1
|
Rukthanapitak P, Saito K, Kobayashi R, Kaweewan I, Kodani S. Heterologous production of a new lanthipeptide boletupeptin using a cryptic biosynthetic gene cluster of the myxobacterium Melittangium boletus. J Biosci Bioeng 2024; 137:354-359. [PMID: 38458885 DOI: 10.1016/j.jbiosc.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 03/10/2024]
Abstract
Myxobacteria have comparatively large genomes that contain many biosynthetic genes with the potential to produce secondary metabolites. Based on genome mining, we discovered a new biosynthetic gene cluster of class III lanthipeptide in the genome of the myxobacterium Melittangium boletus. The biosynthetic gene cluster contained a precursor peptide-coding gene bolA, and a class III lanthipeptide synthetase-coding gene bolKC. The expression vector containing bolA and bolKC was constructed using synthetic DNA with codon-optimized sequences based on the commercially available vector pET29b. Co-expression of the two genes in the host Escherichia coli BL21(DE3) yielded a new class III lanthipeptide named boletupeptin. The structure of boletupeptin was proposed to have one unit of labionin, as determined by mass spectrometry experiments after reductive cleavage. This is the first report of a class III lanthipeptide from a myxobacterial origin.
Collapse
Affiliation(s)
- Pratchaya Rukthanapitak
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Keita Saito
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ryo Kobayashi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Faculty of Medicine, Chiang Mai University, Inthawarorot Rd., Sri Phum, Muang, Chiang Mai 50200, Thailand
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
| |
Collapse
|
2
|
Zhang Z, Zhang L, Zhang L, Chu H, Zhou J, Ju F. Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes. mSystems 2024; 9:e0126323. [PMID: 38470142 PMCID: PMC11019929 DOI: 10.1128/msystems.01263-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly.IMPORTANCEBacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.
Collapse
Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lihan Zhang
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Department of Chemistry, Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou, Zhejiang, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| |
Collapse
|
3
|
Wu Y, Zhuang Y, Wu C, Jia H, He F, Ruan Z. Global emergence of Gram-negative bacteria carrying the mobilised RND-type efflux pump gene cluster tmexCD-toprJ variants. Lancet Microbe 2024; 5:e105. [PMID: 37972633 DOI: 10.1016/s2666-5247(23)00338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Affiliation(s)
- Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Yilu Zhuang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Chenghao Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Fang He
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China.
| |
Collapse
|
4
|
Bradshaw AJ, Ramírez-Cruz V, Awan AR, Furci G, Guzmán-Dávalos L, Dentinger BTM. Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster. Proc Natl Acad Sci U S A 2024; 121:e2311245121. [PMID: 38194448 PMCID: PMC10801892 DOI: 10.1073/pnas.2311245121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.
Collapse
Affiliation(s)
- Alexander J. Bradshaw
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
| | - Virginia Ramírez-Cruz
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Ali R. Awan
- Genomics Innovation Unit, Guy’s and St.Thomas’ NHS Foundation Trust, St Thomas’ Hospital, LondonSE1 7EH, United Kingdom
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Bryn T. M. Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
| |
Collapse
|
5
|
Hirsch P, Tagirdzhanov A, Kushnareva A, Olkhovskii I, Graf S, Schmartz GP, Hegemann JD, Bozhüyük KAJ, Müller R, Keller A, Gurevich A. ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome. Nucleic Acids Res 2024; 52:D579-D585. [PMID: 37994699 PMCID: PMC10767846 DOI: 10.1093/nar/gkad1086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.
Collapse
Affiliation(s)
- Pascal Hirsch
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Azat Tagirdzhanov
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Aleksandra Kushnareva
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ilia Olkhovskii
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Simon Graf
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Georges P Schmartz
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Kenan A J Bozhüyük
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alexey Gurevich
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| |
Collapse
|
6
|
Chauhan S, Sen S, Irshad K, Kashyap S, Pushker N, Meel R, Sharma MC. Receptor tyrosine kinase gene expression profiling of orbital rhabdomyosarcoma unveils MET as a potential biomarker and therapeutic target. Hum Cell 2024; 37:297-309. [PMID: 37914903 DOI: 10.1007/s13577-023-00993-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Receptor tyrosine kinases (RTKs) serve as molecular targets for the development of novel personalized therapies in many malignancies. In the present study, expression pattern of receptor tyrosine kinases and its clinical significance in orbital RMS has been explored. Eighteen patients with histopathologically confirmed orbital RMS formed part of this study. Comprehensive q-PCR gene expression profiles of 19 RTKs were generated in the cases and controls. The patients were followed up for 59.53 ± 20.93 years. Clustering and statistical analysis tools were applied to identify the significant combination of RTKs associated with orbital rhabdomyosarcoma patients. mRNA overexpression of RTKs which included MET, AXL, EGFR was seen in 60-80% of cases; EGFR3, IGFR2, FGFR1, RET, PDGFR1, VEGFR2, PDGFR2 in 30-60% of cases; and EGFR4, FGFR3,VEGFR3 and ROS,IGFR1, EGFR1, FGFR2, VEGFR1 in 10-30% of cases. Immunoexpression of MET was seen in 89% of cases. A significant association was seen between MET mRNA and its protein expression. In all the cases MET gene expression was associated with worst overall survival (P = 0.03).There was a significant correlation of MET mRNA expression with RET, ROS, AXL, FGFR1, FGFR3, PDGFR1, IGFR1, VEGFR2, and EGFR3 genes. Association between MET gene and collective expression of RTKs was further evaluated by semi-supervised gene cluster analysis and Principal component analysis, which showed well-separated tumor clusters. MET gene overexpression could be a useful biomarker for identifying high risk orbital rhabdomyosarcoma patients. Well-separated tumor clusters confirmed the association between MET gene and collective expression of RTK genes. Therefore, the therapeutic potential of multi-kinase inhibitors targeting MET and the 9 other significant RTKs needs to be explored.
Collapse
Affiliation(s)
- Sheetal Chauhan
- Ocular Pathology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, Ansari Nagar, Room No. 725, New Delhi, 110029, India
| | - Seema Sen
- Ocular Pathology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, Ansari Nagar, Room No. 725, New Delhi, 110029, India.
| | - Khushboo Irshad
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Seema Kashyap
- Ocular Pathology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, Ansari Nagar, Room No. 725, New Delhi, 110029, India
| | - Neelam Pushker
- Ophthalmoplasty Services, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rachna Meel
- Ophthalmoplasty Services, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| |
Collapse
|
7
|
Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. Nature 2024; 625:312-320. [PMID: 38200293 PMCID: PMC10781624 DOI: 10.1038/s41586-023-06705-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2023] [Indexed: 01/12/2024]
Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
Collapse
Affiliation(s)
- Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alma S Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Ruairidh Macleod
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- UCL Genetics Institute, University College London, London, UK
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Leo Speidel
- UCL Genetics Institute, University College London, London, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Aaron J Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
| |
Collapse
|
8
|
Abstract
Hox genes are important regulators in animal development. They often show a mosaic of conserved (e.g., longitudinal axis patterning) and lineage-specific novel functions (e.g., development of skeletal, sensory, or locomotory systems). Despite extensive research over the past decades, it remains controversial at which node in the animal tree of life the Hox cluster evolved. Its presence already in the last common metazoan ancestor has been proposed, although the genomes of both putative earliest extant metazoan offshoots, the ctenophores and the poriferans, are devoid of Hox sequences. The lack of Hox genes in the supposedly "simple"-built poriferans and their low number in cnidarians and the basally branching bilaterians, the xenacoelomorphs, seems to support the classical notion that the number of Hox genes is correlated with the degree of animal complexity. However, the 4-fold increase of the Hox cluster in xiphosurans, a basally branching chelicerate clade, as well as the situation in some teleost fishes that show a multitude of Hox genes compared to, e.g., human, demonstrates, that there is no per se direct correlation between organismal complexity and Hox number. Traditional approaches have tried to base homology on the morphological level on shared expression profiles of individual genes, but recent data have shown that, in particular with respect to Hox and other regulatory genes, complex gene-gene interactions rather than expression signatures of individual genes alone are responsible for shaping morphological traits during ontogeny. Accordingly, for sound homology assessments and reconstructions of character evolution on organ system level, additional independent datasets (e.g., morphological, developmental) need to be included in any such analyses. If supported by solid data, proposed structural homology should be regarded as valid and not be rejected solely on the grounds of non-parsimonious distribution of the character over a given phylogenetic topology.
Collapse
Affiliation(s)
- Andreas Wanninger
- University of Vienna, Department of Evolutionary Biology, Unit for Integrative Zoology, Djerassiplatz 1, 1030 Vienna, Austria.
| |
Collapse
|
9
|
Sarquis A, Ladero V, Díaz M, Sánchez-Llana E, Fernández M, Alvarez MA. The gene cluster associated with strong biofilm-formation capacity by histamine-producing Lentilactobacillus parabuchneri encodes a sortase-mediated pilus and is located on a plasmid. Food Res Int 2024; 175:113777. [PMID: 38129064 DOI: 10.1016/j.foodres.2023.113777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Histamine is a biogenic amine synthesized through the enzymatic decarboxylation of the amino acid histidine. It can accumulate at high concentrations in foods through the metabolism of certain bacteria, sometimes leading to adverse reactions in consumers. In cheese, histamine can accumulate at toxic levels; Lentilactobacillus parabuchneri has been identified the major cause of this problem. Previous studies have shown some L. parabuchneri strains to form biofilms on different surfaces, posing a contamination risk during cheese production, particularly for cheeses that are processed post-ripening (e.g., grating or slicing). The food contamination they cause can result in economic losses and even foodborne illness if histamine accumulates in the final product. The aim of the present work was to identify the genes of L. parabuchneri involved in biofilm formation, and to determine their function. The genomes of six strains with different biofilm-production capacities (strong, moderate and weak) were sequenced and analysed. A cluster of four genes, similar to those involved in sortase-mediated pilus formation, was identified in the strong biofilm-producers, suggesting it to have a role in surface adhesion. Cloning and heterologous expression in Lactococcus cremoris NZ9000 confirmed its functionality and involvement in adhesion and, therefore, in biofilm formation. PacBio sequencing showed this cluster to be located on a 33.4 kb plasmid, which might increase its chances of horizontal transmission. These findings provide insight into the genetic factors associated with biofilm formation in histamine-producing L. parabuchneri, and into the risks associated with this bacterium in cheese production.
Collapse
Affiliation(s)
- Agustina Sarquis
- Dairy Research Institute, IPLA, CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain
| | - Víctor Ladero
- Dairy Research Institute, IPLA, CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain.
| | - María Díaz
- Dairy Research Institute, IPLA, CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Spain
| | - Esther Sánchez-Llana
- Dairy Research Institute, IPLA, CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Spain
| | - María Fernández
- Dairy Research Institute, IPLA, CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain
| | - Miguel A Alvarez
- Dairy Research Institute, IPLA, CSIC, Paseo Rio Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain
| |
Collapse
|
10
|
Scott K, Konkel Z, Gluck-Thaler E, Valero David GE, Simmt CF, Grootmyers D, Chaverri P, Slot J. Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma. PLoS One 2023; 18:e0289280. [PMID: 38127903 PMCID: PMC10735191 DOI: 10.1371/journal.pone.0289280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/14/2023] [Indexed: 12/23/2023] Open
Abstract
Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.
Collapse
Affiliation(s)
- Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | | | - Coralie Farinas Simmt
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
| | - Django Grootmyers
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Priscila Chaverri
- Department of Natural Sciences, Bowie State University, Bowie, MD, United States of America
- School of Biology and Natural Products Research Center (CIPRONA), University of Costa Rica, San José, Costa Rica
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States of America
- Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH, United States of America
| |
Collapse
|
11
|
Tang Y, Lei J, Ma X, Li J, Li H, Liu Z. Identification and characterization of a novel bacteriocin gene cluster in Lysinibacillus boronitolerans. Biotechnol Appl Biochem 2023; 70:1860-1869. [PMID: 37431158 DOI: 10.1002/bab.2488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/15/2023] [Indexed: 07/12/2023]
Abstract
Although the antibiotics inhibit or kill pathogens, the abuse leads to the resistance formation and even "Super Bacteria." Therefore, it is urgent to explore the natural and safe alternatives such as bacteriocin. In this study, an uncharacterized bacteriocin gene cluster for Lysinibacillus boronitolerans was first predicted by genome sequencing and bioinformatics analysis, of which including two biosynthetic genes, a regulatory gene, a transport-related gene, and six other genes. Subsequently, the 10.24-kb gene cluster was expressed in Escherichia coli BL21, and the lysate effectively inhibited the growths of pathogenic bacteria containing Bacillus pumilus, Bacillus velezensis, Pseudomonas syringae pv. tomato DC3000, and Xanthomonas axonopodis pv. manihotis. The antibacterial substance was purified by 70% ammonium sulfate precipitation and further identified by liquid chromatography-tandem mass spectrometry. The results showed that the antibacterial substance consisted of 44 amino acids and had 24.1% sequence identity with the cyanobacterin Piricyclamide 7005 E4 PirE4, a bacteriocin analogue. The minimal set of genes required for the biosynthesis of the antibacterial substance was determined by site-directed mutagenesis, suggesting both a transcriptional repressor and a phosphohydroxythreonine transaminase were essential. Subsequently, the evolution and conservation of the two proteins were analyzed among 22 Lysinibacillus species. Among them, the residues responsible for functions were identified. Collectively, our results set a solid foundation for investigation of the biosynthesis and application of bacteriocin.
Collapse
Affiliation(s)
- Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou, China
| | - Junxia Lei
- School of Life Sciences, Hainan University, Haikou, China
| | - Xiang Ma
- School of Life Sciences, Hainan University, Haikou, China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou, China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou, China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| |
Collapse
|
12
|
Palmateer NC, Munro JB, Nagaraj S, Crabtree J, Pelle R, Tallon L, Nene V, Bishop R, Silva JC. The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species. J Mol Evol 2023; 91:897-911. [PMID: 38017120 PMCID: PMC10730637 DOI: 10.1007/s00239-023-10142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/07/2023] [Indexed: 11/30/2023]
Abstract
Multigene families often play an important role in host-parasite interactions. One of the largest multigene families in Theileria parva, the causative agent of East Coast fever, is the T. parva repeat (Tpr) gene family. The function of the putative Tpr proteins remains unknown. The initial publication of the T. parva reference genome identified 39 Tpr family open reading frames (ORFs) sharing a conserved C-terminal domain. Twenty-eight of these are clustered in a central region of chromosome 3, termed the "Tpr locus", while others are dispersed throughout all four nuclear chromosomes. The Tpr locus contains three of the four assembly gaps remaining in the genome, suggesting the presence of additional, as yet uncharacterized, Tpr gene copies. Here, we describe the use of long-read sequencing to attempt to close the gaps in the reference assembly of T. parva (located among multigene families clusters), characterize the full complement of Tpr family ORFs in the T. parva reference genome, and evaluate their evolutionary relationship with Tpr homologs in other Theileria species. We identify three new Tpr family genes in the T. parva reference genome and show that sequence similarity among paralogs in the Tpr locus is significantly higher than between genes outside the Tpr locus. We also identify sequences homologous to the conserved C-terminal domain in five additional Theileria species. Using these sequences, we show that the evolution of this gene family involves conservation of a few orthologs across species, combined with gene gains/losses, and species-specific expansions.
Collapse
Affiliation(s)
- Nicholas C Palmateer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sushma Nagaraj
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roger Pelle
- International Livestock Research Institute, Nairobi, Kenya
| | - Luke Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vish Nene
- International Livestock Research Institute, Nairobi, Kenya
| | - Richard Bishop
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal.
| |
Collapse
|
13
|
Wu Y, Li Y, Zhang Y, Liu Y, Li J, Du G, Lv X, Liu L. Efficient Protein Expression and Biosynthetic Gene Cluster Regulation in Bacillus subtilis Driven by a T7-BOOST System. ACS Synth Biol 2023; 12:3328-3339. [PMID: 37885173 DOI: 10.1021/acssynbio.3c00331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Bacillus subtilis is a generally recognized as safe microorganism that is widely used for protein expression and chemical production, but has a limited number of genetic regulatory components compared with the Gram-negative model microorganism Escherichia coli. In this study, a two-module plug-and-play T7-based optimized output strategy for transcription (T7-BOOST) systems with low leakage expression and a wide dynamic range was constructed based on the inducible promoters Phy-spank and PxylA. The first T7 RNA polymerase-driven module was seamlessly integrated into the genome based on the CRISPR/Cpf1 system, while the second expression control module was introduced into low, medium, and high copy plasmids for characterization. As a proof of concept, the T7-BOOST systems were successfully employed for whole-cell catalysis production of γ-aminobutyric acid (109.8 g/L with a 98.0% conversion rate), expression of human αS1 casein and human lactoferrin, and regulation of exogenous lycopene biosynthetic gene cluster and endogenous riboflavin biosynthetic gene cluster. Overall, the T7-BOOST system serves as a stringent, controllable, and effective tool for regulating gene expression in B. subtilis.
Collapse
Affiliation(s)
- Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yuting Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Baima Future Foods Research Institute, Nanjing 211225, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Baima Future Foods Research Institute, Nanjing 211225, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Baima Future Foods Research Institute, Nanjing 211225, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Baima Future Foods Research Institute, Nanjing 211225, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Baima Future Foods Research Institute, Nanjing 211225, China
| |
Collapse
|
14
|
Khan A, Shah Z, Ali S, Ahmad N, Iqbal M, Ullah A, Ayub F. Genome wide identification, structural characterization and phylogenetic analysis of High-Affinity potassium (HAK) ion transporters in common bean (Phaseolus vulgaris L.). BMC Genom Data 2023; 24:66. [PMID: 37964195 PMCID: PMC10648387 DOI: 10.1186/s12863-023-01163-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND High-Affinity Potassium ions represent one of the most important and large group of potassium transporters. Although HAK genes have been studied in a variety of plant species, yet, remain unexplored in common bean. RESULTS In the current study, 20 HAK genes were identified in common bean genome. Super-family "K_trans" domain was found in all PvHAK genes. Signals for localization of PvHAK proteins were detected in cell membrane. Fifty three HAKs genes, across diverse plant species, were divided into 5 groups based on sequential homology. Twelve pairs of orthologs genes were found in various plant species. PvHAKs genes were distributed unequally on 7 chromosomes with maximum number (7) mapped on chromosome 2 while only 1 PvHAK found on each chromosome 1, 4, and 6. Tandem gene duplication was witnessed in 2 paralog pairs while 1 pair exhibited segmental gene duplication. Five groups were made in PvHAK gene family based on Phylogeny. Maximum PvHAKs (10) were detected in Group-V while group-II composed of only 1 PvHAK gene. Variation was witnessed in number and size of motifs, and structure of PvHAKs associated with different groups. Light and hormone responsive elements contributed 57 and 24% share, respectively, to cis regulatory elements. qRT-PCR based results revealed significant increase in expression of all 4 PvHAK genes under low-potassium stress. CONCLUSION The current study provides valuable information for further functional characterization and uncovering the molecular mechanism associated with Potassium transportation in plants.
Collapse
Affiliation(s)
- Afrasyab Khan
- Department of Biotechnology, University of Science and Technology, Bannu, 28100, Pakistan
| | - Zamarud Shah
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Nisar Ahmad
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, 21300, Pakistan
| | - Maaz Iqbal
- Institute of Biotechnology and Genetic Engineering, University of Agriculture, Peshawar, 25130, Pakistan
| | - Arif Ullah
- Department of Biotechnology, University of Science and Technology, Bannu, 28100, Pakistan
| | - Firdous Ayub
- Department of Computer Science, Women University Swabi, Swabi, 23430, Pakistan
| |
Collapse
|
15
|
Geistodt-Kiener A, Totozafy JC, Le Goff G, Vergne J, Sakai K, Ouazzani J, Mouille G, Viaud M, O'Connell RJ, Dallery JF. Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites. Metab Eng 2023; 80:216-231. [PMID: 37863177 DOI: 10.1016/j.ymben.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Transcriptomic studies have revealed that fungal pathogens of plants activate the expression of numerous biosynthetic gene clusters (BGC) exclusively when in presence of a living host plant. The identification and structural elucidation of the corresponding secondary metabolites remain challenging. The aim was to develop a polycistronic system for heterologous expression of fungal BGCs in Saccharomyces cerevisiae. Here we adapted a polycistronic vector for efficient, seamless and cost-effective cloning of biosynthetic genes using in vivo assembly (also called transformation-assisted recombination) directly in Escherichia coli followed by heterologous expression in S. cerevisiae. Two vectors were generated with different auto-inducible yeast promoters and selection markers. The effectiveness of these vectors was validated with fluorescent proteins. As a proof-of-principle, we applied our approach to the Colletochlorin family of molecules. These polyketide secondary metabolites were known from the phytopathogenic fungus Colletotrichum higginsianum but had never been linked to their biosynthetic genes. Considering the requirement for a halogenase, and by applying comparative genomics, we identified a BGC putatively involved in the biosynthesis of Colletochlorins in C. higginsianum. Following the expression of those genes in S. cerevisiae, we could identify the presence of the precursor Orsellinic acid, Colletochlorins and their non-chlorinated counterparts, the Colletorins. In conclusion, the polycistronic vectors described herein were adapted for the host S. cerevisiae and allowed to link the Colletochlorin compound family to their corresponding biosynthetic genes. This system will now enable the production and purification of infection-specific secondary metabolites of fungal phytopathogens. More widely, this system could be applied to any fungal BGC of interest.
Collapse
Affiliation(s)
| | - Jean Chrisologue Totozafy
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, 78000, Versailles, France
| | - Géraldine Le Goff
- Centre National de La Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, 91190, Gif-sur-Yvette, France
| | - Justine Vergne
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Kaori Sakai
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jamal Ouazzani
- Centre National de La Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, 91190, Gif-sur-Yvette, France
| | - Grégory Mouille
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, 78000, Versailles, France
| | - Muriel Viaud
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | | |
Collapse
|
16
|
Li M, Wang H, Tian S, Zhu Y, Zhang Y. Triticeae-BGC: a web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae. J Genet Genomics 2023; 50:921-923. [PMID: 37806445 DOI: 10.1016/j.jgg.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/10/2023]
Affiliation(s)
- Mingxu Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haoyu Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, Henan 457004, China
| | - Shilong Tian
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
17
|
Sun J, Zhang X, Fu C, Ahmad N, Zhao C, Hou L, Naeem M, Pan J, Wang X, Zhao S. Genome-wide identification and expression analysis of GA20ox and GA3ox genes during pod development in peanut. PeerJ 2023; 11:e16279. [PMID: 37908413 PMCID: PMC10615029 DOI: 10.7717/peerj.16279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023] Open
Abstract
Background Gibberellins (GAs) play important roles in regulating peanut growth and development. GA20ox and GA3ox are key enzymes involved in GA biosynthesis. These enzymes encoded by a multigene family belong to the 2OG-Fe (II) oxygenase superfamily. To date, no genome-wide comparative analysis of peanut AhGA20ox and AhGA3ox-encoding genes has been performed, and the roles of these genes in peanut pod development are not clear. Methods A whole-genome analysis of AhGA20ox and AhGA3ox gene families in peanut was carried out using bioinformatic tools. The expression of these genes at different stage of pod development was analyzed using qRT-PCR. Results In this study, a total of 15 AhGA20ox and five AhGA3ox genes were identified in peanut genome, which were distributed on 14 chromosomes. Phylogenetic analysis divided the GA20oxs and GA3oxs into three groups, but AhGA20oxs and AhGA3oxs in two groups. The conserved pattern of gene structure, cis-elements, and protein motifs further confirmed their evolutionary relationship in peanut. AhGA20ox and AhGA3ox genes were differential expressed at different stages of pod development. The strong expression of AhGA20ox1/AhGA20ox4, AhGA20ox12/AhGA20ox15, AhGA3ox1 and AhGA3ox4/AhGA3ox5 in S1-stage indicated that these genes could have a key role in controlling peg elongation. Furthermore, AhGA20ox and AhGA3ox also showed diverse expression patterns in different peanut tissues including leaves, main stems, flowers and inflorescences. Noticeably, AhGA20ox9/AhGA20ox11 and AhGA3o4/AhGA3ox5 were highly expressed in the main stem, whereas the AhGA3ox1 and AhGA20ox10 were strongly expressed in the inflorescence. The expression levels of AhGA20ox2/AhGA20ox3, AhGA20ox5/AhGA20ox6, AhGA20ox7/AhGA20ox8, AhGA20ox13/AhGA20ox14 and AhGA3ox2/AhGA3ox3 were high in the flowers, suggesting their involvement in flower development. These results provide a basis for deciphering the roles of AhGA20ox and AhGA3ox in peanut growth and development, especially in pod development.
Collapse
Affiliation(s)
- Jie Sun
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiaoqian Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chun Fu
- Weifang Academy of Agricultural Sciences, Weifang, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Lei Hou
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaowen Pan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| |
Collapse
|
18
|
Zhang W, Li H, Li Q, Wang Z, Zeng W, Yin H, Qi K, Zou Y, Hu J, Huang B, Gu P, Qiao X, Zhang S. Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.). BMC Genom Data 2023; 24:58. [PMID: 37789271 PMCID: PMC10548706 DOI: 10.1186/s12863-023-01159-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The cytochrome P450 (CYP) superfamily is the largest enzyme metabolism family in plants identified to date, and it is involved in many biological processes, including secondary metabolite biosynthesis, hormone metabolism and stress resistance. However, the P450 gene superfamily has not been well studied in pear (Pyrus spp.). RESULTS Here, the comprehensive identification and a comparative analysis of P450 superfamily members were conducted in cultivated and wild pear genomes. In total, 338, 299 and 419 P450 genes were identified in Chinese white pear, European pear and the wild pear, respectively. Based on the phylogenetic analyses, pear P450 genes were divided into ten clans, comprising 48 families. The motif and gene structure analyses further supported this classification. The expansion of the pear P450 gene family was attributed to whole-genome and single-gene duplication events. Several P450 gene clusters were detected, which have resulted from tandem and proximal duplications. Purifying selection was the major force imposed on the long-term evolution of P450 genes. Gene dosage balance, subfunctionalization and neofunctionalization jointly drove the retention and functional diversification of P450 gene pairs. Based on the association analysis between transcriptome expression profiles and flavonoid content during fruit development, three candidate genes were identified as being closely associated with the flavonoid biosynthesis, and the expression of one gene was further verified using qRT-PCR and its function was validated through transient transformation in pear fruit. CONCLUSIONS The study results provide insights into the evolution and biological functions of P450 genes in pear.
Collapse
Affiliation(s)
- Wei Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongxiang Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qionghou Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zewen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwei Zeng
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Yin
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Zou
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Hu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baisha Huang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Gu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Qiao
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
19
|
Kramer JC, Böhringer N, Mettal U, Schäberle TF. Functional in vitro and in vivo analysis of biosynthetic genes by heterologous expression in E. coli. STAR Protoc 2023; 4:102531. [PMID: 37682715 PMCID: PMC10493593 DOI: 10.1016/j.xpro.2023.102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/07/2023] [Accepted: 08/01/2023] [Indexed: 09/10/2023] Open
Abstract
Biosynthetic gene clusters of natural products often harbor genes of unknown function, which are difficult to characterize. Here, we present a protocol for the functional analysis in vitro and in vivo of these biosynthetic genes by heterologous expression in E. coli. We describe steps for the expression of genes of interest in an established E. coli strain optimized to heterologously express natural products. We then detail the expression of a His-tagged gene to deduce the specific function of the protein. For complete details on the use and execution of this protocol, please refer to Böhringer et al.1.
Collapse
Affiliation(s)
- Jil-Christine Kramer
- Institute for Insect Biotechnology, Division for Natural Product Research; Justus-Liebig-University Giessen, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Division for Natural Product Research; Justus-Liebig-University Giessen, Ohlebergsweg 12, 35392 Giessen, Germany; German Center for Infection Research (DZIF); Partner Site Giessen-Marburg-Langen, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Ute Mettal
- Institute for Insect Biotechnology, Division for Natural Product Research; Justus-Liebig-University Giessen, Ohlebergsweg 12, 35392 Giessen, Germany.
| | - Till F Schäberle
- Institute for Insect Biotechnology, Division for Natural Product Research; Justus-Liebig-University Giessen, Ohlebergsweg 12, 35392 Giessen, Germany; German Center for Infection Research (DZIF); Partner Site Giessen-Marburg-Langen, Ohlebergsweg 12, 35392 Giessen, Germany; Natural Product Department; Fraunhofer-Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany.
| |
Collapse
|
20
|
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature 2023; 621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
Collapse
Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies Inc., Oxford, UK
| | - Monika Cechova
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivan A Alexandrov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrey V Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Chen-Shan Chin
- GeneDX Holdings Corp, Stamford, CT, USA
- Foundation of Biological Data Science, Belmont, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ariel Gershman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, MO, USA
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nancy F Hansen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jakob Heinz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Hwang
- XDBio Program, Johns Hopkins University, Baltimore, MD, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Rupesh K Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Christopher Markovic
- Genome Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann M Mc Cartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brandy M McNulty
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E Olsen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | | | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Taravella Oill
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison C Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Melissa A Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
21
|
Mukherjee A, Tikariha H, Bandla A, Pavagadhi S, Swarup S. Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes. mSystems 2023; 8:e0038723. [PMID: 37409823 PMCID: PMC10469690 DOI: 10.1128/msystems.00387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
There are gaps in our understandings on how did the evolutionary relationships among members of the phytobiomes shape their ability to produce tremendously complex specialized metabolites under the influence of plant host. To determine these relationships, we investigated the phylogenetic conservation of biosynthetic gene clusters (BGCs) on a global collection of 4,519 high-quality and nonredundant (out of 12,181) bacterial isolates and metagenome-assembled genomes from 47 different plant hosts and soil, by adopting three independent phylogenomic approaches (D-test, Pagel's λ, and consenTRAIT). We report that the BGCs are phylogenetically conserved to varying strengths and depths in their different classes. We show that the ability to produce specialized metabolites qualifies as a complex trait, and the depth of conservation is equivalent to ecologically relevant complex microbial traits. Interestingly, terpene and aryl polyene BGCs had the strongest phylogenetic conservation in the phytobiomes, but not in the soil microbiomes. Furthermore, we showed that terpenes are largely uncharacterized in phytobiomes and pinpointed specific clades that harbor potentially novel terpenes. Taken together, this study sheds light on the evolution of specialized metabolites' biosynthesis potential in phytobiomes under the influence of plant hosts and presents strategies to rationally guide the discovery of potentially novel classes of metabolites. IMPORTANCE This study expands our understandings of the biosynthetic potential of phytobiomes by using such worldwide and extensive collection of microbiomes from plants and soil. Apart from providing such vital resource for the plant microbiome researchers, this study provides fundamental insights into the evolution of biosynthetic gene clusters (BGCs) in phytobiomes under the influence of plant host. Specifically, we report that the strength of phylogenetic conservation in microbiomes varies for different classes of BGCs and is influenced as a result of plant host association. Furthermore, our results indicate that biosynthetic potential of specialized metabolites is deeply conserved equivalent to other complex and ecologically relevant microbial traits. Finally, for the most conserved class of specialized metabolites (terpenes), we identified clades harboring potentially novel class of molecules. Future studies could focus on plant-microbe coevolution and interactions through specialized metabolites building upon these findings.
Collapse
Affiliation(s)
- Arijit Mukherjee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hitesh Tikariha
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Aditya Bandla
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Shruti Pavagadhi
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| |
Collapse
|
22
|
Zhang T, Zhang C, Zhang X, Liang Z, Xia P. Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng. Protoplasma 2023; 260:1081-1096. [PMID: 36564534 DOI: 10.1007/s00709-022-01832-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/17/2022] [Indexed: 06/07/2023]
Abstract
WRKY transcription factors play an important role in the immune system and the innate defense response of plants. WRKY transcription factors have great feedback on nitrogen stress. In this study, bioinformatics was used to detect the WRKYs of Panax notoginseng (PnWRKYs). The response of PnWRKYs under nitrogen stress was also well studied. PnWRKYs were distributed on 11 chromosomes. According to PnWRKY and Arabidopsis thaliana WRKY (AtWRKY) domains, these PnWRKY proteins were divided into three groups by phylogenetic analysis. MEME analysis showed that almost every member contained motif 1 and motif 2. PlantCARE online predicted the cis-acting elements of the promoter. PnWRKY gene family members obtained 22 pairs of repeat fragments by collinearity analysis. The expression levels of PnWRKYs in different parts (roots, flowers, and leafs) were analyzed by the gene expression pattern. They reflected tissue-specific expressions. The qRT-PCR experiments were used to detect 74 PnWRKYs under nitrogen stress. The results showed that the expression levels of 8 PnWRKYs were significantly induced. The PnWRKY gene family may be involved in biotic/abiotic stresses and hormone induction. This study will not only lay the foundation to explore the functions of PnWRKYs but also provide candidate genes for the future improvement of P. notoginseng.
Collapse
Affiliation(s)
- Tingting Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Caijuan Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xuemin Zhang
- Tianjin TASLY Modern Chinese Medicine Resources Co., Ltd, Tianjin, 300402, China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
23
|
Salazar B, Ortiz A, Keswani C, Minkina T, Mandzhieva S, Pratap Singh S, Rekadwad B, Borriss R, Jain A, Singh HB, Sansinenea E. Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations. Microb Ecol 2023; 86:1-24. [PMID: 35604432 DOI: 10.1007/s00248-022-02044-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.
Collapse
Affiliation(s)
- Bruno Salazar
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México
| | - Aurelio Ortiz
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México
| | - Chetan Keswani
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Saglara Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Satyendra Pratap Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Bhagwan Rekadwad
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India
| | - Rainer Borriss
- Institut Für Agrar- Und Gartenbauwissenschaften, Fachgebiet Phytomedizin, Humboldt-Universität Zu Berlin, Lentze-Allee 55-57, 14195, Berlin, Germany
| | - Akansha Jain
- Division of Plant Biology, Bose Institute, CIT Road, Kankurgachi, Kolkata, India
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura, 281406, India
| | - Estibaliz Sansinenea
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México.
| |
Collapse
|
24
|
Miranda RP, Turrini PCG, Bonadio DT, Zerillo MM, Berselli AP, Creste S, Van Sluys MA. Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness. Microbiol Spectr 2023; 11:e0280222. [PMID: 37052486 PMCID: PMC10269729 DOI: 10.1128/spectrum.02802-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 03/03/2023] [Indexed: 04/14/2023] Open
Abstract
An integrative approach combining genomics, transcriptomics, and cell biology is presented to address leaf scald disease, a major problem for the sugarcane industry. To gain insight into the biology of the causal agent, the complete genome sequences of four Brazilian Xanthomonas albilineans strains with differing virulence capabilities are presented and compared to the GPEPC73 reference strain and FJ1. Based on the aggressiveness index, different strains were compared: Xa04 and Xa11 are highly aggressive, Xa26 is intermediate, and Xa21 is the least, while, based on genome structure, Xa04 shares most of its genomic features with Xa26, and Xa11 share most of its genomic features with Xa21. In addition to presenting more clustered regularly interspaced short palindromic repeats (CRISPR) clusters, four more novel prophage insertions are present than the previously sequenced GPEPC73 and FJ1 strains. Incorporating the aggressiveness index and in vitro cell biology into these genome features indicates that disease establishment is not a result of a single determinant factor, as in most other Xanthomonas species. The Brazilian strains lack the previously described plasmids but present more prophage regions. In pairs, the most virulent and the least virulent share unique prophages. In vitro transcriptomics shed light on the 54 most highly expressed genes among the 4 strains compared to ribosomal proteins (RPs), of these, 3 outer membrane proteins. Finally, comparative albicidin inhibition rings and in vitro growth curves of the four strains also do not correlate with pathogenicity. In conclusion, the results disclose that leaf scald disease is not associated with a single shared characteristic between the most or the least pathogenic strains. IMPORTANCE An integrative approach is presented which combines genomics, transcriptomics, and cell biology to address leaf scald disease. The results presented here disclose that the disease is not associated with a single shared characteristic between the most pathogenic strains or a unique genomic pattern. Sequence data from four Brazilian strains are presented that differ in pathogenicity index: Xa04 and Xa11 are highly virulent, Xa26 is intermediate, and Xa21 is the least pathogenic strain, while, based on genome structure, Xa04 shares with Xa26, and Xa11 shares with X21 most of the genome features. Other than presenting more CRISPR clusters and prophages than the previously sequenced strains, the integration of aggressiveness and cell biology points out that disease establishment is not a result of a single determinant factor as in other xanthomonads.
Collapse
Affiliation(s)
- Raquel P. Miranda
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Paula C. G. Turrini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Dora T. Bonadio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Marcelo M. Zerillo
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Arthur P. Berselli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Silvana Creste
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Campinas, São Paulo, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| |
Collapse
|
25
|
Saito K, Mukai K, Kaweewan I, Nakagawa H, Hosaka T, Kodani S. Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense. J Microbiol 2023; 61:641-648. [PMID: 37306831 DOI: 10.1007/s12275-023-00059-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 06/13/2023]
Abstract
Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.
Collapse
Affiliation(s)
- Keita Saito
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Keiichiro Mukai
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hiroyuki Nakagawa
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization (NARO), Ibaraki, 305-8642, Japan
| | - Takeshi Hosaka
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan.
| |
Collapse
|
26
|
Peng F, Zhou L, Lu W, Gan R, Lu M, Li Z, Zhang X, Wang Y, Gui J. Genomic and Transcriptional Profiles of Kelch-like ( klhl) Gene Family in Polyploid Carassius Complex. Int J Mol Sci 2023; 24:8367. [PMID: 37176071 PMCID: PMC10179623 DOI: 10.3390/ijms24098367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.
Collapse
Affiliation(s)
- Fang Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijia Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruihai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaojuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
27
|
Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD. Complete integration of carbene-transfer chemistry into biosynthesis. Nature 2023; 617:403-408. [PMID: 37138074 DOI: 10.1038/s41586-023-06027-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions1. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis2,3, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule-styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.
Collapse
Affiliation(s)
- Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Andrew Quest
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pablo Cruz-Morales
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kai Deng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Jose Henrique Pereira
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Devon Van Cura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ramu Kakumanu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Qingyun Dan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
| |
Collapse
|
28
|
Bai Y, Dou Y, Xie Y, Zheng H, Gao J. Phylogeny, transcriptional profile, and auxin-induced phosphorylation modification characteristics of conserved PIN proteins in Moso bamboo (Phyllostachys edulis). Int J Biol Macromol 2023; 234:123671. [PMID: 36801226 DOI: 10.1016/j.ijbiomac.2023.123671] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Auxin polar transport is an important way for auxin to exercise its function, and auxin plays an irreplaceable role in the rapid growth of Moso bamboo. We identified and performed the structural analysis of PIN-FORMED auxin efflux carriers in Moso bamboo and obtained a total of 23 PhePIN genes from five gene subfamilies. We also performed chromosome localization and intra- and inter-species synthesis analysis. Phylogenetic analyses of 216 PIN genes showed that PIN genes are relatively conserved in the evolution of the Bambusoideae and have undergone intra-family segment replication in Moso bamboo. The PIN genes' transcriptional patterns showed that the PIN1 subfamily plays a major regulatory role. PIN genes and auxin biosynthesis maintain a high degree of consistency in spatial and temporal distribution. Phosphoproteomics analysis identified many phosphorylated protein kinases that respond to auxin regulation through autophosphorylation and phosphorylation of PIN proteins. The protein interaction network showed that there is a plant hormone interaction regulatory network with PIN protein as the core. We provide a comprehensive PIN protein analysis that complements the auxin regulatory pathway in Moso bamboo and paves the way for further auxin regulatory studies in bamboo.
Collapse
Affiliation(s)
- Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Yali Xie
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Huifang Zheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China.
| |
Collapse
|
29
|
Deng L, Zhao Z, Liu L, Zhong Z, Xie W, Zhou F, Xu W, Zhang Y, Deng Z, Sun Y. Dissection of 3D chromosome organization in Streptomyces coelicolor A3(2) leads to biosynthetic gene cluster overexpression. Proc Natl Acad Sci U S A 2023; 120:e2222045120. [PMID: 36877856 PMCID: PMC10242723 DOI: 10.1073/pnas.2222045120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
The soil-dwelling filamentous bacteria, Streptomyces, is widely known for its ability to produce numerous bioactive natural products. Despite many efforts toward their overproduction and reconstitution, our limited understanding of the relationship between the host's chromosome three dimension (3D) structure and the yield of the natural products escaped notice. Here, we report the 3D chromosome organization and its dynamics of the model strain, Streptomyces coelicolor, during the different growth phases. The chromosome undergoes a dramatic global structural change from primary to secondary metabolism, while some biosynthetic gene clusters (BGCs) form special local structures when highly expressed. Strikingly, transcription levels of endogenous genes are found to be highly correlated to the local chromosomal interaction frequency as defined by the value of the frequently interacting regions (FIREs). Following the criterion, an exogenous single reporter gene and even complex BGC can achieve a higher expression after being integrated into the chosen loci, which may represent a unique strategy to activate or enhance the production of natural products based on the local chromosomal 3D organization.
Collapse
Affiliation(s)
- Liang Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Zhihu Zhao
- Department of Protein Engineering, Beijing Institute of Biotechnology, Beijing100071, China
| | - Lin Liu
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Wenxinyu Xie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Fan Zhou
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Wei Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| |
Collapse
|
30
|
Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. Plant J 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
Collapse
Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| |
Collapse
|
31
|
Wu XS, He XY, Ipsaro JJ, Huang YH, Preall JB, Ng D, Shue YT, Sage J, Egeblad M, Joshua-Tor L, Vakoc CR. OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage. Nature 2022; 607:169-175. [PMID: 35576971 PMCID: PMC9419707 DOI: 10.1038/s41586-022-04842-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 05/09/2022] [Indexed: 12/13/2022]
Abstract
Tuft cells are a rare chemosensory lineage that coordinates immune and neural responses to foreign pathogens in mucosal tissues1. Recent studies have also revealed tuft-cell-like human tumours2,3, particularly as a variant of small-cell lung cancer. Both normal and neoplastic tuft cells share a genetic requirement for the transcription factor POU2F3 (refs. 2,4), although the transcriptional mechanisms that generate this cell type are poorly understood. Here we show that binding of POU2F3 to the uncharacterized proteins C11orf53 and COLCA2 (renamed here OCA-T1/POU2AF2 and OCA-T2/POU2AF3, respectively) is critical in the tuft cell lineage. OCA-T1 and OCA-T2 are paralogues of the B-cell-specific coactivator OCA-B; all three proteins are encoded in a gene cluster and contain a conserved peptide that binds to class II POU transcription factors and a DNA octamer motif in a bivalent manner. We demonstrate that binding between POU2F3 and OCA-T1 or OCA-T2 is essential in tuft-cell-like small-cell lung cancer. Moreover, we generated OCA-T1-deficient mice, which are viable but lack tuft cells in several mucosal tissues. These findings reveal that the POU2F3-OCA-T complex is the master regulator of tuft cell identity and a molecular vulnerability of tuft-cell-like small-cell lung cancer.
Collapse
Affiliation(s)
- Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Genetics Program, Stony Brook University, Stony Brook, NY, USA
| | - Xue-Yan He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jonathan J Ipsaro
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - David Ng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | |
Collapse
|
32
|
Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I. Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet 2022; 18:e1010020. [PMID: 35653398 PMCID: PMC9162365 DOI: 10.1371/journal.pgen.1010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.
Collapse
Affiliation(s)
- Bardya Djahanschiri
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jennifer Breisch
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Beate Averhoff
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | | | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- * E-mail:
| |
Collapse
|
33
|
Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. Mar Biotechnol (NY) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
Collapse
Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| |
Collapse
|
34
|
Wu D, Jiang B, Ye CY, Timko MP, Fan L. Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants. Plant Commun 2022; 3:100320. [PMID: 35576160 PMCID: PMC9251436 DOI: 10.1016/j.xplc.2022.100320] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 05/11/2023]
Abstract
Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1-Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.
Collapse
Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
35
|
Polturak G, Dippe M, Stephenson MJ, Chandra Misra R, Owen C, Ramirez-Gonzalez RH, Haidoulis JF, Schoonbeek HJ, Chartrain L, Borrill P, Nelson DR, Brown JK, Nicholson P, Uauy C, Osbourn A. Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat. Proc Natl Acad Sci U S A 2022; 119:e2123299119. [PMID: 35412884 PMCID: PMC9169793 DOI: 10.1073/pnas.2123299119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022] Open
Abstract
Wheat is a widely grown food crop that suffers major yield losses due to attack by pests and pathogens. A better understanding of biotic stress responses in wheat is thus of major importance. The recently assembled bread wheat genome coupled with extensive transcriptomic resources provides unprecedented new opportunities to investigate responses to pathogen challenge. Here, we analyze gene coexpression networks to identify modules showing consistent induction in response to pathogen exposure. Within the top pathogen-induced modules, we identify multiple clusters of physically adjacent genes that correspond to six pathogen-induced biosynthetic pathways that share a common regulatory network. Functional analysis reveals that these pathways, all of which are encoded by biosynthetic gene clusters, produce various different classes of compounds—namely, flavonoids, diterpenes, and triterpenes, including the defense-related compound ellarinacin. Through comparative genomics, we also identify associations with the known rice phytoalexins momilactones, as well as with a defense-related gene cluster in the grass model plant Brachypodium distachyon. Our results significantly advance the understanding of chemical defenses in wheat and open up avenues for enhancing disease resistance in this agriculturally important crop. They also exemplify the power of transcriptional networks to discover the biosynthesis of chemical defenses in plants with large, complex genomes.
Collapse
Affiliation(s)
- Guy Polturak
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Dippe
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Michael J. Stephenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rajesh Chandra Misra
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Charlotte Owen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - John F. Haidoulis
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Henk-Jan Schoonbeek
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Laetitia Chartrain
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Philippa Borrill
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - James K.M. Brown
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| |
Collapse
|
36
|
Handayani DP, Isnansetyo A, Istiqomah I, Jumina J. New Report: Genome Mining Untaps the Antibiotics Biosynthetic Gene Cluster of Pseudoalteromonas xiamenensis STKMTI.2 from a Mangrove Soil Sediment. Mar Biotechnol (NY) 2022; 24:190-202. [PMID: 35166965 DOI: 10.1007/s10126-022-10096-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
The marine bacterium Pseudoalteromonas xiamenensis STKMTI.2 was isolated from a mangrove soil sediment on Setokok Island, Batam, Indonesia. The genome of this bacterium consisted of 4,563,326 bp (GC content: 43.2%) with 1 chromosome, 2 circular plasmids, 2 linear plasmids, 4,824 protein-coding sequences, 25 rRNAs, 104 tRNAs, 4 ncRNAs, and 1 clustered, regularly interspaced, short palindromic repeated (CRISPR). This strain possessed cluster genes which are responsible for the production of brominated marine pyrroles/phenols (bmp), namely, bmp8 and bmp9. Other gene clusters responsible for the synthesis of secondary metabolites were identified using antiSMASH and BAGEL4, which yielded five results, namely, non-ribosomal peptides, polyketide-like butyrolactone, Lant class I, and RiPP-like, detected in chromosome 1, while prodigiosin was detected in the unnamed plasmid 5. This suggests that these whole genome data will be of remarkable importance for the improved understanding of the biosynthesis of industrially important bioactive and antibacterial compounds produced by P. xiamenensis STKMTI.2.
Collapse
Affiliation(s)
- Desy Putri Handayani
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Alim Isnansetyo
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Indah Istiqomah
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jumina Jumina
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| |
Collapse
|
37
|
Jia R, Li C, Wang Y, Qin X, Meng L, Sun X. Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobiumcatenatum. Int J Mol Sci 2022; 23:ijms23042089. [PMID: 35216201 PMCID: PMC8877895 DOI: 10.3390/ijms23042089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family comprises plant-specific transcription factors that control cell proliferation and differentiation during growth and development in many plant species. However, to date, no studies of the LBD gene family in Dendrobium catenatum have been reported. In this study, a genome-wide analysis of LBD genes was performed in D. catenatum and 24 LBD genes were identified. The genes were classified into two classes (I and II) based on phylogenetic relationships and motif structure. Subcellular localization analysis for DcaLBD6 and DcaLBD18 from class I and DcaLBD37 and DcaLBD41 from class II revealed that the proteins were localized in the nucleus. Transient expression analysis of DcaLBD6, DcaLBD18, DcaLBD37, and DcaLBD41 indicated that class I and class II members have opposite roles in regulating VASCULAR-RELATED NAC-DOMAIN 7 (VND7) expression. DcaLBD genes showed diverse expression patterns in response to different phytohormone treatments. Heat maps revealed diverse patterns of DcaLBD gene expression in different organs. These results lay the foundation for further detailed studies of the LBD gene family in D. catenatum.
Collapse
Affiliation(s)
- Ru Jia
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Cheng Li
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhua Wang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangshi Qin
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
| | - Lihua Meng
- School of Life Sciences, Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650500, China;
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
| | - Xudong Sun
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (C.L.); (Y.W.); (X.Q.)
- Correspondence: (L.M.); (X.S.); Tel.: +86-871-65230873 (X.S.)
| |
Collapse
|
38
|
Sehrish S, Sumbal W, Xie M, Zhao C, Zuo R, Gao F, Liu S. Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L. Int J Mol Sci 2022; 23:ijms23041936. [PMID: 35216050 PMCID: PMC8879272 DOI: 10.3390/ijms23041936] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022] Open
Abstract
SET domain group encoding proteins function as histone lysine methyltransferases. These proteins are involved in various biological processes, including plant development and adaption to the environment by modifying the chromatin structures. So far, the SET domain genes (SDGs) have not been systematically investigated in Brassica napus (B. napus). In the current study, through genome-wide analysis, a total of 122 SDGs were identified in the B. napus genome. These BnSDGs were subdivided into seven (I-VII) classes based on phylogeny analysis, domain configurations, and motif distribution. Segmental duplication was involved in the evolution of this family, and the duplicated genes were under strong purifying selection. The promoter sequence of BnSDGs consisted of various growth, hormones, and stress-related cis-acting elements along with transcription factor binding sites (TFBSs) for 20 TF families in 59 of the 122 BnSDGs. The gene ontology (GO) analysis revealed that BnSDGs were closely associated with histone and non-histone methylation and metal binding capacity localized mostly in the nucleus. The in silico expression analysis at four developmental stages in leaf, stem root, floral organ, silique, and seed tissues showed a broad range of tissue and stage-specific expression pattern. The expression analysis under four abiotic stresses (dehydration, cold, ABA, and salinity) also provided evidence for the importance of BnSDGs in stress environments. Based on expression analysis, we performed reverse transcription-quantitative PCR for 15 target BnSDGs in eight tissues (young leaf, mature leaf, root, stem, carpel, stamen, sepal, and petals). Our results were in accordance with the in silico expression data, suggesting the importance of these genes in plant development. In conclusion, this study lays a foundation for future functional studies on SDGs in B. napus.
Collapse
|
39
|
Dennehy R, Duggan N, Dignam S, McCormack S, Dillon E, Molony J, Romano M, Hou Y, Ardill L, Whelan MVX, Drulis‐Kawa Z, Ó'Cróinín T, Valvano MA, Berisio R, McClean S. Protein with negative surface charge distribution, Bnr1, shows characteristics of a DNA-mimic protein and may be involved in the adaptation of Burkholderia cenocepacia. Microbiologyopen 2022; 11:e1264. [PMID: 35212475 PMCID: PMC9060813 DOI: 10.1002/mbo3.1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022] Open
Abstract
Adaptation of opportunistic pathogens to their host environment requires reprogramming of a vast array of genes to facilitate survival in the host. Burkholderia cenocepacia, a Gram-negative bacterium with a large genome of ∼8 Mb that colonizes environmental niches, is exquisitely adaptable to the hypoxic environment of the cystic fibrosis lung and survives in macrophages. We previously identified an immunoreactive acidic protein encoded on replicon 3, BCAS0292. Deletion of the BCAS0292 gene significantly altered the abundance of 979 proteins by 1.5-fold or more; 19 proteins became undetectable while 545 proteins showed ≥1.5-fold reduced abundance, suggesting the BCAS0292 protein is a global regulator. Moreover, the ∆BCAS0292 mutant showed a range of pleiotropic effects: virulence and host-cell attachment were reduced, antibiotic susceptibility was altered, and biofilm formation enhanced. Its growth and survival were impaired in 6% oxygen. In silico prediction of its three-dimensional structure revealed BCAS0292 presents a dimeric β-structure with a negative surface charge. The ΔBCAS0292 mutant displayed altered DNA supercoiling, implicated in global regulation of gene expression. Three proteins were identified in pull-downs with FLAG-tagged BCAS0292, including the Histone H1-like protein, HctB, which is recognized as a global transcriptional regulator. We propose that BCAS0292 protein, which we have named Burkholderia negatively surface-charged regulatory protein 1 (Bnr1), acts as a DNA-mimic and binds to DNA-binding proteins, altering DNA topology and regulating the expression of multiple genes, thereby enabling the adaptation of B. cenocepacia to highly diverse environments.
Collapse
Affiliation(s)
- Ruth Dennehy
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Niamh Duggan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Simon Dignam
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Sarah McCormack
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Eugene Dillon
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Jessica Molony
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Maria Romano
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Yueran Hou
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Laura Ardill
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Matthew V. X. Whelan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and MicrobiologyUniversity of WroclawWroclawPoland
| | - Tadhg Ó'Cróinín
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Miguel A. Valvano
- School of Medicine, Dentistry and Biomedical Sciences, Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| |
Collapse
|
40
|
Olkkonen VM, Ikonen E. Cholesterol transport in the late endocytic pathway: Roles of ORP family proteins. J Steroid Biochem Mol Biol 2022; 216:106040. [PMID: 34864207 DOI: 10.1016/j.jsbmb.2021.106040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 12/29/2022]
Abstract
Oxysterol-binding protein (OSBP) homologues, designated ORP or OSBPL proteins, constitute one of the largest families of intracellular lipid-binding/transfer proteins (LTP). This review summarizes the mounting evidence that several members of this family participate in the machinery facilitating cholesterol trafficking in the late endocytic pathway. There are indications that OSBP, besides acting as a cholesterol/phosphatidylinositol 4-phosphate (PI4P) exchanger at the endoplasmic reticulum (ER)-trans-Golgi network (TGN) membrane contact sites (MCS), also exchanges these lipids at ER-lysosome (Lys) contacts, increasing Lys cholesterol content. The long isoform of ORP1 (ORP1L), which also targets ER-late endosome (LE)/Lys MCS, has the capacity to mediate cholesterol transport either from ER to LE or in the opposite direction. Moreover, it regulates the motility, positioning and fusion of LE as well as autophagic flux. ORP2, the closest relative of ORP1, is mainly cytosolic, but also targets PI(4,5)P2-rich endosomal compartments. Our latest data suggest that ORP2 transfers cholesterol from LE to recycling endosomes (RE) in exchange for PI(4,5)P2, thus stimulating the recruitment of focal adhesion kinase (FAK) on the RE and cell adhesion. FAK activates phosphoinositide kinase on the RE to enhance PI(4,5)P2 synthesis. ORP2 in turn transfers PI(4,5)P2 from RE to LE, thus regulating LE tubule formation and transport activity.
Collapse
Affiliation(s)
- Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland.
| | - Elina Ikonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
41
|
Montaño ET, Nideffer JF, Brumage L, Erb M, Busch J, Fernandez L, Derman AI, Davis JP, Estrada E, Fu S, Le D, Vuppala A, Tran C, Luterstein E, Lakkaraju S, Panchagnula S, Ren C, Doan J, Tran S, Soriano J, Fujita Y, Gutala P, Fujii Q, Lee M, Bui A, Villarreal C, Shing SR, Kim S, Freeman D, Racha V, Ho A, Kumar P, Falah K, Dawson T, Enustun E, Prichard A, Gomez A, Khanna K, Trigg S, Pogliano K, Pogliano J. Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals. PLoS One 2022; 17:e0262354. [PMID: 35061755 PMCID: PMC8782336 DOI: 10.1371/journal.pone.0262354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare’s most potent antibiotics are becoming obsolete. Approximately two-thirds of the world’s antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 104 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.
Collapse
Affiliation(s)
- Elizabeth T. Montaño
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jason F. Nideffer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Lauren Brumage
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Marcella Erb
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Julia Busch
- Department of Immunology, Duke University, Durham, North Carolina, United Stated of America
| | - Lynley Fernandez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alan I. Derman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - John Paul Davis
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elena Estrada
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Fu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Le
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aishwarya Vuppala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Cassidy Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elaine Luterstein
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shivani Lakkaraju
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sriya Panchagnula
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Caroline Ren
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer Doan
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jamielyn Soriano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Yuya Fujita
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Pranathi Gutala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Quinn Fujii
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Minda Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Anthony Bui
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Carleen Villarreal
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Samuel R. Shing
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sean Kim
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Freeman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Vipula Racha
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alicia Ho
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Prianka Kumar
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kian Falah
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Thomas Dawson
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Amy Prichard
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Ana Gomez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shelly Trigg
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
42
|
Zhang X, Xiao K, Li S, Li J, Huang J, Chen R, Pang S, Zhou X. Genome-wide analysis of the NAAT, DMAS, TOM, and ENA gene families in maize suggests their roles in mediating iron homeostasis. BMC Plant Biol 2022; 22:37. [PMID: 35039017 PMCID: PMC8762928 DOI: 10.1186/s12870-021-03422-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Nicotianamine (NA), 2'-deoxymugineic acid (DMA), and mugineic acid (MA) are chelators required for iron uptake and transport in plants. Nicotianamine aminotransferase (NAAT), 2'-deoxymugineic acid synthase (DMAS), transporter of MAs (TOM), and efflux transporter of NA (ENA) are involved in iron uptake and transport in rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare); however, these families have not been fully identified and comprehensively analyzed in maize (Zea mays L.). RESULTS Here, we identified 5 ZmNAAT, 9 ZmDMAS, 11 ZmTOM, and 2 ZmENA genes by genome mining. RNA-sequencing and quantitative real-time PCR analysis revealed that these genes are expressed in various tissues and respond differently to high and low iron conditions. In particular, iron deficiency stimulated the expression of ZmDMAS1, ZmTOM1, ZmTOM3, and ZmENA1. Furthermore, we determined protein subcellular localization by transient expression of green fluorescent protein fusions in maize mesophyll protoplasts. ZmNAAT1, ZmNAAT-L4, ZmDMAS1, and ZmDMAS-L1 localized in the cytoplasm, whereas ZmTOMs and ZmENAs targeted to plasma and tonoplast membranes, endomembranes, and vesicles. CONCLUSIONS Our results suggest that the different gene expression profiles and subcellular localizations of ZmNAAT, ZmDMAS, ZmTOM, and ZmENA family members may enable specific regulation of phytosiderophore metabolism in different tissues and under different external conditions, shedding light on iron homeostasis in maize and providing candidate genes for breeding iron-rich maize varieties.
Collapse
Affiliation(s)
- Xin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
- Center for Biological Science and Technology, Institute of Natural Science, Beijing Normal University, Zhuhai, 519087, China
| | - Ke Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Suzhen Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Li
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jiaxing Huang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China
| | - Rumei Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sen Pang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, China.
| | - Xiaojin Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
43
|
Abstract
The application of CRISPR/Cas9 system for gene editing, as a technical coup for biotechnology, is worldwide and encompasses multiple of species. The inactivation of catalytical site in Cas9 (dCas9) has been reprogrammed as an effective approach to regulate the transcriptional level of target genes, especially for the functionally essential genes and redundant genes. Here, we exploited the CRISPR/dCas9 system to manipulate the transcriptional level of target genes in common wheat. To improve target gene's expression, we generated transcriptional activator by fusing 6×TAL-VP128 activation domain to the C-terminus of dCas9 in frame. For target gene's repressing expression transcriptionally, 3×SRDX repression domain was conjugated to the C-terminus of dCas9 in frame. Our results showed that dCas9 fused activation or repression domain could increase or decrease the transcriptional level of target gene effectively in stable transgenic lines of wheat. The study on the tRNA-processing system in CRISPR/dCas9 based transcriptional regulation system demonstrated that this robust multiplex targeted tool can be incorporated to the CRISPR/dCas9 system to facilitate the target regulation of several genes' transcriptional level. Our data broaden the application of CRISPR/dCas9 based transcriptional regulation and provide great opportunities to investigate the function of essential genes in common wheat.
Collapse
Affiliation(s)
- Huajie Zhou
- College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Lixia District, Jinan 250014, Shandong, China
| | - Lei Xu
- College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Lixia District, Jinan 250014, Shandong, China
| | - Feng Li
- Shandong Shunfeng Biotechnology Co. Ltd., 11 Floor, Main Building, QiLu Innovalley Incubator, High-tech Industry Development Zone, Jinan 250000, Shandong, China
| | - Yansha Li
- Shandong Shunfeng Biotechnology Co. Ltd., 11 Floor, Main Building, QiLu Innovalley Incubator, High-tech Industry Development Zone, Jinan 250000, Shandong, China.
| |
Collapse
|
44
|
Ma R, Liu W, Li S, Zhu X, Yang J, Zhang N, Si H. Genome-Wide Identification, Characterization and Expression Analysis of the CIPK Gene Family in Potato ( Solanum tuberosum L.) and the Role of StCIPK10 in Response to Drought and Osmotic Stress. Int J Mol Sci 2021; 22:ijms222413535. [PMID: 34948331 PMCID: PMC8708990 DOI: 10.3390/ijms222413535] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
The potato (Solanum tuberosum L.), one of the most important food crops worldwide, is sensitive to environmental stresses. Sensor–responder complexes comprising calcineurin B-like (CBL) proteins and CBL-interacting protein kinases (CIPKs) not only modulate plant growth and development but also mediate numerous stress responses. Here, using a Hidden Markov Model and BLAST searches, 27 CIPK genes were identified in potato and divided into five groups by phylogenetic analysis and into two clades (intron-poor and intron-rich) by gene structure analysis. Quantitative reverse-transcription PCR (qRT-PCR) assays revealed that StCIPK genes play important roles in plant growth, development and abiotic stress tolerance. Up-regulated expression of StCIPK10 was significantly induced by drought, PEG6000 and ABA. StCIPK10 enhances both the ability of potato to scavenge reactive oxygen species and the content of corresponding osmoregulation substances, thereby strengthening tolerance to drought and osmotic stress. StCIPK10 is located at the intersection between the abscisic acid and abiotic stress signaling pathways, which control both root growth and stomatal closure in potato. In addition, StCIPK10 interacts with StCBL1, StCBL4, StCBL6, StCBL7, StCBL8, StCBL11 and StCBL12, and is specifically recruited to the plasma membrane by StCBL11.
Collapse
Affiliation(s)
- Rui Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Dingxi Academy of Agricultural Sciences, Dingxi 743000, China
| | - Weigang Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Shigui Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xi Zhu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangwei Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; (R.M.); (W.L.); (S.L.); (X.Z.); (J.Y.); (N.Z.)
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-931-763-1875
| |
Collapse
|
45
|
Shen S, Peng M, Fang H, Wang Z, Zhou S, Jing X, Zhang M, Yang C, Guo H, Li Y, Lei L, Shi Y, Sun Y, Liu X, Xu C, Tohge T, Yuan M, Fernie AR, Ning Y, Wang GL, Luo J. An Oryza-specific hydroxycinnamoyl tyramine gene cluster contributes to enhanced disease resistance. Sci Bull (Beijing) 2021; 66:2369-2380. [PMID: 36654123 DOI: 10.1016/j.scib.2021.03.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/16/2020] [Accepted: 01/07/2021] [Indexed: 02/03/2023]
Abstract
Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine (HT) gene cluster in rice. This cluster contains a pyridoxamine 5'-phosphate oxidase (OsPDX3) producing the cofactor pyridoxal 5'-phosphate (PLP), a PLP-dependent tyrosine decarboxylase (OsTyDC1), and two duplicated hydroxycinnamoyl transferases (OsTHT1 and OsTHT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of OsTyDC1 and OsTHT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and fungal pathogen Magnaporthe oryzae (M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.
Collapse
Affiliation(s)
- Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent 9052, Belgium
| | - Hong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zixuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shen Zhou
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xinyu Jing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Guo
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Long Lei
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuheng Shi
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yangyang Sun
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Congping Xu
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Takayuki Tohge
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma Nara 630-0192, Japan
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus OH 43210, USA
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou 570228, China.
| |
Collapse
|
46
|
Hu M, Li M, Wang J. Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors. Genes (Basel) 2021; 12:genes12121848. [PMID: 34946800 PMCID: PMC8701781 DOI: 10.3390/genes12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.
Collapse
Affiliation(s)
- Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
- Correspondence:
| |
Collapse
|
47
|
Fang Y, Cao D, Yang H, Guo W, Ouyang W, Chen H, Shan Z, Yang Z, Chen S, Li X, Chen L, Zhou X. Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses. Int J Mol Sci 2021; 22:12515. [PMID: 34830397 PMCID: PMC8624885 DOI: 10.3390/ijms222212515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.
Collapse
Affiliation(s)
- Yisheng Fang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China;
| | - Dong Cao
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Hongli Yang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Wei Guo
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Wenqi Ouyang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Haifeng Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Zhihui Shan
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Zhonglu Yang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Shuilian Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan 430070, China;
| | - Limiao Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| | - Xinan Zhou
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (Y.F.); (H.Y.); (W.G.); (W.O.); (H.C.); (Z.S.); (Z.Y.); (S.C.); (D.C.)
| |
Collapse
|
48
|
Santiago-Algarra D, Souaid C, Singh H, Dao LTM, Hussain S, Medina-Rivera A, Ramirez-Navarro L, Castro-Mondragon JA, Sadouni N, Charbonnier G, Spicuglia S. Epromoters function as a hub to recruit key transcription factors required for the inflammatory response. Nat Commun 2021; 12:6660. [PMID: 34795220 PMCID: PMC8602369 DOI: 10.1038/s41467-021-26861-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
Gene expression is controlled by the involvement of gene-proximal (promoters) and distal (enhancers) regulatory elements. Our previous results demonstrated that a subset of gene promoters, termed Epromoters, work as bona fide enhancers and regulate distal gene expression. Here, we hypothesized that Epromoters play a key role in the coordination of rapid gene induction during the inflammatory response. Using a high-throughput reporter assay we explored the function of Epromoters in response to type I interferon. We find that clusters of IFNa-induced genes are frequently associated with Epromoters and that these regulatory elements preferentially recruit the STAT1/2 and IRF transcription factors and distally regulate the activation of interferon-response genes. Consistently, we identified and validated the involvement of Epromoter-containing clusters in the regulation of LPS-stimulated macrophages. Our findings suggest that Epromoters function as a local hub recruiting the key TFs required for coordinated regulation of gene clusters during the inflammatory response.
Collapse
Affiliation(s)
- David Santiago-Algarra
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Charbel Souaid
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Himanshu Singh
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Lan T M Dao
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Vinmec Research Institute of Stem cell and Gene technology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Saadat Hussain
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Lucia Ramirez-Navarro
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Jaime A Castro-Mondragon
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway
| | - Nori Sadouni
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France.
- Equipe Labellisée Ligue Contre le Cancer, Paris, France.
| |
Collapse
|
49
|
Paul A, Srivastava AP, Subrahmanya S, Shen G, Mishra N. In-silico genome wide analysis of Mitogen activated protein kinase kinase kinase gene family in C. sinensis. PLoS One 2021; 16:e0258657. [PMID: 34735479 PMCID: PMC8568164 DOI: 10.1371/journal.pone.0258657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022] Open
Abstract
Mitogen activated protein kinase kinase kinase (MAPKKK) form the upstream component of MAPK cascade. It is well characterized in several plants such as Arabidopsis and rice however the knowledge about MAPKKKs in tea plant is largely unknown. In the present study, MAPKKK genes of tea were obtained through a genome wide search using Arabidopsis thaliana as the reference genome. Among 59 candidate MAPKKK genes in tea, 17 genes were MEKK-like, 31 genes were Raf-like and 11 genes were ZIK- like. Additionally, phylogenetic relationships were established along with structural analysis, which includes gene structure, its location as well as conserved motifs, cis-acting regulatory elements and functional domain signatures that were systematically examined. Also, on the basis of one orthologous gene found between tea and Arabidopsis, functional interaction was carried out in C. sinensis based on an Arabidopsis association model. The expressional profiles indicated major involvement of MAPKKK genes from tea in response to various abiotic stress factors. Taken together, this study provides the targets for additional inclusive identification, functional study, and provides comprehensive knowledge for a better understanding of the MAPKKK cascade regulatory network in C. sinensis.
Collapse
Affiliation(s)
- Abhirup Paul
- Department of Biochemistry, REVA University, Bangalore, Karnataka, India
| | - Anurag P. Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Shreya Subrahmanya
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, Karnataka, India
| | - Guoxin Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Neelam Mishra
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, Karnataka, India
| |
Collapse
|
50
|
Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Cell-type specialization is encoded by specific chromatin topologies. Nature 2021; 599:684-691. [PMID: 34789882 PMCID: PMC8612935 DOI: 10.1038/s41586-021-04081-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/30/2021] [Indexed: 11/09/2022]
Abstract
The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4-6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.
Collapse
Affiliation(s)
- Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany.
| | - Alexander Kukalev
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Izabela Harabula
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luna Zea-Redondo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Szabó
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Serebreni
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Yingnan Zhang
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Simona Bianco
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Andrea M Chiariello
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Ibai Irastorza-Azcarate
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Christoph J Thieme
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Thomas M Sparks
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Sílvia Carvalho
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology, Universidade do Porto, Porto, Portugal
| | - Luca Fiorillo
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Francesco Musella
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Ehsan Irani
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Elena Torlai Triglia
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aleksandra A Kolodziejczyk
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas Abentung
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Eleanor J Paul
- Institute of Clinical Sciences, Imperial College London, London, UK
- Center for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Center for Neurodevelopmental Disorders, King's College London, London, UK
| | - Vedran Franke
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Bioinformatics and Omics Data Science Platform, Berlin, Germany
| | - Rieke Kempfer
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Altuna Akalin
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Bioinformatics and Omics Data Science Platform, Berlin, Germany
| | - Sarah A Teichmann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Mark A Ungless
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - Mario Nicodemi
- Dipartimentio di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
- Berlin Institute of Health, Berlin, Germany
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany.
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
| |
Collapse
|