1
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Li G, Zhao X, Yang J, Hu S, Ponnu J, Kimura S, Hwang I, Torii KU, Hou H. Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39076061 DOI: 10.1111/pce.15050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024]
Abstract
Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Hu
- Laboratory of Marine Biological Resources Development and Utilization, Zhejiang Marine Development Research Institute, Zhoushan, Zhejiang, China
| | - Jathish Ponnu
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, Texas, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Ruickoldt J, Jeoung JH, Rudolph MA, Lennartz F, Kreibich J, Schomäcker R, Dobbek H. Coupling CO 2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis. Angew Chem Int Ed Engl 2024; 63:e202405120. [PMID: 38743001 DOI: 10.1002/anie.202405120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. In this study, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.
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Affiliation(s)
- Jakob Ruickoldt
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Maik Alexander Rudolph
- Technische Universität Berlin, Institut für Chemie - Technische Chemie, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Frank Lennartz
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489, Berlin, Germany
| | - Julian Kreibich
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Reinhard Schomäcker
- Technische Universität Berlin, Institut für Chemie - Technische Chemie, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
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3
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Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
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Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
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4
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Mikhailova AA, Dohmen E, Harrison MC. Major changes in domain arrangements are associated with the evolution of termites. J Evol Biol 2024; 37:758-769. [PMID: 38630634 DOI: 10.1093/jeb/voae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 12/18/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
Domains as functional protein units and their rearrangements along the phylogeny can shed light on the functional changes of proteomes associated with the evolution of complex traits like eusociality. This complex trait is associated with sterile soldiers and workers, and long-lived, highly fecund reproductives. Unlike in Hymenoptera (ants, bees, and wasps), the evolution of eusociality within Blattodea, where termites evolved from within cockroaches, was accompanied by a reduction in proteome size, raising the question of whether functional novelty was achieved with existing rather than novel proteins. To address this, we investigated the role of domain rearrangements during the evolution of termite eusociality. Analysing domain rearrangements in the proteomes of three solitary cockroaches and five eusocial termites, we inferred more than 5,000 rearrangements over the phylogeny of Blattodea. The 90 novel domain arrangements that emerged at the origin of termites were enriched for several functions related to longevity, such as protein homeostasis, DNA repair, mitochondrial activity, and nutrient sensing. Many domain rearrangements were related to changes in developmental pathways, important for the emergence of novel castes. Along with the elaboration of social complexity, including permanently sterile workers and larger, foraging colonies, we found 110 further domain arrangements with functions related to protein glycosylation and ion transport. We found an enrichment of caste-biased expression and splicing within rearranged genes, highlighting their importance for the evolution of castes. Furthermore, we found increased levels of DNA methylation among rearranged compared to non-rearranged genes suggesting fundamental differences in their regulation. Our findings indicate the importance of domain rearrangements in the generation of functional novelty necessary for termite eusociality to evolve.
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Affiliation(s)
- Alina A Mikhailova
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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5
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Chen Y, Feng L, Lin H, Liu J, Hu Q. Chromosome-level genome assembly of Helwingia omeiensis: the first genome in the family Helwingiaceae. Sci Data 2024; 11:719. [PMID: 38956089 PMCID: PMC11220072 DOI: 10.1038/s41597-024-03568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
Helwingia, a shrub of the monotypic cosmopolitan family Helwingiaceae, is distinguished by its inflorescence, in which flowers are borne on the midrib of the leaf-a trait not commonly observed in related plant families. Previous studies have investigated the development of this unusual structure using comparative anatomical methods. However, the scarcity of genomic data has hindered our understanding of the origins and evolutionary history of this uncommon trait at the molecular level. Here, we report the first high-quality genome of the family Helwingiaceae. Assembled using HiFi sequencing and Hi-C technologies, the genome of H. omeiensis is anchored to 19 chromosomes, with a total length of 2.75 Gb and a contig N50 length of 6.78 Mb. The BUSCO completeness score of the assembled genome was 98.2%. 53,951 genes were identified, of which 99.7% were annotated in at least one protein database. The high-quality reference genome of H. omeiensis provides an essential genetic resource and sheds light on the phylogeny and evolution of specific traits in the family Helwingiaceae.
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Affiliation(s)
- Yanyu Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Landi Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Hao Lin
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Quanjun Hu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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Wang Z, He J, Qi Q, Wang K, Tang H, Feng Y, Zhao X, Yi S, Zhao Y, Xu D. Chromosome-level genome assembly of Cnidium monnieri, a highly demanded traditional Chinese medicine. Sci Data 2024; 11:667. [PMID: 38909038 PMCID: PMC11193713 DOI: 10.1038/s41597-024-03523-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024] Open
Abstract
Cnidium monnieri, a medicinal herb of the Cnidium genus and the Apiaceae family, is among the most important traditional Chinese medicines and is widely distributed in China. However, to date, no C. monnieri-related genomic information has been described. In this study, we assembled the C. monnieri genome of approximately 1210.23 Mb with a contig N50 of 83.14 Mb. Using PacBio HiFi and Hi-C sequencing data, we successfully anchored 93.86% of the assembled sequences to 10 pseudochromosomes (2n = 20). We predicted a total of 37,460 protein-coding genes, with 97.02% of them being functionally annotated in Non-Redundant, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and other databases. In addition, we identified 2,778 tRNAs, 4,180 rRNAs, 258 miRNAs, and 1,700 snRNAs in the genome. This is the first reported C. monnieri genome. Hopefully, the availability of this chromosome-level reference genome provides a significant basis for upcoming natural product-related biosynthetic pathway assessment in C. monnieri.
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Affiliation(s)
- Zixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jiaxin He
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi Qi
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Kaixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Huanying Tang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yimeng Feng
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xinyue Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
- Medical Botanical Garden, China Pharmaceutical University, Nanjing, 210009, China.
| | - Dingqiao Xu
- School of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712046, China.
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7
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Urhan A, Cosma BM, Earl AM, Manson AL, Abeel T. SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings. Bioinformatics 2024; 40:btae328. [PMID: 38775729 PMCID: PMC11147799 DOI: 10.1093/bioinformatics/btae328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/08/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
MOTIVATION Today, we know the function of only a small fraction of the protein sequences predicted from genomic data. This problem is even more salient for bacteria, which represent some of the most phylogenetically and metabolically diverse taxa on Earth. This low rate of bacterial gene annotation is compounded by the fact that most function prediction algorithms have focused on eukaryotes, and conventional annotation approaches rely on the presence of similar sequences in existing databases. However, often there are no such sequences for novel bacterial proteins. Thus, we need improved gene function prediction methods tailored for bacteria. Recently, transformer-based language models-adopted from the natural language processing field-have been used to obtain new representations of proteins, to replace amino acid sequences. These representations, referred to as protein embeddings, have shown promise for improving annotation of eukaryotes, but there have been only limited applications on bacterial genomes. RESULTS To predict gene functions in bacteria, we developed SAFPred, a novel synteny-aware gene function prediction tool based on protein embeddings from state-of-the-art protein language models. SAFpred also leverages the unique operon structure of bacteria through conserved synteny. SAFPred outperformed both conventional sequence-based annotation methods and state-of-the-art methods on multiple bacterial species, including for distant homolog detection, where the sequence similarity to the proteins in the training set was as low as 40%. Using SAFPred to identify gene functions across diverse enterococci, of which some species are major clinical threats, we identified 11 previously unrecognized putative novel toxins, with potential significance to human and animal health. AVAILABILITY AND IMPLEMENTATION https://github.com/AbeelLab/safpred.
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Affiliation(s)
- Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Delft XE 2628, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Bianca-Maria Cosma
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Delft XE 2628, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology Van Mourik, Delft XE 2628, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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8
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Ulusoy E, Doğan T. Mutual annotation-based prediction of protein domain functions with Domain2GO. Protein Sci 2024; 33:e4988. [PMID: 38757367 PMCID: PMC11099699 DOI: 10.1002/pro.4988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 03/30/2024] [Indexed: 05/18/2024]
Abstract
Identifying unknown functional properties of proteins is essential for understanding their roles in both health and disease states. The domain composition of a protein can reveal critical information in this context, as domains are structural and functional units that dictate how the protein should act at the molecular level. The expensive and time-consuming nature of wet-lab experimental approaches prompted researchers to develop computational strategies for predicting the functions of proteins. In this study, we proposed a new method called Domain2GO that infers associations between protein domains and function-defining gene ontology (GO) terms, thus redefining the problem as domain function prediction. Domain2GO uses documented protein-level GO annotations together with proteins' domain annotations. Co-annotation patterns of domains and GO terms in the same proteins are examined using statistical resampling to obtain reliable associations. As a use-case study, we evaluated the biological relevance of examples selected from the Domain2GO-generated domain-GO term mappings via literature review. Then, we applied Domain2GO to predict unknown protein functions by propagating domain-associated GO terms to proteins annotated with these domains. For function prediction performance evaluation and comparison against other methods, we employed Critical Assessment of Function Annotation 3 (CAFA3) challenge datasets. The results demonstrated the high potential of Domain2GO, particularly for predicting molecular function and biological process terms, along with advantages such as producing interpretable results and having an exceptionally low computational cost. The approach presented here can be extended to other ontologies and biological entities to investigate unknown relationships in complex and large-scale biological data. The source code, datasets, results, and user instructions for Domain2GO are available at https://github.com/HUBioDataLab/Domain2GO. Additionally, we offer a user-friendly online tool at https://huggingface.co/spaces/HUBioDataLab/Domain2GO, which simplifies the prediction of functions of previously unannotated proteins solely using amino acid sequences.
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Affiliation(s)
- Erva Ulusoy
- Biological Data Science Lab, Department of Computer EngineeringHacettepe UniversityAnkaraTurkey
- Department of BioinformaticsGraduate School of Health Sciences, Hacettepe UniversityAnkaraTurkey
| | - Tunca Doğan
- Biological Data Science Lab, Department of Computer EngineeringHacettepe UniversityAnkaraTurkey
- Department of BioinformaticsGraduate School of Health Sciences, Hacettepe UniversityAnkaraTurkey
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Lin B, Luo X, Liu Y, Jin X. A comprehensive review and comparison of existing computational methods for protein function prediction. Brief Bioinform 2024; 25:bbae289. [PMID: 39003530 PMCID: PMC11246557 DOI: 10.1093/bib/bbae289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/18/2024] [Indexed: 07/15/2024] Open
Abstract
Protein function prediction is critical for understanding the cellular physiological and biochemical processes, and it opens up new possibilities for advancements in fields such as disease research and drug discovery. During the past decades, with the exponential growth of protein sequence data, many computational methods for predicting protein function have been proposed. Therefore, a systematic review and comparison of these methods are necessary. In this study, we divide these methods into four different categories, including sequence-based methods, 3D structure-based methods, PPI network-based methods and hybrid information-based methods. Furthermore, their advantages and disadvantages are discussed, and then their performance is comprehensively evaluated and compared. Finally, we discuss the challenges and opportunities present in this field.
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Affiliation(s)
- Baohui Lin
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong 518118, China
| | - Xiaoling Luo
- Guangdong Provincial Key Laboratory of Novel Security Intelligence Technologies, Shenzhen, Guangdong, China
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong 518061, China
| | - Yumeng Liu
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong 518118, China
| | - Xiaopeng Jin
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong 518118, China
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10
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Armah-Sekum RE, Szedmak S, Rousu J. Protein function prediction through multi-view multi-label latent tensor reconstruction. BMC Bioinformatics 2024; 25:174. [PMID: 38698340 PMCID: PMC11067221 DOI: 10.1186/s12859-024-05789-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND In last two decades, the use of high-throughput sequencing technologies has accelerated the pace of discovery of proteins. However, due to the time and resource limitations of rigorous experimental functional characterization, the functions of a vast majority of them remain unknown. As a result, computational methods offering accurate, fast and large-scale assignment of functions to new and previously unannotated proteins are sought after. Leveraging the underlying associations between the multiplicity of features that describe proteins could reveal functional insights into the diverse roles of proteins and improve performance on the automatic function prediction task. RESULTS We present GO-LTR, a multi-view multi-label prediction model that relies on a high-order tensor approximation of model weights combined with non-linear activation functions. The model is capable of learning high-order relationships between multiple input views representing the proteins and predicting high-dimensional multi-label output consisting of protein functional categories. We demonstrate the competitiveness of our method on various performance measures. Experiments show that GO-LTR learns polynomial combinations between different protein features, resulting in improved performance. Additional investigations establish GO-LTR's practical potential in assigning functions to proteins under diverse challenging scenarios: very low sequence similarity to previously observed sequences, rarely observed and highly specific terms in the gene ontology. IMPLEMENTATION The code and data used for training GO-LTR is available at https://github.com/aalto-ics-kepaco/GO-LTR-prediction .
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Affiliation(s)
- Robert Ebo Armah-Sekum
- Department of Computer Science, Aalto University, Konemiehentie 2, 02150, Espoo, Finland.
| | - Sandor Szedmak
- Department of Computer Science, Aalto University, Konemiehentie 2, 02150, Espoo, Finland
| | - Juho Rousu
- Department of Computer Science, Aalto University, Konemiehentie 2, 02150, Espoo, Finland.
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11
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Van Gray JB, Ayayee P. Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization. Environ Microbiol 2024; 26:e16628. [PMID: 38757470 DOI: 10.1111/1462-2920.16628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
The degradation of freshwater systems by salt pollution is a threat to global freshwater resources. Salinization is commonly identified by increased specific conductance (conductivity), a proxy for salt concentrations. However, conductivity fails to account for the diversity of salts entering freshwaters and the potential implications this has on microbial communities and functions. We tested 4 types of salt pollution-MgCl2, MgSO4, NaCl, and Na2SO4-on bacterial taxonomic and functional α-, β-diversity of communities originating from streams in two distinct localities (Nebraska [NE] and Ohio [OH], USA). Community responses depended on the site of origin, with NE and OH exhibiting more pronounced decreases in community diversity in response to Na2SO4 and MgCl2 than other salt amendments. A closer examination of taxonomic and functional diversity metrics suggests that core features of communities are more resistant to induced salt stress and that marginal features at both a population and functional level are more likely to exhibit significant structural shifts based on salt specificity. The lack of uniformity in community response highlights the need to consider the compositional complexities of salinization to accurately identify the ecological consequences of instances of salt pollution.
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Affiliation(s)
- Jonathon B Van Gray
- The Ohio State University CFAES Wooster, Agriculture Technical Institute, Wooster, Ohio, USA
| | - Paul Ayayee
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
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12
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Li S, Xiong X, Qiu S, Shen Z, He Y, Gao Z, Wan S. Chromosome-level genome assembly of the yellow-cheek carp Elopichthys bambusa. Sci Data 2024; 11:426. [PMID: 38658574 PMCID: PMC11043341 DOI: 10.1038/s41597-024-03262-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Yellow-cheek carp (Elopichthys bambusa) is a typical large and ferocious carnivorous fish endemic to East Asia, with high growth rate, nutritional value and economic value. In this study, a chromosome-level genome of yellow-cheek carp was generated by combining PacBio reads, Illumina reads and Hi-C data. The genome size is 827.63 Mb with a scaffold N50 size of 33.65 Mb, and 99.51% (823.61 Mb) of the assembled sequences were anchored to 24 pseudo-chromosomes. The genome is predicted to contain 24,153 protein-coding genes, with 95.54% having functional annotations. Repeat elements account for approximately 55.17% of the genomic landscape. The completeness of yellow-cheek carp genome assembly is highlighted by a BUSCO score of 98.4%. This genome will help us understand the genetic diversity of yellow-cheek carp and facilitate its conservation planning.
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Affiliation(s)
- Shunyao Li
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuemei Xiong
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Siyu Qiu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhigang Shen
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan He
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| | - Shiming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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13
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Papageorgiou L, Papa L, Papakonstantinou E, Mataragka A, Dragoumani K, Chaniotis D, Beloukas A, Iliopoulos C, Bongcam-Rudloff E, Chrousos GP, Kossida S, Eliopoulos E, Vlachakis D. SNP and Structural Study of the Notch Superfamily Provides Insights and Novel Pharmacological Targets against the CADASIL Syndrome and Neurodegenerative Diseases. Genes (Basel) 2024; 15:529. [PMID: 38790158 PMCID: PMC11120892 DOI: 10.3390/genes15050529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionary conserved Notch signaling pathway functions as a mediator of direct cell-cell communication between neighboring cells during development. Notch plays a crucial role in various fundamental biological processes in a wide range of tissues. Accordingly, the aberrant signaling of this pathway underlies multiple genetic pathologies such as developmental syndromes, congenital disorders, neurodegenerative diseases, and cancer. Over the last two decades, significant data have shown that the Notch signaling pathway displays a significant function in the mature brains of vertebrates and invertebrates beyond neuronal development and specification during embryonic development. Neuronal connection, synaptic plasticity, learning, and memory appear to be regulated by this pathway. Specific mutations in human Notch family proteins have been linked to several neurodegenerative diseases including Alzheimer's disease, CADASIL, and ischemic injury. Neurodegenerative diseases are incurable disorders of the central nervous system that cause the progressive degeneration and/or death of brain nerve cells, affecting both mental function and movement (ataxia). There is currently a lot of study being conducted to better understand the molecular mechanisms by which Notch plays an essential role in the mature brain. In this study, an in silico analysis of polymorphisms and mutations in human Notch family members that lead to neurodegenerative diseases was performed in order to investigate the correlations among Notch family proteins and neurodegenerative diseases. Particular emphasis was placed on the study of mutations in the Notch3 protein and the structure analysis of the mutant Notch3 protein that leads to the manifestation of the CADASIL syndrome in order to spot possible conserved mutations and interpret the effect of these mutations in the Notch3 protein structure. Conserved mutations of cysteine residues may be candidate pharmacological targets for the potential therapy of CADASIL syndrome.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
- Department of Biomedical Sciences, School of Health and Care Sciences, University of West Attica, Agioy Spyridonos, 12243 Egaleo, Greece; (D.C.); (A.B.)
| | - Lefteria Papa
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece;
| | - Antonia Mataragka
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
| | - Dimitrios Chaniotis
- Department of Biomedical Sciences, School of Health and Care Sciences, University of West Attica, Agioy Spyridonos, 12243 Egaleo, Greece; (D.C.); (A.B.)
| | - Apostolos Beloukas
- Department of Biomedical Sciences, School of Health and Care Sciences, University of West Attica, Agioy Spyridonos, 12243 Egaleo, Greece; (D.C.); (A.B.)
| | - Costas Iliopoulos
- School of Informatics, Faculty of Natural & Mathematical Sciences, King’s College London, Bush House, Strand, London WC2R 2LS, UK;
| | - Erik Bongcam-Rudloff
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden;
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece;
| | - Sofia Kossida
- IMGT, The International ImMunoGenetics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), 34000 Montpellier, France;
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; (L.P.); (L.P.); (E.P.); (A.M.); (K.D.); (E.E.)
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, 11527 Athens, Greece;
- School of Informatics, Faculty of Natural & Mathematical Sciences, King’s College London, Bush House, Strand, London WC2R 2LS, UK;
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14
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Hoepflinger MC, Barman M, Dötterl S, Tenhaken R. A novel O-methyltransferase Cp4MP-OMT catalyses the final step in the biosynthesis of the volatile 1,4-dimethoxybenzene in pumpkin (Cucurbita pepo) flowers. BMC PLANT BIOLOGY 2024; 24:294. [PMID: 38632532 PMCID: PMC11022444 DOI: 10.1186/s12870-024-04955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Floral scents play a crucial role in attracting insect pollinators. Among the compounds attractive to pollinators is 1,4-dimethoxybenzene (1,4-DMB). It is a significant contributor to the scent profile of plants from various genera, including economically important Cucurbita species. Despite its importance, the biosynthetic pathway for the formation of 1,4-DMB was not elucidated so far. RESULTS In this study we showed the catalysis of 1,4-DMB in the presence of 4-methoxyphenol (4-MP) by protein extract from Styrian oil pumpkin (Cucurbita pepo) flowers. Based on this finding, we identified a novel O-methyltransferase gene, Cp4MP-OMT, whose expression is highly upregulated in the volatile-producing tissue of pumpkin flowers when compared to vegetative tissues. OMT activity was verified by purified recombinant Cp4MP-OMT, illustrating its ability to catalyse the methylation of 4-MP to 1,4-DMB in the presence of cofactor SAM (S-(5'-adenosyl)-L-methionine). CONCLUSIONS Cp4MP-OMT is a novel O-methyltransferase from C. pepo, responsible for the final step in the biosynthesis of the floral scent compound 1,4-DMB. Considering the significance of 1,4-DMB in attracting insects for pollination and in the further course fruit formation, enhanced understanding of its biosynthetic pathways holds great promise for both ecological insights and advancements in plant breeding initiatives.
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Affiliation(s)
- Marion Christine Hoepflinger
- Department of Environment & Biodiversity, Paris Lodron University Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria
| | - Monica Barman
- Department of Environment & Biodiversity, Paris Lodron University Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Stefan Dötterl
- Department of Environment & Biodiversity, Paris Lodron University Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria
| | - Raimund Tenhaken
- Department of Environment & Biodiversity, Paris Lodron University Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria.
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15
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Kumar S, Behera SK, Gururaj K, Chaurasia A, Murmu S, Prabha R, Angadi UB, Pawaiya RS, Rai A. In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors. J Biomol Struct Dyn 2024; 42:2257-2269. [PMID: 37129165 DOI: 10.1080/07391102.2023.2204362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Enterotoxaemia (ET) is a severe disease that affects domestic ruminants, including sheep and goats, and is caused by Clostridium perfringens type B and D strains. The disease is characterized by the production of Epsilon toxin (ETX), which has a significant impact on the farming industry due to its high lethality. The binding of ETX to the host cell receptor is crucial, but still poorly understood. Therefore, the structural features of goat Myelin and lymphocytic (MAL) protein were investigated and defined in this study. We induced the mutations in aromatic amino acid residues of ETX and substituted them with aliphatic residues at domains I and II. Subsequently, protein-protein interactions (PPI) were performed between ETX (wild)-MAL and ETX (mutated)-MAL protein predicting the domain sites of ETX structure. Further, molecular dynamics (MD) simulation studies were performed for both complexes to investigate the dynamic behavior of the proteins. The binding efficiency between 'ETX (wild)-MAL protein' and 'ETX (mutated)-MAL protein complex' interactions were compared and showed that the former had stronger interactions and binding efficiency due to the higher stability of the complex. The MD analysis showed destabilization and higher fluctuations in the PPI of the mutated heterodimeric ETX-MAL complex which is otherwise essential for its functional conformation. Such kind of interactions with mutated functional domains of ligands provided much-needed clarity in understanding the pre-pore complex formation of epsilon toxin with the MAL protein receptor of goats. The findings from this study would provide an impetus for designing a novel vaccine for Enterotoxaemia in goats.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Kumaresan Gururaj
- ICAR-Central Institute for Research on Goats, Makhdoom, Mathura, India
| | | | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - U B Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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16
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Shams MH, Sohrabi SM, Jafari R, Sheikhian A, Motedayyen H, Baharvand PA, Hasanvand A, Fouladvand A, Assarehzadegan MA. Designing a T-cell epitope-based vaccine using in silico approaches against the Sal k 1 allergen of Salsola kali plant. Sci Rep 2024; 14:5040. [PMID: 38424208 PMCID: PMC10904830 DOI: 10.1038/s41598-024-55788-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Allergens originated from Salsola kali (Russian thistle) pollen grains are one of the most important sources of aeroallergens causing pollinosis in desert and semi-desert regions. T-cell epitope-based vaccines (TEV) are more effective among different therapeutic approaches developed to alleviate allergic diseases. The physicochemical properties, and B as well as T cell epitopes of Sal k 1 (a major allergen of S. kali) were predicted using immunoinformatic tools. A TEV was constructed using the linkers EAAAK, GPGPG and the most suitable CD4+ T cell epitopes. RS04 adjuvant was added as a TLR4 agonist to the amino (N) and carboxyl (C) terminus of the TEV protein. The secondary and tertiary structures, solubility, allergenicity, toxicity, stability, physicochemical properties, docking with immune receptors, BLASTp against the human and microbiota proteomes, and in silico cloning of the designed TEV were assessed using immunoinformatic analyses. Two CD4+ T cell epitopes of Sal k1 that had high affinity with different alleles of MHC-II were selected and used in the TEV. The molecular docking of the TEV with HLADRB1, and TLR4 showed TEV strong interactions and stable binding pose to these receptors. Moreover, the codon optimized TEV sequence was cloned between NcoI and XhoI restriction sites of pET-28a(+) expression plasmid. The designed TEV can be used as a promising candidate in allergen-specific immunotherapy against S. kali. Nonetheless, effectiveness of this vaccine should be validated through immunological bioassays.
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Affiliation(s)
- Mohammad Hossein Shams
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetic, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Box 6814993165, Ahvaz, Iran
| | - Reza Jafari
- School of Allied Medical Sciences, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Ali Sheikhian
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Hossein Motedayyen
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Peyman Amanolahi Baharvand
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Amin Hasanvand
- Department of Physiology and Pharmacology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Ali Fouladvand
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohammad-Ali Assarehzadegan
- Immunology Research Center, Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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17
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Oggenfuss U, Badet T, Croll D. A systematic screen for co-option of transposable elements across the fungal kingdom. Mob DNA 2024; 15:2. [PMID: 38245743 PMCID: PMC10799480 DOI: 10.1186/s13100-024-00312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Microbiology and Immunology, University of Minnesota, Medical School, Minneapolis, Minnesota, United States of America
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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18
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Viner C, Ishak CA, Johnson J, Walker NJ, Shi H, Sjöberg-Herrera MK, Shen SY, Lardo SM, Adams DJ, Ferguson-Smith AC, De Carvalho DD, Hainer SJ, Bailey TL, Hoffman MM. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome Biol 2024; 25:11. [PMID: 38191487 PMCID: PMC10773111 DOI: 10.1186/s13059-023-03070-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/21/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult. RESULTS Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We adapt the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet. Using these methods, we identify modification-sensitive transcription factor binding motifs. We confirm established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs. CONCLUSIONS Using known binding preferences to tune model parameters, we discover novel modified motifs for a wide array of transcription factors. Finally, we validate our binding preference predictions for OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.
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Affiliation(s)
- Coby Viner
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James Johnson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicolas J Walker
- Department of Genetics, University of Cambridge, Cambridge, England
| | - Hui Shi
- Department of Genetics, University of Cambridge, Cambridge, England
| | - Marcela K Sjöberg-Herrera
- Wellcome Sanger Institute, Cambridge, England
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy L Bailey
- Department of Pharmacology, University of Nevada, Reno, Reno, NV, USA
| | - Michael M Hoffman
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
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19
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Kasperski A, Heng HH. The Digital World of Cytogenetic and Cytogenomic Web Resources. Methods Mol Biol 2024; 2825:361-391. [PMID: 38913321 DOI: 10.1007/978-1-0716-3946-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
The dynamic growth of technological capabilities at the cellular and molecular level has led to a rapid increase in the amount of data on the genes and genomes of organisms. In order to store, access, compare, validate, classify, and understand the massive data generated by different researchers, and to promote effective communication among research communities, various genome and cytogenetic online databases have been established. These data platforms/resources are essential not only for computational analyses and theoretical syntheses but also for helping researchers select future research topics and prioritize molecular targets. Furthermore, they are valuable for identifying shared recurrent genomic patterns related to human diseases and for avoiding unnecessary duplications among different researchers. The website interface, menu, graphics, animations, text layout, and data from databases are displayed by a front end on the screen of a monitor or smartphone. A database front-end refers to the user interface or application that enables accessing tabular, structured, or raw data stored in the database. The Internet makes it possible to reach a greater number of users around the world and gives them quick access to information stored in databases. The number of ways of presenting this data by front-ends increases as well. This requires unifying the ways of operating and presenting information by front-ends and ensuring contextual switching between front-ends of different databases. This chapter aims to present selected cytogenetic and cytogenomic Internet resources in terms of obtaining the needed information and to indicate how to increase the efficiency of access to stored information. Through a brief introduction of these databases and by providing examples of their usage in cytogenetic analyses, we aim to bridge the gap between cytogenetics and molecular genomics by encouraging their utilization.
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Affiliation(s)
- Andrzej Kasperski
- Institute of Biological Sciences, Department of Biotechnology, Laboratory of Bioinformatics and Control of Bioprocesses, University of Zielona Góra, Zielona Góra, Poland.
| | - Henry H Heng
- Center for Molecular Medicine and Genetics, and Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
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20
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Holstein T, Muth T. Bioinformatic Workflows for Metaproteomics. Methods Mol Biol 2024; 2820:187-213. [PMID: 38941024 DOI: 10.1007/978-1-0716-3910-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.
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Affiliation(s)
- Tanja Holstein
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
- VIB-UGent Center for Medical Biotechnology, VIB and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Data Competence Center, Robert Koch Institute, Berlin, Deutschland
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany.
- Data Competence Center, Robert Koch Institute, Berlin, Deutschland.
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21
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Srivastava SK, Parker C, O'Brien CN, Tucker MS, Thompson PC, Rosenthal BM, Dubey JP, Khan A, Jenkins MC. Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella. Sci Rep 2023; 13:22802. [PMID: 38129566 PMCID: PMC10739835 DOI: 10.1038/s41598-023-50117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, "ERR296879") share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.
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Affiliation(s)
- Subodh K Srivastava
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Carolyn Parker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Celia N O'Brien
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Matthew S Tucker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Peter C Thompson
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Benjamin M Rosenthal
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Jitender P Dubey
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Asis Khan
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Mark C Jenkins
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
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22
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Jin W, Yan W, Ma M, Hasi A, Che G. Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development. BMC Genomics 2023; 24:771. [PMID: 38093236 PMCID: PMC10720240 DOI: 10.1186/s12864-023-09868-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Proteins with the jumonji (JMJ)-C domain belong to the histone demethylase family and contribute to reverse histone methylation. Although JMJ-C family genes have an essential role in regulating plant growth and development, the characterization of the JMJ-C family genes in melon has not been uncovered. RESULTS In this study, a total of 17 JMJ-C proteins were identified in melon (Cucumis melo L.). CmJMJs were categorized into five subfamilies based on the specific conserved domain: KDM4/JHDM3, KDM5/JARID1, JMJD6, KDM3/JHDM2, and JMJ-C domain-only. The chromosome localization analyses showed that 17 CmJMJs were distributed on nine chromosomes. Cis-acting element analyses of the 17 CmJMJ genes showed numerous hormone, light, and stress response elements distributed in the promoter region. Covariance analysis revealed one pair of replicated fragments (CmJMJ3a and CmJMJ3b) in 17 CmJMJ genes. We investigated the expression profile of 17 CmJMJ genes in different lateral organs and four developmental stages of fruit by RNA-seq transcriptome analysis and RT-qPCR. The results revealed that most CmJMJ genes were prominently expressed in female flowers, ovaries, and developing fruits, suggesting their active role in melon fruit development. Subcellular localization showed that the fruit-related CmJMJ5a protein is specifically localized in the cell nucleus. CONCLUSIONS This study provides a comprehensive understanding of the gene structure, classification, and evolution of JMJ-C in melon and supports the clarification of the JMJ-C functions in further research.
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Affiliation(s)
- Wuyun Jin
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wei Yan
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ming Ma
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Agula Hasi
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Gen Che
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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23
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Zhang JF, Chu HH, Liao D, Ma GJ, Tong YK, Liu YY, Li J, Ren F. Comprehensive Evolution and Expression anaLysis of PHOSPHATE 1 Gene Family in Allotetraploid Brassica napus and Its Diploid Ancestors. Biochem Genet 2023; 61:2330-2347. [PMID: 37036640 DOI: 10.1007/s10528-023-10375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
The members of PHOSPHATE 1 (PHO1) family play important roles in plant phosphate (Pi) transport and adaptation to Pi deficiency. The functions of PHO1 family proteins have been reported in several plant species, with the exception of Brassica species. Here, we identified 23, 23, and 44 putative PHO1 family genes in Brassica rapa, Brassica oleracea, and Brassica napus by whole genome analysis, respectively. The phylogenetic analysis divided PHO1 family proteins into eight groups, which represented the orthologous relationships among PHO1 members. The gene structure and the conserved motif analysis indicated that the most PHO1 family genes had similar gene structures and the PHO1 proteins shared mutual conserved motifs. The chromosome distribution analysis showed that the majority of BnPHO1 family genes distributed analogously at chromosomes with BrPHO1 and BoPHO1 family genes. The data showed that PHO1 family genes were highly conserved during evolution from diploid to tetraploid. Furthermore, the expression analysis showed that PHO1 family genes had different expression patterns in plant tissues, suggesting the diversity of gene functions in Brassica species. Meanwhile, the expression analysis also revealed that some PHO1 family genes were significantly responsive to Pi deficiency, suggesting that PHO1 family genes play critical roles in Pi uptake and homeostasis under low Pi stress. Altogether, the characteristics of PHO1 family genes provide a reliable groundwork for further dissecting their functions in Brassica species.
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Affiliation(s)
- Jian-Feng Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Hui-Hui Chu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Dan Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guang-Jing Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yi-Kai Tong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying-Ying Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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24
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Bhadola P, Deo N. Exploring complexity of class-A Beta-lactamase family using physiochemical-based multiplex networks. Sci Rep 2023; 13:20626. [PMID: 37996629 PMCID: PMC10667273 DOI: 10.1038/s41598-023-48128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
The Beta-lactamase protein family is vital in countering Beta-lactam antibiotics, a widely used antimicrobial. To enhance our understanding of this family, we adopted a novel approach employing a multiplex network representation of its multiple sequence alignment. Each network layer, derived from the physiochemical properties of amino acids, unveils distinct insights into the intricate interactions among nodes, thereby enabling the identification of key motifs. Nodes with identical property signs tend to aggregate, providing evidence of the presence of consequential functional and evolutionary constraints shaping the Beta-lactamase family. We further investigate the distribution of evolutionary links across various layers. We observe that polarity manifests the highest number of unique links at lower thresholds, followed by hydrophobicity and polarizability, wherein hydrophobicity exerts dominance at higher thresholds. Further, the combinations of polarizability and volume, exhibit multiple simultaneous connections at all thresholds. The combination of hydrophobicity, polarizability, and volume uncovers shared links exclusive to these layers, implying substantial evolutionary impacts that may have functional or structural implications. By assessing the multi-degree of nodes, we unveil the hierarchical influence of properties at each position, identifying crucial properties responsible for the protein's functionality and providing valuable insights into potential targets for modulating enzymatic activity.
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Affiliation(s)
- Pradeep Bhadola
- Centre for Theoretical Physics & Natural Philosophy, Mahidol University, Nakhonsawan Campus, Phayuha Khiri, NakhonSawan, 60130, Thailand.
| | - Nivedita Deo
- Department of Physics and Astrophysics, University of Delhi, Delhi, 110007, India.
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25
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Lu B. Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity. Animals (Basel) 2023; 13:3449. [PMID: 38003067 PMCID: PMC10668855 DOI: 10.3390/ani13223449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The extant amphibians have developed uncanny abilities to adapt to their environment. I compared the genes of amphibians to those of other vertebrates to investigate the genetic changes underlying their unique traits, especially salamanders' regeneration and longevity. Using the well-supported Batrachia tree, I found that salamander genomes have undergone accelerated adaptive evolution, especially for development-related genes. The group-based comparison showed that several genes are under positive selection, rapid evolution, and unexpected parallel evolution with traits shared by distantly related species, such as the tail-regenerative lizard and the longer-lived naked mole rat. The genes, such as EEF1E1, PAFAH1B1, and OGFR, may be involved in salamander regeneration, as they are involved in the apoptotic process, blastema formation, and cell proliferation, respectively. The genes PCNA and SIRT1 may be involved in extending lifespan, as they are involved in DNA repair and histone modification, respectively. Some genes, such as PCNA and OGFR, have dual roles in regeneration and aging, which suggests that these two processes are interconnected. My experiment validated the time course differential expression pattern of SERPINI1 and OGFR, two genes that have evolved in parallel in salamanders and lizards during the regeneration process of salamander limbs. In addition, I found several candidate genes responsible for frogs' frequent vocalization and caecilians' degenerative vision. This study provides much-needed insights into the processes of regeneration and aging, and the discovery of the critical genes paves the way for further functional analysis, which could open up new avenues for exploiting the genetic potential of humans and improving human well-being.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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26
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Ibtehaz N, Kagaya Y, Kihara D. Domain-PFP allows protein function prediction using function-aware domain embedding representations. Commun Biol 2023; 6:1103. [PMID: 37907681 PMCID: PMC10618451 DOI: 10.1038/s42003-023-05476-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Domains are functional and structural units of proteins that govern various biological functions performed by the proteins. Therefore, the characterization of domains in a protein can serve as a proper functional representation of proteins. Here, we employ a self-supervised protocol to derive functionally consistent representations for domains by learning domain-Gene Ontology (GO) co-occurrences and associations. The domain embeddings we constructed turned out to be effective in performing actual function prediction tasks. Extensive evaluations showed that protein representations using the domain embeddings are superior to those of large-scale protein language models in GO prediction tasks. Moreover, the new function prediction method built on the domain embeddings, named Domain-PFP, substantially outperformed the state-of-the-art function predictors. Additionally, Domain-PFP demonstrated competitive performance in the CAFA3 evaluation, achieving overall the best performance among the top teams that participated in the assessment.
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Affiliation(s)
- Nabil Ibtehaz
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Yuki Kagaya
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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27
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Sarker P, Mitro A, Hoque H, Hasan MN, Nurnabi Azad Jewel GM. Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Comput Biol Med 2023; 165:107436. [PMID: 37690289 DOI: 10.1016/j.compbiomed.2023.107436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.
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Affiliation(s)
- Parth Sarker
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Arnob Mitro
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Hammadul Hoque
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - Md Nazmul Hasan
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - G M Nurnabi Azad Jewel
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh.
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28
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Schreiber L, Hunnie B, Altshuler I, Góngora E, Ellis M, Maynard C, Tremblay J, Wasserscheid J, Fortin N, Lee K, Stern G, Greer CW. Long-term biodegradation of crude oil in high-arctic backshore sediments: The Baffin Island Oil Spill (BIOS) after nearly four decades. ENVIRONMENTAL RESEARCH 2023; 233:116421. [PMID: 37327845 DOI: 10.1016/j.envres.2023.116421] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/30/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
With an on-going disproportional warming of the Arctic Ocean and the reduction of the sea ice cover, the risk of an accidental oil spill from ships or future oil exploration is increasing. It is hence important to know how crude oil weathers in this environment and what factors affect oil biodegradation in the Arctic. However, this topic is currently poorly studied. In the 1980s, the Baffin Island Oil Spill (BIOS) project carried out a series of simulated oil spills in the backshore zone of beaches located on Baffin Island in the Canadian High Arctic. In this study two BIOS sites were re-visited, offering the unique opportunity to study the long-term weathering of crude oil under Arctic conditions. Here we show that residual oil remains present at these sites even after almost four decades since the original oiling. Oil at both BIOS sites appears to have attenuated very slowly with estimated loss rates of 1.8-2.7% per year. The presence of residual oil continues to significantly affect sediment microbial communities at the sites as manifested by a significantly decreased diversity, differences in the abundance of microorganisms and an enrichment of putative oil-degrading bacteria in oiled sediments. Reconstructed genomes of putative oil degraders suggest that only a subset is specifically adapted for growth under psychrothermic conditions, further reducing the time for biodegradation during the already short Arctic summers. Altogether, this study shows that crude oil spilled in the Arctic can persist and significantly affect the Arctic ecosystem for a long time, in the order of several decades.
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Affiliation(s)
- Lars Schreiber
- Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada.
| | - Blake Hunnie
- Centre for Earth Observation Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
| | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
| | - Madison Ellis
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
| | - Christine Maynard
- Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nathalie Fortin
- Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, Ontario, Canada
| | - Gary Stern
- Centre for Earth Observation Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Centre, National Research Council Canada, Montreal, Quebec, Canada; Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
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29
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Liu F, Zhao J, Sun H, Xiong C, Sun X, Wang X, Wang Z, Jarret R, Wang J, Tang B, Xu H, Hu B, Suo H, Yang B, Ou L, Li X, Zhou S, Yang S, Liu Z, Yuan F, Pei Z, Ma Y, Dai X, Wu S, Fei Z, Zou X. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nat Commun 2023; 14:5487. [PMID: 37679363 PMCID: PMC10484947 DOI: 10.1038/s41467-023-41251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
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Affiliation(s)
- Feng Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Jiantao Zhao
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Cheng Xiong
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Xin Wang
- Boyce Thompson Institute, Ithaca, NY, USA
- Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Zhongyi Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Robert Jarret
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Jin Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bingqian Tang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Hao Xu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bowen Hu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Huan Suo
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bozhi Yang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Lijun Ou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuefeng Li
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Shudong Zhou
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Sha Yang
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhoubing Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Fang Yuan
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Zhenming Pei
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yanqing Ma
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xiongze Dai
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Xuexiao Zou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China.
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Ibtehaz N, Kagaya Y, Kihara D. Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554486. [PMID: 37662252 PMCID: PMC10473699 DOI: 10.1101/2023.08.23.554486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Domains are functional and structural units of proteins that govern various biological functions performed by the proteins. Therefore, the characterization of domains in a protein can serve as a proper functional representation of proteins. Here, we employ a self-supervised protocol to derive functionally consistent representations for domains by learning domain-Gene Ontology (GO) co-occurrences and associations. The domain embeddings we constructed turned out to be effective in performing actual function prediction tasks. Extensive evaluations showed that protein representations using the domain embeddings are superior to those of large-scale protein language models in GO prediction tasks. Moreover, the new function prediction method built on the domain embeddings, named Domain-PFP, significantly outperformed the state-of-the-art function predictors. Additionally, Domain-PFP demonstrated competitive performance in the CAFA3 evaluation, achieving overall the best performance among the top teams that participated in the assessment.
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Affiliation(s)
- Nabil Ibtehaz
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | - Yuki Kagaya
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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Chu T, Shang J, Jian H, Song C, Yang R, Bao D, Tan Q, Tang L. Potential Role of Lysine Acetylation and Autophagy in Brown Film Formation and Postripening of Lentinula edodes Mycelium. Microbiol Spectr 2023; 11:e0282322. [PMID: 37347174 PMCID: PMC10434168 DOI: 10.1128/spectrum.02823-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Lentinula edodes is one of the most widely cultivated edible mushrooms in the world. When cultivated in sawdust, the surface mycelium of L. edodes needs a long postripening stage wherein it forms a brown film (BF) by secreting and accumulating pigments. BF formation is critical for the high quality and yield of fruiting bodies. Protein lysine acetylation (KAC) is an important post-translational modification that regulates growth and development. Previous studies have shown that deacetylase levels are significantly increased during BF formation in the postripening stage of L. edodes. The aim of this study was to assess the role of protein acetylation during BF formation. To this end, we compared the acetylome of L. edodes mycelia before and after BF formation using anti-acetyl antibody-based label-free quantitative proteomics. We identified 5,613 acetylation sites in 1,991 proteins, and quantitative information was available for 4,848 of these sites in 1,815 proteins. Comparative acetylome analysis showed that the modification of 699 sites increased and that of 562 sites decreased during BF formation. Bioinformatics analysis of the differentially acetylated proteins showed significant enrichment in the tricarboxylic acid (TCA) cycle and proteasome pathways. Furthermore, functional assays showed that BF formation is associated with significant changes in the activities of proteasome, citrate synthase, and isocitrate dehydrogenase. Consistent with this hypothesis, the lysine deacetylase inhibitor trichostatin (TSA) delayed autophagy and BF formation in L. edodes. Taken together, KAC and autophagy play important roles in the mycelial BF formation and postripening stage of L. edodes. IMPORTANCE Mycelial BF formation and postripening of L. edodes affects the quality and quantity of its edible fruiting bodies. In this study, we explored the role of protein KAC in this biological process, with the aim of optimizing the cultivation and yield of L. edodes.
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Affiliation(s)
- Ting Chu
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- School of Food Sciences and Technology, Shanghai Ocean University, Shanghai, China
| | - Junjun Shang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Song
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ruiheng Yang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qi Tan
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lihua Tang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Wang T, Koukoulis TF, Vella LJ, Su H, Purnianto A, Nie S, Ang CS, Ma G, Korhonen PK, Taki AC, Williamson NA, Reid GE, Gasser RB. The Proteome and Lipidome of Extracellular Vesicles from Haemonchus contortus to Underpin Explorations of Host-Parasite Cross-Talk. Int J Mol Sci 2023; 24:10955. [PMID: 37446130 DOI: 10.3390/ijms241310955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Many parasitic worms have a major adverse impact on human and animal populations worldwide due to the chronicity of their infections. There is a growing body of evidence indicating that extracellular vesicles (EVs) are intimately involved in modulating (suppressing) inflammatory/immune host responses and parasitism. As one of the most pathogenic nematodes of livestock animals, Haemonchus contortus is an ideal model system for EV exploration. Here, employing a multi-step enrichment process (in vitro culture, followed by ultracentrifugation, size exclusion and filtration), we enriched EVs from H. contortus and undertook the first comprehensive (qualitative and quantitative) multi-omic investigation of EV proteins and lipids using advanced liquid chromatography-mass spectrometry and informatics methods. We identified and quantified 561 proteins and 446 lipids in EVs and compared these molecules with those of adult worms. We identified unique molecules in EVs, such as proteins linked to lipid transportation and lipid species (i.e., sphingolipids) associated with signalling, indicating the involvement of these molecules in parasite-host cross-talk. This work provides a solid starting point to explore the functional roles of EV-specific proteins and lipids in modulating parasite-host cross-talk, and the prospect of finding ways of disrupting or interrupting this relationship to suppress or eliminate parasite infection.
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Affiliation(s)
- Tao Wang
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tiana F Koukoulis
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura J Vella
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Adityas Purnianto
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Guangxu Ma
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pasi K Korhonen
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Aya C Taki
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Gavin E Reid
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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Khan A, Chen S, Fatima S, Ahamad L, Siddiqui MA. Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions. PLANTS (BASEL, SWITZERLAND) 2023; 12:2387. [PMID: 37376010 DOI: 10.3390/plants12122387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.
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Affiliation(s)
- Arshad Khan
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Saba Fatima
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Lukman Ahamad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
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Armstrong EJ, Lê-Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nat Commun 2023; 14:3056. [PMID: 37264036 DOI: 10.1038/s41467-023-38610-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.
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Affiliation(s)
- Eric J Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, La Paz, Baja California Sur, 23096, México
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Emilie Boissin
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Guillaume Iwankow
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan institute, University of Galway, University Road H91TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Oregon State University, Department of Microbiology, 220 Nash Hall, 97331, Corvallis, OR, USA
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860, Perpignan Cedex, France
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Principality of Monaco, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Principality of Monaco, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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Li M, Shi W, Zhang F, Zeng M, Li Y. A Deep Learning Framework for Predicting Protein Functions With Co-Occurrence of GO Terms. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:833-842. [PMID: 35476573 DOI: 10.1109/tcbb.2022.3170719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The understanding of protein functions is critical to many biological problems such as the development of new drugs and new crops. To reduce the huge gap between the increase of protein sequences and annotations of protein functions, many methods have been proposed to deal with this problem. These methods use Gene Ontology (GO) to classify the functions of proteins and consider one GO term as a class label. However, they ignore the co-occurrence of GO terms that is helpful for protein function prediction. We propose a new deep learning model, named DeepPFP-CO, which uses Graph Convolutional Network (GCN) to explore and capture the co-occurrence of GO terms to improve the protein function prediction performance. In this way, we can further deduce the protein functions by fusing the predicted propensity of the center function and its co-occurrence functions. We use Fmax and AUPR to evaluate the performance of DeepPFP-CO and compare DeepPFP-CO with state-of-the-art methods such as DeepGOPlus and DeepGOA. The computational results show that DeepPFP-CO outperforms DeepGOPlus and other methods. Moreover, we further analyze our model at the protein level. The results have demonstrated that DeepPFP-CO improves the performance of protein function prediction. DeepPFP-CO is available at https://csuligroup.com/DeepPFP/.
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Ye YX, Li DT, Zhang SY, Shen ZC, Zhang CX. Chromosome-level Genome Assembly and Sex-specific Differential Transcriptome of the White-backed Planthopper, Sogatella furcifera. Curr Genomics 2023; 23:400-411. [PMID: 37920557 PMCID: PMC10173415 DOI: 10.2174/1389202924666230102092822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/14/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
Background The white-backed planthopper (WBPH), Sogatella furcifera, causes great damage to many crops (mainly rice) by direct feeding or transmitting plant viruses. The previous genome assembly was generated by second-generation sequencing technologies, with a contig N50 of only 51.5 kb, and contained a lot of heterozygous sequences. Methods We utilized third-generation sequencing technologies and Hi-C data to generate a high-quality chromosome-level assembly. We also provide a large amount of transcriptome data for full-length transcriptome analysis and gender differential expression analysis. Results The final assembly comprised 56.38 Mb, with a contig N50 of 2.20 Mb and a scaffold N50 of 45.25 Mb. Fourteen autosomes and one X chromosome were identified. More than 99.5% of the assembled bases located on the 15 chromosomes. 95.9% of the complete BUSCO Hemiptera genes were detected in the final assembly and 16,880 genes were annotated. 722 genes were relatively highly expressed in males, while 60 in the females. Conclusion The integrated genome, definite sex chromosomes, comprehensive transcriptome profiles, high efficiency of RNA interference and short life cycle substantially made WBPH an efficient research object for functional genomics.
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Affiliation(s)
- Yu-Xuan Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- The rural development academy, Zhejiang University, Hangzhou, 310058, China
| | - Dan-Ting Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Si-Yu Zhang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhi-Cheng Shen
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan-Xi Zhang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
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37
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Lechuga-Paredes P, Segura-León OL, Cibrián-Tovar J, Torres-Huerta B, Velázquez-González JC, Cruz-Jaramillo JL. Odorant-Binding and Chemosensory Proteins in Anthonomus eugenii (Coleoptera: Curculionidae) and Their Tissue Expression. Int J Mol Sci 2023; 24:ijms24043406. [PMID: 36834814 PMCID: PMC9961831 DOI: 10.3390/ijms24043406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
The pepper weevil Anthonomus eugenii is one of the most damaging pests to the pepper crop. To offer alternative management strategies to insecticides, several studies have identified the semiochemicals that are involved in the pepper weevil's aggregation and mating behavior; however, there is no information on its perireceptor molecular mechanism, to date. In this study, bioinformatics tools were used to functionally annotate and characterize the A. eugenii head transcriptome and their probable coding proteins. We identified twenty-two transcripts belonging to families related to chemosensory processes, seventeen corresponding to odorant-binding proteins (OBP), and six to chemosensory proteins (CSP). All results matched with closely related Coleoptera: Curculionidae homologous proteins. Likewise, twelve OBP and three CSP transcripts were experimentally characterized by RT-PCR in different female and male tissues. The results by sex and tissue display the different expression patterns of the AeugOBPs and AeugCSPs; some are present in both sexes and all tissues, while others show expressions with higher specificity, which suggests diverse physiological functions in addition to chemo-detection. This study provides information to support the understanding of odor perception in the pepper weevil.
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Affiliation(s)
- Pablo Lechuga-Paredes
- Colegio de Postgraduados, Campus Montecillo, Mexico-Texcoco Highway, Km. 36.5 Montecillo, Texcoco 56230, Mexico
| | - Obdulia Lourdes Segura-León
- Colegio de Postgraduados, Campus Montecillo, Mexico-Texcoco Highway, Km. 36.5 Montecillo, Texcoco 56230, Mexico
- Correspondence: ; Tel.: +52-554-009-3079
| | - Juan Cibrián-Tovar
- Colegio de Postgraduados, Campus Montecillo, Mexico-Texcoco Highway, Km. 36.5 Montecillo, Texcoco 56230, Mexico
| | - Brenda Torres-Huerta
- Colegio de Postgraduados, Campus Montecillo, Mexico-Texcoco Highway, Km. 36.5 Montecillo, Texcoco 56230, Mexico
| | | | - José Luis Cruz-Jaramillo
- Bioinformatics and Technologies Department, Solaria Biodata, Antonio Ortega 817, Benito Juárez, Mexico City 03100, Mexico
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The genome of a Far Eastern isolate of Diaporthe caulivora, a soybean fungal pathogen. Appl Microbiol Biotechnol 2023; 107:1311-1327. [PMID: 36650392 DOI: 10.1007/s00253-023-12370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/26/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023]
Abstract
Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. KEY POINTS: • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.
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Zhang X, Jiang Z, Jiao X, Yu Y, Wang Z, Hou Y, Duan G, Du W, Ruan C, Zhang J, Hu Y. Genome Assembly and Comparative Analysis of the Egg Parasitoid Wasp Trichogramma dendrolimi Shed Light on the Composition and Evolution of Olfactory Receptors and Venoms. INSECTS 2023; 14:144. [PMID: 36835713 PMCID: PMC9960361 DOI: 10.3390/insects14020144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Trichogramma dendrolimi is one of the most successfully industrialized Trichogramma species used to control agricultural and forestry pests in China. However, the molecular mechanisms underlying its host recognition and parasitism remain largely unknown, partially due to the limited genome information of this parasitoid wasp. Here, we present a high-quality de novo assembly of T. dendrolimi through a combination of Illumina and PacBio sequencing technologies. The final assembly had a length of 215.2 Mb and contains 316 scaffolds with a scaffold N50 size of 1.41 Mb. Repetitive sequences with a length of 63.4 Mb and 12,785 protein-coding genes were identified. Significantly expanded gene families were identified to be involved in the development and regulatory processes, while remarkably contracted gene families were involved in the transport processes in T. dendrolimi. The olfactory and venom-associated genes were identified in T. dendrolimi and 24 other hymenopteran species, using uniform methods combining BLAST and HMM profiling. The identified venom genes of T. dendrolimi were enriched in antioxidant activity, tricarboxylic acid cycle, response to oxidative stress and cell redox homeostasis. Our study provides an important resource for comparative genomics and functional studies to interpret the molecular mechanisms underlying host recognition and parasitism of Trichogramma species.
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Affiliation(s)
- Xue Zhang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Zhuo Jiang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Xilin Jiao
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Yang Yu
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Zhenan Wang
- Department of Plant Pathology, College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yangyang Hou
- Department of Entomology, College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Guohua Duan
- Department of Plant Pathology, College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Wenmei Du
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Changchun Ruan
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Junjie Zhang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Ying Hu
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
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Wang C, Liu Y, Cui M, Liu B. Systematic analysis reveals novel insight into the molecular determinants of function, diversity and evolution of sweet taste receptors T1R2/T1R3 in primates. Front Mol Biosci 2023; 10:1037966. [PMID: 36762208 PMCID: PMC9905694 DOI: 10.3389/fmolb.2023.1037966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Sweet taste is a primary sensation for the preference and adaption of primates to diet, which is crucial for their survival and fitness. It is clear now that the sweet perception is mediated by a G protein-coupled receptor (GPCR)-sweet taste receptor T1R2/T1R3, and many behavioral or physiological experiments have described the diverse sweet taste sensitivities in primates. However, the structure-function relationship of T1R2s/T1R3s in primates, especially the molecular basis for their species-dependent sweet taste, has not been well understood until now. In this study, we performed a comprehensive sequence, structural and functional analysis of sweet taste receptors in primates to elucidate the molecular determinants mediating their species-dependent sweet taste recognition. Our results reveal distinct taxonomic distribution and significant characteristics (interaction, coevolution and epistasis) of specific key function-related residues, which could partly account for the previously reported behavioral results of taste perception in primates. Moreover, the prosimians Lemuriformes species, which were reported to have no sensitivity to aspartame, could be proposed to be aspartame tasters based on the present analysis. Collectively, our study provides new insights and promotes a better understanding for the diversity, function and evolution of sweet taste receptors in primates.
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Affiliation(s)
- Congrui Wang
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yi Liu
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States,*Correspondence: Meng Cui, ; Bo Liu,
| | - Bo Liu
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China,*Correspondence: Meng Cui, ; Bo Liu,
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Gautam A, Zeng W, Huson DH. DIAMOND + MEGAN Microbiome Analysis. Methods Mol Biol 2023; 2649:107-131. [PMID: 37258860 DOI: 10.1007/978-1-0716-3072-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.
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Affiliation(s)
- Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Wenhuan Zeng
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
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Roy R, Lorca C, Mulet M, Sánchez Milán JA, Baratas A, de la Casa M, Espinet C, Serra A, Gallart-Palau X. Altered ureido protein modification profiles in seminal plasma extracellular vesicles of non-normozoospermic men. Front Endocrinol (Lausanne) 2023; 14:1113824. [PMID: 37033249 PMCID: PMC10073716 DOI: 10.3389/fendo.2023.1113824] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
INTRODUCTION Extracellular vesicles (EVs) have been recognized as key players in numerous physiological functions. These vesicles alter their compositions attuned to the health and disease states of the organism. In men, significant changes in the proteomic composition(s) of seminal plasma EVs (sEVs) have already been found to be related to infertility. METHODS Methods: In this study, we analyze the posttranslational configuration of sEV proteomes from normozoospermic (NZ) men and non-normozoospermic (non-NZ) men diagnosed with teratozoospermia and/or asthenozoospermia by unbiased, discovery-driven proteomics and advanced bioinformatics, specifically focusing on citrulline (Cit) and homocitrulline (hCit) posttranscriptional residues, both considered product of ureido protein modifications. RESULTS AND DISCUSSION Significant increase in the proteome-wide cumulative presence of hCit together with downregulation of Cit in specific proteins related to decisive molecular functions have been encountered in sEVs of non-NZ subjects. These findings identify novel culprits with a higher chance of affecting fundamental aspects of sperm functional quality and define potential specific diagnostic and prognostic non-invasive markers for male infertility.
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Affiliation(s)
- Rosa Roy
- Department of Biology, Genetics Unit, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Cristina Lorca
- Biomedical Research Institute of Lleida (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), Neuroscience Area, University Hospital Arnau de Vilanova (HUAV), Lleida, Spain
- IMDEA-Food Research Institute, Campus of International Excellence UAM+CSIC, Old Cantoblanco Hospital, Madrid, Spain
| | - María Mulet
- Biomedical Research Institute of Lleida (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), Neuroscience Area, University Hospital Arnau de Vilanova (HUAV), Lleida, Spain
- IMDEA-Food Research Institute, Campus of International Excellence UAM+CSIC, Old Cantoblanco Hospital, Madrid, Spain
| | - José Antonio Sánchez Milán
- Biomedical Research Institute of Lleida (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), Neuroscience Area, University Hospital Arnau de Vilanova (HUAV), Lleida, Spain
| | - Alejandro Baratas
- Department of Biology, Genetics Unit, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Moisés de la Casa
- Department of Biology, Genetics Unit, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- GINEFIV, Assisted Reproduction Centre, Madrid, Spain
| | - Carme Espinet
- Department of Medical Basic Sciences, University of Lleida (UdL), Lleida, Spain
| | - Aida Serra
- Biomedical Research Institute of Lleida (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), Neuroscience Area, University Hospital Arnau de Vilanova (HUAV), Lleida, Spain
- IMDEA-Food Research Institute, Campus of International Excellence UAM+CSIC, Old Cantoblanco Hospital, Madrid, Spain
- Department of Medical Basic Sciences, University of Lleida (UdL), Lleida, Spain
- *Correspondence: Aida Serra, ; Xavier Gallart-Palau,
| | - Xavier Gallart-Palau
- Biomedical Research Institute of Lleida (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), Neuroscience Area, University Hospital Arnau de Vilanova (HUAV), Lleida, Spain
- Department of Psychology, University of Lleida (UdL), Lleida, Spain
- *Correspondence: Aida Serra, ; Xavier Gallart-Palau,
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Bing XL, Xia CB, Ye QT, Gong X, Cui JR, Peng CW, Hong XY. Wolbachia manipulates reproduction of spider mites by influencing herbivore salivary proteins. PEST MANAGEMENT SCIENCE 2023; 79:315-323. [PMID: 36151871 DOI: 10.1002/ps.7201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The endosymbiont Wolbachia is known for manipulating host reproduction. Wolbachia also can affect host fitness by mediating interactions between plant and herbivores. However, it remains unclear whether saliva proteins are involved in this process. RESULTS We found that Wolbachia infection decreased the number of deposited eggs but increased the egg hatching rate in the spider mite Tetranychus urticae Koch (Acari: Tetranychidae), a cosmopolitan pest that infects >1000 species of plants. Transcriptomic and proteomic analyses revealed that Wolbachia-infected mites upregulated the gene expression levels of many T. urticae salivary proteins including a cluster of Tetranychidae-specific, functionally uncharacterized SHOT1s (secreted host-responsive proteins of Tetranychidae). The SHOT1 genes were expressed more in the feeding stages (nymphs and adults) of mites than in eggs and highly enriched in the proterosomas. RNA interference experiments showed that knockdown of SHOT1s significantly decreased Wolbachia density, increased the number of deposited eggs and decreased the egg hatching rate. CONCLUSION Together, these results indicate that SHOT1s are positively correlated with Wolbachia density and account for Wolbachia-mediated phenotypes. Our results provide new evidence that herbivore salivary proteins are related to Wolbachia-mediated manipulations of host performance on plants. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Cai-Bei Xia
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Qing-Tong Ye
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xue Gong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jia-Rong Cui
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Chang-Wu Peng
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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Hossain MA, Al Ashik SA, Mahin MR, Al Amin M, Rahman MH, Khan MA, Emran AA. Systems biology and in silico-based analysis of PCOS revealed the risk of metabolic disorders. Heliyon 2022; 8:e12480. [PMID: 36619413 PMCID: PMC9816984 DOI: 10.1016/j.heliyon.2022.e12480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/18/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background Polycystic ovarian syndrome (PCOS) is a common condition of hyperandrogenism, chronic ovulation, and polycystic ovaries in females during the reproduction and maturation of the ovum. Although PCOS has been associated with metabolic disorders, including type 2 diabetes (T2D), obesity (OBE), and cardiovascular disease (CVD), Causal connection and molecular features are still unknown. Purpose Therefore, we investigated the shared common differentially expressed genes (DEGs), pathways, and networks of associated proteins in PCOS and metabolic diseases with therapeutic intervention. Methods We have used a bioinformatics pipeline to analyze transcriptome data for the polycystic ovarian syndrome (PCOS), type 2 diabetes (T2D), obesity (OBE), and cardiovascular diseases (CVD) in female patients. Then we employed gene-disease association network, gene ontology (GO) and signaling pathway analysis, selection of hub genes from protein-protein interaction (PPI) network, molecular docking, and gold benchmarking approach to screen potential hub proteins. Result We discovered 2225 DEGs in PCOS patients relative to healthy controls and 34, 91, and 205 significant DEGs with T2D, Obesity, and CVD, respectively. Gene Ontology analysis revealed several significant shared and metabolic pathways from signaling pathway analysis. Furthermore, we identified ten potential hub proteins from PPI analysis that may serve as a therapeutic intervention in the future. Finally, we targeted one significant hub protein, IGF2R (PDB ID: 2V5O), out of ten hub proteins based on the Maximal clique centrality (MCC) algorithm and literature review for molecular docking study. Enzastaurin (-12.5), Kaempferol (-9.1), Quercetin (-9.0), and Coumestrol (-8.9) kcal/mol showed higher binding affinity in the molecular docking approach than 19 drug compounds. We have also found that the selected four compounds displayed favorable ADMET properties compared to the native ligand. Conclusion Our in-silico research findings identified a shared molecular etiology between PCOS and metabolic diseases that may suggest new therapeutic targets and warrants future experimental validation of the key targets.
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Affiliation(s)
- Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1092, Bangladesh
| | - Sheikh Abdullah Al Ashik
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1092, Bangladesh
| | - Moshiur Rahman Mahin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1092, Bangladesh
| | - Md. Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1092, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Md. Arif Khan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1092, Bangladesh,Department of Biotechnology and Genetic Engineering, University of Development Alternative, 4/4B, Block A, Lalmatia, Dhaka, 1209, Bangladesh
| | - Abdullah Al Emran
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1092, Bangladesh,Corresponding author.
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Lei S, Lei X, Liu L. Drug repositioning based on heterogeneous networks and variational graph autoencoders. Front Pharmacol 2022; 13:1056605. [PMID: 36618933 PMCID: PMC9812491 DOI: 10.3389/fphar.2022.1056605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Predicting new therapeutic effects (drug repositioning) of existing drugs plays an important role in drug development. However, traditional wet experimental prediction methods are usually time-consuming and costly. The emergence of more and more artificial intelligence-based drug repositioning methods in the past 2 years has facilitated drug development. In this study we propose a drug repositioning method, VGAEDR, based on a heterogeneous network of multiple drug attributes and a variational graph autoencoder. First, a drug-disease heterogeneous network is established based on three drug attributes, disease semantic information, and known drug-disease associations. Second, low-dimensional feature representations for heterogeneous networks are learned through a variational graph autoencoder module and a multi-layer convolutional module. Finally, the feature representation is fed to a fully connected layer and a Softmax layer to predict new drug-disease associations. Comparative experiments with other baseline methods on three datasets demonstrate the excellent performance of VGAEDR. In the case study, we predicted the top 10 possible anti-COVID-19 drugs on the existing drug and disease data, and six of them were verified by other literatures.
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Añorga M, Urriza M, Ramos C, Murillo J. Multiple relaxases contribute to the horizontal transfer of the virulence plasmids from the tumorigenic bacterium Pseudomonas syringae pv. savastanoi NCPPB 3335. Front Microbiol 2022; 13:1076710. [PMID: 36578579 PMCID: PMC9791958 DOI: 10.3389/fmicb.2022.1076710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas syringae pv. savastanoi NCPPB 3335 is the causal agent of olive knot disease and contains three virulence plasmids: pPsv48A (pA), 80 kb; pPsv48B (pB), 45 kb, and pPsv48C (pC), 42 kb. Here we show that pB contains a complete MPFT (previously type IVA secretion system) and a functional origin of conjugational transfer adjacent to a relaxase of the MOBP family; pC also contains a functional oriT-MOBP array, whereas pA contains an incomplete MPFI (previously type IVB secretion system), but not a recognizable oriT. Plasmid transfer occurred on solid and in liquid media, and on leaf surfaces of a non-host plant (Phaseolus vulgaris) with high (pB) or moderate frequency (pC); pA was transferred only occasionally after cointegration with pB. We found three plasmid-borne and three chromosomal relaxase genes, although the chromosomal relaxases did not contribute to plasmid dissemination. The MOBP relaxase genes of pB and pC were functionally interchangeable, although with differing efficiencies. We also identified a functional MOBQ mobilization region in pC, which could only mobilize this plasmid. Plasmid pB could be efficiently transferred to strains of six phylogroups of P. syringae sensu lato, whereas pC could only be mobilized to two strains of phylogroup 3 (genomospecies 2). In two of the recipient strains, pB was stably maintained after 21 subcultures in liquid medium. The carriage of several relaxases by the native plasmids of P. syringae impacts their transfer frequency and, by providing functional diversity and redundancy, adds robustness to the conjugation system.
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Affiliation(s)
- Maite Añorga
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain
| | - Miriam Urriza
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain,Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Jesús Murillo
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra (UPNA), Edificio de Agrobiotecnología, Mutilva Baja, Spain,*Correspondence: Jesús Murillo
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Truong AD, Tran HTT, Nguyen HT, Chu NT, Hong YH, Lillehoj HS, Dang HV, Song KD. Molecular and functional characterization of chicken interleukin 1 receptor 2 (chIL-1R2). Poult Sci 2022; 102:102399. [PMID: 36586293 PMCID: PMC9811199 DOI: 10.1016/j.psj.2022.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/24/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Interleukin-1 receptor type 2 (IL1R2) is a decoy receptor for exogenous IL-1. However, its functional role in chicken immunity is poorly understood. Herein, chicken IL-1R2 (chIL-1R2) was identified and functionally characterized in vivo and in vitro. The chIL-1R2 coding sequence includes 1,236 nucleotides encoding 412 amino acids, is highly conserved, and has a close relationship with its mammalian counterpart. Its extracellular region has three Ig-like domains but no TIR domain for intracellular signaling. Using ELISA, the recombinant chIL-1R2 protein was demonstrated to specifically bind to the chicken IL-1β. ChIL-1R2 mRNA expression was shown to be higher in the spleen, lung, kidney, small intestine, and liver. The expression of chIL-1R2 and chIL-1R1 was significantly upregulated in DF-1 cells treated with poly (I:C), but significantly downregulated in the presence of NF-κB, JNK, and MEK inhibitors, indicating that the NF-κB, JNK, and MEK signaling pathways are required for the transcriptional regulation of chIL-1R1 and chIL-1R2 expression. It is worth noting that while the p30 MAPK pathway was required for chIL-1R1 expression, it was not required for chIL-1R2 expression. Furthermore, chIL-1R2 expression increased as early as day 1, and then significantly decreased until day 3, while chIL-1R1 was dramatically upregulated in four organs of chickens infected with the highly pathogenic avian influenza virus (HPAIV). These findings indicate that chIL-1R1 and chIL-1R2 may play a crucial in innate and adaptive immune responses toward HPAIV infection. In summary the present study showed that chIL-1R2 binds to chIL-1β antibody. ChIL-1R2 expression can be induced by a viral infection, and may be regulated through NF-κB/JNK/MEK-mediated signaling pathways.
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Affiliation(s)
- Anh Duc Truong
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, Dong Da, Ha Noi, 100000, Vietnam
| | - Ha Thi Thanh Tran
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, Dong Da, Ha Noi, 100000, Vietnam
| | - Huyen Thi Nguyen
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, Dong Da, Ha Noi, 100000, Vietnam
| | - Nhu Thi Chu
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, Dong Da, Ha Noi, 100000, Vietnam
| | - Yeong Ho Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hyun S. Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hoang Vu Dang
- Department of Biochemistry and Immunology, National Institute of Veterinary Research, Dong Da, Ha Noi, 100000, Vietnam
| | - Ki-Duk Song
- The Animal Molecular Genetics and Breeding Center & Department of Agricultural Convergence Technology, JeonBuk National University, Jeonju, 54896, Republic of Korea,Corresponding author:
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Wang T, Gasser RB, Korhonen PK, Young ND, Ang CS, Williamson NA, Ma G, Samarawickrama GR, Fernando DD, Fischer K. Proteomic analysis of Sarcoptes scabiei reveals that proteins differentially expressed between eggs and female adult stages are involved predominantly in genetic information processing, metabolism and/or host-parasite interactions. PLoS Negl Trop Dis 2022; 16:e0010946. [PMID: 36472966 PMCID: PMC9725168 DOI: 10.1371/journal.pntd.0010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Presently, there is a dearth of proteomic data for parasitic mites and their relationship with the host animals. Here, using a high throughput LC-MS/MS-based approach, we undertook the first comprehensive, large-scale proteomic investigation of egg and adult female stages of the scabies mite, Sarcoptes scabiei-one of the most important parasitic mites of humans and other animals worldwide. In total, 1,761 S. scabiei proteins were identified and quantified with high confidence. Bioinformatic analyses revealed differentially expressed proteins to be involved predominantly in biological pathways or processes including genetic information processing, energy (oxidative phosphorylation), nucleotide, amino acid, carbohydrate and/or lipid metabolism, and some adaptive processes. Selected, constitutively and highly expressed proteins, such as peptidases, scabies mite inactivated protease paralogues (SMIPPs) and muscle proteins (myosin and troponin), are proposed to be involved in key biological processes within S. scabiei, host-parasite interactions and/or the pathogenesis of scabies. These proteomic data will enable future molecular, biochemical and physiological investigations of early developmental stages of S. scabiei and the discovery of novel interventions, targeting the egg stage, given its non-susceptibility to acaricides currently approved for the treatment of scabies in humans.
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Affiliation(s)
- Tao Wang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
- * E-mail:
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Australia
| | - Nicholas A. Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Australia
| | - Guangxu Ma
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Gangi R. Samarawickrama
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Deepani D. Fernando
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Katja Fischer
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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49
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Cheng S, Fahmi NA, Park M, Sun J, Thao K, Yeh HS, Zhang W, Yong J. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing. Int J Mol Sci 2022; 23:ijms232012416. [PMID: 36293270 PMCID: PMC9604279 DOI: 10.3390/ijms232012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3′-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
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Affiliation(s)
- Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Kaitlyn Thao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
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50
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Farci D, Cocco E, Tanas M, Kirkpatrick J, Maxia A, Tamburini E, Schröder WP, Piano D. Isolation and characterization of a main porin from the outer membrane of Salinibacter ruber. J Bioenerg Biomembr 2022; 54:273-281. [PMID: 36229623 DOI: 10.1007/s10863-022-09950-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022]
Abstract
Salinibacter ruber is an extremophilic bacterium able to grow in high-salts environments, such as saltern crystallizer ponds. This halophilic bacterium is red-pigmented due to the production of several carotenoids and their derivatives. Two of these pigment molecules, salinixanthin and retinal, are reported to be essential cofactors of the xanthorhodopsin, a light-driven proton pump unique to this bacterium. Here, we isolate and characterize an outer membrane porin-like protein that retains salinixanthin. The characterization by mass spectrometry identified an unknown protein whose structure, predicted by AlphaFold, consists of a 8 strands beta-barrel transmembrane organization typical of porins. The protein is found to be part of a functional network clearly involved in the outer membrane trafficking. Cryo-EM micrographs showed the shape and dimensions of a particle comparable with the ones of the predicted structure. Functional implications, with respect to the high representativity of this protein in the outer membrane fraction, are discussed considering its possible role in primary functions such as the nutrients uptake and the homeostatic balance. Finally, also a possible involvement in balancing the charge perturbation associated with the xanthorhodopsin and ATP synthase activities is considered.
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Affiliation(s)
- Domenica Farci
- Department of Chemistry, Umeå University, Linnaeus väg 6, 90736, Umeå, Sweden. .,Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy.
| | - Emma Cocco
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | - Marta Tanas
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | | | - Andrea Maxia
- Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | - Elena Tamburini
- Department of Biomedical Sciences, Università degli Studi di Cagliari, Cittadella Universitaria sp. 8, 09042, Monserrato, CA, Italy
| | - Wolfgang P Schröder
- Department of Chemistry, Umeå University, Linnaeus väg 6, 90736, Umeå, Sweden
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy.
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