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Osman MEM, Osman RSH, Elmubarak SA, Dirar AI, Konozy EHE. Phoenix dactylifera (date palm; Arecaceae) putative lectin homologs: Genome-wide search, architecture analysis, and evolutionary relationship. Saudi J Biol Sci 2023; 30:103676. [PMID: 37213699 PMCID: PMC10197109 DOI: 10.1016/j.sjbs.2023.103676] [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: 02/25/2023] [Revised: 04/10/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023] Open
Abstract
The date palm, Phoenix dactylifera, is a vital crop in nations in the Middle East and North Africa. The date palm was thought to have outstanding traditional medicinal value because it was abundant in phytochemicals with diverse chemical structures. The date palm's ability to withstand harsh environments could be partly attributed to a class of proteins known as lectins, which are carbohydrate-binding proteins that can bind sugar moieties reversibly and without changing their chemical structures. After scanning the genome of P. dactylifera (GCF 009389715.1), this in silico study discovered 196 possible lectin homologs from 11 different families, some specific to plants. At the same time, others could also be found in other kingdoms of life. Their domain architectures and functional amino acid residues were investigated, and they yielded a 40% true-lectin with known conserved carbohydrate-binding residues. Further, their probable subcellular localization, physiochemical and phylogenetic analyses were also performed. Scanning all putative lectin homologs against the anticancer peptide (ACP) dataset found in the AntiCP2.0 webpage identified 26 genes with protein kinase receptors (Lec-KRs) belonging to 5 lectin families, which are reported to have at least one ACP motif. Our study offers the first account of Phoenix-lectins and their organization that can be used for further structural and functional analysis and investigating their potential as anticancer proteins.
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Affiliation(s)
| | | | - Sara A.A Elmubarak
- Department of Biotechnology, Africa City of Technology (ACT), Khartoum, Sudan
| | - Amina I. Dirar
- Medicinal, Aromatic Plants and Traditional Medicine Research Institute (MAPTRI), National Center for Research, Mek Nimr Street, Khartoum, Sudan
| | - Emadeldin Hassan E. Konozy
- Department of Biotechnology, Africa City of Technology (ACT), Khartoum, Sudan
- Pharmaceutical Research and Development, Centre Faculty of Pharmacy, Karary University, Omdurman, Khartoum State, Sudan
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52
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Jin J, Diao Y, Xiong X, Yu C, Tian Y, Li C, Liu H. The Regulation of the Growth and Pathogenicity of Valsa mali by the Carbon Metabolism Repressor CreA. Int J Mol Sci 2023; 24:ijms24119252. [PMID: 37298203 DOI: 10.3390/ijms24119252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Carbon catabolite repression (CCR) is a very important mechanism for efficient use of carbon sources in the environment and is necessary for the regulation of fungal growth, development, and pathogenesis. Although there have been extensive studies conducted regarding this mechanism in fungi, little is yet known about the effects of CreA genes on Valsa mali. However, based on the results obtained in this study for the identification of the VmCreA gene in V. mali, it was determined that the gene was expressed at all stages of fungal growth, with self-repression observed at the transcriptional level. Furthermore, the functional analysis results of the gene deletion mutants (ΔVmCreA) and complements (CTΔVmCreA) showed that the VmCreA gene played an important role in the growth, development, pathogenicity, and carbon source utilization of V. mali.
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Affiliation(s)
- Jiyang Jin
- Mountain Tai Forest Ecosystem Research Station of State Forestry Administration, Key Laboratory of Ecological Protection and Safety Prevention of the Lower Yellow River, Forestry College, Shandong Agricultural University, Tai'an 271018, China
| | - Yufei Diao
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Xiong Xiong
- Mountain Tai Forest Ecosystem Research Station of State Forestry Administration, Key Laboratory of Ecological Protection and Safety Prevention of the Lower Yellow River, Forestry College, Shandong Agricultural University, Tai'an 271018, China
| | - Chengming Yu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Yehan Tian
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Chuanrong Li
- Mountain Tai Forest Ecosystem Research Station of State Forestry Administration, Key Laboratory of Ecological Protection and Safety Prevention of the Lower Yellow River, Forestry College, Shandong Agricultural University, Tai'an 271018, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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Gavande PV, Goyal A. Molecular dynamics-based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans. J Mol Model 2023; 29:186. [PMID: 37221261 DOI: 10.1007/s00894-023-05575-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023]
Abstract
CONTEXT The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)8-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of - 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm2), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm2) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of - 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector. METHODS The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.
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Affiliation(s)
- Parmeshwar Vitthal Gavande
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Shui K, Wang C, Zhang X, Ma S, Li Q, Ning W, Zhang W, Chen M, Peng D, Hu H, Fang Z, Guo A, Gao G, Ye M, Zhang L, Xue Y. Small-sample learning reveals propionylation in determining global protein homeostasis. Nat Commun 2023; 14:2813. [PMID: 37198164 DOI: 10.1038/s41467-023-38414-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Proteostasis is fundamental for maintaining organismal health. However, the mechanisms underlying its dynamic regulation and how its disruptions lead to diseases are largely unclear. Here, we conduct in-depth propionylomic profiling in Drosophila, and develop a small-sample learning framework to prioritize the propionylation at lysine 17 of H2B (H2BK17pr) to be functionally important. Mutating H2BK17 which eliminates propionylation leads to elevated total protein level in vivo. Further analyses reveal that H2BK17pr modulates the expression of 14.7-16.3% of genes in the proteostasis network, and determines global protein level by regulating the expression of genes involved in the ubiquitin-proteasome system. In addition, H2BK17pr exhibits daily oscillation, mediating the influences of feeding/fasting cycles to drive rhythmic expression of proteasomal genes. Our study not only reveals a role of lysine propionylation in regulating proteostasis, but also implements a generally applicable method which can be extended to other issues with little prior knowledge.
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Affiliation(s)
- Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xuedi Zhang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Shanshan Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qinyu Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Wanshan Ning
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Miaomiao Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Hui Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Guanjun Gao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, 430022, Hubei, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, 210031, Jiangsu, China.
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Prozzillo Y, Fattorini G, Ferreri D, Leo M, Dimitri P, Messina G. Knockdown of DOM/Tip60 Complex Subunits Impairs Male Meiosis of Drosophila melanogaster. Cells 2023; 12:1348. [PMID: 37408183 DOI: 10.3390/cells12101348] [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: 03/27/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 07/07/2023] Open
Abstract
ATP-dependent chromatin remodeling complexes are involved in nucleosome sliding and eviction and/or the incorporation of histone variants into chromatin to facilitate several cellular and biological processes, including DNA transcription, replication and repair. The DOM/TIP60 chromatin remodeling complex of Drosophila melanogaster contains 18 subunits, including the DOMINO (DOM), an ATPase that catalyzes the exchange of the canonical H2A with its variant (H2A.V), and TIP60, a lysine-acetyltransferase that acetylates H4, H2A and H2A.V histones. In recent decades, experimental evidence has shown that ATP-dependent chromatin remodeling factors, in addition to their role in chromatin organization, have a functional relevance in cell division. In particular, emerging studies suggested the direct roles of ATP-dependent chromatin remodeling complex subunits in controlling mitosis and cytokinesis in both humans and D. melanogaster. However, little is known about their possible involvement during meiosis. The results of this work show that the knockdown of 12 of DOM/TIP60 complex subunits generates cell division defects that, in turn, cause total/partial sterility in Drosophila males, providing new insights into the functions of chromatin remodelers in cell division control during gametogenesis.
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Affiliation(s)
- Yuri Prozzillo
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Gaia Fattorini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), Sapienza University of Rome, 00185 Rome, Italy
| | - Diego Ferreri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Manuela Leo
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy
| | - Patrizio Dimitri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Giovanni Messina
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Pasteur Institute, Fondazione Cenci-Bolognetti, 00161 Rome, Italy
- Department of Biotechnology and Biosciences, Milano-Bicocca University, 20126 Milan, Italy
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56
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Shafieipour N, Jafari Khamirani H, Kamal N, Tabei SMB, Dianatpour M, Dastgheib SA. The third patient of ACACA-related acetyl-CoA carboxylase deficiency with seizure and literature review. Eur J Med Genet 2023; 66:104707. [PMID: 36709796 DOI: 10.1016/j.ejmg.2023.104707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/30/2022] [Accepted: 01/15/2023] [Indexed: 01/27/2023]
Abstract
Pathogenic variants in ACACA are the cause of acetyl-CoA carboxylase deficiency with an autosomal recessive inheritance that is identified by hypotonia, motor, and intellectual developmental delay. In this article, we describe a seven-year-old boy who is the child of consanguineous parents with a homozygous variant in ACACA (NM_198834.3:c.6641C > A, p.P2214H) that was detected by Whole-Exome Sequencing and confirmed by Sanger sequencing. This is the first reported patient of acetyl-CoA carboxylase deficiency that results from a homozygous pathogenic variant in the ACACA gene in the Iranian family. The proband presents with motor and intellectual developmental delay, muscle weakness, language disorder, facial dysmorphism, and poor growth. The patient discussed here is similar to other patients that were previously published; however, we were able to identify seizure that has hitherto not been reported. This paper describes the third person with a novel variant in the ACACA gene in the world that accounts for acetyl-CoA carboxylase deficiency and implicates the clinical spectrum of the disease. Finally, we describe an individual-based review of the symptoms associated with acetyl-CoA carboxylase deficiency. So far, only two acetyl-CoA carboxylase deficiency patients have been reviewed in the literature.
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Affiliation(s)
- Negin Shafieipour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Iran
| | | | - Neda Kamal
- Department of Medical Genetics, Shiraz University of Medical Sciences, Iran
| | - Seyed Mohammad Bagher Tabei
- Department of Medical Genetics, Shiraz University of Medical Sciences, Iran; Maternal-fetal Medicine Research Center, Shiraz University of Medical Sciences, Iran
| | - Mehdi Dianatpour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Iran; Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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57
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Neyroud AS, Rudinger-Thirion J, Frugier M, Riley LG, Bidet M, Akloul L, Simpson A, Gilot D, Christodoulou J, Ravel C, Sinclair AH, Belaud-Rotureau MA, Tucker EJ, Jaillard S. LARS2 variants can present as premature ovarian insufficiency in the absence of overt hearing loss. Eur J Hum Genet 2023; 31:453-460. [PMID: 36450801 PMCID: PMC10133321 DOI: 10.1038/s41431-022-01252-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Premature ovarian insufficiency (POI) affects 1 in 100 women and is a leading cause of female infertility. There are over 80 genes in which variants can cause POI, with these explaining only a minority of cases. Whole exome sequencing (WES) can be a useful tool for POI patient management, allowing clinical care to be personalized to underlying cause. We performed WES to investigate two French sisters, whose only clinical complaint was POI. Surprisingly, they shared one known and one novel likely pathogenic variant in the Perrault syndrome gene, LARS2. Using amino-acylation studies, we established that the novel missense variant significantly impairs LARS2 function. Perrault syndrome is characterized by sensorineural hearing loss in addition to POI. This molecular diagnosis alerted the sisters to the significance of their difficulty in following conversation. Subsequent audiology assessment revealed a mild bilateral hearing loss. We describe the first cases presenting with perceived isolated POI and causative variants in a Perrault syndrome gene. Our study expands the phenotypic spectrum associated with LARS2 variants and highlights the clinical benefit of having a genetic diagnosis, with prediction of potential co-morbidity and prompt and appropriate medical care, in this case by an audiologist for early detection of hearing loss.
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Affiliation(s)
- Anne Sophie Neyroud
- CHU Rennes, Service de Biologie de la Reproduction-CECOS, F-35033, Rennes, France
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, F-35000, Rennes, France
| | - Joëlle Rudinger-Thirion
- Université de Strasbourg, Architecture et Réactivité de l'ARN, CNRS, IBMC, Strasbourg, France
| | - Magali Frugier
- Université de Strasbourg, Architecture et Réactivité de l'ARN, CNRS, IBMC, Strasbourg, France
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, NSW, Australia
- Specialty of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Maud Bidet
- Clinique Mutualiste La Sagesse, Service of AMP, 35000, Rennes, France
| | - Linda Akloul
- CHU Rennes, Service de Génétique Clinique, CLAD Ouest, F-35033, Rennes, France
| | - Andrea Simpson
- School of Allied Health, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC, Australia
- College of Health and Human Services, Charles Darwin University, Darwin, NT, Australia
| | - David Gilot
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France
- INSERM U1242, COSS, Université Rennes 1, F-35032, Rennes, France
| | - John Christodoulou
- Specialty of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Célia Ravel
- CHU Rennes, Service de Biologie de la Reproduction-CECOS, F-35033, Rennes, France
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, F-35000, Rennes, France
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Marc-Antoine Belaud-Rotureau
- CHU Rennes, Service de Biologie de la Reproduction-CECOS, F-35033, Rennes, France
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, F-35000, Rennes, France
- School of Allied Health, College of Science, Health and Engineering, La Trobe University, Bundoora, VIC, Australia
| | - Elena J Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
| | - Sylvie Jaillard
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, F-35000, Rennes, France.
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033, Rennes, France.
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Du Q, Peng F, Xiong Q, Xu K, Yang KY, Wang M, Wu Z, Li S, Cheng X, Rao X, Wang Y, Tsui SKW, Zeng X. Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences. Viruses 2023; 15:v15040909. [PMID: 37112889 PMCID: PMC10145014 DOI: 10.3390/v15040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/11/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone H4 or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.
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Affiliation(s)
- Qiao Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Kejin Xu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhitian Wu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanying Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaorui Cheng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinjie Rao
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyouye Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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59
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Velayuthan LP, Moretto L, Tågerud S, Ušaj M, Månsson A. Virus-free transfection, transient expression, and purification of human cardiac myosin in mammalian muscle cells for biochemical and biophysical assays. Sci Rep 2023; 13:4101. [PMID: 36907906 PMCID: PMC10008826 DOI: 10.1038/s41598-023-30576-1] [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: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023] Open
Abstract
Myosin expression and purification is important for mechanistic insights into normal function and mutation induced changes. The latter is particularly important for striated muscle myosin II where mutations cause several debilitating diseases. However, the heavy chain of this myosin is challenging to express and the standard protocol, using C2C12 cells, relies on viral infection. This is time and work intensive and associated with infrastructural demands and biological hazards, limiting widespread use and hampering fast generation of a wide range of mutations. We here develop a virus-free method to overcome these challenges. We use this system to transfect C2C12 cells with the motor domain of the human cardiac myosin heavy chain. After optimizing cell transfection, cultivation and harvesting conditions, we functionally characterized the expressed protein, co-purified with murine essential and regulatory light chains. The gliding velocity (1.5-1.7 µm/s; 25 °C) in the in vitro motility assay as well as maximum actin activated catalytic activity (kcat; 8-9 s-1) and actin concentration for half maximal activity (KATPase; 70-80 µM) were similar to those found previously using virus based infection. The results should allow new types of studies, e.g., screening of a wide range of mutations to be selected for further characterization.
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Affiliation(s)
- Lok Priya Velayuthan
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 391 82, Kalmar, Sweden
| | - Luisa Moretto
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 391 82, Kalmar, Sweden
| | - Sven Tågerud
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 391 82, Kalmar, Sweden
| | - Marko Ušaj
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 391 82, Kalmar, Sweden.
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 391 82, Kalmar, Sweden.
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Mohammadi S, Jafari Khamirani H, Baneshi M, Kamal N, Manoocheri J, Saffar M, Dianatpour M, Tabei SMB, Dastgheib SA. A novel nonsense variant in the ATL3 gene is associated with disturbed pain sensitivity, numbness of distal limbs and muscle weakness. Ann Hum Genet 2023. [PMID: 36856139 DOI: 10.1111/ahg.12501] [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: 07/06/2022] [Revised: 01/09/2023] [Accepted: 01/27/2023] [Indexed: 03/02/2023]
Abstract
Introduction Hereditary sensory neuropathy (HSN) describes as a heterogeneous group of peripheral neuropathies. HSN type 1 (HSN1) is one subtype characterized by distal sensory impairment that occurs in the form of numbness, tingling, or pain. To date, only two variants in the atlastin GTPase 3 (ATL3) gene have been identified that result in hereditary sensory neuropathy type 1F (HSN1F) with autosomal dominantinheritance. Methods We sudied and examined who present with sensory disturbances and muscle weakness in their lower limb. Patients underwent Whole Exome Sequencing and Sanger sequencing was performed in families for validation of detected variant. Results Here, we identified two Iranian families carrying the novel heterozygous stop variant NM_015459.5: c.16C>T, p.Arg6Ter in ATL3 that led to disturbed pain and touch sensitivity. This variant in the ATL3 gene was detected in both families (NM_015459.5: c.16C>T, p.Arg6Ter) by whole-exome sequencing and confirmed by Sanger sequencing. Conclusion In this study, the subjects manifested weakness of distal limb muscles and numbness of the lower extremities. In addition, some unusual features, including hearing problems and inability to sit and walk presented in one of the patients. Eventually, we provide a case-based review of the clinical features associated with HSN1F. Hitherto, only 11 patients with HSN1F have been reported. We compared our findings to previously reported cases, suggesting that the clinical features are generally variable in the HSN1F patients.
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Affiliation(s)
- Sanaz Mohammadi
- Comprehensive Medical Genetic Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Maryam Baneshi
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Kamal
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Manoocheri
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsa Saffar
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Dianatpour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran.,Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Bagher Tabei
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran.,Maternal-fetal Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Effects of glutamate oxaloacetate transaminase on reactive oxygen species in Ganoderma lucidum. Appl Microbiol Biotechnol 2023; 107:1845-1861. [PMID: 36754884 DOI: 10.1007/s00253-023-12417-3] [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: 08/05/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/10/2023]
Abstract
Nitrogen metabolism can regulate mycelial growth and secondary metabolism in Ganoderma lucidum. As an important enzyme in intracellular amino acid metabolism, glutamate oxaloacetate transaminase (GOT) has many physiological functions in animals and plants, but its function in fungi has been less studied. In the present study, two GOT isoenzymes were found in G. lucidum; one is located in the mitochondria (GOT1), and the other is located in the cytoplasm (GOT2). The reactive oxygen species (ROS) level was increased in got1 silenced strains and was approximately 1.5-fold higher than that in the wild-type (WT) strain, while silencing got2 did not affect the ROS level. To explore how GOT affects ROS in G. lucidum, experiments related to the generation and elimination of intracellular ROS were conducted. First, compared with that in the WT strain, the glutamate content, one of the substrates of GOT, decreased when got1 or got2 was knocked down, and the glutathione (l-γ-glutamyl-l-cysteinylglycine) (GSH) content decreased by approximately 38.6%, 19.3%, and 40.1% in got1 silenced strains, got2 silenced strains, and got1/2 co-silenced strains respectively. Second, GOT also affects glucose metabolism. The pyruvate (PA), acetyl-CoA and α-ketoglutarate (α-KG) contents decreased in got1 and got2 silenced strains, and the transcription levels of most genes involved in the glycolytic pathway and the tricarboxylic acid cycle increased. The NADH content was increased in got1 silenced strains and got2 silenced strains, and the NAD+/NADH ratio was decreased, which might result in mitochondrial ROS production. Compared with the WT strain, the mitochondrial ROS level was approximately 1.5-fold higher in the got1 silenced strains. In addition, silencing of got1 or got2 resulted in a decrease in antioxidant enzymes, including superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase. Finally, ganoderic acid (GA) was increased by approximately 40% in got1 silenced strains compared with the WT strain, while silencing of got2 resulted in a 10% increase in GA biosynthesis. These findings provide new insights into the effect of GOT on ROS and secondary metabolism in fungi. KEY POINTS: • GOT plays important roles in ROS level in Ganoderma lucidum. • Silencing of got1 resulted in decrease in GSH content and antioxidant enzymes activities, but an increase in mitochondrial ROS level in G. lucidum. • Silencing of got1 and got2 resulted in an increase in ganoderic acid biosynthesis in G. lucidum.
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Chen B, Liu Y, Xiang C, Zhang D, Liu Z, Liu Y, Chen J. Identification and in vitro enzymatic activity analysis of the AOP2 gene family associated with glucosinolate biosynthesis in Tumorous stem mustard ( Brassica juncea var. tumida). FRONTIERS IN PLANT SCIENCE 2023; 14:1111418. [PMID: 36909383 PMCID: PMC9992552 DOI: 10.3389/fpls.2023.1111418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The major enzyme encoded by the glucosinolate biosynthetic gene AOP2 is involved in catalyzing the conversion of glucoiberin (GIB) into sinigrin (SIN) in Brassicaceae crops. The AOP2 proteins have previously been identified in several Brassicaceae species, but not in Tumorous stem mustard. As per this research, the five identified members of the AOP2 family from the whole genome of Brassica juncea named BjuAOP2.1-BjuAOP2.5 were found to be evenly distributed on five chromosomes. The subcellular localization results implied that BjuAOP2 proteins were mainly concentrated in the cytoplasm. Phylogenetic analysis of the AOP2 proteins from the sequenced Brassicaceae species in BRAD showed that BjuAOP2 genes were more closely linked to Brassica carinata and Brassica rapa than Arabidopsis. In comparison with other Brassicaceae plants, the BjuAOP2 members were conserved in terms of gene structures, protein sequences, and motifs. The light response and hormone response elements were included in the BjuAOP2 genes' cis-regulatory elements. The expression pattern of BjuAOP2 genes was influenced by the different stages of development and the type of tissue being examined. The BjuAOP2 proteins were used to perform the heterologous expression experiment. The results showed that all the five BjuAOP2 proteins can catalyze the conversion of GIB to SIN with different catalytic activity. These results provide the basis for further investigation of the functional study of BjuAOP2 in Tumorous stem mustard glucosinolate biosynthesis.
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Affiliation(s)
| | | | | | | | | | - Yihua Liu
- *Correspondence: Yihua Liu, ; Jingjing Chen,
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Beutler M, Harnischfeger J, Weber MHW, Hahnel SR, Quack T, Blohm A, Ueberall ME, Timm T, Lochnit G, Rennar GA, Gallinger TL, Houhou H, Rahlfs S, Falcone FH, Becker K, Schlitzer M, Haeberlein S, Czermak P, Salzig D, Grevelding CG. Identification and characterisation of the tegument-expressed aldehyde dehydrogenase SmALDH_312 of Schistosoma mansoni, a target of disulfiram. Eur J Med Chem 2023; 251:115179. [PMID: 36948075 DOI: 10.1016/j.ejmech.2023.115179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Schistosomiasis is an infectious disease caused by blood flukes of the genus Schistosoma and affects approximately 200 million people worldwide. Since Praziquantel (PZQ) is the only drug for schistosomiasis, alternatives are needed. By a biochemical approach, we identified a tegumentally expressed aldehyde dehydrogenase (ALDH) of S. mansoni, SmALDH_312. Molecular analyses of adult parasites showed Smaldh_312 transcripts in both genders and different tissues. Physiological and cell-biological experiments exhibited detrimental effects of the drug disulfiram (DSF), a known ALDH inhibitor, on larval and adult schistosomes in vitro. DSF also reduced stem-cell proliferation and caused severe tegument damage in treated worms. In silico-modelling of SmALDH_312 and docking analyses predicted DSF binding, which we finally confirmed by enzyme assays with recombinant SmALDH_312. Furthermore, we identified compounds of the Medicine for Malaria Venture (MMV) pathogen box inhibiting SmALDH_312 activity. Our findings represent a promising starting point for further development towards new drugs for schistosomiasis.
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Affiliation(s)
- Mandy Beutler
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Julie Harnischfeger
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Michael H W Weber
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Steffen R Hahnel
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Thomas Quack
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Ariane Blohm
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Monique E Ueberall
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany; Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Justus Liebig University Giessen, Germany
| | - Günter Lochnit
- Protein Analytics, Institute of Biochemistry, Justus Liebig University Giessen, Germany
| | - Georg A Rennar
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Germany, Germany
| | - Tom L Gallinger
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Germany, Germany
| | - Hicham Houhou
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Stefan Rahlfs
- Institute for Biochemistry and Molecular Biology, Interdisciplinary Research Centre, Justus Liebig University, Germany
| | - Franco H Falcone
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Katja Becker
- Institute for Biochemistry and Molecular Biology, Interdisciplinary Research Centre, Justus Liebig University, Germany
| | - Martin Schlitzer
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Germany, Germany
| | - Simone Haeberlein
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Denise Salzig
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
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De la Merced-García DS, Sánchez-Barrera Á, Hernández-Yonca J, Mancilla I, García-López G, Díaz NF, Terrazas LI, Molina-Hernández A. Increased Nuclear FOXP2 Is Related to Reduced Neural Stem Cell Number and Increased Neurogenesis in the Dorsal Telencephalon of Embryos of Diabetic Rats through Histamine H 1 Receptors. Cells 2023; 12:cells12030510. [PMID: 36766852 PMCID: PMC9914739 DOI: 10.3390/cells12030510] [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: 12/12/2022] [Accepted: 12/27/2022] [Indexed: 02/09/2023] Open
Abstract
Diabetic rat embryos have increased cortical neurogenesis and neuron maturation, and their offspring presented altered neuron polarity, lamination, and diminished neuron excitability. The FOXP2 overexpression results in higher cortical neurogenesis by increasing the transition of radial glia to the intermediate progenitor. Similarly, histamine through H1-receptor activation increases cortical neuron differentiation. Indeed, blocking the H1-receptor by the systemic administration of chlorpheniramine to diabetic pregnant rats prevents increased neurogenesis. Here, we explore the relationship between the H1-receptor and FOXP2 on embryo neurogenesis from diabetic dams. Through qRT-PCR, Western blot, immunohistofluorescence, and flow cytometry, we showed an increased FOXP2 expression and nuclear localization, a reduced Nestin expression and -positive cells number, and a higher PKCα expression in the cortical neuroepithelium of fourteen-day-old embryos from diabetic rats. Interestingly, this scenario was prevented by the chlorpheniramine systemic administration to diabetic pregnant rats at embryo day twelve. These data, together with the bioinformatic analysis, suggest that higher H1-receptor activity in embryos under high glucose increases FOXP2 nuclear translocation, presumably through PKCα phosphorylation, impairing the transition of radial glia to intermediate progenitor and increasing neuron differentiation in embryos of diabetic rats.
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Affiliation(s)
- Diana Sarahi De la Merced-García
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
| | - Ángel Sánchez-Barrera
- Unidad de Biomedicina, Facultad de Estudios Superiores (FES)-Iztacala, Universidad Nacional Autónoma de México (UNAM), Av. de los Barrios, Los Reyes Iztacala, Tlanepantla 54090, Mexico
| | - Juan Hernández-Yonca
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
| | - Ismael Mancilla
- Departamento de Infectología, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
| | - Guadalupe García-López
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
| | - Néstor Fabián Díaz
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
| | - Luis Ignacio Terrazas
- Departamento de Infectología, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
- Laboratorio Nacional en Salud FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), Av. de los Barrios, Los Reyes Iztacala, Tlanepantla 54090, Mexico
| | - Anayansi Molina-Hernández
- Departamento de Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Miguel Hidalgo, Ciudad de Mexico 11000, Mexico
- Correspondence:
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Glendinning S, Fitzgibbon QP, Smith GG, Ventura T. Unravelling the neuropeptidome of the ornate spiny lobster Panulirus ornatus: A focus on peptide hormones and their processing enzymes expressed in the reproductive tissues. Gen Comp Endocrinol 2023; 332:114183. [PMID: 36471526 DOI: 10.1016/j.ygcen.2022.114183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
Neuropeptides are commonly produced in the neural tissues yet can have effects on far-reaching targets, with varied biological responses. We describe here the neuropeptidome of the ornate spiny lobster, Panulirus ornatus, a species of emerging importance to closed-system aquaculture, with a focus on peptide hormones produced by the reproductive tissues. Transcripts for a precursor to one neuropeptide, adipokinetic hormone/corazonin-related peptide (ACP) were identified in high numbers in the sperm duct of adult spiny lobsters suggesting a role for ACP in the reproduction of this species. Neuropeptide production in the sperm duct may be linked with physiological control of spermatophore production in the male, or alternatively may function in signalling to the female. The enzymes which process nascent neuropeptide precursors into their mature, active forms have seldom been studied in decapods, and never before at the multi-tissue level. We have identified transcripts for multiple members of the proprotein convertase subtisilin/kexin family in the ornate spiny lobster, with some enzymes showing specificity to certain tissues. In addition, other enzyme transcripts involved with neuropeptide processing are identified along with their tissue and life stage expression patterns.
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Affiliation(s)
- Susan Glendinning
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia; School of Science and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia.
| | - Quinn P Fitzgibbon
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 49, Hobart, Tasmania 7001, Australia
| | - Gregory G Smith
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 49, Hobart, Tasmania 7001, Australia
| | - Tomer Ventura
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD, Australia; School of Science and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
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Ji S, Gavande PV, Choudhury B, Goyal A. Computational design and structure dynamics analysis of bifunctional chimera of endoxylanase from Clostridium thermocellum and xylosidase from Bacteroides ovatus. 3 Biotech 2023; 13:59. [PMID: 36714550 PMCID: PMC9877272 DOI: 10.1007/s13205-023-03482-6] [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: 08/27/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Development of chimeric enzymes by protein engineering can more efficiently contribute toward biomass conversion for bioenergy generation. Therefore, prior to experimental validation, a computational approach by modeling and molecular dynamic simulation can assess the structural and functional behavior of chimeric enzymes. In this study, a bifunctional chimera, CtXyn11A-BoGH43A comprising an efficient endoxylanase (CtXyn11A) from Clostridium thermocellum and xylosidase (BoGH43A) from Bacteroides ovatus was computationally designed and its binding and stability analysis with xylooligosaccharides were performed. The modeled chimera showed β-jellyroll fold for CtXyn11A and 5-bladed β-propeller fold for BoGH43A module. Stereo-chemical properties analyzed by Ramachandran plot showed 98.8% residues in allowed region, validating the modeled chimera. The catalytic residues identified by multiple sequence alignment were Glu94 and Glu184 for CtXyn11A and Asp229 and Glu384 for BoGH43A modules. CtXyn11A followed retaining-type, whereas BoGH43A enforced inverting-type of reaction mechanism during xylan hydrolysis as revealed by superposition and GH11 and GH43 familial analyses. Molecular docking studies showed binding energy, (ΔG) - 4.54 and - 4.18 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylobiose, while - 3.94 and - 3.82 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylotriose. MD simulation of CtXyn11A-BoGH43A complexed with xylobiose and xylotriose till 100 ns displayed stability by RMSD, compactness by R g and conformational stability by SASA analyses. The lowered values of RMSF in active-site residues, Glu94, Glu184, Asp229, Asp335 and Glu384 confirmed the efficient binding of chimera with xylobiose and xylotriose. These results were in agreement with the earlier experimental studies on CtXyn11A releasing xylooligosaccharides from xylan and BoGH43A releasing d-xylose from xylooligosaccharides and xylobiose. The chimera showed stronger affinity in terms of total short-range interaction energy; - 190 and - 121 kJ/mol for with xylobiose and xylotriose, respectively. The bifunctional chimera, CtXyn11A-BoGH43A showed stability and integrity with xylobiose and xylotriose. The designed chimera can be constructed and applied for efficient biomass conversion.
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Affiliation(s)
- Shyam Ji
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Parmeshwar Vitthal Gavande
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Bipasha Choudhury
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
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Shcherbakova L, Pardo M, Roumeliotis T, Choudhary J. Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry. Wellcome Open Res 2023; 6:260. [PMID: 35865489 PMCID: PMC9270653 DOI: 10.12688/wellcomeopenres.17160.1] [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] [Accepted: 09/24/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising XL-MS to characterise individual protein complexes' topology have been carried out on over-expressed or recombinant proteins, which might not accurately represent native cellular conditions. Methods: We performed XL-MS using MS-cleavable crosslinker disuccinimidyl sulfoxide (DSSO) after immunoprecipitation of endogenous BRG/Brahma-associated factors (BAF) complex and co-purifying proteins. Data are available via ProteomeXchange with identifier PXD027611. Results: Although we did not detect the expected enrichment of crosslinks within the BAF complex, we identified numerous crosslinks between three co-purifying proteins, namely Thrap3, Bclaf1 and Erh. Thrap3 and Bclaf1 are mostly disordered proteins for which no 3D structure is available. The XL data allowed us to map interaction surfaces on these proteins, which overlap with the non-disordered portions of both proteins. The identified XLs are in agreement with homology-modelled structures suggesting that the interaction surfaces are globular. Conclusions: Our data shows that MS-cleavable crosslinker DSSO can be used to characterise in detail the topology and interaction surfaces of endogenous protein complexes without the need for overexpression. We demonstrate that Bclaf1, Erh and Thrap3 interact closely with each other, suggesting they might form a novel complex, hereby referred to as BET complex. This data can be exploited for modelling protein-protein docking to characterise the three-dimensional structure of the complex. Endogenous XL-MS might be challenging due to crosslinker accessibility, protein complex abundance or isolation efficiency, and require further optimisation for some complexes like the BAF complex to detect a substantial number of crosslinks.
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Affiliation(s)
| | - Mercedes Pardo
- Cancer Biology, Institute of Cancer Research, UK, London, UK
| | | | - Jyoti Choudhary
- Cancer Biology, Institute of Cancer Research, UK, London, UK,
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Shcherbakova L, Pardo M, Roumeliotis T, Choudhary J. Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry. Wellcome Open Res 2023; 6:260. [PMID: 35865489 PMCID: PMC9270653 DOI: 10.12688/wellcomeopenres.17160.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising XL-MS to characterise individual protein complexes' topology have been carried out on over-expressed or recombinant proteins, which might not accurately represent native cellular conditions. Methods: We performed XL-MS using MS-cleavable crosslinker disuccinimidyl sulfoxide (DSSO) after immunoprecipitation of endogenous BRG/Brahma-associated factors (BAF) complex and co-purifying proteins. Data are available via ProteomeXchange with identifier PXD027611. Results: Although we did not detect the expected enrichment of crosslinks within the BAF complex, we identified numerous crosslinks between three co-purifying proteins, namely Thrap3, Bclaf1 and Erh. Thrap3 and Bclaf1 are mostly disordered proteins for which no 3D structure is available. The XL data allowed us to map interaction surfaces on these proteins, which overlap with the non-disordered portions of both proteins. The identified XLs are in agreement with homology-modelled structures suggesting that the interaction surfaces are globular. Conclusions: Our data shows that MS-cleavable crosslinker DSSO can be used to characterise in detail the topology and interaction surfaces of endogenous protein complexes without the need for overexpression. We demonstrate that Bclaf1, Erh and Thrap3 interact closely with each other, suggesting they might form a novel complex, hereby referred to as TEB complex. This data can be exploited for modelling protein-protein docking to characterise the three-dimensional structure of the complex. Endogenous XL-MS might be challenging due to crosslinker accessibility, protein complex abundance or isolation efficiency, and require further optimisation for some complexes like the BAF complex to detect a substantial number of crosslinks.
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Affiliation(s)
| | - Mercedes Pardo
- Cancer Biology, Institute of Cancer Research, UK, London, UK
| | | | - Jyoti Choudhary
- Cancer Biology, Institute of Cancer Research, UK, London, UK,
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Zhang X, Xiao N, Cao Y, Peng Y, Lian A, Chen Y, Wang P, Gu W, Xiao B, Yu J, Wang H, Shu L. De novo variants in MAST4 related to neurodevelopmental disorders with developmental delay and infantile spasms: Genotype-phenotype association. Front Mol Neurosci 2023; 16:1097553. [PMID: 36910266 PMCID: PMC9992645 DOI: 10.3389/fnmol.2023.1097553] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Objective This study aims to prove that the de novo variants in MAST4 gene are associated with neurodevelopmental disorders (NDD) with developmental delay (DD) and infantile spasm (IS) and to determine the genotype-phenotype correlations. Methods Trio-based exome sequencing (ES) was performed on the four families enrolled in this study. We collected and systematically reviewed the four probands' clinical data, magnetic resonance images (MRI), and electroencephalography (EEG). We also carried out bioinformatics analysis by integrating published exome/genome sequencing data and human brain transcriptomic data. Results We described four patients whose median age of seizure onset was 5 months. The primary manifestation was infantile spasms with typical hypsarrhythmia on EEG. Developmental delays or intellectual disabilities varied among the four individuals. Three de novo missense variants in MAST4 gene were identified from four families, including chr5:66438324 (c.2693T > C: p.Ile898Thr) z, chr5:66459419 (c.4412C > T: p.Thr1471Ile), and chr5:66462662 (c.7655C > G:p.Ser2552Trp). The missense variant p.Ile898Thr is mapped to the AGC-kinase C-terminal with phosphatase activity. The other variant p.Ser2552Trp is located in a phosphoserine-modified residue which may affect cell membrane stability and signal transduction. Besides, the variant p.Thr1471Ile is a recurrent site screened out in two unrelated patients. Compared to private mutations (found only in a single family or a small population) of MAST4 in the gnomAD non-neuro subset, all de novo variants were predicted to be damaging or probably damaging through different bioinformatic analyses. Significantly higher CADD scores of the variant p.Thr1471Ile indicate more deleteriousness of the recurrent site. And the affected amino acids are highly conserved across multiple species. According to the Brainspan Atlas database, MAST4 is expressed primarily in the mediodorsal nucleus of the thalamus and medial prefrontal cortex during the prenatal period, potentially contributing to embryonic brain development. Conclusion Our results revealed that the variants of MAST4 gene might lead to neurodevelopmental disorders with developmental delay and infantile spasm. Thus, MAST4 variants should be considered the potential candidate gene in patients with neurodevelopmental disorders clinically marked by infantile spasms.
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Affiliation(s)
- Xi Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Neng Xiao
- Department of Pediatric Neurology, Chenzhou First People's Hospital, Chenzhou, China
| | - Yang Cao
- Department of Radiology, Chenzhou First People's Hospital, Chenzhou, China
| | - Ying Peng
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Aojie Lian
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Clinical Research Center for Placental Medicine in Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Yuanlu Chen
- Department of Pharmacy, Chenzhou First People's Hospital, Chenzhou, China
| | - Pengchao Wang
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, China
| | - Weiyue Gu
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Yu
- Department of Neurology, Children's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, China
| | - Li Shu
- Department of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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Structural and functional insights into the glycoside hydrolase family 30 xylanase of the rumen bacterium Ruminococcus flavefaciens. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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71
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Dalakouras A, Katsaouni A, Avramidou M, Dadami E, Tsiouri O, Vasileiadis S, Makris A, Georgopoulou ME, Papadopoulou KK. A beneficial fungal root endophyte triggers systemic RNA silencing and DNA methylation of a host reporter gene. RNA Biol 2023; 20:20-30. [PMID: 36573793 PMCID: PMC9809956 DOI: 10.1080/15476286.2022.2159158] [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] [Indexed: 12/28/2022] Open
Abstract
A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional trans-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms have been elusive to this date. To determine whether root endophytes can induce systemic RNAi responses to their host plants, we designed an experimental reporter-based system consisting of the root-restricted, beneficial fungal endophyte, Fusarium solani strain K (FsK) and its host Nicotiana benthamiana. Since not all fungi encode the RNAi machinery, we first needed to validate that FsK does so, by identifying its core RNAi enzymes (2 Dicer-like genes, 2 Argonautes and 4 RNA-dependent RNA polymerases) and by showing its susceptibility to in vitro RNAi upon exogenous application of double stranded RNAs (dsRNAs). Upon establishing this, we transformed FsK with a hairpin RNA (hpRNA) construct designed to target a reporter gene in its host N. benthamiana. The hpRNA was processed by FsK RNAi machinery predominantly into 21-24-nt small RNAs that triggered RNA silencing but not DNA methylation in the fungal hyphae. Importantly, when the hpRNA-expressing FsK was used to inoculate N. benthamiana, systemic RNA silencing and DNA methylation of the host reporter gene was recorded. Our data suggest that RNAi signals can be translocated by root endophytes to their hosts and can modulate gene expression during mutualism, which may be translated to beneficial phenotypes.
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Affiliation(s)
- Athanasios Dalakouras
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece,Hellenic Agricultural Organization Demeter, Institute of Industrial and Forage Crops, Larissa, Greece,CONTACT Athanasios Dalakouras University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece; Hellenic Agricultural Organization Demeter, Institute of Industrial and Forage Crops, Larissa, Greece
| | - Afrodite Katsaouni
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Marianna Avramidou
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Elena Dadami
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Olga Tsiouri
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
| | - Athanasios Makris
- University of Thessaly, Department of Biochemistry & Biotechnology, Larissa, Greece
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Krchlíková V, Hron T, Těšický M, Li T, Ungrová L, Hejnar J, Vinkler M, Elleder D. Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET. Viruses 2022; 15:3. [PMID: 36680044 PMCID: PMC9861763 DOI: 10.3390/v15010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are key RNA virus sensors belonging to the RIG-I-like receptor (RLR) family. The activation of the RLR inflammasome leads to the establishment of antiviral state, mainly through interferon-mediated signaling. The evolutionary dynamics of RLRs has been studied mainly in mammals, where rare cases of RLR gene losses were described. By in silico screening of avian genomes, we previously described two independent disruptions of MDA5 in two bird orders. Here, we extend this analysis to approximately 150 avian genomes and report 16 independent evolutionary events of RIG-I inactivation. Interestingly, in almost all cases, these inactivations are coupled with genetic disruptions of RIPLET/RNF135, an ubiquitin ligase RIG-I regulator. Complete absence of any detectable RIG-I sequences is unique to several galliform species, including the domestic chicken (Gallus gallus). We further aimed to determine compensatory evolution of MDA5 in RIG-I-deficient species. While we were unable to show any specific global pattern of adaptive evolution in RIG-I-deficient species, in galliforms, the analyses of positive selection and surface charge distribution support the hypothesis of some compensatory evolution in MDA5 after RIG-I loss. This work highlights the dynamic nature of evolution in bird RNA virus sensors.
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Affiliation(s)
- Veronika Krchlíková
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Lenka Ungrová
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Daniel Elleder
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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Akhter S, Sami AA, Toma TI, Jahan B, Islam T. Caffeoyl-CoA 3-O-methyltransferase gene family in jute: Genome-wide identification, evolutionary progression and transcript profiling under different quandaries. FRONTIERS IN PLANT SCIENCE 2022; 13:1035383. [PMID: 36589126 PMCID: PMC9798919 DOI: 10.3389/fpls.2022.1035383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Jute (Corchorus sp.), is a versatile, naturally occurring, biodegradable material that holds the promising possibility of diminishing the extensive use of plastic bags. One of the major components of the cell wall, lignin plays both positive and negative roles in fiber fineness and quality. Although it gives mechanical strength to plants, an excess amount of it is responsible for the diminution of fiber quality. Among various gene families involved in the lignin biosynthesis, Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is the most significant and has remained mostly unexplored. In this study, an extensive in-silico characterization of the CCoAOMT gene family was carried out in two jute species (C. capsularis L. and C. olitoroius L.) by analyzing their structural, functional, molecular and evolutionary characteristics. A total of 6 CCoAOMT gene members were identified in each of the two species using published reference genomes. These two jute species showed high syntenic conservation and the identified CCoAOMT genes formed four clusters in the phylogenetic tree. Histochemical assay of lignin in both jute species could shed light on the deposition pattern in stems and how it changes in response to abiotic stresses. Furthermore, expression profiling using qPCR showed considerable alteration of CCoAOMT transcripts under various abiotic stresses and hormonal treatment. This study will lay a base for further analysis and exploration of target candidates for overexpression of gene silencing using modern biotechnological techniques to enhance the quality of this economically important fiber crop.
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Prabu S, Jing D, Jurat-Fuentes JL, Wang Z, He K. Hemocyte response to treatment of susceptible and resistant Asian corn borer ( Ostrinia furnacalis) larvae with Cry1F toxin from Bacillus thuringiensis. Front Immunol 2022; 13:1022445. [PMID: 36466886 PMCID: PMC9714555 DOI: 10.3389/fimmu.2022.1022445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/31/2022] [Indexed: 10/12/2023] Open
Abstract
Midgut receptors have been recognized as the major mechanism of resistance to Cry proteins in lepidopteran larvae, while there is a dearth of data on the role of hemocyte's response to Cry intoxication and resistance development. We aimed at investigating the role of circulating hemocytes in the intoxication of Cry1F toxin in larvae from susceptible (ACB-BtS) and resistant (ACB-FR) strains of the Asian corn borer (ACB), Ostrinia furnacalis. Transcriptome and proteome profiling identified genes and proteins involved in immune-related (tetraspanin and C-type lectins) and detoxification pathways as significantly up-regulated in the hemocytes of Cry1F treated ACB-FR. High-throughput in vitro assays revealed the binding affinity of Cry1F with the tetraspanin and C-type lectin family proteins. We found significant activation of MAPKinase (ERK 1/2, p38α, and JNK 1/2) in the hemocytes of Cry1F treated ACB-FR. In testing plausible crosstalk between a tetraspanin (CD63) and downstream MAPK signaling, we knocked down CD63 expression by RNAi and detected an alteration in JNK 1/2 level but a significant increase in susceptibility of ACB-FR larvae to Cry1F toxin. Information from this study advances a change in knowledge on the cellular immune response to Cry intoxication and its potential role in resistance in a lepidopteran pest.
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Affiliation(s)
- Sivaprasath Prabu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dapeng Jing
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Luis Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Zhenying Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kanglai He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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75
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [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] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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Bai J, Cao J, Zhang Y, Xu Z, Li L, Liang L, Ma X, Han R, Ma W, Xu L, Ma L. Comparative analysis of the immune system and expression profiling of Lymantria dispar infected by Beauveria bassiana. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 187:105212. [PMID: 36127056 DOI: 10.1016/j.pestbp.2022.105212] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Lymantria dispar is one of the most devastating forest pests worldwide. Fungal biopesticides have great potential as alternatives owing to their high lethality to pests and eco-friendly feature, which is, however, often severely compromised by the pests' innate immunity. A better understanding of the antifungal immune system in L. dispar would significantly facilitate the development of the biopesticide. Here, we investigated phylogenetic characteristics of immunity-related genes as well as the tissue expression patterns in L. dispar after the infection of an entomopathogen Beauveria bassiana using RNA-sequencing data. Results showed most immune genes remain at a low level of response after 24 h post-infection (HPI). Almost all genes in the Toll pathway were significantly up-regulated at 48 HPI, and SPH1, SPN6, Toll6, Toll12, Myd88, pelle, and Drosal were significantly down-regulated at 72 HPI. Immunoblotting analysis revealed that the protein levels of βGRP3 and PPO1 were significantly upregulated at 24 and 48 HPI, while Myd88 was downregulated at 24 HPI, which was further confirmed by Quantitative real-time PCR experiments. Moreover, the relative content of H2O2, a potent reactive oxygen species (ROS), was significantly increased with the decrease of the total antioxidant capacity, indicating that oxidative stress system positively participates in the clearance of the pathogenic fungus. Together, our study provides detailed genetic characteristics of antifungal immunity as well as profiling of the host defense against entomopathogenic infection, and comprehensive insight into molecular interaction between L. dispar and the entomopathogen.
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Affiliation(s)
- Jianyang Bai
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Jingyu Cao
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yue Zhang
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhe Xu
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Lu Li
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Liwei Liang
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Xiaoqian Ma
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China; Institute of Forest Protection, Heilongjiang Academy of Forestry, Harbin 150081, China
| | - Runhua Han
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Wei Ma
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China.
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China.
| | - Ling Ma
- Department of Forest protection, College of Forestry, Northeast Forestry University, Harbin 150040, China; Forest Protection Technology Innovation Center, Harbin, China.
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Ng WM, Fedosyuk S, English S, Augusto G, Berg A, Thorley L, Haselon AS, Segireddy RR, Bowden TA, Douglas AD. Structure of trimeric pre-fusion rabies virus glycoprotein in complex with two protective antibodies. Cell Host Microbe 2022; 30:1219-1230.e7. [PMID: 35985336 PMCID: PMC9605875 DOI: 10.1016/j.chom.2022.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/07/2022] [Accepted: 07/19/2022] [Indexed: 11/03/2022]
Abstract
Rabies virus (RABV) causes lethal encephalitis and is responsible for approximately 60,000 deaths per year. As the sole virion-surface protein, the rabies virus glycoprotein (RABV-G) mediates host-cell entry. RABV-G's pre-fusion trimeric conformation displays epitopes bound by protective neutralizing antibodies that can be induced by vaccination or passively administered for post-exposure prophylaxis. We report a 2.8-Å structure of a RABV-G trimer in the pre-fusion conformation, in complex with two neutralizing and protective monoclonal antibodies, 17C7 and 1112-1, that recognize distinct epitopes. One of these antibodies is a licensed prophylactic (17C7, Rabishield), which we show locks the protein in pre-fusion conformation. Targeted mutations can similarly stabilize RABV-G in the pre-fusion conformation, a key step toward structure-guided vaccine design. These data reveal the higher-order architecture of a key therapeutic target and the structural basis of neutralization by antibodies binding two key antigenic sites, and this will facilitate the development of improved vaccines and prophylactic antibodies.
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Affiliation(s)
- Weng M Ng
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sofiya Fedosyuk
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Solomon English
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Gilles Augusto
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Adam Berg
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Luke Thorley
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Anna-Sophie Haselon
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Rameswara R Segireddy
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alexander D Douglas
- Jenner Institute, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
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Genome-Wide Analysis of Calmodulin Binding Transcription Activator (CAMTA) Gene Family in Peach ( Prunus persica L. Batsch) and Ectopic Expression of PpCAMTA1 in Arabidopsis camta2,3 Mutant Restore Plant Development. Int J Mol Sci 2022; 23:ijms231810500. [PMID: 36142414 PMCID: PMC9499639 DOI: 10.3390/ijms231810500] [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: 06/10/2022] [Revised: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Calmodulin-binding transcription activator (CAMTA) is a transcription factor family containing calmodulin (CaM) binding sites and is involved in plant development. Although CAMTAs in Arabidopsis have been extensively investigated, the functions of CAMTAs remain largely unclear in peaches. In this study, we identified five peach CAMTAs which contained conserved CG-1 box, ANK repeats, CaM binding domain (CaMBD) and IQ motifs. Overexpression in tobacco showed that PpCAMTA1/2/3 were located in the nucleus, while PpCAMTA4 and PpCAMTA5 were located in the plasma membrane. Increased expression levels were observed for PpCAMTA1 and PpCAMTA3 during peach fruit ripening. Expression of PpCAMTA1 was induced by cold treatment and was inhibited by ultraviolet B irradiation (UV-B). Driven by AtCAMTA3 promoter, PpCAMTA1/2/3 were overexpressed in Arabidopsis mutant. Here, we characterized peach PpCAMTA1, representing an ortholog of AtCAMTA3. PpCAMTA1 expression in Arabidopsis complements the developmental deficiencies of the camta2,3 mutant, and restored the plant size to the wild type level. Moreover, overexpressing PpCAMTA1 in camta2,3 mutant inhibited salicylic acid (SA) biosynthesis and expression of SA-related genes, resulting in a susceptibility phenotype to Pst DC3000. Taken together, our results provide new insights for CAMTAs in peach fruit and indicate that PpCAMTA1 is associated with response to stresses during development.
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Penugurti V, Mishra YG, Manavathi B. AMPK: An odyssey of a metabolic regulator, a tumor suppressor, and now a contextual oncogene. Biochim Biophys Acta Rev Cancer 2022; 1877:188785. [PMID: 36031088 DOI: 10.1016/j.bbcan.2022.188785] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022]
Abstract
Metabolic reprogramming is a unique but complex biochemical adaptation that allows solid tumors to tolerate various stresses that challenge cancer cells for survival. Under conditions of metabolic stress, mammalian cells employ adenosine monophosphate (AMP)-activated protein kinase (AMPK) to regulate energy homeostasis by controlling cellular metabolism. AMPK has been described as a cellular energy sensor that communicates with various metabolic pathways and networks to maintain energy balance. Earlier studies characterized AMPK as a tumor suppressor in the context of cancer. Later, a paradigm shift occurred in support of the oncogenic nature of AMPK, considering it a contextual oncogene. In support of this, various cellular and mouse models of tumorigenesis and clinicopathological studies demonstrated increased AMPK activity in various cancers. This review will describe AMPK's pro-tumorigenic activity in various malignancies and explain the rationale and context for using AMPK inhibitors in combination with anti-metabolite drugs to treat AMPK-driven cancers.
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Affiliation(s)
- Vasudevarao Penugurti
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Yasaswi Gayatri Mishra
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Bramanandam Manavathi
- Molecular and Cellular Oncology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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Qin L, Yang L, Zhao J, Zeng W, Su M, Wang S, Yuan J. GTPase Rac Regulates Conidiation, AFB1 Production and Stress Response in Pathogenic Fungus Aspergillus flavus. Toxins (Basel) 2022; 14:toxins14090581. [PMID: 36136519 PMCID: PMC9503438 DOI: 10.3390/toxins14090581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
As a member of the Rho family, Rac plays important roles in many species, including proliferation, differentiation, apoptosis, DNA damage responses, metabolism, angiogenesis, and immunosuppression. In this study, by constructing Rac-deleted mutants in Aspergillus flavus, it was found that the deletion of Rac gene led to the decline of growth and development, conidia production, AFB1 toxin synthesis, and seed infection ability of A. flavus. The deletion of Rac gene also caused the disappearance of A. flavus sclerotium, indicating that Rac is required for sclerotium formation in A. flavus. The sensitivity of Rac-deficient strains responding to cell wall stress and osmotic pressure stress increased when compared to A.flavus WT. The Western blot result showed that mitogen-activated serine/threonine-protein kinase Slt2 and mitogen-activated protein kinase Hog1 proteins were no longer phosphorylated in Rac-deficient strains of A. flavus, showing that Rac may be used as a molecular switch to control the Slt2-MAPK cascade pathway and regulate the osmotic Hog-MAPK cascade pathway in A. flavus in response to external stress. Altogether, these results indicated that Rac was involved in regulating the growth and development, conidia formation and AFB1 synthesis, and response to cell wall stress and osmotic pressure stress in A. flavus.
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Suntharalingham JP, Ishida M, Del Valle I, Stalman SE, Solanky N, Wakeling E, Moore GE, Achermann JC, Buonocore F. Emerging phenotypes linked to variants in SAMD9 and MIRAGE syndrome. Front Endocrinol (Lausanne) 2022; 13:953707. [PMID: 36060959 PMCID: PMC9433874 DOI: 10.3389/fendo.2022.953707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Heterozygous de novo variants in SAMD9 cause MIRAGE syndrome, a complex multisystem disorder involving Myelodysplasia, Infection, Restriction of growth, Adrenal hypoplasia, Genital phenotypes, and Enteropathy. The range of additional clinical associations is expanding and includes disrupted placental development, poor post-natal growth and endocrine features. Increasingly, milder phenotypic features such as hypospadias in small for gestational age (SGA) boys and normal adrenal function are reported. Some children present with isolated myelodysplastic syndrome (MDS/monosomy 7) without MIRAGE features. Objective We aimed to investigate: 1) the range of reported SAMD9 variants, clinical features, and possible genotype-phenotype correlations; 2) whether SAMD9 disruption affects placental function and leads to pregnancy loss/recurrent miscarriage (RM); 3) and if pathogenic variants are associated with isolated fetal growth restriction (FGR). Methods Published data were analyzed, particularly reviewing position/type of variant, pregnancy, growth data, and associated endocrine features. Genetic analysis of SAMD9 was performed in products of conception (POC, n=26), RM couples, (couples n=48; individuals n=96), children with FGR (n=44), SGA (n=20), and clinical Silver-Russell Syndrome (SRS, n=8), (total n=194). Results To date, SAMD9 variants are reported in 116 individuals [MDS/monosomy 7, 64 (55.2%); MIRAGE, 52 (44.8%)]. Children with MIRAGE features are increasingly reported without an adrenal phenotype (11/52, 21.2%). Infants without adrenal dysfunction were heavier at birth (median 1515 g versus 1020 g; P < 0.05) and born later (median 34.5 weeks versus 31.0; P < 0.05) compared to those with adrenal insufficiency. In MIRAGE patients, hypospadias is a common feature. Additional endocrinopathies include hypothyroidism, hypo- and hyper-glycemia, short stature and panhypopituitarism. Despite this increasing range of phenotypes, genetic analysis did not reveal any likely pathogenic variants/enrichment of specific variants in SAMD9 in the pregnancy loss/growth restriction cohorts studied. Conclusion MIRAGE syndrome is more phenotypically diverse than originally reported and includes growth restriction and multisystem features, but without adrenal insufficiency. Endocrinopathies might be overlooked or develop gradually, and may be underreported. As clinical features including FGR, severe infections, anemia and lung problems can be non-specific and are often seen in neonatal medicine, SAMD9-associated conditions may be underdiagnosed. Reaching a specific diagnosis of MIRAGE syndrome is critical for personalized management.
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Affiliation(s)
- Jenifer P. Suntharalingham
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Miho Ishida
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ignacio Del Valle
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Susanne E. Stalman
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Nita Solanky
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital, London, United Kingdom
| | - Gudrun E. Moore
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John C. Achermann
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Federica Buonocore
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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Dutta M, Raturi V, Gahlaut V, Kumar A, Sharma P, Verma V, Gupta VK, Sood S, Zinta G. The interplay of DNA methyltransferases and demethylases with tuberization genes in potato ( Solanum tuberosum L.) genotypes under high temperature. FRONTIERS IN PLANT SCIENCE 2022; 13:933740. [PMID: 36051291 PMCID: PMC9425917 DOI: 10.3389/fpls.2022.933740] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Potato is a temperate crop consumed globally as a staple food. High temperature negatively impacts the tuberization process, eventually affecting crop yield. DNA methylation plays an important role in various developmental and physiological processes in plants. It is a conserved epigenetic mark determined by the dynamic concurrent action of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases (DeMets). However, C5-MTases and DeMets remain unidentified in potato, and their expression patterns are unknown under high temperatures. Here, we performed genome-wide analysis and identified 10 C5-MTases and 8 DeMets in potatoes. Analysis of their conserved motifs, gene structures, and phylogenetic analysis grouped C5-MTases into four subfamilies (StMET, StCMT3, StDRM, and StDNMT2) and DeMets into three subfamilies (StROS, StDML, and StDME). Promoter analysis showed the presence of multiple cis-regulatory elements involved in plant development, hormone, and stress response. Furthermore, expression dynamics of C5-MTases and DeMets were determined in the different tissues (leaf, flower, and stolon) of heat-sensitive (HS) and heat-tolerant (HT) genotypes under high temperature. qPCR results revealed that high temperature resulted in pronounced upregulation of CMT and DRM genes in the HT genotype. Likewise, demethylases showed strong upregulation in HT genotype as compared to HS genotype. Several positive (StSP6A and StBEL5) and negative (StSP5G, StSUT4, and StRAP1) regulators are involved in the potato tuberization. Expression analysis of these genes revealed that high temperature induces the expression of positive regulators in the leaf and stolon samples of HT genotype, possibly through active DNA demethylation and RNA-directed DNA methylation (RdDM) pathway components. Our findings lay a framework for understanding how epigenetic pathways synergistically or antagonistically regulate the tuberization process under high-temperature stress in potatoes. Uncovering such mechanisms will contribute to potato breeding for developing thermotolerant potato varieties.
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Affiliation(s)
- Madhushree Dutta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vidhi Raturi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Akhil Kumar
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Paras Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | | | - Salej Sood
- Division of Crop Improvement, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Arenas NE, Pieffet G, Rocha-Roa C, Guerrero MI. Design of a specific peptide against phenolic glycolipid-1 from Mycobacterium leprae and its implications in leprosy bacilli entry. Mem Inst Oswaldo Cruz 2022; 117:e220025. [PMID: 35857971 PMCID: PMC9296141 DOI: 10.1590/0074-02760220025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Mycobacterium leprae, the causative agent of Hansen’s
disease, causes neural damage through the specific interaction between the
external phenolic glycolipid-1 (PGL-1) and laminin subunit alpha-2 (LAMA2)
from Schwann cells. OBJECTIVE To design a LAMA2-based peptide that targets PGL-1 from M.
leprae. METHODS We retrieved the protein sequence of human LAMA2 and designed a specific
peptide using the Antimicrobial Peptide Database and physicochemical
parameters for antimycobacterial peptide-lipid interactions. We used the
AlphaFold2 server to predict its three-dimensional structure, AUTODOCK-VINA
for docking, and GROMACS programs for molecular dynamics simulations. FINDINGS We analysed 52 candidate peptides from LAMA2, and subsequent screening
resulted in a single 60-mer peptide. The mapped peptide comprises four
β-sheets and a random coiled region. This peptide exhibits a 45% hydrophobic
ratio, in which one-third covers the same surface. Molecular dynamics
simulations show that our predicted peptide is stable in aqueous solution
and remains stable upon interaction with PGL-1 binding. In addition, we
found that PGL-1 has a preference for one of the two faces of the predicted
peptide, which could act as the preferential binding site of PGL-1. MAIN CONCLUSIONS Our LAMA2-based peptide targeting PGL-1 might have the potential to
specifically block this key molecule, suggesting that the preferential
region of the peptide is involved in the initial contact during the
attachment of leprosy bacilli to Schwann cells.
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Affiliation(s)
- Nelson Enrique Arenas
- Hospital Universitario, Centro Dermatológico Federico Lleras Acosta, Bogotá, Colombia
| | - Gilles Pieffet
- Universidad de los Andes, Departamento de Química, Bogotá, Colombia
| | - Cristian Rocha-Roa
- Universidad del Quindío, Facultad de Ciencias de la Salud, Grupo de Estudio en Parasitología y Micología Molecular-GEPAMOL, Armenia, Quindío, Colombia
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Xie Y, Li H, Luo X, Li H, Gao Q, Zhang L, Teng Y, Zhao Q, Zuo Z, Ren J. IBS 2.0: an upgraded illustrator for the visualization of biological sequences. Nucleic Acids Res 2022; 50:W420-W426. [PMID: 35580044 PMCID: PMC9252815 DOI: 10.1093/nar/gkac373] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/23/2022] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field of molecular and cellular biology. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. Here, we present a professional tool called IBS 2.0 for illustrating the organization of both protein and nucleotide sequences. With the abundant graphical elements provided in IBS 2.0, biological sequences can be easily represented in a concise and clear way. Moreover, we implemented a database visualization module in IBS 2.0, enabling batch visualization of biological sequences from the UniProt and the NCBI RefSeq databases. Furthermore, to increase the design efficiency, a resource platform that allows uploading, retrieval, and browsing of existing biological sequence diagrams has been integrated into IBS 2.0. In addition, a lightweight JS library was developed in IBS 2.0 to assist the visualization of biological sequences in customized web services. To obtain the latest version of IBS 2.0, please visit https://ibs.renlab.org.
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Affiliation(s)
- Yubin Xie
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Huiqin Li
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Xiaotong Luo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Hongyu Li
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Qiuyuan Gao
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Luowanyue Zhang
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Yuyan Teng
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Ren
- School of Life Sciences, Precision Medicine Institute, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
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Islam MS, Mohtasim M, Islam T, Ghosh A. Aldehyde dehydrogenase superfamily in sorghum: genome-wide identification, evolution, and transcript profiling during development stages and stress conditions. BMC PLANT BIOLOGY 2022; 22:316. [PMID: 35786175 PMCID: PMC9252066 DOI: 10.1186/s12870-022-03708-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/23/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND Aldehyde dehydrogenases (ALDHs) are a family of NAD(P)+ dependent enzymes that detoxify aldehydes by promoting their oxidation to respective carboxylic acids. The role of ALDH enzymes in various plant species has been extensively studied, revealing their critical role in salinity, drought, heat, and heavy metal stress tolerance. Despite their physiological significance, ALDH genes in Sorghum bicolor have yet to be studied thoroughly. RESULTS In this study, a total of 19 ALDH genes have been identified that have been grouped into ten families based on the criteria of the ALDH gene nomenclature committee. Segmental duplication assisted more in the enhancement of SbALDH gene family members than tandem duplication. All the identified SbALDH members made a cluster with monocot rice and maize in the phylogenetic tree rather than dicot species, suggesting the pre-eudicot-monocot separation of the ALDH superfamily members. The gene structure and protein domain were found to be mostly conserved in separate phylogenetic classes, indicating that each family played an important role in evolution. Expression analysis revealed that several SbALDHs were expressed in various tissues, developmental stages, and in response to abiotic stresses, indicating that they can play roles in plant growth, development, or stress adaptation. Interestingly, the majority of the SbALDH genes were found to be highly responsive to drought stress, and the SbALDH18B1 transcript showed maximum enhancement in all the stress conditions. The presence of cis-acting elements (mainly ABRE and MBS) in the promoter region of these genes might have a significant role in drought tolerance. CONCLUSIONS Our findings add to the current understanding, evolutionary history, and contribution of SbALDHs in stress tolerance, and smooth the path of further functional validation of these genes.
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Affiliation(s)
- Md Sifatul Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Munira Mohtasim
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tahmina Islam
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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Asmani F, Khavari-Nejad RA, Salmanian AH, Amani J. Immunological evaluation of recombinant chimeric construct from Enterotoxigenic E. coli expressed in hairy roots. Mol Immunol 2022; 147:81-89. [DOI: 10.1016/j.molimm.2022.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/26/2022] [Accepted: 02/09/2022] [Indexed: 01/05/2023]
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Wang H, Zhang X, Ding S, Huang Y, Wang S, Chen H, Chen Y, Li Y. VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features. BMC Genomics 2022; 23:472. [PMID: 35761171 PMCID: PMC9235191 DOI: 10.1186/s12864-022-08713-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Background Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures. Results We developed a user-friendly, independent R package and Shiny web application named “VisProDom”. VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use. Conclusion VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08713-3.
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Amarante ADM, da Silva ICDA, Carneiro VC, Vicentino ARR, Pinto MDA, Higa LM, Moharana KC, Talyuli OAC, Venancio TM, de Oliveira PL, Fantappié MR. Zika virus infection drives epigenetic modulation of immunity by the histone acetyltransferase CBP of Aedes aegypti. PLoS Negl Trop Dis 2022; 16:e0010559. [PMID: 35759510 PMCID: PMC9269902 DOI: 10.1371/journal.pntd.0010559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/08/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022] Open
Abstract
Epigenetic mechanisms are responsible for a wide range of biological phenomena in insects, controlling embryonic development, growth, aging and nutrition. Despite this, the role of epigenetics in shaping insect-pathogen interactions has received little attention. Gene expression in eukaryotes is regulated by histone acetylation/deacetylation, an epigenetic process mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, we explored the role of the Aedes aegypti histone acetyltransferase CBP (AaCBP) after infection with Zika virus (ZIKV), focusing on the two main immune tissues, the midgut and fat body. We showed that the expression and activity of AaCBP could be positively modulated by blood meal and ZIKV infection. Nevertheless, Zika-infected mosquitoes that were silenced for AaCBP revealed a significant reduction in the acetylation of H3K27 (CBP target marker), followed by downmodulation of the expression of immune genes, higher titers of ZIKV and lower survival rates. Importantly, in Zika-infected mosquitoes that were treated with sodium butyrate, a histone deacetylase inhibitor, their capacity to fight virus infection was rescued. Our data point to a direct correlation among histone hyperacetylation by AaCBP, upregulation of antimicrobial peptide genes and increased survival of Zika-infected-A. aegypti.
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Affiliation(s)
- Anderson de Mendonça Amarante
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Vitor Coutinho Carneiro
- Division of Epigenetics, German Cancer Research Center, Im Neuenheimer Feld, Heidelberg, Germany
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcia de Amorim Pinto
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Luiza Mendonça Higa
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Kanhu Charan Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brasil
| | - Octavio A. C. Talyuli
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Thiago Motta Venancio
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brasil
| | - Pedro Lagerblad de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- * E-mail:
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Wang H, Zhou X, Sun Y, Sun X, Guo M. Differences in Protein Profiles of Kefir Grains from Different Origins When Subcultured in Goat Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7515-7524. [PMID: 35687069 DOI: 10.1021/acs.jafc.2c01391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteins not only serve as a nitrogen source for microorganisms but are the main skeleton of kefir grains. After subculturing in goat milk for 4 months, proteins and peptides in three kefir grains from China, Germany, and the United States were analyzed. Except for the S-layer protein from special Lactobacillus sp., αs1-casein, αs2-casein, and β-casein from goat milk were found in kefir grains. These proteins could form aggregates through a covalent interaction with polysaccharides to maintain the morphological stability of the grains. Furthermore, they were highly related to the microbiota in kefir grains. Additionally, a number of hydrophilic/hydrophobic peptides that were hydrolyzed by extracellular proteases were found from kefir grains. A correlation may exist between peptides and Lactobacillus sp. in kefir grains. Bioactive peptides, including DKIHPF, LGPVRGPFP, and QEPVLGPVRGPFP, were found from these kefir grains. The results indicated that goat milk as a substrate affects the protein and peptide composition of kefir grains.
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Affiliation(s)
- Hao Wang
- Department of Food Quality and Safety, College of Food Science and Technology, Ocean University of China, Qingdao, Shandong 266100, China
- Key Laboratory of Dairy Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xinhui Zhou
- Key Laboratory of Dairy Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Yuxue Sun
- Key Laboratory of Dairy Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xiaomeng Sun
- Key Laboratory of Dairy Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Mingruo Guo
- Department of Nutrition and Food Sciences, College of Agriculture and Life Sciences, University of Vermont, Burlington, Vermont 05405, United States
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Li W, Hu J, Li L, Zhang M, Cui Q, Ma Y, Su H, Zhang X, Xu H, Wang M. New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain. Front Microbiol 2022; 13:896916. [PMID: 35801099 PMCID: PMC9253605 DOI: 10.3389/fmicb.2022.896916] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
Daptomycin (DAP), a last-resort antibiotic for treating Gram-positive bacterial infection, has been widely used in the treatment of vancomycin-resistant enterococci (VRE). Resistance to both daptomycin and vancomycin leads to difficulties in controlling infections of enterococci. A clinical multidrug-resistant Enterococcus faecium EF332 strain that shows resistance to both daptomycin and vancomycin was identified, for which resistance mechanisms were investigated in this work. Whole-genome sequencing and comparative genomic analysis were performed by third-generation PacBio sequencing, showing that E. faecium EF332 contains four plasmids, including a new multidrug-resistant pEF332-2 plasmid. Two vancomycin resistance-conferring gene clusters vanA and vanM were found on this plasmid, making it the second reported vancomycin-resistant plasmid containing both clusters. New mutations in chromosomal genes cls and gdpD that, respectively, encode cardiolipin synthase and glycerophosphoryl diester phosphodiesterase were identified. Their potential roles in leading to daptomycin resistance were further investigated. Through molecular cloning and phenotypic screening, two-dimensional thin-layer chromatography, fluorescence surface charge test, and analysis of cardiolipin distribution patterns, we found that mutations in cls decrease surface negative charges of the cell membrane (CM) and led to redistribution of lipids of CM. Both events contribute to the DAP resistance of E. faecium EF332. Mutation in gdpD leads to changes in CM phospholipid compositions, but cannot confer DAP resistance. Neither mutation could result in changes in cellular septa. Therefore, we conclude that the daptomycin resistance of E. faecium EF332 is conferred by new cls mutations. This work reports the genetic basis for vancomycin and daptomycin resistance of a multidrug-resistant E. faecium strain, with the finding of new mutations of cls that leads to daptomycin resistance.
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Affiliation(s)
- Weiwei Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- Division of Science and Technology, Ludong University, Yantai, China
| | - Jiamin Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Mengge Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qingyu Cui
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yanan Ma
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Hainan Su
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xuhua Zhang
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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91
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Kong X, Wang H, Guo G, Li P, Tong P, Liu M, Ma X, Dong C, Li Y, Zhang H, Zhang W. Duck sewage source coliphage P762 can lyse STEC and APEC. Virus Genes 2022; 58:436-447. [PMID: 35705841 DOI: 10.1007/s11262-022-01915-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Multiple pathogenic types or serotypes restrict treatment for colibacillosis. In addition, rising antibiotic resistance has heightened public awareness to prevent and control pathogenic Escherichia coli. The bacteriophage is a viable technique to treat colibacillosis as an alternative to antibiotics. P762, a coliphage isolated from duck farm sewage, was demonstrated to cloud lyse Shiga toxin-producing Escherichia Coli serotypes O157 and non-O157 (17/39), Avian pathogenic E. coli covered serotype O78, O83, and O9 (5/19), and other pathogenic Escherichia coli (5/17). Additional fundamental biological characteristics analysis revealed that P762 is stable at pH 3 ~ 11 and temperature between 4 °C and 60 °C, and its optimum multiplicity of infection (MOI) is 0.1. The one-step curve of P762 exhibited three bursts of growth stage: two rapid and one slow stage. Furthermore, the first rapid burst size is 80 CFU/PFU, the burst size of the slow stage is 10 CFU/PFU, and the second rapid burst size is about 990 CFU/PFU. In addition, P762 can form a "halo" on a double agar plate, implying that the phage secretes depolymerase. With 95.14% identity and 90% query coverage, genome sequence analysis revealed that P762 is most closely related to Escherichia phage DY1, which belongs to the genus Kayfunavirus. After screening using RAST and VFDB, no virulence factors were discovered in P762. In vitro antibacterial tests revealed that P762 has high bactericidal activity in lettuce leaves contaminated with STEC. In conclusion, phage P762 might be employed in the future to prevent and control pathogenic Escherichia coli.
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Affiliation(s)
- Xuewei Kong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pei Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Panpan Tong
- College of Veterinary Medicine, Shihezi Agricultural University, Xinjiang, China
| | - Maojun Liu
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xun Ma
- College of Animal Science and Technology, Xinjiang Agricultural University, Xinjiang, China
| | - Chen Dong
- Jiangsu Province CDC: Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yubao Li
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Haiyan Zhang
- Department of Food and Biology Engineering, Wuhu Institute of Technology, Wuhu, China.
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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92
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Sun R, Gong J, Liu Y, Chen Z, Zhang F, Gao J, Cao J, Chen X, Zhang S, Zhao C, Gao S. Comprehensive molecular evaluation of the histone methyltransferase gene family and their important roles in two-line hybrid wheat. BMC PLANT BIOLOGY 2022; 22:290. [PMID: 35698040 PMCID: PMC9190116 DOI: 10.1186/s12870-022-03639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Histone methylation usually plays important roles in plant development through post-translational regulation and may provide a new visual field for heterosis. The histone methyltransferase gene family has been identified in various plants, but its members and functions in hybrid wheat related in heterosis is poorly studied. RESULTS In this study, 175 histone methyltransferase (HMT) genes were identified in wheat, including 152 histone lysine methyltransferase (HKMT) genes and 23 protein arginine methyltransferase (PRMT) genes. Gene structure analysis, physicochemical properties and subcellular localization predictions of the proteins, exhibited the adequate complexity of this gene family. As an allohexaploid species, the number of the genes (seven HKMTs orthologous groups and four PRMTs orthologous groups) in wheat were about three times than those in diploids and showed certain degrees of conservation, while only a small number of subfamilies such as ASH-like and Su-(var) subfamilies have expanded their members. Transcriptome analysis showed that HMT genes were mainly expressed in the reproductive organs. Expression analysis showed that some TaHMT genes with different trends in various hybrid combinations may be regulated by lncRNAs with similar expression trends. Pearson correlation analysis of the expression of TaHMT genes and two yield traits indicated that four DEGs may participate in the yield heterosis of two-line hybrid wheat. ChIP-qPCR results showed that the histone modifications (H3K4me3, H3K36me3 and H3K9ac) enriched in promoter regions of three TaCCA1 genes which are homologous to Arabidopsis heterosis-related CCA1/LHY genes. The higher expression levels of TaCCA1 in F1 than its parents are positive with these histone modifications. These results showed that histone modifications may play important roles in wheat heterosis. CONCLUSIONS Our study identified characteristics of the histone methyltransferase gene family and enhances the understanding of the evolution and function of these members in allohexaploid wheat. The causes of heterosis of two-line hybrid wheat were partially explained from the perspective of histone modifications.
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Affiliation(s)
- Renwei Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Jie Gong
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Yongjie Liu
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Jiangang Gao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Junmei Cao
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Xianchao Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
| | - Changping Zhao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
| | - Shiqing Gao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
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93
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Zhang J, Xu Y, Zhang Y, Bossila EA, Shi M, Zhao Y. Bioinformatic analysis as a first step to predict the compatibility of hematopoiesis and immune system genes between humans and pigs. Xenotransplantation 2022; 29:e12764. [PMID: 35695327 DOI: 10.1111/xen.12764] [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: 02/15/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022]
Abstract
The shortage of allogeneic donor organs leaves its supply far short of clinical need. There are great expectations on xenotransplantation, especially with pigs' organs. With the genetic modification of donor pigs, the rejection and cross-species transmission issues have now been widely addressed. However, research on the compatibility of genes between humans and pigs was limited. We performed a systematic screening analysis of predicted incompatible genes between humans and pigs, judged by low protein sequence similarities or different predicted protein domain compositions. By combining with gene set enrichment analysis, we screened out several key genes of hematopoiesis and the immune system with possible incompatibilities, which might be important for establishing chimera and xenotransplantation between humans and pigs. There were seven chemokine genes, including CCL1, CCL5, CCL24, CCL25, CCL28, CXCL12, and CXCL16, that exhibited limited similarity between humans and pigs (similarity < 0.8). Among hematopoiesis process-related genes, 15 genes of adhesion molecules, Notch ligands, and cytokine receptors exhibited differences between humans and pigs. In complement and coagulation cascades, 19 genes showed low similarity and 77 genes had different domain compositions between humans and pigs. Our study provides a good reference for further genetic modification of pigs, which might be beneficial for xenotransplantation.
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Affiliation(s)
- Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingzi Zhang
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elhusseny A Bossila
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Biotechnology Department, Faculty of Agriculture Al-Azhar University, Cairo, Egypt
| | - Mingpu Shi
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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94
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Genome-Wide Identification and Characterization of the Calmodulin-Binding Transcription Activator (CAMTA) Gene Family in Plants and the Expression Pattern Analysis of CAMTA3/SR1 in Tomato under Abiotic Stress. Int J Mol Sci 2022; 23:ijms23116264. [PMID: 35682943 PMCID: PMC9181194 DOI: 10.3390/ijms23116264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Calmodulin-binding transcription activator (CAMTA) plays an important regulatory role in plant growth, development, and stress response. This study identified the phylogenetic relationships of the CAMTA family in 42 plant species using a genome-wide search approach. Subsequently, the evolutionary relationships, gene structures, and conservative structural domain of CAMTA3/SR1 in different plants were analyzed. Meanwhile, in the promoter region, the cis-acting elements, protein clustering interaction, and tissue-specific expression of CAMTA3/SR1 in tomato were identified. The results show that SlCAMTA3/SR1 genes possess numerous cis-acting elements related to hormones, light response, and stress in the promoter regions. SlCAMTA3 might act together with other Ca2+ signaling components to regulate Ca2+-related biological processes. Then, the expression pattern of SlCAMTA3/SR1 was also investigated by quantitative real-time PCR (qRT-PCR) analysis. The results show that SlCAMTA3/SR1 might respond positively to various abiotic stresses, especially Cd stress. The expression of SlCAMTA3/SR1 was scarcely detected in tomato leaf at the seedling and flowering stages, whereas SlCAMTA3/SR1 was highly expressed in the root at the seedling stage. In addition, SlCAMTA3/SR1 had the highest expression levels in flowers at the reproductive stage. Here, we provide a basic reference for further studies about the functions of CAMTA3/SR1 proteins in plants.
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95
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Chen Y, Lv M, Liang Z, Liu Z, Zhou J, Zhang L. Cyclic di-GMP modulates sessile-motile phenotypes and virulence in Dickeya oryzae via two PilZ domain receptors. MOLECULAR PLANT PATHOLOGY 2022; 23:870-884. [PMID: 35254732 PMCID: PMC9104268 DOI: 10.1111/mpp.13200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/23/2022] [Accepted: 02/08/2022] [Indexed: 05/03/2023]
Abstract
Dickeya oryzae is a bacterial pathogen causing the severe rice stem rot disease in China and other rice-growing countries. We showed recently that the universal bacterial second messenger c-di-GMP plays an important role in modulation of bacterial motility and pathogenicity, but the mechanism of regulation remains unknown. In this study, bioinformatics analysis of the D. oryzae EC1 genome led to the identification of two proteins, YcgR and BcsA, both of which contain a conserved c-di-GMP receptor domain, known as the PilZ-domain. By deleting all the genes encoding c-di-GMP-degrading enzymes in D. oryzae EC1, the resultant mutant 7ΔPDE with high c-di-GMP levels became nonmotile, formed hyperbiofilm, and lost the ability to colonize and invade rice seeds. These phenotypes were partially reversed by deletion of ycgR in the mutant 7ΔPDE, whereas deletion of bcsA only reversed the hyperbiofilm phenotype of mutant 7ΔPDE. Significantly, double deletion of ycgR and bcsA in mutant 7ΔPDE rescued its motility, biofilm formation, and virulence to levels of wild-type EC1. In vitro biochemical experiments and in vivo phenotypic assays further validated that YcgR and BcsA proteins are the receptors for c-di-GMP, which together play a critical role in regulating the c-di-GMP-associated functionality. The findings from this study fill a gap in our understanding of how c-di-GMP modulates bacterial motility and biofilm formation, and provide useful clues for further elucidation of sophisticated virulence regulatory mechanisms in this important plant pathogen.
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Affiliation(s)
- Yufan Chen
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Mingfa Lv
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Zhibin Liang
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Zhiqing Liu
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Lian‐Hui Zhang
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
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96
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Jin S, Deng Z, Xu S, Zhang H, Han Z. Genome-wide identification and low-salinity stress analysis of the Hsp70 gene family in swimming crab (Portunus trituberculatus). Int J Biol Macromol 2022; 208:126-135. [PMID: 35301000 DOI: 10.1016/j.ijbiomac.2022.03.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 01/01/2023]
Abstract
No genome-wide identification and expression analysis have been performed on the heat shock protein 70 (Hsp70) gene family, which is essential to key cellular processes and responses to environmental change, in decapods. In the present study, we identified nine members of the Hsp70 gene family within the genome of swimming crab (Portunus trituberculatus) and provided insights into their response to long-term low-salinity stress. Results demonstrated that gene structure and motifs are conserved among members of this gene family in P. trituberculatus. Under low-salinity stress, the expression of this gene family in the gill of P. trituberculatus showed that hsc70l.2 was significantly upregulated, hyou1 was significantly downregulated. The hsc70l.4 was not expressed. Furthermore, selection test on duplicated genes showed a negative selection on hsc70l.1, hsc70l.2, hsc70l.3, and hsc70l.4, suggesting functional redundancy. This may be the first study that systematically identified and analyzed the Hsp70 gene family in decapods. These results can provide fundamental data for the biological research of P. trituberculatus and enhance understanding of the biological function of Hsp70 in crustaceans adapting to salinity changes.
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Affiliation(s)
- Shihuai Jin
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Zhaochao Deng
- Ocean Academy, Zhejiang University, Zhoushan, Zhejiang 316021, China
| | - Shengyong Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Haobo Zhang
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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97
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Comprehensive Analysis of N6-Methyladenosine Regulatory Genes from Citrus grandis and Expression Profilings in the Fruits of “Huajuhong” (C. grandis “Tomentosa”) during Various Development Stages. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Citrus grandis “Tomentosa” (“Huajuhong”) is a famous traditional Chinese medicine. The aim of the present study is to provide a comprehensive characterization of the m6A regulatory genes from C. grandis, and examine their expression patterns in fruits of C. grandis “Tomentosa” during various developmental stages. A total of 26 N6-methyladenosine (m6A) regulatory proteins were identified from the genome of C. grandis, which were distributed across nine chromosomes in C. grandis. Phylogenetic relationships revealed that all m6A regulatory genes were divided into groups of m6A writers, erasers, and readers. The m6A writer groups included CgMTA, CgMTB, and CgMTC three MTs (methyltransferases), one CgVIR (virilizer), one CgHAKAI (E3 ubiquitin ligase HAKAI), and one CgFIP37 (FKBP interacting protein 37). Moreover, 10 CgALKBH (α-ketoglutarate-dependent dioxygenase homolog) members (numbered from CgALKBH1 to CgALKBH10) and 10 CgECT (C-terminal region) members (numbered from CgECT1 to CgECT10) in C. grandis were identified as m6A erasers and readers, respectively. The domain structures and motif architectures among the groups of m6A writers, erasers, and readers were diverse. Cis-acting elements in the promoters of the 26 m6A regulatory genes predicted that the abscisic acid-responsive (ABA) element (ABRE) was present on the promoters of 19 genes. In addition, the expression profiles of all m6A regulatory genes were examined in the fruits of two varieties of C. grandis “Tomentosa” during different growth stages to give basic hints for further investigation of the function of the N6-methyladenosine regulatory genes in C. grandis “Tomentosa”.
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98
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Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
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99
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Wang X, Zhang X, Lu BH, Gao J. The periplasmic chaperone protein Psg_2795 contributes to the virulence of Pseudomonas savastanoi pv. glycinea: the causal agent of bacterial blight of soybean. J Microbiol 2022; 60:478-487. [PMID: 35246805 DOI: 10.1007/s12275-022-1469-5] [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: 09/08/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
Abstract
Pseudomonas savastanoi pv. glycinea (Psg also named P. syringae pv. glycinea and P. amygdali pv. glycinea) is the causative agent of bacterial blight in soybean. The identification of virulence factors is essential for understanding the pathogenesis of Psg. In this study, a mini-Tn5 transposon mutant library of Psg strain PsgNC12 was screened on soybean, and one low-virulent mini-Tn5 mutant, designated as 4573, was identified. Sequence analysis of the 4573-mutant revealed that the mini-Tn5 transposon was inserted in the Psg_2795 gene. Psg_2795 encodes a FimC-domain protein that is highly conserved in Pseudomonas. Further analysis revealed that the mutation and knockout of Psg_2795 results in a reduced virulence phenotype on soybean, decreased motility, weakened bacterial attachment to a glass surface and delayed the population growth within soybean leaves. The phenotype of the 4573-mutant could be complemented nearly to wild-type levels using an intact Psg_2795 gene. Collectively, our results demonstrate that Psg_2795 plays an important role in the virulence, motility, attachment and the population growth of PsgNC12 in soybean. This finding provides a new insight into the function of periplasmic chaperone proteins in a type I pilus and provides reference information for identifying Psg_2795 homologues in P. savastanoi and other bacteria.
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Affiliation(s)
- Xiuhua Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China
| | - Xiaoyan Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China
| | - Bao-Hui Lu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China.
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China.
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Ng WM, Sahin M, Krumm SA, Seow J, Zeltina A, Harlos K, Paesen GC, Pinschewer DD, Doores KJ, Bowden TA. Contrasting Modes of New World Arenavirus Neutralization by Immunization-Elicited Monoclonal Antibodies. mBio 2022; 13:e0265021. [PMID: 35315691 PMCID: PMC9040744 DOI: 10.1128/mbio.02650-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/28/2022] [Indexed: 12/31/2022] Open
Abstract
Transmission of the New World hemorrhagic fever arenaviruses Junín virus (JUNV) and Machupo virus (MACV) to humans is facilitated, in part, by the interaction between the arenavirus GP1 glycoprotein and the human transferrin receptor 1 (hTfR1). We utilize a mouse model of live-attenuated immunization with envelope exchange viruses to isolate neutralizing monoclonal antibodies (NAbs) specific to JUNV GP1 and MACV GP1. Structures of two NAbs, termed JUN1 and MAC1, demonstrate that they neutralize through disruption of hTfR1 recognition. JUN1 utilizes a binding mode common to all characterized infection- and vaccine-elicited JUNV-specific NAbs, which involves mimicking hTfR1 binding through the insertion of a tyrosine into the receptor-binding site. In contrast, MAC1 undergoes a tyrosine-mediated mode of antigen recognition distinct from that used by the reported anti-JUNV NAbs and the only other characterized anti-MACV NAb. These data reveal the varied modes of GP1-specific recognition among New World arenaviruses by the antibody-mediated immune response. IMPORTANCE The GP1 subcomponent of the New World arenavirus GP is a primary target of the neutralizing antibody response, which has been shown to be effective in the prevention and treatment of infection. Here, we characterize the structural basis of the antibody-mediated immune response that arises from immunization of mice against Junín virus and Machupo virus, two rodent-borne zoonotic New World arenaviruses. We isolate a panel of GP1-specific monoclonal antibodies that recognize overlapping epitopes and exhibit neutralizing behavior, in vitro. Structural characterization of two of these antibodies indicates that antibody recognition likely interferes with GP1-mediated recognition of the transferrin receptor 1. These data provide molecular-level detail for a key region of vulnerability on the New World arenavirus surface and a blueprint for therapeutic antibody development.
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Affiliation(s)
- Weng M. Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mehmet Sahin
- Department of Biomedicine, Division of Experimental Virology, University of Basel, Basel, Switzerland
| | - Stefanie A. Krumm
- Kings College London, Department of Infectious Diseases, Guy’s Hospital, London, United Kingdom
| | - Jeffrey Seow
- Kings College London, Department of Infectious Diseases, Guy’s Hospital, London, United Kingdom
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Guido C. Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Daniel D. Pinschewer
- Department of Biomedicine, Division of Experimental Virology, University of Basel, Basel, Switzerland
| | - Katie J. Doores
- Kings College London, Department of Infectious Diseases, Guy’s Hospital, London, United Kingdom
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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