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Chanket W, Pipatthana M, Sangphukieo A, Harnvoravongchai P, Chankhamhaengdecha S, Janvilisri T, Phanchana M. The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective. Comput Struct Biotechnol J 2024; 23:2358-2374. [PMID: 38873647 PMCID: PMC11170357 DOI: 10.1016/j.csbj.2024.05.027] [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: 02/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.
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Affiliation(s)
- Wannarat Chanket
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Methinee Pipatthana
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Apiwat Sangphukieo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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2
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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [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: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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3
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Liu J, Li Y, Zhang A, Zhong H, Jiang H, Tsui MTK, Li M, Pan K. Impact of geochemistry and microbes on the methylmercury production in mangrove sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135627. [PMID: 39217948 DOI: 10.1016/j.jhazmat.2024.135627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/05/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Unraveling the geochemical and microbial controls on methylmercury (MeHg) dynamics in mangrove sediments is important, as MeHg can potentially pose risks to marine biota and people that rely on these ecosystems. While the important role of sulfate-reducing bacteria in MeHg formation has been examined in this ecologically important habitat, the contribution of non-Hg methylating communities on MeHg production remains particularly unclear. Here, we collected sediment samples from 13 mangrove forests in south China and examined the geochemical parameters and microbial communities related to the Hg methylation. MeHg concentrations were significantly correlated to the OM-related parameters such as organic carbon content, total nitrogen, and dissolved organic carbon concentrations, suggesting the importance of OM in the MeHg production. Sulfate-reducing bacteria were the major Hg-methylators in mangrove sediments. Desulfobacteraceae and Desulfobulbaceae dominated the Hg-methylating microbes. Classification random forest analysis detected strong co-occurrence between Hg methylators and putative non-Hg methylators, thus suggesting that both types of microorganisms contribute to the MeHg dynamics in the sediments. Our study provides an overview of MeHg contamination in south China and advances our understanding of Hg methylation in mangrove ecosystems.
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Affiliation(s)
- Jingli Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yanping Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Aijia Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Huan Zhong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province 210046, China
| | - Hao Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Martin Tsz-Ki Tsui
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
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4
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Douradinha B. Computational strategies in Klebsiella pneumoniae vaccine design: navigating the landscape of in silico insights. Biotechnol Adv 2024; 76:108437. [PMID: 39216613 DOI: 10.1016/j.biotechadv.2024.108437] [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: 05/28/2024] [Revised: 07/07/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
The emergence of multidrug-resistant Klebsiella pneumoniae poses a grave threat to global public health, necessitating urgent strategies for vaccine development. In this context, computational tools have emerged as indispensable assets, offering unprecedented insights into klebsiellal biology and facilitating the design of effective vaccines. Here, a review of the application of computational methods in the development of K. pneumoniae vaccines is presented, elucidating the transformative impact of in silico approaches. Through a systematic exploration of bioinformatics, structural biology, and immunoinformatics techniques, the complex landscape of K. pneumoniae pathogenesis and antigenicity was unravelled. Key insights into virulence factors, antigen discovery, and immune response mechanisms are discussed, highlighting the pivotal role of computational tools in accelerating vaccine development efforts. Advancements in epitope prediction, antigen selection, and vaccine design optimisation are examined, highlighting the potential of in silico approaches to update vaccine development pipelines. Furthermore, challenges and future directions in leveraging computational tools to combat K. pneumoniae are discussed, emphasizing the importance of multidisciplinary collaboration and data integration. This review provides a comprehensive overview of the current state of computational contributions to K. pneumoniae vaccine development, offering insights into innovative strategies for addressing this urgent global health challenge.
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Tang C, Tamura-Nakano M, Kobayakawa K, Ozawa T, Onojima T, Kajitani R, Itoh T, Tachibana K. A single gene determines allorecognition in hydrozoan jellyfish Cladonema radiatum inbred lines. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:1002-1020. [PMID: 38973306 DOI: 10.1002/jez.2853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/10/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
Allorecognition-the ability of an organism to discriminate between self and nonself-is crucial to colonial marine animals to avoid invasion by other individuals in the same habitat. The cnidarian hydroid Hydractinia has long been a major research model in studying invertebrate allorecognition, establishing a rich knowledge foundation. In this study, we introduce a new cnidarian model Cladonema radiatum (C. radiatum). C. radiatum is a hydroid jellyfish which also forms polyp colonies interconnected with stolons. Allorecognition responses-fusion or regression of stolons-are observed when stolons encounter each other. By transmission electron microscopy, we observe rapid tissue remodeling contributing to gastrovascular system connection in fusion. Meanwhile, rejection responses are regulated by reconstruction of the chitinous exoskeleton perisarc, and induction of necrotic and autophagic cellular responses at cells in contact with the opponent. Genetic analysis identifies allorecognition genes: six Alr genes located on the putative allorecognition complex and four immunoglobulin superfamily genes on a separate genome region. C. radiatum allorecognition genes show notable conservation with the Hydractinia Alr family. Remarkedly, stolon encounter assays of inbred lines reveal that genotypes of Alr1 solely determine allorecognition outcomes in C. radiatum.
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Affiliation(s)
- Crystal Tang
- Laboratory of Chronobiology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Miwa Tamura-Nakano
- Research Institute National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenta Kobayakawa
- Laboratory of Chronobiology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takuto Ozawa
- Laboratory of Chronobiology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takao Onojima
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-Ku, Tokyo, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-Ku, Tokyo, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-Ku, Tokyo, Japan
| | - Kazunori Tachibana
- Laboratory of Chronobiology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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6
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Gül C, Gül A, Karakavuk T, Erkunt Alak S, Karakavuk M, Can H, Değirmenci Döşkaya A, Yavuz İ, Kaplan S, Erel Akbaba G, Şen Karaman D, Akbaba H, Efe Köseoğlu A, Ovayurt T, Yüksel Gürüz A, Ün C, Kantarcı AG, Döşkaya M. A novel DNA vaccine encoding the SRS13 protein administered by electroporation confers protection against chronic toxoplasmosis. Vaccine 2024; 42:126065. [PMID: 38880692 DOI: 10.1016/j.vaccine.2024.06.032] [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: 02/16/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/18/2024]
Abstract
Toxoplasma gondii is an obligate intracellular parasite that can infect a variety of mammals including humans and causes toxoplasmosis. Unfortunately, a protective and safe vaccine against toxoplasmosis hasn't been developed yet. In this study, we developed a DNA vaccine encoding the SRS13 protein and immunized BALB/c mice thrice with pVAX1-SRS13 through the intramuscular route (IM) or intradermally using an electroporation device (ID + EP). The immunogenicity of pVAX1-SRS13 was analyzed by ELISA, Western blot, cytokine ELISA, and flow cytometry. The protective efficacy of the pVAX1-SRS13 was investigated by challenging mice orally with T. gondii PRU strain tissue cysts. The results revealed that pVAX1-SRS13 administered through IM or ID + EP routes induced high level of anti-SRS13 IgG antibody responses (P = 0.0037 and P < 0.0001). The IFN-γ level elicited by the pVAX1-SRS13 (ID + EP) was significantly higher compared to the control group (P = 0.00159). In mice administered with pVAX1-SRS13 (ID + EP), CD8+ cells secreting IFN-γ was significantly higher compared to pVAX1-SRS13 (IM) (P = 0.0035) and the control group (P = 0.0068). Mice vaccinated with the SRS13 DNA vaccine did not induce significant IL-4 level. Moreover, a significant reduction in the number of tissue cysts and the load of T. gondii DNA was detected in brains of mice administered with pVAX1-SRS13 through ID + EP and IM routes compared to controls. In conclusion, the SRS13 DNA vaccine was found to be highly immunogenic and confers strong protection against chronic toxoplasmosis.
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Affiliation(s)
- Ceren Gül
- Ege University, Graduate School of Natural and Applied Sciences, Department of Biotechnology, İzmir, Türkiye; Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye
| | - Aytül Gül
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Faculty of Engineering, Department of Bioengineering, İzmir, Türkiye
| | - Tuğba Karakavuk
- Ege University, Graduate School of Natural and Applied Sciences, Department of Biotechnology, İzmir, Türkiye; Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye
| | - Sedef Erkunt Alak
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Faculty of Science, Department of Biology Molecular Biology Section, İzmir, Türkiye
| | - Muhammet Karakavuk
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Ödemiş Vocational School, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye
| | - Hüseyin Can
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Faculty of Science, Department of Biology Molecular Biology Section, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye
| | - Aysu Değirmenci Döşkaya
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, İzmir, Türkiye
| | - İrem Yavuz
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye
| | - Seren Kaplan
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye
| | - Gülşah Erel Akbaba
- İzmir Katip Çelebi University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, İzmir, Türkiye
| | - Didem Şen Karaman
- İzmir Katip Çelebi University, Faculty of Engineering and Architecture, Department of Biomedical Engineering, İzmir, Türkiye
| | - Hasan Akbaba
- Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye; Ege University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, İzmir, Türkiye
| | - Ahmet Efe Köseoğlu
- Ege University, Faculty of Science, Department of Biology Molecular Biology Section, İzmir, Türkiye; Duisburg-Essen University, Faculty of Chemistry, Department of Environmental Microbiology and Biotechnology, Essen, Germany
| | - Tolga Ovayurt
- İzmir Katip Çelebi University, Graduate School of Natural and Applied Sciences, Department of Biomedical Technology, İzmir, Türkiye
| | - Adnan Yüksel Gürüz
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, İzmir, Türkiye
| | - Cemal Ün
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Faculty of Science, Department of Biology Molecular Biology Section, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye
| | - Ayşe Gülten Kantarcı
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye; Ege University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, İzmir, Türkiye
| | - Mert Döşkaya
- Ege University, Vaccine Development Application and Research Center, İzmir, Türkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, İzmir, Türkiye
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Zhou X, Jiang D, Zhang Z, Shen X, Pan J, Ouyang H, Xu D, Tian Y, Huang Y. Effect of active immunization with OPN5 on follicular development and egg production in quail under different photoperiods. Theriogenology 2024; 228:81-92. [PMID: 39116655 DOI: 10.1016/j.theriogenology.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/14/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
OPN5 is one of the main deep brain photoreceptors (DBPs), converting photoperiodic information into neuroendocrine signals to regulate reproduction in birds. This study investigated the mechanism of OPN5-mediated photoperiodic regulation of reproduction by active immunization against OPN5. 96 female quail were divided into OPN5-immunized and control group under the same photoperiod: 16 L:8 D (d 1 to d 35), 8 L:16 D (d 36 to d 70) and 12 L:12 D (d 71 to d 126). OPN5-immunized group was conducted with OPN5 protein vaccination and control group was given a blank vaccine. Samples were collected on d 1, d 30, d 60, and d 126. Results showed switching photoperiod to 8 L:16 D decreased the laying rate, GSI%, numbers of YFs and WFs, serum levels of PRL, P4 and E2, and pituitary PRL and TSHβ protein expressions in both groups (P < 0.05). Whereas the OPN5-immunized group exhibited higher laying rates than the control group (P < 0.05). The control group showed reduced GnRHR and TSHβ gene expressions in the pituitary and increased GnIH and DIO3 transcript and/or protein abundance in the hypothalamus. (P < 0.05). The OPN5-immunized group had lower DIO3 expression at both mRNA and protein levels. (P < 0.05). Switching photoperiod from 8 L:16 D to 12 L:12 D increased the laying rates, GSI%, numbers of YFs and WFs, serum levels of PRL, and PRL protein expression in both groups (P < 0.05), and the responses were more pronounced in OPN5-immunized group (P < 0.05). In contrast to the control group, quail with OPN5-immunization had higher OPN5 and DIO2 transcript and/or protein levels but lower DIO3 expressions in the hypothalamus along the transition photoperiods (P < 0.05). The results revealed that OPN5 responds to photoperiod transition, and its activation mediates related signaling to up-regulate TSH-DIO2/DIO3 pathway and VIP-PRL secretion to prime quail reproductive functions.
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Affiliation(s)
- Xiaoli Zhou
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Danli Jiang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhuoshen Zhang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xu Shen
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jianqiu Pan
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hongjia Ouyang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Danning Xu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yunbo Tian
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yunmao Huang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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Kowalczyk J, Kłodawska K, Zych M, Burczyk J, Malec P. Ubiquitin-like and ubiquitinylated proteins associated with the maternal cell walls of Scenedesmus obliquus 633 as identified by immunochemistry and LC-MS/MS proteomics. PROTOPLASMA 2024:10.1007/s00709-024-01994-3. [PMID: 39365352 DOI: 10.1007/s00709-024-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 09/23/2024] [Indexed: 10/05/2024]
Abstract
The cell walls of green algae Scenedesmus obliquus are complex, polymeric structures including an inner cellulose layer surrounded by an algaenan-containing trilaminar sheath. The process of autosporulation leads to the formation of sporangial (maternal) cell walls, which are released into the medium after sporangial autolysis. In this study, a fraction of maternal cell wall material (CWM) was isolated from the stationary phase cultures of Scenedesmus obliquus 633 and subjected to immunofluorescence microscopy using polyclonal anti-ubiquitin antibodies. The water-extracted polypeptide fraction from the maternal cell walls was then analyzed using immunoblotting and LC-MS/MS. An immunoanalysis showed the presence of several peptides reactive with polyclonal anti-ubiquitin serum, with apparent molecular masses of c. 12, 70, 120, 200, and > 250 kDa. Cell wall-associated peptides were identified on the basis of LC-MS/MS spectra across NCBI databases, including the Scenedesmaceae family (58 records), the Chlorophyceae class (37 records), and Chlamydomonas reinhardtii (18 records) corresponding to the signatures of 95 identified proteins. In particular, three signatures identified ubiquitin and ubiquitin-related proteins. In the maternal cell walls, immunoblotting analysis, immunofluorescence microscopy, and LC-MS/MS proteomics collectively demonstrated the presence of ubiquitin-like epitopes, ubiquitin-specific peptide signatures, and several putative ubiquitin conjugates of a higher molecular mass. These results support the presence of ubiquitin-like proteins in the extramembranous compartment of Scenedesmus obliquus 633 and suggest that protein ubiquitination plays a significant role in the formation and functional integrity of the maternal cell walls in green algae.
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Affiliation(s)
- Justyna Kowalczyk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348, Kraków, Poland
| | - Kinga Kłodawska
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Maria Zych
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jagiellońska 4, 41-200, Sosnowiec, Poland
| | - Jan Burczyk
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jagiellońska 4, 41-200, Sosnowiec, Poland
- Laboratory of Biotechnology, Puńcowska 74, 43-400, Cieszyn, Poland
| | - Przemysław Malec
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland.
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9
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Liu M, Yang W, Gu X, Xiao Y, Yang L, Zhang Z, Wei T, Hsiang T, Zhang Y, Li G. A Nanopore-sequenced high-quality genome of the Bipolaris oryzae strain Bo-1. Microbiol Resour Announc 2024:e0038824. [PMID: 39365042 DOI: 10.1128/mra.00388-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 09/10/2024] [Indexed: 10/05/2024] Open
Abstract
Brown spot disease of rice caused by Bipolaris oryzae results in severe yield losses. A high-quality genome was assembled using Nanopore sequencing data, resulting in a 36-Mb nuclear genome with 19 contigs and a mitogenome. This assembly provides valuable genetic resources for investigations of rice-B. oryzae interactions.
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Affiliation(s)
- Meng Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Wei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Xinyi Gu
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yongxin Xiao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Lei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Zhaowu Zhang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Tom Hsiang
- Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Yaling Zhang
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
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10
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Frink B, Burger M, Yarkoni M, Shevtsov-Tal S, Zer H, Yamaoka S, Ostersetzer-Biran O, Takenaka M. PCIS1, Encoded by a Pentatricopeptide Protein Co-expressed Gene, Is Required for Splicing of Three Mitochondrial nad Transcripts in Angiosperms. PLANT & CELL PHYSIOLOGY 2024; 65:1474-1485. [PMID: 39092566 DOI: 10.1093/pcp/pcae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/13/2024] [Accepted: 08/01/2024] [Indexed: 08/04/2024]
Abstract
Group II introns are large catalytic RNAs, which reside mainly within genes encoding respiratory complex I (CI) subunits in angiosperms' mitochondria. Genetic and biochemical analyses led to the identification of many nuclear-encoded factors that facilitate the splicing of the degenerated organellar introns in plants. Here, we describe the analysis of the pentatricopeptide repeat (PPR) co-expressed intron splicing-1 (PCIS1) factor, which was identified in silico by its co-expression pattern with many PPR proteins. PCIS1 is well conserved in land plants but has no sequence similarity with any known protein motifs. PCIS1 mutant lines are arrested in embryogenesis and can be maintained by the temporal expression of the gene under the embryo-specific ABI3 promoter. The pABI3::PCIS1 mutant plants display low germination and stunted growth phenotypes. RNA-sequencing and quantitative RT-PCR analyses of wild-type and mutant plants indicated that PCIS1 is a novel splicing cofactor that is pivotal for the maturation of several nad transcripts in Arabidopsis mitochondria. These phenotypes are tightly associated with respiratory CI defects and altered plant growth. Our data further emphasize the key roles of nuclear-encoded cofactors that regulate the maturation and expression of mitochondrial transcripts for the biogenesis of the oxidative phosphorylation system, and hence for plant physiology. The discovery of novel splicing factors other than typical RNA-binding proteins suggests further complexity of splicing mechanisms in plant mitochondria.
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Affiliation(s)
- Brody Frink
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Matthias Burger
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, Ulm D-89069, Germany
| | - Maya Yarkoni
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat-Ram, Jerusalem 9190401, Israel
| | - Sofia Shevtsov-Tal
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat-Ram, Jerusalem 9190401, Israel
| | - Hagit Zer
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat-Ram, Jerusalem 9190401, Israel
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat-Ram, Jerusalem 9190401, Israel
| | - Mizuki Takenaka
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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11
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Lian Q, Zhang S, Wu Z, Zhang C, Negrão S. Assembly and comparative analysis of the mitochondrial genome in diploid potatoes. PLANT CELL REPORTS 2024; 43:249. [PMID: 39358565 DOI: 10.1007/s00299-024-03326-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024]
Abstract
KEY MESSAGE We report the mitochondrial genome of 39 diploid potatoes and identify a candidate ORF potentially linked to cytoplasmic male sterility in potatoes. Potato (Solanum tuberosum L.) holds a critical position as the foremost non-grain food crop, playing a pivotal role in ensuring global food security. Diploid potatoes constitute a vital genetic resource pool, harboring the potential to revolutionize modern potato breeding. Nevertheless, diploid potatoes are relatively understudied, and mitochondrial DNA can provide valuable insights into key potato breeding traits such as CMS. In this study, we examine and assemble the mitochondrial genome evolution and diversity of 39 accessions of diploid potatoes using high-fidelity (HiFi) sequencing. We annotated 54 genes for all the investigated accessions, comprising 34 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. Our analyses revealed differences in repeats sequences between wild and cultivated landraces. To understand the evolution of diploid maternal lineage inheritance, we conducted phylogenetic analysis, which clearly distinguished mitochondrial from nuclear gene trees, further supporting the evidence-based of clustering between wild and cultivated landraces accessions. Our study discovers new candidate ORFs associated with CMS in potatoes, including ORF137, which is homologous to other CMS in Solanaceae. Ultimately, this work bridges the gap in mitochondrial genome research for diploid potatoes, providing a steppingstone into evolutionary studies and potato breeding.
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Affiliation(s)
- Qun Lian
- School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Genome Analysis Laboratory of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Genome Analysis Laboratory of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Genome Analysis Laboratory of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Genome Analysis Laboratory of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Sónia Negrão
- School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland.
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12
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Sapio MR, Staedtler ES, King DM, Maric D, Jahanipour J, Ghetti A, Jacobson KA, Mannes AJ, Iadarola MJ. Analgesic candidate adenosine A 3 receptors are expressed by perineuronal peripheral macrophages in human dorsal root ganglion and spinal cord microglia. Pain 2024; 165:2323-2343. [PMID: 38691673 PMCID: PMC11408117 DOI: 10.1097/j.pain.0000000000003242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/22/2024] [Indexed: 05/03/2024]
Abstract
ABSTRACT Adenosine receptors are a family of purinergic G protein-coupled receptors that are widely distributed in bodily organs and in the peripheral and central nervous systems. Recently, antihyperalgesic actions have been suggested for the adenosine A 3 receptor, and its agonists have been proposed as new neuropathic pain treatments. We hypothesized that these receptors may be expressed in nociceptive primary afferent neurons. However, RNA sequencing across species, eg, rat, mouse, dog, and human, suggests that dorsal root ganglion (DRG) expression of ADORA3 is inconsistent. In rat and mouse, Adora3 shows very weak to no expression in DRG, whereas it is well expressed in human DRG. However, the cell types in human DRG that express ADORA3 have not been delineated. An examination of DRG cell types using in situ hybridization clearly detected ADORA3 transcripts in peripheral macrophages that are in close apposition to the neuronal perikarya but not in peripheral sensory neurons. By contrast, ADORA1 was found primarily in neurons, where it is broadly expressed at low levels. These results suggest that a more complex or indirect mechanism involving modulation of macrophage and/or microglial cells may underlie the potential analgesic action of adenosine A 3 receptor agonism.
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Affiliation(s)
- Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Ellen S Staedtler
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Diana M King
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Dragan Maric
- National Institute of Neurological Disorders and Stroke, Flow and Imaging Cytometry Core Facility, Bethesda, MD, United States
| | - Jahandar Jahanipour
- National Institute of Neurological Disorders and Stroke, Flow and Imaging Cytometry Core Facility, Bethesda, MD, United States
| | - Andre Ghetti
- AnaBios Corporation, San Diego, CA, United States
| | - Kenneth A Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Laboratory of Bioorganic Chemistry, Bethesda, MD, United States
| | - Andrew J Mannes
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
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13
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Güney G, Cedden D, Körnig J, Ulber B, Beran F, Scholten S, Rostás M. Physiological and transcriptional changes associated with obligate aestivation in the cabbage stem flea beetle (Psylliodes chrysocephala). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 173:104165. [PMID: 39089389 DOI: 10.1016/j.ibmb.2024.104165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Aestivation is a form of seasonal dormancy observed in various insect species, usually coinciding with the summer season. The cabbage stem flea beetle, Psylliodes chrysocephala (Coleoptera: Chrysomelidae), is a key pest of oilseed rape that obligatorily aestivates as adult in late summer. Since the physiological and transcriptional processes linked to aestivation in P. chrysocephala are still little understood, we analyzed relevant physiological parameters and performed RNA-seq analyses on laboratory-reared beetles in their pre-aestivation, aestivation, and post-aestivation stages. We found that the beetles reached aestivation at 15 days post-eclosion, showing strongly reduced metabolic activity, with less than 50% CO2 production, compared to pre-aestivating individuals. Under constant laboratory conditions, the beetles aestivated for about 25 days. Female beetles reached reproductive maturity at a median of 52 days post-eclosion. Furthermore, aestivating beetles had significantly reduced carbohydrate reserves and increased lipid reserves compared with pre-aestivating beetles, indicating that aestivation is associated with drastic changes in energy metabolism. Aestivating beetles contained 30% less water and their survival rates under high-temperature conditions (30 °C) were 40% higher compared to pre-aestivating beetles. RNA-seq studies showed that, in particular, gene ontology terms related to carbohydrate and lipid metabolism, digestion, and mitochondrial activity were enriched, with clear differences in transcript abundance between beetles in aestivation compared to pre- or post-aestivation. Specifically, mitochondrial transcripts, such as respiratory chain I subunits, and digestion-related transcripts, such as trypsin, were less abundant during aestivation, which supports the idea that aestivation is associated with decreased metabolic activity. This study represents the first exploration of the transcriptomic and physiological processes linked to aestivation in P. chrysocephala.
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Affiliation(s)
- Gözde Güney
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, D-37077, Göttingen, Germany.
| | - Doga Cedden
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, D-37077, Göttingen, Germany
| | - Johannes Körnig
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany; Population Ecology Group, Friedrich Schiller University, D-07743, Jena, Germany
| | - Bernd Ulber
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, D-37077, Göttingen, Germany
| | - Franziska Beran
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany; Population Ecology Group, Friedrich Schiller University, D-07743, Jena, Germany
| | - Stefan Scholten
- Division of Crop Plant Genetics, Department of Crop Sciences, University of Göttingen, D-37075, Göttingen, Germany
| | - Michael Rostás
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, D-37077, Göttingen, Germany.
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14
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Qiu C, Zhang H, Liu Z. Alternaria solani core effector Aex59 is a new member of the Alt a 1 protein family and is recognized as a PAMP. Int J Biol Macromol 2024; 278:134918. [PMID: 39179073 DOI: 10.1016/j.ijbiomac.2024.134918] [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: 05/06/2024] [Revised: 08/18/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Early blight caused by Alternaria solani is a destructive disease in potato production. Here, through systematically screening of an effector protein pool consisting of 115 small cysteine-containing candidate Aex (Alternariaextracellular proteins) in A. solani, we identified a core effector protein named Aex59, a pathogen-associated molecular pattern (PAMP) molecule. Aex59 is uniquely present in the Ascomycota of fungi and can activate defense responses in multiple plants. Targeted gene disruption showed that Aex59 is a virulence factor and participates in spore development. Perception of Aex59 in Nicotiana benthamiana does not depend on the receptor-like kinases Brassinosteroid-associated kinase1 (BAK1) and Suppressor of BIR1-1 (SOBIR1), which are required for multiple pattern recognition receptors (PRR) pathways. Sequence analysis revealed that Aex59 is a new member of the Alt a 1 protein family and is a potential molecular marker capable of aiding in the classification of the fungi Alternaria spp.
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Affiliation(s)
- Chaodong Qiu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Huajian Zhang
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei, Anhui 230036, China
| | - Zhenyu Liu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei, Anhui 230036, China.
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15
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Huang Y, Zhang Z, Hattori M. Recent advances in expression screening and sample evaluation for structural studies of membrane proteins. J Mol Biol 2024:168809. [PMID: 39362625 DOI: 10.1016/j.jmb.2024.168809] [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: 08/27/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/05/2024]
Abstract
Membrane proteins are involved in numerous biological processes and represent more than half of all drug targets; thus, structural information on these proteins is invaluable. However, the low expression level of membrane proteins, as well as their poor stability in solution and tendency to precipitate and aggregate, are major bottlenecks in the preparation of purified membrane proteins for structural studies. Traditionally, the evaluation of membrane protein constructs for structural studies has been quite time consuming and expensive since it is necessary to express and purify the proteins on a large scale, particularly for X-ray crystallography. The emergence of fluorescence detection size exclusion chromatography (FSEC) has drastically changed this situation, as this method can be used to rapidly evaluate the expression and behavior of membrane proteins on a small scale without the need for purification. FSEC has become the most widely used method for the screening of expression conditions and sample evaluation for membrane proteins, leading to the successful determination of numerous structures. Even in the era of cryo-EM, FSEC and the new generation of FSEC derivative methods are being widely used in various manners to facilitate structural analysis. In addition, the application of FSEC is not limited to structural analysis; this method is also widely used for functional analysis of membrane proteins, including for analysis of oligomerization state, screening of antibodies and ligands, and affinity profiling. This review presents the latest advances and applications in membrane protein expression screening and sample evaluation, with a particular focus on FSEC methods.
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Affiliation(s)
- Yichen Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziyi Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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16
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Liu Y, Liu J, Sun M, Mao Y, Feng S, Shen S, Liu T, Cao Z, Li Z, Hao Z, Dong J. The genome sequencing and comparative genomics analysis of Rhizoctonia solani reveals a novel effector family owning a uinque domain in Basidiomycetes. Int J Biol Macromol 2024; 278:134328. [PMID: 39098663 DOI: 10.1016/j.ijbiomac.2024.134328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/26/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
Rhizoctonia solani is a soil-borne pathogen with 14 anastomosis groups (AGs), and different subgroups are genetically diverse. However, the genetic factors contributing to the pathogenicity of the fungus have not been well characterized. In this study, the genome of R. solani AG1-ZJ was sequenced. As the result, a 41.57 Mb draft genome containing 12,197 putative coding genes was obtained. Comparative genomic analysis of 11 different AGs revealed conservation and unique characteristics between the AGs. Furthermore, a novel effector family containing a 68 amino acid conserved domain unique in basidiomycetous fungi was characterized. Two effectors containing the conserved domain in AG4-JY were identified, and named as RsUEB1 and RsUEB2. Furthermore, the spray-induced gene silencing strategy was used to generate a dsRNA capable of silencing the conserved domain sequence of RsUEB1 and RsUEB2. This dsRNA can significantly reduce the expression of RsUEB1 and RsUEB2 and the pathogenicity of AG4-JY on foxtail millet, maize, rice and wheat. In conclusion, this study provides significant insights into the pathogenicity mechanisms of R. solani. The identification of the conserved domain and the successful use of dsRNA silencing of the gene containing the conserved domain will offer a new strategy for controlling sheath blight in cereal crops.
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Affiliation(s)
- Yuwei Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Jiayue Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Mingqing Sun
- Shijiazhuang Agricultural Technology Extension Center, Shijiazhuang, 050051, China
| | - Yanan Mao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Shang Feng
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Shen Shen
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Tingting Liu
- Shijiazhuang Agricultural Technology Extension Center, Shijiazhuang, 050051, China
| | - Zhiyan Cao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China; College of Plant Protection/Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhiyong Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/Key Laboratory of Minor Cereal Crops of Hebei Province, Shijiazhuang, Hebei, 050035, China.
| | - Zhimin Hao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China.
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China; College of Plant Protection/Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei 071001, China.
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17
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Langleib M, Calvelo J, Costábile A, Castillo E, Tort JF, Hoffmann FG, Protasio AV, Koziol U, Iriarte A. Evolutionary analysis of species-specific duplications in flatworm genomes. Mol Phylogenet Evol 2024; 199:108141. [PMID: 38964593 DOI: 10.1016/j.ympev.2024.108141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 06/15/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.
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Affiliation(s)
- Mauricio Langleib
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Alicia Costábile
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Estela Castillo
- Laboratorio de Biología Parasitaria, Instituto de Higiene, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, United States of America; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, United States of America
| | - Anna V Protasio
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, United Kingdom
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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18
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Shrivastava D, Abboud E, Ramchandra JP, Jha A, Marq JB, Chaurasia A, Mitra K, Sadik M, Siddiqi MI, Soldati-Favre D, Kloehn J, Habib S. ATM1, an essential conserved transporter in Apicomplexa, bridges mitochondrial and cytosolic [Fe-S] biogenesis. PLoS Pathog 2024; 20:e1012593. [PMID: 39348385 DOI: 10.1371/journal.ppat.1012593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 09/13/2024] [Indexed: 10/02/2024] Open
Abstract
The Apicomplexa phylum encompasses numerous obligate intracellular parasites, some associated with severe implications for human health, including Plasmodium, Cryptosporidium, and Toxoplasma gondii. The iron-sulfur cluster [Fe-S] biogenesis ISC pathway, localized within the mitochondrion or mitosome of these parasites, is vital for parasite survival and development. Previous work on T. gondii and Plasmodium falciparum provided insights into the mechanisms of [Fe-S] biogenesis within this phylum, while the transporter linking mitochondria-generated [Fe-S] with the cytosolic [Fe-S] assembly (CIA) pathway remained elusive. This critical step is catalyzed by a well-conserved ABC transporter, termed ATM1 in yeast, ATM3 in plants and ABCB7 in mammals. Here, we identify and characterize this transporter in two clinically relevant Apicomplexa. We demonstrate that depletion of TgATM1 does not specifically impair mitochondrial metabolism. Instead, proteomic analyses reveal that TgATM1 expression levels inversely correlate with the abundance of proteins that participate in the transfer of [Fe-S] to cytosolic proteins at the outer mitochondrial membrane. Further insights into the role of TgATM1 are gained through functional complementation with the well-characterized yeast homolog. Biochemical characterization of PfATM1 confirms its role as a functional ABC transporter, modulated by oxidized glutathione (GSSG) and [4Fe-4S].
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Affiliation(s)
- Deepti Shrivastava
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ernest Abboud
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Jadhav Prasad Ramchandra
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Akanksha Jha
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Jean-Baptiste Marq
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Animesh Chaurasia
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalyan Mitra
- Sophisticated Analytical Instrument Facility and Research Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Sadik
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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19
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Loivamaa I, Sillanpää A, Deptula P, Chamlagain B, Edelmann M, Auvinen P, Nyman TA, Savijoki K, Piironen V, Varmanen P. Aerobic adaptation and metabolic dynamics of Propionibacterium freudenreichii DSM 20271: insights from comparative transcriptomics and surfaceome analysis. mSystems 2024:e0061524. [PMID: 39345151 DOI: 10.1128/msystems.00615-24] [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: 04/29/2024] [Accepted: 09/08/2024] [Indexed: 10/01/2024] Open
Abstract
Propionibacterium freudenreichii (PFR) DSM 20271T is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271T to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of vitamin B12, pseudovitamin-B12, propionate, and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, tricarboxylic acid cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and α-ketoglutarate availability. Furthermore, in liquid culture, FeSO4 supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding of PFR's physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications. IMPORTANCE The study of the response of Propionibacterium freudenreichii to aerobic growth is crucial for understanding how this bacterium adapts to different environments and produces essential compounds like vitamin B12. By investigating its physiological changes under aerobic conditions, we can gain insights into its metabolic adjustments and potential for enhanced growth. These findings not only deepen our understanding of P. freudenreichii's responses to oxygen availability but also offer valuable information for optimizing its growth in industrial applications. This research sheds light on the adaptive mechanisms of this bacterium, providing a foundation for further exploration and potential applications in various fields.
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Affiliation(s)
- Iida Loivamaa
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Annika Sillanpää
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Paulina Deptula
- Department of Food Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Bhawani Chamlagain
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Minnamari Edelmann
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Tuula A Nyman
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kirsi Savijoki
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
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20
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Sahi U, Kottury NG, Kottury NR, Kotturi H. Complete genome sequence of Mycobacteriophage Eaglepride. Microbiol Resour Announc 2024:e0059924. [PMID: 39345163 DOI: 10.1128/mra.00599-24] [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: 06/04/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
Eaglepride is a mycobacteriophage isolated using Mycobacterium smegmatis mc2155. The genome length is 50,926 bp with 89 open reading frames and 1 tRNA gene. Based on gene content similarity to actinobacteriophages, Eaglepride is assigned to phage subcluster A10 and shares the highest nucleotide identity with mycobacteriophage OKCentral2016.
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Affiliation(s)
- Umar Sahi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, USA
| | | | | | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, USA
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21
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Galindo-Torres P, Rosas C, Ramos-Rodríguez S, Galindo-Sánchez CE. Chronic thermal stress on Octopus maya embryos down-regulates epigenome-related genes and those involved in the nervous system development and morphogenesis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101332. [PMID: 39366120 DOI: 10.1016/j.cbd.2024.101332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 09/20/2024] [Accepted: 09/22/2024] [Indexed: 10/06/2024]
Abstract
Red Octopus maya is strongly influenced by temperature. Recent studies have reported negative reproduction effects on males and females when exposed to temperatures higher than 27 °C. Embryos under thermal stress show morphological and physiological alterations; similar phenotypes have been reported in embryos from stressed females, evidencing transgenerational consequences. Transcriptomic profiles were characterized along embryo development during normal-under thermal stress and epigenetic alterations through DNA methylation and damage quantification. Total RNA in organogenesis, activation, and growth stages in control and thermal stress were sequenced with Illumina RNA-Seq. Similarly, total DNA was used for DNA methylation and damage quantification between temperatures and embryo stages. Differential gene expression analyses showed that embryos express genes associated with oxygen transport, morphogenesis, nervous system, neuroendocrine cell differentiation, spermatogenesis, and male sex differentiation. Conversely, embryos turn off genes involved mainly in nervous system development, morphogenesis, and gene expression regulation when exposed to thermal stress - consistent with O. maya embryo phenotypes showing abnormal arms, eyes, and body development. No significant differences were observed in quantifying DNA methylation between temperatures but they were for DNA damage quantification. Epigenetic alterations are hypothesized to occur since several genes found downregulated belong to the epigenetic machinery but at histone tail level.
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Affiliation(s)
- Pavel Galindo-Torres
- Centro de Investigacion Cientifica y de Educacion Superior de Ensenada (CICESE), Carretera Tijuana-Ensenada No. 3918, Zona Playitas, Ensenada, Baja California CP 22860, Mexico.
| | - Carlos Rosas
- Unidad Multidisciplinaria de Docencia e Investigacion (UMDI), Facultad de Ciencias, Universidad Nacional Autonoma de Mexico (UNAM), Puerto DE Abrigo s/n, Sisal, Hunucma, Yucatan CP97355, Mexico.
| | - Sadot Ramos-Rodríguez
- Centro de Investigacion Cientifica y de Educacion Superior de Ensenada (CICESE), Carretera Tijuana-Ensenada No. 3918, Zona Playitas, Ensenada, Baja California CP 22860, Mexico.
| | - Clara E Galindo-Sánchez
- Centro de Investigacion Cientifica y de Educacion Superior de Ensenada (CICESE), Carretera Tijuana-Ensenada No. 3918, Zona Playitas, Ensenada, Baja California CP 22860, Mexico.
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22
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Lu Q, Hitch TCA, Zhou JY, Dwidar M, Sangwan N, Lawrence D, Nolan LS, Espenschied ST, Newhall KP, Han Y, Karell PE, Salazar V, Baldridge MT, Clavel T, Stappenbeck TS. A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency. Science 2024; 385:eadk2536. [PMID: 39325906 DOI: 10.1126/science.adk2536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 05/12/2024] [Accepted: 07/26/2024] [Indexed: 09/28/2024]
Abstract
Harnessing the microbiome to benefit human health requires an initial step in determining the identity and function of causative microorganisms that affect specific host physiological functions. We show a functional screen of the bacterial microbiota from mice with low intestinal immunoglobulin A (IgA) levels; we identified a Gram-negative bacterium, proposed as Tomasiella immunophila, that induces and degrades IgA in the mouse intestine. Mice harboring T. immunophila are susceptible to infections and show poor mucosal repair. T. immunophila is auxotrophic for the bacterial cell wall amino sugar N-acetylmuramic acid. It delivers immunoglobulin-degrading proteases into outer membrane vesicles that preferentially degrade rodent antibodies with kappa but not lambda light chains. This work indicates a role for symbionts in immunodeficiency, which might be applicable to human disease.
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Affiliation(s)
- Qiuhe Lu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Julie Y Zhou
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dylan Lawrence
- Department of Medicine, Washington University, Saint Louis, MO 63110, USA
| | - Lila S Nolan
- Department of Medicine, Washington University, Saint Louis, MO 63110, USA
| | - Scott T Espenschied
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin P Newhall
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yi Han
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E Karell
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Vanessa Salazar
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Megan T Baldridge
- Department of Medicine, Washington University, Saint Louis, MO 63110, USA
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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23
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Wiśniewska MM, Salomaki ED, Silberman JD, Terpis KX, Mazancová E, Táborský P, Jinatham V, Gentekaki E, Čepička I, Kolisko M. Expanded gene and taxon sampling of diplomonads shows multiple switches to parasitic and free-living lifestyle. BMC Biol 2024; 22:217. [PMID: 39334206 PMCID: PMC11437800 DOI: 10.1186/s12915-024-02013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Diplomonads are anaerobic flagellates classified within Metamonada. They contain both host-associated commensals and parasites that reside in the intestinal tracts of animals, including humans (e.g., Giardia intestinalis), as well as free-living representatives that inhabit freshwater and marine anoxic sediments (e.g., Hexamita inflata). The evolutionary trajectories within this group are particularly unusual as the free-living taxa appear to be nested within a clade of host-associated species, suggesting a reversal from host-dependence to a secondarily free-living lifestyle. This is thought to be an exceedingly rare event as parasites often lose genes for metabolic pathways that are essential to a free-living life strategy, as they become increasingly reliant on their host for nutrients and metabolites. To revert to a free-living lifestyle would require the reconstruction of numerous metabolic pathways. All previous studies of diplomonad evolution suffered from either low taxon sampling, low gene sampling, or both, especially among free-living diplomonads, which has weakened the phylogenetic resolution and hindered evolutionary insights into this fascinating transition. RESULTS We sequenced transcriptomes from 1 host-associated and 13 free-living diplomonad isolates; expanding the genome scale data sampling for diplomonads by roughly threefold. Phylogenomic analyses clearly show that free-living diplomonads form several branches nested within endobiotic species. Moreover, the phylogenetic distribution of genes related to an endobiotic lifestyle suggest their acquisition at the root of diplomonads, while traces of these genes have been identified in free-living diplomonads as well. Based on these results, we propose an evolutionary scenario of ancestral and derived lifestyle transitions across diplomonads. CONCLUSIONS Free-living taxa form several clades nested within endobiotic taxa in our phylogenomic analyses, implying multiple transitions between free-living and endobiotic lifestyles. The evolutionary history of numerous virulence factors corroborates the inference of an endobiotic ancestry of diplomonads, suggesting that there have been several reversals to a free-living lifestyle. Regaining host independence may have been facilitated by a subset of laterally transferred genes. We conclude that the extant diversity of diplomonads has evolved from a non-specialized endobiont, with some taxa becoming highly specialized parasites, others becoming free-living, and some becoming capable of both free-living and endobiotic lifestyles.
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Affiliation(s)
- Monika M Wiśniewska
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, Branišovská 1160/31, 2, České Budějovice, 370 05, Czech Republic.
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculturein Krakow, 29 Listopada Ave. 54, Kraków, 31-425, Poland.
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, České Budějovice, 370 05, Czech Republic.
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, Branišovská 1160/31, 2, České Budějovice, 370 05, Czech Republic
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, RI, USA
| | - Jeffrey D Silberman
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, Branišovská 1160/31, 2, České Budějovice, 370 05, Czech Republic
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Kristina X Terpis
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - Eva Mazancová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, 252 42, Czech Republic
| | - Petr Táborský
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, Branišovská 1160/31, 2, České Budějovice, 370 05, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Vasana Jinatham
- School of Science, Mae Fah Luang University, 333 Moo1Chiang Rai 57100, Thasud, Muang, Thailand
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, 333 Moo1Chiang Rai 57100, Thasud, Muang, Thailand
- Department of Veterinary Medicine, University of Nicosia Veterinary School, 93 Agiou Nikolaou Street, Nicosia, 2414, Cyprus
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, Branišovská 1160/31, 2, České Budějovice, 370 05, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, České Budějovice, 370 05, Czech Republic.
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24
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Polasa A, Badiee SA, Moradi M. Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase. J Phys Chem B 2024. [PMID: 39329451 DOI: 10.1021/acs.jpcb.4c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer in bacteria. YidC facilitates the insertion and folding of membrane proteins, both in conjunction with the Sec complex and independently. Additionally, YidC acts as a chaperone during the folding of proteins. Multiple investigations have conclusively shown that Gram-positive bacterial YidC has Sec-independent insertion mechanisms. Through the use of microsecond-level all-atom molecular dynamics (MD) simulations, we have carried out an in-depth investigation of the YidC protein originating from Gram-negative bacteria. This research sheds light on the significance of multiple domains of the YidC structure at a detailed molecular level by utilizing equilibrium MD simulations. Specifically, multiple models of YidC embedded in the lipid bilayer were constructed to characterize the critical role of the C2 loop and the periplasmic domain (PD) present in Gram-negative YidC, which is absent in its Gram-positive counterpart. Based on our results, the C2 loop plays a role in the overall stabilization of the protein, most notably in the transmembrane (TM) region, and it also has an allosteric influence on the PD region. We have found critical inter- and intradomain interactions that contribute to the stability of the protein and its function. Finally, our study provides a hypothetical Sec-independent insertion mechanism for Gram-negative bacterial YidC.
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Affiliation(s)
- Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Shadi A Badiee
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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25
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Banerjee A, Roychoudhury A. Molecular characterization of a phytomelatonin receptor and its overexpression as a 'one-stop' solution to nullify the toxic effects of hazardous inorganic agro-pollutants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024:125041. [PMID: 39343345 DOI: 10.1016/j.envpol.2024.125041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/22/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
Inorganic toxicants like arsenic, copper, lead, nickel and fluoride are notorious agro-pollutants, impeding plant-productivity due to high bioaccumulation. Consumption of such contaminated plant-parts causes irreversible health hazards. We identified a G-protein coupled receptor, serving as melatonin receptor (MelR) in Nicotiana tabacum (NtMelR), that relayed downstream-signaling after binding melatonin, a potent growth regulator and antioxidant. Using inhibitors against G-protein-α and NADPH oxidase (NOX), and by supplementing epidermal strips with exogenous melatonin and H2O2, we established that NtMelR acted upstream of reactive oxygen species (ROS) production in guard cells. Transgenic lines overexpressing NtMelR maintained constitutive melatonin-signaling via MelR, leading to efficient stomatal closure for preventing desiccation during oxidative stress. Melatonin biosynthesis was stimulated in the transgenic lines, exposed to different agro-pollutant stress, providing a steady-abundance of ligand for NtMelR binding and activating the defence machinery, comprising of enzymatic-antioxidants like superoxide dismutase, catalase, peroxidases and glyoxalases. Due to increased antioxidant capacity, the transgenics exhibited less molecular injuries (electrolyte leakage, methylglyoxal accumulation and NOX activity), generated less ROS and bioaccumulated significantly lower levels of toxicants. Unlike the wild-type counterparts, the transgenics maintained high relative water content, photosynthetic efficiency, could flower abundantly and even produce seeds. Overall, we established that overexpression of NtMelR is a single-window strategy to generate multiple-stress tolerant genotypes.
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Affiliation(s)
- Aditya Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata - 700016, West Bengal, India
| | - Aryadeep Roychoudhury
- Discipline of Life Sciences, School of Sciences, Indira Gandhi National Open University, Maidan Garhi, New Delhi - 110068, India.
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26
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Buma S, Urayama SI, Suo R, Itoi S, Okada S, Ninomiya A. Mycoviruses from Aspergillus fungi involved in fermentation of dried bonito. Virus Res 2024:199470. [PMID: 39321926 DOI: 10.1016/j.virusres.2024.199470] [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: 07/31/2024] [Revised: 09/17/2024] [Accepted: 09/18/2024] [Indexed: 09/27/2024]
Abstract
Fungi are exploited for fermentation of foods such as cheese, Japanese sake, and soy sauce. However, the diversity of viruses that infect fungi involved in food fermentation is poorly understood. Fermented dried bonito ("katsuobushi") is one of the most important processed marine products in Japan. Fungi involved in katsuobushi fermentation are called katsuobushi molds, and Aspergillus spp. have been reported to be dominant on the surface of katsuobushi during fermentation. Because various mycoviruses have been found in members of the genus Aspergillus, we hypothesized that katsuobushi molds are also infected with mycoviruses. Here, we describe seven novel mycoviruses belonging to six families (Chrysoviridae, Fusariviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and Pseudototiviridae) from isolated katsuobushi molds (Aspergillus chevalieri and A. sulphureus) detected by fragmented and primer-ligated double-stranded RNA sequencing. Aspergillus chevalieri fusarivirus 1 has a unique bi-segmented genome, whereas other known fusariviruses have a single genomic segment. Phenotypic comparison between the parental A. chevalieri strain infected with Aspergillus chevalieri polymycovirus 1 (AchPmV1) and isogenic AchPmV1-free isolates indicated that AchPmV1 inhibits the early growth of the host. This study reveals the diversity of mycoviruses that infect katsuobushi molds, and provides insight into the effect of mycoviruses on fungi involved in fermentation.
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Affiliation(s)
- Seiji Buma
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Syun-Ichi Urayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan; Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Rei Suo
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Shiro Itoi
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Shigeru Okada
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Akihiro Ninomiya
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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27
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Das D, Podder S. Microscale marvels: unveiling the macroscopic significance of micropeptides in human health. Brief Funct Genomics 2024; 23:624-638. [PMID: 38706311 DOI: 10.1093/bfgp/elae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Non-coding RNA encodes micropeptides from small open reading frames located within the RNA. Interestingly, these micropeptides are involved in a variety of functions within the body. They are emerging as the resolving piece of the puzzle for complex biomolecular signaling pathways within the body. Recent studies highlight the pivotal role of small peptides in regulating important biological processes like DNA repair, gene expression, muscle regeneration, immune responses, etc. On the contrary, altered expression of micropeptides also plays a pivotal role in the progression of various diseases like cardiovascular diseases, neurological disorders and several types of cancer, including colorectal cancer, hepatocellular cancer, lung cancer, etc. This review delves into the dual impact of micropeptides on health and pathology, exploring their pivotal role in preserving normal physiological homeostasis and probing their involvement in the triggering and progression of diseases.
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Affiliation(s)
- Deepyaman Das
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
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28
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Pei H, Xie G, Yao X, Wang S, Yan J, Dai L, Wang Y. Exploring the binding affinity and characteristics of DcitOBP9 in citrus psyllids. Gene 2024; 923:148551. [PMID: 38759737 DOI: 10.1016/j.gene.2024.148551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Odorant-binding proteins (OBPs) are crucial in insect olfaction. The most abundant expressed OBP of citrus psyllids, DcitOBP9 encodes 148 amino acids. DcitOBP9 lacks a transmembrane structure and possesses a 17-amino acid signal peptide at the N-terminus. Characterized by the six conserved cysteine sites, DcitOBP9 is classified as the Classical-OBP family. RT-qPCR experiments revealed ubiquitous expression of DcitOBP9 across all developmental stages of the citrus psyllid, with predominant expression in adults antennae. Fluorescence competitive binding assays demonstrated DcitOBP9's strong affinity for ocimene, linalool, dodecanoic acid, and citral, and moderate affinity for dimethyl trisulfide. Additionally, it binds to myrcia, (-)-trans-caryophyllene, (±)-Citronellal, nonanal, and (+)-α-pinene. Among them, ocimene, linalool, and dodecanoic acid were dynamically bound to DcitOBP9, while citral was statically bound to DcitOBP9. Molecular docking simulations with the top five ligands indicated that amino acid residues V92, S72, P128, L91, L75, and A76 are pivotal in the interaction between DcitOBP9 and these odorants. These findings suggest DcitOBP9's involvement in the citrus psyllid's host plant recognition and selection behaviors, thereby laying a foundation for elucidating the potential physiological and biological functions of DcitOBP9 and developing attractants.
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Affiliation(s)
- Haoran Pei
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Gang Xie
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiang Yao
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Shenghui Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jin Yan
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China.
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China.
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29
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Chen L, Zhang L, Li Y, Qiao L, Kumar S. Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach. Arch Microbiol 2024; 206:415. [PMID: 39320535 DOI: 10.1007/s00203-024-04140-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 09/02/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024]
Abstract
This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.
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Affiliation(s)
- Lei Chen
- Jiangsu Vocational College of Medicine, Yancheng, China
- School of Graduate Studies, Management and Science University, Shah Alam, Malaysia
| | - Lihu Zhang
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Yanping Li
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Liang Qiao
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, University Drive, Off Persiaran Olahraga, 40100, Shah Alam, Selangor, Malaysia.
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Karagöl A, Karagöl T, Zhang S. Molecular Dynamic Simulations Reveal that Water-Soluble QTY-Variants of Glutamate Transporters EAA1, EAA2 and EAA3 Retain the Conformational Characteristics of Native Transporters. Pharm Res 2024:10.1007/s11095-024-03769-0. [PMID: 39322794 DOI: 10.1007/s11095-024-03769-0] [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: 07/31/2024] [Accepted: 09/13/2024] [Indexed: 09/27/2024]
Abstract
OBJECTIVE Glutamate transporters play a crucial role in neurotransmitter homeostasis, but studying their structure and function is challenging due to their membrane-bound nature. This study aims to investigate whether water-soluble QTY-variants of glutamate transporters EAA1, EAA2 and EAA3 retain the conformational characteristics and dynamics of native membrane-bound transporters. METHODS Molecular dynamics simulations and comparative genomics were used to analyze the structural dynamics of both native transporters and their QTY-variants. Native transporters were simulated in lipid bilayers, while QTY-variants were simulated in aqueous solution. Lipid distortions, relative solvent accessibilities, and conformational changes were examined. Evolutionary conservation profiles were correlated with structural dynamics. Statistical analyses included multivariate analysis to account for confounding variables. RESULTS QTY-variants exhibited similar residue-wise conformational dynamics to their native counterparts, with correlation coefficients of 0.73 and 0.56 for EAA1 and EAA3, respectively (p < 0.001). Hydrophobic interactions of native helices correlated with water interactions of QTY- helices (rs = 0.4753, p < 0.001 for EAA1). QTY-variants underwent conformational changes resembling the outward-to-inward transition of native transporters. CONCLUSIONS Water-soluble QTY-variants retain key structural properties of native glutamate transporters and mimic aspects of native lipid interactions, including conformational flexibility. This research provides valuable insights into the conformational changes and molecular mechanisms of glutamate transport, potentially offering a new approach for studying membrane protein dynamics and drug interactions.
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Affiliation(s)
- Alper Karagöl
- Istanbul University Istanbul Medical Faculty, Istanbul, Turkey
| | - Taner Karagöl
- Istanbul University Istanbul Medical Faculty, Istanbul, Turkey
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Massachusetts Avenue, Cambridge, MA, 02139, USA.
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Pal DC, Anik TA, Rahman AA, Mahfujur Rahman SM. Identification and Functional Annotation of Hypothetical Proteins of Pan-Drug-Resistant Providencia rettgeri Strain MRSN845308 Toward Designing Antimicrobial Drug Targets. Bioinform Biol Insights 2024; 18:11779322241280580. [PMID: 39372506 PMCID: PMC11452876 DOI: 10.1177/11779322241280580] [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: 04/18/2024] [Accepted: 08/08/2024] [Indexed: 10/08/2024] Open
Abstract
Providencia rettgeri has increasingly been responsible for several infections, including urinary tract, post-burn wounds, neonatal sepsis, and others. The emergence of drug-resistant isolates of P rettgeri, accompanied by intrinsic and acquired antibiotic resistance, has exacerbated the challenge of treating such infections, necessitating the development of novel therapeutics. Hypothetical proteins (HPs) form a major portion of cellular proteins and can be targeted by these novel therapeutics. In this study, 410 HPs from a pan-drug-resistant (PDR) P rettgeri strain (MRSN845308) were functionally annotated and characterized by physicochemical properties, localization, virulence, essentiality, druggability, and functionality. Among 410 HPs, the VirulentPred 2.0 tool and VICMpred combinedly predicted 33 HPs as virulent, whereas 48 HPs were highly interacting proteins based on the STRING v12 database. BlastKOALA and eggNOG-mapper v2.1.12 predicted 13 HPs involved in several metabolic pathways like Riboflavin metabolism and Lipopolysaccharide biosynthesis. Overall, 83 HPs were selected as primary drug targets; however, only 80 remained after nonhomology searching and essentiality analysis. In addition, all were detected as novel drug targets according to DrugBank 5.1.12. Considering the potential of membrane and extracellular proteins, 29 HPs (extracellular, outer, and inner membrane) were selected based on the combined prediction from PSORTb v3.0.3, CELLO v.2.5, BUSCA, SOSUIGramN, and PSLpred. According to the prevalence of those HPs in different strains of P rettgeri sequences in National Center for Biotechnology Information Identical Protein Groups (NCBI-IPG), 5 HPs were selected as final drug targets. In addition, 5 other HPs annotated as transporter proteins were also added to the list. As no crystal structures of our targets are present, 3-dimensional structures of selected HPs were predicted by the AlphaFold Server powered by AlphaFold 3. Our findings might facilitate a better understanding of the mechanism of virulence and pathogenesis, and up-to-date annotations can make uncharacterized HPs easy to identify as targets for novel therapeutics.
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Desai M, Sun B. Protein Visualizer 2.0: Intuitive and Interactive Visualization of Protein Topology and Co/Post-Translational Modifications. ACS Chem Biol 2024; 19:1930-1934. [PMID: 39250597 DOI: 10.1021/acschembio.4c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Topology and post-translational modifications (PTMs) are critical features in studying the structures and functions of proteins. Several popular and detailed protein visualization algorithms are available for such studies, such as PyMOL, NCBI's iCn3D, UniProt PTM viewing, and Protter. However, none of the studies depict the special relationships between key structural features such as N-glycosylation, disulfide bonds, potential N-glycosylation sites (free sequons), potential disulfide bonds (free cysteine sites), and protein topology in a way conducive to detailed analyses. We introduce Protein Visualizer 2.0 (https://sfu-sun-lab.github.io/protein-visualizer-2.0/), a web-based tool that visualizes these features and the topology of all human proteins. This tool allows users to readily assess potential conflicts among predicted protein topology and known co/post-translational modifications. This tool also helps to reveal hidden relationships among displayed structural features.
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Affiliation(s)
- Manthan Desai
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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Listian SA, Mazur AC, Kol M, Ufelmann E, Eising S, Fröhlich F, Walter S, Holthuis JCM, Barisch C. Complex sphingolipid profiling and identification of an inositol-phosphorylceramide synthase in Dictyostelium discoideum. iScience 2024; 27:110609. [PMID: 39286488 PMCID: PMC11402645 DOI: 10.1016/j.isci.2024.110609] [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: 01/09/2024] [Revised: 06/12/2024] [Accepted: 07/26/2024] [Indexed: 09/19/2024] Open
Abstract
Dictyostelium discoideum is a professional phagocyte frequently used to study cellular processes underlying the recognition, engulfment, and infection course of microbial pathogens. Sphingolipids are abundant components of the plasma membrane that bind cholesterol, control membrane properties, participate in signal transmission, and serve as adhesion molecules in recognition processes relevant to immunity and infection. By combining lipidomics with a bioinformatics-based cloning strategy, we show here that D. discoideum produces phosphoinositol-containing sphingolipids with predominantly phytoceramide backbones. Cell-free expression of candidate inositol-phosphorylceramide (IPC) synthases from D. discoideum enabled identification of an enzyme that selectively catalyzes the transfer of phosphoinositol from phosphatidylinositol onto ceramide. The IPC synthase, DdIPCS1, shares multiple sequence motifs with yeast IPC and human sphingomyelin synthases and localizes to the Golgi apparatus as well as the contractile vacuole of D. discoideum. These findings open up important opportunities for exploring a role of sphingolipids in phagocytosis and infection across major evolutionary boundaries.
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Affiliation(s)
- Stevanus A Listian
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Anna-Carina Mazur
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel (FZB) - Leibniz Lung Center, Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| | - Matthijs Kol
- Division of Molecular Cell Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Edwin Ufelmann
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Sebastian Eising
- Division of Molecular Membrane Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Division of Molecular Membrane Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Joost C M Holthuis
- Division of Molecular Cell Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Caroline Barisch
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel (FZB) - Leibniz Lung Center, Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
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Zatorski N, Sun Y, Elmas A, Dallago C, Karl T, Stein D, Rost B, Huang KL, Walsh M, Schlessinger A. Structural analysis of genomic and proteomic signatures reveal dynamic expression of intrinsically disordered regions in breast cancer. iScience 2024; 27:110640. [PMID: 39310778 PMCID: PMC11416222 DOI: 10.1016/j.isci.2024.110640] [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: 07/25/2023] [Revised: 05/05/2024] [Accepted: 07/30/2024] [Indexed: 09/25/2024] Open
Abstract
Structural features of proteins capture underlying information about protein evolution and function, which enhances the analysis of proteomic and transcriptomic data. Here, we develop Structural Analysis of Gene and protein Expression Signatures (SAGES), a method that describes expression data using features calculated from sequence-based prediction methods and 3D structural models. We used SAGES, along with machine learning, to characterize tissues from healthy individuals and those with breast cancer. We analyzed gene expression data from 23 breast cancer patients and genetic mutation data from the Catalog of Somatic Mutations In Cancer database as well as 17 breast tumor protein expression profiles. We identified prominent expression of intrinsically disordered regions in breast cancer proteins as well as relationships between drug perturbation signatures and breast cancer disease signatures. Our results suggest that SAGES is generally applicable to describe diverse biological phenomena including disease states and drug effects.
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Affiliation(s)
- Nicole Zatorski
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
| | - Abdulkadir Elmas
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
| | - Christian Dallago
- NVIDIA DE GmbH, Einsteinstraße 172, 81677 München, Germany
- Faculty of Informatics, Bioinformatics & Computational Biology, Technical University Munich (TUM), 85748 Garching, Germany
| | - Timothy Karl
- Faculty of Informatics, Bioinformatics & Computational Biology, Technical University Munich (TUM), 85748 Garching, Germany
| | - David Stein
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
| | - Burkhard Rost
- Faculty of Informatics, Bioinformatics & Computational Biology, Technical University Munich (TUM), 85748 Garching, Germany
| | - Kuan-Lin Huang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
| | - Martin Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levey Pl, New York, NY 10029, USA
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Anderson AC, Schultz BJ, Snow ED, Brott AS, Stangherlin S, Malloch T, London JR, Walker S, Clarke AJ. The mechanism of peptidoglycan O-acetylation in Gram-negative bacteria typifies bacterial MBOAT-SGNH acyltransferases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613324. [PMID: 39345430 PMCID: PMC11429678 DOI: 10.1101/2024.09.17.613324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Bacterial cell envelope polymers are commonly modified with acyl groups that provide fitness advantages. Many polymer acylation pathways involve pairs of membrane-bound O -acyltransferase (MBOAT) and SGNH family proteins. As an example, the MBOAT protein PatA and the SGNH protein PatB are required in Gram-negative bacteria for peptidoglycan O-acetylation. The mechanism for how MBOAT-SGNH transferases move acyl groups from acyl-CoA donors made in the cytoplasm to extracellular polymers is unclear. Using the peptidoglycan O -acetyltransferase proteins PatAB, we explore the mechanism of MBOAT-SGNH pairs. We find that the MBOAT protein PatA catalyzes auto-acetylation of an invariant Tyr residue in its conserved C-terminal hexapeptide motif. We also show that PatB can use a synthetic hexapeptide containing an acetylated tyrosine to donate an acetyl group to a peptidoglycan mimetic. Finally, we report the structure of PatB, finding that it has structural features that shape its activity as an O -acetyltransferase and distinguish it from other SGNH esterases and hydrolases. Taken together, our results support a model for peptidoglycan acylation in which a tyrosine-containing peptide at the MBOAT's C-terminus shuttles an acyl group from the MBOAT active site to the SGNH active site, where it is transferred to peptidoglycan. This model likely applies to other systems containing MBOAT-SGNH pairs, such as those that O-acetylate alginate, cellulose, and secondary cell wall polysaccharides. The use of an acyl-tyrosine intermediate for MBOAT-SGNH acyl transfer is also shared with AT3-SGNH proteins, a second major group of acyltransferases that modify cell envelope polymers.
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Liu X, Wang C, Gai W, Sun Z, Fang L, Hua Z. Critical role of msgA in invasive capacity and intracellular survivability of Salmonella. Appl Environ Microbiol 2024; 90:e0020124. [PMID: 39136487 PMCID: PMC11409701 DOI: 10.1128/aem.00201-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/04/2024] [Indexed: 09/19/2024] Open
Abstract
Salmonella enterica serovar Typhimurium, which is a common foodborne pathogen, causes both intestinal and systemic infections in hosts. Salmonella has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability, which hampers research on virulence of Salmonella. The virulence of Salmonella is primarily studied through Salmonella pathogenicity islands (SPIs). However, there are also genes outside these SPIs that significantly impact virulence. Macrophage survival gene msgA is positioned at a region independent of the SPIs and conserved in Salmonella. However, there has been limited research on msgA to date. This study aims to investigate the virulent function of msgA to deepen our understanding of Salmonella virulence. Proteomic and RT-qPCR analyses reveal that MsgA influences multiple metabolic pathways and the expression of SPIs. The depletion of msgA led to the significantly reduced invasive capacity and intracellular survivability, and thus the decreased virulence of Salmonella. In conclusion, our study suggests that MsgA is an important regulator that mainly regulates virulence. Further research into the function of MsgA will enhance the understanding of Salmonella pathogenesis and promote the application of Salmonella for medical treatment. IMPORTANCE Salmonella enterica serovar Typhimurium is a common foodborne pathogen, it has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability. The virulence of Salmonella is primarily studied through its pathogenicity islands. In contrast, virulence genes located outside the Salmonella pathogenicity islands (SPIs) have received less attention. Macrophage survival gene (MsgA) is positioned at a region independent of the SPIs and conserved in Salmonella. Our research indicates that MsgA is a novel global regulator influencing the metabolic pathways and SPIs. Further research into the function of MsgA will enhance the understanding of Salmonella pathogenesis and promote the application of Salmonella for medical treatment.
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Affiliation(s)
- Xinqi Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chengzhi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Wenhua Gai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhaotong Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Zichun Hua
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Changzhou High-Tech Research Institute of Nanjing University and Jiangsu Target Pharma Laboratories Inc, Changzhou, China
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Liu L, Yang C, Liang F, Li C, Zeng Q, Han S, Li S, Liu Y. Genome-wide survey of the bipartite structure and pathogenesis-related genes of Neostagonosporella sichuanensis, a causal agent of Fishscale bamboo rhombic-spot disease. Front Microbiol 2024; 15:1456993. [PMID: 39360322 PMCID: PMC11444983 DOI: 10.3389/fmicb.2024.1456993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024] Open
Abstract
Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16-0001 and strain SICAUCC 23-0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within AT-rich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis, including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo.
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Affiliation(s)
- Lijuan Liu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Chunlin Yang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Fang Liang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Chengsong Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Qian Zeng
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yinggao Liu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
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Brackenridge S, John N, He W, Früh K, Borrow P, McMichael A. Regulation of the cell surface expression of classical and non-classical MHC proteins by the human cytomegalovirus UL40 and rhesus cytomegalovirus Rh67 proteins. J Virol 2024; 98:e0120624. [PMID: 39207137 PMCID: PMC11406984 DOI: 10.1128/jvi.01206-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
The signal sequences of the human cytomegalovirus (CMV) UL40 protein and its rhesus CMV (RhCMV) counterpart, Rh67, contain a peptide (VMAPRT[L/V][F/I/L/V]L, VL9) that is presented by major histocompatibility complex (MHC) antigen E (MHC-E). The CMV VL9 peptides replace VL9 peptides derived from classical MHC (Ia) signal sequences, which are lost when CMV disrupts antigen processing and presentation and MHC Ia expression. This allows infected cells to maintain MHC-E surface expression and escape killing by Natural Killer cells. We demonstrate that processing of the Rh67 VL9 peptide mirrors that of UL40, despite the lack of sequence conservation between the two proteins. Processing of both VL9 peptides is dependent on cleavage of their signal sequences by the host protease signal peptide peptidase. As previously shown for UL40, up-regulation of MHC-E expression by Rh67 requires only its signal sequence, with sequences upstream of VL9 critical for conferring independence from TAP, the transporter associated with antigen processing. Our results also suggest that the mature UL40 and Rh67 proteins contribute to CMV immune evasion by decreasing surface expression of MHC Ia. Unexpectedly, while the Rh67 VL9 peptide is resistant to the effects of Rh67, UL40 can partially counteract the up-regulation of MHC-E expression mediated by its own VL9 peptide. This suggests differences in the mechanisms by which the two VL9 peptides up-regulate MHC-E, and further work will be required to determine if any such differences have implications for translating a RhCMV-vectored simian immunodeficiency virus (SIV) vaccine to HIV-1 using human CMV as a vector. IMPORTANCE The protective immune response induced by a rhesus cytomegalovirus (RhCMV)-vectored simian immunodeficiency virus (SIV) vaccine in rhesus macaques depends on the presence of the viral Rh67 gene in the vaccine. The Rh67 protein contains a peptide that allows the RhCMV-infected cells to maintain expression of major histocompatibility complex (MHC) antigen E at the cell surface. We show that production of this peptide, referred to as "VL9," mirrors that of the equivalent peptide present in the human cytomegalovirus (CMV) protein UL40, despite the little sequence similarity between the two CMV proteins. We also show that the mature UL40 and Rh67 proteins, which have no previously described function, also contribute to CMV immune evasion by reducing cell surface expression of MHC proteins important for the immune system to detect infected cells. Despite these similarities, our work also reveals possible differences between Rh67 and UL40, and these may have implications for the use of human CMV as the vector for a potential HIV-1 vaccine.
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Affiliation(s)
- Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nessy John
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Wanlin He
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Klaus Früh
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew McMichael
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Fan Y, He Y, Li Y, Yin Z, Shi J, Tian T, Shang K, Shi H, Zhang F, Wen H. Design of a novel EmTSP-3 and EmTIP based multi-epitope vaccine against Echinococcus multilocularis infection. Front Immunol 2024; 15:1425603. [PMID: 39351224 PMCID: PMC11439721 DOI: 10.3389/fimmu.2024.1425603] [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: 04/30/2024] [Accepted: 08/20/2024] [Indexed: 10/04/2024] Open
Abstract
Background Current treatments and prevention strategies for echinococcosis are inadequate. Recent advancements in molecular vaccine development show promise against Echinococcus granulosus; however, Echinococcus multilocularis remains a challenge. A Multi-epitope Vaccine could potentially induce specific B and T lymphocyte responses, thereby offering protection against Echinococcus multilocularis infection. Methods This study aimed to develop a MEV against alveolar echinococcosis. Key epitopes from the Echinococcus multilocularis proteins EmTSP3 and EmTIP were identified using immunoinformatics analyses. These analyses were conducted to assess the MEV feasibility, structural characteristics, molecular docking, molecular dynamics simulations, and immune simulations. The immunogenicity and antigenicity of the vaccine were evaluated through in vitro and in vivo experiments, employing ELISA, Western blotting, FCM, challenge infection experiments, and ELISPOT. Results The effective antigenicity and immunogenicity of MEV were demonstrated through immunoinformatics, as well as in vitro and in vivo experiments. In vitro experiments revealed that MEV increased the secretion of IFN-γ and IL-4 in PBMC and successfully bound to specific antibodies in patient serum. Furthermore, mice immunized with MEV developed a robust immune response, characterized by elevated levels of CD4+ and CD8+ T-cells, increased secretion of IFN-γ and IL-4 by specific Th1 and Th2 cells, and heightened serum antibody levels. Importantly, MEV reduced the weight of cysts by conferring resistance against echinococcosis. These findings suggest that MEV is a promising candidate for the prevention of Echinococcus multilocularis infection. Conclusion A total of 7 CTL, 7 HTL, 5 linear B-cell, and 2 conformational B-cell epitopes were identified. The vaccine has demonstrated effective antigenicity and immunogenicity against AE through molecular docking, immune simulation, molecular dynamics studies, and both in vitro and in vivo experiments. It provides effective protection against Echinococcus multilocularis infection, thereby laying a foundation for further development.
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Affiliation(s)
- Yichen Fan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhengwei Yin
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Juan Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Tingting Tian
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Kaiyu Shang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Huidong Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Escobar-Sierra C, Cañedo-Argüelles M, Vinyoles D, Lampert KP. Unraveling the molecular mechanisms of fish physiological response to freshwater salinization: A comparative multi-tissue transcriptomic study in a river polluted by potash mining. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124400. [PMID: 38906407 DOI: 10.1016/j.envpol.2024.124400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, including fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.
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Affiliation(s)
- Camilo Escobar-Sierra
- Institute of Zoology, Universität zu Köln Mathematisch-Naturwissenschaftliche Fakultät, Zülpicher Str. 47b, Köln, NRW, 50674, Germany.
| | - Miguel Cañedo-Argüelles
- FEHM-Lab, Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Dolors Vinyoles
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Avda. Diagonal 643, Barcelona, 08028, Catalonia, Spain
| | - Kathrin P Lampert
- Institute of Zoology, Universität zu Köln Mathematisch-Naturwissenschaftliche Fakultät, Zülpicher Str. 47b, Köln, NRW, 50674, Germany
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Versini R, Baaden M, Cavellini L, Cohen MM, Taly A, Fuchs PFJ. Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion. Structure 2024:S0969-2126(24)00334-4. [PMID: 39299234 DOI: 10.1016/j.str.2024.08.017] [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: 12/22/2023] [Revised: 05/06/2024] [Accepted: 08/23/2024] [Indexed: 09/22/2024]
Abstract
Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion.
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Affiliation(s)
- Raphaëlle Versini
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, 75005 Paris, France; Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, 75005 Paris, France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, 75005 Paris, France
| | - Laetitia Cavellini
- Laboratoire de Biologie Cellulaire et Moléculaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Mickaël M Cohen
- Laboratoire de Biologie Cellulaire et Moléculaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, 75005 Paris, France.
| | - Patrick F J Fuchs
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, 75005 Paris, France; Université Paris Cité, 75006 Paris, France.
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Wenlong Z, Yadong W, Andrew E, Martin G. Characterization of two carbonic anhydrase isoforms in the pulmonate snail (Lymnaea Stagnalis) and their involvement in Molluskan calcification. Comp Biochem Physiol B Biochem Mol Biol 2024; 275:111028. [PMID: 39271049 DOI: 10.1016/j.cbpb.2024.111028] [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: 07/20/2024] [Revised: 09/02/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024]
Abstract
Calcifying organisms are suffering from negative impacts induced by climate change, such as CO2-induced acidification, which may impair external calcified structures. Freshwater mollusks have the potential to suffer more from CO2-induced acidification than marine calcifiers due to the lower buffering capacity of many freshwater systems. One of the most important enzymes contributing to the biomineralization reaction is carbonic anhydrase (CA), which catalyzes the reversible conversion of CO2 to bicarbonate, the major carbon source of the calcareous structure in calcifiers. In this study we characterized two α-CA isoforms (LsCA1 and LsCA4) from the freshwater snail Lymnaea stagnalis using a combination of gene sequencing, gene expression, phylogenetic analysis and biochemical assays. Both CA isoforms demonstrated high expression levels in the mantle tissue, the major site for biomineralization. Furthermore, expression of LsCA4 during development parallels shell formation. The primary protein structure analysis, active site configuration and the catalytic activity of LsCA4 together suggest that the LsCA4 is embedded in the apical and basolateral membranes of mantle cells; while LsCA1 is proposed to be cytosolic and might play an important role in acid-base regulation. These findings of LsCA isoforms form a strong basis for a more detailed physiological understanding of the effects of elevated CO2 on calcification in freshwater mollusks.
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Affiliation(s)
- Zhang Wenlong
- Rosenstiel School of Marine, Atmospheric and Earth Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America.
| | - Wang Yadong
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 N.E. Pacific St., Seattle, WA 98195, United States of America
| | - Esbaugh Andrew
- University of Texas at Austin, Marine Science Institute. 750 Channel View Drive, Port Aransas, TX 78373, United States of America
| | - Grosell Martin
- Rosenstiel School of Marine, Atmospheric and Earth Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
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Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIOPHYSICAL REPORTS 2024; 4:100167. [PMID: 38909903 PMCID: PMC11305224 DOI: 10.1016/j.bpr.2024.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. In addition, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from noncoding ones in otherwise ambiguous cases.
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Affiliation(s)
- A M Whited
- BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts
| | - Jeffre Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | | | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts
| | - John L Rinn
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado Boulder, Boulder, Colorado.
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Kors S, Schuster M, Maddison DC, Kilaru S, Schrader TA, Costello JL, Islinger M, Smith GA, Schrader M. New insights into the functions of ACBD4/5-like proteins using a combined phylogenetic and experimental approach across model organisms. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119843. [PMID: 39271061 DOI: 10.1016/j.bbamcr.2024.119843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024]
Abstract
Acyl-CoA binding domain-containing proteins (ACBDs) perform diverse but often uncharacterised functions linked to cellular lipid metabolism. Human ACBD4 and ACBD5 are closely related peroxisomal membrane proteins, involved in tethering of peroxisomes to the ER and capturing fatty acids for peroxisomal β-oxidation. ACBD5 deficiency causes neurological abnormalities including ataxia and white matter disease. Peroxisome-ER contacts depend on an ACBD4/5-FFAT motif, which interacts with ER-resident VAP proteins. As ACBD4/5-like proteins are present in most fungi and all animals, we combined phylogenetic analyses with experimental approaches to improve understanding of their evolution and functions. Notably, all vertebrates exhibit gene sequences for both ACBD4 and ACBD5, while invertebrates and fungi possess only a single ACBD4/5-like protein. Our analyses revealed alterations in domain structure and FFAT sequences, which help understanding functional diversification of ACBD4/5-like proteins. We show that the Drosophila melanogaster ACBD4/5-like protein possesses a functional FFAT motif to tether peroxisomes to the ER via Dm_Vap33. Depletion of Dm_Acbd4/5 caused peroxisome redistribution in wing neurons and reduced life expectancy. In contrast, the ACBD4/5-like protein of the filamentous fungus Ustilago maydis lacks a FFAT motif and does not interact with Um_Vap33. Loss of Um_Acbd4/5 resulted in an accumulation of peroxisomes and early endosomes at the hyphal tip. Moreover, lipid droplet numbers increased, and mitochondrial membrane potential declined, implying altered lipid homeostasis. Our findings reveal differences between tethering and metabolic functions of ACBD4/5-like proteins across evolution, improving our understanding of ACBD4/5 function in health and disease. The need for a unifying nomenclature for ACBD proteins is discussed.
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Affiliation(s)
- Suzan Kors
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Martin Schuster
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Daniel C Maddison
- School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Sreedhar Kilaru
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tina A Schrader
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Joseph L Costello
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gaynor A Smith
- School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Michael Schrader
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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Grafakou A, Mosterd C, Beck MH, Kelleher P, McDonnell B, de Waal PP, van Rijswijck IMH, van Peij NNME, Cambillau C, Mahony J, van Sinderen D. Discovery of antiphage systems in the lactococcal plasmidome. Nucleic Acids Res 2024; 52:9760-9776. [PMID: 39119896 PMCID: PMC11381338 DOI: 10.1093/nar/gkae671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Until the late 2000s, lactococci substantially contributed to the discovery of various plasmid-borne phage defence systems, rendering these bacteria an excellent antiphage discovery resource. Recently, there has been a resurgence of interest in identifying novel antiphage systems in lactic acid bacteria owing to recent reports of so-called 'defence islands' in diverse bacterial genera. Here, 321 plasmid sequences from 53 lactococcal strains were scrutinized for the presence of antiphage systems. Systematic evaluation of 198 candidates facilitated the discovery of seven not previously described antiphage systems, as well as five systems, of which homologues had been described in other bacteria. All described systems confer resistance against the most prevalent lactococcal phages, and act post phage DNA injection, while all except one behave like abortive infection systems. Structure and domain predictions provided insights into their mechanism of action and allow grouping of several genetically distinct systems. Although rare within our plasmid collection, homologues of the seven novel systems appear to be widespread among bacteria. This study highlights plasmids as a rich repository of as yet undiscovered antiphage systems.
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Affiliation(s)
- Andriana Grafakou
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Cas Mosterd
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Matthias H Beck
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Brian McDonnell
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Paul P de Waal
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Irma M H van Rijswijck
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Noël N M E van Peij
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université - CNRS, UMR 7255 Marseille, France
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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Bhowmick S, Viveros RP, Latoscha A, Commichau FM, Wrede C, Al-Bassam MM, Tschowri N. Cell shape and division septa positioning in filamentous Streptomyces require a functional cell wall glycopolymer ligase CglA. mBio 2024:e0149224. [PMID: 39248520 DOI: 10.1128/mbio.01492-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024] Open
Abstract
The cell wall of monoderm bacteria consists of peptidoglycan and glycopolymers in roughly equal proportions and is crucial for cellular integrity, cell shape, and bacterial vitality. Despite the immense value of Streptomyces in biotechnology and medicine as antibiotic producers, we know very little about their cell wall biogenesis, composition, and functions. Here, we have identified the LCP-LytR_C domain protein CglA (Vnz_13690) as a key glycopolymer ligase, which specifically localizes in zones of cell wall biosynthesis in S. venezuelae. Reduced amount of glycopolymers in the cglA mutant results in enlarged vegetative hyphae and failures in FtsZ-rings formation and positioning. Consequently, division septa are misplaced leading to the formation of aberrant cell compartments, misshaped spores, and reduced cell vitality. In addition, we report our discovery that c-di-AMP signaling and decoration of the cell wall with glycopolymers are physiologically linked in Streptomyces since the deletion of cglA restores growth of the S. venezuelae disA mutant at high salt. Altogether, we have identified and characterized CglA as a novel component of cell wall biogenesis in Streptomyces, which is required for cell shape maintenance and cellular vitality in filamentous, multicellular bacteria.IMPORTANCEStreptomyces are our key producers of antibitiotics and other bioactive molecules and are, therefore, of high value for medicine and biotechnology. They proliferate by apical extension and branching of hyphae and undergo complex cell differentiation from filaments to spores during their life cycle. For both, growth and sporulation, coordinated cell wall biogenesis is crucial. However, our knowledge about cell wall biosynthesis, functions, and architecture in Streptomyces and in other Actinomycetota is still very limited. Here, we identify CglA as the key enzyme needed for the attachment of glycopolymers to the cell wall of S. venezuelae. We demonstrate that defects in the cell wall glycopolymer content result in loss of cell shape in these filamentous bacteria and show that division-competent FtsZ-rings cannot assemble properly and fail to be positioned correctly. As a consequence, cell septa placement is disturbed leading to the formation of misshaped spores with reduced viability.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Ruth P Viveros
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Andreas Latoscha
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fabian M Commichau
- Institute of Biology, FG Molecular Microbiology 190 h, Universität Hohenheim, Stuttgart, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Mahmoud M Al-Bassam
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
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Tian Q, Yu T, Dong M, Hu Y, Chen X, Xue Y, Fang Y, Zhang J, Zhang X, Xue D. Identification and Characterization of Shaker Potassium Channel Gene Family and Response to Salt and Chilling Stress in Rice. Int J Mol Sci 2024; 25:9728. [PMID: 39273675 PMCID: PMC11395327 DOI: 10.3390/ijms25179728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/30/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
Shaker potassium channel proteins are a class of voltage-gated ion channels responsible for K+ uptake and translocation, playing a crucial role in plant growth and salt tolerance. In this study, bioinformatic analysis was performed to identify the members within the Shaker gene family. Moreover, the expression patterns of rice Shaker(OsShaker) K+ channel genes were analyzed in different tissues and salt treatment by RT-qPCR. The results revealed that there were eight OsShaker K+ channel genes distributed on chromosomes 1, 2, 5, 6 and 7 in rice, and their promoters contained a variety of cis-regulatory elements, including hormone-responsive, light-responsive, and stress-responsive elements, etc. Most of the OsShaker K+ channel genes were expressed in all tissues of rice, but at different levels in different tissues. In addition, the expression of OsShaker K+ channel genes differed in the timing, organization and intensity of response to salt and chilling stress. In conclusion, our findings provide a reference for the understanding of OsShaker K+ channel genes, as well as their potential functions in response to salt and chilling stress in rice.
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Affiliation(s)
- Quanxiang Tian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Tongyuan Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Mengyuan Dong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yue Hu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiaoguang Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuan Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
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Kim HS, Haley OC, Portwood Ii JL, Harding S, Proctor RH, Woodhouse MR, Sen TZ, Andorf CM. Fusarium Protein Toolkit: a web-based resource for structural and variant analysis of Fusarium species. BMC Microbiol 2024; 24:326. [PMID: 39243017 PMCID: PMC11378500 DOI: 10.1186/s12866-024-03480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND The genus Fusarium poses significant threats to food security and safety worldwide because numerous species of the fungus cause destructive diseases and/or mycotoxin contamination in crops. The adverse effects of climate change are exacerbating some existing threats and causing new problems. These challenges highlight the need for innovative solutions, including the development of advanced tools to identify targets for control strategies. DESCRIPTION In response to these challenges, we developed the Fusarium Protein Toolkit (FPT), a web-based tool that allows users to interrogate the structural and variant landscape within the Fusarium pan-genome. The tool displays both AlphaFold and ESMFold-generated protein structure models from six Fusarium species. The structures are accessible through a user-friendly web portal and facilitate comparative analysis, functional annotation inference, and identification of related protein structures. Using a protein language model, FPT predicts the impact of over 270 million coding variants in two of the most agriculturally important species, Fusarium graminearum and F. verticillioides. To facilitate the assessment of naturally occurring genetic variation, FPT provides variant effect scores for proteins in a Fusarium pan-genome based on 22 diverse species. The scores indicate potential functional consequences of amino acid substitutions and are displayed as intuitive heatmaps using the PanEffect framework. CONCLUSION FPT fills a knowledge gap by providing previously unavailable tools to assess structural and missense variation in proteins produced by Fusarium. FPT has the potential to deepen our understanding of pathogenic mechanisms in Fusarium, and aid the identification of genetic targets for control strategies that reduce crop diseases and mycotoxin contamination. Such targets are vital to solving the agricultural problems incited by Fusarium, particularly evolving threats resulting from climate change. Thus, FPT has the potential to contribute to improving food security and safety worldwide.
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Grants
- 5010-11420-001-000-D and 5010-42000-053-000-D USDA, Agricultural Research Service, United States
- 0201-88888-003-000D and 0201-88888-002-000D USDA, Agricultural Research Service, United States
- 5030-21000-072-00-D USDA, Agricultural Research Service, United States
- 5010-11420-001-000-D and 5010-42000-053-000-D USDA, Agricultural Research Service, United States
- 5010-11420-001-000-D and 5010-42000-053-000-D USDA, Agricultural Research Service, United States
- 5030-21000-072-00-D USDA, Agricultural Research Service, United States
- 2030-21000-056-000-D USDA, Agricultural Research Service, United States
- 5030-21000-072-00-D USDA, Agricultural Research Service, United States
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Affiliation(s)
- Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St, Peoria, IL, 61604, USA
| | - Olivia C Haley
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Rd. Ames, IA, 50011, USA
| | - John L Portwood Ii
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Rd. Ames, IA, 50011, USA
| | - Stephen Harding
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St, Peoria, IL, 61604, USA
| | - Robert H Proctor
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St, Peoria, IL, 61604, USA
| | - Margaret R Woodhouse
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Rd. Ames, IA, 50011, USA
| | - Taner Z Sen
- USDA, Agricultural Research Service, Crop Improvement and Genetics Research Unit, 800 Buchanan St. Albany, CA, 94710, USA
- Department of Bioengineering, University of California, 306 Stanley Hall, Berkeley, CA, 94720, USA
| | - Carson M Andorf
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Rd. Ames, IA, 50011, USA.
- Department of Computer Science, Iowa State University, 2434 Osborn Dr, Ames,, IA, 50011, USA.
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Chen Y, Yang J, Zhao X, Sun Z, Li G, Hussain S, Li X, Zhang L, Wang Z, Gong H, Hou H. Effects of SpGSH1 and SpPCS1 overexpression or co-overexpression on cadmium accumulation in yeast and Spirodela polyrhiza. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109097. [PMID: 39244885 DOI: 10.1016/j.plaphy.2024.109097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/13/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
Cadmium (Cd) is one of the most toxic elements to all organisms. Glutathione (GSH)-dependent phytochelatin (PC) synthesis pathway is considered an extremely important mechanism in Cd detoxification in plants. However, few studies have focused on the roles of glutamate-cysteine ligase (GSH1) and phytochelatin synthase (PCS1) in Cd accumulation and detoxification in plants. In this study, SpGSH1 and SpPCS1 were identified and cloned from Spirodela polyrhiza and analyzed their functions in yeast and S. polyrhiza via single- or dual-gene (SpGP1) overexpression. The findings of this study showed that SpGSH1, SpPCS1, and SpGP1 could dramatically rescue the growth of the yeast mutant Δycf1. In S. polyrhiza, SpGSH1 was located in the cytoplasm and could promote Mn and Ca accumulation. SpPCS1 was located in the cytoplasm and nucleus, mainly expressed in meristem regions, and promoted Cd, Fe, Mn, and Ca accumulation. SpGSH1 and SpPCS1 co-overexpression increased the Cd, Mn, and Ca contents. Based on the growth data of S. polyrhiza, it was recommended that biomass as the preferable indicator for assessing plant tolerance to Cd stress compared to frond number in duckweeds. Collectively, this study for the first time systematically elaborated the function of SpGSH1 and SpPCS1 for Cd detoxification in S. polyrhiza.
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Affiliation(s)
- Yan Chen
- Special Agricultural Resources in Tuojiang River Basin Sharing and Service Platform of Sichuan Province, Analysis and Testing Center, College of Chemistry and Chemical Engineering, Neijiang Normal University, Neijiang, 641112, Sichuan, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Zuoliang Sun
- Shandong Provincial University Laboratory for Protected Horticulture, Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Sajid Hussain
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 310006, Hangzhou, China; Soil and Water Testing Laboratory Marketing Division, Pakarab, Khanewal Road, Multan, 36000, Pakistan
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Liyuan Zhang
- Special Agricultural Resources in Tuojiang River Basin Sharing and Service Platform of Sichuan Province, Analysis and Testing Center, College of Chemistry and Chemical Engineering, Neijiang Normal University, Neijiang, 641112, Sichuan, China
| | - Zhenye Wang
- Special Agricultural Resources in Tuojiang River Basin Sharing and Service Platform of Sichuan Province, Analysis and Testing Center, College of Chemistry and Chemical Engineering, Neijiang Normal University, Neijiang, 641112, Sichuan, China
| | - Huihua Gong
- Special Agricultural Resources in Tuojiang River Basin Sharing and Service Platform of Sichuan Province, Analysis and Testing Center, College of Chemistry and Chemical Engineering, Neijiang Normal University, Neijiang, 641112, Sichuan, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
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Easterling KA, Marshall AT, Pitino M, Walker WB, Cooper WR. Gene expression profiling of Cacopsylla pyricola (Hemiptera: Psyllidae) infected with Ca. Phytoplasma pyri (Acholeplasmatales: Acholeplasmataceae) reveals candidate effectors and mechanisms of infection. ENVIRONMENTAL ENTOMOLOGY 2024:nvae074. [PMID: 39235989 DOI: 10.1093/ee/nvae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/31/2024] [Accepted: 08/20/2024] [Indexed: 09/07/2024]
Abstract
Phytoplasmas can negatively or positively alter vector host fitness. "Candidatus Phytoplasma pyri," is the causal agent of pear decline in commercial pear (Pyrus communis L.; Rosales: Rosaceae) and peach yellow leafroll in peach [Prunus persica (L.); Rosaceae]. This plant pathogen is transmitted by several species of pear psyllids (Cacopsylla spp. Hemiptera: Psyllidae). We sought to explore the relationship between the pear decline phytoplasma and its US vector, Cacopsylla pyricola (Förster), at the molecular genetic level through transcriptomic analysis using RNA-sequencing methodology. We also focused on phytoplasma and insect effectors, which are secreted proteins that can modulate interactions within a pathosystem. In this study, we identified 30 differentially expressed genes, 14 candidate insect effector genes, and 8 Ca. Phytoplasma pyri candidate effectors. Two strains of Ca. Phytoplasma pyri were identified based on immunodominant membrane protein sequence analysis from C. pyricola collected in the Pacific Northwest agricultural region. Here, we present a first genetic look at the pear decline pathosystem and report gene candidates for further exploration of infection mechanisms and potential tools for integrated pest management.
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Affiliation(s)
| | - Adrian T Marshall
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
| | - Marco Pitino
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
| | - William B Walker
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
| | - W Rodney Cooper
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
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