751
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Quintieri L, Fanelli F, Zühlke D, Caputo L, Logrieco AF, Albrecht D, Riedel K. Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage. Front Microbiol 2020; 11:991. [PMID: 32670211 PMCID: PMC7326052 DOI: 10.3389/fmicb.2020.00991] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/23/2020] [Indexed: 12/22/2022] Open
Abstract
In food chain, Pseudomonas spp. cause spoilage by reducing shelf life of fresh products, especially during cold storage, with a high economic burden for industries. However, recent studies have shed new light on health risks occurring when they colonize immunocompromised patient tissues. Likewise to P. aeruginosa, they exhibit antibiotic resistance and biofilm formation, responsible for their spread and persistence in the environment. Biofilm formation might be induced by environmental stresses, such as temperature fluctuations causing physiological and metabolic changes exacerbating food spoilage (by protease and pigment synthesis), and the production of adhesion molecules, chemotactic or underestimated virulence factors. In order to provide a new insight into phenotypic biodiversity of Pseudomonas spoilers isolated from cold stored cheese, in this work 19 Pseudomonas spp. were investigated for biofilm, pigments, exopolysaccharide production and motility at low temperature. Only nine strains showed these phenotypic traits and the blue pigmenting cheese strain P. fluorescens ITEM 17298 was the most distinctive. In addition, this strain decreased the survival probability of infected Galleria mellonella larvae, showing, for the first time, a pathogenic potential. Genomic and proteomic analyses performed on the ITEM 17298 planktonic cells treated or not with lactoferrin derived antibiofilm peptides allowed to reveal specific biofilm related-pathways as well as proteins involved in pathogenesis. Indeed, several genes were found related to signaling system by cGMP-dependent protein kinases, cellulose, rhamnolipid and alginate synthesis, antibiotic resistance, adhesion and virulence factors. The proteome of the untreated ITEM 17298, growing at low temperature, showed that most of the proteins associated with biofilm regulation, pigmentation motility, antibiotic resistance and pathogenecity were repressed, or decreased their levels in comparison to that of the untreated cultures. Thus, the results of this work shed light on the complex pathways network allowing psychrotrophic pseudomonads to adapt themselves to food-refrigerated conditions and enhance their spoilage. In addition, the discovery of virulence factors and antibiotic resistance determinants raises some questions about the need to deeper investigate these underestimated bacteria in order to increase awareness and provide input to update legislation on their detection limits in foods.
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Affiliation(s)
- Laura Quintieri
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | - Francesca Fanelli
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Leonardo Caputo
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | | | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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752
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Shamimuzzaman M, Le Tourneau JJ, Unni DR, Diesh CM, Triant DA, Walsh AT, Tayal A, Conant GC, Hagen DE, Elsik CG. Bovine Genome Database: new annotation tools for a new reference genome. Nucleic Acids Res 2020; 48:D676-D681. [PMID: 31647100 PMCID: PMC7145693 DOI: 10.1093/nar/gkz944] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.
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Affiliation(s)
- Md Shamimuzzaman
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Deepak R Unni
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Colin M Diesh
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Deborah A Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Amy T Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Aditi Tayal
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.,Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
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753
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Abstract
DNA methylation is an important epigenetic mark that contributes to various regulations in all domains of life. Giant viruses are widespread dsDNA viruses with gene contents overlapping the cellular world that also encode DNA methyltransferases. Yet, virtually nothing is known about the methylation of their DNA. Here, we use single-molecule real-time sequencing to study the complete methylome of a large spectrum of giant viruses. We show that DNA methylation is widespread, affecting 2/3 of the tested families, although unevenly distributed. We also identify the corresponding viral methyltransferases and show that they are subject to intricate gene transfers between bacteria, viruses and their eukaryotic host. Most methyltransferases are conserved, functional and under purifying selection, suggesting that they increase the viruses' fitness. Some virally encoded methyltransferases are also paired with restriction endonucleases forming Restriction-Modification systems. Our data suggest that giant viruses' methyltransferases are involved in diverse forms of virus-pathogens interactions during coinfections.
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754
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Kuleshov MV, Diaz JEL, Flamholz ZN, Keenan AB, Lachmann A, Wojciechowicz ML, Cagan RL, Ma'ayan A. modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Res 2020; 47:W183-W190. [PMID: 31069376 PMCID: PMC6602483 DOI: 10.1093/nar/gkz347] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set libraries within FishEnrichr, FlyEnrichr, WormEnrichr and YeastEnrichr are created from the Gene Ontology, mRNA expression profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific resources. Additionally, libraries were created by predicting gene function from RNA-seq co-expression data processed uniformly from the gene expression omnibus for each organism. The modEnrichr suite of tools provides the ability to convert gene lists across species using an ortholog conversion tool that automatically detects the species. For complex analyses, modEnrichr provides API access that enables submitting batch queries. In summary, modEnrichr leverages existing model organism databases and other resources to facilitate comprehensive hypothesis generation through data integration.
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Affiliation(s)
- Maxim V Kuleshov
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Jennifer E L Diaz
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020, New York, NY 10029, USA
| | - Zachary N Flamholz
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Alexandra B Keenan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Megan L Wojciechowicz
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
| | - Ross L Cagan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1020, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, NY 10029, USA
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755
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Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Marchler GH, Song JS, Thanki N, Yamashita RA, Yang M, Zhang D, Zheng C, Lanczycki CJ, Marchler-Bauer A. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res 2020; 48:D265-D268. [PMID: 31777944 DOI: 10.1093/nar/gkz991] [Citation(s) in RCA: 1553] [Impact Index Per Article: 388.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/11/2019] [Accepted: 11/13/2019] [Indexed: 11/12/2022] Open
Abstract
As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
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Affiliation(s)
- Shennan Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Farideh Chitsaz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Myra K Derbyshire
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Renata C Geer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Noreen R Gonzales
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Marc Gwadz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - David I Hurwitz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Gabriele H Marchler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - James S Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Narmada Thanki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Roxanne A Yamashita
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Mingzhang Yang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Dachuan Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Chanjuan Zheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Christopher J Lanczycki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
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756
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Lima WC, Gasteiger E, Marcatili P, Duek P, Bairoch A, Cosson P. The ABCD database: a repository for chemically defined antibodies. Nucleic Acids Res 2020; 48:D261-D264. [PMID: 31410491 PMCID: PMC6943046 DOI: 10.1093/nar/gkz714] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
The ABCD (for AntiBodies Chemically Defined) database is a repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized databases of chemical and protein entities. It is freely available to the academic community, accessible through the ExPASy server (https://web.expasy.org/abcd/). The ABCD database aims at helping to improve reproducibility in academic research by providing a unique, unambiguous identifier associated to each antibody sequence. It also allows to determine rapidly if a sequenced antibody is available for a given antigen.
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Affiliation(s)
- Wanessa C Lima
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Elisabeth Gasteiger
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Paula Duek
- CALIPHO Group, Faculty of Medicine, University of Geneva and SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Amos Bairoch
- CALIPHO Group, Faculty of Medicine, University of Geneva and SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Pierre Cosson
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
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757
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Miyazaki T, Park EY. Crystal structure of the Enterococcus faecalis α-N-acetylgalactosaminidase, a member of the glycoside hydrolase family 31. FEBS Lett 2020; 594:2282-2293. [PMID: 32367553 DOI: 10.1002/1873-3468.13804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Glycoside hydrolases catalyze the hydrolysis of glycosidic linkages in carbohydrates. The glycoside hydrolase family 31 (GH31) contains α-glucosidase, α-xylosidase, α-galactosidase, and α-transglycosylase. Recent work has expanded the diversity of substrate specificity of GH31 enzymes, and α-N-acetylgalactosaminidases (αGalNAcases) belonging to GH31 have been identified in human gut bacteria. Here, we determined the first crystal structure of a truncated form of GH31 αGalNAcase from the human gut bacterium Enterococcus faecalis. The enzyme has a similar fold to other reported GH31 enzymes and an additional fibronectin type 3-like domain. Additionally, the structure in complex with N-acetylgalactosamine reveals that conformations of the active site residues, including its catalytic nucleophile, change to recognize the ligand. Our structural analysis provides insight into the substrate recognition and catalytic mechanism of GH31 αGalNAcases.
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Affiliation(s)
- Takatsugu Miyazaki
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Japan
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Japan
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758
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Andrighetti T, Bohar B, Lemke N, Sudhakar P, Korcsmaros T. MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. Cells 2020; 9:cells9051278. [PMID: 32455748 PMCID: PMC7291277 DOI: 10.3390/cells9051278] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Microbiome–host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe–host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions—as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn’s disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.
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Affiliation(s)
- Tahila Andrighetti
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Institute of Biosciences, São Paulo University (UNESP), Botucatu 18618-689, SP, Brazil;
| | - Balazs Bohar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Department of Genetics, Eötvös Loránd University, Budapest 1117, Hungary
| | - Ney Lemke
- Institute of Biosciences, São Paulo University (UNESP), Botucatu 18618-689, SP, Brazil;
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Department of Chronic Diseases, Metabolism and Ageing, KU Leuven BE-3000, Leuven, Belgium
- Correspondence: (T.K.); (P.S.)
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Correspondence: (T.K.); (P.S.)
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759
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Damle NP, Köhn M. The human DEPhOsphorylation Database DEPOD: 2019 update. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5677402. [PMID: 31836896 PMCID: PMC6911163 DOI: 10.1093/database/baz133] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/06/2019] [Accepted: 10/29/2019] [Indexed: 01/04/2023]
Abstract
The human Dephosphorylation Database (DEPOD) is a manually curated resource that harbors human phosphatases, their protein and non-protein substrates, dephosphorylation sites and the associated signaling pathways. We report here an update to DEPOD by integrating and/or linking to annotations from 69 other open access databases including disease associations, phosphorylating kinases, protein interactions, and also genome browsers. We also provide tools to visualize protein interactions, protein structures, phosphorylation networks, evolutionary conservation of proteins, dephosphorylation sites, and short linear motifs within various proteins. The updated version of DEPOD contains 254 human phosphatases, 336 protein and 83 non-protein substrates, and 1215 manually curated phosphatase-substrate relationships. In addition, we have improved the data access as all the data in DEPOD can now be easily downloaded in a user-friendly format. With multiple significant improvements, DEPOD continues serving as a key resource for research on phosphatase-kinase networks. Database URL: www.depod.org
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Affiliation(s)
- Nikhil P Damle
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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760
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Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A, Finn RD. MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res 2020; 48:D570-D578. [PMID: 31696235 PMCID: PMC7145632 DOI: 10.1093/nar/gkz1035] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022] Open
Abstract
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.
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Affiliation(s)
- Alex L Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Martin Beracochea
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Miguel Boland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josephine Burgin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael R Crusoe
- Common Workflow Language, a project of the Software Freedom Conservancy, Inc. 137 Montague Street, Suite 380, Brooklyn, NY 11201-3548, USA
| | - Varsha Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon C Potter
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lorna J Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ekaterina Sakharova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Maxim Scheremetjew
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnologies, Saint Petersburg State University, Russia
| | - Alex Shlemov
- Center for Algorithmic Biotechnologies, Saint Petersburg State University, Russia
| | - Olga Kunyavskaya
- Center for Algorithmic Biotechnologies, Saint Petersburg State University, Russia
| | - Alla Lapidus
- Center for Algorithmic Biotechnologies, Saint Petersburg State University, Russia
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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761
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Wang X, Gao Y, Guan Z, Xie Z, Zhang D, Yin P, Yang G, Hong D, Xin Q. Structural analysis of the meiosis-related protein MS5 reveals non-canonical papain enhancement by cystatin-like folds. FEBS Lett 2020; 594:2462-2471. [PMID: 32415887 DOI: 10.1002/1873-3468.13817] [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: 01/17/2020] [Revised: 05/06/2020] [Accepted: 05/10/2020] [Indexed: 11/05/2022]
Abstract
MS5 is a meiosis-related protein belonging to the Brassicaceae-specific domain of unknown function family and characterized by the MS5 superfamily domain (MSD). In this study, we elucidated the three-dimensional crystal structure and potential biochemical function of the MSD. It was observed that the MSD adopts a cystatin-like fold, mainly consisting of a central α-helix and four- or five-stranded antiparallel β-sheets that wrap around it. However, unlike cystatins, which inhibit cysteine proteases, the MSD displayed allosteric activation of papain. We believe that our study provides insight into novel mechanisms of proteolytic enzyme regulation and may serve as a basis for functional studies of the MS5 family proteins in plants.
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Affiliation(s)
- Xiang Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yupeng Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhaoqi Xie
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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762
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Wang D, Fan W, Guo X, Wu K, Zhou S, Chen Z, Li D, Wang K, Zhu Y, Zhou Y. MaGenDB: a functional genomics hub for Malvaceae plants. Nucleic Acids Res 2020; 48:D1076-D1084. [PMID: 31665439 PMCID: PMC7145696 DOI: 10.1093/nar/gkz953] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
Malvaceae is a family of flowering plants containing many economically important plant species including cotton, cacao and durian. Recently, the genomes of several Malvaceae species have been decoded, and many omics data were generated for individual species. However, no integrative database of multiple species, enabling users to jointly compare and analyse relevant data, is available for Malvaceae. Thus, we developed a user-friendly database named MaGenDB (http://magen.whu.edu.cn) as a functional genomics hub for the plant community. We collected the genomes of 13 Malvaceae species, and comprehensively annotated genes from different perspectives including functional RNA/protein element, gene ontology, KEGG orthology, and gene family. We processed 374 sets of diverse omics data with the ENCODE pipelines and integrated them into a customised genome browser, and designed multiple dynamic charts to present gene/RNA/protein-level knowledge such as dynamic expression profiles and functional elements. We also implemented a smart search system for efficiently mining genes. In addition, we constructed a functional comparison system to help comparative analysis between genes on multiple features in one species or across closely related species. This database and associated tools will allow users to quickly retrieve large-scale functional information for biological discovery.
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Affiliation(s)
- Dehe Wang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- State Key Laboratory of Virology, Wuhan University, Wuhan 430072, China
| | - Weiliang Fan
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaolong Guo
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- State Key Laboratory of Virology, Wuhan University, Wuhan 430072, China
| | - Kai Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- State Key Laboratory of Virology, Wuhan University, Wuhan 430072, China
| | - Siyu Zhou
- College of Information Science and Engineering, Hunan University, Changsha 410082, China
| | - Zonggui Chen
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Danyang Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence may also be addressed to Kun Wang. Tel: +86 27 68754887;
| | - Yuxian Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
- Correspondence may also be addressed to Yuxian Zhu. Tel: +86 27 68752987;
| | - Yu Zhou
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- State Key Laboratory of Virology, Wuhan University, Wuhan 430072, China
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
- To whom correspondence should be addressed. Tel: +86 27 68756749;
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763
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Mead HL, Roe CC, Higgins Keppler EA, Van Dyke MCC, Laux KL, Funke AL, Miller KJ, Bean HD, Sahl JW, Barker BM. Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. Front Genet 2020; 11:483. [PMID: 32499817 PMCID: PMC7243461 DOI: 10.3389/fgene.2020.00483] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Coccidioides immitis and C. posadasii are soil dwelling dimorphic fungi found in North and South America. Inhalation of aerosolized asexual conidia can result in asymptomatic, acute, or chronic respiratory infection. In the United States there are approximately 350,000 new infections per year. The Coccidioides genus is the only known fungal pathogen to make specialized parasitic spherules, which contain endospores that are released into the host upon spherule rupture. The molecular determinants involved in this key step of infection remain largely elusive as 49% of genes are hypothetical with unknown function. An attenuated mutant strain C. posadasii Δcts2/Δard1/Δcts3 in which chitinase genes 2 and 3 were deleted was previously created for vaccine development. This strain does not complete endospore development, which prevents completion of the parasitic lifecycle. We sought to identify pathways active in the wild-type strain during spherule remodeling and endospore formation that have been affected by gene deletion in the mutant. We compared the transcriptome and volatile metabolome of the mutant Δcts2/Δard1/Δcts3 to the wild-type C735. First, the global transcriptome was compared for both isolates using RNA sequencing. The raw reads were aligned to the reference genome using TOPHAT2 and analyzed using the Cufflinks package. Genes of interest were screened in an in vivo model using NanoString technology. Using solid phase microextraction (SPME) and comprehensive two-dimensional gas chromatography - time-of-flight mass spectrometry (GC × GC-TOFMS) volatile organic compounds (VOCs) were collected and analyzed. Our RNA-Seq analyses reveal approximately 280 significantly differentially regulated transcripts that are either absent or show opposite expression patterns in the mutant compared to the parent strain. This suggests that these genes are tied to networks impacted by deletion and may be critical for endospore development and/or spherule rupture in the wild-type strain. Of these genes, 14 were specific to the Coccidioides genus. We also found that the wild-type and mutant strains differed significantly in their production versus consumption of metabolites, with the mutant displaying increased nutrient scavenging. Overall, our results provide the first targeted list of key genes that are active during endospore formation and demonstrate that this approach can define targets for functional assays in future studies.
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Affiliation(s)
- H L Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - C C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - E A Higgins Keppler
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - M C Caballero Van Dyke
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - K L Laux
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - A L Funke
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States.,Imaging Histology Core Facility, Northern Arizona University, Flagstaff AZ, United States
| | - K J Miller
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - H D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - J W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - B M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
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764
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The Biotechnological Potential of the Marine Diatom Skeletonema dohrnii to the Elevated Temperature and pCO 2 Concentration. Mar Drugs 2020; 18:md18050259. [PMID: 32429035 PMCID: PMC7281586 DOI: 10.3390/md18050259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Marine diatoms are promising candidates for biotechnological applications, since they contain high-value compounds, naturally. To facilitate the production of these compounds, stress conditions are often preferable; however, challenges remain with respect to maximizing a metabolic potential for the large-scale cultivation. Here, we sequenced the transcriptome of diatom Skeletonema dohrnii under the actual (21 °C, 400 ppm) and elevated (25 °C, 1000 ppm) temperature and pCO2 condition. Results indicated that cells grown at higher temperature and pCO2 showed increasing growth rate, pigment composition, and biochemical productivity as did the expression of chlorophyll, carotenoid and bioactive compound related genes or transcripts. Furthermore, performing de novo transcriptome, we identified 32,884 transcript clusters and found 10,974 of them were differentially expressed between these two conditions. Analyzing the functions of differentially expressed transcripts, we found many of them involved in core metabolic and biosynthesis pathways, including chlorophyll metabolism, carotenoid, phenylpropanoid, phenylalanine and tyrosine, and flavonoid biosynthesis was upregulated. Moreover, we here demonstrated that utilizing a unique bio-fixation ability, S. dohrnii is capable of suppressing central carbon metabolism to promote lipid productivity, fatty acid contents and other bioactive compounds under high temperature and pCO2 treatment. Our study suggests that this S. dohrnii species could be a potential candidate for wide-scale biotechnological applications under elevated temperature and CO2 conditions.
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765
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Álvarez B, Nieto-Pelegrín E, Martínez de la Riva P, Toki D, Poderoso T, Revilla C, Uenishi H, Ezquerra A, Domínguez J. Characterization of the Porcine CLEC12A and Analysis of Its Expression on Blood Dendritic Cell Subsets. Front Immunol 2020; 11:863. [PMID: 32477350 PMCID: PMC7237735 DOI: 10.3389/fimmu.2020.00863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/15/2020] [Indexed: 12/28/2022] Open
Abstract
CLEC12A has been proposed as a suitable target for delivering antigen to dendritic cells (DCs) to enhance vaccine efficacy both in human and mouse. In this study, we have characterized the porcine homolog of CLEC12A (poCLEC12A). Using new monoclonal antibodies (mAb), raised against its ectodomain, poCLEC12A was found to be expressed on alveolar macrophages, blood conventional type 1 and type 2 DCs and plasmacytoid DCs, but not on monocytes, T cells, B cells or NK cells, in contrast to its human and murine homologs. Western blot analysis showed that in alveolar macrophages this receptor is expressed both as a monomer and a dimer. After binding to DCs, anti- poCLEC12A mAb was efficiently internalized. No significant changes were observed in TNFα or IFNα secretion by plasmacytoid DCs stimulated with either CpGs (ODN2216) or polyinosinic-polycytidylic acid (poly I:C), upon incubation with mAb. These results provide the basis for future investigations aimed to assess the ability of anti-poCLEC12A mAbs to improve vaccine efficacy by targeting antigen to DCs.
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Affiliation(s)
- Belén Álvarez
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Elvira Nieto-Pelegrín
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Paloma Martínez de la Riva
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Daisuke Toki
- Animal Research Division, Institute of Japan Association for Techno-Innovation in Agriculture, Forestry and Fisheries, Tsukuba, Japan
| | - Teresa Poderoso
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Concepción Revilla
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Hirohide Uenishi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Angel Ezquerra
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Javier Domínguez
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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766
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You R, Yao S, Xiong Y, Huang X, Sun F, Mamitsuka H, Zhu S. NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res 2020; 47:W379-W387. [PMID: 31106361 PMCID: PMC6602452 DOI: 10.1093/nar/gkz388] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 01/19/2023] Open
Abstract
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Based on our GOLabeler—a state-of-the-art method for the third critical assessment of functional annotation (CAFA3), in this paper we propose NetGO, a web server that is able to further improve the performance of the large-scale AFP by incorporating massive protein-protein network information. Specifically, the advantages of NetGO are threefold in using network information: (i) NetGO relies on a powerful learning to rank framework from machine learning to effectively integrate both sequence and network information of proteins; (ii) NetGO uses the massive network information of all species (>2000) in STRING (other than only some specific species) and (iii) NetGO still can use network information to annotate a protein by homology transfer, even if it is not contained in STRING. Separating training and testing data with the same time-delayed settings of CAFA, we comprehensively examined the performance of NetGO. Experimental results have clearly demonstrated that NetGO significantly outperforms GOLabeler and other competing methods. The NetGO web server is freely available at http://issubmission.sjtu.edu.cn/netgo/.
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Affiliation(s)
- Ronghui You
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China
| | - Shuwei Yao
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China
| | - Yi Xiong
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University
| | - Xiaodi Huang
- School of Computing and Mathematics, Charles Sturt University, Albury, NSW 2640, Australia
| | - Fengzhu Sun
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China.,Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Hiroshi Mamitsuka
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan.,Department of Computer Science, Aalto University, Espoo and Helsinki, Finland
| | - Shanfeng Zhu
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China
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767
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Piovesan D, Tosatto SCE. INGA 2.0: improving protein function prediction for the dark proteome. Nucleic Acids Res 2020; 47:W373-W378. [PMID: 31073595 PMCID: PMC6602455 DOI: 10.1093/nar/gkz375] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/21/2022] Open
Abstract
Our current knowledge of complex biological systems is stored in a computable form through the Gene Ontology (GO) which provides a comprehensive description of genes function. Prediction of GO terms from the sequence remains, however, a challenging task, which is particularly critical for novel genomes. Here we present INGA 2.0, a new version of the INGA software for protein function prediction. INGA exploits homology, domain architecture, interaction networks and information from the ‘dark proteome’, like transmembrane and intrinsically disordered regions, to generate a consensus prediction. INGA was ranked in the top ten methods on both CAFA2 and CAFA3 blind tests. The new algorithm can process entire genomes in a few hours or even less when additional input files are provided. The new interface provides a better user experience by integrating filters and widgets to explore the graph structure of the predicted terms. The INGA web server, databases and benchmarking are available from URL: https://inga.bio.unipd.it/.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,CNR Institute of Neuroscience, Padua, Italy
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768
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Han G, Li C, Xiang F, Zhao Q, Zhao Y, Cai R, Cheng B, Wang X, Tao F. Genome-wide association study leads to novel genetic insights into resistance to Aspergillus flavus in maize kernels. BMC PLANT BIOLOGY 2020; 20:206. [PMID: 32393173 PMCID: PMC7216483 DOI: 10.1186/s12870-020-02404-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Fungus infection in staple grains affects the food storage and threatens food security. The Aspergillus flavus is known to infect multiple grains and produce mycotoxin Aflatoxin B1, which is mutagenic, teratogenic and causes immunosuppression in animals. However, the molecular mechanism of maize resistance to A. flavus is largely unknown. RESULTS Here we used corn kernels to investigate resistance genes to A. flavus using genome-wide association study (GWAS) of 313 inbred lines. We characterized the resistance levels of kernels after inoculating with A. flavus. The GWAS with 558,529 SNPs identified four associated loci involving 29 candidate genes that were linked to seed development, resistance or infection, and involved in signal pathways, seed development, germination, dormancy, epigenetic modification, and antimicrobial activity. In addition, a few candidate genes were also associated with several G-protein signaling and phytohormones that might involve in synergistic work conferring different resistance during seed development. Expression of 16 genes out of 29 during kernel development was also associated with resistance levels. CONCLUSIONS We characterized the resistance levels of 313 maize kernels after inoculating with A. flavus, and found four associated loci and 16 candidate maize genes. The expressed 16 genes involved in kernel structure and kernel composition most likely contribute to mature maize kernels' resistance to A. flavus, and in particular, in the development of pericarp. The linked candidate genes could be experimentally transformed to validate and manipulate fungal resistance. Thus this result adds value to maize kernels in breeding programs.
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Affiliation(s)
- Guomin Han
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
| | - Cuiping Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Fangzhi Xiang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Qianqian Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yang Zhao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
| | - Ronghao Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Beijiu Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, 230036 China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, 30602 USA
| | - Fang Tao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
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769
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Karow M, Fischer S, Meßling S, Konertz R, Riehl J, Xiong Q, Rijal R, Wagle P, S. Clemen C, Eichinger L. Functional Characterisation of the Autophagy ATG12~5/16 Complex in Dictyostelium discoideum. Cells 2020; 9:cells9051179. [PMID: 32397394 PMCID: PMC7290328 DOI: 10.3390/cells9051179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Macroautophagy, a highly conserved and complex intracellular degradative pathway, involves more than 20 core autophagy (ATG) proteins, among them the hexameric ATG12~5/16 complex, which is part of the essential ubiquitin-like conjugation systems in autophagy. Dictyostelium discoideumatg5 single, atg5/12 double, and atg5/12/16 triple gene knock-out mutant strains displayed similar defects in the conjugation of ATG8 to phosphatidylethanolamine, development, and cell viability upon nitrogen starvation. This implies that ATG5, 12 and 16 act as a functional unit in canonical autophagy. Macropinocytosis of TRITC dextran and phagocytosis of yeast were significantly decreased in ATG5¯ and ATG5¯/12¯ and even further in ATG5¯/12¯/16¯ cells. In contrast, plaque growth on Klebsiella aerogenes was about twice as fast for ATG5¯ and ATG5¯/12¯/16¯ cells in comparison to AX2, but strongly decreased for ATG5¯/12¯ cells. Along this line, phagocytic uptake of Escherichia coli was significantly reduced in ATG5¯/12¯ cells, while no difference in uptake, but a strong increase in membrane association of E. coli, was seen for ATG5¯ and ATG5¯/12¯/16¯ cells. Proteasomal activity was also disturbed in a complex fashion, consistent with an inhibitory activity of ATG16 in the absence of ATG5 and/or ATG12. Our results confirm the essential function of the ATG12~5/16 complex in canonical autophagy, and furthermore are consistent with autophagy-independent functions of the complex and its individual components. They also strongly support the placement of autophagy upstream of the ubiquitin-proteasome system (UPS), as a fully functional UPS depends on autophagy.
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Affiliation(s)
- Malte Karow
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Sarah Fischer
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Susanne Meßling
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Roman Konertz
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Jana Riehl
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
| | - Qiuhong Xiong
- Institute of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, Taiyuan 030006, China;
| | - Ramesh Rijal
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA;
| | - Prerana Wagle
- Bioinformatics Core Facility, CECAD Research Center, University of Cologne, 50931 Cologne, Germany;
| | - Christoph S. Clemen
- Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany;
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, 50931 Cologne, Germany
- Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Ludwig Eichinger
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany; (M.K.); (S.F.); (S.M.); (R.K.); (J.R.)
- Correspondence: ; Tel.: +49-221-478-6928; Fax: +49-221-478-97524
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770
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Li J, Zhang M, Sun J, Mao X, Wang J, Liu H, Zheng H, Li X, Zhao H, Zou D. Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. Front Genet 2020; 11:477. [PMID: 32457808 PMCID: PMC7225358 DOI: 10.3389/fgene.2020.00477] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 04/17/2020] [Indexed: 11/26/2022] Open
Abstract
Heavy metal exposure is a serious environmental stress in plants. However, plants have evolved several strategies to improve their heavy metal tolerance. Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Here, we identified 46 and 55 HMPs in rice and Arabidopsis, respectively, and named them OsHMP 1–46 and AtHMP 1–55 according to their chromosomal locations. The HMPs from both plants were divided into six clades based on the characteristics of their heavy metal-associated domains (HMA). The HMP gene structures and motifs varied greatly among the different classifications. The HMPs had high collinearity and were segmentally duplicated. A cis-element analysis revealed that the HMPs may be regulated by different transcription factors. An expression profile analysis disclosed that only eight OsHMPs were constitutive in rice tissues. Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. For Arabidopsis, nine AtHMPs presented with very high transcript levels in all organs. Most of the selected OsHMPs were differentially expressed in various tissues under different heavy metal stresses. Only OsHMP09, OsHMP18, and OsHMP22 showed higher expression levels in all tissues under different heavy metal stresses. In contrast, most of the selected AtHMPs had nearly constant expression levels in different tissues under various heavy metal stresses. The AtHMP20, AtHMP23, AtHMP25, AtHMP31, AtHMP35, AtHMP46 expression levels under different heavy metal stresses were higher in the leaves and roots. The foregoing discoveries elucidated HMP evolution in monocotyledonous and dicotyledonous plants and may helpful functionally characterize HMPs in the future.
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Affiliation(s)
- Jiaming Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xinrui Mao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xianwei Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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771
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Schrad JR, Abrahão JS, Cortines JR, Parent KN. Structural and Proteomic Characterization of the Initiation of Giant Virus Infection. Cell 2020; 181:1046-1061.e6. [PMID: 32392465 DOI: 10.1016/j.cell.2020.04.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/07/2020] [Accepted: 04/17/2020] [Indexed: 12/26/2022]
Abstract
Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
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Affiliation(s)
- Jason R Schrad
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jônatas S Abrahão
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Juliana R Cortines
- Department of Virology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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772
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Li R, Zhang W, Lu J, Zhang Z, Mu C, Song W, Migaud H, Wang C, Bekaert M. The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus. Front Genet 2020; 11:440. [PMID: 32457802 PMCID: PMC7227121 DOI: 10.3389/fgene.2020.00440] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/09/2020] [Indexed: 01/13/2023] Open
Abstract
The hard-shelled mussel (Mytilus coruscus) is an economically important shellfish that has been cultivated for the last decade. Due to over-exploitation, most mussel stocks have dramatically declined. Efforts to study this species' natural distribution, genetics, breeding, and cultivation have been hindered by the lack of a high-quality reference genome. To address this, we produced a hybrid high-quality reference genome of M. coruscus using a long-read platform to assemble the genome and short-read, high-quality technology to accurately correct for sequence errors. The genome was assembled into 10,484 scaffolds, a total length of 1.90 Gb, and a scaffold N50 of 898 kb. Ab initio annotation of the M. coruscus genome assembly identified a total of 42,684 genes. This accurate reference genome of M. coruscus provides an essential resource with the advantage of enabling the genome-scale selective breeding of M. coruscus. More importantly, it will also help in deciphering the speciation and local adaptation of the Mytilus species.
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Affiliation(s)
- Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China.,Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Weijia Zhang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Junkai Lu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Zhouyi Zhang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Weiwei Song
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Herve Migaud
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China.,Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Michaël Bekaert
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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773
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Frawley D, Stroe MC, Oakley BR, Heinekamp T, Straßburger M, Fleming AB, Brakhage AA, Bayram Ö. The Pheromone Module SteC-MkkB-MpkB-SteD-HamE Regulates Development, Stress Responses and Secondary Metabolism in Aspergillus fumigatus. Front Microbiol 2020; 11:811. [PMID: 32457716 PMCID: PMC7223695 DOI: 10.3389/fmicb.2020.00811] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
In order for eukaryotes to efficiently detect and respond to environmental stimuli, a myriad of protein signaling pathways are utilized. An example of highly conserved signaling pathways in eukaryotes are the mitogen-activated protein kinase (MAPK) pathways. In fungi, MAPK pathways have been shown to regulate a diverse array of biological processes, such as asexual and sexual development, stress responses and the production of secondary metabolites (SMs). In the model fungus Aspergillus nidulans, a MAPK pathway known as the pheromone module is utilized to regulate both development and SM production. This signaling cascade consists of the three kinases SteC, MkkB, and MpkB, as well as the SteD adaptor protein and the HamE scaffold. In this study, homologs of each of these proteins have been identified in the opportunistic human pathogen A. fumigatus. By performing epitope tagging and mass spectrometry experiments, we have shown that these proteins form a pentameric complex, similar to what is observed in A. nidulans. This complex has been shown to assemble in the cytoplasm and MpkB enters the nucleus, where it would presumably interact with various transcription factors. Pheromone module mutant strains exhibit drastic reductions in asexual sporulation, vegetative growth rate and production of SMs, such as gliotoxin. Mutants also display increased sensitivity to cell wall and oxidative stress agents. Overall, these data provide evidence of the existence of a conserved MAP kinase signaling pathway in Aspergillus species and suggest that this pathway is critical for the regulation of fungal development and secondary metabolism.
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Affiliation(s)
- Dean Frawley
- Department of Biology, Fungal Genetics and Secondary Metabolism Laboratory, Maynooth University, Maynooth, Ireland
| | - Maria C Stroe
- Department of Molecular and Applied Microbiology, Hans Knöll Institute (HKI), Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Hans Knöll Institute (HKI), Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Maria Straßburger
- Transfer Group Antiinfectives, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany
| | - Alastair B Fleming
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Hans Knöll Institute (HKI), Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Özgür Bayram
- Department of Biology, Fungal Genetics and Secondary Metabolism Laboratory, Maynooth University, Maynooth, Ireland
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774
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Horesh G, Fino C, Harms A, Dorman MJ, Parts L, Gerdes K, Heinz E, Thomson NR. Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population. Nucleic Acids Res 2020; 48:4357-4370. [PMID: 32232417 PMCID: PMC7192599 DOI: 10.1093/nar/gkaa198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/21/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022] Open
Abstract
The Klebsiella pneumoniae species complex includes important opportunistic pathogens which have become public health priorities linked to major hospital outbreaks and the recent emergence of multidrug-resistant hypervirulent strains. Bacterial virulence and the spread of multidrug resistance have previously been linked to toxin-antitoxin (TA) systems. TA systems encode a toxin that disrupts essential cellular processes, and a cognate antitoxin which counteracts this activity. Whilst associated with the maintenance of plasmids, they also act in bacterial immunity and antibiotic tolerance. However, the evolutionary dynamics and distribution of TA systems in clinical pathogens are not well understood. Here, we present a comprehensive survey and description of the diversity of TA systems in 259 clinically relevant genomes of K. pneumoniae. We show that TA systems are highly prevalent with a median of 20 loci per strain. Importantly, these toxins differ substantially in their distribution patterns and in their range of cognate antitoxins. Classification along these properties suggests different roles of TA systems and highlights the association and co-evolution of toxins and antitoxins.
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Affiliation(s)
- Gal Horesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
| | - Cinzia Fino
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Alexander Harms
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
- Department of Computer Science, University of Tartu, Tartu, 50090, Estonia
| | - Kenn Gerdes
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Eva Heinz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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775
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Ebert A, Monod M, Salamin K, Burmester A, Uhrlaß S, Wiegand C, Hipler UC, Krüger C, Koch D, Wittig F, Verma SB, Singal A, Gupta S, Vasani R, Saraswat A, Madhu R, Panda S, Das A, Kura MM, Kumar A, Poojary S, Schirm S, Gräser Y, Paasch U, Nenoff P. Alarming India-wide phenomenon of antifungal resistance in dermatophytes: A multicentre study. Mycoses 2020; 63:717-728. [PMID: 32301159 DOI: 10.1111/myc.13091] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND An alarming increase in recalcitrant dermatophytosis has been witnessed in India over the past decade. Drug resistance may play a major role in this scenario. OBJECTIVES The aim of the present study was to determine the prevalence of in vitro resistance to terbinafine, itraconazole and voriconazole in dermatophytes, and to identify underlying mutations in the fungal squalene epoxidase (SQLE) gene. PATIENTS/METHODS We analysed skin samples from 402 patients originating from eight locations in India. Fungi were identified by microbiological and molecular methods, tested for antifungal susceptibility (terbinafine, itraconazole, voriconazole), and investigated for missense mutations in SQLE. RESULTS Trichophyton (T.) mentagrophytes internal transcribed spacer (ITS) Type VIII was found in 314 (78%) samples. Eighteen (5%) samples harboured species identified up to the T interdigitale/mentagrophytes complex, and T rubrum was detected in 19 (5%) samples. 71% of isolates were resistant to terbinafine. The amino acid substitution Phe397Leu in the squalene epoxidase of resistant T mentagrophytes was highly prevalent (91%). Two novel substitutions in resistant Trichophyton strains, Ser395Pro and Ser443Pro, were discovered. The substitution Ala448Thr was found in terbinafine-sensitive and terbinafine-resistant isolates but was associated with increased MICs of itraconazole and voriconazole. CONCLUSIONS The high frequencies of terbinafine resistance in dermatophytes are worrisome and demand monitoring and further research. Squalene epoxidase substitutions between Leu393 and Ser443 could serve as markers of resistance in the future.
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Affiliation(s)
- Andreas Ebert
- Medizinische Fakultät, Universität Leipzig, Leipzig, Germany.,Labor für medizinische Mikrobiologie, Rötha, Germany
| | - Michel Monod
- Service de Dermatologie et Vénéréologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Karine Salamin
- Service de Dermatologie et Vénéréologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Anke Burmester
- Klinik für Hautkrankheiten, Universitätsklinikum Jena, Jena, Germany
| | - Silke Uhrlaß
- Labor für medizinische Mikrobiologie, Rötha, Germany
| | - Cornelia Wiegand
- Klinik für Hautkrankheiten, Universitätsklinikum Jena, Jena, Germany
| | | | | | - Daniela Koch
- Labor für medizinische Mikrobiologie, Rötha, Germany
| | | | | | - Archana Singal
- Department of Dermatology and STD, University College of Medical Sciences and GTB Hospital, Delhi, India
| | - Sanjeev Gupta
- M M Institute of Medical Sciences and Research, MM Deemed to be University, Ambala, India
| | - Resham Vasani
- Department of Dermatology, Bhojani Clinic, Mumbai, India
| | - Abir Saraswat
- Department of Dermatology, Indushree Skin Clinic, Lucknow, India
| | - Rengarajan Madhu
- Department of Dermatology (Mycology), Madras Medical College, Chennai, India
| | - Saumya Panda
- Department of Dermatology, KPC Medical College, Kolkata, India
| | - Anupam Das
- Department of Dermatology, KPC Medical College, Kolkata, India
| | - Mahendra M Kura
- Department of Dermatology, Grant Medical College & Sir J J Group of Hospitals, Mumbai, India
| | - Akshy Kumar
- Department of Dermatology, Government Medical College, Kota, India
| | - Shital Poojary
- Department of Dermatology, K J Somaiya Medical College, Mumbai, India
| | - Sibylle Schirm
- Institut für Medizinische Informatik, Statistik und Epidemiologie, Leipzig, Germany
| | - Yvonne Gräser
- Institut für Mikrobiologie und Hygiene, Nationales Konsiliarlabor für Dermatophyten, Universitätsmedizin Berlin Charité, Berlin, Germany
| | - Uwe Paasch
- Klinik und Poliklinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Pietro Nenoff
- Labor für medizinische Mikrobiologie, Rötha, Germany
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776
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Dabravolski S. Multi-faceted nature of the tRNA isopentenyltransferase. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:475-485. [PMID: 32345433 DOI: 10.1071/fp19255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/26/2019] [Indexed: 06/11/2023]
Abstract
Transfer RNA isopentenylation an adenine 37 position (A37) is a universal modification known in prokaryotes and eukaryotes. A set of highly homologous enzymes catalyse a series of reactions, leading to tRNA modifications, aimed to increase adaptation to environmental condition through the control of translation efficiency and reading frame maintenance. Transfer RNA-isopentenylation-related (TI-related) functions are well studied in bacteria, mitochondria of yeast and human, but completely unexplored in plants. Transfer RNA-isopentenylation-unrelated (TI-unrelated) functions participate in adaptation to environmental stresses via the regulation of sterol metabolism, gene silencing/suppression and amyloid fibrils formation. TI-unrelated functions are mostly studied in yeast. Finally, the degradation of A37-modified tRNA releases a set of bioactive compounds known as cis-cytokinins. Although all organisms are able to produce cis-cytokinins, its physiological role is still a matter of debates. For several species of bacteria and fungi, cis-cytokinins are known to play a crucial role in pathogenesis. In mammalian and human models cis-cytokinins have tumour-suppressing and anti-inflammation effects. This review aims to summarise current knowledge of the TI-related and TI-unrelated functions and main bioactive by-products of isopentenylated tRNA degradation.
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Affiliation(s)
- Siarhei Dabravolski
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 78371 Olomouc, Czech Republic.
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777
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Yu X, Han J, Li L, Zhang Q, Yang G, He G. Wheat PP2C-a10 regulates seed germination and drought tolerance in transgenic Arabidopsis. PLANT CELL REPORTS 2020; 39:635-651. [PMID: 32065246 PMCID: PMC7165162 DOI: 10.1007/s00299-020-02520-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/04/2020] [Indexed: 05/13/2023]
Abstract
A wheat protein phosphatase PP2C-a10, which interacted with TaDOG1L1 and TaDOG1L4, promoted seed germination and decreased drought tolerance of transgenic Arabidopsis. Seed dormancy and germination are critical to plant fitness. DELAY OF GERMINATION 1 (DOG1) is a quantitative trait locus for dormancy in Arabidopsis thaliana. Some interactions between DOG1 and the type 2C protein phosphatases (PP2Cs) have been reported in Arabidopsis. However, the research on molecular functions and regulations of DOG1Ls and group A PP2Cs in wheat (Triticum aestivum. L), an important crop plant, is rare. In this study, the whole TaDOG1L family was identified. Expression analysis revealed that TaDOG1L2, TaDOG1L4 and TaDOG1L-N2 specially expressed in wheat grains, while others displayed distinct expression patterns. Yeast two-hybrid analysis of TaDOG1Ls and group A TaPP2Cs revealed interaction patterns differed from those in Arabidopsis, and TaDOG1L1 and TaDOG1L4 interacted with TaPP2C-a10. The qRT-PCR analysis showed that TaPP2C-a10 exhibited the highest transcript level in wheat grains. Further investigation showed that ectopic expression of TaPP2C-a10 in Arabidopsis promoted seed germination and decreased sensitivity to ABA during germination stage. Additionally, TaPP2C-a10 transgenic Arabidopsis exhibited decreased tolerance to drought stress. Finally, the phylogenetic analysis indicated that TaPP2C-a10 gene was conserved in angiosperm during evolutionary process. Overall, our results reveal the role of TaPP2C-a10 in seed germination and abiotic stress response, as well as the functional diversity of TaDOG1L family.
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Affiliation(s)
- Xiaofen Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiapeng Han
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Li Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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778
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Liu Z, Ma H, Jung S, Main D, Guo L. Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:547-573. [PMID: 32442388 DOI: 10.1146/annurev-arplant-111119-021700] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
| | - Hong Ma
- Department of Biology, Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
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779
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Liu B, Leng L, Sun X, Wang Y, Ma J, Zhu Y. ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence. PeerJ 2020; 8:e9066. [PMID: 32377454 PMCID: PMC7195829 DOI: 10.7717/peerj.9066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/05/2020] [Indexed: 01/28/2023] Open
Abstract
Extracellular matrix (ECM) proteins play an essential role in various biological processes in multicellular organisms, and their abnormal regulation can lead to many diseases. For large-scale ECM protein identification, especially through proteomic-based techniques, a theoretical reference database of ECM proteins is required. In this study, based on the experimentally verified ECM datasets and by the integration of protein domain features and a machine learning model, we developed ECMPride, a flexible and scalable tool for predicting ECM proteins. ECMPride achieved excellent performance in predicting ECM proteins, with appropriate balanced accuracy and sensitivity, and the performance of ECMPride was shown to be superior to the previously developed tool. A new theoretical dataset of human ECM components was also established by applying ECMPride to all human entries in the SwissProt database, containing a significant number of putative ECM proteins as well as the abundant biological annotations. This dataset might serve as a valuable reference resource for ECM protein identification.
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Affiliation(s)
- Binghui Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Ling Leng
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xuer Sun
- Tissue Engineering Lab, Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Yunfang Wang
- Tissue Engineering Lab, Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China.,Basic Medical School, Anhui Medical University, Anhui, China
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780
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Cammarata-Mouchtouris A, Nguyen XH, Acker A, Bonnay F, Goto A, Orian A, Fauvarque MO, Boutros M, Reichhart JM, Matt N. Hyd ubiquitinates the NF-κB co-factor Akirin to operate an effective immune response in Drosophila. PLoS Pathog 2020; 16:e1008458. [PMID: 32339205 PMCID: PMC7205318 DOI: 10.1371/journal.ppat.1008458] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/07/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023] Open
Abstract
The Immune Deficiency (IMD) pathway in Drosophila melanogaster is activated upon microbial challenge with Gram-negative bacteria to trigger the innate immune response. In order to decipher this nuclear factor κB (NF-κB) signaling pathway, we undertook an in vitro RNAi screen targeting E3 ubiquitin ligases specifically and identified the HECT-type E3 ubiquitin ligase Hyperplastic discs (Hyd) as a new actor in the IMD pathway. Hyd mediated Lys63 (K63)-linked polyubiquitination of the NF-κB cofactor Akirin was required for efficient binding of Akirin to the NF-κB transcription factor Relish. We showed that this Hyd-dependent interaction was required for the transcription of immunity-related genes that are activated by both Relish and Akirin but was dispensable for the transcription of genes that depend solely on Relish. Therefore Hyd is key in NF-κB transcriptional selectivity downstream of the IMD pathway. Drosophila depleted of Akirin or Hyd failed to express the full set of genes encoding immune-induced anti-microbial peptides and succumbed to immune challenges. We showed further that UBR5, the mammalian homolog of Hyd, was also required downstream of the NF-κB pathway for the activation of Interleukin 6 (IL6) transcription by LPS or IL-1β in cultured human cells. Our findings link the action of an E3 ubiquitin ligase to the activation of immune effector genes, deepening our understanding of the involvement of ubiquitination in inflammation and identifying a potential target for the control of inflammatory diseases. Ubiquitination has been recently identified in pathogenesis and progression of various diseases where inflammation is critical. NF-κB transcription factors are key actors in the transcriptional cascade leading to inflammation as they activate genes with pro- or anti-inflammatory activities. The similarity between the immune pathways in flies and mammals makes Drosophila melanogaster an excellent model to study the innate response. Accordingly, we decided to identify E3 ubiquitin-ligases involved in the regulation of NF-κB pathway, using Drosophila as a model system. A RNAi based screen in immortalized embryonic macrophage-like Drosophila cells points to the HECT-E3 ubiquitin ligase Hyd as a new regulator of the Immune-deficiency (IMD) NF-κB pathway, activated after Gram-negative immune challenge. More precisely, we showed that Hyd acts at the level of Akirin, an evolutionarily conserved player in the NF-κB pathway, required for the transcription of pro-inflammatory genes, but not for the NF-κB-dependent genes contributing to the down-regulation of inflammation. In addition, we could show that the human homologue of Hyd (UBR5) acts genetically at the level of human AKIRIN2, pointing to a unique dichotomy between Hyd/Akirin-dependent and -independent gene activation, allowing for the decoupling activation and resolution of inflammation. These results identified UBR5 as a putative target for anti-inflammatory compounds.
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Affiliation(s)
| | - Xuan-Hung Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology (VRISG) and College of Health Sciences, VinUniversity Hanoi, Vietnam
| | - Adrian Acker
- Université de Strasbourg, CNRS, M3I UPR 9022, Strasbourg, France
| | - François Bonnay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Akira Goto
- Université de Strasbourg, CNRS, M3I UPR 9022, Strasbourg, France
| | - Amir Orian
- Rappaport Research Institute and Rappaport Faculty of Medicine, Technion Integrated Cancer Center, Technion—Israel Institute of Technology, Haifa, Israel
| | | | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), and Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | | | - Nicolas Matt
- Université de Strasbourg, CNRS, M3I UPR 9022, Strasbourg, France
- * E-mail:
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781
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Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. Proc Natl Acad Sci U S A 2020; 117:10511-10519. [PMID: 32341166 PMCID: PMC7229680 DOI: 10.1073/pnas.1921859117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study uses viral-like particle purification and subsequent unbiased genome sequencing to identify prokaryotic viruses associated with Apis mellifera. Interestingly, bacteriophages found in honey bees show a high diversity and span different viral taxa. This diversity sharply contrasts with the state-of-the-art knowledge on the relatively simple bee bacterial microbiome. The identification of multiple auxiliary metabolic genes suggests that these bacteriophages possess the coding potential to intervene in essential microbial pathways related to health and possibly also to disease. This study sheds light on a neglected part of the bee microbiota and opens avenues of in vivo research on the interaction of bacteriophages with their bacterial host, which likely has strongly underappreciated consequences on bee health. Honey bees (Apis mellifera) produce an enormous economic value through their pollination activities and play a central role in the biodiversity of entire ecosystems. Recent efforts have revealed the substantial influence that the gut microbiota exert on bee development, food digestion, and homeostasis in general. In this study, deep sequencing was used to characterize prokaryotic viral communities associated with honey bees, which was a blind spot in research up until now. The vast majority of the prokaryotic viral populations are novel at the genus level, and most of the encoded proteins comprise unknown functions. Nevertheless, genomes of bacteriophages were predicted to infect nearly every major bee-gut bacterium, and functional annotation and auxiliary metabolic gene discovery imply the potential to influence microbial metabolism. Furthermore, undiscovered genes involved in the synthesis of secondary metabolic biosynthetic gene clusters reflect a wealth of previously untapped enzymatic resources hidden in the bee bacteriophage community.
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782
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Pranavathiyani G, Prava J, Rajeev AC, Pan A. Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. Front Cell Infect Microbiol 2020; 10:109. [PMID: 32318354 PMCID: PMC7146069 DOI: 10.3389/fcimb.2020.00109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 11/13/2022] Open
Abstract
The opportunistic pathogen Klebsiella pneumoniae is a causative agent of several hospital-acquired infections. It has become resistant to a wide range of currently available antibiotics, leading to high mortality rates among patients; this has further led to a demand for novel therapeutic intervention to treat such infections. Using a series of in silico analyses, the present study aims to explore novel drug/vaccine candidates from the hypothetical proteins of K. pneumoniae. A total of 540 proteins were found to be hypothetical in this organism. Analysis of these 540 hypothetical proteins revealed 30 pathogen-specific proteins essential for pathogen survival. A motifs/domain family analysis, similarity search against known proteins, gene ontology, and protein–protein interaction analysis of the shortlisted 30 proteins led to functional assignment for 17 proteins. They were mainly cataloged as enzymes, lipoproteins, stress-induced proteins, transporters, and other proteins (viz., two-component proteins, skeletal proteins and toxins). Among the annotated proteins, 16 proteins, located in the cytoplasm, periplasm, and inner membrane, were considered as potential drug targets, and one extracellular protein was considered as a vaccine candidate. A druggability analysis indicated that the identified 17 drug/vaccine candidates were “novel”. Furthermore, a host–pathogen interaction analysis of these identified target candidates revealed a betaine/carnitine/choline transporters (BCCT) family protein showing interactions with five host proteins. Structure prediction and validation were carried out for this protein, which could aid in structure-based inhibitor design.
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Affiliation(s)
- G Pranavathiyani
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Jyoti Prava
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Athira C Rajeev
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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783
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Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Nat Commun 2020; 11:1960. [PMID: 32327655 PMCID: PMC7181641 DOI: 10.1038/s41467-020-15876-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.
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784
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Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Res 2020; 9. [PMID: 32566135 PMCID: PMC7284151 DOI: 10.12688/f1000research.20559.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.
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Affiliation(s)
- Christine Orengo
- Structural and Molecular Biology Department, University College, London, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Shoshana Wodak
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Vincent Zoete
- Department of Oncology, Lausanne University, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandre M J J Bonvin
- Bijvoet Center, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Arne Elofsson
- Science for Life Laboratory, Stockholm University, Solna, S-17121, Sweden
| | - K Anton Feenstra
- Dept. Computer Science, Center for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit, Amsterdam, 1081 HV, The Netherlands
| | - Dietland L Gerloff
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Thomas Hamelryck
- Bioinformatics center, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | | | | | - Adam Hospital
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | | | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, D-20146, Germany
| | - Claudio Soares
- Instituto de Tecnologia Química e Biológica Antonio Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Pierre Tuffery
- Ressource Parisienne en Bioinformatique Structurale, Université de Paris, Paris, F-75205, France
| | - Gabor Tusnady
- Membrane Bioinformatics Research Group, Institute of Enzymology, Budapest, H-1117, Hungary
| | | | - Tiina Salminen
- Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, FI-20500, Finland
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, CZ-25250, Czech Republic
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785
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Wiebe DS, Omelyanchuk NA, Mukhin AM, Grosse I, Lashin SA, Zemlyanskaya EV, Mironova VV. Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. Genes (Basel) 2020; 11:genes11040434. [PMID: 32316383 PMCID: PMC7230499 DOI: 10.3390/genes11040434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies Gene Ontology (GO) terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g., weakly, moderately, or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments, and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, Singular Enrichment Analysis (SEA), and Gene Set Enrichment Analysis (GSEA). These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers, and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server.
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Affiliation(s)
- Daniil S. Wiebe
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Nadezhda A. Omelyanchuk
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Aleksei M. Mukhin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Sergey A. Lashin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Victoria V. Mironova
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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786
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Su WC, Harrison PM. Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives. PeerJ 2020; 8:e9023. [PMID: 32337108 PMCID: PMC7169965 DOI: 10.7717/peerj.9023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Pub1 protein is an important RNA-binding protein functional in stress granule assembly in budding yeast Saccharomyces cerevisiae and, as its co-ortholog Tia1, in humans. It is unique among proteins in evidencing prion-like aggregation in both its yeast and human forms. Previously, we noted that Pub1/Tia1 was the only protein linked to human disease that has prion-like character and and has demonstrated such aggregation in both species. Thus, we were motivated to probe further into the evolution of the Pub1/Tia1 family (and its close relative Nam8 and its orthologs) to gain a picture of how such a protein has evolved over deep evolutionary time since the last common ancestor of eukaryotes. Here, we discover that the prion-like composition of this protein family is deeply conserved across eukaryotes, as is the prion-like composition of its close relative Nam8/Ngr1. A sizeable minority of protein orthologs have multiple prion-like domains within their sequences (6-20% depending on criteria). The number of RNA-binding RRM domains is conserved at three copies over >86% of the Pub1 family (>71% of the Nam8 family), but proteins with just one or two RRM domains occur frequently in some clades, indicating that these are not due to annotation errors. Overall, our results indicate that a basic scaffold comprising three RNA-binding domains and at least one prion-like region has been largely conserved since the last common ancestor of eukaryotes, providing further evidence that prion-like aggregation may be a very ancient and conserved phenomenon for certain specific proteins.
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Affiliation(s)
- Wan-Chun Su
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Paul M Harrison
- Department of Biology, McGill University, Montreal, QC, Canada
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787
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Cabral A, Azinheira HG, Talhinhas P, Batista D, Ramos AP, Silva MDC, Oliveira H, Várzea V. Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E502. [PMID: 32295225 PMCID: PMC7238176 DOI: 10.3390/plants9040502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/20/2022]
Abstract
The genus Colletotrichum has witnessed tremendous variations over the years in the number of species recognized, ranging from 11 to several hundreds. Host-specific fungal species, once the rule, are now the exception, with polyphagous behavior regarded as normal in this genus. The species Colletotrichum kahawae was created to accommodate the pathogens that have the unique ability to infect green developing coffee berries causing the devastating Coffee Berry Disease in Africa, but its close phylogenetic relationship to a polyphagous group of fungi in the C. gloeosporioides species complex led some researchers to regard these pathogens as members of a wider species. In this work we combine pathological, morphological, cytogenomic, biochemical, and molecular data of a comprehensive set of phylogenetically-related isolates to show that the Coffee Berry Disease pathogen forms a separate species, C. kahawae, and also to assign the closely related fungi, previously in C. kahawae subsp. cigarro, to a new species, C. cigarro comb. et stat. nov. This taxonomic clarification provides an opportunity to link phylogeny and functional biology, and additionally enables a much-needed tool for plant pathology and agronomy, associating exclusively C. kahawae to the Coffee Berry Disease pathogen.
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Affiliation(s)
- Ana Cabral
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Helena G. Azinheira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Dora Batista
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Ana Paula Ramos
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Laboratório de Patologia Vegetal “Veríssimo de Almeida”, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Maria do Céu Silva
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Helena Oliveira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
| | - Vítor Várzea
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
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788
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Blango MG, Pschibul A, Rivieccio F, Krüger T, Rafiq M, Jia LJ, Zheng T, Goldmann M, Voltersen V, Li J, Panagiotou G, Kniemeyer O, Brakhage AA. Dynamic Surface Proteomes of Allergenic Fungal Conidia. J Proteome Res 2020; 19:2092-2104. [PMID: 32233371 DOI: 10.1021/acs.jproteome.0c00013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fungal spores and hyphal fragments play an important role as allergens in respiratory diseases. In this study, we performed trypsin shaving and secretome analyses to identify the surface-exposed proteins and secreted/shed proteins of Aspergillus fumigatus conidia, respectively. We investigated the surface proteome under different conditions, including temperature variation and germination. We found that the surface proteome of resting A. fumigatus conidia is not static but instead unexpectedly dynamic, as evidenced by drastically different surface proteomes under different growth conditions. Knockouts of two abundant A. fumigatus surface proteins, ScwA and CweA, were found to function only in fine-tuning the cell wall stress response, implying that the conidial surface is very robust against perturbations. We then compared the surface proteome of A. fumigatus to other allergy-inducing molds, including Alternaria alternata, Penicillium rubens, and Cladosporium herbarum, and performed comparative proteomics on resting and swollen conidia, as well as secreted proteins from germinating conidia. We detected 125 protein ortholog groups, including 80 with putative catalytic activity, in the extracellular region of all four molds, and 42 nonorthologous proteins produced solely by A. fumigatus. Ultimately, this study highlights the dynamic nature of the A. fumigatus conidial surface and provides targets for future diagnostics and immunotherapy.
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Affiliation(s)
- Matthew G Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Annica Pschibul
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Flora Rivieccio
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Muhammad Rafiq
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Lei-Jie Jia
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Tingting Zheng
- Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Marie Goldmann
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Vera Voltersen
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong S.A.R., China.,School of Data Science, City University of Hong Kong, Kowloon, Hong Kong S.A.R., China
| | - Gianni Panagiotou
- Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena 07745, Germany
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789
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Vitorino I, Albuquerque L, Wiegand S, Kallscheuer N, da Costa MS, Lobo-da-Cunha A, Jogler C, Lage OM. Alienimonas chondri sp. nov., a novel planctomycete isolated from the biofilm of the red alga Chondrus crispus. Syst Appl Microbiol 2020; 43:126083. [PMID: 32360272 DOI: 10.1016/j.syapm.2020.126083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 11/26/2022]
Abstract
The phylum Planctomycetes comprises bacteria with peculiar and very unique characteristics among prokaryotes. In marine environments, macroalgae biofilms are well known for harboring planctomycetal diversity. Here, we describe a novel isolate obtained from the biofilm of the red alga Chondrus crispus collected at a rocky beach in Porto, Portugal. The novel strain LzC2T is motile, rosette-forming with spherical- to ovoid-shaped cells. LzC2T forms magenta- to pinkish-colored colonies in M13 and M14 media. Transmission and scanning electron microscopy observations showed a division by polar and lateral budding. Mother cells are connected to the daughter cells by a tubular neck-like structure. The strain requires salt for growth. Vitamins are not required for growth. Optimal growth occurs from 15 to 30°C and within a pH range from 5.5 to 10.0. Major fatty acids are anteiso-C15:0 (54.2%) and iso-C15:0 (19.5%). Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid represent the main lipids and menaquinone 6 (MK-6) is the only quinone present. 16S rRNA gene-based phylogenetic analysis supports the affiliation to the phylum Planctomycetes and family Planctomycetaceae, with Alienimonas as the closest relative. Strain LzC2T shares 97% 16S rRNA gene sequence similarity with Alienimonas californiensis. LzC2T has a genome size of 5.3 Mb and a G+C content of 68.3%. Genotypic and phenotypic comparison with the closest relatives strongly suggest that LzC2T (=CECT 30038T=LMG XXXT) is a new species of the genus Alienimonas, for which we propose the name Alienimonas chondri sp. nov., represented by LzC2T as type strain. 16S rRNA gene accession number: GenBank=MN757873.1. Genome accession number: GenBank=WTPX00000000.
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Affiliation(s)
- Inês Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/no., 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Luciana Albuquerque
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Milton S da Costa
- Departamento de Ciências da Vida, Apartado 3046, Universidade de Coimbra, 3001-401 Coimbra, Portugal
| | - Alexandre Lobo-da-Cunha
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal; Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Christian Jogler
- Institute of Microbiology, Department of Microbial Interactions, Friedrich-Schiller University Jena, Philosophenweg 12, Jena, Germany
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/no., 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
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790
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Mann E, Kimber MS, Whitfield C. Bioinformatics analysis of diversity in bacterial glycan chain-termination chemistry and organization of carbohydrate-binding modules linked to ABC transporters. Glycobiology 2020; 29:822-838. [PMID: 31504498 DOI: 10.1093/glycob/cwz066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
The structures of bacterial cell surface glycans are remarkably diverse. In spite of this diversity, the general strategies used for their assembly are limited. In one of the major processes, found in both Gram-positive and Gram-negative bacteria, the glycan is polymerized in the cytoplasm on a polyprenol lipid carrier and exported from the cytoplasm by an ATP-binding cassette (ABC) transporter. The ABC transporter actively participates in determining the chain length of the glycan substrate, which impacts functional properties of the glycoconjugate products. A subset of these systems employs an additional elaborate glycan capping strategy that dictates the size distribution of the products. The hallmarks of prototypical capped glycan systems are a chain-terminating enzyme possessing a coiled-coil molecular ruler and an ABC transporter possessing a carbohydrate-binding module, which recognizes the glycan cap. To date, detailed investigations are limited to a small number of prototypes, and here, we used our current understanding of these processes for a bioinformatics census of other examples in available genome sequences. This study not only revealed additional instances of existing terminators but also predicted new chemistries as well as systems that diverge from the established prototypes. These analyses enable some new functional hypotheses and offer a roadmap for future research.
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Affiliation(s)
- Evan Mann
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. East, Guelph, Ontario N1G 2W1, Canada
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. East, Guelph, Ontario N1G 2W1, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. East, Guelph, Ontario N1G 2W1, Canada
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791
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Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22. 3 Biotech 2020; 10:160. [PMID: 32206494 DOI: 10.1007/s13205-020-2148-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, a bacterial strain CP22 with ability to produce cellulase, xylanase and mannanase was isolated from the oil palm compost. Based on the 16S rRNA gene analysis, the strain was affiliated to genus Micromonospora. To further investigate genes that are related to cellulose and hemicellulose degradation, the genome of strain CP22 was sequenced, annotated and analyzed. The de novo assembled genome of strain CP22 featured a size of 5,856,203 bp with G + C content of 70.84%. Detailed genome analysis on lignocellulose degradation revealed a total of 60 genes consisting of 47 glycoside hydrolase domains and 16 carbohydrate esterase domains predicted to be involved in cellulolytic and hemicellulolytic deconstruction. Particularly, 20 genes encode for cellulases (8 endoglucanases, 3 exoglucanases and 9 β-glucosidases) and 40 genes encode for hemicellulases (15 endo-1,4-β-xylanase, 3 β-xylosidase, 3 α-arabinofuranosidase, 10 acetyl xylan esterase, 6 polysaccharide deacetylase, 1 β-mannanase, 1 β-mannosidase and 1 α-galactosidase). Thirty-two genes encoding carbohydrate-binding modules (CBM) from six different families (CBM2, CBM4, CBM6, CBM9, CBM13 and CBM22) were present in the genome of strain CP22. These CBMs were found in 27 cellulolytic and hemicellulolytic genes, indicating their potential role in enhancing the substrate-binding capability of the enzymes. CBM2 and CBM13 are the major CBMs present in cellulases and hemicellulases (xylanases and mannanases), respectively. Moreover, a GH10 xylanase was found to contain 3 CBMs (1 CBM9 and 2 CBM22) and these CBMs were reported to bind specifically to xylan. This genome-based analysis could facilitate the exploration of this strain for lignocellulosic biomass degradation.
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792
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de Castro I, Mendo S, Caetano T. Antibiotics from Haloarchaea: What Can We Learn from Comparative Genomics? MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:308-316. [PMID: 32048095 DOI: 10.1007/s10126-020-09952-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
The knowledge of antibiotics produced by Archaea (archaeocins) is still limited. So far, only two types of archaeocins are known: (i) sulfolobicins, produced by the extremely thermophilic Sulfolobus spp. and (ii) haloarcheocins, produced by halophilic archaea. Haloarcheocins were first discovered in the 1980s, but most of their characterisation was solely based on supernatant-based assays. Only a few were successfully purified and sequenced, and even fewer have a proposed biosynthetic model. Furthermore, their mode of action, ecological role and biotechnological potential are still to be explored. Haloarcheocin C8 (HalC8) is the best well-characterised haloarcheocin. We applied an approach of comparative genomics in order to go a step further in the knowledge of their biosynthetic clusters as well as the clusters encoding HalC8-like peptides. These peptides can be classified, at least, into 4 different clades, and there is low gene conservation between them. However, the putative function of some proteins is conserved. These include uncharacterized major facilitator superfamily proteins, transmembrane peptides, DNA-binding transcriptional regulators and proteins with extracellular domains. Our analysis reinforces the association of these proteins with HalC8/HalC8-like biosynthesis. Their functionality is unknown, and, in an era where it is known that haloarchaea are not confined to high salt habitats, the advance in the knowledge of their specialised metabolites will be imperative.
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Affiliation(s)
- Inês de Castro
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Sónia Mendo
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Tânia Caetano
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal.
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793
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Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet 2020; 16:e1008462. [PMID: 32236090 PMCID: PMC7112179 DOI: 10.1371/journal.pgen.1008462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.
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Affiliation(s)
- Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sam Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Erica Unger-Wallace
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Rex A. Cole
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Antony M. Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik Vollbrecht
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Interdepartmental Genetics, Iowa State University, Ames, Iowa, United States of America
| | - Matthew M. S. Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - John E. Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
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794
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Kim A, Chen J, Khare D, Jin JY, Yamaoka Y, Maeshima M, Zhao Y, Martinoia E, Hwang JU, Lee Y. Non-intrinsic ATP-binding cassette proteins ABCI19, ABCI20 and ABCI21 modulate cytokinin response at the endoplasmic reticulum in Arabidopsis thaliana. PLANT CELL REPORTS 2020; 39:473-487. [PMID: 32016506 PMCID: PMC7346704 DOI: 10.1007/s00299-019-02503-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/23/2019] [Indexed: 05/13/2023]
Abstract
The non-intrinsic ABC proteins ABCI20 and ABCI21 are induced by light under HY5 regulation, localize to the ER, and ameliorate cytokinin-driven growth inhibition in young Arabidopsis thaliana seedlings. The plant ATP-binding cassette (ABC) I subfamily (ABCIs) comprises heterogeneous proteins containing any of the domains found in other ABC proteins. Some ABCIs are known to function in basic metabolism and stress responses, but many remain functionally uncharacterized. ABCI19, ABCI20, and ABCI21 of Arabidopsis thaliana cluster together in a phylogenetic tree, and are suggested to be targets of the transcription factor ELONGATED HYPOCOTYL 5 (HY5). Here, we reveal that these three ABCIs are involved in modulating cytokinin responses during early seedling development. The ABCI19, ABCI20 and ABCI21 promoters harbor HY5-binding motifs, and ABCI20 and ABCI21 expression was induced by light in a HY5-dependent manner. abci19 abci20 abci21 triple and abci20 abci21 double knockout mutants were hypersensitive to cytokinin in seedling growth retardation assays, but did not show phenotypic differences from the wild type in either control medium or auxin-, ABA-, GA-, ACC- or BR-containing media. ABCI19, ABCI20, and ABCI21 were expressed in young seedlings and the three proteins interacted with each other, forming a large protein complex at the endoplasmic reticulum (ER) membrane. These results suggest that ABCI19, ABCI20, and ABCI21 fine-tune the cytokinin response at the ER under the control of HY5 at the young seedling stage.
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Affiliation(s)
- Areum Kim
- Department of Life Science, POSTECH, Pohang, 37673, Republic of Korea
| | - Jilin Chen
- Section of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
| | - Deepa Khare
- Department of Life Science, POSTECH, Pohang, 37673, Republic of Korea
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, India
| | - Jun-Young Jin
- Department of Life Science, POSTECH, Pohang, 37673, Republic of Korea
| | - Yasuyo Yamaoka
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Republic of Korea
| | - Masayoshi Maeshima
- Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California, San Diego, San Diego, CA, USA
| | - Enrico Martinoia
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Republic of Korea
| | - Jae-Ung Hwang
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Republic of Korea
| | - Youngsook Lee
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Republic of Korea.
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795
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Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J. Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control. EMBO J 2020; 39:e103852. [PMID: 32227509 PMCID: PMC7196914 DOI: 10.15252/embj.2019103852] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
RNA–protein interactions are the crucial basis for many steps of bacterial gene expression, including post‐transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram‐negative bacteria, knowledge about RNA–protein complexes in Gram‐positive species remains scarce. Here, we used the Grad‐seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% of the transcripts and ~ 62% of the proteins of this important human pathogen. Analysis of in‐gradient distributions and subsequent tag‐based protein capture identified interactions of the exoribonuclease Cbf1/YhaM with sRNAs that control bacterial competence for DNA uptake. Unexpectedly, the nucleolytic activity of Cbf1 stabilizes these sRNAs, thereby promoting their function as repressors of competence. Overall, these results provide the first RNA/protein complexome resource of a Gram‐positive species and illustrate how this can be utilized to identify new molecular factors with functions in RNA‐based regulation of virulence‐relevant pathways.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Geneviève Garriss
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Silvia Di Giorgio
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,ZB MED-Information Centre for Life Sciences, Cologne, Germany
| | - Lisa-Marie Hack
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- ZB MED-Information Centre for Life Sciences, Cologne, Germany.,Faculty of Information Science and Communication Studies, TH Köln, Cologne, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,SCELSE and LKC, Nanyang Technological University, NTU, Singapore, Singapore
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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796
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Sakalauskaite J, Plasseraud L, Thomas J, Albéric M, Thoury M, Perrin J, Jamme F, Broussard C, Demarchi B, Marin F. The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization. J Struct Biol 2020; 211:107497. [PMID: 32220629 DOI: 10.1016/j.jsb.2020.107497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 11/18/2022]
Abstract
Molluscs, the largest marine phylum, display extraordinary shell diversity and sophisticated biomineral architectures. However, mineral-associated biomolecules involved in biomineralization are still poorly characterised. We report the first comprehensive structural and biomolecular study of Spondylus gaederopus, a pectinoid bivalve with a peculiar shell texture. Used since prehistoric times, this is the best-known shell of Europe's cultural heritage. We find that Spondylus microstructure is very poor in mineral-bound organics, which are mostly intercrystalline and concentrated at the interface between structural layers. Using high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) we characterized several shell protein fractions, isolated following different bleaching treatments. Several peptides were identified as well as six shell proteins, which display features and domains typically found in biomineralized tissues, including the prevalence of intrinsically disordered regions. It is very likely that these sequences only partially represent the full proteome of Spondylus, considering the lack of genomics data for this genus and the fact that most of the reconstructed peptides do not match with any known shell proteins, representing consequently lineage-specific sequences. This work sheds light onto the shell matrix involved in the biomineralization in spondylids. Our proteomics data suggest that Spondylus has evolved a shell-forming toolkit, distinct from that of other better studied pectinoids - fine-tuned to produce shell structures with high mechanical properties, while limited in organic content. This study therefore represents an important milestone for future studies on biomineralized skeletons and provides the first reference dataset for forthcoming molecular studies of Spondylus archaeological artifacts.
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Affiliation(s)
- Jorune Sakalauskaite
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy; Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France.
| | - Laurent Plasseraud
- Institute of Molecular Chemistry, ICMUB UMR CNRS 6302, University of Burgundy-Franche-Comté (UBFC), 9 Avenue Alain Savary, 21000 Dijon, France
| | - Jérôme Thomas
- Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France
| | - Marie Albéric
- Laboratoire Chimie de la Matière Condensée de Paris, UMR, CNRS 7574, Sorbonne Université, Place Jussieu 4, 75252 Paris, France
| | - Mathieu Thoury
- IPANEMA, CNRS, ministère de la Culture, UVSQ, USR3461, Université Paris-Saclay, F-91192 Gif-sur-Yvette, France
| | - Jonathan Perrin
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif sur Yvette Cedex, France
| | - Frédéric Jamme
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif sur Yvette Cedex, France
| | - Cédric Broussard
- 3P5 Proteomic Platform, University of Paris, Cochin Institute, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy
| | - Frédéric Marin
- Biogeosciences, UMR CNRS 6282, University of Burgundy-Franche-Comté (UBFC), 6 Boulevard Gabriel, 21000 Dijon, France.
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797
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Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent. PLoS Pathog 2020; 16:e1007969. [PMID: 32191774 PMCID: PMC7108748 DOI: 10.1371/journal.ppat.1007969] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 03/31/2020] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae is recognized as an urgent threat to human health due to the increasing isolation of multidrug resistant strains. Hypervirulent strains are a major concern due to their ability to cause life-threating infections in healthy hosts. The type VI secretion system (T6SS) is widely implicated in microbial antagonism, and it mediates interactions with host eukaryotic cells in some cases. In silico search for genes orthologous to T6SS component genes and T6SS effector genes across 700 K. pneumoniae genomes shows extensive diversity in T6SS genes across the K. pneumoniae species. Temperature, oxygen tension, pH, osmolarity, iron levels, and NaCl regulate the expression of the T6SS encoded by a hypervirulent K. pneumoniae strain. Polymyxins and human defensin 3 also increase the activity of the T6SS. A screen for regulators governing T6SS uncover the correlation between the transcription of the T6SS and the ability to kill E. coli prey. Whereas H-NS represses the T6SS, PhoPQ, PmrAB, Hfq, Fur, RpoS and RpoN positively regulate the T6SS. K. pneumoniae T6SS mediates intra and inter species bacterial competition. This antagonism is only evident when the prey possesses an active T6SS. The PhoPQ two component system governs the activation of K. pneumoniae T6SS in bacterial competitions. Mechanistically, PhoQ periplasmic domain, and the acid patch within, is essential to activate K. pneumoniae T6SS. Klebsiella T6SS also mediates anti-fungal competition. We have delineated the contribution of each of the individual VgrGs in microbial competition and identified VgrG4 as a T6SS effector. The DUF2345 domain of VgrG4 is sufficient to intoxicate bacteria and yeast. ROS generation mediates the antibacterial effects of VgrG4, and the antitoxin Sel1E protects against the toxic activity of VgrG4. Our findings provide a better understanding of the regulation of the T6SS in bacterial competitions, and place ROS as an early event in microbial competition. Klebsiella pneumoniae has been singled out as an “urgent threat to human health” due to extremely drug resistant strains. Numerous studies investigate the molecular mechanisms underlying antibiotic resistance in K. pneumoniae, while others dissect the virulence strategies of this pathogen. However, there is still limited knowledge on the fitness of Klebsiella in the environment, and, particularly, the competition of Klebsiella with other species. Here, we demonstrate that Klebsiella exploits the type VI secretion system (T6SS) nanoweapon to kill bacterial competitors and fungi. K. pneumoniae perceives T6SS attacks from bacterial competitors, resulting in retaliation against the aggressive cell. The perception of the attack involved the sensor PhoPQ and led to the up-regulation of the T6SS. We identified one of the toxins deployed by the T6SS to antagonize other microbes and revealed how Klebsiella protects itself from this toxin. Our findings provide a better understanding of the T6SS role in microbial competition and uncover new aspects on how bacteria regulate T6SS-mediated microbial antagonism.
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798
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Li WJ, Narancic T, Kenny ST, Niehoff PJ, O’Connor K, Blank LM, Wierckx N. Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440. Front Microbiol 2020; 11:382. [PMID: 32256468 PMCID: PMC7090098 DOI: 10.3389/fmicb.2020.00382] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
Plastics, in all forms, are a ubiquitous cornerstone of modern civilization. Although humanity undoubtedly benefits from the versatility and durability of plastics, they also cause a tremendous burden for the environment. Bio-upcycling is a promising approach to reduce this burden, especially for polymers that are currently not amenable to mechanical recycling. Wildtype P. putida KT2440 is able to grow on 1,4-butanediol as sole carbon source, but only very slowly. Adaptive laboratory evolution (ALE) led to the isolation of several strains with significantly enhanced growth rate and yield. Genome re-sequencing and proteomic analysis were applied to characterize the genomic and metabolic basis of efficient 1,4-butanediol metabolism. Initially, 1,4-butanediol is oxidized to 4-hydroxybutyrate, in which the highly expressed dehydrogenase enzymes encoded within the PP_2674-2680 ped gene cluster play an essential role. The resulting 4-hydroxybutyrate can be metabolized through three possible pathways: (i) oxidation to succinate, (ii) CoA activation and subsequent oxidation to succinyl-CoA, and (iii) beta oxidation to glycolyl-CoA and acetyl-CoA. The evolved strains were both mutated in a transcriptional regulator (PP_2046) of an operon encoding both beta-oxidation related genes and an alcohol dehydrogenase. When either the regulator or the alcohol dehydrogenase is deleted, no 1,4-butanediol uptake or growth could be detected. Using a reverse engineering approach, PP_2046 was replaced by a synthetic promotor (14g) to overexpress the downstream operon (PP_2047-2051), thereby enhancing growth on 1,4-butanediol. This work provides a deeper understanding of microbial 1,4-butanediol metabolism in P. putida, which is also expandable to other aliphatic alpha-omega diols. It enables the more efficient metabolism of these diols, thereby enabling biotechnological valorization of plastic monomers in a bio-upcycling approach.
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Affiliation(s)
- Wing-Jin Li
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Tanja Narancic
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- BEACON – SFI Bioeconomy Research Centre, University College Dublin, Dublin, Ireland
| | - Shane T. Kenny
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Paul-Joachim Niehoff
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Kevin O’Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- BEACON – SFI Bioeconomy Research Centre, University College Dublin, Dublin, Ireland
| | - Lars M. Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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799
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Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Wikidata as a knowledge graph for the life sciences. eLife 2020; 9:e52614. [PMID: 32180547 PMCID: PMC7077981 DOI: 10.7554/elife.52614] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/28/2020] [Indexed: 12/22/2022] Open
Abstract
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
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Affiliation(s)
| | - Gregory Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sebastian Burgstaller-Muehlbacher
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of ViennaViennaAustria
| | - Benjamin M Good
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | | | - Toby S Hudson
- School of Chemistry, The University of SydneySydneyAustralia
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of WashingtonSeattleUnited States
| | - Sarah M Keating
- European Bioinformatics Institute (EMBL-EBI)HinxtonUnited Kingdom
| | - Magnus Manske
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Michael Mayers
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Daniel Mietchen
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Elvira Mitraka
- University of Maryland School of MedicineBaltimoreUnited States
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Timothy Putman
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Anders Riutta
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Nuria Queralt-Rosinach
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Lynn M Schriml
- University of Maryland School of MedicineBaltimoreUnited States
| | - Thomas Shafee
- Department of Animal Plant and Soil Sciences, La Trobe UniversityMelbourneAustralia
| | - Denise Slenter
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | | | | | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Roger Tu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sabah Ul-Hasan
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
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800
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Xu XW, Shao CW, Xu H, Zhou Q, You F, Wang N, Li WL, Li M, Chen SL. Draft genomes of female and male turbot Scophthalmus maximus. Sci Data 2020; 7:90. [PMID: 32165614 PMCID: PMC7067757 DOI: 10.1038/s41597-020-0426-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 02/20/2020] [Indexed: 01/14/2023] Open
Abstract
Turbot (Scophthalmus maximus) is a commercially important flatfish species in aquaculture. It has a drastic sexual dimorphism, with females growing faster than males. In the present study, we sequenced and de novo assembled female and male turbot genomes. The assembled female genome was 568 Mb (scaffold N50, 6.2 Mb, BUSCO 97.4%), and the male genome was 584 Mb (scaffold N50, 5.9 Mb, BUSCO 96.6%). Using two genetic maps, we anchored female scaffolds representing 535 Mb onto 22 chromosomes. Annotation of the female anchored genome identified 87.8 Mb transposon elements and 20,134 genes. We identified 17,936 gene families, of which 369 gene families were flatfish specific. Phylogenetic analysis showed that the turbot, Japanese flounder and Chinese tongue sole form a clade that diverged from other teleosts approximately 78 Mya. This report of female and male turbot draft genomes and annotated genes provides a new resource for identifying sex determination genes, elucidating the evolution of adaptive traits in flatfish and developing genetic techniques to increase the sustainability of turbot aquaculture.
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Affiliation(s)
- Xi-Wen Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Chang-Wei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Hao Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Feng You
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Na Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Wen-Long Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Ming Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Song-Lin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.
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