1
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Wen J, Zhang H, Chu D, Chen X, Feng J, Wang Y, Liu G, Zhang Y, Li Y, Ning K. Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages. Nucleic Acids Res 2024:gkae966. [PMID: 39460615 DOI: 10.1093/nar/gkae966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/26/2024] [Accepted: 10/12/2024] [Indexed: 10/28/2024] Open
Abstract
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.
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Affiliation(s)
- Jiejie Wen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Haobo Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongliang Chu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaoke Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jingru Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yucen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Guanxi Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yuhao Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yuxue Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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2
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Chanin RB, West PT, Wirbel J, Gill MO, Green GZM, Park RM, Enright N, Miklos AM, Hickey AS, Brooks EF, Lum KK, Cristea IM, Bhatt AS. Intragenic DNA inversions expand bacterial coding capacity. Nature 2024; 634:234-242. [PMID: 39322669 DOI: 10.1038/s41586-024-07970-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 08/20/2024] [Indexed: 09/27/2024]
Abstract
Bacterial populations that originate from a single bacterium are not strictly clonal and often contain subgroups with distinct phenotypes1. Bacteria can generate heterogeneity through phase variation-a preprogrammed, reversible mechanism that alters gene expression levels across a population1. One well-studied type of phase variation involves enzyme-mediated inversion of specific regions of genomic DNA2. Frequently, these DNA inversions flip the orientation of promoters, turning transcription of adjacent coding regions on or off2. Through this mechanism, inversion can affect fitness, survival or group dynamics3,4. Here, we describe the development of PhaVa, a computational tool that identifies DNA inversions using long-read datasets. We also identify 372 'intragenic invertons', a novel class of DNA inversions found entirely within genes, in genomes of bacterial and archaeal isolates. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We validate ten intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, and experimentally characterize an intragenic inverton in the thiamine biosynthesis gene thiC.
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Affiliation(s)
- Rachael B Chanin
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Patrick T West
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Jakob Wirbel
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Matthew O Gill
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gabriella Z M Green
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Ryan M Park
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Nora Enright
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Arjun M Miklos
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Angela S Hickey
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Erin F Brooks
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Krystal K Lum
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ami S Bhatt
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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3
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Arif B, Yasir S, Saeed M, Fatmi MQ. Natural products can be potential inhibitors of metalloproteinase II from Bacteroides fragilis to intervene colorectal cancer. Heliyon 2024; 10:e32838. [PMID: 39005891 PMCID: PMC11239599 DOI: 10.1016/j.heliyon.2024.e32838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Bacteroides fragilis, a gram negative and obligate anaerobe bacterium, is a member of normal gut microbiota and facilitates many essential roles being performed in human body in normal circumstances specifically in Gastrointestinal or GI tract. Sometimes, due to genetics, epigenetics, and environmental factors, Bacteroides fragilis and their protein(s) start interacting with intestinal epithelium thus damaging the lining leading to colorectal cancers (CRC). To identify these protein(s), we incorporated a novel subtractive proteomics approach in the study. Metalloproteinase II (MPII), a Bacteroides fragilis toxin (bft), was investigated for its virulence and unique pathways to demonstrate its specificity and uniqueness in pathogenicity followed by molecular docking against a set of small drug-like natural molecules to discover potential inhibitors against the toxin. All these identified inhibitor-like molecules were analyzed for their ADMET calculations and detailed physiochemical properties to predict their druggability, GI absorption, blood brain barrier and skin permeation, and others. Resultantly, a total of ten compounds with the least binding energies were obtained and were subjected to protein-compound interaction analysis. Interaction analysis revealed the most common ligand-interacting residues in MPII are His 345, Glu 346, His 339, Gly 310, Tyr 341, Pro 340, Asp 187, Phe 309, Lys 307, Ile 185, Thr 308, and Pro 184. Therefore, top three compounds complexed with MPII having best binding energies were selected in order to analyze their trajectories. RMSD, RMSF, Rg and MMPBSA analysis revealed that all compounds showed good binding and keeping the complex stable and compact throughout the simulation time in addition to all properties and qualities of being a potential inhibitor against MPII.
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Affiliation(s)
- Bushra Arif
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - Saba Yasir
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Muhammad Saeed
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - M. Qaiser Fatmi
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
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4
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy M, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Murat Eren A, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540287. [PMID: 37214927 PMCID: PMC10197588 DOI: 10.1101/2023.05.11.540287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Miette Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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6
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Chanin RB, West PT, Park RM, Wirbel J, Green GZM, Miklos AM, Gill MO, Hickey AS, Brooks EF, Bhatt AS. Intragenic DNA inversions expand bacterial coding capacity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532203. [PMID: 36945655 PMCID: PMC10028968 DOI: 10.1101/2023.03.11.532203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Bacterial populations that originate from a single bacterium are not strictly clonal. Often, they contain subgroups with distinct phenotypes. Bacteria can generate heterogeneity through phase variation: a preprogrammed, reversible mechanism that alters gene expression levels across a population. One well studied type of phase variation involves enzyme-mediated inversion of specific intergenic regions of genomic DNA. Frequently, these DNA inversions flip the orientation of promoters, turning ON or OFF adjacent coding regions within otherwise isogenic populations. Through this mechanism, inversion can affect fitness, survival, or group dynamics. Here, we develop and apply bioinformatic approaches to discover thousands of previously undescribed phase-variable regions in prokaryotes using long-read datasets. We identify 'intragenic invertons', a surprising new class of invertible elements found entirely within genes, in bacteria and archaea. To date, inversions within single genes have not been described. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We experimentally characterize specific intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, presenting a 'roadmap' for investigating this new gene-diversifying phenomenon.
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Affiliation(s)
- Rachael B. Chanin
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Patrick T. West
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Ryan M. Park
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Jakob Wirbel
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Gabriella Z. M. Green
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Arjun M. Miklos
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | | | | | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Ami S. Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
- Department of Genetics, Stanford University; Stanford, USA
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7
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Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A 2021; 118:e2007595118. [PMID: 33972416 PMCID: PMC8157926 DOI: 10.1073/pnas.2007595118] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Active inflammatory bowel disease (IBD) often coincides with increases of Ruminococcus gnavus, a gut microbe found in nearly everyone. It was not known how, or if, this correlation contributed to disease. We investigated clinical isolates of R. gnavus to identify molecular mechanisms that would link R. gnavus to inflammation. Here, we show that only some isolates of R. gnavus produce a capsular polysaccharide that promotes a tolerogenic immune response, whereas isolates lacking functional capsule biosynthetic genes elicit robust proinflammatory responses in vitro. Germ-free mice colonized with an isolate of R. gnavus lacking a capsule show increased measures of gut inflammation compared to those colonized with an encapsulated isolate in vivo. These observations in the context of our earlier identification of an inflammatory cell-wall polysaccharide reveal how some strains of R. gnavus could drive the inflammatory responses that characterize IBD.
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Affiliation(s)
- Matthew T Henke
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Eric M Brown
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chelsi D Cassilly
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Hera Vlamakis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114
| | - Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
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8
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Ben-Assa N, Coyne MJ, Fomenkov A, Livny J, Robins WP, Muniesa M, Carey V, Carasso S, Gefen T, Jofre J, Roberts RJ, Comstock LE, Geva-Zatorsky N. Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis. Nucleic Acids Res 2020; 48:11040-11053. [PMID: 33045731 PMCID: PMC7641763 DOI: 10.1093/nar/gkaa824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/10/2020] [Accepted: 10/06/2020] [Indexed: 11/28/2022] Open
Abstract
The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.
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Affiliation(s)
- Nadav Ben-Assa
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel
| | - Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William P Robins
- Department of Microbiology, Harvard Medical School, Boston, 02115, MA, USA
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Avda. Diagonal 643 08028 Barcelona Spain
| | - Vincent Carey
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shaqed Carasso
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel
| | - Tal Gefen
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Avda. Diagonal 643 08028 Barcelona Spain
| | | | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, 3525422 Israel.,Canadian Institute for Advanced Research (CIFAR) Azrieli Global Scholar, MaRS Centre, West Tower 661 University Ave., Suite 505 Toronto, ON M5G 1M1, Canada
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9
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Trzilova D, Tamayo R. Site-Specific Recombination - How Simple DNA Inversions Produce Complex Phenotypic Heterogeneity in Bacterial Populations. Trends Genet 2020; 37:59-72. [PMID: 33008627 DOI: 10.1016/j.tig.2020.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
Many bacterial species generate phenotypically heterogeneous subpopulations as a strategy for ensuring the survival of the population as a whole - an environmental stress that eradicates one subpopulation may leave other phenotypic groups unharmed, allowing the lineage to continue. Phase variation, a process that functions as an ON/OFF switch for gene expression, is one way that bacteria achieve phenotypic heterogeneity. Phase variation occurs stochastically and reversibly, and in the presence of a selective pressure the advantageous phenotype(s) predominates in the population. Phase variation can occur through multiple genetic and epigenetic mechanisms. This review focuses on conservative site-specific recombination that generates reversible DNA inversions as a genetic mechanism mediating phase variation. Recent studies have sparked a renewed interest in phase variation mediated through DNA inversion, revealing a high level of complexity beyond simple ON/OFF switching, including unusual modes of gene regulation, and highlighting an underappreciation of the use of these mechanisms by bacteria.
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Affiliation(s)
- Dominika Trzilova
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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10
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Yekani M, Baghi HB, Naghili B, Vahed SZ, Sóki J, Memar MY. To resist and persist: Important factors in the pathogenesis of Bacteroides fragilis. Microb Pathog 2020; 149:104506. [PMID: 32950639 DOI: 10.1016/j.micpath.2020.104506] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/15/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Bacteroides fragilis is a most frequent anaerobic pathogen isolated from human infections, particularly found in the abdominal cavity. Different factors contribute to the pathogenesis and persistence of B. fragilis at infection sites. The knowledge of the virulence factors can provide applicable information for finding alternative options for the antibiotic therapy and treatment of B. fragilis caused infections. Herein, a comprehensive review of the important B. fragilis virulence factors was prepared. In addition to B. fragilis toxin (BFT) and its potential role in the diarrhea and cancer development, some other important virulence factors and characteristics of B. fragilis are described including capsular polysaccharides, iron acquisition, resistance to antimicrobial agents, and survival during the prolonged oxidative stress, quorum sensing, and secretion systems.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee,Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - József Sóki
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Microbiology Department, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
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11
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Xiong Z, Hussain A, Lee J, Lee HS. Food waste fermentation in a leach bed reactor: Reactor performance, and microbial ecology and dynamics. BIORESOURCE TECHNOLOGY 2019; 274:153-161. [PMID: 30502606 DOI: 10.1016/j.biortech.2018.11.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Food waste fermentation was investigated in a leach bed reactor operated at acidic, neutral and alkaline conditions. Highest solids reduction of 87% was obtained at pH 7 in 14 days of reaction time with minimum mixing. The concentration of volatile fatty acids increased to 28.6 g COD/L under pH 7, while the highest butyric acid of 16 g COD/L was obtained at pH 6. Bacterial community structure was narrowed down to Bifidobacterium and Clostridium at pH 6, while Bacteroides and Dysgonomonas were identified as main players at both pH 7 and 8. Bacterial populations in the food residue generally reflected those in the leachate, but some bacteria were selectively enriched in the leachate or the food residue. Bacterial community dynamics suggested that biodegradable food waste was first fermented by one of dominant players (e.g., Clostridium) and the other degraded resistant dietary fibers later (e.g., Bifidobacterium, Bacteroides, Dysgonomonas).
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Affiliation(s)
- Ziyi Xiong
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Ontario N2L3G1, Canada
| | - Abid Hussain
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Ontario N2L3G1, Canada; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Jangho Lee
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Ontario N2L3G1, Canada
| | - Hyung-Sool Lee
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Ontario N2L3G1, Canada.
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12
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Nakayama-Imaohji H, Hirota K, Yamasaki H, Yoneda S, Nariya H, Suzuki M, Secher T, Miyake Y, Oswald E, Hayashi T, Kuwahara T. DNA Inversion Regulates Outer Membrane Vesicle Production in Bacteroides fragilis. PLoS One 2016; 11:e0148887. [PMID: 26859882 PMCID: PMC4747536 DOI: 10.1371/journal.pone.0148887] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 02/06/2023] Open
Abstract
Phase changes in Bacteroides fragilis, a member of the human colonic microbiota, mediate variations in a vast array of cell surface molecules, such as capsular polysaccharides and outer membrane proteins through DNA inversion. The results of the present study show that outer membrane vesicle (OMV) formation in this anaerobe is also controlled by DNA inversions at two distantly localized promoters, IVp-I and IVp-II that are associated with extracellular polysaccharide biosynthesis and the expression of outer membrane proteins. These promoter inversions are mediated by a single tyrosine recombinase encoded by BF2766 (orthologous to tsr19 in strain NCTC9343) in B. fragilis YCH46, which is located near IVp-I. A series of BF2766 mutants were constructed in which the two promoters were locked in different configurations (IVp-I/IVp-II = ON/ON, OFF/OFF, ON/OFF or OFF/ON). ON/ON B. fragilis mutants exhibited hypervesiculating, whereas the other mutants formed only a trace amount of OMVs. The hypervesiculating ON/ON mutants showed higher resistance to treatment with bile, LL-37, and human β-defensin 2. Incubation of wild-type cells with 5% bile increased the population of cells with the ON/ON genotype. These results indicate that B. fragilis regulates the formation of OMVs through DNA inversions at two distantly related promoter regions in response to membrane stress, although the mechanism underlying the interplay between the two regions controlled by the invertible promoters remains unknown.
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Affiliation(s)
- Haruyuki Nakayama-Imaohji
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Katsuhiko Hirota
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770–8503, Japan
| | - Hisashi Yamasaki
- Department of Cellular and Molecular Medicine, Wakayama Medical University Graduate School of Medicine, Wakayama 641–8509, Japan
| | - Saori Yoneda
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Hirofumi Nariya
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Motoo Suzuki
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
| | - Thomas Secher
- Inserm UMR1043 Toulouse, France
- INRA USC 1360 Toulouse, France
- CNRS UMR5282 Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
| | - Yoichiro Miyake
- Department of Oral Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770–8503, Japan
| | - Eric Oswald
- Inserm UMR1043 Toulouse, France
- INRA USC 1360 Toulouse, France
- CNRS UMR5282 Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de bactériologie-hygiène, Toulouse, France
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812–8582, Japan
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, 1750–1 Miki, Kagawa 761–0793, Japan
- * E-mail:
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13
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The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
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14
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Genome sequence of Vibrio diabolicus and identification of the exopolysaccharide HE800 biosynthesis locus. Appl Microbiol Biotechnol 2014; 98:10165-76. [PMID: 25273176 DOI: 10.1007/s00253-014-6086-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 09/01/2014] [Accepted: 09/03/2014] [Indexed: 01/08/2023]
Abstract
Vibrio diabolicus, a marine bacterium originating from deep-sea hydrothermal vents, produces the HE800 exopolysaccharide with high value for biotechnological purposes, especially for human health. Its genome was sequenced and analyzed; phylogenetic analysis using the core genome revealed V. diabolicus is close to another deep-sea Vibrio sp. (Ex25) within the Harveyi clade and Alginolyticus group. A genetic locus homologous to the syp cluster from Vibrio fischeri was demonstrated to be involved in the HE800 production. However, few genetic particularities suggest that the regulation of syp expression may be different in V. diabolicus. The presence of several types of glycosyltransferases within the locus indicates a capacity to generate diversity in the glycosidic structure, which may confer an adaptability to environmental conditions. These results contribute to better understanding exopolysaccharide biosynthesis and for developing new efficient processes to produce this molecule for biotechnological applications.
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15
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Fanning S, Hall LJ, van Sinderen D. Bifidobacterium breve UCC2003 surface exopolysaccharide production is a beneficial trait mediating commensal-host interaction through immune modulation and pathogen protection. Gut Microbes 2013; 3:420-5. [PMID: 22713271 DOI: 10.4161/gmic.20630] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bifidobacteria constitute a substantial proportion of the human gut microbiota. There are currently many bifidobacterial strains with claimed probiotic attributes. The mechanism through which these strains reside within their host and exert benefits to the host is far from fully understood. We have shown in the case of Bifidobacterium breve UCC2003 that a cell surface exopolysaccharide (EPS) plays a role in in vivo persistence. Biosynthesis of two possible EPSs is controlled by a bidirectional gene cluster which guides alternate EPS synthesis by means of a reorienting promoter. The presence of EPS impacts on host immune response: the wild type, EPS-positive B. breve UCC2003 efficiently evades the adaptive B-cell host response, while its isogenic, EPS-deficient equivalent elicits a strong adaptive immune response. Functionally, EPS positive strains were more resilient to presence of acid and bile and were responsible for reduced colonization levels of Citrobacter rodentium, a gut pathogen. In conclusion, we have found that EPS is important in host interactions and pathogen protection, the latter indicative of a probiotic ability for the EPS of B. breve UCC2003.
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Affiliation(s)
- Saranna Fanning
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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16
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UDP-glucuronic acid decarboxylases of Bacteroides fragilis and their prevalence in bacteria. J Bacteriol 2011; 193:5252-9. [PMID: 21804000 DOI: 10.1128/jb.05337-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylose is rarely described as a component of bacterial glycans. UDP-xylose is the nucleotide-activated form necessary for incorporation of xylose into glycans and is synthesized by the decarboxylation of UDP-glucuronic acid (UDP-GlcA). Enzymes with UDP-GlcA decarboxylase activity include those that lead to the formation of UDP-xylose as the end product (Uxs type) and those synthesizing UDP-xylose as an intermediate (ArnA and RsU4kpxs types). In this report, we identify and confirm the activities of two Uxs-type UDP-GlcA decarboxylases of Bacteroides fragilis, designated BfUxs1 and BfUxs2. Bfuxs1 is located in a conserved region of the B. fragilis genome, whereas Bfuxs2 is in the heterogeneous capsular polysaccharide F (PSF) biosynthesis locus. Deletion of either gene separately does not result in the loss of a detectable phenotype, but deletion of both genes abrogates PSF synthesis, strongly suggesting that they are functional paralogs and that the B. fragilis NCTC 9343 PSF repeat unit contains xylose. UDP-GlcA decarboxylases are often annotated incorrectly as NAD-dependent epimerases/dehydratases; therefore, their prevalence in bacteria is underappreciated. Using available structural and mutational data, we devised a sequence pattern to detect bacterial genes encoding UDP-GlcA decarboxylase activity. We identified 826 predicted UDP-GlcA decarboxylase enzymes in diverse bacterial species, with the ArnA and RsU4kpxs types confined largely to proteobacterial species. These data suggest that xylose, or a monosaccharide requiring a UDP-xylose intermediate, is more prevalent in bacterial glycans than previously appreciated. Genes encoding BfUxs1-like enzymes are highly conserved in Bacteroides species, indicating that these abundant intestinal microbes may synthesize a conserved xylose-containing glycan.
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17
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Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J. Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis. MICROBIOLOGY (READING, ENGLAND) 2010; 156:3255-3269. [PMID: 20829291 PMCID: PMC3090145 DOI: 10.1099/mic.0.042978-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Comparison of the complete genome sequence of Bacteroides fragilis 638R, originally isolated in the USA, was made with two previously sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The presence of 10 loci containing genes associated with polysaccharide (PS) biosynthesis, each including a putative Wzx flippase and Wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between NCTC 9343 and 638R surface PS-specific antibodies by immunolabelling and microscopy. Genomic comparisons revealed an exceptional level of PS biosynthesis locus diversity. Of the 10 divergent PS-associated loci apparent in each strain, none is similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC 9343, confirmed by mAb labelling, and a second different locus with 638R, making a total of 28 divergent PS biosynthesis loci amongst the three strains. The lack of expression of the phase-variable large capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due to a point mutation that generates a stop codon within a putative initiating glycosyltransferase, necessary for the expression of the LC in NCTC 9343. Other major sequence differences were observed to arise from different numbers and variety of inserted extra-chromosomal elements, in particular prophages. Extensive horizontal gene transfer has occurred within these strains, despite the presence of a significant number of divergent DNA restriction and modification systems that act to prevent acquisition of foreign DNA. The level of amongst-strain diversity in PS biosynthesis loci is unprecedented.
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Affiliation(s)
- Sheila Patrick
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Garry W Blakely
- Institute of Cell Biology, University of Edinburgh, Darwin Building, Kings Buildings, Edinburgh EH9 3JR, UK
| | - Simon Houston
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Jane Moore
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Valerie R Abratt
- Department of Molecular and Cell Biology, University of Cape Town, South Africa
| | - Marcelo Bertalan
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ana M Cerdeño-Tárraga
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Michael A Quail
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Nicola Corton
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Craig Corton
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Alexandra Bignell
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew Barron
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Louise Clark
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen D Bentley
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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18
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Abstract
This study describes refined electroporation parameters for efficient transformation of Bacteroides fragilis by plasmids prepared from laboratory strains of Escherichia coli. Development of the method used included determination of the optimal growth conditions for competent cell preparation, selectable antimicrobial resistance markers, electric field strength, and postpulse incubation time. Of the four E. coli-Bacteroides shuttle plasmids tested (pVAL-1, pVAL-2, pNLY1, and pLYL05), pLYL05 containing the cefoxitin resistance marker was found to be the most suitable for B. fragilis transformation, and it generated 2- to 900-fold more transformants (about 10(4) transformants per microg pLYL05 DNA) than the other plasmids. For the 72-h cultivation period tested, B. fragilis cells harvested at 48 h yielded the highest numbers of transformants. The transformation efficiency of pLYL05 increased linearly with the electric field strength over a range from 5.0 to 12.5 kV/cm. At least 3 h of postpulse incubation was required to maximize the transformation efficiency. For deletion of B. fragilis genes by homologous recombination, competent cells grown to early exponential phase and 12 h of postpulse incubation were required for efficient integration of the pLYL05-based suicide vector into the target site. The expected integration was obtained in B. fragilis strain NCTC9343 only when a homologously prepared (i.e., in vivo methylated) suicide vector was used. Spontaneous resolution of the diploid successfully deleted the expected genetic region. Our simple and efficient plasmid transfer method enabled disruption of a B. fragilis gene using in vivo-methylated targeted vectors. Our optimized electroporation parameters provide a useful tool for genetic manipulation of Bacteroides species.
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19
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Identification of the site-specific DNA invertase responsible for the phase variation of SusC/SusD family outer membrane proteins in Bacteroides fragilis. J Bacteriol 2009; 191:6003-11. [PMID: 19648246 DOI: 10.1128/jb.00687-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human gut microbe Bacteroides fragilis can alter the expression of its surface molecules, such as capsular polysaccharides and SusC/SusD family outer membrane proteins, through reversible DNA inversions. We demonstrate here that DNA inversions at 12 invertible regions, including three gene clusters for SusC/SusD family proteins, were controlled by a single tyrosine site-specific recombinase (Tsr0667) encoded by BF0667 in B. fragilis strain YCH46. Genetic disruption of BF0667 diminished or attenuated shufflon-type DNA inversions at all three susC/susD genes clusters, as well as simple DNA inversions at nine other loci, most of which colocalized with susC/susD family genes. The inverted repeat sequences found within the Tsr0667-regulated invertible regions shared the consensus motif sequence AGTYYYN(4)GDACT. Tsr0667 specifically mediated the DNA inversions of 10 of the 12 regions, even under an Escherichia coli background when the invertible regions were exposed to BF0667 in E. coli cells. Thus, Tsr0667 is an additional globally acting DNA invertase in B. fragilis, which probably involves the selective expression of SusC/SusD family outer membrane proteins.
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20
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Comstock LE. Importance of glycans to the host-bacteroides mutualism in the mammalian intestine. Cell Host Microbe 2009; 5:522-6. [PMID: 19527880 DOI: 10.1016/j.chom.2009.05.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Much of the mutualistic relationship between humans and their resident intestinal Bacteroides species is founded on glycans. The host provides plant polysaccharides and host-derived glycans and, in return, receives beneficial end products of bacterial fermentation. Glycans from the bacteria themselves are required for the establishment and survival of these organisms in the colonic ecosystem and provide immunomodulatory properties to the host. Coordinated synthesis and catabolism of bacterial glycans is likely to contribute to the host-bacterial mutualism.
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Affiliation(s)
- Laurie E Comstock
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
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21
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Patrick S, Houston S, Thacker Z, Blakely GW. Mutational analysis of genes implicated in LPS and capsular polysaccharide biosynthesis in the opportunistic pathogen Bacteroides fragilis. MICROBIOLOGY-SGM 2009; 155:1039-1049. [PMID: 19332806 DOI: 10.1099/mic.0.025361-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The obligate anaerobe Bacteroides fragilis is a normal resident of the human gastrointestinal tract. The clinically derived B. fragilis strain NCTC 9343 produces an extensive array of extracellular polysaccharides (EPS), including antigenically distinct large, small and micro- capsules. The genome of NCTC 9343 encodes multiple gene clusters potentially involved in the biosynthesis of EPS, eight of which are implicated in production of the antigenically variable micro-capsule. We have developed a rapid and robust method for generating marked and markerless deletions, together with efficient electroporation using unmodified plasmid DNA to enable complementation of mutations. We show that deletion of a putative wzz homologue prevents production of high-molecular-mass polysaccharides (HMMPS), which form the micro-capsule. This observation suggests that micro-capsule HMMPS constitute the distal component of LPS in B. fragilis. The long chain length of this polysaccharide is strikingly different from classical enteric O-antigen, which consists of short-chain polysaccharides. We also demonstrate that deletion of a putative wbaP homologue prevents expression of the phase-variable large capsule and that expression can be restored by complementation. This suggests that synthesis of the large capsule is mechanistically equivalent to production of Escherichia coli group 1 and 4 capsules.
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Affiliation(s)
- Sheila Patrick
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Simon Houston
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Zubin Thacker
- Institute of Cell Biology, University of Edinburgh, Darwin Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Garry W Blakely
- Institute of Cell Biology, University of Edinburgh, Darwin Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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22
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Mastropaolo MD, Thorson ML, Stevens AM. Comparison of Bacteroides thetaiotaomicron and Escherichia coli 16S rRNA gene expression signals. MICROBIOLOGY-SGM 2009; 155:2683-2693. [PMID: 19443545 DOI: 10.1099/mic.0.027748-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There are barriers to cross-expression of genes between Bacteroides spp. and Escherichia coli. In this study, a lux-based reporter system was developed for Bacteroides and used to compare the promoter structure and function of a Bacteroides thetaiotaomicron 4001 (BT4001) 16S rRNA promoter with those of E. coli in vivo. Analysis of the BT4001 sequences upstream of the 16S rRNA gene revealed the same overall structure known for E. coli 16S rRNA promoters in that there were two promoters separated by approximately 150 bp. However, the BT4001 16S rRNA promoter contains the proposed Bacteroides -7 and -33 consensus sequences instead of the E. coli -10 and -35 consensus sequences. The biological activity of various configurations of the BT4001 16S rRNA promoter was analysed. Experiments pairing the BT4001 16S rRNA promoter with an E. coli RBS, and vice-versa, confirmed that gene expression between the two species is restricted at the level of transcription. In Bacteroides, a difference in translation initiation also appears to limit expression of foreign genes.
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MESH Headings
- Bacteroides/genetics
- Bacteroides/metabolism
- Base Sequence
- Consensus Sequence
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genes, Reporter
- Genes, rRNA
- Luminescent Measurements/methods
- Molecular Sequence Data
- Photorhabdus/genetics
- Promoter Regions, Genetic
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Matthew D Mastropaolo
- Department of Biological Sciences, Virginia Tech, 219 Life Sciences 1, Washington Street, Blacksburg, VA 24061-0910, USA
| | - Mary L Thorson
- Department of Biological Sciences, Virginia Tech, 219 Life Sciences 1, Washington Street, Blacksburg, VA 24061-0910, USA
| | - Ann M Stevens
- Department of Biological Sciences, Virginia Tech, 219 Life Sciences 1, Washington Street, Blacksburg, VA 24061-0910, USA
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Pivotal roles of the outer membrane polysaccharide export and polysaccharide copolymerase protein families in export of extracellular polysaccharides in gram-negative bacteria. Microbiol Mol Biol Rev 2009; 73:155-77. [PMID: 19258536 PMCID: PMC2650888 DOI: 10.1128/mmbr.00024-08] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Many bacteria export extracellular polysaccharides (EPS) and capsular polysaccharides (CPS). These polymers exhibit remarkably diverse structures and play important roles in the biology of free-living, commensal, and pathogenic bacteria. EPS and CPS production represents a major challenge because these high-molecular-weight hydrophilic polymers must be assembled and exported in a process spanning the envelope, without compromising the essential barrier properties of the envelope. Emerging evidence points to the existence of molecular scaffolds that perform these critical polymer-trafficking functions. Two major pathways with different polymer biosynthesis strategies are involved in the assembly of most EPS/CPS: the Wzy-dependent and ATP-binding cassette (ABC) transporter-dependent pathways. They converge in an outer membrane export step mediated by a member of the outer membrane auxiliary (OMA) protein family. OMA proteins form outer membrane efflux channels for the polymers, and here we propose the revised name outer membrane polysaccharide export (OPX) proteins. Proteins in the polysaccharide copolymerase (PCP) family have been implicated in several aspects of polymer biogenesis, but there is unequivocal evidence for some systems that PCP and OPX proteins interact to form a trans-envelope scaffold for polymer export. Understanding of the precise functions of the OPX and PCP proteins has been advanced by recent findings from biochemistry and structural biology approaches and by parallel studies of other macromolecular trafficking events. Phylogenetic analyses reported here also contribute important new insight into the distribution, structural relationships, and function of the OPX and PCP proteins. This review is intended as an update on progress in this important area of microbial cell biology.
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24
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Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. Proc Natl Acad Sci U S A 2008; 105:13099-104. [PMID: 18723678 DOI: 10.1073/pnas.0804220105] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Bacteroides species are the most abundant Gram-negative bacteria of the human colonic microbiota. These endogenous organisms are unique in that they synthesize an extensive number of phase-variable surface polysaccharides. Pathogenic bacteria phase vary expression of surface molecules for immune evasion, but the importance of the synthesis of multiple phase-variable polysaccharides to these commensal bacteria is unknown. We previously showed that a Bacteroides fragilis mutant unable to synthesize 4 of the 8 capsular polysaccharides and unable to glycosylate proteins properly is rapidly outcompeted by the wild-type strain for colonization of the gnotobiotic mouse intestine. In the present study, we constructed mutants defective only in capsule polysaccharide synthesis to define better the importance of these surface molecules to intestinal colonization. We discovered a key enzymatic activity required for synthesis of 7 of the 8 capsular polysaccharides. Deletion of its gene resulted in the first B. fragilis mutant able to synthesize only one phase-variable polysaccharide, and further mutation resulted in a stable acapsular mutant. We show that the acapsular mutant is rapidly outcompeted, but synthesis of a single polysaccharide is sufficient for the organism to colonize the gnotobiotic intestine competitively. These data demonstrate that initial colonization of the gnotobiotic mouse intestine by B. fragilis requires that the organism synthesize only a single polysaccharide and suggest that the synthesis of multiple phase-variable polysaccharides is important for the bacteria's long-term maintenance in the normally complex and competitive ecosystem.
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