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Tomatsidou A, Krunic M, Missiakas D. Contribution of TagA-Like Glycosyltransferases to the Assembly of the Secondary Cell Wall Polysaccharide in Bacillus anthracis. J Bacteriol 2022; 204:e0025322. [PMID: 35997505 PMCID: PMC9487633 DOI: 10.1128/jb.00253-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis elaborates a secondary cell wall polysaccharide (SCWP) made of 6 to 12 trisaccharide units. Pyruvyl and acetyl substitutions of the distal unit are prerequisites for the noncovalent retention of 22 secreted Bacillus S-layer (Bsl)-associated proteins bearing an S-layer homology (SLH) domain. Surface display of Bsl proteins contributes to cell separation as well as virulence. Earlier work suggested that TagO initiates the synthesis of SCWP while GneY and GneZ, two UDP-GlcNAc 2-epimerases, synthesize ManNAc that is later incorporated in the repeat unit (→4)-ManNAc-(β1→4)-GlcNAc-(β1→6)-GlcNAc-(α1→). In organisms that synthesize wall teichoic acid, TagA catalysts have been shown to form the glycosidic bond ManNAc-(β1→4)-GlcNAc. Here, we show that genes bas2675 and bas5272, predicted to encode glycosyltransferases of the WecB/TagA/CpsF family (PFAM03808; CAZy GT26), are required for B. anthracis SCWP synthesis and S-layer assembly. Similar to tagO or gneY gneZ mutants, B. anthracis strains depleted of tagA1 (bas5272) cannot maintain cell shape, support vegetative growth, or synthesize SCWP. Expression of tagA2 (bas2675), or Staphylococcus aureus tagA on a plasmid, rescues the nonviable tagA1 mutant. We propose that TagA1 and TagA2 fulfill overlapping and key glycosyltransferase functions for the synthesis of repeat units of the SCWP of B. anthracis. IMPORTANCE Glycosyltransferases (GTs) catalyze the transfer of sugar moieties from activated donor molecules to acceptor molecules to form glycosidic bonds using a retaining or inverting mechanism. Based on the structural relatedness of their catalytic and carbohydrate-binding modules, GTs have been grouped into 115 families in the Carbohydrate-Active EnZyme (CAZy) database. For complex products, the functional assignment of GTs remains highly challenging without the knowledge of the chemical structure of the assembled polymer. Here, we propose that two uncharacterized GTs of B. anthracis belonging to the WecB/TagA/CpsF family incorporate ManNAc in repeat units of the secondary cell wall polymer of bacilli species.
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Affiliation(s)
- Anastasia Tomatsidou
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
| | - Maria Krunic
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
| | - Dominique Missiakas
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
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2
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Chateau A, Van der Verren SE, Remaut H, Fioravanti A. The Bacillus anthracis Cell Envelope: Composition, Physiological Role, and Clinical Relevance. Microorganisms 2020; 8:E1864. [PMID: 33255913 PMCID: PMC7759979 DOI: 10.3390/microorganisms8121864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/31/2022] Open
Abstract
Anthrax is a highly resilient and deadly disease caused by the spore-forming bacterial pathogen Bacillus anthracis. The bacterium presents a complex and dynamic composition of its cell envelope, which changes in response to developmental and environmental conditions and host-dependent signals. Because of their easy to access extracellular locations, B. anthracis cell envelope components represent interesting targets for the identification and development of novel therapeutic and vaccine strategies. This review will focus on the novel insights regarding the composition, physiological role, and clinical relevance of B. anthracis cell envelope components.
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Affiliation(s)
- Alice Chateau
- Avignon Université, INRAE, UMR SQPOV, F-84914 Avignon, France;
| | - Sander E. Van der Verren
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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Liu Y, Li L, Yu F, Luo Y, Liang W, Yang Q, Wang R, Li M, Tang J, Gu Q, Luo Z, Chen M. Genome-wide analysis revealed the virulence attenuation mechanism of the fish-derived oral attenuated Streptococcus iniae vaccine strain YM011. FISH & SHELLFISH IMMUNOLOGY 2020; 106:546-554. [PMID: 32781206 DOI: 10.1016/j.fsi.2020.07.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Streptococcus iniae has become one the most serious aquatic pathogens causing invasive diseases in farmed marine and freshwater fish worldwide, and orally attenuated vaccine is still the best option in protecting these invasive diseases. In this study, the safety, stability, immunogenicity of the S. iniae attenuated strain YM011 were evaluated, and comprehensively analyzed its virulence weakening mechanism at whole genome level. The results shown that attenuated S. iniae strain YM011 completely lost its pathogenicity to tilapia and had good immunogenicity with relative percent survival being 93.25% at 15 days and 90.31% at 30 days via IP injection, respectively, and 76.81% at 15 days and 56.69% at 30 days via oral gavage, respectively. Back-passage safety assay indicated that YM011 did not cause diseases or death in tilapia after 100 generations of serial passaging. Comparative genome-wide sequencing shown that YM011 had a 0.4 M large inversion fragment compared with its parental strain virulent strain GX005, which encoded 372 genes including drug resistance genes pbp2A and tet, as well as known virulence factors including hemolysin transport system gene, recA, and mutator family transposase. The attenuated S. iniae strain YM011 is an ideal attenuated oral vaccine candidate with good immunogenicity, safety and stability. Abnormal expression of important drug resistance genes as well as known virulence factors due to inversion of a 0.4 M large fragment is the leading mechanism underlying its attenuated virulence.
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Affiliation(s)
- Yu Liu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Liping Li
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Fangzhao Yu
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, China
| | - Yongju Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Wanwen Liang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiong Yang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Rui Wang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Li
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Jiayou Tang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qunhong Gu
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, China
| | - Zhiping Luo
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, China
| | - Ming Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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4
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Chateau A, Oh SY, Tomatsidou A, Brockhausen I, Schneewind O, Missiakas D. Distinct Pathways Carry Out α and β Galactosylation of Secondary Cell Wall Polysaccharide in Bacillus anthracis. J Bacteriol 2020; 202:e00191-20. [PMID: 32457049 PMCID: PMC7348550 DOI: 10.1128/jb.00191-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 05/15/2020] [Indexed: 12/26/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, elaborates a secondary cell wall polysaccharide (SCWP) that is required for the retention of surface layer (S-layer) and S-layer homology (SLH) domain proteins. Genetic disruption of the SCWP biosynthetic pathway impairs growth and cell division. B. anthracis SCWP is comprised of trisaccharide repeats composed of one ManNAc and two GlcNAc residues with O-3-α-Gal and O-4-β-Gal substitutions. UDP-Gal, synthesized by GalE1, is the substrate of galactosyltransferases that modify the SCWP repeat. Here, we show that the gtsE gene, which encodes a predicted glycosyltransferase with a GT-A fold, is required for O-4-β-Gal modification of trisaccharide repeats. We identify a DXD motif critical for GtsE activity. Three distinct genes, gtsA, gtsB, and gtsC, are required for O-3-α-Gal modification of trisaccharide repeats. Based on the similarity with other three-component glycosyltransferase systems, we propose that GtsA transfers Gal from cytosolic UDP-Gal to undecaprenyl phosphate (C55-P), GtsB flips the C55-P-Gal intermediate to the trans side of the membrane, and GtsC transfers Gal onto trisaccharide repeats. The deletion of galE1 does not affect growth in vitro, suggesting that galactosyl modifications are dispensable for the function of SCWP. The deletion of gtsA, gtsB, or gtsC leads to a loss of viability, yet gtsA and gtsC can be deleted in strains lacking galE1 or gtsE We propose that the loss of viability is caused by the accumulation of undecaprenol-bound precursors and present an updated model for SCWP assembly in B. anthracis to account for the galactosylation of repeat units.IMPORTANCE Peptidoglycan is a conserved extracellular macromolecule that protects bacterial cells from turgor pressure. Peptidoglycan of Gram-positive bacteria serves as a scaffold for the attachment of polymers that provide defined bacterial interactions with their environment. One such polymer, B. anthracis SCWP, is pyruvylated at its distal end to serve as a receptor for secreted proteins bearing the S-layer homology domain. Repeat units of SCWP carry three galactoses in B. anthracis Glycosylation is a recurring theme in nature and often represents a means to mask or alter conserved molecular signatures from intruders such as bacteriophages. Several glycosyltransferase families have been described based on bioinformatics prediction, but few have been studied. Here, we describe the glycosyltransferases that mediate the galactosylation of B. anthracis SCWP.
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Affiliation(s)
- Alice Chateau
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - So Young Oh
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - Anastasia Tomatsidou
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - Inka Brockhausen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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5
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Andreazza AP, Cardoso RLA, Cocco J, Guizelini D, Faoro H, Tadra-Sfeir MZ, Balsanelli E, Cruz LM, Fadel-Picheth CMT, Donatti L, Souza EM, Foerster LA, Pedrosa FO, Chubatsu LS. Genome Analysis of Entomopathogenic Bacillus sp. ABP14 Isolated from a Lignocellulosic Compost. Genome Biol Evol 2019; 11:1658-1662. [PMID: 31135033 PMCID: PMC6573470 DOI: 10.1093/gbe/evz114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 01/08/2023] Open
Abstract
We report the complete genome sequence of Bacillus sp. strain ABP14 isolated from lignocellulosic compost and selected by its ability in hydrolyzing carboxymethyl cellulose. This strain does not produce a Cry-like protein but showed an insecticidal activity against larvae of Anticarsia gemmatalis (Lepidoptera). Genome-based taxonomic analysis revealed that the ABP14 chromosome is genetically close to Bacillus thuringiensis serovar finitimus YBT020. ABP14 also carries one plasmid which showed no similarity with those from YBT020. Genome analysis of ABP14 identified unique genes related to cell surface structures, cell wall, metabolic competence, and virulence factors that may contribute for its survival and environmental adaptation, as well as its entomopathogenic activity.
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Affiliation(s)
- Ana Paula Andreazza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Rodrigo L A Cardoso
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Jessica Cocco
- Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Dieval Guizelini
- Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, Paraná , Brazil
| | - Helisson Faoro
- Carlos Chagas Institute, Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Michelle Z Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Leonardo M Cruz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | | | - Lucélia Donatti
- Department of Cellular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Luís A Foerster
- Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Leda S Chubatsu
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
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6
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Abstract
Bacillus anthracis, the anthrax agent, is a member of the Bacillus cereus sensu lato group, which includes invasive pathogens of mammals or insects as well as nonpathogenic environmental strains. The genes for anthrax pathogenesis are located on two large virulence plasmids. Similar virulence plasmids have been acquired by other B. cereus strains and enable the pathogenesis of anthrax-like diseases. Among the virulence factors of B. anthracis is the S-layer-associated protein BslA, which endows bacilli with invasive attributes for mammalian hosts. BslA surface display and function are dependent on the bacterial S-layer, whose constituents assemble by binding to the secondary cell wall polysaccharide (SCWP) via S-layer homology (SLH) domains. B. anthracis and other pathogenic B. cereus isolates harbor genes for the secretion of S-layer proteins, for S-layer assembly, and for synthesis of the SCWP. We review here recent insights into the assembly and function of the S-layer and the SCWP.
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Affiliation(s)
- Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois 60649.,Department of Microbiology, University of Chicago, Chicago, Illinois 60637;
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois 60649.,Department of Microbiology, University of Chicago, Chicago, Illinois 60637;
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7
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Méric G, Mageiros L, Pascoe B, Woodcock DJ, Mourkas E, Lamble S, Bowden R, Jolley KA, Raymond B, Sheppard SK. Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group. Mol Ecol 2018; 27:1524-1540. [PMID: 29509989 PMCID: PMC5947300 DOI: 10.1111/mec.14546] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 12/20/2022]
Abstract
Bacterial plasmids can vary from small selfish genetic elements to large autonomous replicons that constitute a significant proportion of total cellular DNA. By conferring novel function to the cell, plasmids may facilitate evolution but their mobility may be opposed by co-evolutionary relationships with chromosomes or encouraged via the infectious sharing of genes encoding public goods. Here, we explore these hypotheses through large-scale examination of the association between plasmids and chromosomal DNA in the phenotypically diverse Bacillus cereus group. This complex group is rich in plasmids, many of which encode essential virulence factors (Cry toxins) that are known public goods. We characterized population genomic structure, gene content and plasmid distribution to investigate the role of mobile elements in diversification. We analysed coding sequence within the core and accessory genome of 190 B. cereus group isolates, including 23 novel sequences and genes from 410 reference plasmid genomes. While cry genes were widely distributed, those with invertebrate toxicity were predominantly associated with one sequence cluster (clade 2) and phenotypically defined Bacillus thuringiensis. Cry toxin plasmids in clade 2 showed evidence of recent horizontal transfer and variable gene content, a pattern of plasmid segregation consistent with transfer during infectious cooperation. Nevertheless, comparison between clades suggests that co-evolutionary interactions may drive association between plasmids and chromosomes and limit wider transfer of key virulence traits. Proliferation of successful plasmid and chromosome combinations is a feature of specialized pathogens with characteristic niches (Bacillus anthracis, B. thuringiensis) and has occurred multiple times in the B. cereus group.
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Affiliation(s)
- Guillaume Méric
- The Milner Centre for EvolutionDepartment of Biology and BiochemistryUniversity of BathBathUK
| | | | - Ben Pascoe
- The Milner Centre for EvolutionDepartment of Biology and BiochemistryUniversity of BathBathUK
- MRC CLIMB ConsortiumUniversity of BathBathUK
| | - Dan J. Woodcock
- Mathematics Institute and Zeeman Institute for Systems Biology and Infectious Epidemiology ResearchUniversity of WarwickCoventryUK
| | - Evangelos Mourkas
- The Milner Centre for EvolutionDepartment of Biology and BiochemistryUniversity of BathBathUK
| | - Sarah Lamble
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rory Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | | | - Ben Raymond
- Department of Life SciencesFaculty of Natural SciencesImperial College LondonAscotUK
- Department of BiosciencesUniversity of ExeterExeterUK
| | - Samuel K. Sheppard
- The Milner Centre for EvolutionDepartment of Biology and BiochemistryUniversity of BathBathUK
- MRC CLIMB ConsortiumUniversity of BathBathUK
- Department of ZoologyUniversity of OxfordOxfordUK
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8
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Chateau A, Lunderberg JM, Oh SY, Abshire T, Friedlander A, Quinn CP, Missiakas DM, Schneewind O. Galactosylation of the Secondary Cell Wall Polysaccharide of Bacillus anthracis and Its Contribution to Anthrax Pathogenesis. J Bacteriol 2018; 200:e00562-17. [PMID: 29229702 PMCID: PMC5809694 DOI: 10.1128/jb.00562-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 12/05/2017] [Indexed: 12/13/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, elaborates a secondary cell wall polysaccharide (SCWP) that is essential for bacterial growth and cell division. B. anthracis SCWP is comprised of trisaccharide repeats with the structure, [→4)-β-ManNAc-(1→4)-β-GlcNAc(O3-α-Gal)-(1→6)-α-GlcNAc(O3-α-Gal, O4-β-Gal)-(1→]6-12 The genes whose products promote the galactosylation of B. anthracis SCWP are not yet known. We show here that the expression of galE1, encoding a UDP-glucose 4-epimerase necessary for the synthesis of UDP-galactose, is required for B. anthracis SCWP galactosylation. The galE1 mutant assembles surface (S) layer and S layer-associated proteins that associate with ketal-pyruvylated SCWP via their S layer homology domains similarly to wild-type B. anthracis, but the mutant displays a defect in γ-phage murein hydrolase binding to SCWP. Furthermore, deletion of galE1 diminishes the capsulation of B. anthracis with poly-d-γ-glutamic acid (PDGA) and causes a reduction in bacterial virulence. These data suggest that SCWP galactosylation is required for the physiologic assembly of the B. anthracis cell wall envelope and for the pathogenesis of anthrax disease.IMPORTANCE Unlike virulent Bacillus anthracis isolates, B. anthracis strain CDC684 synthesizes secondary cell wall polysaccharide (SCWP) trisaccharide repeats without galactosyl modification, exhibits diminished growth in vitro in broth cultures, and is severely attenuated in an animal model of anthrax. To examine whether SCWP galactosylation is a requirement for anthrax disease, we generated variants of B. anthracis strains Sterne 34F2 and Ames lacking UDP-glucose 4-epimerase by mutating the genes galE1 and galE2 We identified galE1 as necessary for SCWP galactosylation. Deletion of galE1 decreased the poly-d-γ-glutamic acid (PDGA) capsulation of the vegetative form of B. anthracis and increased the bacterial inoculum required to produce lethal disease in mice, indicating that SCWP galactosylation is indeed a determinant of anthrax disease.
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Affiliation(s)
- Alice Chateau
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Justin Mark Lunderberg
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - So Young Oh
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Teresa Abshire
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Arthur Friedlander
- Headquarters, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Conrad P Quinn
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dominique M Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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9
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Valdebenito B, Tullume-Vergara PO, González W, Kreth J, Giacaman RA. In silico analysis of the competition between Streptococcus sanguinis and Streptococcus mutans in the dental biofilm. Mol Oral Microbiol 2018; 33:168-180. [PMID: 29237244 DOI: 10.1111/omi.12209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2017] [Indexed: 01/03/2023]
Abstract
During dental caries, the dental biofilm modifies the composition of the hundreds of involved bacterial species. Changing environmental conditions influence competition. A pertinent model to exemplify the complex interplay of the microorganisms in the human dental biofilm is the competition between Streptococcus sanguinis and Streptococcus mutans. It has been reported that children and adults harbor greater numbers of S. sanguinis in the oral cavity, associated with caries-free teeth. Conversely, S. mutans is predominant in individuals with a high number of carious lesions. Competition between both microorganisms stems from the production of H2 O2 by S. sanguinis and mutacins, a type of bacteriocins, by S. mutans. There is limited evidence on how S. sanguinis survives its own H2 O2 levels, or if it has other mechanisms that might aid in the competition against S. mutans, nonetheless. We performed a genomic and metabolic pathway comparison, coupled with a comprehensive literature review, to better understand the competition between these two species. Results indicated that S. sanguinis can outcompete S. mutans by the production of an enzyme capable of metabolizing H2 O2 . S. mutans, however, lacks the enzyme and is susceptible to the peroxide from S. sanguinis. In addition, S. sanguinis can generate energy through gluconeogenesis and seems to have evolved different communication mechanisms, indicating that novel proteins may be responsible for intra-species communication.
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Affiliation(s)
- B Valdebenito
- Centro de Bioinformática y Simulación Molecular (CBSM), University of Talca, Talca, Chile
| | - P O Tullume-Vergara
- Facultad de Ciencias Biológicas, Universidad Nacional Pedro Ruiz Gallo, Lambayeque, Peru
| | - W González
- Centro de Bioinformática y Simulación Molecular (CBSM), University of Talca, Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Talca, Chile
| | - J Kreth
- Department of Restorative Dentistry, Oregon Health & Science University, Portland, OR, USA
| | - R A Giacaman
- Cariology Unit, Department of Oral Rehabilitation and Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), University of Talca, Talca, Chile
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10
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Derzelle S, Aguilar-Bultet L, Frey J. Comparative genomics of Bacillus anthracis from the wool industry highlights polymorphisms of lineage A.Br.Vollum. INFECTION GENETICS AND EVOLUTION 2016; 46:50-58. [PMID: 27793731 DOI: 10.1016/j.meegid.2016.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 10/21/2016] [Accepted: 10/22/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND With the advent of affordable next-generation sequencing (NGS) technologies, major progress has been made in the understanding of the population structure and evolution of the B. anthracis species. Here we report the use of whole genome sequencing and computer-based comparative analyses to characterize six strains belonging to the A.Br.Vollum lineage. These strains were isolated in Switzerland, in 1981, during iterative cases of anthrax involving workers in a textile plant processing cashmere wool from the Indian subcontinent. RESULTS We took advantage of the hundreds of currently available B. anthracis genomes in public databases, to investigate the genetic diversity existing within the A.Br.Vollum lineage and to position the six Swiss isolates into the worldwide B. anthracis phylogeny. Thirty additional genomes related to the A.Br.Vollum group were identified by whole-genome single nucleotide polymorphism (SNP) analysis, including two strains forming a new evolutionary branch at the basis of the A.Br.Vollum lineage. This new phylogenetic lineage (termed A.Br.H9401) splits off the branch leading to the A.Br.Vollum group soon after its divergence to the other lineages of the major A clade (i.e. 6 SNPs). The available dataset of A.Br.Vollum genomes were resolved into 2 distinct groups. Isolates from the Swiss wool processing facility clustered together with two strains from Pakistan and one strain of unknown origin isolated from yarn. They were clearly differentiated (69 SNPs) from the twenty-five other A.Br.Vollum strains located on the branch leading to the terminal reference strain A0488 of the lineage. Novel analytic assays specific to these new subgroups were developed for the purpose of rapid molecular epidemiology. CONCLUSIONS Whole genome SNP surveys greatly expand upon our knowledge on the sub-structure of the A.Br.Vollum lineage. Possible origin and route of spread of this lineage worldwide are discussed.
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Affiliation(s)
- Sylviane Derzelle
- Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland.
| | - Lisandra Aguilar-Bultet
- Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland.
| | - Joachim Frey
- Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland.
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11
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A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics. Sci Rep 2016; 6:23747. [PMID: 27030530 PMCID: PMC4814877 DOI: 10.1038/srep23747] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 03/14/2016] [Indexed: 12/17/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1.
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Naseeb S, Carter Z, Minnis D, Donaldson I, Zeef L, Delneri D. Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering. Mol Biol Evol 2016; 33:1679-96. [PMID: 26929245 PMCID: PMC4915352 DOI: 10.1093/molbev/msw045] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces “sensu stricto” species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible paracentric and pericentric inversions between Ty1 elements, a natural substrate for rearrangements. We found that 4 inversions were lethal, while the other 12 did not show any fitness advantage or disadvantage in rich and minimal media. At meiosis, only a weak negative correlation with fitness was seen with the size of the inverted region. However, significantly lower fertility was seen in heterozygote invertant strains carrying recombination hotspots within the breakpoints. Altered transcription was observed throughout the genome rather than being overrepresented within the inversions. In spite of the large difference in gene expression in the inverted strains, mitotic fitness was not impaired in the majority of the 94 conditions tested, indicating that the robustness of the expression network buffers the deleterious effects of structural changes in several environments. Overall, our results support the notion that transcriptional changes may compensate for Ty-mediated rearrangements resulting in the maintenance of a constant phenotype, and suggest that large inversions in yeast are unlikely to be a selectable trait during vegetative growth.
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Affiliation(s)
- Samina Naseeb
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Zorana Carter
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David Minnis
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian Donaldson
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Leo Zeef
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Daniela Delneri
- Computational and Evolutionary Biology Research Theme, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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Vergnaud G, Girault G, Thierry S, Pourcel C, Madani N, Blouin Y. Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade. PLoS One 2016; 11:e0146216. [PMID: 26901621 PMCID: PMC4763433 DOI: 10.1371/journal.pone.0146216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
Background Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French B. anthracis lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins. Results A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant B. anthracis lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France. Conclusions/Significance The present work extends the range of observed substitution rate heterogeneity within B. anthracis, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.
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Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
- * E-mail:
| | - Guillaume Girault
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Simon Thierry
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Nora Madani
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
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14
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Genomic and transcriptomic insights into the efficient entomopathogenicity of Bacillus thuringiensis. Sci Rep 2015; 5:14129. [PMID: 26411888 PMCID: PMC4585936 DOI: 10.1038/srep14129] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/31/2015] [Indexed: 11/19/2022] Open
Abstract
Bacillus thuringiensis has been globally used as a microbial pesticide for over 70 years. However, information regarding its various adaptions and virulence factors and their roles in the entomopathogenic process remains limited. In this work, we present the complete genomes of two industrially patented Bacillus thuringiensis strains (HD-1 and YBT-1520). A comparative genomic analysis showed a larger and more complicated genome constitution that included novel insecticidal toxicity-related genes (ITRGs). All of the putative ITRGs were summarized according to the steps of infection. A comparative genomic analysis showed that highly toxic strains contained significantly more ITRGs, thereby providing additional strategies for infection, immune evasion, and cadaver utilization. Furthermore, a comparative transcriptomic analysis suggested that a high expression of these ITRGs was a key factor in efficient entomopathogenicity. We identified an active extra urease synthesis system in the highly toxic strains that may aid B. thuringiensis survival in insects (similar to previous results with well-known pathogens). Taken together, these results explain the efficient entomopathogenicity of B. thuringiensis. It provides novel insights into the strategies used by B. thuringiensis to resist and overcome host immune defenses and helps identify novel toxicity factors.
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15
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Derzelle S, Girault G, Roest HIJ, Koene M. Molecular diversity of Bacillus anthracis in the Netherlands: Investigating the relationship to the worldwide population using whole-genome SNP discovery. INFECTION GENETICS AND EVOLUTION 2015; 32:370-6. [DOI: 10.1016/j.meegid.2015.03.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 01/01/2023]
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16
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Goldberg A, Fridman O, Ronin I, Balaban NQ. Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli. Genome Med 2014; 6:112. [PMID: 25530806 PMCID: PMC4272514 DOI: 10.1186/s13073-014-0112-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.
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Affiliation(s)
- Amir Goldberg
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
| | - Ofer Fridman
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
| | - Irine Ronin
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
| | - Nathalie Q Balaban
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
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17
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Rouli L, MBengue M, Robert C, Ndiaye M, La Scola B, Raoult D. Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium. New Microbes New Infect 2014; 2:161-9. [PMID: 25566394 PMCID: PMC4265047 DOI: 10.1002/nmi2.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/04/2014] [Accepted: 08/08/2014] [Indexed: 01/31/2023] Open
Abstract
Bacillus anthracis is the causative agent of anthrax and is classified as a
‘Category A’ biological weapon. Six complete genomes of
B. anthracis (A0248, Ames, Ames Ancestor, CDC684, H0491, and Sterne) are
currently available. In this report, we add three African strain genomes: Sen2Col2, Sen3 and Gmb1.
To study the pan-genome of B. anthracis, we used bioinformatics tools, such
as Cluster of Orthologous Groups, and performed phylogenetic analysis. We found that the three
African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the
plcR gene and the four known prophages. These strains are most similar to the
CDC684 strain and belong to the A cluster. We estimated that the
B. anthracis pan-genome has 2893 core genes (99% of the genome size)
and 85 accessory genes. We validated the hypothesis that B. anthracis has a
closed pan-genome and found that the three African strains carry the two plasmids associated with
bacterial virulence. The pan-genome nature of B. anthracis confirms its lack
of exchange (similar to Clostridium tetani) and supports its exclusively pathogenic
role, despite its survival in the environment. Moreover, thanks to the study of the core content
single nucleotide polymorphisms, we can see that our three African strains diverged very recently
from the other B. anthracis strains.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - M MBengue
- Laboratoire National d'Elevage et des Recherches Vétérinaires (LNERV), Institut Sénégalais de Recherches Agricoles (ISRA) Hann, Dakar, Senegal
| | - C Robert
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - M Ndiaye
- Laboratoire de Biologie Cellulaire, Faculté des Sciences et Techniques de l'Université Cheikh Anta DIOP de Dakar (UCAD) Dakar, Senegal
| | - B La Scola
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
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Abstract
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations. Bacterial chromosomes are dynamic structures shaped by long histories of evolution. Among genomic changes, large-scale DNA rearrangements can have important effects on the presence, order, and expression of genes. Whole-genome sequencing that relies on short DNA reads cannot identify all large-scale rearrangements. Therefore, deciphering changes in the overall organization of genomes requires alternative methods, such as optical mapping. We analyzed the longest-running microbial evolution experiment (more than 25 years of evolution in the laboratory) by optical mapping, genome sequencing, and PCR analyses. We found multiple large genome rearrangements in all 12 independently evolving populations. In most cases, it is unclear whether these changes were beneficial themselves or, alternatively, hitchhiked to fixation with other beneficial mutations. In any case, many genome rearrangements accumulated over decades of evolution, providing these populations with genetic plasticity reminiscent of that observed in some pathogenic bacteria.
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Periwal V, Scaria V. Insights into structural variations and genome rearrangements in prokaryotic genomes. ACTA ACUST UNITED AC 2014; 31:1-9. [PMID: 25189783 DOI: 10.1093/bioinformatics/btu600] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing.
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Affiliation(s)
- Vinita Periwal
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
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20
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Lunderberg JM, Nguyen-Mau SM, Richter GS, Wang YT, Dworkin J, Missiakas DM, Schneewind O. Bacillus anthracis acetyltransferases PatA1 and PatA2 modify the secondary cell wall polysaccharide and affect the assembly of S-layer proteins. J Bacteriol 2013; 195:977-89. [PMID: 23243307 PMCID: PMC3571321 DOI: 10.1128/jb.01274-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/09/2012] [Indexed: 11/20/2022] Open
Abstract
The envelope of Bacillus anthracis encompasses a proteinaceous S-layer with two S-layer proteins (Sap and EA1). Protein assembly in the envelope of B. anthracis requires S-layer homology domains (SLH) within S-layer proteins and S-layer-associated proteins (BSLs), which associate with the secondary cell wall polysaccharide (SCWP), an acetylated carbohydrate that is tethered to peptidoglycan. Here, we investigated the contributions of two putative acetyltransferases, PatA1 and PatA2, on SCWP acetylation and S-layer assembly. We show that mutations in patA1 and patA2 affect the chain lengths of B. anthracis vegetative forms and perturb the deposition of the BslO murein hydrolase at cell division septa. The patA1 and patA2 mutants are defective for the assembly of EA1 in the envelope but retain the ability of S-layer formation with Sap. SCWP isolated from the patA1 patA2 mutant lacked acetyl moieties identified in wild-type polysaccharide and failed to associate with the SLH domains of EA1. A model is discussed whereby patA1- and patA2-mediated acetylation of SCWP enables the deposition of EA1 as well as BslO near the septal region of the B. anthracis envelope.
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Affiliation(s)
- J. Mark Lunderberg
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Sao-Mai Nguyen-Mau
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - G. Stefan Richter
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Ya-Ting Wang
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, Columbia University, New York, New York, USA
| | - Dominique M. Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis. GENOME ANNOUNCEMENTS 2013; 1:genomeA00067-12. [PMID: 23405332 PMCID: PMC3569327 DOI: 10.1128/genomea.00067-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 11/07/2012] [Indexed: 11/20/2022]
Abstract
The Bacillus anthracis Carbosap genome, which includes the pXO1 and pXO2 plasmids, has been shown to encode the major B. anthracis virulence factors, yet this strain’s attenuation has not yet been explained. Here we report the draft genome sequence of this strain, and a comparison to fully virulent B. anthracis.
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Forsberg LS, Abshire TG, Friedlander A, Quinn CP, Kannenberg EL, Carlson RW. Localization and structural analysis of a conserved pyruvylated epitope in Bacillus anthracis secondary cell wall polysaccharides and characterization of the galactose-deficient wall polysaccharide from avirulent B. anthracis CDC 684. Glycobiology 2012; 22:1103-17. [PMID: 22556058 DOI: 10.1093/glycob/cws080] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacillus anthracis CDC 684 is a naturally occurring, avirulent variant and close relative of the highly pathogenic B. anthracis Vollum. Bacillus anthracis CDC 684 contains both virulence plasmids, pXO1 and pXO2, yet is non-pathogenic in animal models, prompting closer scrutiny of the molecular basis of attenuation. We structurally characterized the secondary cell wall polysaccharide (SCWP) of B. anthracis CDC 684 (Ba684) using chemical and NMR spectroscopy analysis. The SCWP consists of a HexNAc trisaccharide backbone having identical structure as that of B. anthracis Pasteur, Sterne and Ames, →4)-β-d-ManpNAc-(1 → 4)-β-d-GlcpNAc-(1 → 6)-α-d-GlcpNAc-(1→. Remarkably, although the backbone is fully polymerized, the SCWP is the devoid of all galactosyl side residues, a feature which normally comprises 50% of the glycosyl residues on the highly galactosylated SCWPs from pathogenic strains. This observation highlights the role of defective wall assembly in virulence and indicates that polymerization occurs independently of galactose side residue attachment. Of particular interest, the polymerized Ba684 backbone retains the substoichiometric pyruvate acetal, O-acetate and amino group modifications found on SCWPs from normal B. anthracis strains, and immunofluorescence analysis confirms that SCWP expression coincides with the ability to bind the surface layer homology (SLH) domain containing S-layer protein extractable antigen-1. Pyruvate was previously demonstrated as part of a conserved epitope, mediating SLH-domain protein attachment to the underlying peptidoglycan layer. We find that a single repeating unit, located at the distal (non-reducing) end of the Ba684 SCWP, is structurally modified and that this modification is present in identical manner in the SCWPs of normal B. anthracis strains. These polysaccharides terminate in the sequence: (S)-4,6-O-(1-carboxyethylidene)-β-d-ManpNAc-(1 → 4)-[3-O-acetyl]-β-d-GlcpNAc-(1 → 6)-α-d-GlcpNH(2)-(1→.
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Affiliation(s)
- L Scott Forsberg
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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