1
|
Liu Y, Liu Q, Zhang C, Zhao J, Zhang H, Chen W, Zhai Q. Strain-specific effects of Akkermansia muciniphila on the regulation of intestinal barrier. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
2
|
Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
Collapse
Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
3
|
Beskrovnaya P, Sexton DL, Golmohammadzadeh M, Hashimi A, Tocheva EI. Structural, Metabolic and Evolutionary Comparison of Bacterial Endospore and Exospore Formation. Front Microbiol 2021; 12:630573. [PMID: 33767680 PMCID: PMC7985256 DOI: 10.3389/fmicb.2021.630573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
Sporulation is a specialized developmental program employed by a diverse set of bacteria which culminates in the formation of dormant cells displaying increased resilience to stressors. This represents a major survival strategy for bacteria facing harsh environmental conditions, including nutrient limitation, heat, desiccation, and exposure to antimicrobial compounds. Through dispersal to new environments via biotic or abiotic factors, sporulation provides a means for disseminating genetic material and promotes encounters with preferable environments thus promoting environmental selection. Several types of bacterial sporulation have been characterized, each involving numerous morphological changes regulated and performed by non-homologous pathways. Despite their likely independent evolutionary origins, all known modes of sporulation are typically triggered by limited nutrients and require extensive membrane and peptidoglycan remodeling. While distinct modes of sporulation have been observed in diverse species, two major types are at the forefront of understanding the role of sporulation in human health, and microbial population dynamics and survival. Here, we outline endospore and exospore formation by members of the phyla Firmicutes and Actinobacteria, respectively. Using recent advances in molecular and structural biology, we point to the regulatory, genetic, and morphological differences unique to endo- and exospore formation, discuss shared characteristics that contribute to the enhanced environmental survival of spores and, finally, cover the evolutionary aspects of sporulation that contribute to bacterial species diversification.
Collapse
Affiliation(s)
| | | | | | | | - Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
4
|
Mašlaňová I, Wertheimer Z, Sedláček I, Švec P, Indráková A, Kovařovic V, Schumann P, Spröer C, Králová S, Šedo O, Krištofová L, Vrbovská V, Füzik T, Petráš P, Zdráhal Z, Ružičková V, Doškař J, Pantuček R. Description and Comparative Genomics of Macrococcus caseolyticus subsp. hominis subsp. nov., Macrococcus goetzii sp. nov., Macrococcus epidermidis sp. nov., and Macrococcus bohemicus sp. nov., Novel Macrococci From Human Clinical Material With Virulence Potential and Suspected Uptake of Foreign DNA by Natural Transformation. Front Microbiol 2018; 9:1178. [PMID: 29951040 PMCID: PMC6008420 DOI: 10.3389/fmicb.2018.01178] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/15/2018] [Indexed: 11/30/2022] Open
Abstract
The genus Macrococcus is a close relative of the genus Staphylococcus. Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as Macrococcus sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus Macrococcus. Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a com operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCCmec-like element containing a unique mec gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus Macrococcus, for which the names Macrococcus caseolyticus subsp. hominis subsp. nov. (type strain CCM 7927T = DSM 103682T), Macrococcus goetzii sp. nov. (type strain CCM 4927T = DSM 103683T), Macrococcus epidermidis sp. nov. (type strain CCM 7099T = DSM 103681T), and Macrococcus bohemicus sp. nov. (type strain CCM 7100T = DSM 103680T) are proposed. Moreover, a formal description of Macrococcus caseolyticus subsp. caseolyticus subsp. nov. and an emended description of the genus Macrococcus are provided.
Collapse
Affiliation(s)
- Ivana Mašlaňová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zuzana Wertheimer
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Adéla Indráková
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Kovařovic
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Peter Schumann
- Leibniz Institute Deutsche Sammlung von Mikroorganismen und Zellkulturen—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute Deutsche Sammlung von Mikroorganismen und Zellkulturen—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stanislava Králová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Lucie Krištofová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Veronika Vrbovská
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Prague, Czechia
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vladislava Ružičková
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Doškař
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Roman Pantuček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| |
Collapse
|
5
|
Abstract
Bacterial endospores possess multiple integument layers, one of which is the cortex peptidoglycan wall. The cortex is essential for the maintenance of spore core dehydration and dormancy and contains structural modifications that differentiate it from vegetative cell peptidoglycan and determine its fate during spore germination. Following the engulfment stage of sporulation, the cortex is synthesized within the intermembrane space surrounding the forespore. Proteins responsible for cortex synthesis are produced in both the forespore and mother cell compartments. While some of these proteins also contribute to vegetative cell wall synthesis, others are sporulation specific. In order for the bacterial endospore to germinate and resume metabolism, the cortex peptidoglycan must first be degraded through the action of germination-specific lytic enzymes. These enzymes are present, yet inactive, in the dormant spore and recognize the muramic-δ-lactam modification present in the cortex. Germination-specific lytic enzymes across Bacillaceae and Clostridiaceae share this specificity determinant, which ensures that the spore cortex is hydrolyzed while the vegetative cell wall remains unharmed. Bacillus species tend to possess two redundant enzymes, SleB and CwlJ, capable of sufficient cortex degradation, while the clostridia have only one, SleC. Additional enzymes are often present that cannot initiate the cortex degradation process, but which can increase the rate of release of small fragments into the medium. Between the two families, the enzymes also differ in the enzymatic activities they possess and the mechanisms acting to restrict their activation until germination has been initiated.
Collapse
|
6
|
Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA. Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. Cell Syst 2017; 4:291-305.e7. [PMID: 28189581 DOI: 10.1016/j.cels.2016.12.013] [Citation(s) in RCA: 348] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 11/19/2016] [Accepted: 12/21/2016] [Indexed: 12/16/2022]
Abstract
A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria.
Collapse
Affiliation(s)
- Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - George Kritikos
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kenneth Tong
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Harvey Kimsey
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ilan Wapinski
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Galardini
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Angelo Cabal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason M Peters
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna-Barbara Hachmann
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
7
|
Emami K, Guyet A, Kawai Y, Devi J, Wu LJ, Allenby N, Daniel RA, Errington J. RodA as the missing glycosyltransferase in Bacillus subtilis and antibiotic discovery for the peptidoglycan polymerase pathway. Nat Microbiol 2017; 2:16253. [PMID: 28085152 PMCID: PMC5568705 DOI: 10.1038/nmicrobiol.2016.253] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/15/2016] [Indexed: 11/08/2022]
Abstract
The bacterial cell wall is a highly conserved essential component of most bacterial groups. It is the target for our most frequently used antibiotics and provides important small molecules that trigger powerful innate immune responses. The wall is composed of glycan strands crosslinked by short peptides. For many years, the penicillin-binding proteins were thought to be the key enzymes required for wall synthesis. RodA and possibly other proteins in the wider SEDS (shape, elongation, division and sporulation) family have now emerged as a previously unknown class of essential glycosyltranferase enzymes, which play key morphogenetic roles in bacterial cell wall synthesis. We provide evidence in support of this role and the discovery of small natural product molecules that probably target these enzymes. The SEDS proteins have exceptional potential as targets for new antibacterial therapeutic agents.
Collapse
Affiliation(s)
- Kaveh Emami
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Aurelie Guyet
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Yoshikazu Kawai
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Jenny Devi
- Demuris Ltd, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Ling J Wu
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Nick Allenby
- Demuris Ltd, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Richard A Daniel
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Jeff Errington
- The Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
- Demuris Ltd, Newcastle Biomedicine Bio-Incubators, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
8
|
Elhenawy W, Davis RM, Fero J, Salama NR, Felman MF, Ruiz N. The O-Antigen Flippase Wzk Can Substitute for MurJ in Peptidoglycan Synthesis in Helicobacter pylori and Escherichia coli. PLoS One 2016; 11:e0161587. [PMID: 27537185 PMCID: PMC4990322 DOI: 10.1371/journal.pone.0161587] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/08/2016] [Indexed: 11/19/2022] Open
Abstract
The peptidoglycan (PG) cell wall is an essential component of the cell envelope of most bacteria. Biogenesis of PG involves a lipid-linked disaccharide-pentapeptide intermediate called lipid II, which must be translocated across the cytoplasmic membrane after it is synthesized in the inner leaflet of this bilayer. Accordingly, it has been demonstrated that MurJ, the proposed lipid II flippase in Escherichia coli, is required for PG biogenesis, and thereby viability. In contrast, MurJ is not essential in Bacillus subtilis because this bacterium produces AmJ, an unrelated protein that is functionally redundant with MurJ. In this study, we investigated why MurJ is not essential in the prominent gastric pathogen, Helicobacter pylori. We found that in this bacterium, Wzk, the ABC (ATP-binding cassette) transporter that flips the lipid-linked O- or Lewis- antigen precursors across the inner membrane, is redundant with MurJ for cell viability. Heterologous expression of wzk in E. coli also suppresses the lethality caused by the loss of murJ. Furthermore, we show that this cross-species complementation is abolished when Wzk is inactivated by mutations that target a domain predicted to be required for ATPase activity. Our results suggest that Wzk can flip lipid II, implying that Wzk is the flippase with the most relaxed specificity for lipid-linked saccharides ever identified.
Collapse
Affiliation(s)
- Wael Elhenawy
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Rebecca M. Davis
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, United States of America
| | - Jutta Fero
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States of America
| | - Nina R. Salama
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States of America
| | - Mario F. Felman
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, United States of America
- * E-mail:
| |
Collapse
|
9
|
SEDS proteins are a widespread family of bacterial cell wall polymerases. Nature 2016; 537:634-638. [PMID: 27525505 PMCID: PMC5161649 DOI: 10.1038/nature19331] [Citation(s) in RCA: 333] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022]
Abstract
Elongation of rod-shaped bacteria is mediated by a dynamic peptidoglycan synthetic machinery called the Rod complex. We report that in Bacillus subtilis this complex is functional in the absence of all known peptidoglycan polymerases. Cells lacking these enzymes survive by inducing an envelope stress response that increases expression of RodA, a widely conserved core component of the Rod complex. RodA is a member of the SEDS family of proteins that play essential but ill-defined roles in cell wall biogenesis during growth, division and sporulation. Our genetic and biochemical analyses indicate that SEDS proteins constitute a new family of peptidoglycan polymerases. Thus, B. subtilis and likely most bacteria use two distinct classes of polymerases to synthesize their exoskeleton. Our findings indicate that SEDS family proteins are core cell wall synthases of the cell elongation and division machinery, and represent attractive targets for antibiotic development.
Collapse
|
10
|
Ruiz N. Lipid Flippases for Bacterial Peptidoglycan Biosynthesis. Lipid Insights 2016; 8:21-31. [PMID: 26792999 PMCID: PMC4714577 DOI: 10.4137/lpi.s31783] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/10/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
The biosynthesis of cellular polysaccharides and glycoconjugates often involves lipid-linked intermediates that need to be translocated across membranes. Essential pathways such as N-glycosylation in eukaryotes and biogenesis of the peptidoglycan (PG) cell wall in bacteria share a common strategy where nucleotide-sugars are used to build a membrane-bound oligosaccharide precursor that is linked to a phosphorylated isoprenoid lipid. Once made, these lipid-linked intermediates must be translocated across a membrane so that they can serve as substrates in a different cellular compartment. How translocation occurs is poorly understood, although it clearly requires a transporter or flippase. Identification of these transporters is notoriously difficult, and, in particular, the identity of the flippase of lipid II, an intermediate required for PG biogenesis, has been the subject of much debate. Here, I will review the body of work that has recently fueled this controversy, centered on proposed flippase candidates FtsW, MurJ, and AmJ.
Collapse
Affiliation(s)
- Natividad Ruiz
- Associate Professor, Department of Microbiology, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
11
|
Meeske AJ, Rodrigues CDA, Brady J, Lim HC, Bernhardt TG, Rudner DZ. High-Throughput Genetic Screens Identify a Large and Diverse Collection of New Sporulation Genes in Bacillus subtilis. PLoS Biol 2016; 14:e1002341. [PMID: 26735940 PMCID: PMC4703394 DOI: 10.1371/journal.pbio.1002341] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/25/2015] [Indexed: 01/09/2023] Open
Abstract
The differentiation of the bacterium Bacillus subtilis into a dormant spore is among the most well-characterized developmental pathways in biology. Classical genetic screens performed over the past half century identified scores of factors involved in every step of this morphological process. More recently, transcriptional profiling uncovered additional sporulation-induced genes required for successful spore development. Here, we used transposon-sequencing (Tn-seq) to assess whether there were any sporulation genes left to be discovered. Our screen identified 133 out of the 148 genes with known sporulation defects. Surprisingly, we discovered 24 additional genes that had not been previously implicated in spore formation. To investigate their functions, we used fluorescence microscopy to survey early, middle, and late stages of differentiation of null mutants from the B. subtilis ordered knockout collection. This analysis identified mutants that are delayed in the initiation of sporulation, defective in membrane remodeling, and impaired in spore maturation. Several mutants had novel sporulation phenotypes. We performed in-depth characterization of two new factors that participate in cell–cell signaling pathways during sporulation. One (SpoIIT) functions in the activation of σE in the mother cell; the other (SpoIIIL) is required for σG activity in the forespore. Our analysis also revealed that as many as 36 sporulation-induced genes with no previously reported mutant phenotypes are required for timely spore maturation. Finally, we discovered a large set of transposon insertions that trigger premature initiation of sporulation. Our results highlight the power of Tn-seq for the discovery of new genes and novel pathways in sporulation and, combined with the recently completed null mutant collection, open the door for similar screens in other, less well-characterized processes. Transposon sequencing enables the recovery of virtually all previously characterized genes required for the differentiation of the bacterium Bacillus subtilis into a dormant spore and identifies 24 new ones. When starved of nutrients, the bacterium Bacillus subtilis differentiates into a dormant spore that is impervious to environmental insults. Decades of research have uncovered over 100 genes required for spore formation. Molecular dissection of these genes has revealed factors that act at every stage of this developmental process. In this study, we used a high-throughput genetic screening method called transposon sequencing to assess whether there were any sporulation genes left to be discovered. This approach identified virtually all of the known sporulation genes, as well as 24 new ones. Furthermore, transposon sequencing enabled the discovery of two new sets of mutants in which the sporulation process was either delayed or accelerated. Using fluorescence microscopy, we determined the developmental stage at which each mutant was impaired and discovered mutants that are delayed in initiation of sporulation, or defective in morphogenesis, cell–cell signaling, or spore maturation. Our findings exemplify the utility of transposon sequencing to uncover new biology in well-studied processes, suggesting that it could similarly be used to identify novel genes required for other aspects of bacterial physiology, such as natural competence, stationary phase survival, or the responses to cell envelope stress and DNA damage.
Collapse
Affiliation(s)
- Alexander J. Meeske
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christopher D. A. Rodrigues
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jacqueline Brady
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hoong Chuin Lim
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas G. Bernhardt
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Z. Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
12
|
Improvements to a Markerless Allelic Exchange System for Bacillus anthracis. PLoS One 2015; 10:e0142758. [PMID: 26624016 PMCID: PMC4666636 DOI: 10.1371/journal.pone.0142758] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/20/2015] [Indexed: 11/25/2022] Open
Abstract
A system was previously developed for conducting I-SceI-mediated allelic exchange in Bacillus anthracis. In this system, recombinational loss of a chromosomally-integrated allelic exchange vector is stimulated by creation of a double-stranded break within the vector by the homing endonuclease I-SceI. Although this system is reasonably efficient and represents an improvement in the tools available for allelic exchange in B. anthracis, researchers are nonetheless required to “pick and patch” colonies in order to identify candidate "exchangeants." In the present study, a number of improvements have been made to this system: 1) an improved I-SceI-producing plasmid includes oriT so that both plasmids can now be introduced by conjugation, thus avoiding the need for preparing electro-competent cells of each integration intermediate; 2) antibiotic markers have been changed to allow the use of the system in select agent strains; and 3) both plasmids have been marked with fluorescent proteins, allowing the visualization of plasmid segregation on a plate and obviating the need for “picking and patching.” These modifications have made the process easier, faster, and more efficient, allowing for parallel construction of larger numbers of mutant strains. Using this improved system, the genes encoding the tripartite anthrax toxin were deleted singly and in combination from plasmid pXO1 of Sterne strain 34F2. In the course of this study, we determined that DNA transfer to B. anthracis could be accomplished by conjugation directly from a methylation-competent E. coli strain.
Collapse
|
13
|
Teo ACK, Roper DI. Core Steps of Membrane-Bound Peptidoglycan Biosynthesis: Recent Advances, Insight and Opportunities. Antibiotics (Basel) 2015; 4:495-520. [PMID: 27025638 PMCID: PMC4790310 DOI: 10.3390/antibiotics4040495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/03/2015] [Accepted: 10/26/2015] [Indexed: 11/16/2022] Open
Abstract
We are entering an era where the efficacy of current antibiotics is declining, due to the development and widespread dispersion of antibiotic resistance mechanisms. These factors highlight the need for novel antimicrobial discovery. A large number of antimicrobial natural products elicit their effect by directly targeting discrete areas of peptidoglycan metabolism. Many such natural products bind directly to the essential cell wall precursor Lipid II and its metabolites, i.e., preventing the utlisation of vital substrates by direct binding rather than inhibiting the metabolising enzymes themselves. Concurrently, there has been an increase in the knowledge surrounding the proteins essential to the metabolism of Lipid II at and across the cytoplasmic membrane. In this review, we draw these elements together and look to future antimicrobial opportunities in this area.
Collapse
Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - David I Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| |
Collapse
|
14
|
MurJ and a novel lipid II flippase are required for cell wall biogenesis in Bacillus subtilis. Proc Natl Acad Sci U S A 2015; 112:6437-42. [PMID: 25918422 DOI: 10.1073/pnas.1504967112] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial surface polysaccharides are synthesized from lipid-linked precursors at the inner surface of the cytoplasmic membrane before being translocated across the bilayer for envelope assembly. Transport of the cell wall precursor lipid II in Escherichia coli requires the broadly conserved and essential multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily member MurJ. Here, we show that Bacillus subtilis cells lacking all 10 MOP superfamily members are viable with only minor morphological defects, arguing for the existence of an alternate lipid II flippase. To identify this factor, we screened for synthetic lethal partners of MOP family members using transposon sequencing. We discovered that an uncharacterized gene amj (alternate to MurJ; ydaH) and B. subtilis MurJ (murJBs; formerly ytgP) are a synthetic lethal pair. Cells defective for both Amj and MurJBs exhibit cell shape defects and lyse. Furthermore, expression of Amj or MurJBs in E. coli supports lipid II flipping and viability in the absence of E. coli MurJ. Amj is present in a subset of gram-negative and gram-positive bacteria and is the founding member of a novel family of flippases. Finally, we show that Amj is expressed under the control of the cell envelope stress-response transcription factor σ(M) and cells lacking MurJBs increase amj transcription. These findings raise the possibility that antagonists of the canonical MurJ flippase trigger expression of an alternate translocase that can resist inhibition.
Collapse
|
15
|
Mohamed YF, Valvano MA. A Burkholderia cenocepacia MurJ (MviN) homolog is essential for cell wall peptidoglycan synthesis and bacterial viability. Glycobiology 2014; 24:564-76. [PMID: 24688094 DOI: 10.1093/glycob/cwu025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cell wall peptidoglycan (PG) of Burkholderia cenocepacia, an opportunistic pathogen, has not yet been characterized. However, the B. cenocepacia genome contains homologs of genes encoding PG biosynthetic functions in other bacteria. PG biosynthesis involves the formation of the undecaprenyl-pyrophosphate-linked N-acetyl glucosamine-N-acetyl muramic acid-pentapeptide, known as lipid II, which is built on the cytosolic face of the cell membrane. Lipid II is then translocated across the membrane and its glycopeptide moiety becomes incorporated into the growing cell wall mesh; this translocation step is critical to PG synthesis. We have investigated candidate flippase homologs of the MurJ family in B. cenocepacia. Our results show that BCAL2764, herein referred to as murJBc, is indispensable for viability. Viable B. cenocepacia could only be obtained through a conditional mutagenesis strategy by placing murJBc under the control of a rhamnose-inducible promoter. Under rhamnose depletion, the conditional strain stopped growing and individual cells displayed morphological abnormalities consistent with a defect in PG synthesis. Bacterial cells unable to express MurJBc underwent cell lysis, while partial MurJBc depletion sensitized the mutant to the action of β-lactam antibiotics. Depletion of MurJBc caused accumulation of PG precursors consistent with the notion that this protein plays a role in lipid II flipping to the periplasmic compartment. Reciprocal complementation experiments of conditional murJ mutants in B. cenocepacia and Escherichia coli with plasmids expressing MurJ from each strain indicated that MurJBc and MurJEc are functional homologs. Together, our results are consistent with the notion that MurJBc is a PG lipid II flippase in B. cenocepacia.
Collapse
|
16
|
Getsin I, Nalbandian GH, Yee DC, Vastermark A, Paparoditis PCG, Reddy VS, Saier MH. Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor. BMC Microbiol 2013; 13:279. [PMID: 24304716 PMCID: PMC3924187 DOI: 10.1186/1471-2180-13-279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/20/2013] [Indexed: 01/11/2023] Open
Abstract
Background Two of the largest fully sequenced prokaryotic genomes are those of the actinobacterium, Streptomyces coelicolor (Sco), and the δ-proteobacterium, Myxococcus xanthus (Mxa), both differentiating, sporulating, antibiotic producing, soil microbes. Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa. Results Surprisingly, Sco has 93% more identifiable transport proteins than Mxa. This is because Sco has amplified several specific types of its transport protein genes, while Mxa has done so to a much lesser extent. Amplification is substrate- and family-specific. For example, Sco but not Mxa has amplified its voltage-gated ion channels but not its aquaporins and mechano-sensitive channels. Sco but not Mxa has also amplified drug efflux pumps of the DHA2 Family of the Major Facilitator Superfamily (MFS) (49 versus 6), amino acid transporters of the APC Family (17 versus 2), ABC-type sugar transport proteins (85 versus 6), and organic anion transporters of several families. Sco has not amplified most other types of transporters. Mxa has selectively amplified one family of macrolid exporters relative to Sco (16 versus 1), consistent with the observation that Mxa makes more macrolids than does Sco. Conclusions Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently. A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives. The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene amplification.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Milton H Saier
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
| |
Collapse
|
17
|
Wang J, Mei H, Qian H, Tang Q, Liu X, Yu Z, He J. Expression profile and regulation of spore and parasporal crystal formation-associated genes in Bacillus thuringiensis. J Proteome Res 2013; 12:5487-501. [PMID: 24215520 DOI: 10.1021/pr4003728] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus thuringiensis, a Gram-positive endospore-forming bacterium, is characterized by the formation of parasporal crystals consisting of insecticidal crystal proteins (ICPs) during sporulation. We reveal gene expression profiles and regulatory mechanisms associated with spore and parasporal crystal formation based on transcriptomics and proteomics data of B. thuringiensis strain CT-43. During sporulation, five ICP genes encoded by CT-43 were specifically transcribed; moreover, most of the spore structure-, assembly-, and maturation-associated genes were specifically expressed or significantly up-regulated, with significant characteristics of temporal regulation. These findings suggest that it is essential for the cell to maintain efficient operation of transcriptional and translational machinery during sporulation. Our results indicate that the RNA polymerase complex δ and ω subunits, cold shock proteins, sigma factors, and transcriptional factors as well as the E2 subunit of the pyruvate dehydrogenase complex could cooperatively participate in transcriptional regulation via different mechanisms. In particular, differences in processing and modification of ribosomal proteins, rRNA, and tRNA combined with derepression of translational inhibition could boost the rate of ribosome recycling and assembly as well as translation initiation, elongation, and termination efficiency, thereby compensating for the reduction in ribosomal levels. The efficient operation of translational machineries and powerful protein-quality controlling systems would thus ensure biosyntheses of a large quantity of proteins with normal biological functions during sporulation.
Collapse
Affiliation(s)
- Jieping Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan, Hubei 430070, China
| | | | | | | | | | | | | |
Collapse
|
18
|
Higgins D, Dworkin J. Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev 2011; 36:131-48. [PMID: 22091839 DOI: 10.1111/j.1574-6976.2011.00310.x] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 08/25/2011] [Accepted: 09/02/2011] [Indexed: 11/29/2022] Open
Abstract
The Gram-positive bacterium Bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. Here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, DNA translocation, cell-cell communication, protein localization and spore morphogenesis. The progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-specific proteins are involved in vegetative growth.
Collapse
Affiliation(s)
- Douglas Higgins
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | |
Collapse
|
19
|
Eichenberger P. The red-ox status of a penicillin-binding protein is an on/off switch for spore peptidoglycan synthesis in Bacillus subtilis. Mol Microbiol 2009; 75:10-2. [PMID: 19919674 DOI: 10.1111/j.1365-2958.2009.06963.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Thiol-disulphide oxidoreductases catalyse the formation or breakage of disulphide bonds to control the red-ox status of a variety of proteins. Their activity is compartmentalized, as exemplified by the distinct roles these enzymes play in the cytoplasm and periplasm of Gram-negative bacteria. In this issue of Molecular Microbiology, an article from Lars Hederstedt and collaborators at Lund University sheds light on another member of this superfamily of proteins, the thioredoxin-like protein StoA from Bacillus subtilis. Interestingly, StoA function is required in yet another subcellular compartment: the intermembrane space that separates forespores from mother cells in endospore-forming bacteria. Specifically, this study demonstrates that the high-molecular-weight penicillin-binding protein SpoVD, which contains two exposed cysteine residues and whose extracellular domain is located in the intermembrane space, is a substrate of StoA. As formation of a disulphide bond most likely inactivates SpoVD activity, the converse breakage of that bond in a process catalysed by StoA appears to be the trigger that initiates peptidoglycan synthesis in sporulating cells.
Collapse
Affiliation(s)
- Patrick Eichenberger
- Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, New York, NY 10003, USA.
| |
Collapse
|
20
|
Liu Y, Carlsson Möller M, Petersen L, Söderberg CAG, Hederstedt L. Penicillin-binding protein SpoVD disulphide is a target for StoA in Bacillus subtilis forespores. Mol Microbiol 2009; 75:46-60. [PMID: 19919673 DOI: 10.1111/j.1365-2958.2009.06964.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial endospore is a dormant and heat-resistant form of life. StoA (SpoIVH) in Bacillus subtilis is a membrane-bound thioredoxin-like protein involved in endospore cortex synthesis. It is proposed to reduce disulphide bonds in hitherto unknown proteins in the intermembrane compartment of developing forespores. Starting with a bioinformatic analysis combined with mutant studies we identified the sporulation-specific, high-molecular-weight, class B penicillin-binding protein SpoVD as a putative target for StoA. We then demonstrate that SpoVD is a membrane-bound protein with two exposed redox-active cysteine residues. Structural modelling of SpoVD, based on the well characterized orthologue PBP2x of Streptococcus pneumoniae, confirmed that a disulphide bond can form close to the active site of the penicillin-binding domain restricting access of enzyme substrate or functional association with other cortex biogenic proteins. Finally, by exploiting combinations of mutations in the spoVD, stoA and ccdA genes in B. subtilis cells, we present strong in vivo evidence that supports the conclusion that StoA functions to specifically break the disulphide bond in the SpoVD protein in the forespore envelope. The findings contribute to our understanding of endospore biogenesis and open a new angle to regulation of cell wall synthesis and penicillin-binding protein activity.
Collapse
Affiliation(s)
- Yiming Liu
- Department of Cell & Organism Biology, Lund University, Lund, Sweden
| | | | | | | | | |
Collapse
|