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Hugonneau-Beaufet I, Barnier JP, Thiriet-Rupert S, Létoffé S, Mainardi JL, Ghigo JM, Beloin C, Arthur M. Characterization of Pseudomonas aeruginosa l,d-Transpeptidases and Evaluation of Their Role in Peptidoglycan Adaptation to Biofilm Growth. Microbiol Spectr 2023; 11:e0521722. [PMID: 37255442 PMCID: PMC10434034 DOI: 10.1128/spectrum.05217-22] [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: 12/20/2022] [Accepted: 04/18/2023] [Indexed: 06/01/2023] Open
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that sustains the turgor pressure of the cytoplasm, determines cell shape, and acts as a scaffold for the anchoring of envelope polymers such as lipoproteins. The final cross-linking step of peptidoglycan polymerization is performed by classical d,d-transpeptidases belonging to the penicillin-binding protein (PBP) family and by l,d-transpeptidases (LDTs), which are dispensable for growth in most bacterial species and whose physiological functions remain elusive. In this study, we investigated the contribution of LDTs to cell envelope synthesis in Pseudomonas aeruginosa grown in planktonic and biofilm conditions. We first assigned a function to each of the three P. aeruginosa LDTs by gene inactivation in P. aeruginosa, heterospecific gene expression in Escherichia coli, and, for one of them, direct determination of its enzymatic activity. We found that the three P. aeruginosa LDTs catalyze peptidoglycan cross-linking (LdtPae1), the anchoring of lipoprotein OprI to the peptidoglycan (LdtPae2), and the hydrolysis of the resulting peptidoglycan-OprI amide bond (LdtPae3). Construction of a phylogram revealed that LDTs performing each of these three functions in various species cannot be assigned to distinct evolutionary lineages, in contrast to what has been observed with PBPs. We showed that biofilm, but not planktonic bacteria, displayed an increase proportion of peptidoglycan cross-links formed by LdtPae1 and a greater extent of OprI anchoring to peptidoglycan, which is controlled by LdtPae2 and LdtPae3. Consistently, deletion of each of the ldt genes impaired biofilm formation and potentiated the bactericidal activity of EDTA. These results indicate that LDTs contribute to the stabilization of the bacterial cell envelope and to the adaptation of peptidoglycan metabolism to growth in biofilm. IMPORTANCE Active-site cysteine LDTs form a functionally heterologous family of enzymes that contribute to the biogenesis of the bacterial cell envelope through formation of peptidoglycan cross-links and through the dynamic anchoring of lipoproteins to peptidoglycan. Here, we report the role of three P. aeruginosa LDTs that had not been previously characterized. We show that these enzymes contribute to resistance to the bactericidal activity of EDTA and to the adaptation of cell envelope polymers to conditions that prevail in biofilms. These results indicate that LDTs should be considered putative targets in the development of drug-EDTA associations for the control of biofilm-related infections.
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Affiliation(s)
- Inès Hugonneau-Beaufet
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Jean-Philippe Barnier
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, Faculté de Santé, UFR de Médecine, Paris, France
| | - Stanislas Thiriet-Rupert
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Sylvie Létoffé
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Jean-Luc Mainardi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, Faculté de Santé, UFR de Médecine, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
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Peptidoglycan Remodeling by an L,D-Transpeptidase, LdtD during Cold Shock in Escherichia coli. J Bacteriol 2023; 205:e0038222. [PMID: 36507682 PMCID: PMC9879098 DOI: 10.1128/jb.00382-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan (PG) is a unique and essential component of the bacterial cell envelope. It is made up of several linear glycan polymers cross-linked through covalently attached stem peptides making it a fortified mesh-like sacculus around the bacterial cytosolic membrane. In most bacteria, including Escherichia coli, the stem peptide is made up of l-alanine (l-Ala1), d-glutamate (d-Glu2), meso-diaminopimelic acid (mDAP3), d-alanine (d-Ala4), and d-Ala5 with cross-links occurring either between d-ala4 and mDAP3 or between two mDAP3 residues. Of these, the cross-links of the 4-3 (d-Ala4-mDAP3) type are the most predominant and are formed by penicillin-binding D,D-transpeptidases, whereas the formation of less frequent 3-3 linkages (mDAP3-mDAP3) is catalyzed by L,D-transpeptidases. In this study, we found that the frequency of the 3-3 cross-linkages increased upon cold shock in exponentially growing E. coli and that the increase was mediated by an L,D-transpeptidase, LdtD. We found that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation resulting in an increased abundance of 3-3 cross-linkages during cold shock. However, DeaD was also required for optimal expression of LdtD during growth at ambient temperature. Overall, our study finds that E. coli undergoes PG remodeling during cold shock by altering the frequency of 3-3 cross-linkages, implying a role for these modifications in conferring fitness and survival advantage to bacteria growing in diverse environmental conditions. IMPORTANCE Most bacteria are surrounded by a protective exoskeleton called peptidoglycan (PG), an extensively cross-linked mesh-like macromolecule. In bacteria, such as Escherichia coli, the cross-links in the PG are of two types: a major fraction is of 4-3 type whereas a minor fraction is of 3-3 type. Here, we showed that E. coli exposed to cold shock had elevated levels of 3-3 cross-links due to the upregulation of an enzyme, LdtD, that catalyzed their formation. We showed that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation, resulting in increased 3-3 cross-links during cold shock. Our results suggest that PG remodeling contributes to the survival and fitness of bacteria growing in conditions of cold stress.
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LdtC Is a Key l,d-Transpeptidase for Peptidoglycan Assembly in Mycobacterium smegmatis. J Bacteriol 2023; 205:e0042422. [PMID: 36541811 PMCID: PMC9879121 DOI: 10.1128/jb.00424-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The peptidoglycan of mycobacteria has two types of direct cross-links, classical 4-3 cross-links that occur between diaminopimelate (DAP) and alanine residues, and nonclassical 3-3 cross-links that occur between DAP residues on adjacent peptides. The 3-3 cross-links are synthesized by the concerted action of d,d-carboxypeptidases and l,d-transpeptidases (Ldts). Mycobacterial genomes encode several Ldt proteins that can be classified into six classes based upon sequence identity. As a group, the Ldt enzymes are resistant to most β-lactam antibiotics but are susceptible to carbapenem antibiotics, with the exception of LdtC, a class 5 enzyme. In previous work, we showed that loss of LdtC has the greatest effect on the carbapenem susceptibility phenotype of Mycobacterium smegmatis (also known as Mycolicibacterium smegmatis) compared to other ldt deletion mutants. In this work, we show that a M. smegmatis mutant lacking the five ldt genes other than ldtC has a wild-type phenotype with the exception of increased susceptibility to rifampin. In contrast, a mutant lacking all six ldt genes has pleiotropic cell envelope defects, is temperature sensitive, and has increased susceptibility to a variety of antibiotics. These results indicate that LdtC is capable of functioning as the sole l,d-transpeptidase in M. smegmatis and suggest that it may represent a carbapenem-resistant pathway for peptidoglycan biosynthesis. IMPORTANCE Mycobacteria have several enzymes to catalyze nonclassical 3-3 linkages in the cell wall peptidoglycan. Understanding the biology of these cross-links is important for the development of antibiotic therapies to target peptidoglycan biosynthesis. Our work provides evidence that LdtC can function as the sole enzyme for 3-3 cross-link formation in M. smegmatis and suggests that LdtC may be part of a carbapenem-resistant l,d-transpeptidase pathway.
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Organomercurial lyase (MerB)-mediated demethylation decreases bacterial methylmercury resistance in the absence of mercuric reductase (MerA). Appl Environ Microbiol 2022; 88:e0001022. [PMID: 35138926 DOI: 10.1128/aem.00010-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mer operon encodes enzymes that transform and detoxify methylmercury (MeHg) and/or inorganic mercury (Hg(II)). Organomercurial lyase (MerB) and mercuric reductase (MerA) can act sequentially to demethylate MeHg to Hg(II) and reduce Hg(II) to volatile elemental mercury (Hg0) that can escape from the cell, conferring resistance to MeHg and Hg(II). Most identified mer operons encode either MerA and MerB in tandem or MerA alone, however, microbial genomes were recently identified that encode only MerB. Yet, the effects of potentially producing intracellular Hg(II) via demethylation of MeHg by MerB, independent of a mechanism to further detoxify or sequester the metal is not well understood. Here, we investigate MeHg biotransformation in Escherichia coli strains engineered to express MerA and MerB, together or separately, and characterize cell viability and Hg detoxification kinetics when these strains are grown in the presence of MeHg. Strains expressing only MerB are capable of demethylating MeHg to Hg(II). Compared to strains that express both MerA and MerB, strains expressing only MerB exhibit a lower minimum inhibitory concentration with MeHg exposure, which parallels a redistribution of Hg from the cell-associated fraction to the culture medium, consistent with cell lysis occurring. The data support a model whereby intracellular production of Hg(II), in the absence of reduction or other forms of demobilization, results in a greater cytotoxicity compared to the parent MeHg compound. Collectively, these results suggest that in the context of MeHg detoxification, MerB must be accompanied by an additional mechanism(s) to reduce, sequester, or re-distribute generated Hg(II). Importance: Mercury is a globally distributed pollutant that poses a risk to wildlife and human health. The toxicity of mercury is influenced largely by microbially mediated biotransformation between its organic (methylmercury) and inorganic (Hg(II) and Hg0) forms. Here we show in a relevant cellular context that the organomercurial lyase (MerB) enzyme is capable of MeHg demethylation without subsequent mercuric reductase (MerA)-mediated reduction of Hg(II). Demethylation of MeHg without subsequent Hg(II) reduction results in a greater cytotoxicity and increased cell lysis. Microbes carrying MerB alone have recently been identified but have yet to be characterized. Our results demonstrate that mer operons encoding MerB but not MerA put the cell at a disadvantage in the context of MeHg exposure, unless subsequent mechanisms of reduction or Hg(II) sequestration exist. These findings may help uncover the existence of alternative mechanisms of Hg(II) detoxification in addition to revealing the drivers of mer operon evolution.
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Tian D, Han M. Bacterial peptidoglycan muropeptides benefit mitochondrial homeostasis and animal physiology by acting as ATP synthase agonists. Dev Cell 2022; 57:361-372.e5. [PMID: 35045336 PMCID: PMC8825754 DOI: 10.1016/j.devcel.2021.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
The symbiotic relationship between commensal microbes and host animals predicts unidentified beneficial impacts of individual bacterial metabolites on animal physiology. Peptidoglycan fragments (muropeptides) from the bacterial cell wall are known for their roles in pathogenicity and for inducing host immune responses. However, the potential beneficial usage of muropeptides from commensal bacteria by the host needs exploration. We identified a striking role for muropeptides in supporting mitochondrial homeostasis, development, and behaviors in Caenorhabditis elegans. We determined that the beneficial molecules are disaccharide muropeptides containing a short AA chain, and they enter intestinal-cell mitochondria to repress oxidative stress. Further analyses indicate that muropeptides execute this role by binding to and promoting the activity of ATP synthase. Therefore, given the exceptional structural conservation of ATP synthase, the role of muropeptides as a rare agonist of the ATP synthase presents a major conceptual modification regarding the impact of bacterial cell metabolites on animal physiology.
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Affiliation(s)
- Dong Tian
- Department of MCDB, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Min Han
- Department of MCDB, University of Colorado at Boulder, Boulder, CO 80309, USA.
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Acinetobacter baumannii Can Survive with an Outer Membrane Lacking Lipooligosaccharide Due to Structural Support from Elongasome Peptidoglycan Synthesis. mBio 2021; 12:e0309921. [PMID: 34844428 PMCID: PMC8630537 DOI: 10.1128/mbio.03099-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative bacteria resist external stresses due to cell envelope rigidity, which is provided by two membranes and a peptidoglycan layer. The outer membrane (OM) surface contains lipopolysaccharide (LPS; contains O-antigen) or lipooligosaccharide (LOS). LPS/LOS are essential in most Gram-negative bacteria and may contribute to cellular rigidity. Acinetobacter baumannii is a useful tool for testing these hypotheses as it can survive without LOS. Previously, our group found that strains with naturally high levels of penicillin binding protein 1A (PBP1A) could not become LOS deficient unless the gene encoding it was deleted, highlighting the relevance of peptidoglycan biosynthesis and suggesting that high PBP1A levels were toxic during LOS deficiency. Transposon sequencing and follow-up analysis found that axial peptidoglycan synthesis by the elongasome and a peptidoglycan recycling enzyme, ElsL, were vital in LOS-deficient cells. The toxicity of high PBP1A levels during LOS deficiency was clarified to be due to a negative impact on elongasome function. Our data suggest that during LOS deficiency, the strength of the peptidoglycan specifically imparted by elongasome synthesis becomes essential, supporting that the OM and peptidoglycan contribute to cell rigidity.
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7
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Gupta R, Al-Kharji NMSA, Alqurafi MA, Nguyen TQ, Chai W, Quan P, Malhotra R, Simcox BS, Mortimer P, Brammer Basta LA, Rohde KH, Buynak JD. Atypically Modified Carbapenem Antibiotics Display Improved Antimycobacterial Activity in the Absence of β-Lactamase Inhibitors. ACS Infect Dis 2021; 7:2425-2436. [PMID: 34191496 PMCID: PMC8369493 DOI: 10.1021/acsinfecdis.1c00185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Commercial carbapenem
antibiotics are being used to treat multidrug
resistant (MDR) and extensively drug resistant (XDR) tuberculosis.
Like other β-lactams, carbapenems are irreversible inhibitors
of serine d,d-transpeptidases involved in peptidoglycan biosynthesis.
In addition to d,d-transpeptidases, mycobacteria also utilize
nonhomologous cysteine l,d-transpeptidases (Ldts) to cross-link
the stem peptides of peptidoglycan, and carbapenems form long-lived
acyl-enzymes with Ldts. Commercial carbapenems are C2 modifications
of a common scaffold. This study describes the synthesis of a series
of atypical, C5α modifications of the carbapenem scaffold, microbiological
evaluation against Mycobacterium tuberculosis (Mtb) and the nontuberculous mycobacterial species, Mycobacterium abscessus (Mab), as well
as acylation of an important mycobacterial target Ldt, LdtMt2. In vitro evaluation of these C5α-modified
carbapenems revealed compounds with standalone (i.e., in the absence of a β-lactamase inhibitor) minimum inhibitory
concentrations (MICs) superior to meropenem-clavulanate for Mtb, and meropenem-avibactam for Mab. Time-kill
kinetics assays showed better killing (2–4 log decrease) of Mtb and Mab with lower concentrations of
compound 10a as compared to meropenem. Although susceptibility
of clinical isolates to meropenem varied by nearly 100-fold, 10a maintained excellent activity against all Mtb and Mab strains. High resolution mass spectrometry
revealed that 10a acylates LdtMt2 at a rate
comparable to meropenem, but subsequently undergoes an unprecedented
carbapenem fragmentation, leading to an acyl-enzyme with mass of Δm = +86 Da. Rationale for the divergence of the nonhydrolytic
fragmentation of the LdtMt2 acyl-enzymes is proposed. The
observed activity illustrates the potential of novel atypical carbapenems
as prospective candidates for treatment of Mtb and Mab infections.
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Affiliation(s)
- Rashmi Gupta
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | | | - Maha A. Alqurafi
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Thu Q. Nguyen
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Weirui Chai
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Pojun Quan
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Riya Malhotra
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Breven S. Simcox
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Phil Mortimer
- Department of Chemistry, Mass Spectrometry Facility, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Leighanne A. Brammer Basta
- Chemistry Department, United States Naval Academy, 572M Holloway Road, Annapolis, Maryland 21402, United States
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
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Voedts H, Dorchêne D, Lodge A, Vollmer W, Arthur M, Hugonnet JE. Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes in Escherichia coli. EMBO J 2021; 40:e108126. [PMID: 34382698 DOI: 10.15252/embj.2021108126] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria resist to the turgor pressure of the cytoplasm through a net-like macromolecule, the peptidoglycan, made of glycan strands connected via peptides cross-linked by penicillin-binding proteins (PBPs). We recently reported the emergence of β-lactam resistance resulting from a bypass of PBPs by the YcbB L,D-transpeptidase (LdtD), which form chemically distinct 3→3 cross-links compared to 4→3 formed by PBPs. Here we show that peptidoglycan expansion requires controlled hydrolysis of cross-links and identify among eight endopeptidase paralogues the minimum enzyme complements essential for bacterial growth with 4→3 (MepM) and 3→3 (MepM and MepK) cross-links. Purified Mep endopeptidases unexpectedly displayed a 4→3 and 3→3 dual specificity implying recognition of a common motif in the two cross-link types. Uncoupling of the polymerization of glycan chains from the 4→3 cross-linking reaction was found to facilitate the bypass of PBPs by YcbB. These results illustrate the plasticity of the peptidoglycan polymerization machinery in response to the selective pressure of β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
| | - Delphine Dorchêne
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
| | - Adam Lodge
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Paris, France
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Gurnani Serrano CK, Winkle M, Martorana AM, Biboy J, Morè N, Moynihan P, Banzhaf M, Vollmer W, Polissi A. ActS activates peptidoglycan amidases during outer membrane stress in Escherichia coli. Mol Microbiol 2021; 116:329-342. [PMID: 33660879 PMCID: PMC8360153 DOI: 10.1111/mmi.14712] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/22/2022]
Abstract
The integrity of the cell envelope of E. coli relies on the concerted activity of multi-protein machineries that synthesize the peptidoglycan (PG) and the outer membrane (OM). Our previous work found that the depletion of lipopolysaccharide (LPS) export to the OM induces an essential PG remodeling process involving LD-transpeptidases (LDTs), the glycosyltransferase function of PBP1B and the carboxypeptidase PBP6a. Consequently, cells with defective OM biogenesis lyse if they lack any of these PG enzymes. Here we report that the morphological defects, and lysis associated with a ldtF mutant with impaired LPS transport, are alleviated by the loss of the predicted OM-anchored lipoprotein ActS (formerly YgeR). We show that ActS is an inactive member of LytM-type peptidoglycan endopeptidases due to a degenerated catalytic domain. ActS is capable of activating all three main periplasmic peptidoglycan amidases, AmiA, AmiB, and AmiC, which were previously reported to be activated only by EnvC and/or NlpD. Our data also suggest that in vivo ActS preferentially activates AmiC and that its function is linked to cell envelope stress.
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Affiliation(s)
| | - Matthias Winkle
- The Centre for Bacterial Cell BiologyBiosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Alessandra M. Martorana
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Jacob Biboy
- The Centre for Bacterial Cell BiologyBiosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Niccolo Morè
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
- Present address:
Nikon Instruments Europe B.VAmsterdamNorth HollandNetherlands
| | - Patrick Moynihan
- Institute of Microbiology and InfectionSchool of Biological SciencesUniversity of BirminghamBirminghamUK
| | - Manuel Banzhaf
- Institute of Microbiology and InfectionSchool of Biological SciencesUniversity of BirminghamBirminghamUK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell BiologyBiosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
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Cleavage of Braun's lipoprotein Lpp from the bacterial peptidoglycan by a paralog of l,d-transpeptidases, LdtF. Proc Natl Acad Sci U S A 2021; 118:2101989118. [PMID: 33941679 DOI: 10.1073/pnas.2101989118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gram-negative bacterial cell envelope is made up of an outer membrane (OM), an inner membrane (IM) that surrounds the cytoplasm, and a periplasmic space between the two membranes containing peptidoglycan (PG or murein). PG is an elastic polymer that forms a mesh-like sacculus around the IM, protecting cells from turgor and environmental stress conditions. In several bacteria, including Escherichia coli, the OM is tethered to PG by an abundant OM lipoprotein, Lpp (or Braun's lipoprotein), that functions to maintain the structural and functional integrity of the cell envelope. Since its discovery, Lpp has been studied extensively, and although l,d-transpeptidases, the enzymes that catalyze the formation of PG-Lpp linkages, have been earlier identified, it is not known how these linkages are modulated. Here, using genetic and biochemical approaches, we show that LdtF (formerly yafK), a newly identified paralog of l,d-transpeptidases in E. coli, is a murein hydrolytic enzyme that catalyzes cleavage of Lpp from the PG sacculus. LdtF also exhibits glycine-specific carboxypeptidase activity on muropeptides containing a terminal glycine residue. LdtF was earlier presumed to be an l,d-transpeptidase; however, our results show that it is indeed an l,d-endopeptidase that hydrolyzes the products generated by the l,d-transpeptidases. To summarize, this study describes the discovery of a murein endopeptidase with a hitherto unknown catalytic specificity that removes the PG-Lpp cross-links, suggesting a role for LdtF in the regulation of PG-OM linkages to maintain the structural integrity of the bacterial cell envelope.
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11
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García-Del Portillo F. Building peptidoglycan inside eukaryotic cells: A view from symbiotic and pathogenic bacteria. Mol Microbiol 2020; 113:613-626. [PMID: 32185832 PMCID: PMC7154730 DOI: 10.1111/mmi.14452] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/08/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022]
Abstract
The peptidoglycan (PG), as the exoskeleton of most prokaryotes, maintains a defined shape and ensures cell integrity against the high internal turgor pressure. These important roles have attracted researchers to target PG metabolism in order to control bacterial infections. Most studies, however, have been performed in bacteria grown under laboratory conditions, leading to only a partial view on how the PG is synthetized in natural environments. As a case in point, PG metabolism and its regulation remain poorly understood in symbiotic and pathogenic bacteria living inside eukaryotic cells. This review focuses on the PG metabolism of intracellular bacteria, emphasizing the necessity of more in vivo studies involving the analysis of enzymes produced in the intracellular niche and the isolation of PG from bacteria residing within eukaryotic cells. The review also points to persistent infections caused by some intracellular bacterial pathogens and the extent at which the PG could contribute to establish such physiological state. Based on recent evidences, I speculate on the idea that certain structural features of the PG may facilitate attenuation of intracellular growth. Lastly, I discuss recent findings in endosymbionts supporting a cooperation between host and bacterial enzymes to assemble a mature PG.
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12
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The Twin-Arginine Translocation System Is Important for Stress Resistance and Virulence of Brucella melitensis. Infect Immun 2020; 88:IAI.00389-20. [PMID: 32778612 DOI: 10.1128/iai.00389-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/03/2020] [Indexed: 12/25/2022] Open
Abstract
Brucella, the causative agent of brucellosis, is a stealthy intracellular pathogen that is highly pathogenic to a range of mammals, including humans. The twin-arginine translocation (Tat) pathway transports folded proteins across the cytoplasmic membrane and has been implicated in virulence in many bacterial pathogens. However, the roles of the Tat system and related substrates in Brucella remain unclear. We report here that disruption of Tat increases the sensitivity of Brucella melitensis M28 to the membrane stressor sodium dodecyl sulfate (SDS), indicating cell envelope defects, as well as to EDTA. In addition, mutating Tat renders M28 bacteria more sensitive to oxidative stress caused by H2O2 Further, loss of Tat significantly attenuates B. melitensis infection in murine macrophages ex vivo Using a mouse model for persistent infection, we demonstrate that Tat is required for full virulence of B. melitensis M28. Genome-wide in silico prediction combined with an in vivo amidase reporter assay indicates that at least 23 proteins are authentic Tat substrates, and they are functionally categorized into solute-binding proteins, oxidoreductases, cell envelope biosynthesis enzymes, and others. A comprehensive deletion study revealed that 6 substrates contribute significantly to Brucella virulence, including an l,d-transpeptidase, an ABC transporter solute-binding protein, and a methionine sulfoxide reductase. Collectively, our work establishes that the Tat pathway plays a critical role in Brucella virulence.
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Palmer T, Finney AJ, Saha CK, Atkinson GC, Sargent F. A holin/peptidoglycan hydrolase-dependent protein secretion system. Mol Microbiol 2020; 115:345-355. [PMID: 32885520 DOI: 10.1111/mmi.14599] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022]
Abstract
Gram-negative bacteria have evolved numerous pathways to secrete proteins across their complex cell envelopes. Here, we describe a protein secretion system that uses a holin membrane protein in tandem with a cell wall-editing enzyme to mediate the secretion of substrate proteins from the periplasm to the cell exterior. The identity of the cell wall-editing enzymes involved was found to vary across biological systems. For instance, the chitinase secretion pathway of Serratia marcescens uses an endopeptidase to facilitate secretion, whereas the secretion of Typhoid toxin in Salmonella enterica serovar Typhi relies on a muramidase. Various families of holins are also predicted to be involved. Genomic analysis indicates that this pathway is conserved and implicated in the secretion of hydrolytic enzymes and toxins for a range of bacteria. The pairing of holins from different families with various types of peptidoglycan hydrolases suggests that this secretion pathway evolved multiple times. We suggest that the complementary bodies of evidence presented is sufficient to propose that the pathway be named the Type 10 Secretion System (TXSS).
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Affiliation(s)
- Tracy Palmer
- Microbes in Health & Disease, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Alexander J Finney
- Plant & Microbial Biology, School of Natural and Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne, UK
| | - Chayan Kumar Saha
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Gemma C Atkinson
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Frank Sargent
- Plant & Microbial Biology, School of Natural and Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne, UK
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Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. Front Microbiol 2019; 10:331. [PMID: 30873139 PMCID: PMC6403190 DOI: 10.3389/fmicb.2019.00331] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
The cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | | | - Magdalena Popowska
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
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15
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Abstract
In Gram-negative bacteria, the outer membrane protects the cell against many toxic molecules, and the peptidoglycan layer provides protection against osmotic challenges, allowing bacterial cells to survive in changing environments. Maintaining cell envelope integrity is therefore a question of life or death for a bacterial cell. Here we show that Escherichia coli cells activate the LD-transpeptidase LdtD to introduce 3-3 cross-links in the peptidoglycan layer when the integrity of the outer membrane is compromised, and this response is required to avoid cell lysis. This peptidoglycan remodeling program is a strategy to increase the overall robustness of the bacterial cell envelope in response to defects in the outer membrane. Gram-negative bacteria have a tripartite cell envelope with the cytoplasmic membrane (CM), a stress-bearing peptidoglycan (PG) layer, and the asymmetric outer membrane (OM) containing lipopolysaccharide (LPS) in the outer leaflet. Cells must tightly coordinate the growth of their complex envelope to maintain cellular integrity and OM permeability barrier function. The biogenesis of PG and LPS relies on specialized macromolecular complexes that span the entire envelope. In this work, we show that Escherichia coli cells are capable of avoiding lysis when the transport of LPS to the OM is compromised, by utilizing LD-transpeptidases (LDTs) to generate 3-3 cross-links in the PG. This PG remodeling program relies mainly on the activities of the stress response LDT, LdtD, together with the major PG synthase PBP1B, its cognate activator LpoB, and the carboxypeptidase PBP6a. Our data support a model according to which these proteins cooperate to strengthen the PG in response to defective OM synthesis.
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16
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Stankeviciute G, Miguel AV, Radkov A, Chou S, Huang KC, Klein EA. Differential modes of crosslinking establish spatially distinct regions of peptidoglycan in
Caulobacter crescentus. Mol Microbiol 2019; 111:995-1008. [DOI: 10.1111/mmi.14199] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriele Stankeviciute
- Center for Computational and Integrative Biology Rutgers University‐Camden Camden NJ 08102USA
| | - Amanda V. Miguel
- Department of Bioengineering Stanford University Stanford CA 94305USA
| | - Atanas Radkov
- Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94158USA
| | - Seemay Chou
- Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94158USA
- Chan Zuckerberg Biohub San Francisco CA 94158USA
| | - Kerwyn Casey Huang
- Department of Bioengineering Stanford University Stanford CA 94305USA
- Chan Zuckerberg Biohub San Francisco CA 94158USA
- Department of Microbiology and Immunology Stanford University School of Medicine Stanford CA 94305USA
| | - Eric A. Klein
- Center for Computational and Integrative Biology Rutgers University‐Camden Camden NJ 08102USA
- Biology Department Rutgers University‐Camden Camden NJ 08102USA
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Schaub RE, Dillard JP. The Pathogenic Neisseria Use a Streamlined Set of Peptidoglycan Degradation Proteins for Peptidoglycan Remodeling, Recycling, and Toxic Fragment Release. Front Microbiol 2019; 10:73. [PMID: 30766523 PMCID: PMC6365954 DOI: 10.3389/fmicb.2019.00073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 01/15/2019] [Indexed: 12/26/2022] Open
Abstract
Neisseria gonorrhoeae and Neisseria meningitidis release peptidoglycan (PG) fragments from the cell as the bacteria grow. For N. gonorrhoeae these PG fragments are known to cause damage to human Fallopian tube tissue in organ culture that mimics the damage seen in patients with pelvic inflammatory disease. N. meningitidis also releases pro-inflammatory PG fragments, but in smaller amounts than those from N. gonorrhoeae. It is not yet known if PG fragment release contributes to the highly inflammatory conditions of meningitis and meningococcemia caused by N. meningitidis. Examination of the mechanisms of PG degradation and recycling identified proteins required for these processes. In comparison to the model organism E. coli, the pathogenic Neisseria have far fewer PG degradation proteins, and some of these proteins show differences in subcellular localization compared to their E. coli homologs. In particular, some N. gonorrhoeae PG degradation proteins were demonstrated to be in the outer membrane while their homologs in E. coli were found free in the periplasm or in the cytoplasm. The localization of two of these proteins was demonstrated to affect PG fragment release. Another major factor for PG fragment release is the allele of ampG. Gonococcal AmpG was found to be slightly defective compared to related PG fragment permeases, thus leading to increased release of PG. A number of additional PG-related factors affect other virulence functions in Neisseria. Endopeptidases and carboxypeptidases were found to be required for type IV pilus production and resistance to hydrogen peroxide. Also, deacetylation of PG was required for virulence of N. meningitidis as well as normal cell size. Overall, we describe the processes involved in PG degradation and recycling and how certain characteristics of these proteins influence the interactions of these pathogens with their host.
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Affiliation(s)
- Ryan E Schaub
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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18
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Neisseria gonorrhoeae PBP3 and PBP4 Facilitate NOD1 Agonist Peptidoglycan Fragment Release and Survival in Stationary Phase. Infect Immun 2019; 87:IAI.00833-18. [PMID: 30510100 DOI: 10.1128/iai.00833-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/25/2018] [Indexed: 01/16/2023] Open
Abstract
Neisseria gonorrhoeae releases peptidoglycan fragments during growth, and these molecules induce an inflammatory response in the human host. The proinflammatory molecules include peptidoglycan monomers, peptidoglycan dimers, and free peptides. These molecules can be released by the actions of lytic transglycosylases or an amidase. However, >40% of the gonococcal cell wall is cross-linked, where the peptide stem on one peptidoglycan strand is linked to the peptide stem on a neighboring strand, suggesting that endopeptidases may be required for the release of many peptidoglycan fragments. Therefore, we characterized mutants with individual or combined mutations in genes for the low-molecular-mass penicillin-binding proteins PBP3 and PBP4. Mutations in either dacB, encoding PBP3, or pbpG, encoding PBP4, did not significantly reduce the release of peptidoglycan monomers or free peptides. A mutation in dacB caused the appearance of a larger-sized peptidoglycan monomer, the pentapeptide monomer, and an increased release of peptidoglycan dimers, suggesting the involvement of this enzyme in both the removal of C-terminal d-Ala residues from stem peptides and the cleavage of cross-linked peptidoglycan. Mutation of both dacB and pbpG eliminated the release of tripeptide-containing peptidoglycan fragments concomitantly with the appearance of pentapeptide and dipeptide peptidoglycan fragments and higher-molecular-weight peptidoglycan dimers. In accord with the loss of tripeptide peptidoglycan fragments, the level of human NOD1 activation by the dacB pbpG mutants was significantly lower than that by the wild type. We conclude that PBP3 and PBP4 overlap in function for cross-link cleavage and that these endopeptidases act in the normal release of peptidoglycan fragments during growth.
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Abstract
The peptidoglycan sacculus is a net-like polymer that surrounds the cytoplasmic membrane in most bacteria. It is essential to maintain the bacterial cell shape and protect from turgor. The peptidoglycan has a basic composition, common to all bacteria, with species-specific variations that can modify its biophysical properties or the pathogenicity of the bacteria. The synthesis of peptidoglycan starts in the cytoplasm and the precursor lipid II is flipped across the cytoplasmic membrane. The new peptidoglycan strands are synthesised and incorporated into the pre-existing sacculus by the coordinated activities of peptidoglycan synthases and hydrolases. In the model organism Escherichia coli there are two complexes required for the elongation and division. Each of them is regulated by different proteins from both the cytoplasmic and periplasmic sides that ensure the well-coordinated synthesis of new peptidoglycan.
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Hisham Y, Ashhab Y. Identification of Cross-Protective Potential Antigens against Pathogenic Brucella spp. through Combining Pan-Genome Analysis with Reverse Vaccinology. J Immunol Res 2018; 2018:1474517. [PMID: 30622973 PMCID: PMC6304850 DOI: 10.1155/2018/1474517] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/04/2018] [Indexed: 01/18/2023] Open
Abstract
Brucellosis is a zoonotic infectious disease caused by bacteria of the genus Brucella. Brucella melitensis, Brucella abortus, and Brucella suis are the most pathogenic species of this genus causing the majority of human and domestic animal brucellosis. There is a need to develop a safe and potent subunit vaccine to overcome the serious drawbacks of the live attenuated Brucella vaccines. The aim of this work was to discover antigen candidates conserved among the three pathogenic species. In this study, we employed a reverse vaccinology strategy to compute the core proteome of 90 completed genomes: 55 B. melitensis, 17 B. abortus, and 18 B. suis. The core proteome was analyzed by a metasubcellular localization prediction pipeline to identify surface-associated proteins. The identified proteins were thoroughly analyzed using various in silico tools to obtain the most potential protective antigens. The number of core proteins obtained from analyzing the 90 proteomes was 1939 proteins. The surface-associated proteins were 177. The number of potential antigens was 87; those with adhesion score ≥ 0.5 were considered antigen with "high potential," while those with a score of 0.4-0.5 were considered antigens with "intermediate potential." According to a cumulative score derived from protein antigenicity, density of MHC-I and MHC-II epitopes, MHC allele coverage, and B-cell epitope density scores, a final list of 34 potential antigens was obtained. Remarkably, most of the 34 proteins are associated with bacterial adhesion, invasion, evasion, and adaptation to the hostile intracellular environment of macrophages which is adjusted to deprive Brucella of required nutrients. Our results provide a manageable list of potential protective antigens for developing a potent vaccine against brucellosis. Moreover, our elaborated analysis can provide further insights into novel Brucella virulence factors. Our next step is to test some of these antigens using an appropriate antigen delivery system.
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Affiliation(s)
- Yasmin Hisham
- Palestine-Korea Biotechnology Center, Palestine Polytechnic University, Hebron, State of Palestine
| | - Yaqoub Ashhab
- Palestine-Korea Biotechnology Center, Palestine Polytechnic University, Hebron, State of Palestine
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21
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Coyle JF, Pagliai FA, Zhang D, Lorca GL, Gonzalez CF. Purification and partial characterization of LdtP, a cell envelope modifying enzyme in Liberibacter asiaticus. BMC Microbiol 2018; 18:201. [PMID: 30497377 PMCID: PMC6267092 DOI: 10.1186/s12866-018-1348-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
Background The aggressive spread of Liberibacter asiaticus, a bacterium closely associated with citrus greening, has given rise to an acute crisis in the citrus industry, making it imperative to expand the scientific knowledge base regarding L. asiaticus. Despite several endeavors to culture L. asiaticus, this bacterium has yet to be maintained in axenic culture, rendering identification and analysis of potential treatment targets challenging. Accordingly, a thorough understanding of biological mechanisms involved in the citrus host-microbe relationship is critical as a means of directing the search for future treatment targets. In this study, we evaluate the biochemical characteristics of CLIBASIA_01175, renamed LdtP (L,D-transpeptidase). Surrogate strains were used to evaluate its potential biological significance in gram-negative bacteria. A strain of E. coli carrying quintuple knock-outs of all genes encoding L,D-transpeptidases was utilized to demonstrate the activity of L. asiaticus LdtP. Results This complementation study demonstrated the periplasmic localization of mature LdtP and provided evidence for the biological role of LdtP in peptidoglycan modification. Further investigation highlighted the role of LdtP as a periplasmic esterase involved in modification of the lipid A moiety of the lipopolysaccharide. This work described, for the first time, an enzyme of the L,D-transpeptidase family with moonlighting enzyme activity directed to the modification of the bacterial cell wall and LPS. Conclusions Taken together, the data indicates that LdtP is a novel protein involved in an alternative pathway for modification of the bacterial cell, potentially affording L. asiaticus a means to survive within the host. Electronic supplementary material The online version of this article (10.1186/s12866-018-1348-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janelle F Coyle
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Fernando A Pagliai
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Dan Zhang
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
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22
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Yadav AK, Espaillat A, Cava F. Bacterial Strategies to Preserve Cell Wall Integrity Against Environmental Threats. Front Microbiol 2018; 9:2064. [PMID: 30233540 PMCID: PMC6127315 DOI: 10.3389/fmicb.2018.02064] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
Bacterial cells are surrounded by an exoskeleton-like structure, the cell wall, composed primarily of the peptidoglycan (PG) sacculus. This structure is made up of glycan strands cross-linked by short peptides generating a covalent mesh that shapes bacteria and prevents their lysis due to their high internal osmotic pressure. Even though the PG is virtually universal in bacteria, there is a notable degree of diversity in its chemical structure. Modifications in both the sugars and peptides are known to be instrumental for bacteria to cope with diverse environmental challenges. In this review, we summarize and discuss the cell wall strategies to withstand biotic and abiotic environmental insults such as the effect of antibiotics targeting cell wall enzymes, predatory PG hydrolytic proteins, and PG signaling systems. Finally we will discuss the opportunities that species-specific PG variability might open to develop antimicrobial therapies.
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Affiliation(s)
- Akhilesh K Yadav
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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23
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Asmar AT, Collet JF. Lpp, the Braun lipoprotein, turns 50—major achievements and remaining issues. FEMS Microbiol Lett 2018; 365:5071948. [DOI: 10.1093/femsle/fny199] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Abir T Asmar
- WELBIO, Université catholique de Louvain, avenue Hippocrate 75, Brussels 1200, Belgium
- De Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
| | - Jean-François Collet
- WELBIO, Université catholique de Louvain, avenue Hippocrate 75, Brussels 1200, Belgium
- De Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, Brussels 1200, Belgium
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24
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Abstract
Peptidoglycan is an essential component of the cell wall that protects bacteria from environmental stress. A carefully coordinated biosynthesis of peptidoglycan during cell elongation and division is required for cell viability. This biosynthesis involves sophisticated enzyme machineries that dynamically synthesize, remodel, and degrade peptidoglycan. However, when and where bacteria build peptidoglycan, and how this is coordinated with cell growth, have been long-standing questions in the field. The improvement of microscopy techniques has provided powerful approaches to study peptidoglycan biosynthesis with high spatiotemporal resolution. Recent development of molecular probes further accelerated the growth of the field, which has advanced our knowledge of peptidoglycan biosynthesis dynamics and mechanisms. Here, we review the technologies for imaging the bacterial cell wall and its biosynthesis activity. We focus on the applications of fluorescent d-amino acids, a newly developed type of probe, to visualize and study peptidoglycan synthesis and dynamics, and we provide direction for prospective research.
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Affiliation(s)
- Atanas D Radkov
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.,Current affiliation: Biophysics and Biochemistry Department, University of California, San Francisco, California 94158, USA;
| | - Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
| | - Michael S VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; , ,
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25
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Zhao H, Patel V, Helmann JD, Dörr T. Don't let sleeping dogmas lie: new views of peptidoglycan synthesis and its regulation. Mol Microbiol 2017; 106:847-860. [PMID: 28975672 DOI: 10.1111/mmi.13853] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/24/2022]
Abstract
Bacterial cell wall synthesis is the target for some of our most powerful antibiotics and has thus been the subject of intense research focus for more than 50 years. Surprisingly, we still lack a fundamental understanding of how bacteria build, maintain and expand their cell wall. Due to technical limitations, directly testing hypotheses about the coordination and biochemistry of cell wall synthesis enzymes or architecture has been challenging, and interpretation of data has therefore often relied on circumstantial evidence and implicit assumptions. A number of recent papers have exploited new technologies, like single molecule tracking and real-time, high resolution temporal mapping of cell wall synthesis processes, to address fundamental questions of bacterial cell wall biogenesis. The results have challenged established dogmas and it is therefore timely to integrate new data and old observations into a new model of cell wall biogenesis in rod-shaped bacteria.
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Affiliation(s)
- Heng Zhao
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Vaidehi Patel
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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26
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Fluorescent D-amino-acids reveal bi-cellular cell wall modifications important for Bdellovibrio bacteriovorus predation. Nat Microbiol 2017; 2:1648-1657. [PMID: 28974693 PMCID: PMC5705579 DOI: 10.1038/s41564-017-0029-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/11/2017] [Indexed: 01/05/2023]
Abstract
Modification of essential bacterial peptidoglycan (PG) containing cell
walls can lead to antibiotic resistance, for example β-lactam resistance
by L,D-transpeptidase activities. Predatory Bdellovibrio
bacteriovorus are naturally antibacterial and combat infections by
traversing, modifying and finally destroying walls of Gram-negative prey
bacteria, modifying their own PG as they grow inside prey. Historically, these
multi-enzymatic processes on two similar PG walls have proved challenging to
elucidate. Here, with a PG labelling approach utilizing timed pulses of multiple
fluorescent D-amino acids (FDAAs), we illuminate dynamic changes that predator
and prey walls go through during the different phases of bacteria:bacteria
invasion. We show formation of a reinforced circular port-hole in the prey wall;
L,D-transpeptidaseBd mediated D-amino acid modifications
strengthening prey PG during Bdellovibrio invasion and a zonal
mode of predator-elongation. This process is followed by unconventional,
multi-point and synchronous septation of the intracellular
Bdellovibrio, accommodating odd- and even-numbered progeny
formation by non-binary division.
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27
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Appropriate Regulation of the σ E-Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli. J Bacteriol 2017; 199:JB.00089-17. [PMID: 28373273 DOI: 10.1128/jb.00089-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
The alternative sigma factor σE is a key component of the Escherichia coli response to cell envelope stress and is required for viability even in the absence of stress. The activity of σE increases during entry into stationary phase, suggesting an important role for σE when nutrients are limiting. Elevated σE activity has been proposed to activate a pathway leading to the lysis of nonculturable cells that accumulate during early stationary phase. To better understand σE-directed cell lysis and the role of σE in stationary phase, we investigated the effects of elevated σE activity in cultures grown for 10 days. We demonstrate that high σE activity is lethal for all cells in stationary phase, not only those that are nonculturable. Spontaneous mutants with reduced σE activity, due primarily to point mutations in the region of σE that binds the -35 promoter motif, arise and take over cultures within 5 to 6 days after entry into stationary phase. High σE activity leads to large reductions in the levels of outer membrane porins and increased membrane permeability, indicating membrane defects. These defects can be counteracted and stationary-phase lethality delayed significantly by stabilizing membranes with Mg2+ and buffering the growth medium or by deleting the σE-dependent small RNAs (sRNAs) MicA, RybB, and MicL, which inhibit the expression of porins and Lpp. Expression of these sRNAs also reverses the loss of viability following depletion of σE activity. Our results demonstrate that appropriate regulation of σE activity, ensuring that it is neither too high nor too low, is critical for envelope integrity and cell viability.IMPORTANCE The Gram-negative cell envelope and cytoplasm differ significantly, and separate responses have evolved to combat stress in each compartment. An array of cell envelope stress responses exist, each of which is focused on different parts of the envelope. The σE response is conserved in many enterobacteria and is tuned to monitor pathways for the maturation and delivery of outer membrane porins, lipoproteins, and lipopolysaccharide to the outer membrane. The activity of σE is tightly regulated to match the production of σE regulon members to the needs of the cell. In E. coli, loss of σE results in lethality. Here we demonstrate that excessive σE activity is also lethal and results in decreased membrane integrity, the very phenotype the system is designed to prevent.
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The secondary resistome of multidrug-resistant Klebsiella pneumoniae. Sci Rep 2017; 7:42483. [PMID: 28198411 PMCID: PMC5309761 DOI: 10.1038/srep42483] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/11/2017] [Indexed: 12/22/2022] Open
Abstract
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258). We constructed a high-density transposon mutant library of >430,000 unique Tn5 insertions and measured mutant depletion upon exposure to three clinically relevant antimicrobials (colistin, imipenem or ciprofloxacin) by Transposon Directed Insertion-site Sequencing (TraDIS). Using this high-throughput approach, we defined three sets of chromosomal non-essential genes essential for growth during exposure to colistin (n = 35), imipenem (n = 1) or ciprofloxacin (n = 1) in addition to known resistance determinants, collectively termed the "secondary resistome". As proof of principle, we demonstrated that inactivation of a non-essential gene not previously found linked to colistin resistance (dedA) restored colistin susceptibility by reducing the minimum inhibitory concentration from 8 to 0.5 μg/ml, 4-fold below the susceptibility breakpoint (S ≤ 2 μg/ml). This finding suggests that the secondary resistome is a potential target for developing antimicrobial "helper" drugs that restore the efficacy of existing antimicrobials.
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Abstract
The complex cell envelope is a hallmark of mycobacteria and is anchored by the peptidoglycan layer, which is similar to that of Escherichia coli and a number of other bacteria but with modifications to the monomeric units and other structural complexities that are likely related to a role for the peptidoglycan in stabilizing the mycolyl-arabinogalactan-peptidoglycan complex (MAPc). In this article, we will review the genetics of several aspects of peptidoglycan biosynthesis in mycobacteria, including the production of monomeric precursors in the cytoplasm, assembly of the monomers into the mature wall, cell wall turnover, and cell division. Finally, we will touch upon the resistance of mycobacteria to β-lactam antibiotics, an important class of drugs that, until recently, have not been extensively exploited as potential antimycobacterial agents. We will also note areas of research where there are still unanswered questions.
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Rioseras B, Yagüe P, López-García MT, Gonzalez-Quiñonez N, Binda E, Marinelli F, Manteca A. Characterization of SCO4439, a D-alanyl-D-alanine carboxypeptidase involved in spore cell wall maturation, resistance, and germination in Streptomyces coelicolor. Sci Rep 2016; 6:21659. [PMID: 26867711 PMCID: PMC4751497 DOI: 10.1038/srep21659] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/28/2016] [Indexed: 11/24/2022] Open
Abstract
This work contributes to the understanding of cell wall modifications during sporulation and germination in Streptomyces by assessing the biological function and biochemical properties of SCO4439, a D-alanyl-D-alanine carboxypeptidase (DD-CPase) constitutively expressed during development. SCO4439 harbors a DD-CPase domain and a putative transcriptional regulator domain, separated by a putative transmembrane region. The recombinant protein shows that DD-CPase activity is inhibited by penicillin G. The spores of the SCO4439::Tn5062 mutant are affected in their resistance to heat and acid and showed a dramatic increase in swelling during germination. The mycelium of the SCO4439::Tn5062 mutant is more sensitive to glycopeptide antibiotics (vancomycin and teicoplanin). The DD-CPase domain and the hydrophobic transmembrane region are highly conserved in Streptomyces, and both are essential for complementing the wild type phenotypes in the mutant. A model for the biological mechanism behind the observed phenotypes is proposed, in which SCO4439 DD-CPase releases D-Ala from peptidoglycan (PG) precursors, thereby reducing the substrate pool for PG crosslinking (transpeptidation). PG crosslinking regulates spore physical resistance and germination, and modulates mycelium resistance to glycopeptides. This study is the first demonstration of the role of a DD-CPase in the maturation of the spore cell wall.
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Affiliation(s)
- Beatriz Rioseras
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Paula Yagüe
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - María Teresa López-García
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Nathaly Gonzalez-Quiñonez
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy.,"The Protein Factory" Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, 21100 Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy.,"The Protein Factory" Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, 21100 Varese, Italy
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
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Ye Y, Jiao R, Gao J, Li H, Ling N, Wu Q, Zhang J, Xu X. Proteins involved in responses to biofilm and planktonic modes in Cronobacter sakazakii. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.09.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hsu YP, Meng X, VanNieuwenhze M. Methods for visualization of peptidoglycan biosynthesis. METHODS IN MICROBIOLOGY 2016. [DOI: 10.1016/bs.mim.2016.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Brammer Basta LA, Ghosh A, Pan Y, Jakoncic J, Lloyd EP, Townsend CA, Lamichhane G, Bianchet MA. Loss of a Functionally and Structurally Distinct ld-Transpeptidase, LdtMt5, Compromises Cell Wall Integrity in Mycobacterium tuberculosis. J Biol Chem 2015; 290:25670-85. [PMID: 26304120 DOI: 10.1074/jbc.m115.660753] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 11/06/2022] Open
Abstract
The final step of peptidoglycan (PG) biosynthesis in bacteria involves cross-linking of peptide side chains. This step in Mycobacterium tuberculosis is catalyzed by ld- and dd-transpeptidases that generate 3→3 and 4→3 transpeptide linkages, respectively. M. tuberculosis PG is predominantly 3→3 cross-linked, and LdtMt2 is the dominant ld-transpeptidase. There are four additional sequence paralogs of LdtMt2 encoded by the genome of this pathogen, and the reason for this apparent redundancy is unknown. Here, we studied one of the paralogs, LdtMt5, and found it to be structurally and functionally distinct. The structures of apo-LdtMt5 and its meropenem adduct presented here demonstrate that, despite overall architectural similarity to LdtMt2, the LdtMt5 active site has marked differences. The presence of a structurally divergent catalytic site and a proline-rich C-terminal subdomain suggest that this protein may have a distinct role in PG metabolism, perhaps involving other cell wall-anchored proteins. Furthermore, M. tuberculosis lacking a functional copy of LdtMt5 displayed aberrant growth and was more susceptible to killing by crystal violet, osmotic shock, and select carbapenem antibiotics. Therefore, we conclude that LdtMt5 is not a functionally redundant ld-transpeptidase, but rather it serves a unique and important role in maintaining the integrity of the M. tuberculosis cell wall.
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Affiliation(s)
- Leighanne A Brammer Basta
- From the Taskforce to study Resistance Emergence and Antimicrobial development Technology (TREAT) and Division of Infectious Diseases, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Anita Ghosh
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry and
| | - Ying Pan
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry and
| | - Jean Jakoncic
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, and
| | - Evan P Lloyd
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Gyanu Lamichhane
- From the Taskforce to study Resistance Emergence and Antimicrobial development Technology (TREAT) and Division of Infectious Diseases, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231,
| | - Mario A Bianchet
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry and Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205,
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Sublethal concentrations of carbapenems alter cell morphology and genomic expression of Klebsiella pneumoniae biofilms. Antimicrob Agents Chemother 2015; 59:1707-17. [PMID: 25583711 DOI: 10.1128/aac.04581-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae, a Gram-negative bacterium, is normally associated with pneumonia in patients with weakened immune systems. However, it is also a prevalent nosocomial infectious agent that can be found in infected surgical sites and combat wounds. Many of these clinical strains display multidrug resistance. We have worked with a clinical strain of K. pneumoniae that was initially isolated from a wound of an injured soldier. This strain demonstrated resistance to many commonly used antibiotics but sensitivity to carbapenems. This isolate was capable of forming biofilms in vitro, contributing to its increased antibiotic resistance and impaired clearance. We were interested in determining how sublethal concentrations of carbapenem treatment specifically affect K. pneumoniae biofilms both in morphology and in genomic expression. Scanning electron microscopy showed striking morphological differences between untreated and treated biofilms, including rounding, blebbing, and dimpling of treated cells. Comparative transcriptome analysis using RNA sequencing (RNA-Seq) technology identified a large number of open reading frames (ORFs) differentially regulated in response to carbapenem treatment at 2 and 24 h. ORFs upregulated with carbapenem treatment included genes involved in resistance, as well as those coding for antiporters and autoinducers. ORFs downregulated included those coding for metal transporters, membrane biosynthesis proteins, and motility proteins. Quantitative real-time PCR validated the general trend of some of these differentially regulated ORFs. Treatment of K. pneumoniae biofilms with sublethal concentrations of carbapenems induced a wide range of phenotypic and gene expression changes. This study reveals some of the mechanisms underlying how sublethal amounts of carbapenems could affect the overall fitness and pathogenic potential of K. pneumoniae biofilm cells.
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Lowry RC, Parker JL, Kumbhar R, Mesnage S, Shaw JG, Stafford GP. The Aeromonas caviae AHA0618 gene modulates cell length and influences swimming and swarming motility. Microbiologyopen 2014; 4:220-234. [PMID: 25515520 PMCID: PMC4398505 DOI: 10.1002/mbo3.233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/17/2014] [Accepted: 11/24/2014] [Indexed: 01/12/2023] Open
Abstract
Aeromonas caviae is motile via a polar flagellum in liquid culture, with a lateral flagella system used for swarming on solid surfaces. The polar flagellum also has a role in cellular adherence and biofilm formation. The two subunits of the polar flagellum, FlaA and FlaB, are posttranslationally modified by O-linked glycosylation with pseudaminic acid on 6–8 serine and threonine residues within the central region of these proteins. This modification is essential for the formation of the flagellum. Aeromonas caviae possesses the simplest set of genes required for bacterial glycosylation currently known, with the putative glycosyltransferase, Maf1, being described recently. Here, we investigated the role of the AHA0618 gene, which shares homology (37% at the amino acid level) with the central region of a putative deglycosylation enzyme (HP0518) from the human pathogen Helicobacter pylori, which also glycosylates its flagellin and is proposed to be part of a flagellin deglycosylation pathway. Phenotypic analysis of an AHA0618 A. caviae mutant revealed increased swimming and swarming motility compared to the wild-type strain but without any detectable effects on the glycosylation status of the polar flagellins when analyzed by western blot analysis or mass spectroscopy. Bioinformatic analysis of the protein AHA0618, demonstrated homology to a family of l,d-transpeptidases involved in cell wall biology and peptidoglycan cross-linking (YkuD-like). Scanning electron microscopy (SEM) and fluorescence microscopy analysis of the wild-type and AHA0618-mutant A. caviae strains revealed the mutant to be subtly but significantly shorter than wild-type cells; a phenomenon that could be recovered when either AHA0618 or H. pylori HP0518 were introduced. We can therefore conclude that AHA0618 does not affect A. caviae behavior by altering polar flagellin glycosylation levels but is likely to have a role in peptidoglycan processing at the bacterial cell wall, consequently altering cell length and hence influencing motility.
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Affiliation(s)
- Rebecca C Lowry
- Department of Infection and Immunity, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Jennifer L Parker
- Department of Infection and Immunity, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Ramhari Kumbhar
- Department of Infection and Immunity, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Stephane Mesnage
- Department of Molecular Biology and Biotechnology, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jonathan G Shaw
- Department of Infection and Immunity, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Graham P Stafford
- School of Clinical Dentistry, Claremont Crescent, University of Sheffield, Sheffield, S10 2TA, UK
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The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU. J Bacteriol 2014; 197:603-14. [PMID: 25422305 DOI: 10.1128/jb.02449-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Cpx envelope stress response mediates a complex adaptation to conditions that cause protein misfolding in the periplasm. A recent microarray study demonstrated that Cpx response activation led to changes in the expression of genes known, or predicted, to be involved in cell wall remodeling. We sought to characterize the changes that the cell wall undergoes during activation of the Cpx pathway in Escherichia coli. Luminescent reporters of gene expression confirmed that LdtD, a putative l,d-transpeptidase; YgaU, a protein of unknown function; and Slt, a lytic transglycosylase, are upregulated in response to Cpx-inducing conditions. Phosphorylated CpxR binds to the upstream regions of these genes, which contain putative CpxR binding sites, suggesting that regulation is direct. We show that the activation of the Cpx response causes an increase in the abundance of diaminopimelic acid (DAP)-DAP cross-links that involves LdtD and YgaU. Altogether, our data indicate that changes in peptidoglycan structure are part of the Cpx-mediated adaptation to envelope stress and indicate a role for the uncharacterized gene ygaU in regulating cross-linking.
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Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A. Mapping Cell Envelope and Periplasm Protein Interactions of Escherichia coli Respiratory Formate Dehydrogenases by Chemical Cross-Linking and Mass Spectrometry. J Proteome Res 2014; 13:5524-35. [DOI: 10.1021/pr5004906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Michael Zorn
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | | | | | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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Tsui HCT, Boersma MJ, Vella SA, Kocaoglu O, Kuru E, Peceny JK, Carlson EE, VanNieuwenhze MS, Brun YV, Shaw SL, Winkler ME. Pbp2x localizes separately from Pbp2b and other peptidoglycan synthesis proteins during later stages of cell division of Streptococcus pneumoniae D39. Mol Microbiol 2014; 94:21-40. [PMID: 25099088 PMCID: PMC4209751 DOI: 10.1111/mmi.12745] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2014] [Indexed: 11/27/2022]
Abstract
The relative localization patterns of class B penicillin-binding proteins Pbp2x and Pbp2b were used as positional indicators of septal and peripheral (side-wall-like) peptidoglycan (PG) synthesis, respectively, in the mid-cell regions of Streptococcus pneumoniae cells at different stages of division. We confirm that Pbp2x and Pbp2b are essential in the strain D39 genetic background, which differs from that of laboratory strains. We show that Pbp2b, like Pbp2x and class A Pbp1a, follows a different localization pattern than FtsZ and remains at division septa after FtsZ reappears at the equators of daughter cells. Pulse-experiments with fluorescent D-amino acids (FDAAs) were performed in wild-type cells and in cells in which Pbp2x activity was preferentially inhibited by methicillin or Pbp2x amount was depleted. These experiments show that Pbp2x activity separates from that of other PBPs to the centres of constricting septa in mid-to-late divisional cells resolved by high-resolution 3D-SIM microscopy. Dual-protein and protein-fluorescent vancomycin 2D and 3D-SIM immunofluorescence microscopy (IFM) of cells at different division stages corroborate that Pbp2x separates to the centres of septa surrounded by an adjacent constricting ring containing Pbp2b, Pbp1a and regulators, StkP and MreC. The separate localization of Pbp2x suggests distinctive roles in completing septal PG synthesis and remodelling.
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Affiliation(s)
- Ho-Ching T. Tsui
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
| | - Michael J. Boersma
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
| | - Stephen A. Vella
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
| | - Ozden Kocaoglu
- Department of Molecular and Cellular Biochemistry, Indiana
University Bloomington, Bloomington, IN 47405
| | - Erkin Kuru
- Department of Molecular and Cellular Biochemistry, Indiana
University Bloomington, Bloomington, IN 47405
| | - Julia K. Peceny
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
| | - Erin E. Carlson
- Department of Molecular and Cellular Biochemistry, Indiana
University Bloomington, Bloomington, IN 47405
- Department of Chemistry, Indiana University Bloomington,
Bloomington, IN 47405
| | - Michael S. VanNieuwenhze
- Department of Molecular and Cellular Biochemistry, Indiana
University Bloomington, Bloomington, IN 47405
- Department of Chemistry, Indiana University Bloomington,
Bloomington, IN 47405
| | - Yves V. Brun
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana
University Bloomington, Bloomington, IN 47405
| | - Sidney L. Shaw
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington,
Bloomington, IN 47405
- Department of Molecular and Cellular Biochemistry, Indiana
University Bloomington, Bloomington, IN 47405
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Orfanoudaki G, Economou A. Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). Mol Cell Proteomics 2014; 13:3674-87. [PMID: 25210196 DOI: 10.1074/mcp.o114.041137] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cell compartmentalization serves both the isolation and the specialization of cell functions. After synthesis in the cytoplasm, over a third of all proteins are targeted to other subcellular compartments. Knowing how proteins are distributed within the cell and how they interact is a prerequisite for understanding it as a whole. Surface and secreted proteins are important pathogenicity determinants. Here we present the STEP database (STEPdb) that contains a comprehensive characterization of subcellular localization and topology of the complete proteome of Escherichia coli. Two widely used E. coli proteomes (K-12 and BL21) are presented organized into thirteen subcellular classes. STEPdb exploits the wealth of genetic, proteomic, biochemical, and functional information on protein localization, secretion, and targeting in E. coli, one of the best understood model organisms. Subcellular annotations were derived from a combination of bioinformatics prediction, proteomic, biochemical, functional, topological data and extensive literature re-examination that were refined through manual curation. Strong experimental support for the location of 1553 out of 4303 proteins was based on 426 articles and some experimental indications for another 526. Annotations were provided for another 320 proteins based on firm bioinformatic predictions. STEPdb is the first database that contains an extensive set of peripheral IM proteins (PIM proteins) and includes their graphical visualization into complexes, cellular functions, and interactions. It also summarizes all currently known protein export machineries of E. coli K-12 and pairs them, where available, with the secretory proteins that use them. It catalogs the Sec- and TAT-utilizing secretomes and summarizes their topological features such as signal peptides and transmembrane regions, transmembrane topologies and orientations. It also catalogs physicochemical and structural features that influence topology such as abundance, solubility, disorder, heat resistance, and structural domain families. Finally, STEPdb incorporates prediction tools for topology (TMHMM, SignalP, and Phobius) and disorder (IUPred) and implements the BLAST2STEP that performs protein homology searches against the STEPdb.
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Affiliation(s)
- Georgia Orfanoudaki
- From the ‡Institute of Molecular Biology and Biotechnology-FoRTH and §Department of Biology-University of Crete, P.O. Box 1385, Iraklio, Crete, Greece
| | - Anastassios Economou
- From the ‡Institute of Molecular Biology and Biotechnology-FoRTH and §Department of Biology-University of Crete, P.O. Box 1385, Iraklio, Crete, Greece; ¶Laboratory of Molecular Bacteriology; Rega Institute, Department of Microbiology and Immunology, KU Leuven, Herrestraat 49, B-3000 Leuven, Belgium
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Peptidoglycan synthesis machinery in Agrobacterium tumefaciens during unipolar growth and cell division. mBio 2014; 5:e01219-14. [PMID: 24865559 PMCID: PMC4045076 DOI: 10.1128/mbio.01219-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The synthesis of peptidoglycan (PG) in bacteria is a crucial process controlling cell shape and vitality. In contrast to bacteria such as Escherichia coli that grow by dispersed lateral insertion of PG, little is known of the processes that direct polar PG synthesis in other bacteria such as the Rhizobiales. To better understand polar growth in the Rhizobiales Agrobacterium tumefaciens, we first surveyed its genome to identify homologs of (~70) well-known PG synthesis components. Since most of the canonical cell elongation components are absent from A. tumefaciens, we made fluorescent protein fusions to other putative PG synthesis components to assay their subcellular localization patterns. The cell division scaffolds FtsZ and FtsA, PBP1a, and a Rhizobiales- and Rhodobacterales-specific l,d-transpeptidase (LDT) all associate with the elongating cell pole. All four proteins also localize to the septum during cell division. Examination of the dimensions of growing cells revealed that new cell compartments gradually increase in width as they grow in length. This increase in cell width is coincident with an expanded region of LDT-mediated PG synthesis activity, as measured directly through incorporation of exogenous d-amino acids. Thus, unipolar growth in the Rhizobiales is surprisingly dynamic and represents a significant departure from the canonical growth mechanism of E. coli and other well-studied bacilli. Many rod-shaped bacteria, including pathogens such as Brucella and Mycobacterium, grow by adding new material to their cell poles, and yet the proteins and mechanisms contributing to this process are not yet well defined. The polarly growing plant pathogen Agrobacterium tumefaciens was used as a model bacterium to explore these polar growth mechanisms. The results obtained indicate that polar growth in this organism is facilitated by repurposed cell division components and an otherwise obscure class of alternative peptidoglycan transpeptidases (l,d-transpeptidases). This growth results in dynamically changing cell widths as the poles expand to maturity and contrasts with the tightly regulated cell widths characteristic of canonical rod-shaped growth. Furthermore, the abundance and/or activity of l,d-transpeptidases appears to associate with polar growth strategies, suggesting that these enzymes may serve as attractive targets for specifically inhibiting growth of Rhizobiales, Actinomycetales, and other polarly growing bacterial pathogens.
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Sanders AN, Wright LF, Pavelka MS. Genetic characterization of mycobacterial L,D-transpeptidases. MICROBIOLOGY-SGM 2014; 160:1795-1806. [PMID: 24855140 DOI: 10.1099/mic.0.078980-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
l,d-Transpeptidases (Ldts) catalyse the formation of 3-3 cross-links in peptidoglycans (PGs); however, the role of these enzymes in cell envelope physiology is not well understood. Mycobacterial PG contains a higher percentage of 3-3 cross-links (~30-80 %) than the PG in most other bacteria, suggesting that they are particularly important to mycobacterial cell wall biology. The genomes of Mycobacterium tuberculosis and Mycobacterium smegmatis encode multiple Ldt genes, but it is not clear if they are redundant. We compared the sequences of the Ldt proteins from 18 mycobacterial genomes and found that they can be grouped into six classes. We then constructed M. smegmatis strains lacking single or multiple Ldt genes to determine the physiological consequence of the loss of these enzymes. We report that of the single mutants, only one, ΔldtC (MSMEG_0929, class 5), displayed an increased susceptibility to imipenem - a carbapenem antibiotic that inhibits the Ldt enzymes. The invariant cysteine in the active site of LdtC was required for function, consistent with its role as an Ldt. A triple mutant missing ldtC and both of the class 2 genes displayed hypersusceptibility to antibiotics, lysozyme and d-methionine, and had an altered cellular morphology. These data demonstrated that the distinct classes of mycobacterial Ldts may reflect different, non-redundant functions and that the class 5 Ldt was peculiar in that its loss, alone and with the class 2 proteins, had the most profound effect on phenotype.
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Affiliation(s)
- Akeisha N Sanders
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Lori F Wright
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S Pavelka
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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Nonclassical transpeptidases of Mycobacterium tuberculosis alter cell size, morphology, the cytosolic matrix, protein localization, virulence, and resistance to β-lactams. J Bacteriol 2014; 196:1394-402. [PMID: 24464457 DOI: 10.1128/jb.01396-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virtually all bacteria possess a peptidoglycan layer that is essential for their growth and survival. The β-lactams, the most widely used class of antibiotics in human history, inhibit D,D-transpeptidases, which catalyze the final step in peptidoglycan biosynthesis. The existence of a second class of transpeptidases, the L,D-transpeptidases, was recently reported. Mycobacterium tuberculosis, an infectious pathogen that causes tuberculosis (TB), is known to possess as many as five proteins with L,D-transpeptidase activity. Here, for the first time, we demonstrate that loss of L,D-transpeptidases 1 and 2 of M. tuberculosis (LdtMt1 and LdtMt2) alters cell surface morphology, shape, size, organization of the intracellular matrix, sorting of some low-molecular-weight proteins that are targeted to the membrane or secreted, cellular physiology, growth, virulence, and resistance of M. tuberculosis to amoxicillin-clavulanate and vancomycin.
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