1
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Roodsant TJ, van der Putten B, Brizuela J, Coolen JPM, Baltussen TJH, Schipper K, Pannekoek Y, van der Ark KCH, Schultsz C. The streptococcal phase-variable type I restriction modification system SsuCC20p dictates the methylome of Streptococcus suis impacting the transcriptome and virulence in a zebrafish larvae infection model. mBio 2024; 15:e0225923. [PMID: 38063379 PMCID: PMC10790761 DOI: 10.1128/mbio.02259-23] [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: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Phase variation allows a single strain to produce phenotypic diverse subpopulations. Phase-variable restriction modification (RM) systems are systems that allow for such phase variation via epigenetic regulation of gene expression levels. The phase-variable RM system SsuCC20p was found in multiple streptococcal species and was acquired by an emerging zoonotic lineage of Streptococcus suis. We show that the phase variability of SsuCC20p is dependent on a recombinase encoded within the SsuCC20p locus. We characterized the genome methylation profiles of the different phases of SsuCC20p and demonstrated the consequential impact on the transcriptome and virulence in a zebrafish infection model. Acquiring mobile genetic elements containing epigenetic regulatory systems, like phase-variable RM systems, enables bacterial pathogens to produce diverse phenotypic subpopulations that are better adapted to specific (host) environments encountered during infection.
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Affiliation(s)
- Thomas J. Roodsant
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Boas van der Putten
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jaime Brizuela
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Kim Schipper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Kees C. H. van der Ark
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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2
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Kobras CM, Monteith W, Somerville S, Delaney JM, Khan I, Brimble C, Corrigan RM, Sheppard SK, Fenton AK. Loss of Pde1 function acts as an evolutionary gateway to penicillin resistance in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2023; 120:e2308029120. [PMID: 37796984 PMCID: PMC10576035 DOI: 10.1073/pnas.2308029120] [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: 05/14/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen and rising resistance to β-lactam antibiotics, such as penicillin, is a significant threat to global public health. Mutations occurring in the penicillin-binding proteins (PBPs) can confer high-level penicillin resistance but other poorly understood genetic factors are also important. Here, we combined strictly controlled laboratory experiments and population analyses to identify a new penicillin resistance pathway that is independent of PBP modification. Initial laboratory selection experiments identified high-frequency pde1 mutations conferring S. pneumoniae penicillin resistance. The importance of variation at the pde1 locus was confirmed in natural and clinical populations in an analysis of >7,200 S. pneumoniae genomes. The pde1 mutations identified by these approaches reduce the hydrolytic activity of the Pde1 enzyme in bacterial cells and thereby elevate levels of cyclic-di-adenosine monophosphate and penicillin resistance. Our results reveal rapid de novo loss of function mutations in pde1 as an evolutionary gateway conferring low-level penicillin resistance. This relatively simple genomic change allows cells to persist in populations on an adaptive evolutionary pathway to acquire further genetic changes and high-level penicillin resistance.
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Affiliation(s)
- Carolin M. Kobras
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - William Monteith
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Sophie Somerville
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - James M. Delaney
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Imran Khan
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Camilla Brimble
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Rebecca M. Corrigan
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Samuel K. Sheppard
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Andrew K. Fenton
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
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3
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Bazant J, Ott B, Hudel M, Hain T, Lucas R, Mraheil MA. Impact of Endogenous Pneumococcal Hydrogen Peroxide on the Activity and Release of Pneumolysin. Toxins (Basel) 2023; 15:593. [PMID: 37888624 PMCID: PMC10611280 DOI: 10.3390/toxins15100593] [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: 08/10/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Streptococcus pneumoniae is the leading cause of community-acquired pneumonia. The pore-forming cholesterol-dependent cytolysin (CDC) pneumolysin (PLY) and the physiological metabolite hydrogen peroxide (H2O2) can greatly increase the virulence of pneumococci. Although most studies have focused on the contribution of both virulence factors to the course of pneumococcal infection, it is unknown whether or how H2O2 can affect PLY activity. Of note, S. pneumoniae exploits endogenous H2O2 as an intracellular signalling molecule to modulate the activity of several proteins. Here, we demonstrate that H2O2 negatively affects the haemolytic activity of PLY in a concentration-dependent manner. Prevention of cysteine-dependent sulfenylation upon substitution of the unique and highly conserved cysteine residue to serine in PLY significantly reduces the toxin's susceptibility to H2O2 treatment and completely abolishes the ability of DTT to activate PLY. We also detect a clear gradual correlation between endogenous H2O2 generation and PLY release, with decreased H2O2 production causing a decline in the release of PLY. Comparative transcriptome sequencing analysis of the wild-type S. pneumoniae strain and three mutants impaired in H2O2 production indicates enhanced expression of several genes involved in peptidoglycan (PG) synthesis and in the production of choline-binding proteins (CPBs). One explanation for the impact of H2O2 on PLY release is the observed upregulation of the PG bridge formation alanyltransferases MurM and MurN, which evidentially negatively affect the PLY release. Our findings shed light on the significance of endogenous pneumococcal H2O2 in controlling PLY activity and release.
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Affiliation(s)
- Jasmin Bazant
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (J.B.); (B.O.); (M.H.); (T.H.)
| | - Benjamin Ott
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (J.B.); (B.O.); (M.H.); (T.H.)
| | - Martina Hudel
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (J.B.); (B.O.); (M.H.); (T.H.)
| | - Torsten Hain
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (J.B.); (B.O.); (M.H.); (T.H.)
| | - Rudolf Lucas
- Vascular Biology Center, Department of Pharmacology and Toxicology and Division of Pulmonary Critical Care Medicine, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA;
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (J.B.); (B.O.); (M.H.); (T.H.)
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4
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Gibson PS, Veening JW. Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae. Curr Opin Microbiol 2023; 72:102261. [PMID: 36638546 DOI: 10.1016/j.mib.2022.102261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 01/13/2023]
Abstract
Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, and one of the main pathogens responsible for otitis media infections in children. Amoxicillin (AMX) is a broad-spectrum β-lactam antibiotic, used frequently for the treatment of bacterial respiratory tract infections. Here, we discuss the pneumococcal response to AMX, including the mode of action of AMX, the effects on autolysin regulation, and the evolution of resistance through natural transformation. We discuss current knowledge gaps in the synthesis and translocation of peptidoglycan and teichoic acids, major constituents of the pneumococcal cell wall and critical to AMX activity. Furthermore, an outlook of AMX resistance research is presented, including the development of natural competence inhibitors to block evolution via horizontal gene transfer, and the use of high-throughput essentiality screens for the discovery of novel cotherapeutics.
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Affiliation(s)
- Paddy S Gibson
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.
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5
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Li L, Ma J, Yu Z, Li M, Zhang W, Sun H. Epidemiological characteristics and antibiotic resistance mechanisms of Streptococcus pneumoniae: An updated review. Microbiol Res 2023; 266:127221. [DOI: 10.1016/j.micres.2022.127221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/13/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022]
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6
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Nishimoto AT, Dao TH, Jia Q, Ortiz-Marquez JC, Echlin H, Vogel P, van Opijnen T, Rosch JW. Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae. Cell Rep 2022; 41:111835. [PMID: 36516783 PMCID: PMC9850807 DOI: 10.1016/j.celrep.2022.111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.
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Affiliation(s)
- Andrew T. Nishimoto
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | | | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology and Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Boston, MA 02467, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Lead contact,Correspondence:
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7
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Gibson PS, Bexkens E, Zuber S, Cowley LA, Veening JW. The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci. PLoS Pathog 2022; 18:e1010727. [PMID: 35877768 PMCID: PMC9352194 DOI: 10.1371/journal.ppat.1010727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/04/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.
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Affiliation(s)
- Paddy S. Gibson
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Evan Bexkens
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sylvia Zuber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lauren A. Cowley
- Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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8
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Kwack KH, Lee JH, Moon JH. Whole genome and RNA sequencing of oral commensal bacterium Streptococcus anginosus subsp. anginosus with vancomycin tolerance. J Microbiol 2022; 60:167-176. [PMID: 34997538 DOI: 10.1007/s12275-022-1425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022]
Abstract
"Antibiotic tolerance" promotes the rapid subsequent evolution of "antibiotic resistance," however, it is often overlooked because it is difficult to distinguish between tolerant and susceptible organisms. A commensal bacterium S. anginosus subsp. anginosus strain KHUD_S1, isolated from dental biofilm was found to exhibit a high MBC/MIC ratio of 32 against vancomycin. We observed KHUD_S1 cells exposed to vancomycin did not grow but maintained viability. Transmission electron microscope showed KHUD_S1 cells possessed a dense, thick capsule and maintained the cell wall integrity upon vancomycin exposure. To infer the underlying mechanisms of the vancomycin tolerance in KHUD_S1, we performed whole genome sequencing and RNA sequencing. The KHUD_S1 genome carried three genes encoding branching enzymes that can affect peptidoglycan structure through interpeptide bridge formation. Global gene expression profiling revealed that the vancomycin-induced downregulation of carbohydrate and inorganic ion transport/metabolism as well as translation is less prominent in KHUD_S1 than in the vancomycin susceptible strain KHUD_S3. Based on the transcriptional levels of genes related to peptidoglycan synthesis, KHUD_S1 was determined to have a 3D peptidoglycan architecture distinct from KHUD_S3. It was found that, under vancomycin exposure, the peptidoglycan was remodeled through changes in the interpeptide bridge and transpeptidation reactions. Collectively, these features of S. anginosus KHUD_S1, including a dense capsule and differential gene expression in peptidoglycan synthesis, may contribute to vancomycin tolerance. Our results showing the occurrence of vancomycin tolerance amongst oral commensal bacteria highlight the need for considering future strategies for screening of antibiotic tolerance as an effort to reduce antibiotic resistance.
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Affiliation(s)
- Kyu Hwan Kwack
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
- Present address: Department of Oral Biology, University at Buffalo School of Dental Medicine, Buffalo, New York, 14214, USA
| | - Jae-Hyung Lee
- Department of Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Ji-Hoi Moon
- Department of Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, 02447, Republic of Korea.
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9
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D'Aeth JC, van der Linden MPG, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, Croucher NJ. The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci. eLife 2021; 10:e67113. [PMID: 34259624 PMCID: PMC8321556 DOI: 10.7554/elife.67113] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.
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Affiliation(s)
- Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Mark PG van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital RWTH AachenAachenGermany
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller UniversityNew YorkUnited States
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Jae-Hoon Song
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - Stephanie W Lo
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Rebecca A Gladstone
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory UniversityAtlantaUnited States
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Stephen D Bentley
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
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10
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York A, Lloyd AJ, Del Genio CI, Shearer J, Hinxman KJ, Fritz K, Fulop V, Dowson CG, Khalid S, Roper DI. Structure-based modeling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant present at the cytoplasmic membrane. Structure 2021; 29:731-742.e6. [PMID: 33740396 PMCID: PMC8280954 DOI: 10.1016/j.str.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022]
Abstract
Branched Lipid II, required for the formation of indirectly crosslinked peptidoglycan, is generated by MurM, a protein essential for high-level penicillin resistance in the human pathogen Streptococcus pneumoniae. We have solved the X-ray crystal structure of Staphylococcus aureus FemX, an isofunctional homolog, and have used this as a template to generate a MurM homology model. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of MurM with the phospholipid bilayer and the membrane-embedded Lipid II substrate. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and experimental evidence confirms that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. The spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may therefore be critical to the final architecture of peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
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Affiliation(s)
- Anna York
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Adrian J Lloyd
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, University of Coventry, West Midlands CV1 5FB, UK
| | - Jonathan Shearer
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Karen J Hinxman
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Konstantin Fritz
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Vilmos Fulop
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Christopher G Dowson
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK.
| | - David I Roper
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK; Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
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11
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Varghese R, Veeraraghavan B. Decoding the Penicillin Resistance of Streptococcus pneumoniae for Invasive and Noninvasive Infections. Microb Drug Resist 2021; 27:942-950. [DOI: 10.1089/mdr.2020.0233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
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12
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Aggarwal SD, Lloyd AJ, Yerneni SS, Narciso AR, Shepherd J, Roper DI, Dowson CG, Filipe SR, Hiller NL. A molecular link between cell wall biosynthesis, translation fidelity, and stringent response in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2021; 118:e2018089118. [PMID: 33785594 PMCID: PMC8040666 DOI: 10.1073/pnas.2018089118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Survival in the human host requires bacteria to respond to unfavorable conditions. In the important Gram-positive pathogen Streptococcus pneumoniae, cell wall biosynthesis proteins MurM and MurN are tRNA-dependent amino acyl transferases which lead to the production of branched muropeptides. We demonstrate that wild-type cells experience optimal growth under mildly acidic stressed conditions, but ΔmurMN strain displays growth arrest and extensive lysis. Furthermore, these stress conditions compromise the efficiency with which alanyl-tRNAAla synthetase can avoid noncognate mischarging of tRNAAla with serine, which is toxic to cells. The observed growth defects are rescued by inhibition of the stringent response pathway or by overexpression of the editing domain of alanyl-tRNAAla synthetase that enables detoxification of tRNA misacylation. Furthermore, MurM can incorporate seryl groups from mischarged Seryl-tRNAAlaUGC into cell wall precursors with exquisite specificity. We conclude that MurM contributes to the fidelity of translation control and modulates the stress response by decreasing the pool of mischarged tRNAs. Finally, we show that enhanced lysis of ΔmurMN pneumococci is caused by LytA, and the murMN operon influences macrophage phagocytosis in a LytA-dependent manner. Thus, MurMN attenuates stress responses with consequences for host-pathogen interactions. Our data suggest a causal link between misaminoacylated tRNA accumulation and activation of the stringent response. In order to prevent potential corruption of translation, consumption of seryl-tRNAAla by MurM may represent a first line of defense. When this mechanism is overwhelmed or absent (ΔmurMN), the stringent response shuts down translation to avoid toxic generation of mistranslated/misfolded proteins.
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Affiliation(s)
- Surya D Aggarwal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Adrian J Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | | | - Ana Rita Narciso
- Laboratory of Bacterial Cell Surfaces and Pathogenesis, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 1099-085 Oeiras, Portugal
- Unidade de Ciências Biomoleculares Aplicadas (UCIBIO), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-149 Caparica, Portugal
| | - Jennifer Shepherd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christopher G Dowson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sergio R Filipe
- Laboratory of Bacterial Cell Surfaces and Pathogenesis, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 1099-085 Oeiras, Portugal;
- Unidade de Ciências Biomoleculares Aplicadas (UCIBIO), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-149 Caparica, Portugal
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213;
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The pneumococcal two-component system SirRH is linked to enhanced intracellular survival of Streptococcus pneumoniae in influenza-infected pulmonary cells. PLoS Pathog 2020; 16:e1008761. [PMID: 32790758 PMCID: PMC7447016 DOI: 10.1371/journal.ppat.1008761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 08/25/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
The virus-bacterial synergism implicated in secondary bacterial infections caused by Streptococcus pneumoniae following infection with epidemic or pandemic influenza A virus (IAV) is well documented. However, the molecular mechanisms behind such synergism remain largely ill-defined. In pneumocytes infected with influenza A virus, subsequent infection with S. pneumoniae leads to enhanced pneumococcal intracellular survival. The pneumococcal two-component system SirRH appears essential for such enhanced survival. Through comparative transcriptomic analysis between the ΔsirR and wt strains, a list of 179 differentially expressed genes was defined. Among those, the clpL protein chaperone gene and the psaB Mn+2 transporter gene, which are involved in the stress response, are important in enhancing S. pneumoniae survival in influenza-infected cells. The ΔsirR, ΔclpL and ΔpsaB deletion mutants display increased susceptibility to acidic and oxidative stress and no enhancement of intracellular survival in IAV-infected pneumocyte cells. These results suggest that the SirRH two-component system senses IAV-induced stress conditions and controls adaptive responses that allow survival of S. pneumoniae in IAV-infected pneumocytes.
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Abstract
The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.
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Small-Molecule Acetylation by GCN5-Related N-Acetyltransferases in Bacteria. Microbiol Mol Biol Rev 2020; 84:84/2/e00090-19. [PMID: 32295819 DOI: 10.1128/mmbr.00090-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acetylation is a conserved modification used to regulate a variety of cellular pathways, such as gene expression, protein synthesis, detoxification, and virulence. Acetyltransferase enzymes transfer an acetyl moiety, usually from acetyl coenzyme A (AcCoA), onto a target substrate, thereby modulating activity or stability. Members of the GCN5- N -acetyltransferase (GNAT) protein superfamily are found in all domains of life and are characterized by a core structural domain architecture. These enzymes can modify primary amines of small molecules or of lysyl residues of proteins. From the initial discovery of antibiotic acetylation, GNATs have been shown to modify a myriad of small-molecule substrates, including tRNAs, polyamines, cell wall components, and other toxins. This review focuses on the literature on small-molecule substrates of GNATs in bacteria, including structural examples, to understand ligand binding and catalysis. Understanding the plethora and versatility of substrates helps frame the role of acetylation within the larger context of bacterial cellular physiology.
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Shields RC, Walker AR, Maricic N, Chakraborty B, Underhill SAM, Burne RA. Repurposing the Streptococcus mutans CRISPR-Cas9 System to Understand Essential Gene Function. PLoS Pathog 2020; 16:e1008344. [PMID: 32150575 PMCID: PMC7082069 DOI: 10.1371/journal.ppat.1008344] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/19/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
A recent genome-wide screen identified ~300 essential or growth-supporting genes in the dental caries pathogen Streptococcus mutans. To be able to study these genes, we built a CRISPR interference tool around the Cas9 nuclease (Cas9Smu) encoded in the S. mutans UA159 genome. Using a xylose-inducible dead Cas9Smu with a constitutively active single-guide RNA (sgRNA), we observed titratable repression of GFP fluorescence that compared favorably to that of Streptococcus pyogenes dCas9 (Cas9Spy). We then investigated sgRNA specificity and proto-spacer adjacent motif (PAM) requirements. Interference by sgRNAs did not occur with double or triple base-pair mutations, or if single base-pair mutations were in the 3' end of the sgRNA. Bioinformatic analysis of >450 S. mutans genomes allied with in vivo assays revealed a similar PAM recognition sequence as Cas9Spy. Next, we created a comprehensive library of sgRNA plasmids that were directed at essential and growth-supporting genes. We discovered growth defects for 77% of the CRISPRi strains expressing sgRNAs. Phenotypes of CRISPRi strains, across several biological pathways, were assessed using fluorescence microscopy. A variety of cell structure anomalies were observed, including segregational instability of the chromosome, enlarged cells, and ovococci-to-rod shape transitions. CRISPRi was also employed to observe how silencing of cell wall glycopolysaccharide biosynthesis (rhamnose-glucose polysaccharide, RGP) affected both cell division and pathogenesis in a wax worm model. The CRISPRi tool and sgRNA library are valuable resources for characterizing essential genes in S. mutans, some of which could prove to be promising therapeutic targets.
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Affiliation(s)
- Robert C. Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Alejandro R. Walker
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Natalie Maricic
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Brinta Chakraborty
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Simon A. M. Underhill
- Department of Physics, University of Florida, Gainesville, Florida, United States of America
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
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Porfírio S, Carlson RW, Azadi P. Elucidating Peptidoglycan Structure: An Analytical Toolset. Trends Microbiol 2019; 27:607-622. [DOI: 10.1016/j.tim.2019.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 01/04/2023]
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18
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Monteiro JM, Covas G, Rausch D, Filipe SR, Schneider T, Sahl HG, Pinho MG. The pentaglycine bridges of Staphylococcus aureus peptidoglycan are essential for cell integrity. Sci Rep 2019; 9:5010. [PMID: 30899062 PMCID: PMC6428869 DOI: 10.1038/s41598-019-41461-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/07/2019] [Indexed: 02/04/2023] Open
Abstract
Bacterial cells are surrounded by cell wall, whose main component is peptidoglycan (PG), a macromolecule that withstands the internal turgor of the cell. PG composition can vary considerably between species. The Gram-positive pathogen Staphylococcus aureus possesses highly crosslinked PG due to the presence of cross bridges containing five glycines, which are synthesised by the FemXAB protein family. FemX adds the first glycine of the cross bridge, while FemA and FemB add the second and the third, and the fourth and the fifth glycines, respectively. Of these, FemX was reported to be essential. To investigate the essentiality of FemAB, we constructed a conditional S. aureus mutant of the femAB operon. Depletion of femAB was lethal, with cells appearing as pseudomulticellular forms that eventually lyse due to extensive membrane rupture. This deleterious effect was mitigated by drastically increasing the osmolarity of the medium, indicating that pentaglycine crosslinks are required for S. aureus cells to withstand internal turgor. Despite the absence of canonical membrane targeting domains, FemA has been shown to localise at the membrane. To study its mechanism of localisation, we constructed mutants in key residues present in the putative transferase pocket and the α6 helix of FemA, possibly involved in tRNA binding. Mutations in the α6 helix led to a sharp decrease in protein activity in vivo and in vitro but did not impair correct membrane localisation, indicating that FemA activity is not required for localisation. Our data indicates that, contrarily to what was previously thought, S. aureus cells do not survive in the absence of a pentaglycine cross bridge.
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Affiliation(s)
- João M Monteiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gonçalo Covas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Daniela Rausch
- Institute of Pharmaceutical Microbiology, University of Bonn, 53115, Bonn, Germany
| | - Sérgio R Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Tanja Schneider
- Institute of Pharmaceutical Microbiology, University of Bonn, 53115, Bonn, Germany
| | - Hans-Georg Sahl
- Institute of Pharmaceutical Microbiology, University of Bonn, 53115, Bonn, Germany
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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19
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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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20
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Abstract
The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.
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Cell Wall Glycans Mediate Recognition of the Dairy Bacterium Streptococcus thermophilus by Bacteriophages. Appl Environ Microbiol 2018; 84:AEM.01847-18. [PMID: 30242010 PMCID: PMC6238053 DOI: 10.1128/aem.01847-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/14/2018] [Indexed: 01/21/2023] Open
Abstract
Streptococcus thermophilus is widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants. Receptors on the cell surfaces of bacterial hosts are essential during the infection cycle of bacteriophages. To date, the phage receptors of the industrial relevant dairy starter bacterium Streptococcus thermophilus remain elusive. Thus, we set out to identify cell surface structures that are involved in host recognition by dairy streptococcal phages. Five industrial S. thermophilus strains sensitive to different phages (pac type, cos type, and the new type 987), were selected to generate spontaneous bacteriophage-insensitive mutants (BIMs). Of these, approximately 50% were deselected as clustered regularly interspaced short palindromic repeat (CRISPR) mutants, while the other pool was further characterized to identify receptor mutants. On the basis of genome sequencing data, phage resistance in putative receptor mutants was attributed to nucleotide changes in genes encoding glycan biosynthetic pathways. Superresolution structured illumination microscopy was used to visualize the interactions between S. thermophilus and its phages. The phages were either regularly distributed along the cells or located at division sites of the cells. The cell wall structures mediating the latter type of phage adherence were further analyzed via phenotypic and biochemical assays. Altogether, our data suggested that phage adsorption to S. thermophilus is mediated by glycans associated with the bacterial cell surface. Specifically, the pac-type phage CHPC951 adsorbed to polysaccharides anchored to peptidoglycan, while the 987-type phage CHPC926 recognized exocellular polysaccharides associated with the cell surface. IMPORTANCEStreptococcus thermophilus is widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants.
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Piñas GE, Reinoso-Vizcaino NM, Yandar Barahona NY, Cortes PR, Duran R, Badapanda C, Rathore A, Bichara DR, Cian MB, Olivero NB, Perez DR, Echenique J. Crosstalk between the serine/threonine kinase StkP and the response regulator ComE controls the stress response and intracellular survival of Streptococcus pneumoniae. PLoS Pathog 2018; 14:e1007118. [PMID: 29883472 PMCID: PMC6010298 DOI: 10.1371/journal.ppat.1007118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 06/20/2018] [Accepted: 05/23/2018] [Indexed: 11/30/2022] Open
Abstract
Streptococcus pneumoniae is an opportunistic human bacterial pathogen that usually colonizes the upper respiratory tract, but the invasion and survival mechanism in respiratory epithelial cells remains elusive. Previously, we described that acidic stress-induced lysis (ASIL) and intracellular survival are controlled by ComE through a yet unknown activation mechanism under acidic conditions, which is independent of the ComD histidine kinase that activates this response regulator for competence development at pH 7.8. Here, we demonstrate that the serine/threonine kinase StkP is essential for ASIL, and show that StkP phosphorylates ComE at Thr128. Molecular dynamic simulations predicted that Thr128-phosphorylation induces conformational changes on ComE’s DNA-binding domain. Using nonphosphorylatable (ComET128A) and phosphomimetic (ComET128E) proteins, we confirmed that Thr128-phosphorylation increased the DNA-binding affinity of ComE. The non-phosphorylated form of ComE interacted more strongly with StkP than the phosphomimetic form at acidic pH, suggesting that pH facilitated crosstalk. To identify the ComE-regulated genes under acidic conditions, a comparative transcriptomic analysis was performed between the comET128A and wt strains, and differential expression of 104 genes involved in different cellular processes was detected, suggesting that the StkP/ComE pathway induced global changes in response to acidic stress. In the comET128A mutant, the repression of spxB and sodA correlated with decreased H2O2 production, whereas the reduced expression of murN correlated with an increased resistance to cell wall antibiotic-induced lysis, compatible with cell wall alterations. In the comET128A mutant, ASIL was blocked and acid tolerance response was higher compared to the wt strain. These phenotypes, accompanied with low H2O2 production, are likely responsible for the increased survival in pneumocytes of the comET128A mutant. We propose that the StkP/ComE pathway controls the stress response, thus affecting the intracellular survival of S. pneumoniae in pneumocytes, one of the first barriers that this pathogen must cross to establish an infection. Streptococcus pneumoniae is a major human pathogen and is the causal agent of otitis (media) and sinusitis. It is also responsible for severe infections such as bacteremia, pneumonia, and meningitis, associated with 2 million annual deaths. Although this bacterium is part of the human nasopharynx commensal microbiota, it can become a pathogen and cross the epithelial cell barrier to establishing infections of varying intensity. Although S. pneumoniae is considered to be a typical extracellular pathogen, transient intracellular life forms have been found in eukaryotic cells, suggesting a putative survival mechanism. Here, we report that the serine-threonine kinase StkP was able to phosphorylate the response regulator ComE to control different cellular processes in response to environmental stress. Moreover, the phosphorylation of ComE on Thr128, and the consequent conformational and functional changes resulting from this event, extended the current knowledge of molecular activation mechanisms of response regulators. In this report, we provide evidence for the regulatory control exerted by the StkP/ComE pathway on acid-induced autolysis (associated with pneumolysin release), the acid tolerance response, and H2O2 production to modulate tissue damage and intracellular survival, which are ultimately linked to pneumococcal pathogenesis.
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Affiliation(s)
- Germán E. Piñas
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Nicolás M. Reinoso-Vizcaino
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Nubia Y. Yandar Barahona
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Paulo R. Cortes
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosario Duran
- Instituto Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable, Unidad de Bioquímica y Proteómica Analíticas, Montevideo, Uruguay
| | | | - Ankita Rathore
- Bioinformatics Division, Xcelris Lab Limited, Ahmedabad, India
| | | | - Melina B. Cian
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Nadia B. Olivero
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - José Echenique
- Departamento de Bioquímica Clínica—CIBICI (CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- * E-mail:
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Diversity of Mosaic pbp2x Families in Penicillin-Resistant Streptococcus pneumoniae from Iran and Romania. Antimicrob Agents Chemother 2017; 61:AAC.01535-17. [PMID: 28971878 PMCID: PMC5700355 DOI: 10.1128/aac.01535-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/19/2017] [Indexed: 11/20/2022] Open
Abstract
Penicillin-resistant Streptococcus pneumoniae strains are found at high rates in Romania and Iran. The mosaic structure of PBP2x was investigated in 9 strains from Iran and in 15 strains from Romania to understand their evolutionary history. Mutations potentially important for β-lactam resistance were identified by comparison of the PBP2x sequences with the sequence of the related PBP2x of reference penicillin-sensitive S. mitis strains. Two main PBP2x mosaic gene families were recognized. Eight Iranian strains expressed PBP2x variants in group 1, which had a mosaic block highly related to PBP2x of the Spain23F-1 clone, which is widespread among international penicillin-resistant S. pneumoniae clones. A second unique PBP2x group was observed in Romanian strains; furthermore, three PBP2x single mosaic variants were found. Sequence blocks of penicillin-sensitive strain S. mitis 658 were common among PBP2x variants from strains from both countries. Each PBP2x group contained specific signature mutations within the transpeptidase domain, documenting the existence of distinct mutational pathways for the development of penicillin resistance.
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El Moujaber G, Osman M, Rafei R, Dabboussi F, Hamze M. Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region. J Med Microbiol 2017. [DOI: 10.1099/jmm.0.000503] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Grace El Moujaber
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
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New Aspects of the Interplay between Penicillin Binding Proteins, murM, and the Two-Component System CiaRH of Penicillin-Resistant Streptococcus pneumoniae Serotype 19A Isolates from Hungary. Antimicrob Agents Chemother 2017; 61:AAC.00414-17. [PMID: 28483958 PMCID: PMC5487634 DOI: 10.1128/aac.00414-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/01/2017] [Indexed: 11/23/2022] Open
Abstract
The Streptococcus pneumoniae clone Hungary19A-6 expresses unusually high levels of β-lactam resistance, which is in part due to mutations in the MurM gene, encoding a transferase involved in the synthesis of branched peptidoglycan. Moreover, it contains the allele ciaH232, encoding the histidine kinase CiaH (M. Müller, P. Marx, R. Hakenbeck, and R. Brückner, Microbiology 157:3104–3112, 2011, https://doi.org/10.1099/mic.0.053157-0). High-level penicillin resistance primarily requires the presence of low-affinity (mosaic) penicillin binding protein (PBP) genes, as, for example, in strain Hu17, a closely related member of the Hungary19A-6 lineage. Interestingly, strain Hu15 is β-lactam sensitive due to the absence of mosaic PBPs. This unique situation prompted us to investigate the development of cefotaxime resistance in transformation experiments with genes known to play a role in this phenotype, pbp2x, pbp1a, murM, and ciaH, and penicillin-sensitive recipient strains R6 and Hu15. Characterization of phenotypes, peptidoglycan composition, and CiaR-mediated gene expression revealed several novel aspects of penicillin resistance. The murM gene of strain Hu17 (murMHu17), which is highly similar to murM of Streptococcus mitis, induced morphological changes which were partly reversed by ciaH232. murMHu17 conferred cefotaxime resistance only in the presence of the pbp2x of strain Hu17 (pbp2xHu17). The ciaH232 allele contributed to a remarkable increase in cefotaxime resistance in combination with pbp2xHu17 and pbp1a of strain Hu17 (pbp1aHu17), accompanied by higher levels of expression of CiaR-regulated genes, documenting that ciaH232 responds to PBP1aHu17-mediated changes in cell wall synthesis. Most importantly, the proportion of branched peptides relative to the proportion of linear muropeptides increased in cells containing mosaic PBPs, suggesting an altered enzymatic activity of these proteins.
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Calvez P, Breukink E, Roper DI, Dib M, Contreras-Martel C, Zapun A. Substitutions in PBP2b from β-Lactam-resistant Streptococcus pneumoniae Have Different Effects on Enzymatic Activity and Drug Reactivity. J Biol Chem 2017; 292:2854-2865. [PMID: 28062575 DOI: 10.1074/jbc.m116.764696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Pneumococcus resists β-lactams by expressing variants of its target enzymes, the penicillin-binding proteins (PBPs), with many amino acid substitutions. Up to 10% of the sequence can be modified. These altered PBPs have a much reduced reactivity with the drugs but retain their physiological activity of cross-linking the peptidoglycan, the major constituent of the bacterial cell wall. However, because β-lactams are chemical and structural mimics of the natural substrate, resistance mediated by altered PBPs raises the following paradox: how PBPs that react poorly with the drugs maintain a sufficient level of activity with the physiological substrate. This question is addressed for the first time in this study, which compares the peptidoglycan cross-linking activity of PBP2b from susceptible and resistant strains with their inhibition by different β-lactams. Unexpectedly, the enzymatic activity of the variants did not correlate with their antibiotic reactivity. This finding indicates that some of the numerous amino acid substitutions were selected to restore a viable level of enzymatic activity by a compensatory molecular mechanism.
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Affiliation(s)
- Philippe Calvez
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Eefjan Breukink
- the Department of Chemical Biology and Organic Chemistry, Institute of Biomembranes, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584 CH, The Netherlands, and
| | - David I Roper
- the School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mélanie Dib
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Carlos Contreras-Martel
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - André Zapun
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France,
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Highly improved acarbose production of Actinomyces through the combination of ARTP and penicillin susceptible mutant screening. World J Microbiol Biotechnol 2016; 33:16. [PMID: 27896580 DOI: 10.1007/s11274-016-2156-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
Atmospheric and room temperature plasma (ARTP) was first employed to generate mutants of Actinomyces JN537 for improving acarbose production. To obtain higher acarbose producing strains, the method of screening the strains for susceptibility to penicillin was used after treatment with ARTP. The rationale for the strategy was that mutants showing penicillin susceptibility were likely to be high acarbose producers, as their ability to synthesize cell walls was weak which might enhance metabolic flux to the pathway of acarbose biosynthesis. Acarbose yield of the mutant strain M37 increased by 62.5 % than that of the original strain. The contents of monosaccharides and amino acids of the cell wall of M37 were lower than that of the original strain. The acarbose production ability in mutant strain remained relatively stable after 10 generations. This work provides a promising strategy for obtaining high acarbose-yield strains by combination of ARTP mutation method and efficient screening technique.
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Edgar RJ, Chen J, Kant S, Rechkina E, Rush JS, Forsberg LS, Jaehrig B, Azadi P, Tchesnokova V, Sokurenko EV, Zhu H, Korotkov KV, Pancholi V, Korotkova N. SpyB, a Small Heme-Binding Protein, Affects the Composition of the Cell Wall in Streptococcus pyogenes. Front Cell Infect Microbiol 2016; 6:126. [PMID: 27790410 PMCID: PMC5061733 DOI: 10.3389/fcimb.2016.00126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/27/2016] [Indexed: 12/01/2022] Open
Abstract
Streptococcus pyogenes (Group A Streptococcus or GAS) is a hemolytic human pathogen associated with a wide variety of infections ranging from minor skin and throat infections to life-threatening invasive diseases. The cell wall of GAS consists of peptidoglycan sacculus decorated with a carbohydrate comprising a polyrhamnose backbone with immunodominant N-acetylglucosamine side-chains. All GAS genomes contain the spyBA operon, which encodes a 35-amino-acid membrane protein SpyB, and a membrane-bound C3-like ADP-ribosyltransferase SpyA. In this study, we addressed the function of SpyB in GAS. Phenotypic analysis of a spyB deletion mutant revealed increased bacterial aggregation, and reduced sensitivity to β-lactams of the cephalosporin class and peptidoglycan hydrolase PlyC. Glycosyl composition analysis of cell wall isolated from the spyB mutant suggested an altered carbohydrate structure compared with the wild-type strain. Furthermore, we found that SpyB associates with heme and protoporphyrin IX. Heme binding induces SpyB dimerization, which involves disulfide bond formation between the subunits. Thus, our data suggest the possibility that SpyB activity is regulated by heme.
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Affiliation(s)
- Rebecca J. Edgar
- Department of Molecular and Cellular Biochemistry, University of KentuckyLexington, KY, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of KentuckyLexington, KY, USA
| | - Sashi Kant
- Department of Pathology, Ohio State UniversityColumbus, OH, USA
| | - Elena Rechkina
- Department of Microbiology, University of WashingtonSeattle, WA, USA
| | - Jeffrey S. Rush
- Department of Molecular and Cellular Biochemistry, University of KentuckyLexington, KY, USA
| | | | - Bernhard Jaehrig
- Complex Carbohydrate Research Center, University of GeorgiaAthens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of GeorgiaAthens, GA, USA
| | | | | | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of KentuckyLexington, KY, USA
| | - Konstantin V. Korotkov
- Department of Molecular and Cellular Biochemistry, University of KentuckyLexington, KY, USA
| | - Vijay Pancholi
- Department of Pathology, Ohio State UniversityColumbus, OH, USA
| | - Natalia Korotkova
- Department of Molecular and Cellular Biochemistry, University of KentuckyLexington, KY, USA
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Mengin-Lecreulx D, Lemaitre B. Structure and metabolism of peptidoglycan and molecular requirements allowing its detection by the Drosophila innate immune system. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519050110020601] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Peptidoglycan (murein) is a major essential and specific constituent of the bacterial cell wall. Its main function is to protect cells against the internal osmotic pressure and to maintain the characteristic cell shape. It also serves as a platform for the anchoring of specific proteins and other cell wall components. This giant macromolecule is composed of long glycan chains cross-linked by short peptides. Any alteration of the disaccharide—peptide basic unit results in a global change of peptidoglycan structure and properties. Such global variations are encountered in nature as conserved variations along phyletic lines but have sometimes been acquired as a result of mutations or as a mechanism of resistance against cell-wall targeted antibiotics. During bacterial cell growth and division, the peptidoglycan mesh is constantly broken down by a set of highly specific hydrolases in a maturation process allowing insertion of newly synthesized units in the pre-existing polymerized material. Depending on the bacterial species considered, degradation fragments are either released in the growth medium or efficiently re-utilized for synthesis of new murein in a sequence of events termed the recycling pathway. Peptidoglycan is one of the main pathogen-associated molecular patterns recognized by the host innate immune system. Variations of the structure and metabolism of this cell wall component have been exploited by host defense mechanisms for detection/identification of invading bacterial species. Modification of the peptidoglycan structure could also represent a mechanism allowing bacteria to escape these host defense systems.
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Affiliation(s)
- Dominique Mengin-Lecreulx
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS, Université Paris-Sud, Paris, France, -psud.fr
| | - Bruno Lemaitre
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
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van Opijnen T, Dedrick S, Bento J. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathog 2016; 12:e1005869. [PMID: 27607357 PMCID: PMC5015961 DOI: 10.1371/journal.ppat.1005869] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/19/2022] Open
Abstract
The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.
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Affiliation(s)
- Tim van Opijnen
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - Sandra Dedrick
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - José Bento
- Boston College, Computer Science Department, Massachusetts, United States of America
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Kim L, McGee L, Tomczyk S, Beall B. Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective. Clin Microbiol Rev 2016; 29:525-52. [PMID: 27076637 PMCID: PMC4861989 DOI: 10.1128/cmr.00058-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.
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Affiliation(s)
- Lindsay Kim
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara Tomczyk
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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32
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Favrot L, Blanchard JS, Vergnolle O. Bacterial GCN5-Related N-Acetyltransferases: From Resistance to Regulation. Biochemistry 2016; 55:989-1002. [PMID: 26818562 DOI: 10.1021/acs.biochem.5b01269] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The GCN5-related N-acetyltransferases family (GNAT) is an important family of proteins that includes more than 100000 members among eukaryotes and prokaryotes. Acetylation appears as a major regulatory post-translational modification and is as widespread as phosphorylation. N-Acetyltransferases transfer an acetyl group from acetyl-CoA to a large array of substrates, from small molecules such as aminoglycoside antibiotics to macromolecules. Acetylation of proteins can occur at two different positions, either at the amino-terminal end (αN-acetylation) or at the ε-amino group (εN-acetylation) of an internal lysine residue. GNAT members have been classified into different groups on the basis of their substrate specificity, and in spite of a very low primary sequence identity, GNAT proteins display a common and conserved fold. This Current Topic reviews the different classes of bacterial GNAT proteins, their functions, their structural characteristics, and their mechanism of action.
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Affiliation(s)
- Lorenza Favrot
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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33
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Alvarez L, Hernandez SB, de Pedro MA, Cava F. Ultra-Sensitive, High-Resolution Liquid Chromatography Methods for the High-Throughput Quantitative Analysis of Bacterial Cell Wall Chemistry and Structure. Methods Mol Biol 2016; 1440:11-27. [PMID: 27311661 DOI: 10.1007/978-1-4939-3676-2_2] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
High-performance liquid chromatography (HPLC) analysis has been critical for determining the structural and chemical complexity of the cell wall. However this method is very time consuming in terms of sample preparation and chromatographic separation. Here we describe (1) optimized methods for peptidoglycan isolation from both Gram-negative and Gram-positive bacteria that dramatically reduce the sample preparation time, and (2) the application of the fast and highly efficient ultra-performance liquid chromatography (UPLC) technology to muropeptide separation and quantification. The advances in both analytical instrumentation and stationary-phase chemistry have allowed for evolved protocols which cut run time from hours (2-3 h) to minutes (10-20 min), and sample demands by at least one order of magnitude. Furthermore, development of methods based on organic solvents permits in-line mass spectrometry (MS) of the UPLC-resolved muropeptides. Application of these technologies to high-throughput analysis will expedite the better understanding of the cell wall biology.
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Affiliation(s)
- Laura Alvarez
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90187, Sweden
| | - Sara B Hernandez
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90187, Sweden
| | - Miguel A de Pedro
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90187, Sweden.
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Desmarais SM, Tropini C, Miguel A, Cava F, Monds RD, de Pedro MA, Huang KC. High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography. J Biol Chem 2015; 290:31090-100. [PMID: 26468288 DOI: 10.1074/jbc.m115.661660] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 01/22/2023] Open
Abstract
The bacterial cell wall is a network of glycan strands cross-linked by short peptides (peptidoglycan); it is responsible for the mechanical integrity of the cell and shape determination. Liquid chromatography can be used to measure the abundance of the muropeptide subunits composing the cell wall. Characteristics such as the degree of cross-linking and average glycan strand length are known to vary across species. However, a systematic comparison among strains of a given species has yet to be undertaken, making it difficult to assess the origins of variability in peptidoglycan composition. We present a protocol for muropeptide analysis using ultra performance liquid chromatography (UPLC) and demonstrate that UPLC achieves resolution comparable with that of HPLC while requiring orders of magnitude less injection volume and a fraction of the elution time. We also developed a software platform to automate the identification and quantification of chromatographic peaks, which we demonstrate has improved accuracy relative to other software. This combined experimental and computational methodology revealed that peptidoglycan composition was approximately maintained across strains from three Gram-negative species despite taxonomical and morphological differences. Peptidoglycan composition and density were maintained after we systematically altered cell size in Escherichia coli using the antibiotic A22, indicating that cell shape is largely decoupled from the biochemistry of peptidoglycan synthesis. High-throughput, sensitive UPLC combined with our automated software for chromatographic analysis will accelerate the discovery of peptidoglycan composition and the molecular mechanisms of cell wall structure determination.
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Affiliation(s)
| | - Carolina Tropini
- From the Departments of Bioengineering and the Biophysics Program, Stanford University, Stanford, California 94305
| | | | - Felipe Cava
- the Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, 90187 Sweden
| | - Russell D Monds
- From the Departments of Bioengineering and the Bio-X Program, Stanford University, Stanford, California 94305, and
| | - Miguel A de Pedro
- the Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Kerwyn Casey Huang
- From the Departments of Bioengineering and the Biophysics Program, Stanford University, Stanford, California 94305, the Bio-X Program, Stanford University, Stanford, California 94305, and Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305,
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Peptidoglycan Branched Stem Peptides Contribute to Streptococcus pneumoniae Virulence by Inhibiting Pneumolysin Release. PLoS Pathog 2015; 11:e1004996. [PMID: 26114646 PMCID: PMC4483231 DOI: 10.1371/journal.ppat.1004996] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/02/2015] [Indexed: 11/29/2022] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) colonizes the human nasopharynx and is a significant pathogen worldwide. Pneumolysin (Ply) is a multi-functional, extracellular virulence factor produced by this organism that is critical for pathogenesis. Despite the absence of any apparent secretion or cell surface attachment motifs, Ply localizes to the cell envelope of actively growing cells. We sought to characterize the consequences of this surface localization. Through functional assays with whole cells and subcellular fractions, we determined that Ply activity and its release into the extracellular environment are inhibited by peptidoglycan (PG) structure. The ability of PG to inhibit Ply release was dependent on the stem peptide composition of this macromolecule, which was manipulated by mutation of the murMN operon that encodes proteins responsible for branched stem peptide synthesis. Additionally, removal of choline-binding proteins from the cell surface significantly reduced Ply release to levels observed in a mutant with a high proportion of branched stem peptides suggesting a link between this structural feature and surface-associated choline-binding proteins involved in PG metabolism. Of clinical relevance, we also demonstrate that a hyperactive, mosaic murMN allele associated with penicillin resistance causes decreased Ply release with concomitant increases in the amount of branched stem peptides. Finally, using a murMN deletion mutant, we observed that increased Ply release is detrimental to virulence during a murine model of pneumonia. Taken together, our results reveal a novel role for branched stem peptides in pneumococcal pathogenesis and demonstrate the importance of controlled Ply release during infection. These results highlight the importance of PG composition in pathogenesis and may have broad implications for the diverse PG structures observed in other bacterial pathogens. Pneumolysin (Ply) is a protein toxin produced by Streptococcus pneumoniae that contributes to the ability of this organism to cause invasive disease. Release of this protein from the bacterial cell is necessary for many of its functions but the underlying mechanisms driving this process are not well characterized. Previous research demonstrated that Ply localizes to the cell wall compartment. Here, we address the consequences of this localization and reveal a role for the major cell wall structural component, peptidoglycan, in inhibiting Ply activity and release into the extracellular environment. Peptidoglycan is an essential, mesh-like sac that encases the cell, and alterations affecting its composition lead to differences in the amount of Ply released. How molecules interact with and traverse through the restrictive matrix of the cell wall and its associated structures is incompletely understood, particularly with respect to protein secretion and surface attachment. Our results argue that proper maintenance of cell wall-associated Ply is dependent on surface architecture and may be critical for S. pneumoniae pathogenesis.
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36
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Todorova K, Maurer P, Rieger M, Becker T, Bui NK, Gray J, Vollmer W, Hakenbeck R. Transfer of penicillin resistance from Streptococcus oralis to Streptococcus pneumoniae identifies murE as resistance determinant. Mol Microbiol 2015; 97:866-80. [PMID: 26010014 DOI: 10.1111/mmi.13070] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 01/26/2023]
Abstract
Beta-lactam resistant clinical isolates of Streptococcus pneumoniae contain altered penicillin-binding protein (PBP) genes and occasionally an altered murM, presumably products of interspecies gene transfer. MurM and MurN are responsible for the synthesis of branched lipid II, substrate for the PBP catalyzed transpeptidation reaction. Here we used the high-level beta-lactam resistant S. oralis Uo5 as donor in transformation experiments with the sensitive laboratory strain S. pneumoniae R6 as recipient. Surprisingly, piperacillin-resistant transformants contained no alterations in PBP genes but carried murEUo5 encoding the UDP-N-acetylmuramyl tripeptide synthetase. Codons 83-183 of murEUo5 were sufficient to confer the resistance phenotype. Moreover, the promoter of murEUo5 , which drives a twofold higher expression compared to that of S. pneumoniae R6, could also confer increased resistance. Multiple independent transformations produced S. pneumoniae R6 derivatives containing murEUo5 , pbp2xUo5 , pbp1aUo5 and pbp2bUo5 , but not murMUo5 sequences; however, the resistance level of the donor strain could not be reached. S. oralis Uo5 harbors an unusual murM, and murN is absent. Accordingly, the peptidoglycan of S. oralis Uo5 contained interpeptide bridges with one L-Ala residue only. The data suggest that resistance in S. oralis Uo5 is based on a complex interplay of distinct PBPs and other enzymes involved in peptidoglycan biosynthesis.
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Affiliation(s)
- Katya Todorova
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Patrick Maurer
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Martin Rieger
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tina Becker
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Nhat Khai Bui
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Pinnacle Laboratory, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
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Commensal streptococci serve as a reservoir for β-lactam resistance genes in Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 59:3529-40. [PMID: 25845880 DOI: 10.1128/aac.00429-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/31/2015] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia, meningitis, septicemia, and middle ear infections. The incidence of S. pneumoniae isolates that are not susceptible to penicillin has risen worldwide and may be above 20% in some countries. Beta-lactam antibiotic resistance in pneumococci is associated with significant sequence polymorphism in penicillin-binding proteins (PBPs). Commensal streptococci, especially S. mitis and S. oralis, have been identified as putative donors of mutated gene fragments. However, no studies have compared sequences of the involved pbp genes in large collections of commensal streptococci with those of S. pneumoniae. We therefore investigated the sequence diversity of the transpeptidase region of the three pbp genes, pbp2x, pbp2b, and pbp1a in 107, 96, and 88 susceptible and nonsusceptible strains of commensal streptococci, respectively, at the nucleotide and amino acid levels to determine to what extent homologous recombination between commensal streptococci and S. pneumoniae plays a role in the development of beta-lactam resistance in S. pneumoniae. In contrast to pneumococci, extensive sequence variation in the transpeptidase region of pbp2x, pbp2b, and pbp1a was observed in both susceptible and nonsusceptible strains of commensal streptococci, conceivably reflecting the genetic diversity of the many evolutionary lineages of commensal streptococci combined with the recombination events occurring with intra- and interspecies homologues. Our data support the notion that resistance to beta-lactam antibiotics in pneumococci is due to sequences acquired from commensal Mitis group streptococci, especially S. mitis. However, several amino acid alterations previously linked to beta-lactam resistance in pneumococci appear to represent species signatures of the donor strain rather than being causal of resistance.
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Shepherd J, Ibba M. Bacterial transfer RNAs. FEMS Microbiol Rev 2015; 39:280-300. [PMID: 25796611 DOI: 10.1093/femsre/fuv004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/21/2015] [Indexed: 11/14/2022] Open
Abstract
Transfer RNA is an essential adapter molecule that is found across all three domains of life. The primary role of transfer RNA resides in its critical involvement in the accurate translation of messenger RNA codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. This review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer RNAs. Codon recognition at the ribosome as well as the ever-increasing number of alternative roles for transfer RNA outside of translation will be discussed in the specific context of bacterial cells.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
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Philippe J, Gallet B, Morlot C, Denapaite D, Hakenbeck R, Chen Y, Vernet T, Zapun A. Mechanism of β-lactam action in Streptococcus pneumoniae: the piperacillin paradox. Antimicrob Agents Chemother 2015; 59:609-21. [PMID: 25385114 PMCID: PMC4291406 DOI: 10.1128/aac.04283-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/05/2014] [Indexed: 11/20/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae has been treated for decades with β-lactam antibiotics. Its resistance is now widespread, mediated by the expression of mosaic variants of the target enzymes, the penicillin-binding proteins (PBPs). Understanding the mode of action of β-lactams, not only in molecular detail but also in their physiological consequences, will be crucial to improving these drugs and any counterresistances. In this work, we investigate the piperacillin paradox, by which this β-lactam selects primarily variants of PBP2b, whereas its most reactive target is PBP2x. These PBPs are both essential monofunctional transpeptidases involved in peptidoglycan assembly. PBP2x participates in septal synthesis, while PBP2b functions in peripheral elongation. The formation of the "lemon"-shaped cells induced by piperacillin treatment is consistent with the inhibition of PBP2x. Following the examination of treated and untreated cells by electron microscopy, the localization of the PBPs by epifluorescence microscopy, and the determination of the inhibition time course of the different PBPs, we propose a model of peptidoglycan assembly that accounts for the piperacillin paradox.
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Affiliation(s)
- Jules Philippe
- Université Grenoble Alpes, IBS, Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Benoit Gallet
- Université Grenoble Alpes, IBS, Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Cécile Morlot
- Université Grenoble Alpes, IBS, Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Dalia Denapaite
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany Alfried Krupp Wissenschaftskolleg, Greifswald, Germany
| | - Yuxin Chen
- University of Science and Technology of China, Hefei, China
| | - Thierry Vernet
- Université Grenoble Alpes, IBS, Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - André Zapun
- Université Grenoble Alpes, IBS, Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
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Relaxed substrate specificity leads to extensive tRNA mischarging by Streptococcus pneumoniae class I and class II aminoacyl-tRNA synthetases. mBio 2014; 5:e01656-14. [PMID: 25205097 PMCID: PMC4173786 DOI: 10.1128/mbio.01656-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aminoacyl-tRNA synthetases provide the first step in protein synthesis quality control by discriminating cognate from noncognate amino acid and tRNA substrates. While substrate specificity is enhanced in many instances by cis- and trans-editing pathways, it has been revealed that in organisms such as Streptococcus pneumoniae some aminoacyl-tRNA synthetases display significant tRNA mischarging activity. To investigate the extent of tRNA mischarging in this pathogen, the aminoacylation profiles of class I isoleucyl-tRNA synthetase (IleRS) and class II lysyl-tRNA synthetase (LysRS) were determined. Pneumococcal IleRS mischarged tRNAIle with both Val, as demonstrated in other bacteria, and Leu in a tRNA sequence-dependent manner. IleRS substrate specificity was achieved in an editing-independent manner, indicating that tRNA mischarging would only be significant under growth conditions where Ile is depleted. Pneumococcal LysRS was found to misaminoacylate tRNALys with Ala and to a lesser extent Thr and Ser, with mischarging efficiency modulated by the presence of an unusual U4:G69 wobble pair in the acceptor stems of both pneumococcal tRNALys isoacceptors. Addition of the trans-editing factor MurM, which also functions in peptidoglycan synthesis, reduced Ala-tRNALys production by LysRS, providing evidence for cross talk between the protein synthesis and cell wall biogenesis pathways. Mischarging of tRNALys by AlaRS was also observed, and this would provide additional potential MurM substrates. More broadly, the extensive mischarging activities now described for a number of Streptococcus pneumoniae aminoacyl-tRNA synthetases suggest that adaptive misaminoacylation may contribute significantly to the viability of this pathogen during amino acid starvation. Streptococcus pneumoniae is a common causative agent of several debilitating and potentially life-threatening infections, such as pneumonia, meningitis, and infectious endocarditis. Such infections are increasingly difficult to treat due to widespread development of penicillin resistance. High-level penicillin resistance is known to depend in part upon MurM, a protein involved in both aminoacyl-tRNA-dependent synthesis of indirect amino acid cross-linkages within cell wall peptidoglycan and in translation quality control. The involvement of MurM in both protein synthesis and antibiotic resistance identify it as a potential target for the development of new and potent antibiotics for pneumococcal infections. The goals of this work were to identify and characterize S. pneumoniae pathways that can synthesize mischarged tRNAs and to relate these activities to expected changes in protein and peptidoglycan biosynthesis during antibiotic and nutritional stress.
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Sudhakar P, Reck M, Wang W, He FQ, Wagner-Döbler I, Dobler IW, Zeng AP. Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton. BMC Genomics 2014; 15:362. [PMID: 24884510 PMCID: PMC4048456 DOI: 10.1186/1471-2164-15-362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/17/2014] [Indexed: 11/26/2022] Open
Abstract
Background Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network of S. mutans biofilms upon carolacton treatment was constructed and analyzed. A systems biological approach integrating time-resolved transcriptomic data, reverse engineering, transcription factor binding sites, and experimental validation was carried out. Results The co-expression response network constructed from transcriptomic data using the reverse engineering algorithm called the Trend Correlation method consisted of 8284 gene pairs. The regulatory response network inferred by superimposing transcription factor binding site information into the co-expression network comprised 329 putative transcriptional regulatory interactions and could be classified into 27 sub-networks each co-regulated by a transcription factor. These sub-networks were significantly enriched with genes sharing common functions. The regulatory response network displayed global hierarchy and network motifs as observed in model organisms. The sub-networks modulated by the pyrimidine biosynthesis regulator PyrR, the glutamine synthetase repressor GlnR, the cysteine metabolism regulator CysR, global regulators CcpA and CodY and the two component system response regulators VicR and MbrC among others could putatively be related to the physiological effect of carolacton. The predicted interactions from the regulatory network between MbrC, known to be involved in cell envelope stress response, and the murMN-SMU_718c genes encoding peptidoglycan biosynthetic enzymes were experimentally confirmed using Electro Mobility Shift Assays. Furthermore, gene deletion mutants of five predicted key regulators from the response networks were constructed and their sensitivities towards carolacton were investigated. Deletion of cysR, the node having the highest connectivity among the regulators chosen from the regulatory network, resulted in a mutant which was insensitive to carolacton thus demonstrating not only the essentiality of cysR for the response of S. mutans biofilms to carolacton but also the relevance of the predicted network. Conclusion The network approach used in this study revealed important regulators and interactions as part of the response mechanisms of S. mutans biofilm cells to carolacton. It also opens a door for further studies into novel drug targets against streptococci. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-362) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Irene W Dobler
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, 21073 Hamburg, Germany.
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A low-affinity penicillin-binding protein 2x variant is required for heteroresistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 2014; 58:3934-41. [PMID: 24777105 DOI: 10.1128/aac.02547-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heteroresistance to penicillin in Streptococcus pneumoniae is the ability of subpopulations to grow at a higher antibiotic concentration than expected from the MIC. This may render conventional resistance testing unreliable and lead to therapeutic failure. We investigated the role of the primary β-lactam resistance determinants, penicillin-binding protein 2b (PBP2b) and PBP2x, and the secondary resistance determinant PBP1a in heteroresistance to penicillin. Transformants containing PBP genes from the heteroresistant strain Spain(23F) 2349 in the nonheteroresistant strain R6 background were tested for heteroresistance by population analysis profiling (PAP). We found that pbp2x, but not pbp2b or pbp1a alone, conferred heteroresistance to R6. However, a change of pbp2x expression was not observed, and therefore, expression does not correlate with an increased proportion of resistant subpopulations. In addition, the influence of the CiaRH system, mediating PBP-independent β-lactam resistance, was assessed by PAP on ciaR disruption mutants but revealed no heteroresistant phenotype. We also showed that the highly resistant subpopulations (HOM*) of transformants containing low-affinity pbp2x undergo an increase in resistance upon selection on penicillin plates that partially reverts after passaging on selection-free medium. Shotgun proteomic analysis showed an upregulation of phosphate ABC transporter subunit proteins encoded by pstS, phoU, pstB, and pstC in these highly resistant subpopulations. In conclusion, the presence of low-affinity pbp2x enables certain pneumococcal colonies to survive in the presence of β-lactams. Upregulation of phosphate ABC transporter genes may represent a reversible adaptation to antibiotic stress.
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Verhagen LM, de Jonge MI, Burghout P, Schraa K, Spagnuolo L, Mennens S, Eleveld MJ, van der Gaast-de Jongh CE, Zomer A, Hermans PWM, Bootsma HJ. Genome-wide identification of genes essential for the survival of Streptococcus pneumoniae in human saliva. PLoS One 2014; 9:e89541. [PMID: 24586856 PMCID: PMC3934895 DOI: 10.1371/journal.pone.0089541] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Since Streptococcus pneumoniae transmits through droplet spread, this respiratory tract pathogen may be able to survive in saliva. Here, we show that saliva supports survival of clinically relevant S. pneumoniae strains for more than 24 h in a capsule-independent manner. Moreover, saliva induced growth of S. pneumoniae in growth-permissive conditions, suggesting that S. pneumoniae is well adapted for uptake of nutrients from this bodily fluid. By using Tn-seq, a method for genome-wide negative selection screening, we identified 147 genes potentially required for growth and survival of S. pneumoniae in saliva, among which genes predicted to be involved in cell envelope biosynthesis, cell transport, amino acid metabolism, and stress response predominated. The Tn-seq findings were validated by testing a panel of directed gene deletion mutants for their ability to survive in saliva under two testing conditions: at room temperature without CO2, representing transmission, and at 37°C with CO2, representing in-host carriage. These validation experiments confirmed that the plsX gene and the amiACDEF and aroDEBC operons, involved in respectively fatty acid metabolism, oligopeptide transport, and biosynthesis of aromatic amino acids play an important role in the growth and survival of S. pneumoniae in saliva at 37°C. In conclusion, this study shows that S. pneumoniae is well-adapted for growth and survival in human saliva and provides a genome-wide list of genes potentially involved in adaptation. This notion supports earlier evidence that S. pneumoniae can use human saliva as a vector for transmission.
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Affiliation(s)
- Lilly M. Verhagen
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marien I. de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Peter Burghout
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Kiki Schraa
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Lorenza Spagnuolo
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Svenja Mennens
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marc J. Eleveld
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - Aldert Zomer
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Peter W. M. Hermans
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Hester J. Bootsma
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
- * E-mail:
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Nikolaidis I, Favini-Stabile S, Dessen A. Resistance to antibiotics targeted to the bacterial cell wall. Protein Sci 2014; 23:243-59. [PMID: 24375653 DOI: 10.1002/pro.2414] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 11/10/2022]
Abstract
Peptidoglycan is the main component of the bacterial cell wall. It is a complex, three-dimensional mesh that surrounds the entire cell and is composed of strands of alternating glycan units crosslinked by short peptides. Its biosynthetic machinery has been, for the past five decades, a preferred target for the discovery of antibacterials. Synthesis of the peptidoglycan occurs sequentially within three cellular compartments (cytoplasm, membrane, and periplasm), and inhibitors of proteins that catalyze each stage have been identified, although not all are applicable for clinical use. A number of these antimicrobials, however, have been rendered inactive by resistance mechanisms. The employment of structural biology techniques has been instrumental in the understanding of such processes, as well as the development of strategies to overcome them. This review provides an overview of resistance mechanisms developed toward antibiotics that target bacterial cell wall precursors and its biosynthetic machinery. Strategies toward the development of novel inhibitors that could overcome resistance are also discussed.
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Affiliation(s)
- I Nikolaidis
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, 6 rue Jules Horowitz, 38027, Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France; Centre National de la Recherche Scientifique (CNRS), UMR 5075, Grenoble, France; Bijvoet Center for Biomolecular Research, Department of Biochemistry of Membranes, Utrecht University, Utrecht, The Netherlands
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Genomic analyses of DNA transformation and penicillin resistance in Streptococcus pneumoniae clinical isolates. Antimicrob Agents Chemother 2013; 58:1397-403. [PMID: 24342643 DOI: 10.1128/aac.01311-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alterations in penicillin-binding proteins, the target enzymes for β-lactam antibiotics, are recognized as primary penicillin resistance mechanisms in Streptococcus pneumoniae. Few studies have analyzed penicillin resistance at the genome scale, however, and we report the sequencing of S. pneumoniae R6 transformants generated while reconstructing the penicillin resistance phenotypes from three penicillin-resistant clinical isolates by serial genome transformation. The genome sequences of the three last-level transformants T2-18209, T5-1983, and T3-55938 revealed that 16.2 kb, 82.7 kb, and 137.2 kb of their genomes had been replaced with 5, 20, and 37 recombinant sequence segments derived from their respective parental clinical isolates, documenting the extent of DNA transformation between strains. A role in penicillin resistance was confirmed for some of the mutations identified in the transformants. Several multiple recombination events were also found to have happened at single loci coding for penicillin-binding proteins (PBPs) that increase resistance. Sequencing of the transformants with MICs for penicillin similar to those of the parent clinical strains confirmed the importance of mosaic PBP2x, -2b, and -1a as a driving force in penicillin resistance. A role in resistance for mosaic PBP2a was also observed for two of the resistant clinical isolates.
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Frazão N, Hiller NL, Powell E, Earl J, Ahmed A, Sá-Leão R, de Lencastre H, Ehrlich GD, Tomasz A. Virulence potential and genome-wide characterization of drug resistant Streptococcus pneumoniae clones selected in vivo by the 7-valent pneumococcal conjugate vaccine. PLoS One 2013; 8:e74867. [PMID: 24069360 PMCID: PMC3777985 DOI: 10.1371/journal.pone.0074867] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022] Open
Abstract
We used mouse models of pneumococcal colonization and disease combined with full genome sequencing to characterize three major drug resistant clones of S. pneumoniae that were recovered from the nasopharynx of PCV7-immunized children in Portugal. The three clones--serotype 6A (ST2191), serotype 15A (ST63) and serotype 19A (ST276) carried some of the same drug resistance determinants already identified in nasopharyngeal isolates from the pre-PCV7 era. The three clones were able to colonize efficiently the mouse nasopharyngeal mucosa where populations of these pneumococci were retained for as long as 21 days. During this period, the three clones were able to asymptomatically invade the olfactory bulbs, brain, lungs and the middle ear mucosa and established populations in these tissues. The virulence potential of the three clones was poor even at high inoculum (10(5) CFU per mouse) concentrations in the mouse septicemia model and was undetectable in the pneumonia model. Capsular type 3 transformants of clones 6A and 19A prepared in the laboratory produced lethal infection at low cell concentration (10(3) CFU per mouse) but the same transformants became impaired in their potential to colonize, indicating the importance of the capsular polysaccharide in both disease and colonization. The three clones were compared to the genomes of 56 S. pneumoniae strains for which sequence information was available in the public databank. Clone 15A (ST63) only differed from the serotype 19F clone G54 in a very few genes including serotype so that this clone may be considered the product of a capsular switch. While no strain with comparable degree of similarity to clone 19A (ST276) was found among the sequenced isolates, by MLST this clone is a single locust variant (SLV) of Denmark14-ST230 international clone. Clone 6A (ST2191) was most similar to the penicillin resistant Hungarian serotype 19A clone.
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Affiliation(s)
- Nelson Frazão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - N. Luisa Hiller
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Evan Powell
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Josh Earl
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Azad Ahmed
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - Garth D. Ehrlich
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Alexander Tomasz
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
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Shepherd J, Ibba M. Direction of aminoacylated transfer RNAs into antibiotic synthesis and peptidoglycan-mediated antibiotic resistance. FEBS Lett 2013; 587:2895-904. [PMID: 23907010 DOI: 10.1016/j.febslet.2013.07.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 12/30/2022]
Abstract
Prokaryotic aminoacylated-transfer RNAs often need to be efficiently segregated between translation and other cellular biosynthetic pathways. Many clinically relevant bacteria, including Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa direct some aminoacylated-tRNA species into peptidoglycan biosynthesis and/or membrane phospholipid modification. Subsequent indirect peptidoglycan cross-linkage or change in membrane permeability is often a prerequisite for high-level antibiotic resistance. In Streptomycetes, aminoacylated-tRNA species are used for antibiotic synthesis as well as antibiotic resistance. The direction of coding aminoacylated-tRNA molecules away from translation and into antibiotic resistance and synthesis pathways are discussed in this review.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210-1292, USA
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Effects of low PBP2b levels on cell morphology and peptidoglycan composition in Streptococcus pneumoniae R6. J Bacteriol 2013; 195:4342-54. [PMID: 23873916 DOI: 10.1128/jb.00184-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae produces two class B penicillin-binding proteins, PBP2x and PBP2b, both of which are essential. It is generally assumed that PBP2x is specifically involved in septum formation, while PBP2b is dedicated to peripheral cell wall synthesis. However, little experimental evidence exists to substantiate this belief. In the present study, we obtained evidence that strongly supports the view that PBP2b is essential for peripheral peptidoglycan synthesis. Depletion of PBP2b expression gave rise to long chains of cells in which individual cells were compressed in the direction of the long axis and looked lentil shaped. This morphological change is consistent with a role for pneumococcal PBP2b in the synthesis of the lateral cell wall. Depletion of PBP2x, on the other hand, resulted in lemon-shaped and some elongated cells with a thickened midcell region. Low PBP2b levels gave rise to changes in the peptidoglycan layer that made pneumococci sensitive to exogenously added LytA during logarithmic growth and refractory to chain dispersion upon addition of LytB. Interestingly, analysis of the cell wall composition of PBP2b-depleted pneumococci revealed that they had a larger proportion of branched stem peptides in their peptidoglycan than the corresponding undepleted cells. Furthermore, MurM-deficient mutants, i.e., mutants lacking the ability to synthesize branched muropeptides, were found to require much higher levels of PBP2b to sustain growth than those required by MurM-proficient strains. These findings might help to explain why increased incorporation of branched muropeptides is required for high-level beta-lactam resistance in S. pneumoniae.
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Shepherd J, Ibba M. Lipid II-independent trans editing of mischarged tRNAs by the penicillin resistance factor MurM. J Biol Chem 2013; 288:25915-25923. [PMID: 23867453 DOI: 10.1074/jbc.m113.479824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Streptococcus pneumoniae is a causative agent of nosocomial infections such as pneumonia, meningitis, and septicemia. Penicillin resistance in S. pneumoniae depends in part upon MurM, an aminoacyl-tRNA ligase that attaches L-serine or L-alanine to the stem peptide lysine of Lipid II in cell wall peptidoglycan. To investigate the exact substrates the translation machinery provides MurM, quality control by alanyl-tRNA synthetase (AlaRS) was investigated. AlaRS mischarged serine and glycine to tRNA(Ala), as observed in other bacteria, and also transferred alanine, serine, and glycine to tRNA(Phe). S. pneumoniae tRNA(Phe) has an unusual U4:C69 mismatch in its acceptor stem that prevents editing by phenylalanyl-tRNA synthetase (PheRS), leading to the accumulation of misaminoacylated tRNAs that could serve as substrates for translation or for MurM. Although the peptidoglycan layer of S. pneumoniae tolerates a combination of both branched and linear muropeptides, deletion of MurM results in a reversion to penicillin sensitivity in strains that were previously resistant. However, because MurM is not required for cell viability, the reason for its functional conservation across all strains of S. pneumoniae has remained elusive. We now show that MurM can directly function in translation quality control by acting as a broad specificity lipid-independent trans editing factor that deacylates tRNA. This activity of MurM does not require the presence of its second substrate, Lipid II, and can functionally substitute for the activity of widely conserved editing domain homologues of AlaRS, termed AlaXPs proteins, which are themselves absent from S. pneumoniae.
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Affiliation(s)
| | - Michael Ibba
- From the Department of Microbiology and; Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
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Fani F, Brotherton MC, Leprohon P, Ouellette M. Genomic analysis and reconstruction of cefotaxime resistance in Streptococcus pneumoniae. J Antimicrob Chemother 2013; 68:1718-27. [PMID: 23608923 DOI: 10.1093/jac/dkt113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To identify non-penicillin-binding protein (PBP) mutations contributing to resistance to the third-generation cephalosporin cefotaxime in Streptococcus pneumoniae at the genome-wide scale. METHODS The genomes of two in vitro S. pneumoniae cefotaxime-resistant isolates and of two transformants serially transformed with the genomic DNA of cefotaxime-resistant mutants were determined by next-generation sequencing. A role in cefotaxime resistance for the mutations identified was confirmed by reconstructing resistance in a cefotaxime-susceptible background. RESULTS Analysis of the genome assemblies revealed mutations in genes coding for the PBPs 2x, 2a and 3, of which pbp2x was the only mutated gene common to all mutants. The transformation of altered PBP alleles into S. pneumoniae R6 confirmed the role of PBP mutations in cefotaxime resistance, but these were not sufficient to fully explain the levels of resistance. Thirty-one additional genes were found to be mutated in at least one of the four sequenced genomes. Non-PBP resistance determinants appeared to be mostly lineage specific. Mutations in spr1333, spr0981, spr1704 and spr1098, encoding a peptidoglycan N-acetylglucosamine deacetylase, a glycosyltransferase, an ABC transporter and a sortase, respectively, were implicated in resistance by transformation experiments and allowed the reconstruction of the full level of resistance observed in the parent resistant strains. CONCLUSIONS This whole-genome analysis coupled to functional studies has allowed the discovery of both known and novel cefotaxime resistance genes in S. pneumoniae.
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Affiliation(s)
- Fereshteh Fani
- Centre de recherche en Infectiologie du Centre de recherche du CHUL and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
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