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Miguel-Ruano V, Feltzer R, Batuecas MT, Ramachandran B, El-Araby AM, Avila-Cobian LF, De Benedetti S, Mobashery S, Hermoso JA. Structural characterization of lytic transglycosylase MltD of Pseudomonas aeruginosa, a target for the natural product bulgecin A. Int J Biol Macromol 2024; 267:131420. [PMID: 38583835 DOI: 10.1016/j.ijbiomac.2024.131420] [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: 01/02/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Natural product bulgecin A potentiates the activity of β-lactam antibiotics by inhibition of three lytic transglycosylases in Pseudomonas aeruginosa, of which MltD is one. MltD exhibits both endolytic and exolytic reactions in the turnover of the cell-wall peptidoglycan and tolerates the presence or absence of stem peptides in its substrates. The present study reveals structural features of the multimodular MltD, presenting a catalytic module and four cell-wall-binding LysM modules that account for these attributes. Three X-ray structures are reported herein for MltD that disclose one unpredicted LysM module tightly attached to the catalytic domain, whereas the other LysM modules are mobile, and connected to the catalytic domain through long flexible linkers. The formation of crystals depended on the presence of bulgecin A. The expansive active-site cleft is highlighted by the insertion of a helical region, a hallmark of the family 1D of lytic transglycosylases, which was mapped out in a ternary complex of MltD:bulgecinA:chitotetraose, revealing at the minimum the presence of eight subsites (from -4 to +4, with the seat of reaction at subsites -1 and + 1) for binding of sugars of the substrate for the endolytic reaction. The mechanism of the exolytic reaction is revealed in one of the structures, showing how the substrate's terminal anhydro-NAM moiety could be sequestered at subsite +2. Our results provide the structural insight for both the endolytic and exolytic activities of MltD during cell-wall-turnover events.
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Affiliation(s)
- Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Balajee Ramachandran
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Amr M El-Araby
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Luis F Avila-Cobian
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Stefania De Benedetti
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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2
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Sobe RC, Scharf BE. The swimming defect caused by the absence of the transcriptional regulator LdtR in Sinorhizobium meliloti is restored by mutations in the motility genes motA and motS. Mol Microbiol 2024; 121:954-970. [PMID: 38458990 DOI: 10.1111/mmi.15247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024]
Abstract
The flagellar motor is a powerful macromolecular machine used to propel bacteria through various environments. We determined that flagellar motility of the alpha-proteobacterium Sinorhizobium meliloti is nearly abolished in the absence of the transcriptional regulator LdtR, known to influence peptidoglycan remodeling and stress response. LdtR does not regulate motility gene transcription. Remarkably, the motility defects of the ΔldtR mutant can be restored by secondary mutations in the motility gene motA or a previously uncharacterized gene in the flagellar regulon, which we named motS. MotS is not essential for S. meliloti motility and may serve an accessory role in flagellar motor function. Structural modeling predicts that MotS comprised an N-terminal transmembrane segment, a long-disordered region, and a conserved β-sandwich domain. The C terminus of MotS is localized in the periplasm. Genetics based substitution of MotA with MotAG12S also restored the ΔldtR motility defect. The MotAG12S variant protein features a local polarity shift at the periphery of the MotAB stator units. We propose that MotS may be required for optimal alignment of stators in wild-type flagellar motors but becomes detrimental in cells with altered peptidoglycan. Similarly, the polarity shift in stator units composed of MotB/MotAG12S might stabilize its interaction with altered peptidoglycan.
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Affiliation(s)
- Richard C Sobe
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, Virginia, USA
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3
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Weaver A, Taguchi A, Dörr T. Masters of Misdirection: Peptidoglycan Glycosidases in Bacterial Growth. J Bacteriol 2023; 205:e0042822. [PMID: 36757204 PMCID: PMC10029718 DOI: 10.1128/jb.00428-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The dynamic composition of the peptidoglycan cell wall has been the subject of intense research for decades, yet how bacteria coordinate the synthesis of new peptidoglycan with the turnover and remodeling of existing peptidoglycan remains elusive. Diversity and redundancy within peptidoglycan synthases and peptidoglycan autolysins, enzymes that degrade peptidoglycan, have often made it challenging to assign physiological roles to individual enzymes and determine how those activities are regulated. For these reasons, peptidoglycan glycosidases, which cleave within the glycan strands of peptidoglycan, have proven veritable masters of misdirection over the years. Unlike many of the broadly conserved peptidoglycan synthetic complexes, diverse bacteria can employ unrelated glycosidases to achieve the same physiological outcome. Additionally, although the mechanisms of action for many individual enzymes have been characterized, apparent conserved homologs in other organisms can exhibit an entirely different biochemistry. This flexibility has been recently demonstrated in the context of three functions critical to vegetative growth: (i) release of newly synthesized peptidoglycan strands from their membrane anchors, (ii) processing of peptidoglycan turned over during cell wall expansion, and (iii) removal of peptidoglycan fragments that interfere with daughter cell separation during cell division. Finally, the regulation of glycosidase activity during these cell processes may be a cumulation of many factors, including protein-protein interactions, intrinsic substrate preferences, substrate availability, and subcellular localization. Understanding the true scope of peptidoglycan glycosidase activity will require the exploration of enzymes from diverse organisms with equally diverse growth and division strategies.
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Affiliation(s)
- Anna Weaver
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Atsushi Taguchi
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
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4
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Becker R, Ulrich K, Behrendt U, Schneck V, Ulrich A. Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback. PLANTS (BASEL, SWITZERLAND) 2022; 11:3487. [PMID: 36559599 PMCID: PMC9781493 DOI: 10.3390/plants11243487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.
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Affiliation(s)
- Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Volker Schneck
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
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5
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Rattanachak N, Weawsiangsang S, Daowtak K, Thongsri Y, Ross S, Ross G, Nilsri N, Baldock RA, Pongcharoen S, Jongjitvimol T, Jongjitwimol J. High-Throughput Transcriptomic Profiling Reveals the Inhibitory Effect of Hydroquinine on Virulence Factors in Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:antibiotics11101436. [PMID: 36290094 PMCID: PMC9598861 DOI: 10.3390/antibiotics11101436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/08/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Hydroquinine is an organic alkaloid compound that exhibits antimicrobial activity against several bacterial strains including strains of both drug-sensitive and multidrug-resistant P. aeruginosa. Despite this, the effects of hydroquinine on virulence factors in P. aeruginosa have not yet been characterized. We therefore aimed to uncover the mechanism of P. aeruginosa hydroquinine-sensitivity using high-throughput transcriptomic analysis. We further confirmed whether hydroquinine inhibits specific virulence factors using RT-qPCR and phenotypic analysis. At half the minimum inhibitory concentration (MIC) of hydroquinine (1.250 mg/mL), 254 genes were differentially expressed (97 downregulated and 157 upregulated). We found that flagellar-related genes were downregulated by between −2.93 and −2.18 Log2-fold change. These genes were consistent with the analysis of gene ontology and KEGG pathway. Further validation by RT-qPCR showed that hydroquinine significantly suppressed expression of the flagellar-related genes. By analyzing cellular phenotypes, P. aeruginosa treated with ½MIC of hydroquinine exhibited inhibition of motility (30−54% reduction) and pyocyanin production (~25−27% reduction) and impaired biofilm formation (~57−87% reduction). These findings suggest that hydroquinine possesses anti-virulence factors, through diminishing flagellar, pyocyanin and biofilm formation.
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Affiliation(s)
- Nontaporn Rattanachak
- Biomedical Sciences Program, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Sattaporn Weawsiangsang
- Biomedical Sciences Program, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Krai Daowtak
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Cellular and Molecular Immunology Research Unit, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Yordhathai Thongsri
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Cellular and Molecular Immunology Research Unit, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Sukunya Ross
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
- Centre of Excellence in Biomaterials, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Gareth Ross
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
- Centre of Excellence in Biomaterials, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Nungruthai Nilsri
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Cellular and Molecular Immunology Research Unit, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Robert A. Baldock
- School of Pharmacy and Biomedical Sciences, Faculty of Science and Health, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Sutatip Pongcharoen
- Division of Immunology, Department of Medicine, Faculty of Medicine, Naresuan University, Phitsanulok 65000, Thailand
| | - Touchkanin Jongjitvimol
- Biology Program, Faculty of Science and Technology, Pibulsongkram Rajabhat University, Phitsanulok 65000, Thailand
- Correspondence: (T.J.); (J.J.)
| | - Jirapas Jongjitwimol
- Biomedical Sciences Program, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok 65000, Thailand
- Centre of Excellence in Biomaterials, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
- Correspondence: (T.J.); (J.J.)
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6
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Abstract
Most bacteria are protected from environmental offenses by a cell wall consisting of strong yet elastic peptidoglycan. The cell wall is essential for preserving bacterial morphology and viability, and thus the enzymes involved in the production and turnover of peptidoglycan have become preferred targets for many of our most successful antibiotics. In the past decades, Vibrio cholerae, the gram-negative pathogen causing the diarrheal disease cholera, has become a major model for understanding cell wall genetics, biochemistry, and physiology. More than 100 articles have shed light on novel cell wall genetic determinants, regulatory links, and adaptive mechanisms. Here we provide the first comprehensive review of V. cholerae's cell wall biology and genetics. Special emphasis is placed on the similarities and differences with Escherichia coli, the paradigm for understanding cell wall metabolism and chemical structure in gram-negative bacteria.
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Affiliation(s)
- Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| | - Sara B Hernandez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå SE-90187, Sweden;
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7
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Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria. Nat Commun 2021; 12:4347. [PMID: 34301933 PMCID: PMC8302735 DOI: 10.1038/s41467-021-24645-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for heterologous BGC expression, but its cells undergo early autolysis, hindering further applications. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chitinimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression.
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8
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Morin CD, Déziel E, Gauthier J, Levesque RC, Lau GW. An Organ System-Based Synopsis of Pseudomonas aeruginosa Virulence. Virulence 2021; 12:1469-1507. [PMID: 34180343 PMCID: PMC8237970 DOI: 10.1080/21505594.2021.1926408] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Driven in part by its metabolic versatility, high intrinsic antibiotic resistance, and a large repertoire of virulence factors, Pseudomonas aeruginosa is expertly adapted to thrive in a wide variety of environments, and in the process, making it a notorious opportunistic pathogen. Apart from the extensively studied chronic infection in the lungs of people with cystic fibrosis (CF), P. aeruginosa also causes multiple serious infections encompassing essentially all organs of the human body, among others, lung infection in patients with chronic obstructive pulmonary disease, primary ciliary dyskinesia and ventilator-associated pneumonia; bacteremia and sepsis; soft tissue infection in burns, open wounds and postsurgery patients; urinary tract infection; diabetic foot ulcers; chronic suppurative otitis media and otitis externa; and keratitis associated with extended contact lens use. Although well characterized in the context of CF, pathogenic processes mediated by various P. aeruginosa virulence factors in other organ systems remain poorly understood. In this review, we use an organ system-based approach to provide a synopsis of disease mechanisms exerted by P. aeruginosa virulence determinants that contribute to its success as a versatile pathogen.
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Affiliation(s)
- Charles D Morin
- Centre Armand-Frappier Santé Biotechnologie, Institut National De La Recherche Scientifique (INRS), Laval, Quebec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National De La Recherche Scientifique (INRS), Laval, Quebec, Canada
| | - Jeff Gauthier
- Département De Microbiologie-infectiologie Et Immunologie, Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Roger C Levesque
- Département De Microbiologie-infectiologie Et Immunologie, Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, Quebec, Canada
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, US
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9
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Bouteiller M, Dupont C, Bourigault Y, Latour X, Barbey C, Konto-Ghiorghi Y, Merieau A. Pseudomonas Flagella: Generalities and Specificities. Int J Mol Sci 2021; 22:ijms22073337. [PMID: 33805191 PMCID: PMC8036289 DOI: 10.3390/ijms22073337] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
Flagella-driven motility is an important trait for bacterial colonization and virulence. Flagella rotate and propel bacteria in liquid or semi-liquid media to ensure such bacterial fitness. Bacterial flagella are composed of three parts: a membrane complex, a flexible-hook, and a flagellin filament. The most widely studied models in terms of the flagellar apparatus are E. coli and Salmonella. However, there are many differences between these enteric bacteria and the bacteria of the Pseudomonas genus. Enteric bacteria possess peritrichous flagella, in contrast to Pseudomonads, which possess polar flagella. In addition, flagellar gene expression in Pseudomonas is under a four-tiered regulatory circuit, whereas enteric bacteria express flagellar genes in a three-step manner. Here, we use knowledge of E. coli and Salmonella flagella to describe the general properties of flagella and then focus on the specificities of Pseudomonas flagella. After a description of flagellar structure, which is highly conserved among Gram-negative bacteria, we focus on the steps of flagellar assembly that differ between enteric and polar-flagellated bacteria. In addition, we summarize generalities concerning the fuel used for the production and rotation of the flagellar macromolecular complex. The last part summarizes known regulatory pathways and potential links with the type-six secretion system (T6SS).
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Affiliation(s)
- Mathilde Bouteiller
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yvann Bourigault
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Corinne Barbey
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
- Correspondence:
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10
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Dörr T. Understanding tolerance to cell wall-active antibiotics. Ann N Y Acad Sci 2020; 1496:35-58. [PMID: 33274447 PMCID: PMC8359209 DOI: 10.1111/nyas.14541] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic tolerance-the ability of bacteria to survive for an extended time in the presence of bactericidal antibiotics-is an understudied contributor to antibiotic treatment failure. Herein, I review the manifestations, mechanisms, and clinical relevance of tolerance to cell wall-active (CWA) antibiotics, one of the most important groups of antibiotics at the forefront of clinical use. I discuss definitions of tolerance and assays for tolerance detection, comprehensively discuss the mechanism of action of β-lactams and other CWA antibiotics, and then provide an overview of how cells mitigate the potentially lethal effects of CWA antibiotic-induced cell damage to become tolerant. Lastly, I discuss evidence for a role of CWA antibiotic tolerance in clinical antibiotic treatment failure.
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Affiliation(s)
- Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Department of Microbiology, and Cornell Institute of Host-Pathogen Interactions and Disease, Cornell University, Ithaca, New York
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11
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Shin JH, Sulpizio AG, Kelley A, Alvarez L, Murphy SG, Fan L, Cava F, Mao Y, Saper MA, Dörr T. Structural basis of peptidoglycan endopeptidase regulation. Proc Natl Acad Sci U S A 2020; 117:11692-11702. [PMID: 32393643 PMCID: PMC7261138 DOI: 10.1073/pnas.2001661117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Most bacteria surround themselves with a cell wall, a strong meshwork consisting primarily of the polymerized aminosugar peptidoglycan (PG). PG is essential for structural maintenance of bacterial cells, and thus for viability. PG is also constantly synthesized and turned over; the latter process is mediated by PG cleavage enzymes, for example, the endopeptidases (EPs). EPs themselves are essential for growth but also promote lethal cell wall degradation after exposure to antibiotics that inhibit PG synthases (e.g., β-lactams). Thus, EPs are attractive targets for novel antibiotics and their adjuvants. However, we have a poor understanding of how these enzymes are regulated in vivo, depriving us of novel pathways for the development of such antibiotics. Here, we have solved crystal structures of the LysM/M23 family peptidase ShyA, the primary EP of the cholera pathogen Vibrio cholerae Our data suggest that ShyA assumes two drastically different conformations: a more open form that allows for substrate binding and a closed form, which we predicted to be catalytically inactive. Mutations expected to promote the open conformation caused enhanced activity in vitro and in vivo, and these results were recapitulated in EPs from the divergent pathogens Neisseria gonorrheae and Escherichia coli Our results suggest that LysM/M23 EPs are regulated via release of the inhibitory Domain 1 from the M23 active site, likely through conformational rearrangement in vivo.
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Affiliation(s)
- Jung-Ho Shin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Alan G Sulpizio
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Aaron Kelley
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-5606
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Shannon G Murphy
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD 21702
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Mark A Saper
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-5606
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853;
- Department of Microbiology, Cornell University, Ithaca, NY 14853
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853
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12
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Giovannoni M, Gramegna G, Benedetti M, Mattei B. Industrial Use of Cell Wall Degrading Enzymes: The Fine Line Between Production Strategy and Economic Feasibility. Front Bioeng Biotechnol 2020; 8:356. [PMID: 32411686 PMCID: PMC7200985 DOI: 10.3389/fbioe.2020.00356] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Cell Wall Degrading Enzymes (CWDEs) are a heterogeneous group of enzymes including glycosyl-hydrolases, oxidoreductases, lyases, and esterases. Microbes with degrading activities toward plant cell wall polysaccharides are the most relevant source of CWDEs for industrial applications. These organisms secrete a wide array of CWDEs in amounts strictly necessary for their own sustenance, nonetheless the production of CWDEs from wild type microbes can be increased at large-scale by using optimized fermentation strategies. In the last decades, advances in genetic engineering allowed the expression of recombinant CWDEs also in lab-domesticated organisms such as E. coli, yeasts and plants, dramatically increasing the available options for the large-scale production of CWDEs. The optimization of a CWDE-producing biofactory is a hard challenge that biotechnologists tackle by testing different expression strategies and expression-hosts. Although both the yield and production costs are critical factors to produce biomolecules at industrial scale, these parameters are often disregarded in basic research. This review presents the main characteristics and industrial applications of CWDEs directed toward the cell wall of plants, bacteria, fungi and microalgae. Different biofactories for CWDE expression are compared in order to highlight strengths and weaknesses of each production system and how these aspects impact the final enzyme cost and, consequently, the economic feasibility of using CWDEs for industrial applications.
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Affiliation(s)
- Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Gramegna
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Manuel Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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13
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Bouteiller M, Gallique M, Bourigault Y, Kosta A, Hardouin J, Massier S, Konto-Ghiorghi Y, Barbey C, Latour X, Chane A, Feuilloley M, Merieau A. Crosstalk between the Type VI Secretion System and the Expression of Class IV Flagellar Genes in the Pseudomonas fluorescens MFE01 Strain. Microorganisms 2020; 8:microorganisms8050622. [PMID: 32344878 PMCID: PMC7286023 DOI: 10.3390/microorganisms8050622] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/16/2020] [Accepted: 04/23/2020] [Indexed: 11/16/2022] Open
Abstract
Type VI secretion systems (T6SSs) are contractile bacterial multiprotein nanomachines that enable the injection of toxic effectors into prey cells. The Pseudomonas fluorescens MFE01 strain has T6SS antibacterial activity and can immobilise competitive bacteria through the T6SS. Hcp1 (hemolysin co-regulated protein 1), a constituent of the T6SS inner tube, is involved in such prey cell inhibition of motility. Paradoxically, disruption of the hcp1 or T6SS contractile tail tssC genes results in the loss of the mucoid and motile phenotypes in MFE01. Here, we focused on the relationship between T6SS and flagella-associated motility. Electron microscopy revealed the absence of flagellar filaments for MFE01Δhcp1 and MFE01ΔtssC mutants. Transcriptomic analysis showed a reduction in the transcription of class IV flagellar genes in these T6SS mutants. However, transcription of fliA, the gene encoding the class IV flagellar sigma factor, was unaffected. Over-expression of fliA restored the motile and mucoid phenotypes in both MFE01Δhcp1+fliA, and MFE01ΔtssC+fliA and a fliA mutant displayed the same phenotypes as MFE01Δhcp1 and MFE01ΔtssC. Moreover, the FliA anti-sigma factor FlgM was not secreted in the T6SS mutants, and flgM over-expression reduced both motility and mucoidy. This study provides arguments to unravel the crosstalk between T6SS and motility.
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Affiliation(s)
- Mathilde Bouteiller
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, F-76821 Mont-Saint-Aignan, France
| | - Mathias Gallique
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- Meakins-Christie laboratories, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Chemical Engineering, McGill University, Montreal, QC H3A 0C5, Canada
| | - Yvann Bourigault
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, F-76821 Mont-Saint-Aignan, France
| | - Artemis Kosta
- Plateforme de Microscopie de l’Institut de Microbiologie de la Méditerranée, IMM, Institut de Microbiologie, FR3479, Campus CNRS, 13402 Marseille cedex 20, France;
| | - Julie Hardouin
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, F-76821 Mont-Saint-Aignan cedex, France; (J.H.); (S.M.)
- PISSARO Proteomics Facility, Université de Rouen, F-76821 Mont-Saint-Aignan, France
| | - Sebastien Massier
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, F-76821 Mont-Saint-Aignan cedex, France; (J.H.); (S.M.)
- PISSARO Proteomics Facility, Université de Rouen, F-76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
| | - Corinne Barbey
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, F-76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, F-76821 Mont-Saint-Aignan, France
| | - Andréa Chane
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, F-76821 Mont-Saint-Aignan, France
| | - Marc Feuilloley
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
| | - Annabelle Merieau
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (M.G.); (Y.B.); (Y.K.-G.); (C.B.); (X.L.); (A.C.); (M.F.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, F-76821 Mont-Saint-Aignan, France
- Correspondence:
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14
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A Screen for Antibiotic Resistance Determinants Reveals a Fitness Cost of the Flagellum in Pseudomonas aeruginosa. J Bacteriol 2020; 202:JB.00682-19. [PMID: 31871033 DOI: 10.1128/jb.00682-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/18/2019] [Indexed: 01/09/2023] Open
Abstract
The intrinsic resistance of Pseudomonas aeruginosa to many antibiotics limits treatment options for pseudomonal infections. P. aeruginosa's outer membrane is highly impermeable and decreases antibiotic entry into the cell. We used an unbiased high-throughput approach to examine mechanisms underlying outer membrane-mediated antibiotic exclusion. Insertion sequencing (INSeq) identified genes that altered fitness in the presence of linezolid, rifampin, and vancomycin, antibiotics to which P. aeruginosa is intrinsically resistant. We reasoned that resistance to at least one of these antibiotics would depend on outer membrane barrier function, as previously demonstrated in Escherichia coli and Vibrio cholerae This approach demonstrated a critical role of the outer membrane barrier in vancomycin fitness, while efflux pumps were primary contributors to fitness in the presence of linezolid and rifampin. Disruption of flagellar assembly or function was sufficient to confer a fitness advantage to bacteria exposed to vancomycin. These findings clearly show that loss of flagellar function alone can confer a fitness advantage in the presence of an antibiotic.IMPORTANCE The cell envelopes of Gram-negative bacteria render them intrinsically resistant to many classes of antibiotics. We used insertion sequencing to identify genes whose disruption altered the fitness of a highly antibiotic-resistant pathogen, Pseudomonas aeruginosa, in the presence of antibiotics usually excluded by the cell envelope. This screen identified gene products involved in outer membrane biogenesis and homeostasis, respiration, and efflux as important contributors to fitness. An unanticipated fitness cost of flagellar assembly and function in the presence of the glycopeptide antibiotic vancomycin was further characterized. These findings have clinical relevance for individuals with cystic fibrosis who are infected with P. aeruginosa and undergo treatment with vancomycin for a concurrent Staphylococcus aureus infection.
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15
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Anderson EM, Sychantha D, Brewer D, Clarke AJ, Geddes-McAlister J, Khursigara CM. Peptidoglycomics reveals compositional changes in peptidoglycan between biofilm- and planktonic-derived Pseudomonas aeruginosa. J Biol Chem 2019; 295:504-516. [PMID: 31771981 DOI: 10.1074/jbc.ra119.010505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan (PG) is a critical component of the bacterial cell wall and is composed of a repeating β-1,4-linked disaccharide of N-acetylglucosamine and N-acetylmuramic acid appended with a highly conserved stem peptide. In Gram-negative bacteria, PG is assembled in the cytoplasm and exported into the periplasm where it undergoes considerable maturation, modification, or degradation depending on the growth phase or presence of environmental stressors. These modifications serve important functions in diverse processes, including PG turnover, cell elongation/division, and antibiotic resistance. Conventional methods for analyzing PG composition are complex and time-consuming. We present here a streamlined MS-based method that combines differential analysis with statistical 1D annotation approaches to quantitatively compare PGs produced in planktonic- and biofilm-cultured Pseudomonas aeruginosa We identified a core assembly of PG that is present in high abundance and that does not significantly differ between the two growth states. We also identified an adaptive PG assembly that is present in smaller amounts and fluctuates considerably between growth states in response to physiological changes. Biofilm-derived adaptive PG exhibited significant changes compared with planktonic-derived PG, including amino acid substitutions of the stem peptide and modifications that indicate changes in the activity of amidases, deacetylases, and lytic transglycosylases. The results of this work also provide first evidence of de-N-acetylated muropeptides from P. aeruginosa The method developed here offers a robust and reproducible workflow for accurately determining PG composition in samples that can be used to assess global PG fluctuations in response to changing growth conditions or external stimuli.
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Affiliation(s)
- Erin M Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - David Sychantha
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Dyanne Brewer
- Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada; Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada.
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada; Mass Spectrometry Facility, University of Guelph, Ontario N1G 2W1, Canada.
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16
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Dual RNA-Seq Unveils the Role of the Pseudomonas plecoglossicida fliA Gene in Pathogen-Host Interaction with Larimichthys crocea. Microorganisms 2019; 7:microorganisms7100443. [PMID: 31614635 PMCID: PMC6843279 DOI: 10.3390/microorganisms7100443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 11/17/2022] Open
Abstract
In the present study, Larimichthys crocea and Pseudomonas plecoglossicida were selected as a host-pathogen interaction model for teleosts and prokaryotic pathogens. Five shRNAs were designed and synthesized to silence the fliA gene, all of which resulted in pronounced reductions in fliA mRNA; the mutant strain with the best silencing efficiency of 92.16% was chosen for subsequent analysis. A significant decrease in motility, intracellular survival and escape was observed for the fliA-RNAi strain of P. plecoglossicida, whereby silencing of the fliA gene led to a 30% decrease in mortality and a four-day delay in the onset of infection in L. crocea. Moreover, silencing of P. plecoglossicida fliA resulted in a significant change in both the pathogen and host transcriptome in the spleens of infected L. crocea. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of pathogen transcriptome data showed that silencing fliA resulted in downregulation of 18 flagellum-related genes; KEGG analysis of host transcriptome data revealed that infection with the fliA-RNAi strain caused upregulation of 47 and downregulation of 106 immune-related genes. These pathogen-host interactions might facilitate clearance of P. plecoglossicida by L. crocea, with a significant decrease in fliA-RNAi P. plecoglossicida strain virulence in L. crocea.
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17
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Weaver AI, Jiménez-Ruiz V, Tallavajhala SR, Ransegnola BP, Wong KQ, Dörr T. Lytic transglycosylases RlpA and MltC assist in Vibrio cholerae daughter cell separation. Mol Microbiol 2019; 112:1100-1115. [PMID: 31286580 DOI: 10.1111/mmi.14349] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/21/2022]
Abstract
The cell wall is a crucial structural feature in the vast majority of bacteria and comprises a covalently closed network of peptidoglycan (PG) strands. While PG synthesis is important for survival under many conditions, the cell wall is also a dynamic structure, undergoing degradation and remodeling by 'autolysins', enzymes that break down PG. Cell division, for example, requires extensive PG remodeling, especially during separation of daughter cells, which depends heavily upon the activity of amidases. However, in Vibrio cholerae, we demonstrate that amidase activity alone is insufficient for daughter cell separation and that lytic transglycosylases RlpA and MltC both contribute to this process. MltC and RlpA both localize to the septum and are functionally redundant under normal laboratory conditions; however, only RlpA can support normal cell separation in low-salt media. The division-specific activity of lytic transglycosylases has implications for the local structure of septal PG, suggesting that there may be glycan bridges between daughter cells that cannot be resolved by amidases. We propose that lytic transglycosylases at the septum cleave PG strands that are crosslinked beyond the reach of the highly regulated activity of the amidase and clear PG debris that may block the completion of outer membrane invagination.
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Affiliation(s)
- Anna I Weaver
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Valeria Jiménez-Ruiz
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Srikar R Tallavajhala
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Brett P Ransegnola
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kimberly Q Wong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, 14853, USA
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18
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Jenkins CH, Wallis R, Allcock N, Barnes KB, Richards MI, Auty JM, Galyov EE, Harding SV, Mukamolova GV. The lytic transglycosylase, LtgG, controls cell morphology and virulence in Burkholderia pseudomallei. Sci Rep 2019; 9:11060. [PMID: 31363151 PMCID: PMC6667503 DOI: 10.1038/s41598-019-47483-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of the tropical disease melioidosis. Its genome encodes an arsenal of virulence factors that allow it, when required, to switch from a soil dwelling bacterium to a deadly intracellular pathogen. With a high intrinsic resistance to antibiotics and the ability to overcome challenges from the host immune system, there is an increasing requirement for new antibiotics and a greater understanding into the molecular mechanisms of B. pseudomallei virulence and dormancy. The peptidoglycan remodeling enzymes, lytic transglycosylases (Ltgs) are potential targets for such new antibiotics. Ltgs cleave the glycosidic bonds within bacterial peptidoglycan allowing for the insertion of peptidoglycan precursors during cell growth and division, and cell membrane spanning structures such as flagella and secretion systems. Using bioinformatic analysis we have identified 8 putative Ltgs in B. pseudomallei K96243. We aimed to investigate one of these Ltgs, LtgG (BPSL3046) through the generation of deletion mutants and biochemical analysis. We have shown that LtgG is a key contributor to cellular morphology, division, motility and virulence in BALB/c mice. We have determined the crystal structure of LtgG and have identified various amino acids likely to be important in peptidoglycan binding and catalytic activity. Recombinant protein assays and complementation studies using LtgG containing a site directed mutation in aspartate 343, confirmed the essentiality of this amino acid in the function of LtgG.
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Affiliation(s)
- Christopher H Jenkins
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK. .,Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK.
| | - Russell Wallis
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.,The Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Natalie Allcock
- Electron Microscopy Facility, Core Biotechnology Services, University of Leicester, Leicester, UK
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
| | - Mark I Richards
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK
| | - Joss M Auty
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Edouard E Galyov
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK.,Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Galina V Mukamolova
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK. .,Department of Respiratory Sciences, University of Leicester, Leicester, UK.
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19
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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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20
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Vermassen A, Leroy S, Talon R, Provot C, Popowska M, Desvaux M. Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. Front Microbiol 2019; 10:331. [PMID: 30873139 PMCID: PMC6403190 DOI: 10.3389/fmicb.2019.00331] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
The cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | - Régine Talon
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
| | | | - Magdalena Popowska
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRA, MEDiS, Clermont-Ferrand, France
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21
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Dik DA, Madukoma CS, Tomoshige S, Kim C, Lastochkin E, Boggess WC, Fisher JF, Shrout JD, Mobashery S. Slt, MltD, and MltG of Pseudomonas aeruginosa as Targets of Bulgecin A in Potentiation of β-Lactam Antibiotics. ACS Chem Biol 2019; 14:296-303. [PMID: 30620575 DOI: 10.1021/acschembio.8b01025] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interplay between the activities of lytic transglycosylases (LTs) and penicillin-binding proteins (PBPs) is critical for the health of the bacterial cell wall. Bulgecin A (a natural-product inhibitor of LTs) potentiates the activity of β-lactam antibiotics (inhibitors of PBPs), underscoring this intimate mechanistic interdependence. Bulgecin A in the presence of an appropriate β-lactam causes bulge deformation due to the formation of aberrant peptidoglycan at the division site of the bacterium. As Pseudomonas aeruginosa, a nefarious human pathogen, has 11 LT paralogs, the answer as to which LT activity correlates with β-lactam potentiation is important and is currently unknown. Growth of P. aeruginosa PAO1 strains harboring individual transposon-insertion mutants at each of the 11 genes for LTs, in the presence of the β-lactam antibiotic ceftazidime or meropenem, implicated the gene products of slt, mltD, and mltG (of the 11), in bulge formation and potentiation. Hence, the respective enzymes would be the targets of inhibition by bulgecin A, which was indeed documented. We further demonstrated by imaging in real time and by SEM that cell lysis occurs by the structural failure of this bulge. Upon removal of the β-lactam antibiotic prior to lysis, P. aeruginosa experiences delayed recovery from the elongation and bulge phenotype in the presence of bulgecin A. These observations argue for a collaborative role for the target LTs in the repair of the aberrant cell wall, the absence of activities of which in the presence of bulgecin A results in potentiation of the β-lactam antibiotic.
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Affiliation(s)
- David A. Dik
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
| | - Chinedu S. Madukoma
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, United States
| | - Shusuke Tomoshige
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
| | - Choonkeun Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
| | - William C. Boggess
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, 352 McCourtney Hall, Notre Dame, Indiana 46556, United States
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Juan C, Torrens G, Barceló IM, Oliver A. Interplay between Peptidoglycan Biology and Virulence in Gram-Negative Pathogens. Microbiol Mol Biol Rev 2018; 82:e00033-18. [PMID: 30209071 PMCID: PMC6298613 DOI: 10.1128/mmbr.00033-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The clinical and epidemiological threat of the growing antimicrobial resistance in Gram-negative pathogens, particularly for β-lactams, the most frequently used and relevant antibiotics, urges research to find new therapeutic weapons to combat the infections caused by these microorganisms. An essential previous step in the development of these therapeutic solutions is to identify their potential targets in the biology of the pathogen. This is precisely what we sought to do in this review specifically regarding the barely exploited field analyzing the interplay among the biology of the peptidoglycan and related processes, such as β-lactamase regulation and virulence. Hence, here we gather, analyze, and integrate the knowledge derived from published works that provide information on the topic, starting with those dealing with the historically neglected essential role of the Gram-negative peptidoglycan in virulence, including structural, biogenesis, remodeling, and recycling aspects, in addition to proinflammatory and other interactions with the host. We also review the complex link between intrinsic β-lactamase production and peptidoglycan metabolism, as well as the biological costs potentially associated with the expression of horizontally acquired β-lactamases. Finally, we analyze the existing evidence from multiple perspectives to provide useful clues for identifying targets enabling the future development of therapeutic options attacking the peptidoglycan-virulence interconnection as a key weak point of the Gram-negative pathogens to be used, if not to kill the bacteria, to mitigate their capacity to produce severe infections.
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Affiliation(s)
- Carlos Juan
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Gabriel Torrens
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Isabel Maria Barceló
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
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23
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Dik DA, Batuecas MT, Lee M, Mahasenan KV, Marous DR, Lastochkin E, Fisher JF, Hermoso JA, Mobashery S. A Structural Dissection of the Active Site of the Lytic Transglycosylase MltE from Escherichia coli. Biochemistry 2018; 57:6090-6098. [PMID: 30256085 DOI: 10.1021/acs.biochem.8b00800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lytic transglycosylases (LTs) are bacterial enzymes that catalyze the cleavage of the glycan strands of the bacterial cell wall. The mechanism of this cleavage is a remarkable intramolecular transacetalization reaction, accomplished by an ensemble of active-site residues. Because the LT reaction occurs in parallel with the cell wall bond-forming reactions catalyzed by the penicillin-binding proteins, simultaneous inhibition of both enzymes can be particularly bactericidal to Gram-negative bacteria. The MltE lytic transglycosylase is the smallest of the eight LTs encoded by the Escherichia coli genome. Prior crystallographic and computational studies identified four active-site residues-E64, S73, S75, and Y192-as playing roles in catalysis. Each of these four residues was individually altered by mutation to give four variant enzymes (E64Q, S73A, S75A, and Y192F). All four variants showed reduced catalytic activity [soluble wild type (100%) > soluble Y192F and S75A (both 40%) > S73A (4%) > E64Q (≤1%)]. The crystal structure of each variant protein was determined at the resolution of 2.12 Å for E64Q, 2.33 Å for Y192F, 1.38 Å for S73A, and 1.35 Å for S75A. These variants show alteration of the hydrogen-bond interactions of the active site. Within the framework of a prior computational study of the LT mechanism, we suggest the mechanistic role of these four active-site residues in MltE catalysis.
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Affiliation(s)
- David A Dik
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - María T Batuecas
- Department of Crystallography and Structural Biology , Inst. Química-Física "Rocasolano", CSIC , Serrano 119 , 28006 Madrid , Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Daniel R Marous
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology , Inst. Química-Física "Rocasolano", CSIC , Serrano 119 , 28006 Madrid , Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry , University of Notre Dame , 352 McCourtney Hall , Notre Dame , Indiana 46556 , United States
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24
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Biochemical and Phylogenetic Study of SltF, a Flagellar Lytic Transglycosylase from Rhodobacter sphaeroides. J Bacteriol 2018; 200:JB.00397-18. [PMID: 30061356 DOI: 10.1128/jb.00397-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/27/2018] [Indexed: 11/20/2022] Open
Abstract
In this work, we have characterized the soluble lytic transglycosylase (SltF) from Rhodobacter sphaeroides that interacts with the scaffolding protein FlgJ in the periplasm to open space at the cell wall peptidoglycan heteropolymer for the emerging rod. The characterization of the genetic context of flgJ and sltF in alphaproteobacteria shows that these two separate genes coexist frequently in a flagellar gene cluster. Two domains of unknown function in SltF were studied, and the results show that the deletion of a 17-amino-acid segment near the N terminus does not show a recognizable phenotype, whereas the deletion of 47 and 95 amino acids of the C terminus of SltF disrupts the interaction with FlgJ without affecting the transglycosylase catalytic activity of SltF. These mutant proteins are unable to support swimming, indicating that the physical interaction between SltF and FlgJ is central for flagellar formation. In a maximum likelihood tree of representative lytic transglycosylases, all of the flagellar SltF proteins cluster in subfamily 1F. From this analysis, it was also revealed that the lytic transglycosylases related to the type III secretion systems present in pathogens cluster with the closely related flagellar transglycosylases.IMPORTANCE Flagellar biogenesis is a highly orchestrated event where the flagellar structure spans the bacterial cell envelope. The rod diameter of approximately 4 nm is larger than the estimated pore size of the peptidoglycan layer; hence, its insertion requires the localized and controlled lysis of the cell wall. We found that a 47-residue domain of the C terminus of the lytic transglycosylase (LT) SltF of R. sphaeroides is involved in the recognition of the rod chaperone FlgJ. We also found that in many alphaproteobacteria, the flagellar cluster includes a homolog of SltF and FlgJ, indicating that association of an LT with the flagellar machinery is ancestral. A maximum likelihood tree shows that family 1 of LTs segregates into seven subfamilies.
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25
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Dik DA, Fisher JF, Mobashery S. Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance. Chem Rev 2018; 118:5952-5984. [PMID: 29847102 PMCID: PMC6855303 DOI: 10.1021/acs.chemrev.8b00277] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The importance of the cell wall to the viability of the bacterium is underscored by the breadth of antibiotic structures that act by blocking key enzymes that are tasked with cell-wall creation, preservation, and regulation. The interplay between cell-wall integrity, and the summoning forth of resistance mechanisms to deactivate cell-wall-targeting antibiotics, involves exquisite orchestration among cell-wall synthesis and remodeling and the detection of and response to the antibiotics through modulation of gene regulation by specific effectors. Given the profound importance of antibiotics to the practice of medicine, the assertion that understanding this interplay is among the most fundamentally important questions in bacterial physiology is credible. The enigmatic regulation of the expression of the AmpC β-lactamase, a clinically significant and highly regulated resistance response of certain Gram-negative bacteria to the β-lactam antibiotics, is the exemplar of this challenge. This review gives a current perspective to this compelling, and still not fully solved, 35-year enigma.
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Affiliation(s)
- David A. Dik
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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26
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Dik DA, Marous DR, Fisher JF, Mobashery S. Lytic transglycosylases: concinnity in concision of the bacterial cell wall. Crit Rev Biochem Mol Biol 2017. [PMID: 28644060 DOI: 10.1080/10409238.2017.1337705] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure-function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.
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Affiliation(s)
- David A Dik
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Daniel R Marous
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Jed F Fisher
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
| | - Shahriar Mobashery
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN , USA
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27
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Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases. Curr Opin Struct Biol 2017; 44:87-100. [PMID: 28109980 DOI: 10.1016/j.sbi.2017.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 01/26/2023]
Abstract
The major component of bacterial cell wall is peptidoglycan (PG), a complex polymer formed by long glycan chains cross-linked by peptide stems. PG is in constant equilibrium requiring well-orchestrated coordination between synthesis and degradation. The resulting cell-wall fragments can be recycled, act as messengers for bacterial communication, as effector molecules in immune response or as signaling molecules triggering antibiotics resistance. Tailoring and recycling of PG requires the cleavage of different covalent bonds of the PG sacculi by a diverse set of specific enzymes whose activities are strictly regulated. Here, we review the molecular mechanisms that govern PG remodeling focusing on the structural information available for the bacterial lytic enzymes and the mechanisms by which they recognize their substrates.
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