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Peng F, Zou Y, Liu X, Yang Y, Chen J, Nie J, Huang D, Bai Z. The murein endopeptidase MepA regulated by MtrAB and MprAB participate in cell wall homeostasis. Res Microbiol 2024; 175:104188. [PMID: 38286394 DOI: 10.1016/j.resmic.2024.104188] [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: 04/04/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
The complete genome of Corynebacterium glutamicum contain a gene encoding murein endopeptidase MepA which maintain cell wall homeostasis by regulating peptidoglycan biosynthesis. In this study, we investigate the physiological function, localization and regulator of MepA. The result shows that mepA overexpression lead to peptidoglycan degradation and the defects in cell division. MepA-EGFP was shown to localizes exclusively at the cell cell septum. In addition, mepA overexpression increased cell permeability and reduced the resistance of cells to isoniazid, an antibiotic used to treat Mycobacterium tuberculosis infection. Furthermore, transcription analysis showed that mepA affected cell division and membrane transport pathways, and was coordinately regulated by the two-component systems MtrAB and MprAB(CgtS/R2).
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Affiliation(s)
- Feng Peng
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Yu Zou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China.
| | - Yankun Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Jianqi Nie
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Danni Huang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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2
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Sparks IL, Kado T, Prithviraj M, Nijjer J, Yan J, Morita YS. Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteria. Nat Commun 2024; 15:2191. [PMID: 38467648 PMCID: PMC10928101 DOI: 10.1038/s41467-024-46565-5] [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: 07/14/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
The growth and division of mycobacteria, which include clinically relevant pathogens, deviate from that of canonical bacterial models. Despite their Gram-positive ancestry, mycobacteria synthesize and elongate a diderm envelope asymmetrically from the poles, with the old pole elongating more robustly than the new pole. The phosphatidylinositol-anchored lipoglycans lipomannan (LM) and lipoarabinomannan (LAM) are cell envelope components critical for host-pathogen interactions, but their physiological functions in mycobacteria remained elusive. In this work, using biosynthetic mutants of these lipoglycans, we examine their roles in maintaining cell envelope integrity in Mycobacterium smegmatis and Mycobacterium tuberculosis. We find that mutants defective in producing mature LAM fail to maintain rod cell shape specifically at the new pole and para-septal regions whereas a mutant that produces a larger LAM becomes multi-septated. Therefore, LAM plays critical and distinct roles at subcellular locations associated with division in mycobacteria, including maintenance of local cell wall integrity and septal placement.
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Affiliation(s)
- Ian L Sparks
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
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3
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Samuels V, Mulelu AE, Ndlovu H, Marakalala MJ. Mycobacterial FtsEX-RipC interaction is required for normal growth and cell morphology in rifampicin and low ionic strength conditions. Microbiol Spectr 2024; 12:e0251523. [PMID: 38289931 PMCID: PMC10913748 DOI: 10.1128/spectrum.02515-23] [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: 06/17/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Tuberculosis, a lung disease caused by Mycobacterium tuberculosis (Mtb), remains a major global health problem ranking as the second leading cause of death from a single infectious agent. One of the major factors contributing toward Mtb's success as a pathogen is its unique cell wall and its ability to counteract various arms of the host's immune response. A recent genome-scale study profiled a list of candidate genes that are predicted to be essential for Mtb survival of host-mediated responses. One candidate was FtsEX, a protein complex composed of an ATP-binding domain, FtsE, and a transmembrane domain, FtsX. FtsEX functions through interaction with a periplasmic hydrolase, RipC. Homologs of FtsEX exist in other bacteria and have been linked with playing a key role in regulating peptidoglycan hydrolysis during cell elongation and division. Here, we report on Mycobacterium smegmatis, FtsE, FtsX, and RipC and their protective roles in stressful conditions. We demonstrate that the individual genes of FtsEX complex and RipC are not essential for survival in normal growth conditions but conditionally essential in low-salt media and antibiotic-treated media. Growth defects in these conditions were characterized by short and bulgy cells as well as elongated filamentous cells. Our results suggest that FtsE, FtsX, and RipC are required for both normal cell elongation and division and ultimately for survival in stressful conditions. IMPORTANCE Mycobacterial cell growth and division are coordinated with regulated peptidoglycan hydrolysis. Understanding cell wall gene complexes that govern normal cell division and elongation will aid in the development of tools to disarm the ability of mycobacteria to survive immune-like and antibiotic stresses. We combined genetic analyses and scanning electron microscopy to analyze morphological changes of mycobacterial FtsEX and RipC mutants in stressful conditions. We demonstrate that FtsE, FtsX, FtsEX, and RipC are conditionally required for the survival of Mycobacterium smegmatis during rifampicin treatment and in low-salt conditions. Growth defects in these conditions were characterized by short and bulgy cells as well as elongated filamentous cells. We also show that the FtsEX-RipC interaction is essential for the survival of M. smegmatis in rifampicin. Our results suggest that FtsE, FtsX, and RipC are required for normal cell wall regulation and ultimately for survival in stressful conditions.
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Affiliation(s)
- Veneshley Samuels
- Division of Medical Microbiology, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Andani E. Mulelu
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hlumani Ndlovu
- Division of Chemical Systems Biology, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mohlopheni J. Marakalala
- Division of Immunology, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
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4
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Peterson EJR, Brooks AN, Reiss DJ, Kaur A, Do J, Pan M, Wu WJ, Morrison R, Srinivas V, Carter W, Arrieta-Ortiz ML, Ruiz RA, Bhatt A, Baliga NS. MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance. Cell Rep 2023; 42:112875. [PMID: 37542718 PMCID: PMC10480492 DOI: 10.1016/j.celrep.2023.112875] [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: 08/16/2021] [Revised: 04/21/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023] Open
Abstract
The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability to physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. Analysis of EGRIN 2.0 shows how modulation of the MtrAB two-component signaling system tunes Mtb growth in response to related host microenvironmental cues. Disruption of MtrAB by tunable CRISPR interference confirms that the signaling system regulates multiple peptidoglycan hydrolases, among other targets, that are important for cell division. Further, MtrA decreases the effectiveness of antibiotics by mechanisms of both intrinsic resistance and drug tolerance. Together, the model-enabled dissection of complex MtrA regulation highlights its importance as a drug target and illustrates how EGRIN 2.0 facilitates discovery and mechanistic characterization of Mtb adaptation to specific host microenvironments within the host.
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Affiliation(s)
| | | | - David J Reiss
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Amardeep Kaur
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Julie Do
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Robert Morrison
- Laboratory of Malaria, Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Warren Carter
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Rene A Ruiz
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; Departments of Biology and Microbiology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA; Lawrence Berkeley National Lab, Berkeley, CA 94720, USA.
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5
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Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [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: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
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Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
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6
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Sparks IL, Nijjer J, Yan J, Morita YS. Lipoarabinomannan regulates septation in Mycobacterium smegmatis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534150. [PMID: 36993273 PMCID: PMC10055410 DOI: 10.1101/2023.03.26.534150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The growth and division of mycobacteria, which include several clinically relevant pathogens, deviate significantly from that of canonical bacterial models. Despite their Gram-positive ancestry, mycobacteria synthesize and elongate a diderm envelope asymmetrically from the poles, with the old pole elongating more robustly than the new pole. In addition to being structurally distinct, the molecular components of the mycobacterial envelope are also evolutionarily unique, including the phosphatidylinositol-anchored lipoglycans lipomannan (LM) and lipoarabinomannan (LAM). LM and LAM modulate host immunity during infection, but their role outside of intracellular survival remains poorly understood, despite their widespread conservation among non-pathogenic and opportunistically pathogenic mycobacteria. Previously, Mycobacterium smegmatis and Mycobacterium tuberculosis mutants producing structurally altered LM and LAM were shown to grow slowly under certain conditions and to be more sensitive to antibiotics, suggesting that mycobacterial lipoglycans may support cellular integrity or growth. To test this, we constructed multiple biosynthetic lipoglycan mutants of M. smegmatis and determined the effect of each mutation on cell wall biosynthesis, envelope integrity, and division. We found that mutants deficient in LAM, but not LM, fail to maintain cell wall integrity in a medium-dependent manner, with envelope deformations specifically associated with septa and new poles. Conversely, a mutant producing abnormally large LAM formed multiseptated cells in way distinct from that observed in a septal hydrolase mutant. These results show that LAM plays critical and distinct roles at subcellular locations associated with division in mycobacteria, including maintenance of local cell envelope integrity and septal placement.
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Affiliation(s)
- Ian L. Sparks
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
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7
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Colombatti Olivieri MA, Fresia P, Graña M, Cuerda MX, Nagel A, Alvarado Pinedo F, Romano MI, Caimi K, Berná L, Santangelo MP. Genomic comparison of two strains of Mycobacterium avium subsp. paratuberculosis with contrasting pathogenic phenotype. Tuberculosis (Edinb) 2023; 138:102299. [PMID: 36587510 DOI: 10.1016/j.tube.2022.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
In a previous study, we evaluated the degree of virulence of Mycobacterium avium subsp. paratuberculosis (Map) strains isolated from cattle in Argentina in a murine model. This assay allowed us to differentiate between high-virulent MapARG1347 and low-virulent MapARG1543 strains. To corroborate whether the differences in virulence could be attributed to genetic differences between the strains, we performed Whole Genome Sequencing and compared the genomes and gene content between them and determined the differences related to the reference strain MapK10. We found 233 SNPs/INDELS in one or both strains relative to Map K10. The two strains share most of the variations, but we found 15 mutations present in only one of the strains. Considering NS-SNP/INDELS that produced a severe effect in the coding sequence, we focus the analysis on four predicted proteins, putatively related to virulence. Survival of MapARG1347 strain in bMDM was higher than MapARG1543 and was more resistant to acidic pH and H2O2 stresses than MapK10. The genomic differences between the two strains found in genes MAP1203 (a putative peptidoglycan hydrolase), MAP0403 (a putative serine protease) MAP1003c (a member of the PE-PPE family) and MAP4152 (a putative mycofactocin binding protein) could contribute to explain the contrasting phenotype previously observed in mice models.
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Affiliation(s)
- M A Colombatti Olivieri
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - P Fresia
- Unidad Mixta Pasteur+INIA, Institut Pasteur de Montevideo, Mataojo 2020, CP11400, Montevideo, Uruguay.
| | - M Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Mataojo 2020, CP11400, Montevideo, Uruguay.
| | - M X Cuerda
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - A Nagel
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - F Alvarado Pinedo
- Centro de Diagnóstico e Investigaciones Veterinarias (CEDIVE), Facultad de Ciencias Veterinarias - Universidad de La Plata (UNLP), Chascomus, Buenos Aires, Argentina.
| | - M I Romano
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - K Caimi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - L Berná
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400, Montevideo, Uruguay.
| | - M P Santangelo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
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8
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FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales. Proc Natl Acad Sci U S A 2022; 119:e2214599119. [PMID: 36469781 PMCID: PMC9897464 DOI: 10.1073/pnas.2214599119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bacterial cell wall is a multi-layered mesh, whose major component is peptidoglycan (PG), a sugar polymer cross-linked by short peptide stems. During cell division, a careful balance of PG synthesis and degradation, precisely coordinated both in time and space, is necessary to prevent uncontrolled destruction of the cell wall. In Corynebacteriales, the D,L endopeptidase RipA has emerged as a major PG hydrolase for cell separation, and RipA defaults have major implications for virulence of the human pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. However, the precise mechanisms by which RipA mediates cell separation remain elusive. Here we report phylogenetic, biochemical, and structural analysis of the Corynebacterium glutamicum homologue of RipA, Cg1735. The crystal structures of full-length Cg1735 in two different crystal forms revealed the C-terminal NlpC/P60 catalytic domain obtruded by its N-terminal conserved coiled-coil domain, which locks the enzyme in an autoinhibited state. We show that this autoinhibition is relieved by the extracellular core domain of the transmembrane septal protein Cg1604. The crystal structure of Cg1604 revealed a (β/α) protein with an overall topology similar to that of receiver domains from response regulator proteins. The atomic model of the Cg1735-Cg1604 complex, based on bioinformatical and mutational analysis, indicates that a conserved, distal-membrane helical insertion in Cg1604 is responsible for Cg1735 activation. The reported data provide important insights into how intracellular cell division signal(s), yet to be identified, control PG hydrolysis during RipA-mediated cell separation in Corynebacteriales.
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9
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Wysocka A, Jagielska E, Łężniak Ł, Sabała I. Two New M23 Peptidoglycan Hydrolases With Distinct Net Charge. Front Microbiol 2021; 12:719689. [PMID: 34630350 PMCID: PMC8498115 DOI: 10.3389/fmicb.2021.719689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial peptidoglycan hydrolases play an essential role in cell wall metabolism during bacterial growth, division, and elongation (autolysins) or in the elimination of closely related species from the same ecological niche (bacteriocins). Most studies concerning the peptidoglycan hydrolases present in Gram-positive bacteria have focused on clinically relevant Staphylococcus aureus or the model organism Bacillus subtilis, while knowledge relating to other species remains limited. Here, we report two new peptidoglycan hydrolases from the M23 family of metallopeptidases derived from the same staphylococcal species, Staphylococcus pettenkoferi. They share modular architecture, significant sequence identity (60%), catalytic and binding residue conservation, and similar modes of activation, but differ in gene distribution, putative biological role, and, strikingly, in their isoelectric points (pIs). One of the peptides has a high pI, similar to that reported for all M23 peptidases evaluated to date, whereas the other displays a low pI, a unique feature among M23 peptidases. Consequently, we named them SpM23_B (Staphylococcus pettenkoferi M23 "Basic") and SpM23_A (Staphylococcus pettenkoferi M23 "Acidic"). Using genetic and biochemical approaches, we have characterized these two novel lytic enzymes, both in vitro and in their physiological context. Our study presents a detailed characterization of two novel and clearly distinct peptidoglycan hydrolases to understand their role in bacterial physiology.
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Affiliation(s)
- Alicja Wysocka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Łukasz Łężniak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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10
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Abstract
Mycobacteria have unique cell envelopes, surface properties, and growth dynamics, which all play a part in the ability of these important pathogens to infect, evade host immunity, disseminate, and resist antibiotic challenges. Recent atomic force microscopy (AFM) studies have brought new insights into the nanometer-scale ultrastructural, adhesive, and mechanical properties of mycobacteria. The molecular forces with which mycobacterial adhesins bind to host factors, like heparin and fibronectin, and the hydrophobic properties of the mycomembrane have been unraveled by AFM force spectroscopy studies. Real-time correlative AFM and fluorescence imaging have delineated a complex interplay between surface ultrastructure, tensile stresses within the cell envelope, and cellular processes leading to division. The unique capabilities of AFM, which include subdiffraction-limit topographic imaging and piconewton force sensitivity, have great potential to resolve important questions that remain unanswered on the molecular interactions, surface properties, and growth dynamics of this important class of pathogens.
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11
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Espinosa J, Lin TY, Estrella Y, Kim B, Molina H, Hang HC. Enterococcus NlpC/p60 Peptidoglycan Hydrolase SagA Localizes to Sites of Cell Division and Requires Only a Catalytic Dyad for Protease Activity. Biochemistry 2020; 59:4470-4480. [PMID: 33136372 DOI: 10.1021/acs.biochem.0c00755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptidoglycan is a vital component of the bacterial cell wall, and its dynamic remodeling by NlpC/p60 hydrolases is crucial for proper cell division and survival. Beyond these essential functions, we previously discovered that Enterococcus species express and secrete the NlpC/p60 hydrolase-secreted antigen A (SagA), whose catalytic activity can modulate host immune responses in animal models. However, the localization and peptidoglycan hydrolase activity of SagA in Enterococcus was still unclear. In this study, we show that SagA contributes to a triseptal structure in dividing cells of enterococci and localizes to sites of cell division through its N-terminal coiled-coil domain. Using molecular modeling and site-directed mutagenesis, we identify amino acid residues within the SagA-NlpC/p60 domain that are crucial for catalytic activity and potential substrate binding. Notably, these studies revealed that SagA may function via a catalytic Cys-His dyad instead of the predicted Cys-His-His triad, which is conserved in SagA orthologs from other Enterococcus species. Our results provide key additional insight into peptidoglycan remodeling in Enterococcus by SagA NlpC/p60 hydrolases.
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Affiliation(s)
- Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Ti-Yu Lin
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Yadyvic Estrella
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Byungchul Kim
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States.,Departments of Immunology & Microbiology and Chemistry, Scripps Research, La Jolla, California 92037, United States
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12
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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13
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Mycobacterium smegmatis HtrA Blocks the Toxic Activity of a Putative Cell Wall Amidase. Cell Rep 2020; 27:2468-2479.e3. [PMID: 31116989 PMCID: PMC6538288 DOI: 10.1016/j.celrep.2018.12.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/14/2018] [Accepted: 12/13/2018] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, withstands diverse environmental stresses in the host. The periplasmic protease HtrA is required only to survive extreme conditions in most bacteria but is predicted to be essential for normal growth in mycobacteria. We confirm that HtrA is indeed essential in Mycobacterium smegmatis and interacts with another essential protein of unknown function, LppZ. However, the loss of any of three unlinked genes, including those encoding Ami3, a peptidoglycan muramidase, and Pmt, a mannosyltransferase, suppresses the essentiality of both HtrA and LppZ, indicating the functional relevance of these genes' protein products. Our data indicate that HtrA-LppZ is required to counteract the accumulation of active Ami3, which is toxic under the stabilizing influence of Pmt-based mannosylation. This suggests that HtrA-LppZ blocks the toxicity of a cell wall enzyme to maintain mycobacterial homeostasis.
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14
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Peptidoglycan Hydrolases RipA and Ami1 Are Critical for Replication and Persistence of Mycobacterium tuberculosis in the Host. mBio 2020; 11:mBio.03315-19. [PMID: 32127458 PMCID: PMC7064781 DOI: 10.1128/mbio.03315-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) is a major global heath burden, with 1.6 million people succumbing to the disease every year. The search for new drugs to improve the current chemotherapeutic regimen is crucial to reducing this global health burden. The cell wall polymer peptidoglycan (PG) has emerged as a very successful drug target in bacterial pathogens, as many currently used antibiotics target the synthesis of this macromolecule. However, the multitude of genes encoding PG-synthesizing and PG-modifying enzymes with apparent redundant functions has hindered the identification of novel drug targets in PG synthesis in Mycobacterium tuberculosis. Here, we demonstrate that two PG-cleaving enzymes are important for virulence of M. tuberculosis. In particular, the d,l-endopeptidase RipA represents a potentially attractive drug target, as its depletion results in the clearance of M. tuberculosis from the host and renders the bacteria hypersusceptible to rifampin, a frontline TB drug, and to several cell wall-targeting antibiotics. Synthesis and cleavage of the cell wall polymer peptidoglycan (PG) are carefully orchestrated processes and are essential for the growth and survival of bacteria. Yet, the function and importance of many enzymes that act on PG in Mycobacterium tuberculosis remain to be elucidated. We demonstrate that the activity of the N-acetylmuramyl-l-alanine amidase Ami1 is dispensable for cell division in M. tuberculosisin vitro yet contributes to the bacterium’s ability to persist during chronic infection in mice. Furthermore, the d,l-endopeptidase RipA, a predicted essential enzyme, is dispensable for the viability of M. tuberculosis but required for efficient cell division in vitro and in vivo. Depletion of RipA sensitizes M. tuberculosis to rifampin and to cell envelope-targeting antibiotics. Ami1 helps sustain residual cell division in cells lacking RipA, but the partial redundancy provided by Ami1 is not sufficient during infection, as depletion of RipA prevents M. tuberculosis from replicating in macrophages and leads to dramatic killing of the bacteria in mice. Notably, RipA is essential for persistence of M. tuberculosis in mice, suggesting that cell division is required during chronic mouse infection. Despite the multiplicity of enzymes acting on PG with redundant functions, we have identified two PG hydrolases that are important for M. tuberculosis to replicate and persist in the host.
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15
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Veyron‐Churlet R, Saliou J, Locht C. Protein scaffold involving MSMEG_1285 maintains cell wall organization and mediates penicillin sensitivity in mycobacteria. FEBS J 2020; 287:4415-4426. [DOI: 10.1111/febs.15232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/06/2019] [Accepted: 01/27/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Romain Veyron‐Churlet
- U1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille CNRS Inserm CHU Lille Institut Pasteur de Lille Université de Lille France
| | - Jean‐Michel Saliou
- U1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille CNRS Inserm CHU Lille Institut Pasteur de Lille Université de Lille France
| | - Camille Locht
- U1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille CNRS Inserm CHU Lille Institut Pasteur de Lille Université de Lille France
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16
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Le P, Kunold E, Macsics R, Rox K, Jennings MC, Ugur I, Reinecke M, Chaves-Moreno D, Hackl MW, Fetzer C, Mandl FAM, Lehmann J, Korotkov VS, Hacker SM, Kuster B, Antes I, Pieper DH, Rohde M, Wuest WM, Medina E, Sieber SA. Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms. Nat Chem 2020; 12:145-158. [PMID: 31844194 PMCID: PMC6994260 DOI: 10.1038/s41557-019-0378-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022]
Abstract
New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effectively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltransferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associated antibiotic effects, especially the lack of resistance development, probably stem from the compound's polypharmacology.
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Affiliation(s)
- Philipp Le
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Elena Kunold
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
- SciLifeLab, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Robert Macsics
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research, Partner Site Braunschweig-Hannover, Hannover, Germany
| | - Megan C Jennings
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Ilke Ugur
- Center for Integrated Protein Science, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mathias W Hackl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Franziska A M Mandl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Johannes Lehmann
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Vadim S Korotkov
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Stephan M Hacker
- Department of Chemistry, Technische Universität München, Garching bei München, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
- German Cancer Research Center, Heidelberg, Germany
- Center for Integrated Protein Science Munich, Garching bei München, Germany
| | - Iris Antes
- Center for Integrated Protein Science, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - William M Wuest
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Emory Antibiotic Resistance Center, Emory School of Medicine, Atlanta, GA, USA
| | - Eva Medina
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany.
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany.
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17
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Odermatt PD, Hannebelle MTM, Eskandarian HA, Nievergelt AP, McKinney JD, Fantner GE. Overlapping and essential roles for molecular and mechanical mechanisms in mycobacterial cell division. NATURE PHYSICS 2020; 16:57-62. [PMID: 31921326 PMCID: PMC6952280 DOI: 10.1038/s41567-019-0679-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/04/2019] [Indexed: 05/30/2023]
Abstract
Mechanisms to control cell division are essential for cell proliferation and survival 1. Bacterial cell growth and division require the coordinated activity of peptidoglycan synthases and hydrolytic enzymes 2-4 to maintain mechanical integrity of the cell wall 5. Recent studies suggest that cell separation is governed by mechanical forces 6,7. How mechanical forces interact with molecular mechanisms to control bacterial cell division in space and time is poorly understood. Here, we use a combination of atomic force microscope (AFM) imaging, nanomechanical mapping, and nanomanipulation to show that enzymatic activity and mechanical forces serve overlapping and essential roles in mycobacterial cell division. We find that mechanical stress gradually accumulates in the cell wall concentrated at the future division site, culminating in rapid (millisecond) cleavage of nascent sibling cells. Inhibiting cell wall hydrolysis delays cleavage; conversely, locally increasing cell wall stress causes instantaneous and premature cleavage. Cells deficient in peptidoglycan hydrolytic activity fail to locally decrease their cell wall strength and undergo natural cleavage, instead forming chains of non-growing cells. Cleavage of these cells can be mechanically induced by local application of stress with AFM. These findings establish a direct link between actively controlled molecular mechanisms and passively controlled mechanical forces in bacterial cell division.
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Affiliation(s)
- Pascal D. Odermatt
- Laboratory for Bio- and Nano-Instrumentation, School of Engineering, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
| | - Mélanie T. M. Hannebelle
- Laboratory for Bio- and Nano-Instrumentation, School of Engineering, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
- Laboratory of Microbiology and Microtechnology, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
| | - Haig A. Eskandarian
- Laboratory for Bio- and Nano-Instrumentation, School of Engineering, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
- Laboratory of Microbiology and Microtechnology, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
| | - Adrian P. Nievergelt
- Laboratory for Bio- and Nano-Instrumentation, School of Engineering, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
| | - John D. McKinney
- Laboratory of Microbiology and Microtechnology, School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
| | - Georg E. Fantner
- Laboratory for Bio- and Nano-Instrumentation, School of Engineering, Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland
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18
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Abstract
Abstract
An increasing problem in the field of health protection is the emergence of drug-resistant and multi-drug-resistant bacterial strains. They cause a number of infections, including hospital infections, which currently available antibiotics are unable to fight. Therefore, many studies are devoted to the search for new therapeutic agents with bactericidal and bacteriostatic properties. One of the latest concepts is to search for this type of substances among toxins produced by venomous animals. In this approach, however, special attention is paid to snake venom because it contains molecules with antibacterial properties. Thorough investigations have shown that the phospholipases A2 (PLA2) and l-amino acids oxidases (LAAO), as well as fragments of these enzymes, are mainly responsible for the bactericidal properties of snake venoms. Some preliminary research studies also suggest that fragments of three-finger toxins (3FTx) are bactericidal. It has also been proven that some snakes produce antibacterial peptides (AMP) homologous to human defensins and cathelicidins. The presence of these proteins and peptides means that snake venoms continue to be an interesting material for researchers and can be perceived as a promising source of antibacterial agents.
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19
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Gao B, Wang J, Huang J, Huang X, Sha W, Qin L. The dynamic region of the peptidoglycan synthase gene, Rv0050, induces the growth rate and morphologic heterogeneity in Mycobacteria. INFECTION GENETICS AND EVOLUTION 2019; 72:86-92. [DOI: 10.1016/j.meegid.2018.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022]
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20
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Brunet YR, Wang X, Rudner DZ. SweC and SweD are essential co-factors of the FtsEX-CwlO cell wall hydrolase complex in Bacillus subtilis. PLoS Genet 2019; 15:e1008296. [PMID: 31437162 PMCID: PMC6705773 DOI: 10.1371/journal.pgen.1008296] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/08/2019] [Indexed: 01/10/2023] Open
Abstract
The peptidoglycan (PG) sacculus is composed of long glycan strands cross-linked together by short peptides forming a covalently closed meshwork that protects the bacterial cell from osmotic lysis and specifies its shape. PG hydrolases play essential roles in remodeling this three-dimensional network during growth and division but how these autolytic enzymes are regulated remains poorly understood. The FtsEX ABC transporter-like complex has emerged as a broadly conserved regulatory module in controlling cell wall hydrolases in diverse bacterial species. In most characterized examples, this complex regulates distinct PG hydrolases involved in cell division and is intimately associated with the cytokinetic machinery called the divisome. However, in the gram-positive bacterium Bacillus subtilis the FtsEX complex is required for cell wall elongation where it regulates the PG hydrolase CwlO that acts along the lateral cell wall. To investigate whether additional factors are required for FtsEX function outside the divisome, we performed a synthetic lethal screen taking advantage of the conditional essentiality of CwlO. This screen identified two uncharacterized factors (SweD and SweC) that are required for CwlO activity. We demonstrate that these proteins reside in a membrane complex with FtsX and that amino acid substitutions in residues adjacent to the ATPase domain of FtsE partially bypass the requirement for them. Collectively our data indicate that SweD and SweC function as essential co-factors of FtsEX in controlling CwlO during cell wall elongation. We propose that factors analogous to SweDC function to support FtsEX activity outside the divisome in other bacteria.
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Affiliation(s)
- Yannick R. Brunet
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
| | - Xindan Wang
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
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21
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Squeglia F, Moreira M, Ruggiero A, Berisio R. The Cell Wall Hydrolytic NlpC/P60 Endopeptidases in Mycobacterial Cytokinesis: A Structural Perspective. Cells 2019; 8:cells8060609. [PMID: 31216697 PMCID: PMC6628586 DOI: 10.3390/cells8060609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
In preparation for division, bacteria replicate their DNA and segregate the newly formed chromosomes. A division septum then assembles between the chromosomes, and the mother cell splits into two identical daughters due to septum degradation. A major constituent of bacterial septa and of the whole cell wall is peptidoglycan (PGN), an essential cell wall polymer, formed by glycan chains of β−(1-4)-linked-N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), cross-linked by short peptide stems. Depending on the amino acid located at the third position of the peptide stem, PGN is classified as either Lys-type or meso-diaminopimelic acid (DAP)-type. Hydrolytic enzymes play a crucial role in the degradation of bacterial septa to split the cell wall material shared by adjacent daughter cells to promote their separation. In mycobacteria, a key PGN hydrolase, belonging to the NlpC/P60 endopeptidase family and denoted as RipA, is responsible for the degradation of septa, as the deletion of the gene encoding for this enzyme generates abnormal bacteria with multiple septa. This review provides an update of structural and functional data highlighting the central role of RipA in mycobacterial cytokinesis and the fine regulation of its catalytic activity, which involves multiple molecular partners.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
| | - Miguel Moreira
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
| | - Rita Berisio
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
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22
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Abstract
How do mycobacteria divide? Cell division has been studied extensively in the model rod-shaped bacteria Escherichia coli and Bacillus subtilis, but much less is understood about cell division in mycobacteria, a genus that includes the major human pathogens M. tuberculosis and M. leprae. In general, bacterial cell division requires the concerted effort of many proteins in both space and time to elongate the cell, replicate and segregate the chromosome, and construct and destruct the septum - processes which result in the creation of two new daughter cells. Here, we describe these distinct stages of cell division in B. subtilis and follow with the current knowledge in mycobacteria. As will become apparent, there are many differences between mycobacteria and B. subtilis in terms of both the broad outline of cell division and the molecular details. So, while the fundamental challenge of spatially and temporally organizing cell division is shared between these rod-shaped bacteria, they have solved these challenges in often vastly different ways.
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23
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Everman JL, Danelishvili L, Flores LG, Bermudez LE. MAP1203 Promotes Mycobacterium avium Subspecies paratuberculosis Binding and Invasion to Bovine Epithelial Cells. Front Cell Infect Microbiol 2018; 8:217. [PMID: 29998085 PMCID: PMC6030366 DOI: 10.3389/fcimb.2018.00217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease, chronic and ultimately fatal enteritis that affects ruminant populations worldwide. One mode of MAP transmission is oral when young animals ingest bacteria from the collostrum and milk of infected dams. The exposure to raw milk has a dramatic impact on MAP, resulting in a more invasive and virulent phenotype. The MAP1203 gene is upregulated over 28-fold after exposure of the bacterium to milk. In this study, the role of MAP1203 in binding and invasion of the bovine epithelial cells was investigated. By over-expressing the native MAP1203 gene and two clones of deletion mutant in the signal sequence and of missense mutations changing the integrin domain from RGD into RDE, we demonstrate that MAP1203 plays a role in increasing binding in more than 50% and invasion in 35% of bovine MDBK epithelial cells during early phase of infection. Furthermore, results obtained suggest that MAP1203 is a surface-exposed protein in MAP and the signal sequence is required for processing and expression of functional protein on the surface of the bacterium. Using the protein pull-down assay and far-Western blot, we also demonstrate that MAP1203 interacts with the host dihydropyrimidinase-related protein 2 and glyceraldehyde 3-phosphate dehydrogenase proteins, located on the membrane of epithelial cell and involved in the remodeling of the cytoskeleton. Our data suggests that MAP1203 plays a significant role in the initiation of MAP infection of the bovine epithelium.
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Affiliation(s)
- Jamie L Everman
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Lia Danelishvili
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Lucero G Flores
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Luiz E Bermudez
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
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24
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Steiner EM, Lyngsø J, Guy JE, Bourenkov G, Lindqvist Y, Schneider TR, Pedersen JS, Schneider G, Schnell R. The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity. Proteins 2018; 86:912-923. [DOI: 10.1002/prot.25523] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/17/2018] [Accepted: 04/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Eva Maria Steiner
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm S-17 177 Sweden
| | - Jeppe Lyngsø
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO); Aarhus University, Gustav Wieds Vej 14; Aarhus DK-8000 Denmark
| | - Jodie E. Guy
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm S-17 177 Sweden
| | - Gleb Bourenkov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85; Hamburg 22603 Germany
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm S-17 177 Sweden
| | - Thomas R. Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85; Hamburg 22603 Germany
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO); Aarhus University, Gustav Wieds Vej 14; Aarhus DK-8000 Denmark
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm S-17 177 Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm S-17 177 Sweden
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25
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Characterization of Conserved and Novel Septal Factors in Mycobacterium smegmatis. J Bacteriol 2018; 200:JB.00649-17. [PMID: 29311277 DOI: 10.1128/jb.00649-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Septation in bacteria requires coordinated regulation of cell wall biosynthesis and hydrolysis enzymes so that new septal cross-wall can be appropriately constructed without compromising the integrity of the existing cell wall. Bacteria with different modes of growth and different types of cell wall require different regulators to mediate cell growth and division processes. Mycobacteria have both a cell wall structure and a mode of growth that are distinct from well-studied model organisms and use several different regulatory mechanisms. Here, using Mycobacterium smegmatis, we identify and characterize homologs of the conserved cell division regulators FtsL and FtsB, and show that they appear to function similarly to their homologs in Escherichia coli We identify a number of previously undescribed septally localized factors which could be involved in cell wall regulation. One of these, SepIVA, has a DivIVA domain, is required for mycobacterial septation, and is localized to the septum and the intracellular membrane domain. We propose that SepIVA is a regulator of cell wall precursor enzymes that contribute to construction of the septal cross-wall, similar to the putative elongation function of the other mycobacterial DivIVA homolog, Wag31.IMPORTANCE The enzymes that build bacterial cell walls are essential for cell survival but can cause cell lysis if misregulated; thus, their regulators are also essential. The number and nature of these regulators is likely to vary in bacteria that grow in different ways. The mycobacteria are a genus that have a cell wall whose composition and construction vary greatly from those of well-studied model organisms. In this work, we identify and characterize some of the proteins that regulate the mycobacterial cell wall. We find that some of these regulators appear to be functionally conserved with their structural homologs in evolutionarily distant species such as Escherichia coli, but other proteins have critical regulatory functions that may be unique to the actinomycetes.
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Squeglia F, Ruggiero A, Berisio R. Chemistry of Peptidoglycan in Mycobacterium tuberculosis
Life Cycle: An off-the-wall Balance of Synthesis and Degradation. Chemistry 2017; 24:2533-2546. [DOI: 10.1002/chem.201702973] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
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Botella H, Vaubourgeix J, Lee MH, Song N, Xu W, Makinoshima H, Glickman MS, Ehrt S. Mycobacterium tuberculosis protease MarP activates a peptidoglycan hydrolase during acid stress. EMBO J 2017; 36:536-548. [PMID: 28057704 DOI: 10.15252/embj.201695028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/28/2016] [Accepted: 12/02/2016] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can persist in the human host in a latent state for decades, in part because it has the ability to withstand numerous stresses imposed by host immunity. Prior studies have established the essentiality of the periplasmic protease MarP for Mtb to survive in acidified phagosomes and establish and maintain infection in mice. However, the proteolytic substrates of MarP that mediate these phenotypes were unknown. Here, we used biochemical methods coupled with supravital chemical probes that facilitate imaging of nascent peptidoglycan to demonstrate that during acid stress MarP cleaves the peptidoglycan hydrolase RipA, a process required for RipA's activation. Failure of RipA processing in MarP-deficient cells leads to cell elongation and chain formation, a hallmark of progeny cell separation arrest. Our results suggest that sustaining peptidoglycan hydrolysis, a process required for cell elongation, separation of progeny cells, and cell wall homeostasis in growing cells, may also be essential for Mtb's survival in acidic conditions.
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Affiliation(s)
- Helene Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Myung Hee Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Naomi Song
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Weizhen Xu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Hideki Makinoshima
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael S Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
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Singh V, Dhar N, Pató J, Kolly GS, Korduláková J, Forbak M, Evans JC, Székely R, Rybniker J, Palčeková Z, Zemanová J, Santi I, Signorino-Gelo F, Rodrigues L, Vocat A, Covarrubias AS, Rengifo MG, Johnsson K, Mowbray S, Buechler J, Delorme V, Brodin P, Knott GW, Aínsa JA, Warner DF, Kéri G, Mikušová K, McKinney JD, Cole ST, Mizrahi V, Hartkoorn RC. Identification of aminopyrimidine-sulfonamides as potent modulators of Wag31-mediated cell elongation in mycobacteria. Mol Microbiol 2016; 103:13-25. [PMID: 27677649 DOI: 10.1111/mmi.13535] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 12/01/2022]
Abstract
There is an urgent need to discover new anti-tubercular agents with novel mechanisms of action in order to tackle the scourge of drug-resistant tuberculosis. Here, we report the identification of such a molecule - an AminoPYrimidine-Sulfonamide (APYS1) that has potent, bactericidal activity against M. tuberculosis. Mutations in APYS1-resistant M. tuberculosis mapped exclusively to wag31, a gene that encodes a scaffolding protein thought to orchestrate cell elongation. Recombineering confirmed that a Gln201Arg mutation in Wag31 was sufficient to cause resistance to APYS1, however, neither overexpression nor conditional depletion of wag31 impacted M. tuberculosis susceptibility to this compound. In contrast, expression of the wildtype allele of wag31 in APYS1-resistant M. tuberculosis was dominant and restored susceptibility to APYS1 to wildtype levels. Time-lapse imaging and scanning electron microscopy revealed that APYS1 caused gross malformation of the old pole of M. tuberculosis, with eventual lysis. These effects resembled the morphological changes observed following transcriptional silencing of wag31 in M. tuberculosis. These data show that Wag31 is likely not the direct target of APYS1, but the striking phenotypic similarity between APYS1 exposure and genetic depletion of Wag31 in M. tuberculosis suggests that APYS1 might indirectly affect Wag31 through an as yet unknown mechanism.
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Affiliation(s)
- Vinayak Singh
- Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, South Africa
| | - Neeraj Dhar
- Microbiology and Microsystems, Global Health Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - János Pató
- Vichem Chemie Research Ltd, Herman, Otto u. 15, Budapest, 1022, Hungary
| | - Gaëlle S Kolly
- Microbial Pathogenesis, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jana Korduláková
- Now at: 1st Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Martin Forbak
- Now at: 1st Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Joanna C Evans
- Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, South Africa
| | - Rita Székely
- Microbial Pathogenesis, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jan Rybniker
- Microbial Pathogenesis, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Now at: 1st Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Zuzana Palčeková
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Bratislava, Slovakia
| | - Júlia Zemanová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Bratislava, Slovakia
| | - Isabella Santi
- Microbiology and Microsystems, Global Health Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - François Signorino-Gelo
- Microbiology and Microsystems, Global Health Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Liliana Rodrigues
- Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza, and Fundación ARAID, Zaragoza, Spain; CIBERES, Instituto de Salud Carlos III, Madrid, Zaragoza, Spain
| | - Anthony Vocat
- Microbial Pathogenesis, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrian S Covarrubias
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Monica G Rengifo
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kai Johnsson
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sherry Mowbray
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Joseph Buechler
- Alere (San Diego), Summer Ridge Road, San Diego, CA, 92121, USA
| | - Vincent Delorme
- Center for Infection and Immunity, Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Priscille Brodin
- Center for Infection and Immunity, Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Graham W Knott
- Interdisciplinary Centre for Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - José A Aínsa
- Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza, and Fundación ARAID, Zaragoza, Spain; CIBERES, Instituto de Salud Carlos III, Madrid, Zaragoza, Spain
| | - Digby F Warner
- Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, South Africa
| | - György Kéri
- Vichem Chemie Research Ltd, Herman, Otto u. 15, Budapest, 1022, Hungary
| | - Katarína Mikušová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Bratislava, Slovakia
| | - John D McKinney
- Microbiology and Microsystems, Global Health Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Stewart T Cole
- Microbial Pathogenesis, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Valerie Mizrahi
- Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, South Africa
| | - Ruben C Hartkoorn
- Microbial Pathogenesis, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Filippova EV, Kieser KJ, Luan CH, Wawrzak Z, Kiryukhina O, Rubin EJ, Anderson WF. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. FEBS J 2016; 283:2206-18. [PMID: 27101811 PMCID: PMC5245116 DOI: 10.1111/febs.13738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/30/2016] [Accepted: 04/15/2016] [Indexed: 01/21/2023]
Abstract
UNLABELLED Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic-resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin-binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor-free form and in complex with penicillin V are reported. We used site-directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β-lactams. Structural comparison of the PonA1 apo-form and the antibiotic-bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4'-α3 surrounding the penicillin-binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β-lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall-targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections. DATABASE Structural data are available in the PDB database under the accession numbers 5CRF and 5CXW.
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Affiliation(s)
- Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karen J Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chi-Hao Luan
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Zdzislaw Wawrzak
- Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Evanston, IL, USA
| | - Olga Kiryukhina
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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The RipA and RipB Peptidoglycan Endopeptidases Are Individually Nonessential to Mycobacterium smegmatis. J Bacteriol 2016; 198:1464-75. [PMID: 26977111 DOI: 10.1128/jb.00059-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mycobacteria possess a series of Rip peptidoglycan endopeptidases that have been characterized in various levels of detail. The RipA and RipB proteins have been extensively studied and are DL-endopeptidases, and RipA has been considered essential to Mycobacterium smegmatis and Mycobacterium tuberculosis We show here that the ripA and ripB genes are individually dispensable in M. smegmatis and that at least one of the genes must be expressed for viability. We characterized strains carrying in-frame deletion mutations of ripA and ripB and found that both mutant strains exhibited increased susceptibility to a limited number of antibiotics and to detergent but that only the ΔripA mutant displayed hypersusceptibility to lysozyme. We also constructed and characterized ΔripD and ΔripAΔripD mutants and found that the single mutant had only an intermediate lysozyme hypersusceptibility phenotype compared to that of wild-type cells while loss of ripD in the ΔripA background partially rescued the antibiotic and lysozyme phenotypes of the ΔripA mutant. IMPORTANCE We show that the RipA endopeptidase, which has been considered essential for cell division in certain mycobacteria, is not essential but that at least it or a similar protein, RipB, must be expressed by the bacteria for viability. This work is the first description of strains carrying single deletion mutations of RipA, RipB, and a novel endopeptidase-like protein, RipD.
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Interaction of Mycobacterium tuberculosis Virulence Factor RipA with Chaperone MoxR1 Is Required for Transport through the TAT Secretion System. mBio 2016; 7:e02259. [PMID: 26933057 PMCID: PMC4810496 DOI: 10.1128/mbio.02259-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is a leading cause of death worldwide. The M. tuberculosis TAT (twin-arginine translocation) protein secretion system is present at the cytoplasmic membrane of mycobacteria and is known to transport folded proteins. The TAT secretion system is reported to be essential for many important bacterial processes that include cell wall biosynthesis. The M. tuberculosis secretion and invasion protein RipA has endopeptidase activity and interacts with one of the resuscitation antigens (RpfB) that are expressed during pathogen reactivation. MoxR1, a member of the ATPase family that is associated with various cellular activities, was predicted to interact with RipA based on in silico analyses. A bimolecular fluorescence complementation (BiFC) assay confirmed the interaction of these two proteins in HEK293T cells. The overexpression of RipA in Mycobacterium smegmatis and copurification with MoxR1 further validated their interaction in vivo. Recombinant MoxR1 protein, expressed in Escherichia coli, displays ATP-enhanced chaperone activity. Secretion of recombinant RipA (rRipA) protein into the E. coli culture filtrate was not observed in the absence of RipA-MoxR interaction. Inhibition of this export system in M. tuberculosis, including the key players, will prevent localization of peptidoglycan hydrolase and result in sensitivity to existing β-lactam antibiotics, opening up new candidates for drug repurposing. The virulence mechanism of mycobacteria is very complex. Broadly, the virulence factors can be classified as secretion factors, cell surface components, enzymes involved in cellular metabolism, and transcriptional regulators. The mycobacteria have evolved several mechanisms to secrete its proteins. Here, we have identified one of the virulence proteins of Mycobacterium tuberculosis, RipA, possessing peptidoglycan hydrolase activities secreted by the TAT secretion pathway. We also identified MoxR1 as a protein-protein interaction partner of RipA and demonstrated chaperone activity of this protein. We show that MoxR1-mediated folding is critical for the secretion of RipA within the TAT system. Inhibition of this export system in M. tuberculosis will prevent localization of peptidoglycan hydrolase and result in sensitivity to existing β-lactam antibiotics, opening up new candidates for drug repurposing.
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Malhotra N, Chakraborti PK. Eukaryotic-Type Ser/Thr Protein Kinase Mediated Phosphorylation of Mycobacterial Phosphodiesterase Affects its Localization to the Cell Wall. Front Microbiol 2016; 7:123. [PMID: 26904001 PMCID: PMC4746578 DOI: 10.3389/fmicb.2016.00123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/22/2016] [Indexed: 11/13/2022] Open
Abstract
Phosphodiesterase enzymes, involved in cAMP hydrolysis reaction, are present throughout phylogeny and their phosphorylation mediated regulation remains elusive in prokaryotes. In this context, we focused on this enzyme from Mycobacterium tuberculosis. The gene encoded by Rv0805 was PCR amplified and expressed as a histidine-tagged protein (mPDE) utilizing Escherichia coli based expression system. In kinase assays, upon incubation with mycobacterial Clade I eukaryotic-type Ser/Thr kinases (PknA, PknB, and PknL), Ni-NTA purified mPDE protein exhibited transphosphorylation ability albeit with varying degree. When mPDE was co-expressed one at a time with these kinases in E. coli, it was also recognized by an anti-phosphothreonine antibody, which further indicates its phosphorylating ability. Mass spectrometric analysis identified Thr-309 of mPDE as a phosphosite. In concordance with this observation, anti-phosphothreonine antibody marginally recognized mPDE-T309A mutant protein; however, such alteration did not affect the enzymatic activity. Interestingly, mPDE expressed in Mycobacterium smegmatis yielded a phosphorylated protein that preferentially localized to cell wall. In contrast, mPDE-T309A, the phosphoablative variant of mPDE, did not show such behavior. On the other hand, phosphomimics of mPDE (T309D or T309E), exhibited similar cell wall anchorage as was observed with the wild-type. Thus, our results provide credence to the fact that eukaryotic-type Ser/Thr kinase mediated phosphorylation of mPDE renders negative charge to the protein, promoting its localization on cell wall. Furthermore, multiple sequence alignment revealed that Thr-309 is conserved among mPDE orthologs of M. tuberculosis complex, which presumably emphasizes evolutionary significance of phosphorylation at this residue.
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Affiliation(s)
- Neha Malhotra
- CSIR-Institute of Microbial Technology Chandigarh, India
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33
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Abstract
The complex cell envelope is a hallmark of mycobacteria and is anchored by the peptidoglycan layer, which is similar to that of Escherichia coli and a number of other bacteria but with modifications to the monomeric units and other structural complexities that are likely related to a role for the peptidoglycan in stabilizing the mycolyl-arabinogalactan-peptidoglycan complex (MAPc). In this article, we will review the genetics of several aspects of peptidoglycan biosynthesis in mycobacteria, including the production of monomeric precursors in the cytoplasm, assembly of the monomers into the mature wall, cell wall turnover, and cell division. Finally, we will touch upon the resistance of mycobacteria to β-lactam antibiotics, an important class of drugs that, until recently, have not been extensively exploited as potential antimycobacterial agents. We will also note areas of research where there are still unanswered questions.
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Kieser KJ, Boutte CC, Kester JC, Baer CE, Barczak AK, Meniche X, Chao MC, Rego EH, Sassetti CM, Fortune SM, Rubin EJ. Phosphorylation of the Peptidoglycan Synthase PonA1 Governs the Rate of Polar Elongation in Mycobacteria. PLoS Pathog 2015; 11:e1005010. [PMID: 26114871 PMCID: PMC4483258 DOI: 10.1371/journal.ppat.1005010] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/07/2015] [Indexed: 01/11/2023] Open
Abstract
Cell growth and division are required for the progression of bacterial infections. Most rod-shaped bacteria grow by inserting new cell wall along their mid-section. However, mycobacteria, including the human pathogen Mycobacterium tuberculosis, produce new cell wall material at their poles. How mycobacteria control this different mode of growth is incompletely understood. Here we find that PonA1, a penicillin binding protein (PBP) capable of transglycosylation and transpeptidation of cell wall peptidoglycan (PG), is a major governor of polar growth in mycobacteria. PonA1 is required for growth of Mycobacterium smegmatis and is critical for M. tuberculosis during infection. In both cases, PonA1’s catalytic activities are both required for normal cell length, though loss of transglycosylase activity has a more pronounced effect than transpeptidation. Mutations that alter the amount or the activity of PonA1 result in abnormal formation of cell poles and changes in cell length. Moreover, altered PonA1 activity results in dramatic differences in antibiotic susceptibility, suggesting that a balance between the two enzymatic activities of PonA1 is critical for survival. We also find that phosphorylation of a cytoplasmic region of PonA1 is required for normal activity. Mutations in a critical phosphorylated residue affect transglycosylase activity and result in abnormal rates of cell elongation. Together, our data indicate that PonA1 is a central determinant of polar growth in mycobacteria, and its governance of cell elongation is required for robust cell fitness during both host-induced and antibiotic stress. Bacterial infections rely on continued bacterial growth. Studying cell growth is particularly important for pathogens such as Mycobacterium tuberculosis that grow differently than model organisms. Unlike Escherichia coli or Bacillus subtilis, which grow by incorporating cell wall material along their body, mycobacteria grow from the pole. It remains unclear how mycobacteria construct and extend their poles. Our work identifies a cell wall synthase, PonA1, as a key determinant of mycobacterial polar growth. PonA1 governs polar growth through two enzymatic activities that build the cell wall’s peptidoglycan (PG); both of these activities are required for normal cell growth. Changes in the amount or activity of PonA1 leads to misplaced cell poles and inhibition of cell proliferation. PonA1 is phosphorylated, an unusual modification for PG synthases. This phosphorylation tunes the rate of cell elongation. Changing PonA1’s regulatory or enzymatic activity impacts the survival of cells in the host or when treated with antibiotics. Our work shows how mycobacterial cell pole construction and cell fitness is governed by a major cell wall synthase; these findings may have implications for other bacteria that elongate from their poles.
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Affiliation(s)
- Karen J. Kieser
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Cara C. Boutte
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jemila C. Kester
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christina E. Baer
- Department of Microbiology and Physiological Systems, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amy K. Barczak
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Xavier Meniche
- Department of Microbiology and Physiological Systems, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael C. Chao
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - E. Hesper Rego
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Eric J. Rubin
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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35
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Nikitushkin VD, Demina GR, Shleeva MO, Guryanova SV, Ruggiero A, Berisio R, Kaprelyants AS. A product of RpfB and RipA joint enzymatic action promotes the resuscitation of dormant mycobacteria. FEBS J 2015; 282:2500-11. [PMID: 25846449 DOI: 10.1111/febs.13292] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 11/29/2022]
Abstract
Resuscitation-promoting factor proteins (Rpfs) are known to participate in reactivating the dormant forms of actinobacteria. Structural analysis of the Rpf catalytic domain demonstrates its similarity to lysozyme and to lytic transglycosylases - the groups of enzymes that cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and GlcNAc, and concomitantly form a 1,6-anhydro ring at the MurNAc residue. Analysis of the products formed from mycobacterial peptidoglycan hydrolysis reactions containing a mixture of RpfB and resuscitation-promoting factor interacting protein (RipA) allowed us to identify the suggested product of their action - N-acetylglucosaminyl-β(1 → 4)-N-glycolyl-1,6-anhydromuramyl-L-alanyl-D-isoglutamate. To identify the role of this resulting product in resuscitation, we used a synthetic 1,6-anhydrodisaccharide-dipeptide, and tested its ability to stimulate resuscitation by using the dormant Mycobacterium smegmatis model. It was found that the disaccharide-dipeptide was the minimal structure capable of resuscitating the dormant mycobacterial cells over the concentration range of 9-100 ng · mL(-1). The current study therefore provides the first insights into the molecular mechanism of resuscitation from dormancy involving a product of RpfB/RipA-mediated peptidoglycan cleavage.
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Affiliation(s)
- Vadim D Nikitushkin
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Galina R Demina
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Margarita O Shleeva
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana V Guryanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
| | - Arseny S Kaprelyants
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
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Wong JEMM, Midtgaard SR, Gysel K, Thygesen MB, Sørensen KK, Jensen KJ, Stougaard J, Thirup S, Blaise M. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:592-605. [PMID: 25760608 PMCID: PMC4356369 DOI: 10.1107/s139900471402793x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/22/2014] [Indexed: 11/10/2022]
Abstract
LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.
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Affiliation(s)
- Jaslyn E. M. M. Wong
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Kira Gysel
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Mikkel B. Thygesen
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Kasper K. Sørensen
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Knud J. Jensen
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Søren Thirup
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Mickaël Blaise
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
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Squeglia F, Ruggiero A, Romano M, Vitagliano L, Berisio R. Mutational and structural study of RipA, a key enzyme in Mycobacterium tuberculosis cell division: evidence for the L-to-D inversion of configuration of the catalytic cysteine. ACTA ACUST UNITED AC 2014; 70:2295-300. [PMID: 25195744 DOI: 10.1107/s1399004714013674] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022]
Abstract
RipA is a key cysteine protease of Mycobacterium tuberculosis as it is responsible for bacterial daughter-cell separation. Although it is an important target for antimicrobial development, its mechanism of action and its interaction pattern with its substrate are hitherto unknown. By combining crystallographic and mutational studies with functional assays and molecular modelling, it is shown that the catalytic activity of the enzyme relies on a Cys-His-Glu triad and the impact of the mutation of each residue of the triad on the structure and function of RipA is analysed. Unexpectedly, the crystallographic analyses reveal that mutation of the glutamic acid to alanine results in inversion of the configuration of the catalytic cysteine. The consequent burial of the catalytic cysteine side chain explains the enzyme inactivation upon mutation. These data point to a novel role of the acidic residue often present in the triad of cysteine proteases as a supervisor of cysteine configuration through preservation of the local structural integrity.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Maria Romano
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
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Abstract
Mycobacterium tuberculosis, which is the aetiological agent of tuberculosis, owes much of its success as a pathogen to its unique cell wall and unusual mechanism of growth, which facilitate its adaptation to the human host and could have a role in clinical latency. Asymmetric growth and division increase population heterogeneity, which may promote antibiotic tolerance and the fitness of single cells. In this Review, we describe the unusual mechanisms of mycobacterial growth, cell wall biogenesis and division, and discuss how these processes might affect the survival of M. tuberculosis in vivo and contribute to the persistence of infection.
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Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC. Proc Natl Acad Sci U S A 2014; 111:8037-42. [PMID: 24843173 DOI: 10.1073/pnas.1321812111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial growth and cell division are coordinated with hydrolysis of the peptidoglycan (PG) layer of the cell wall, but the mechanisms of regulation of extracellular PG hydrolases are not well understood. Here we report the biochemical, structural, and genetic analysis of the Mycobacterium tuberculosis homolog of the transmembrane PG-hydrolase regulator, FtsX. The purified FtsX extracellular domain binds the PG peptidase Rv2190c/RipC N-terminal segment, causing a conformational change that activates the enzyme. Deletion of ftsEX and ripC caused similar phenotypes in Mycobacterium smegmatis, as expected for genes in a single pathway. The crystal structure of the FtsX extracellular domain reveals an unprecedented fold containing two lobes connected by a flexible hinge. Mutations in the hydrophobic cleft between the lobes reduce RipC binding in vitro and inhibit FtsX function in M. smegmatis. These studies suggest how FtsX recognizes RipC and support a model in which a conformational change in FtsX links the cell division apparatus with PG hydrolysis.
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Calvanese L, Falcigno L, Maglione C, Marasco D, Ruggiero A, Squeglia F, Berisio R, D'Auria G. Structural and binding properties of the PASTA domain of PonA2, a key penicillin binding protein fromMycobacterium tuberculosis. Biopolymers 2014; 101:712-9. [DOI: 10.1002/bip.22447] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/08/2013] [Indexed: 12/18/2022]
Affiliation(s)
| | - Lucia Falcigno
- CIRPeB; University of Naples Federico II; Naples Italy
- Department of Pharmacy; University of Naples “Federico II,”; via Mezzocannone 16 80134 Naples Italy
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Cira Maglione
- Department of Chemical Sciences; University of Naples “Federico II,”; via Cintia 45 80126 Naples Italy
| | - Daniela Marasco
- Department of Pharmacy; University of Naples “Federico II,”; via Mezzocannone 16 80134 Naples Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Gabriella D'Auria
- CIRPeB; University of Naples Federico II; Naples Italy
- Department of Pharmacy; University of Naples “Federico II,”; via Mezzocannone 16 80134 Naples Italy
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
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Machowski EE, Senzani S, Ealand C, Kana BD. Comparative genomics for mycobacterial peptidoglycan remodelling enzymes reveals extensive genetic multiplicity. BMC Microbiol 2014; 14:75. [PMID: 24661741 PMCID: PMC3987819 DOI: 10.1186/1471-2180-14-75] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/12/2014] [Indexed: 02/04/2023] Open
Abstract
Background Mycobacteria comprise diverse species including non-pathogenic, environmental organisms, animal disease agents and human pathogens, notably Mycobacterium tuberculosis. Considering that the mycobacterial cell wall constitutes a significant barrier to drug penetration, the aim of this study was to conduct a comparative genomics analysis of the repertoire of enzymes involved in peptidoglycan (PG) remodelling to determine the potential of exploiting this area of bacterial metabolism for the discovery of new drug targets. Results We conducted an in silico analysis of 19 mycobacterial species/clinical strains for the presence of genes encoding resuscitation promoting factors (Rpfs), penicillin binding proteins, endopeptidases, L,D-transpeptidases and N-acetylmuramoyl-L-alanine amidases. Our analysis reveals extensive genetic multiplicity, allowing for classification of mycobacterial species into three main categories, primarily based on their rpf gene complement. These include the M. tuberculosis Complex (MTBC), other pathogenic mycobacteria and environmental species. The complement of these genes within the MTBC and other mycobacterial pathogens is highly conserved. In contrast, environmental strains display significant genetic expansion in most of these gene families. Mycobacterium leprae retains more than one functional gene from each enzyme family, underscoring the importance of genetic multiplicity for PG remodelling. Notably, the highest degree of conservation is observed for N-acetylmuramoyl-L-alanine amidases suggesting that these enzymes are essential for growth and survival. Conclusion PG remodelling enzymes in a range of mycobacterial species are associated with extensive genetic multiplicity, suggesting functional diversification within these families of enzymes to allow organisms to adapt.
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Affiliation(s)
| | | | | | - Bavesh Davandra Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, P,O, Box 1038, Johannesburg 2000, South Africa.
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Frirdich E, Gaynor EC. Peptidoglycan hydrolases, bacterial shape, and pathogenesis. Curr Opin Microbiol 2013; 16:767-78. [PMID: 24121030 DOI: 10.1016/j.mib.2013.09.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/08/2013] [Accepted: 09/11/2013] [Indexed: 01/29/2023]
Abstract
Bacterial shape has always been hypothesized to play an important role in the biology of a species and in the ability of certain bacteria to influence human health. The recent discovery of peptidoglycan hydrolases that modulate shape has now allowed this hypothesis to be addressed directly. Genetic, biochemical, and phenotypic studies have found that changes in shape and underlying peptidoglycan structure influence many pathogenic attributes including surviving unfavorable conditions, predation, transmission, colonization, and host interactions. The diversity of bacterial shapes, niches, and lifestyles is also reflected in diverse mechanisms of hydrolase regulation, critical for maintaining peptidoglycan integrity and biological properties of the cell. Future studies will build on the current work described and further elucidate the intersection of peptidoglycan hydrolase activity, shape, and disease outcome.
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Affiliation(s)
- Emilisa Frirdich
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T1Z3
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Cava F, Kuru E, Brun YV, de Pedro MA. Modes of cell wall growth differentiation in rod-shaped bacteria. Curr Opin Microbiol 2013; 16:731-7. [PMID: 24094807 DOI: 10.1016/j.mib.2013.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/21/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
Abstract
A bacterial cell takes on the challenge to preserve and reproduce its shape at every generation against a substantial internal pressure by surrounding itself with a mechanical support, a peptidoglycan cell wall. The enlargement of the cell wall via net incorporation of precursors into the pre-existing wall conditions bacterial growth and morphology. However, generation, reproduction and/or modification of a specific shape requires that the incorporation takes place at precise locations for a defined time period. Much has been learnt in the past few years about the biochemistry of the peptidoglycan synthesis process, but topological approaches to the understanding of shape generation have been hindered by a lack of appropriate techniques. Recent technological advances are paving the way for substantial progress in understanding the mechanisms of bacterial morphogenesis. Here we review the latest developments, focusing on the impact of new techniques on the precise mapping of cell wall growth sites.
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Affiliation(s)
- Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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Rip it up. Nat Chem Biol 2013. [DOI: 10.1038/nchembio.1243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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