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Sundaram K, Vajravelu LK. Functional Analysis of Genes in Mycobacterium tuberculosis Action Against Autophagosome-Lysosome Fusion. Indian J Microbiol 2024; 64:367-375. [PMID: 39011011 PMCID: PMC11246336 DOI: 10.1007/s12088-024-01227-4] [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: 08/03/2023] [Accepted: 02/10/2024] [Indexed: 07/17/2024] Open
Abstract
Tuberculosis is a lethal disease that is one of the world's top ten death-associated infections in humans; Mycobacterium tuberculosis causes tuberculosis, and this bacterium is linked to the lysis of autophagolysosomal fusion action, a self-defense mechanism of its own. Thus, Cytoplasmic bacilli are sequestered by autophagy and transported to lysosomes to be inactivated to destroy intracellular bacteria. Besides this, a macrophage can limit intracellular Mycobacterium by using a type of autophagy, selective autophagy, a cell that marks undesirable ubiquitin existence in cytosolic cargo, acting as a "eat me" sensor in conjunction with cellular homeostasis. Mycobacterium tuberculosis genes of the PE_PGRS protein family inhibit autophagy, increase mycobacterial survival, and lead to latent tuberculosis infection associated with miRNAs. In addition, the family of autophagy-regulated (ATG) gene members are involved in autophagy and controls the initiation, expansion, maturation, and fusion of autophagosomes with lysosomes, among other signaling events that control autophagy flux and reduce inflammatory responses and forward to promote cellular proliferation. In line with the formation of caseous necrosis in macrophages by Mycobacterium tuberculosis and their action on the lysis of autophagosome fusion, it leads to latent tuberculosis infection. Therefore, we aimed to comprehensively analyses the autophagy and self-defense mechanism of Mycobacterium tuberculosis, which is to be gratified future research on novel therapeutic tools and diagnostic markers against tuberculosis.
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Affiliation(s)
- Karthikeyan Sundaram
- Department of Microbiology, SRM Medical College Hospital and Research Centre, Kattangulathur, Chennai, Tamilnadu 603203 India
| | - Leela Kagithakara Vajravelu
- Department of Microbiology, SRM Medical College Hospital and Research Centre, Kattangulathur, Chennai, Tamilnadu 603203 India
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2
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Rabaan AA, Garout M, Aljeldah M, Al Shammari BR, Alawfi A, Alshengeti A, Najim MA, Alrouji M, Almuhanna Y, Alissa M, Mashraqi MM, Alwashmi ASS, Alhajri M, Alateah SM, Farahat RA, Mohapatra RK. Anti-tubercular activity evaluation of natural compounds by targeting Mycobacterium tuberculosis resuscitation promoting factor B inhibition: An in silico study. Mol Divers 2024; 28:1057-1072. [PMID: 36964456 DOI: 10.1007/s11030-023-10632-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Tuberculosis (TB), an infectious disease caused by the Mycobacterium tuberculosis (Mtb), has been responsible for the deaths of millions of individuals around the globe. A vital protein in viral pathogenesis known as resuscitation promoting factor (RpfB) has been identified as a potential therapeutic target of anti-tuberculosis drugs. This study offered an in silico process to examine possible RpfB inhibitors employing a computational drug design pipeline. In this study, a total of 1228 phytomolecules were virtually tested against the RpfB of Mtb. These phytomolecules were sourced from the NP-lib database of the MTi-OpenScreen server, and five top hits (ZINC000044404209, ZINC000059779788, ZINC000001562130, ZINC000014766825, and ZINC000043552589) were prioritized for compute intensive docking with dock score ≤ - 8.5 kcal/mole. Later, molecular dynamics (MD) simulation and principal component analysis (PCA) were used to validate these top five hits. In the list of these top five hits, the ligands ZINC000044404209, ZINC000059779788, and ZINC000043552589 showed hydrogen bond formation with the functional residue Glu292 of the RpfB protein suggesting biological significance of the binding. The RMSD study showed stable protein-ligand complexes and higher conformational consistency for the ligands ZINC000014766825, and ZINC000043552589 with RMSD 3-4 Å during 100 ns MD simulation. The overall analysis performed in the study suggested promising binding of these compounds with the RpfB protein of the Mtb at its functional site, further experimental investigation is needed to validate the computational finding.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, 39831, Saudi Arabia
| | - Basim R Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, 39831, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah41491, Saudi Arabia
- Department of Infection prevention and control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, 41491, Saudi Arabia
| | - Mustafa A Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah, 41411, Saudi Arabia
| | - Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, 11961, Saudi Arabia
| | - Yasir Almuhanna
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, 11961, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, 61441, Saudi Arabia
| | - Ameen S S Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 34212, Saudi Arabia
| | - Souad Mohammed Alateah
- Microbiology laboratory, Central military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, 11159, Saudi Arabia
| | | | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, 758002, India.
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3
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Li J, Xu X, Shi J, Hermoso JA, Sham LT, Luo M. Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis. Nat Commun 2023; 14:7999. [PMID: 38044344 PMCID: PMC10694151 DOI: 10.1038/s41467-023-43770-6] [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: 03/17/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX system directly activates peptidoglycan-hydrolases by a mechanism that remains unclear. Here we report our investigation of Mycobacterium tuberculosis FtsEX as a non-canonical regulator with high basal ATPase activity. The cryo-EM structures of the FtsEX system alone and in complex with RipC, as well as the ATP-activated state, unveil detailed information on the signal transduction mechanism, leading to the activation of RipC. Our findings indicate that RipC is recognized through a "Match and Fit" mechanism, resulting in an asymmetric rearrangement of the extracellular domains of FtsX and a unique inclined binding mode of RipC. This study provides insights into the molecular mechanisms of FtsEX and RipC regulation in the context of a critical human pathogen, guiding the design of drugs targeting peptidoglycan remodeling.
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Affiliation(s)
- Jianwei Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Xin Xu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jian Shi
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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4
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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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5
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Tandukar S, Kwon E, Kim DY. Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA. Structure 2023; 31:619-628.e4. [PMID: 36963396 DOI: 10.1016/j.str.2023.02.013] [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: 12/02/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/26/2023]
Abstract
Peptidoglycan, a physical barrier that protects bacteria from the environment, is constantly degraded and resynthesized for remodeling during cell growth and division. Because excessive or insufficient peptidoglycan hydrolysis affects bacterial homeostasis and viability, peptidoglycan degradation must be precisely regulated. In Bacillus subtilis, DL-endopeptidases play an essential role in peptidoglycan remodeling, and their activity is regulated by IseA. Here, we report the crystal structure of peptidoglycan DL-endopeptidase LytE complexed with IseA. In the crystal structure, the inhibitory loop connecting the two lobes of IseA blocks the active site of LytE by mimicking its substrate. Consistently, mutations in the inhibitory loop resulted in the loss of IseA activity. The structure also shows that conformational rearrangements in both LytE and IseA restrict access of the inhibitory loop to the LytE catalytic site. These results reveal an inhibition mechanism of peptidoglycan DL-endopeptidase in which the inhibitory protein mimics the substrate but is not degraded.
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Affiliation(s)
| | - Eunju Kwon
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, South Korea.
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, South Korea.
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Kwan JMC, Qiao Y. Mechanistic Insights into the Activities of Major Families of Enzymes in Bacterial Peptidoglycan Assembly and Breakdown. Chembiochem 2023; 24:e202200693. [PMID: 36715567 DOI: 10.1002/cbic.202200693] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Serving as an exoskeletal scaffold, peptidoglycan is a polymeric macromolecule that is essential and conserved across all bacteria, yet is absent in mammalian cells; this has made bacterial peptidoglycan a well-established excellent antibiotic target. In addition, soluble peptidoglycan fragments derived from bacteria are increasingly recognised as key signalling molecules in mediating diverse intra- and inter-species communication in nature, including in gut microbiota-host crosstalk. Each bacterial species encodes multiple redundant enzymes for key enzymatic activities involved in peptidoglycan assembly and breakdown. In this review, we discuss recent findings on the biochemical activities of major peptidoglycan enzymes, including peptidoglycan glycosyltransferases (PGT) and transpeptidases (TPs) in the final stage of peptidoglycan assembly, as well as peptidoglycan glycosidases, lytic transglycosylase (LTs), amidases, endopeptidases (EPs) and carboxypeptidases (CPs) in peptidoglycan turnover and metabolism. Biochemical characterisation of these enzymes provides valuable insights into their substrate specificity, regulation mechanisms and potential modes of inhibition.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), 21 Nanyang Link, Singapore, 637371, Singapore.,LKC School of Medicine, Nanyang Technological University (NTU) Singapore, 11 Mandalay Road, Singapore, Singapore, 208232, Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), Singapore, 21 Nanyang Link, Singapore, 637371, Singapore
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7
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A Structural View at Vaccine Development against M. tuberculosis. Cells 2023; 12:cells12020317. [PMID: 36672252 PMCID: PMC9857197 DOI: 10.3390/cells12020317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Tuberculosis (TB) is still the leading global cause of death from an infectious bacterial agent. Limiting tuberculosis epidemic spread is therefore an urgent global public health priority. As stated by the WHO, to stop the spread of the disease we need a new vaccine, with better coverage than the current Mycobacterium bovis BCG vaccine. This vaccine was first used in 1921 and, since then, there are still no new licensed tuberculosis vaccines. However, there is extremely active research in the field, with a steep acceleration in the past decades, due to the advance of technologies and more rational vaccine design strategies. This review aims to gather latest updates in vaccine development in the various clinical phases and to underline the contribution of Structural Vaccinology (SV) to the development of safer and effective antigens. In particular, SV and the development of vaccine adjuvants is making the use of subunit vaccines, which are the safest albeit the less antigenic ones, an achievable goal. Indeed, subunit vaccines overcome safety concerns but need to be rationally re-engineered to enhance their immunostimulating effects. The larger availability of antigen structural information as well as a better understanding of the complex host immune response to TB infection is a strong premise for a further acceleration of TB vaccine development.
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8
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Demina GR, Shleeva MO, Bagaeva DI, Vostroknutova GV, Kaprelyants AS. Detection of “Non-culturable” Mycobacterium tuberculosis Cells by Culture Methods. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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9
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Potential Efficacy of β-Amyrin Targeting Mycobacterial Universal Stress Protein by In Vitro and In Silico Approach. Molecules 2022; 27:molecules27144581. [PMID: 35889451 PMCID: PMC9320329 DOI: 10.3390/molecules27144581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 01/29/2023] Open
Abstract
The emergence of drug resistance and the limited number of approved antitubercular drugs prompted identification and development of new antitubercular compounds to cure Tuberculosis (TB). In this work, an attempt was made to identify potential natural compounds that target mycobacterial proteins. Three plant extracts (A. aspera, C. gigantea and C. procera) were investigated. The ethyl acetate fraction of the aerial part of A. aspera and the flower ash of C. gigantea were found to be effective against M. tuberculosis H37Rv. Furthermore, the GC-MS analysis of the plant fractions confirmed the presence of active compounds in the extracts. The Mycobacterium target proteins, i.e., available PDB dataset proteins and proteins classified in virulence, detoxification, and adaptation, were investigated. A total of ten target proteins were shortlisted for further study, identified as follows: BpoC, RipA, MazF4, RipD, TB15.3, VapC15, VapC20, VapC21, TB31.7, and MazF9. Molecular docking studies showed that β-amyrin interacted with most of these proteins and its highest binding affinity was observed with Mycobacterium Rv1636 (TB15.3) protein. The stability of the protein-ligand complex was assessed by molecular dynamic simulation, which confirmed that β-amyrin most firmly interacted with Rv1636 protein. Rv1636 is a universal stress protein, which regulates Mycobacterium growth in different stress conditions and, thus, targeting Rv1636 makes M. tuberculosis vulnerable to host-derived stress conditions.
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10
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Santos-Beneit F. Expression of the Mycobacterium tuberculosis RipA cell wall hydrolase in Streptomyces coelicolor hampers vancomycin resistance. J Glob Antimicrob Resist 2021; 27:115-117. [PMID: 34492398 DOI: 10.1016/j.jgar.2021.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/08/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Fernando Santos-Beneit
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain; Department of Functional Biology, Microbiology Area, Medical School, University of Oviedo, Oviedo, Spain; Centre for Bacterial Cell Biology, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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Abstract
Mycobacteriophage phiT45-1 is a newly isolated bacteriophage spontaneously released from Mycobacterium abscessus strain Taiwan-45 that lytically infects M. abscessus strain BWH-C; phiT45-1 also infects M. abscessus ATCC 1997 but not Mycobacterium smegmatis. Phage phiT45-1 has a 43,407-bp genome and carries a polymorphic toxin-immunity cassette associated with type VII secretion systems. Mycobacteriophage phiT45-1 is a newly isolated bacteriophage spontaneously released from Mycobacterium abscessus strain Taiwan-45 that lytically infects M. abscessus strain BWH-C; phiT45-1 also infects M. abscessus ATCC 19977 but not Mycobacterium smegmatis. Phage phiT45-1 has a 43,407-bp genome and carries a polymorphic toxin-immunity cassette associated with type VII secretion systems.
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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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Küssau T, Van Wyk N, Johansen MD, Alsarraf HMAB, Neyret A, Hamela C, Sørensen KK, Thygesen MB, Beauvineau C, Kremer L, Blaise M. Functional Characterization of the N-Acetylmuramyl-l-Alanine Amidase, Ami1, from Mycobacterium abscessus. Cells 2020; 9:cells9112410. [PMID: 33158165 PMCID: PMC7694207 DOI: 10.3390/cells9112410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Peptidoglycan (PG) is made of a polymer of disaccharides organized as a three-dimensional mesh-like network connected together by peptidic cross-links. PG is a dynamic structure that is essential for resistance to environmental stressors. Remodeling of PG occurs throughout the bacterial life cycle, particularly during bacterial division and separation into daughter cells. Numerous autolysins with various substrate specificities participate in PG remodeling. Expression of these enzymes must be tightly regulated, as an excess of hydrolytic activity can be detrimental for the bacteria. In non-tuberculous mycobacteria such as Mycobacterium abscessus, the function of PG-modifying enzymes has been poorly investigated. In this study, we characterized the function of the PG amidase, Ami1 from M. abscessus. An ami1 deletion mutant was generated and the phenotypes of the mutant were evaluated with respect to susceptibility to antibiotics and virulence in human macrophages and zebrafish. The capacity of purified Ami1 to hydrolyze muramyl-dipeptide was demonstrated in vitro. In addition, the screening of a 9200 compounds library led to the selection of three compounds inhibiting Ami1 in vitro. We also report the structural characterization of Ami1 which, combined with in silico docking studies, allows us to propose a mode of action for these inhibitors.
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Affiliation(s)
- Tanja Küssau
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
| | - Niël Van Wyk
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
| | - Matt D. Johansen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
| | - Husam M. A. B. Alsarraf
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Aymeric Neyret
- CEMIPAI CNRS UM UMS3725, CEDEX 5, 34293 Montpellier, France;
| | - Claire Hamela
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
| | - Kasper K. Sørensen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark; (K.K.S.); (M.B.T.)
| | - Mikkel B. Thygesen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark; (K.K.S.); (M.B.T.)
| | - Claire Beauvineau
- Chemical Library Institut Curie/CNRS, CNRS UMR9187, INSERM U1196 and CNRS UMR3666, INSERM U1193, Université Paris-Saclay, F-91405 Orsay, France;
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
- INSERM, IRIM, 34293 Montpellier, France
- Correspondence: (L.K.); (M.B.); Tel.: +33-(0)-434-359-447 (L.K. & M.B.)
| | - Mickaël Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, CEDEX 5, 34293 Montpellier, France; (T.K.); (N.V.W.); (M.D.J.); (H.M.A.B.A.); (C.H.)
- Correspondence: (L.K.); (M.B.); Tel.: +33-(0)-434-359-447 (L.K. & M.B.)
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14
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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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15
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Abstract
The NlpC/p60-family of peptidoglycan hydrolases are key enzymes that facilitate bacterial cell division and also modulate microbe-host interactions. These endopeptidases utilize conserved Cys-His residues in their active site and are expressed in most bacterial species as well as some eukaryotes. Here we describe methods for biochemical analysis of Enterococcus faecium SagA-NlpC/p60 peptidoglycan hydrolase activity (Kim et al., 2019; Rangan et al., 2016), which includes recombinant protein preparation and biochemical analysis using both gel-based and LC-MS profiling of peptidoglycan fragments. These protocols should also facilitate the biochemical analysis of other NlpC/p60 peptidoglycan hydrolases.
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16
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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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17
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Calvanese L, Squeglia F, Romano M, D'Auria G, Falcigno L, Berisio R. Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence. J Biomol Struct Dyn 2019; 38:2455-2467. [PMID: 31299874 DOI: 10.1080/07391102.2019.1643786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribonuclease AS (RNase AS) is a crucial enzyme for virulence of Mycobacterium tuberculosis. We previously observed that RNase AS structurally resembles RNase T from Escherichia coli, an important enzyme for tRNA maturation and turnover. Here, we combine X-ray crystallography and molecular dynamics (MD) to investigate the specificity and dynamic properties of substrate binding. Both X-ray and MD data provide structural determinants that corroborate the strict substrate specificity of RNase AS to cleave only adenosine residues, due to the structural features of adenine base. Beside suggesting tRNA as most likely substrate of RNase AS, MD and modeling studies identify key enzyme-ligand interactions, both involving the catalytic site and the double helix region of tRNA, which is locked by interactions with a set of arginine residues. The MD data also evidence a ligand-induced conformational change of the enzyme which is transferred from one chain to the adjacent one. These data will explain the dimeric nature of both RNase AS and RNase T, with two catalytic grooves composed of both chains. Also, they account for the dichotomy of tRNA, which contains both the substrate poly(A) chain and an inhibiting double strand RNA. Indeed, they provide a possible mechanism of allosteric regulation, which unlocks one catalytic groove when the second groove is inhibited by the double strand region of tRNA. Finally, a full comprehension of the molecular details of tRNA maturation processes is essential to develop novel strategies to modulate RNA processing, for therapeutic purposes. AbbreviationsMDmolecular dynamicsPDBProtein Data BankRMSDroot mean square deviationRMSFroot mean square fluctuationRNAribonucleotidic acidRNase ASRibonuclease ASCommunicated by Ramasamy H. Sarma.
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Affiliation(s)
- Luisa Calvanese
- CIRPeB, University of Naples Federico II, Naples, Italy.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Flavia Squeglia
- Institute of Bio-Structures and Bio-Imaging - CNR-IBB, Naples, Italy
| | - Maria Romano
- Department of Life Sciences, Imperial College London, London, UK
| | - Gabriella D'Auria
- CIRPeB, University of Naples Federico II, Naples, Italy.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Lucia Falcigno
- CIRPeB, University of Naples Federico II, Naples, Italy.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Rita Berisio
- Institute of Bio-Structures and Bio-Imaging - CNR-IBB, Naples, Italy
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18
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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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19
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Kim B, Wang YC, Hespen CW, Espinosa J, Salje J, Rangan KJ, Oren DA, Kang JY, Pedicord VA, Hang HC. Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. eLife 2019; 8:e45343. [PMID: 30969170 PMCID: PMC6483599 DOI: 10.7554/elife.45343] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
We discovered that Enterococcus faecium (E. faecium), a ubiquitous commensal bacterium, and its secreted peptidoglycan hydrolase (SagA) were sufficient to enhance intestinal barrier function and pathogen tolerance, but the precise biochemical mechanism was unknown. Here we show E. faecium has unique peptidoglycan composition and remodeling activity through SagA, which generates smaller muropeptides that more effectively activates nucleotide-binding oligomerization domain-containing protein 2 (NOD2) in mammalian cells. Our structural and biochemical studies show that SagA is a NlpC/p60-endopeptidase that preferentially hydrolyzes crosslinked Lys-type peptidoglycan fragments. SagA secretion and NlpC/p60-endopeptidase activity was required for enhancing probiotic bacteria activity against Clostridium difficile pathogenesis in vivo. Our results demonstrate that the peptidoglycan composition and hydrolase activity of specific microbiota species can activate host immune pathways and enhance tolerance to pathogens.
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Affiliation(s)
- Byungchul Kim
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Charles W Hespen
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Kavita J Rangan
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
| | - Deena A Oren
- Structural Biology Resource CenterThe Rockefeller UniversityNew YorkUnited States
| | - Jin Young Kang
- Laboratory of Molecular BiophysicsThe Rockefeller UniversityNew YorkUnited States
| | - Virginia A Pedicord
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
- Cambridge Institute of Therapeutic Immunology & Infectious DiseaseUniversity of CambridgeCambridgeUnited Kingdom
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial PathogenesisThe Rockefeller UniversityNew YorkUnited States
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20
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Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest. Biochem J 2018; 475:3123-3140. [PMID: 30315001 DOI: 10.1042/bcj20180482] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022]
Abstract
The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.
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21
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Calvanese L, Falcigno L, Squeglia F, Berisio R, D’Auria G. PASTA sequence composition is a predictive tool for protein class identification. Amino Acids 2018; 50:1441-1450. [DOI: 10.1007/s00726-018-2621-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/13/2018] [Indexed: 12/18/2022]
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22
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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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23
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Squeglia F, Ruggiero A, De Simone A, Berisio R. A structural overview of mycobacterial adhesins: Key biomarkers for diagnostics and therapeutics. Protein Sci 2017; 27:369-380. [PMID: 29139177 DOI: 10.1002/pro.3346] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/09/2017] [Accepted: 11/09/2017] [Indexed: 01/14/2023]
Abstract
Adherence, colonization, and survival of mycobacteria in host cells require surface adhesins, which are attractive pharmacotherapeutic targets. A large arsenal of pilus and non-pilus adhesins have been identified in mycobacteria. These adhesins are capable of interacting with host cells, including macrophages and epithelial cells and are essential to microbial pathogenesis. In the last decade, several structures of mycobacterial adhesins responsible for adhesion to either macrophages or extra cellular matrix proteins have been elucidated. In addition, key structural and functional information have emerged for the process of mycobacterial adhesion to epithelial cells, mediated by the Heparin-binding hemagglutinin (HBHA). In this review, we provide an overview of the structural and functional features of mycobacterial adhesins and discuss their role as important biomarkers for diagnostics and therapeutics. Based on the reported data, it appears clear that adhesins are endowed with a variety of different structures and functions. Most adhesins play important roles in the cell life of mycobacteria and are key virulence factors. However, they have adapted to an extracellular life to exert a role in host-pathogen interaction. The type of interactions they form with the host and the adhesin regions involved in binding is partly known and is described in this review.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, I-80134, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, I-80134, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, SW7 2AZ, UK
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, I-80134, Italy
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24
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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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25
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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: 35] [Impact Index Per Article: 5.0] [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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26
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Kim SK, Park YM, Jung KH, Chai YG. Deletion of a putative NlpC/P60 endopeptidase BAS1812 affects germination, long-term survival and endospore formation in Bacillus anthracis. MICROBIOLOGY-SGM 2016; 163:144-152. [PMID: 28008818 DOI: 10.1099/mic.0.000416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacillus anthracis, an aetiologic agent of the zoonotic disease anthrax, encodes a putative NlpC/P60 endopeptidase BAS1812. It harbours a signal peptide, three bacterial SH3 domains and an NlpC/P60 family domain. Previous studies showed that BAS1812 is immunogenic in infected hosts and is a potential biomarker for anthrax treatment. To date, however, little information is known about its function and involvement in anthrax pathogenesis. Here we describe the phenotypic effect of BAS1812 deletion in B. anthracis Sterne strain. Transcriptional analysis showed that BAS1812 expression in a host-like environment was enhanced at the end of log phase, started to diminish after entry to stationary phase and increased again late in stationary phase. The constructed BAS1812 mutant showed impaired long-term survival in the stationary growth phase, less resilience to detergent, lesser endospore formation and delayed germination. The mutant also showed diminished ability to degrade peptidoglycan, but its ability to produce anthrax exotoxins was not affected. We hypothesize that BAS1812 is a cell wall hydrolase involved in biological activities related to maintaining cell wall integrity, sporulation and spore germination.
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Affiliation(s)
- Se Kye Kim
- Department of Molecular and Life Science, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Yun Min Park
- Department of Molecular and Life Science, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Kyoung Hwa Jung
- Department of Molecular and Life Science, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, Republic of Korea
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea.,Department of Molecular and Life Science, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, Republic of Korea
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27
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Faheem M, Martins-de-Sa D, Vidal JFD, Álvares ACM, Brandão-Neto J, Bird LE, Tully MD, von Delft F, Souto BM, Quirino BF, Freitas SM, Barbosa JARG. Functional and structural characterization of a novel putative cysteine protease cell wall-modifying multi-domain enzyme selected from a microbial metagenome. Sci Rep 2016; 6:38031. [PMID: 27934875 PMCID: PMC5146660 DOI: 10.1038/srep38031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022] Open
Abstract
A current metagenomics focus is to interpret and transform collected genomic data into biological information. By combining structural, functional and genomic data we have assessed a novel bacterial protein selected from a carbohydrate-related activity screen in a microbial metagenomic library from Capra hircus (domestic goat) gut. This uncharacterized protein was predicted as a bacterial cell wall-modifying enzyme (CWME) and shown to contain four domains: an N-terminal, a cysteine protease, a peptidoglycan-binding and an SH3 bacterial domain. We successfully cloned, expressed and purified this putative cysteine protease (PCP), which presented autoproteolytic activity and inhibition by protease inhibitors. We observed cell wall hydrolytic activity and ampicillin binding capacity, a characteristic of most bacterial CWME. Fluorimetric binding analysis yielded a Kb of 1.8 × 105 M-1 for ampicillin. Small-angle X-ray scattering (SAXS) showed a maximum particle dimension of 95 Å with a real-space Rg of 28.35 Å. The elongated molecular envelope corroborates the dynamic light scattering (DLS) estimated size. Furthermore, homology modeling and SAXS allowed the construction of a model that explains the stability and secondary structural changes observed by circular dichroism (CD). In short, we report a novel cell wall-modifying autoproteolytic PCP with insight into its biochemical, biophysical and structural features.
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Affiliation(s)
- Muhammad Faheem
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Diogo Martins-de-Sa
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Julia F. D. Vidal
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Alice C. M. Álvares
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - José Brandão-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, England
| | - Louise E. Bird
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, OX11 0FA, United Kingdom
| | - Mark D. Tully
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, England
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, England
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Betulia M. Souto
- Embrapa Agroenergia, Parque Estação Biológica - PqEB s/n°, Brasília, DF, 70770-901, Brazil
| | - Betania F. Quirino
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
- Embrapa Agroenergia, Parque Estação Biológica - PqEB s/n°, Brasília, DF, 70770-901, Brazil
| | - Sonia M. Freitas
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - João Alexandre R. G. Barbosa
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
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Calvanese L, Falcigno L, Squeglia F, D'Auria G, Berisio R. Structural and dynamic features of PASTA domains with different functional roles. J Biomol Struct Dyn 2016; 35:2293-2300. [PMID: 27568813 DOI: 10.1080/07391102.2016.1217274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Luisa Calvanese
- a CIRPeB , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy
| | - Lucia Falcigno
- a CIRPeB , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,b Department of Pharmacy , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
| | - Flavia Squeglia
- c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
| | - Gabriella D'Auria
- a CIRPeB , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,b Department of Pharmacy , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
| | - Rita Berisio
- c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
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Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R. Structure and dynamics of the multi-domain resuscitation promoting factor RpfB from Mycobacterium tuberculosis. J Biomol Struct Dyn 2016; 35:1322-1330. [PMID: 27420638 DOI: 10.1080/07391102.2016.1182947] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
RpfB is multidomain protein that is crucial for Mycobacterium tuberculosis resuscitation from dormancy. This protein cleaves cell wall peptidoglycan, an essential bacterial 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. RpfB is structurally complex being composed of five distinct domains, namely a catalytic, a G5 and three DUF348 domains. Here, we have undertaken a combined experimental and computation structural investigations on the entire protein to gain insights into its structure-function relationships. CD spectroscopy and light scattering experiments have provided insights into the protein fold stability and into its oligomeric state. Using the available structure information, we modeled the entire protein structure, which includes the two DUF348 domains whose structure is experimentally unknown, and we analyzed the dynamic behavior of RpfB using molecular dynamics simulations. Present results highlight an intricate mutual influence of the dynamics of the different protein domains. These data provide interesting clues on the functional role of non-catalytic domains of RpfB and on the mechanism of peptidoglycan degradation necessary to resuscitation of M. tuberculosis.
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Affiliation(s)
- Alessia Ruggiero
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Flavia Squeglia
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Maria Romano
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Luigi Vitagliano
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Alfonso De Simone
- b Division of Molecular Biosciences , Imperial College London , London , UK
| | - Rita Berisio
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
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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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31
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Pohane AA, Jain V. Insights into the regulation of bacteriophage endolysin: multiple means to the same end. Microbiology (Reading) 2015; 161:2269-76. [DOI: 10.1099/mic.0.000190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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32
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Iglesias V, de Groot NS, Ventura S. Computational analysis of candidate prion-like proteins in bacteria and their role. Front Microbiol 2015; 6:1123. [PMID: 26528269 PMCID: PMC4606120 DOI: 10.3389/fmicb.2015.01123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/28/2015] [Indexed: 12/02/2022] Open
Abstract
Prion proteins were initially associated with diseases such as Creutzfeldt Jakob and transmissible spongiform encephalopathies. However, deeper research revealed them as versatile tools, exploited by the cells to execute fascinating functions, acting as epigenetic elements or building membrane free compartments in eukaryotes. One of the most intriguing properties of prion proteins is their ability to propagate a conformational assembly, even across species. In this context, it has been observed that bacterial amyloids can trigger the formation of protein aggregates by interacting with host proteins. As our life is closely linked to bacteria, either through a parasitic or symbiotic relationship, prion-like proteins produced by bacterial cells might play a role in this association. Bioinformatics is helping us to understand the factors that determine conformational conversion and infectivity in prion-like proteins. We have used PrionScan to detect prion domains in 839 different bacteria proteomes, detecting 2200 putative prions in these organisms. We studied this set of proteins in order to try to understand their functional role and structural properties. Our results suggest that these bacterial polypeptides are associated to peripheral rearrangement, macromolecular assembly, cell adaptability, and invasion. Overall, these data could reveal new threats and therapeutic targets associated to infectious diseases.
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Affiliation(s)
- Valentin Iglesias
- Departament de Bioquìmica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Natalia S de Groot
- Departament de Bioquìmica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Salvador Ventura
- Departament de Bioquìmica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
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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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Berisio R, Squeglia F, Ruggiero A, Petraccone L, Stellato MI, Del Vecchio P. Differential thermodynamic behaviours of the extra-cellular regions of two Ser/Thr PrkC kinases revealed by calorimetric studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:402-9. [PMID: 25668224 DOI: 10.1016/j.bbapap.2015.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/13/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
Eukaryotic-type Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases (STPK) are widespread in gram positive bacteria, where they regulate several cellular functions. STPKs belong to the protein kinase family named as one-component signal transduction systems, which combine both sensing and regulating properties. Thermodynamic investigations of sensing extra-cellular portions of two important Ser-Thr kinases, PrkC, from Staphylococcus aureus and Bacillus subtilis were conducted by differential scanning calorimetry (DSC) and circular dichroism (CD) melting measurements, coupled with modelling studies. The study of thermodynamic properties of the two domains is challenging since they share a modular domain organization. Consistently, DSC and CD data show that they present similar thermodynamic behaviours and that folding/unfolding transitions do not fit a two-state folding model. However, the thermal unfolding of the two proteins is differentially sensitive to pH. In particular, their unfolding is characteristic of modular structures at the neutral pH, with independent contributions of individual domains to folding. Differently, a cooperative unfolding is evidenced at acidic pH for the B. subtilis member, suggesting that a significant interaction between domains becomes valuable.
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Affiliation(s)
- Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy.
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Marco Ignazio Stellato
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy.
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36
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Mavrici D, Prigozhin DM, Alber T. Mycobacterium tuberculosis RpfE crystal structure reveals a positively charged catalytic cleft. Protein Sci 2015; 23:481-7. [PMID: 24452911 DOI: 10.1002/pro.2431] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/17/2014] [Accepted: 01/17/2014] [Indexed: 11/07/2022]
Abstract
Resuscitation promoting factor (Rpf) proteins, which hydrolyze the sugar chains in cell-wall peptidoglycan (PG), play key roles in prokaryotic cell elongation, division, and escape from dormancy to vegetative growth. Like other bacteria, Mycobacterium tuberculosis (Mtb) expresses multiple Rpfs, none of which is individually essential. This redundancy has left unclear the distinct functions of the different Rpfs. To explore the distinguishing characteristics of the five Mtb Rpfs, we determined the crystal structure of the RpfE catalytic domain. The protein adopts the characteristic Rpf fold, but the catalytic cleft is narrower compared to Mtb RpfB. Also in contrast to RpfB, in which the substrate-binding surfaces are negatively charged, the corresponding RpfE catalytic pocket and predicted peptide-binding sites are more positively charged at neutral pH. The complete reversal of the electrostatic potential of the substrate-binding site suggests that the different Rpfs function optimally at different pHs or most efficiently hydrolyze different micro-domains of PG. These studies provide insights into the molecular determinants of the evolution of functional specialization in Rpfs.
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Affiliation(s)
- Daniela Mavrici
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720
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37
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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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40
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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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41
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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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RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function. Biochem J 2013; 457:33-41. [DOI: 10.1042/bj20131227] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RipD from Mycobacterium tuberculosis represents the first NlpC/p60 domain protein that evolved a non-catalytic cell wall binding function. The structure of the NlpC/p60 domain is presented in this study and the protein is characterized with respect to catalytic activity and peptidoglycan binding.
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Kumar A, Kumar S, Kumar D, Mishra A, Dewangan RP, Shrivastava P, Ramachandran S, Taneja B. The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2543-54. [PMID: 24311595 PMCID: PMC3852659 DOI: 10.1107/s0907444913026371] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/24/2013] [Indexed: 11/16/2022]
Abstract
Bacterial N-acetylmuramoyl-L-alanine amidases are cell-wall hydrolases that hydrolyze the bond between N-acetylmuramic acid and L-alanine in cell-wall glycopeptides. Rv3717 of Mycobacterium tuberculosis has been identified as a unique autolysin that lacks a cell-wall-binding domain (CBD) and its structure has been determined to 1.7 Å resolution by the Pt-SAD phasing method. Rv3717 possesses an α/β-fold and is a zinc-dependent hydrolase. The structure reveals a short flexible hairpin turn that partially occludes the active site and may be involved in autoregulation. This type of autoregulation of activity of PG hydrolases has been observed in Bartonella henselae amidase (AmiB) and may be a general mechanism used by some of the redundant amidases to regulate cell-wall hydrolase activity in bacteria. Rv3717 utilizes its net positive charge for substrate binding and exhibits activity towards a broad spectrum of substrate cell walls. The enzymatic activity of Rv3717 was confirmed by isolation and identification of its enzymatic products by LC/MS. These studies indicate that Rv3717, an N-acetylmuramoyl-L-alanine amidase from M. tuberculosis, represents a new family of lytic amidases that do not have a separate CBD and are regulated conformationally.
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Affiliation(s)
- Atul Kumar
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Sanjiv Kumar
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Dilip Kumar
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Arpit Mishra
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Rikeshwer P. Dewangan
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Priyanka Shrivastava
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | | | - Bhupesh Taneja
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
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van der Woude AD, Stoop EJM, Stiess M, Wang S, Ummels R, van Stempvoort G, Piersma SR, Cascioferro A, Jiménez CR, Houben ENG, Luirink J, Pieters J, van der Sar AM, Bitter W. Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector. Cell Microbiol 2013; 16:280-95. [PMID: 24119166 DOI: 10.1111/cmi.12221] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 09/14/2013] [Accepted: 09/24/2013] [Indexed: 02/03/2023]
Abstract
The pathogenicity of mycobacteria is closely associated with their ability to export virulence factors. For this purpose, mycobacteria possess different protein secretion systems, including the accessory Sec translocation pathway, SecA2. Although this pathway is associated with intracellular survival and virulence, the SecA2-dependent effector proteins remain largely undefined. In this work, we studied a Mycobacterium marinum secA2 mutant with an impaired capacity to initiate granuloma formation in zebrafish embryos. By comparing the proteomic profile of cell envelope fractions from the secA2 mutant with wild type M. marinum, we identified putative SecA2-dependent substrates. Immunoblotting procedures confirmed SecA2-dependent membrane localization for several of these proteins, including the virulence factor protein kinase G (PknG). Interestingly, phenotypical defects of the secA2 mutant are similar to those described for ΔpknG, including phagosomal maturation. Overexpression of PknG in the secA2 mutant restored its localization to the cell envelope. Importantly, PknG-overexpression also partially restored the virulence of the secA2 mutant, as indicated by enhanced infectivity in zebrafish embryos and restored inhibition of phagosomal maturation. These results suggest that SecA2-dependent membrane localization of PknG is an important determinant for M. marinum virulence.
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Affiliation(s)
- Aniek D van der Woude
- Department of Medical Microbiology and Infection Control, VU University Medical Center, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands; Department of Molecular Microbiology, Institute of Molecular Cell Biology, VU University, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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Wong JEMM, Blaise M. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the putative NlpC/P60 endopeptidase, TTHA0266, from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1291-4. [PMID: 24192372 PMCID: PMC3818056 DOI: 10.1107/s1744309113027164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/02/2013] [Indexed: 11/10/2022]
Abstract
Autolysins belong to a protein family involved in peptidoglycan degradation and remodelling. Within this family, NlpC/P60 endopeptidases are involved in the hydrolysis of the peptide arm of peptidoglycan. In this work, the putative NlpC/P60 endopeptidase TTHA0266 from Thermus thermophilus HB8 was overexpressed, purified and crystallized. The crystals diffracted to 2.4 Å resolution and belonged to the hexagonal space group P6(1), with unit-cell parameters a = b = 71.19, c = 198.68 Å, γ = 120°. Selenomethionine-substituted protein was crystallized and the structure was solved by single-wavelength anomalous dispersion.
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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
| | - Mickael 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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46
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Ruggiero A, De Simone P, Smaldone G, Squeglia F, Berisio R. Bacterial cell division regulation by Ser/Thr kinases: a structural perspective. Curr Protein Pept Sci 2013; 13:756-66. [PMID: 23305362 PMCID: PMC3601408 DOI: 10.2174/138920312804871201] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/16/2012] [Accepted: 08/03/2012] [Indexed: 12/17/2022]
Abstract
Recent genetic, biochemical and structural studies have established that eukaryotic-like Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases are widespread in gram-positive bacteria. These data underline a key role of reversible Ser/Thr phosphorylation in bacterial physiology and virulence. Numerous studies have revealed how phosphorylation/dephosphorylation of Ser/Thr protein-kinases governs cell division and cell wall biosynthesis and that Ser/Thr protein kinases are responsible for distinct phenotypes, dependent on different environmental signals. In this review we discuss the current understandings of Ser/Thr protein-kinases functional processes based on structural data.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructure and Bioimaging, CNR, Via Mezzocannone, 16. I-80134, Napoli, Italy.
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47
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Correale S, Ruggiero A, Capparelli R, Pedone E, Berisio R. Structures of free and inhibited forms of theL,D-transpeptidase LdtMt1fromMycobacterium tuberculosis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1697-706. [DOI: 10.1107/s0907444913013085] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/13/2013] [Indexed: 11/10/2022]
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48
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Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3. Biochem J 2013; 454:59-68. [DOI: 10.1042/bj20130193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The recently described T6SS (type VI secretion system) acts as a needle that punctures the membrane of the target cells to deliver effector proteins. Type VI amidase effectors can be classified into four divergent families (Tae1–Tae4). These effectors are secreted into the periplasmic space of neighbouring cells via the T6SS and subsequently rupture peptidoglycan. However, the donor cells are protected from damage because of the presence of their cognate immunity proteins [Tai1 (type VI amidase immunity 1)–Tai4]. In the present paper, we describe the structure of Tae3 in complex with Tai3. The Tae3–Tai3 complex exists as a stable heterohexamer, which is composed of two Tae3 molecules and two Tai3 homodimers (Tae3–Tai34–Tae3). Tae3 shares a common NlpC/P60 fold, which consists of N-terminal and C-terminal subdomains. Structural analysis indicates that two unique loops around the catalytic cleft adopt a closed conformation, resulting in a narrow and extended groove involved in the binding of the substrate. The inhibition of Tae3 is attributed to the insertion of the Ω-loop (loop of α3–α4) of Tai3 into the catalytic groove. Furthermore, a cell viability assay confirmed that a conserved motif (Gln-Asp-Xaa) in Tai3 members may play a key role in the inhibition process. Taken together, the present study has revealed a novel inhibition mechanism and provides insights into the role played by T6SS in interspecific competition.
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Rolain T, Bernard E, Beaussart A, Degand H, Courtin P, Egge-Jacobsen W, Bron PA, Morsomme P, Kleerebezem M, Chapot-Chartier MP, Dufrêne YF, Hols P. O-glycosylation as a novel control mechanism of peptidoglycan hydrolase activity. J Biol Chem 2013; 288:22233-47. [PMID: 23760506 DOI: 10.1074/jbc.m113.470716] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acm2, the major autolysin of Lactobacillus plantarum, is a tripartite protein. Its catalytic domain is surrounded by an O-glycosylated N-terminal region rich in Ala, Ser, and Thr (AST domain), which is of low complexity and unknown function, and a C-terminal region composed of five SH3b peptidoglycan (PG) binding domains. Here, we investigate the contribution of these two accessory domains and of O-glycosylation to Acm2 functionality. We demonstrate that Acm2 is an N-acetylglucosaminidase and identify the pattern of O-glycosylation (21 mono-N-acetylglucosamines) of its AST domain. The O-glycosylation process is species-specific as Acm2 purified from Lactococcus lactis is not glycosylated. We therefore explored the functional role of O-glycosylation by purifying different truncated versions of Acm2 that were either glycosylated or non-glycosylated. We show that SH3b domains are able to bind PG and are responsible for Acm2 targeting to the septum of dividing cells, whereas the AST domain and its O-glycosylation are not involved in this process. Notably, our data reveal that the lack of O-glycosylation of the AST domain significantly increases Acm2 enzymatic activity, whereas removal of SH3b PG binding domains dramatically reduces this activity. Based on this antagonistic role, we propose a model in which access of the Acm2 catalytic domain to its substrate may be hindered by the AST domain where O-glycosylation changes its conformation and/or mediates interdomain interactions. To the best of our knowledge, this is the first time that O-glycosylation is shown to control the activity of a bacterial enzyme.
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Affiliation(s)
- Thomas Rolain
- Institut des Sciences de la Vie, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
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Squeglia F, Romano M, Ruggiero A, Vitagliano L, De Simone A, Berisio R. Carbohydrate recognition by RpfB from Mycobacterium tuberculosis unveiled by crystallographic and molecular dynamics analyses. Biophys J 2013; 104:2530-9. [PMID: 23746526 PMCID: PMC3672874 DOI: 10.1016/j.bpj.2013.04.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 12/24/2022] Open
Abstract
Resuscitation of Mtb is crucial to the etiology of Tuberculosis, because latent tuberculosis is estimated to affect one-third of the world population. The resuscitation-promoting factor RpfB is mainly responsible for Mtb resuscitation from dormancy. Given the impact of latent Tuberculosis, RpfB represents an interesting target for tuberculosis drug discovery. However, no molecular models of substrate binding and catalysis are hitherto available for this enzyme. Here, we identified key interactions involved in substrate binding to RpfB by combining x-ray diffraction studies and computational approaches. The crystal structure of RpfB catalytic domain in complex with N,N',N"-triacetyl-chitotriose, as described here, provides the first, to our knowledge, atomic representation of ligand recognition by RpfB and demonstrates that the strongest interactions are established by the N-acetylglucosamine moiety in the central region of the enzyme binding cleft. Molecular dynamics analyses provided information on the dynamic behavior of protein-substrate interactions and on the role played by the solvent in RpfB function. These data combined with sequence conservation analysis suggest that Glu-292 is the sole residue crucial for catalysis, implying that RpfB acts via the formation of an oxocarbenium ion rather than a covalent intermediate. Present data represent a solid base for the design of effective drug inhibitors of RpfB. Moreover, homology models were generated for the catalytic domains of all members of the Mtb Rpf family (RpfA-E). The analysis of these models unveiled analogies and differences among the different members of the Rpf protein family.
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Key Words
- mtb, mycobacterium tuberculosis
- rpfb, resuscitation promoting factor b
- pdb, protein data bank
- rpfbc, catalytic domain of rpfb
- nag3, n,n',n"-triacetyl-chitotriose
- nag6, hexa-n- acetylchitohexaose
- md, molecular dynamics
- rmsf, root mean-square fluctuation
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
- Department of Chemistry, University of Naples Federico II, Napoli, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
- Seconda Università di Napoli, Caserta, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, United Kingdom
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
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