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Gangakhedkar R, Jain V. Elucidating the molecular properties and anti-mycobacterial activity of cysteine peptidase domain of D29 mycobacteriophage endolysin. J Virol 2024:e0132824. [PMID: 39287392 DOI: 10.1128/jvi.01328-24] [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: 07/30/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
Emergence of antibiotic resistance in pathogenic Mycobacterium tuberculosis (Mtb) has elevated tuberculosis to a serious global threat, necessitating alternate solutions for its eradication. D29 mycobacteriophage can infect and kill several mycobacterial species including Mtb. It encodes an endolysin LysA to hydrolyze host bacteria peptidoglycan for progeny release. We previously showed that out of the two catalytically active domains of LysA [N-terminal domain (NTD) and lysozyme-like domain], NTD, when ectopically expressed in Mycobacterium smegmatis (Msm), is able to kill the bacterium nearly as efficiently as full-length LysA. Here, we dissected the functioning of NTD to develop it as a phage-derived small molecule anti-mycobacterial therapeutic. We performed a large-scale site-directed mutagenesis of the conserved residues in NTD and examined its structure, stability, and function using molecular dynamic simulations coupled with biophysical and biochemical experiments. Our data show that NTD functions as a putative cysteine peptidase with a catalytic triad composed of Cys41, His112, and Glu137, acting as nucleophile, base, and acid, respectively, and showing characteristics similar to the NlpC/P60 family of cysteine peptidases. Additionally, our peptidoglycan hydrolysis assays suggested that NTD hydrolyzes only mycobacterial peptidoglycan and does not act on Gram-positive and Gram-negative bacterial peptidoglycans. More importantly, the combined activity of exogenously added NTD and sub-lethal doses of anti-mycobacterial drugs kills Msm in vitro and exhibits disruption of pre-formed mycobacterial biofilm. We additionally show that NTD treatment increases the permeability of antibiotics in Msm, which reduces the minimum inhibitory concentration of the antibiotics. Collectively, we present NTD as a promising phage-derived therapeutic against mycobacteria.IMPORTANCEMycobacteriophages are the viruses that use mycobacteria as host for their progeny production and, in the process, kill them. Mycobacteriophages are, therefore, considered as promising alternatives to antibiotics for killing pathogenic Mycobacterium tuberculosis. The endolysin LysA produced by mycobacteriophage D29 plays an important role in host cell lysis and virion release. Our work presented here highlights the functioning of LysA's N-terminal catalytic domain (NTD) in order to develop it as phage-derived small molecule therapeutics. We show that combined treatment of exogenously added NTD and sub-lethal doses of anti-mycobacterial drugs kills M. smegmatis, shows synergism by reducing the minimum inhibitory concentration of these antibiotics, and exhibits disruption of pre-formed mature biofilm. These outcomes and our detailed biochemical and biophysical dissection of the protein further pave the way toward engineering and development of NTD as a promising therapeutic against mycobacterial infections such as tuberculosis.
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Affiliation(s)
- Rutuja Gangakhedkar
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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2
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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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3
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Flores-Valdez MA, Peterson EJR, Aceves-Sánchez MDJ, Baliga NS, Morita YS, Sparks IL, Saini DK, Yadav R, Lang R, Mata-Espinosa D, León-Contreras JC, Hernández-Pando R. Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages. Sci Rep 2024; 14:11898. [PMID: 38789479 PMCID: PMC11126594 DOI: 10.1038/s41598-024-61815-8] [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: 02/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
We have previously reported the transcriptomic and lipidomic profile of the first-generation, hygromycin-resistant (HygR) version of the BCGΔBCG1419c vaccine candidate, under biofilm conditions. We recently constructed and characterized the efficacy, safety, whole genome sequence, and proteomic profile of a second-generation version of BCGΔBCG1419c, a strain lacking the BCG1419c gene and devoid of antibiotic markers. Here, we compared the antibiotic-less BCGΔBCG1419c with BCG. We assessed their colonial and ultrastructural morphology, biofilm, c-di-GMP production in vitro, as well as their transcriptomic and lipidomic profiles, including their capacity to activate macrophages via Mincle and Myd88. Our results show that BCGΔBCG1419c colonial and ultrastructural morphology, c-di-GMP, and biofilm production differed from parental BCG, whereas we found no significant changes in its lipidomic profile either in biofilm or planktonic growth conditions. Transcriptomic profiling suggests changes in BCGΔBCG1419c cell wall and showed reduced transcription of some members of the DosR, MtrA, and ArgR regulons. Finally, induction of TNF-α, IL-6 or G-CSF by bone-marrow derived macrophages infected with either BCGΔBCG1419c or BCG required Mincle and Myd88. Our results confirm that some differences already found to occur in HygR BCGΔBCG1419c compared with BCG are maintained in the antibiotic-less version of this vaccine candidate except changes in production of PDIM. Comparison with previous characterizations conducted by OMICs show that some differences observed in BCGΔBCG1419c compared with BCG are maintained whereas others are dependent on the growth condition employed to culture them.
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Affiliation(s)
- Mario Alberto Flores-Valdez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Av. Normalistas 800, Col. Colinas de la Normal, 44270, Guadalajara, Jalisco, Mexico.
| | | | - Michel de Jesús Aceves-Sánchez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Av. Normalistas 800, Col. Colinas de la Normal, 44270, Guadalajara, Jalisco, Mexico
| | | | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 N Pleasant St, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 N Pleasant St, Amherst, MA, 01003, USA
| | - Deepak Kumar Saini
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Rahul Yadav
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Roland Lang
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Dulce Mata-Espinosa
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección 16, Tlalpan, Mexico City, Mexico
| | - Juan Carlos León-Contreras
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección 16, Tlalpan, Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección 16, Tlalpan, Mexico City, Mexico
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4
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Peterson EJR, Brooks AN, Reiss DJ, Kaur A, Do J, Pan M, Wu WJ, Morrison R, Srinivas V, Carter W, Arrieta-Ortiz ML, Ruiz RA, Bhatt A, Baliga NS. MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance. Cell Rep 2023; 42:112875. [PMID: 37542718 PMCID: PMC10480492 DOI: 10.1016/j.celrep.2023.112875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/21/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023] Open
Abstract
The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability to physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. Analysis of EGRIN 2.0 shows how modulation of the MtrAB two-component signaling system tunes Mtb growth in response to related host microenvironmental cues. Disruption of MtrAB by tunable CRISPR interference confirms that the signaling system regulates multiple peptidoglycan hydrolases, among other targets, that are important for cell division. Further, MtrA decreases the effectiveness of antibiotics by mechanisms of both intrinsic resistance and drug tolerance. Together, the model-enabled dissection of complex MtrA regulation highlights its importance as a drug target and illustrates how EGRIN 2.0 facilitates discovery and mechanistic characterization of Mtb adaptation to specific host microenvironments within the host.
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Affiliation(s)
| | | | - David J Reiss
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Amardeep Kaur
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Julie Do
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Robert Morrison
- Laboratory of Malaria, Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Warren Carter
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Rene A Ruiz
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; Departments of Biology and Microbiology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA; Lawrence Berkeley National Lab, Berkeley, CA 94720, USA.
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5
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Griffin ME, Klupt S, Espinosa J, Hang HC. Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions. Cell Chem Biol 2023; 30:436-456. [PMID: 36417916 PMCID: PMC10192474 DOI: 10.1016/j.chembiol.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The bacterial cell wall is composed of a highly crosslinked matrix of glycopeptide polymers known as peptidoglycan that dictates bacterial cell morphology and protects against environmental stresses. Regulation of peptidoglycan turnover is therefore crucial for bacterial survival and growth and is mediated by key protein complexes and enzyme families. Here, we review the prevalence, structure, and activity of NlpC/P60 peptidases, a family of peptidoglycan hydrolases that are crucial for cell wall turnover and division as well as interactions with antibiotics and different hosts. Understanding the molecular functions of NlpC/P60 peptidases should provide important insight into bacterial physiology, their interactions with different kingdoms of life, and the development of new therapeutic approaches.
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Affiliation(s)
- Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Steven Klupt
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Juliel Espinosa
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA; Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.
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6
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Ozhelvaci F, Steczkiewicz K. Identification and Classification of Papain-like Cysteine Proteinases. J Biol Chem 2023:104801. [PMID: 37164157 DOI: 10.1016/j.jbc.2023.104801] [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: 01/23/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Papain-like cysteine peptidases form a big and highly diverse superfamily of proteins involved in many important biological functions, such as protein turnover, deubiquitination, tissue remodeling, blood clotting, virulence, defense, and cell wall remodeling. High sequence and structure diversity observed within these proteins hinders their comprehensive classification as well as the identification of new representatives. Moreover, in general protein databases, many families already classified as papain-like lack details regarding their mechanism of action or biological function. Here, we use transitive remote homology searches and 3D modeling to newly classify 21 families to the papain-like cysteine peptidase superfamily. We attempt to predict their biological function, and provide structural chacterization of 89 protein clusters defined based on sequence similarity altogether spanning 106 papain-like families. Moreover, we systematically discuss observed diversity in sequences, structures, and catalytic sites. Eventually, we expand the list of human papain-related proteins by seven representatives, including dopamine receptor-interacting protein (DRIP1) as potential deubiquitinase, and centriole duplication regulating CEP76 as retaining catalytically active peptidase-like domain. The presented results not only provide structure-based rationales to already existing peptidase databases but also may inspire further experimental research focused on peptidase-related biological processes.
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Affiliation(s)
- Fatih Ozhelvaci
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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7
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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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8
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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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9
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Colombatti Olivieri MA, Fresia P, Graña M, Cuerda MX, Nagel A, Alvarado Pinedo F, Romano MI, Caimi K, Berná L, Santangelo MP. Genomic comparison of two strains of Mycobacterium avium subsp. paratuberculosis with contrasting pathogenic phenotype. Tuberculosis (Edinb) 2023; 138:102299. [PMID: 36587510 DOI: 10.1016/j.tube.2022.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
In a previous study, we evaluated the degree of virulence of Mycobacterium avium subsp. paratuberculosis (Map) strains isolated from cattle in Argentina in a murine model. This assay allowed us to differentiate between high-virulent MapARG1347 and low-virulent MapARG1543 strains. To corroborate whether the differences in virulence could be attributed to genetic differences between the strains, we performed Whole Genome Sequencing and compared the genomes and gene content between them and determined the differences related to the reference strain MapK10. We found 233 SNPs/INDELS in one or both strains relative to Map K10. The two strains share most of the variations, but we found 15 mutations present in only one of the strains. Considering NS-SNP/INDELS that produced a severe effect in the coding sequence, we focus the analysis on four predicted proteins, putatively related to virulence. Survival of MapARG1347 strain in bMDM was higher than MapARG1543 and was more resistant to acidic pH and H2O2 stresses than MapK10. The genomic differences between the two strains found in genes MAP1203 (a putative peptidoglycan hydrolase), MAP0403 (a putative serine protease) MAP1003c (a member of the PE-PPE family) and MAP4152 (a putative mycofactocin binding protein) could contribute to explain the contrasting phenotype previously observed in mice models.
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Affiliation(s)
- M A Colombatti Olivieri
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - P Fresia
- Unidad Mixta Pasteur+INIA, Institut Pasteur de Montevideo, Mataojo 2020, CP11400, Montevideo, Uruguay.
| | - M Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Mataojo 2020, CP11400, Montevideo, Uruguay.
| | - M X Cuerda
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - A Nagel
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - F Alvarado Pinedo
- Centro de Diagnóstico e Investigaciones Veterinarias (CEDIVE), Facultad de Ciencias Veterinarias - Universidad de La Plata (UNLP), Chascomus, Buenos Aires, Argentina.
| | - M I Romano
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - K Caimi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - L Berná
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400, Montevideo, Uruguay.
| | - M P Santangelo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Dr. Nicolás Repetto y De Los Reseros S/Nº B1686IGC, Hurlingham, Buenos Aires, Argentina.
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10
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Kevorkian YL, MacGilvary NJ, Giacalone D, Johnson C, Tan S. Rv0500A is a transcription factor that links Mycobacterium tuberculosis environmental response with division and impacts host colonization. Mol Microbiol 2022; 117:1048-1062. [PMID: 35167150 PMCID: PMC9382876 DOI: 10.1111/mmi.14886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 11/28/2022]
Abstract
For Mycobacterium tuberculosis (Mtb) to successfully infect a host, it must be able to adapt to changes in its microenvironment, including to variations in ionic signals such as pH and chloride (Cl- ), and link these responses to its growth. Transcriptional changes are a key mechanism for Mtb environmental adaptation, and we identify here Rv0500A as a novel transcriptional regulator that links Mtb environmental response and division processes. Global transcriptional profiling revealed that Rv0500A acts as a repressor and influences the expression of genes related to division, with the magnitude of its effect modulated by pH and Cl- . Rv0500A can directly bind the promoters of several of these target genes, and we identify key residues required for its DNA-binding ability and biological effect. Overexpression of rv0500A disrupted Mtb growth morphology, resulting in filamentation that was exacerbated by high environmental Cl- levels and acidic pH. Finally, we show that perturbation of rv0500A leads to attenuation of the ability of Mtb to colonize its host in vivo. Our work highlights the important link between Mtb environmental response and growth characteristics, and uncovers a new transcription factor involved in this critical facet of Mtb biology.
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Affiliation(s)
- Yuzo L Kevorkian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.,Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Nathan J MacGilvary
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.,Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Calvin Johnson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.,Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
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11
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Joshi H, Kandari D, Bhatnagar R. Insights into the molecular determinants involved in Mycobacterium tuberculosis persistence and their therapeutic implications. Virulence 2021; 12:2721-2749. [PMID: 34637683 PMCID: PMC8565819 DOI: 10.1080/21505594.2021.1990660] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/05/2021] [Indexed: 01/08/2023] Open
Abstract
The establishment of persistent infections and the reactivation of persistent bacteria to active bacilli are the two hurdles in effective tuberculosis treatment. Mycobacterium tuberculosis, an etiologic tuberculosis agent, adapts to numerous antibiotics and resists the host immune system causing a disease of public health concern. Extensive research has been employed to combat this disease due to its sheer ability to persist in the host system, undetected, waiting for the opportunity to declare itself. Persisters are a bacterial subpopulation that possesses transient tolerance to high doses of antibiotics. There are certain inherent mechanisms that facilitate the persister cell formation in Mycobacterium tuberculosis, some of those had been characterized in the past namely, stringent response, transcriptional regulators, energy production pathways, lipid metabolism, cell wall remodeling enzymes, phosphate metabolism, and proteasome protein degradation. This article reviews the recent advancements made in various in vitro persistence models that assist to unravel the mechanisms involved in the persister cell formation and to hunt for the possible preventive or treatment measures. To tackle the persister population the immunodominant proteins that express specifically at the latent phase of infection can be used for diagnosis to distinguish between the active and latent tuberculosis, as well as to select potential drug or vaccine candidates. In addition, we discuss the genes engaged in the persistence to get more insights into resuscitation and persister cell formation. The in-depth understanding of persistent cells of mycobacteria can certainly unravel novel ways to target the pathogen and tackle its persistence.
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Affiliation(s)
- Hemant Joshi
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Amity University of Rajasthan, Jaipur, Rajasthan, India
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12
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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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13
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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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Peptidoglycan Hydrolases RipA and Ami1 Are Critical for Replication and Persistence of Mycobacterium tuberculosis in the Host. mBio 2020; 11:mBio.03315-19. [PMID: 32127458 PMCID: PMC7064781 DOI: 10.1128/mbio.03315-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) is a major global heath burden, with 1.6 million people succumbing to the disease every year. The search for new drugs to improve the current chemotherapeutic regimen is crucial to reducing this global health burden. The cell wall polymer peptidoglycan (PG) has emerged as a very successful drug target in bacterial pathogens, as many currently used antibiotics target the synthesis of this macromolecule. However, the multitude of genes encoding PG-synthesizing and PG-modifying enzymes with apparent redundant functions has hindered the identification of novel drug targets in PG synthesis in Mycobacterium tuberculosis. Here, we demonstrate that two PG-cleaving enzymes are important for virulence of M. tuberculosis. In particular, the d,l-endopeptidase RipA represents a potentially attractive drug target, as its depletion results in the clearance of M. tuberculosis from the host and renders the bacteria hypersusceptible to rifampin, a frontline TB drug, and to several cell wall-targeting antibiotics. Synthesis and cleavage of the cell wall polymer peptidoglycan (PG) are carefully orchestrated processes and are essential for the growth and survival of bacteria. Yet, the function and importance of many enzymes that act on PG in Mycobacterium tuberculosis remain to be elucidated. We demonstrate that the activity of the N-acetylmuramyl-l-alanine amidase Ami1 is dispensable for cell division in M. tuberculosisin vitro yet contributes to the bacterium’s ability to persist during chronic infection in mice. Furthermore, the d,l-endopeptidase RipA, a predicted essential enzyme, is dispensable for the viability of M. tuberculosis but required for efficient cell division in vitro and in vivo. Depletion of RipA sensitizes M. tuberculosis to rifampin and to cell envelope-targeting antibiotics. Ami1 helps sustain residual cell division in cells lacking RipA, but the partial redundancy provided by Ami1 is not sufficient during infection, as depletion of RipA prevents M. tuberculosis from replicating in macrophages and leads to dramatic killing of the bacteria in mice. Notably, RipA is essential for persistence of M. tuberculosis in mice, suggesting that cell division is required during chronic mouse infection. Despite the multiplicity of enzymes acting on PG with redundant functions, we have identified two PG hydrolases that are important for M. tuberculosis to replicate and persist in the host.
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17
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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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18
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Abstract
How do mycobacteria divide? Cell division has been studied extensively in the model rod-shaped bacteria Escherichia coli and Bacillus subtilis, but much less is understood about cell division in mycobacteria, a genus that includes the major human pathogens M. tuberculosis and M. leprae. In general, bacterial cell division requires the concerted effort of many proteins in both space and time to elongate the cell, replicate and segregate the chromosome, and construct and destruct the septum - processes which result in the creation of two new daughter cells. Here, we describe these distinct stages of cell division in B. subtilis and follow with the current knowledge in mycobacteria. As will become apparent, there are many differences between mycobacteria and B. subtilis in terms of both the broad outline of cell division and the molecular details. So, while the fundamental challenge of spatially and temporally organizing cell division is shared between these rod-shaped bacteria, they have solved these challenges in often vastly different ways.
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19
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Baranowski C, Welsh MA, Sham LT, Eskandarian HA, Lim HC, Kieser KJ, Wagner JC, McKinney JD, Fantner GE, Ioerger TR, Walker S, Bernhardt TG, Rubin EJ, Rego EH. Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape. eLife 2018; 7:37516. [PMID: 30324906 PMCID: PMC6231781 DOI: 10.7554/elife.37516] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
In most well-studied rod-shaped bacteria, peptidoglycan is primarily crosslinked by penicillin-binding proteins (PBPs). However, in mycobacteria, crosslinks formed by L,D-transpeptidases (LDTs) are highly abundant. To elucidate the role of these unusual crosslinks, we characterized Mycobacterium smegmatis cells lacking all LDTs. We find that crosslinks generate by LDTs are required for rod shape maintenance specifically at sites of aging cell wall, a byproduct of polar elongation. Asymmetric polar growth leads to a non-uniform distribution of these two types of crosslinks in a single cell. Consequently, in the absence of LDT-mediated crosslinks, PBP-catalyzed crosslinks become more important. Because of this, Mycobacterium tuberculosis (Mtb) is more rapidly killed using a combination of drugs capable of PBP- and LDT- inhibition. Thus, knowledge about the spatial and genetic relationship between drug targets can be exploited to more effectively treat this pathogen. Most bacteria have a cell wall that protects them and maintains their shape. Many of these organisms make their cell walls from fibers of proteins and sugars, called peptidoglycan. As bacteria grow, peptidoglycan is constantly broken down and reassembled, and in many species, new units of peptidoglycan are added into the sidewall. However, in a group of bacteria called mycobacteria, which cause tuberculosis and other diseases, the units are added at the tips. The peptidoglycan layer is often a successful target for antibiotic treatments. But, drugs that treat tuberculosis do not attack this layer, partly because we know very little about the cell walls of mycobacteria. Here, Baranowski et al. used genetic manipulation and microscopy to study how mycobacteria build their cell wall. The results showed that these bacteria link peptidoglycan units together in an unusual way. In most bacteria, peptidoglycan units are connected by chemical links known as 4-3 crosslinks. This is initially the same in mycobacteria, but as the cell grows and the cell wall expands, these bonds break and so-called 3-3 crosslinks form. In genetically modified bacteria that could not form these 3-3 bonds, the cell wall became brittle and weak, and the bacteria eventually died. These findings could be important for developing new drugs that treat infections caused by mycobacteria. Baranowski et al. demonstrate that a combination of drugs blocking both 4-3 and 3-3 crosslinks is particularly effective at killing the bacterium that causes tuberculosis.
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Affiliation(s)
- Catherine Baranowski
- Department of Immunology and Infectious Disease, Harvard TH Chan School of Public Health, Boston, United States
| | - Michael A Welsh
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Lok-To Sham
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States.,Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
| | - Haig A Eskandarian
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland.,School of Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Hoong Chuin Lim
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Karen J Kieser
- Department of Immunology and Infectious Disease, Harvard TH Chan School of Public Health, Boston, United States
| | - Jeffrey C Wagner
- Department of Immunology and Infectious Disease, Harvard TH Chan School of Public Health, Boston, United States
| | - John D McKinney
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Georg E Fantner
- School of Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, Texas, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Thomas G Bernhardt
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard TH Chan School of Public Health, Boston, United States.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - E Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
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20
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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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21
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Tang VH, Stewart GA, Chang BJ. Dermatophagoides pteronyssinus lytFM encoding an NlpC/P60 endopeptidase is also present in mite-associated bacteria that express LytFM variants. FEBS Open Bio 2017; 7:1267-1280. [PMID: 28904857 PMCID: PMC5586350 DOI: 10.1002/2211-5463.12263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/05/2017] [Accepted: 06/19/2017] [Indexed: 12/25/2022] Open
Abstract
The bodies and faecal pellets of the house dust mite (HDM), Dermatophagoides pteronyssinus, are the source of many allergenic and nonallergenic proteins. One of these, the 14-kDa bacteriolytic enzyme LytFM, originally isolated from the spent HDM growth medium, may contribute to bacteriolytic activity previously detected by zymography at 14 kDa in the culture supernatants of some bacterial species isolated from surface-sterilised HDM. Based on previously reported findings of lateral gene transfer between microbes and their eukaryotic hosts, we investigated the presence of lytFM in the genomes of nine Gram-positive bacteria from surface-sterilised HDM, and the expression by these isolates of LytFM and its variants LytFM1/LytFM2. The lytFM gene was detected by PCR in the genomes of three of the isolates: Bacillus licheniformis strain 1, B. licheniformis strain 2 and Staphylococcus aureus. Expression of the variant LytFM1 was detected in culture supernatants of these bacteria by mass spectrometry (MS) and ELISA, and the bacterial LytFM proteins were shown by zymography to be able to hydrolyse peptidoglycan. Our previous reports of LytFM homologues in other mite species and their phylogenetic analysis had suggested that they originated from a common mite ancestor. The phylogenetic analysis reported herein and the detection of other D. pteronyssinus proteins by MS in the culture supernatants of the three isolates that secreted LytFM1 further support the hypothesis of lateral gene transfer to the bacterial endosymbionts from their HDM host. The complete sequence homology observed between the genes amplified from the microbes and those in their eukaryotic host indicated that the lateral gene transfer was an event that occurred recently.
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Affiliation(s)
- Vivian H Tang
- Marshall Centre for Infectious Diseases Research and Training School of Biomedical Sciences The University of Western Australia Crawley WA Australia
| | - Geoffrey A Stewart
- Marshall Centre for Infectious Diseases Research and Training School of Biomedical Sciences The University of Western Australia Crawley WA Australia
| | - Barbara J Chang
- Marshall Centre for Infectious Diseases Research and Training School of Biomedical Sciences The University of Western Australia Crawley WA Australia
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22
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Botella H, Vaubourgeix J, Lee MH, Song N, Xu W, Makinoshima H, Glickman MS, Ehrt S. Mycobacterium tuberculosis protease MarP activates a peptidoglycan hydrolase during acid stress. EMBO J 2017; 36:536-548. [PMID: 28057704 DOI: 10.15252/embj.201695028] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/28/2016] [Accepted: 12/02/2016] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can persist in the human host in a latent state for decades, in part because it has the ability to withstand numerous stresses imposed by host immunity. Prior studies have established the essentiality of the periplasmic protease MarP for Mtb to survive in acidified phagosomes and establish and maintain infection in mice. However, the proteolytic substrates of MarP that mediate these phenotypes were unknown. Here, we used biochemical methods coupled with supravital chemical probes that facilitate imaging of nascent peptidoglycan to demonstrate that during acid stress MarP cleaves the peptidoglycan hydrolase RipA, a process required for RipA's activation. Failure of RipA processing in MarP-deficient cells leads to cell elongation and chain formation, a hallmark of progeny cell separation arrest. Our results suggest that sustaining peptidoglycan hydrolysis, a process required for cell elongation, separation of progeny cells, and cell wall homeostasis in growing cells, may also be essential for Mtb's survival in acidic conditions.
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Affiliation(s)
- Helene Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Myung Hee Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Naomi Song
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Weizhen Xu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Hideki Makinoshima
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael S Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
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23
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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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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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Abstract
The complex cell envelope is a hallmark of mycobacteria and is anchored by the peptidoglycan layer, which is similar to that of Escherichia coli and a number of other bacteria but with modifications to the monomeric units and other structural complexities that are likely related to a role for the peptidoglycan in stabilizing the mycolyl-arabinogalactan-peptidoglycan complex (MAPc). In this article, we will review the genetics of several aspects of peptidoglycan biosynthesis in mycobacteria, including the production of monomeric precursors in the cytoplasm, assembly of the monomers into the mature wall, cell wall turnover, and cell division. Finally, we will touch upon the resistance of mycobacteria to β-lactam antibiotics, an important class of drugs that, until recently, have not been extensively exploited as potential antimycobacterial agents. We will also note areas of research where there are still unanswered questions.
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Bannantine JP, Lingle CK, Adam PR, Ramyar KX, McWhorter WJ, Stabel JR, Picking WD, Geisbrecht BV. NlpC/P60 domain-containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan. Protein Sci 2016; 25:840-51. [PMID: 26799947 DOI: 10.1002/pro.2884] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/14/2016] [Accepted: 01/19/2016] [Indexed: 01/22/2023]
Abstract
A subset of proteins containing NlpC/P60 domains are bacterial peptidoglycan hydrolases that cleave noncanonical peptide linkages and contribute to cell wall remodeling as well as cell separation during late stages of division. Some of these proteins have been shown to cleave peptidoglycan in Mycobacterium tuberculosis and play a role in Mycobacterium marinum virulence of zebra fish; however, there are still significant knowledge gaps concerning the molecular function of these proteins in Mycobacterium avium subspecies paratuberculosis (MAP). The MAP genome sequence encodes five NlpC/P60 domain-containing proteins. We describe atomic resolution crystal structures of two such MAP proteins, MAP_1272c and MAP_1204. These crystal structures, combined with functional assays to measure peptidoglycan cleavage activity, led to the observation that MAP_1272c does not have a functional catalytic core for peptidoglycan hydrolysis. Furthermore, the structure and sequence of MAP_1272c demonstrate that the catalytic residues normally required for hydrolysis are absent, and the protein does not bind peptidoglycan as efficiently as MAP_1204. While the NlpC/P60 catalytic triad is present in MAP_1204, changing the catalytic cysteine-155 residue to a serine significantly diminished catalytic activity, but did not affect binding to peptidoglycan. Collectively, these findings suggest a broader functional repertoire for NlpC/P60 domain-containing proteins than simply hydrolases.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa
| | - Cari K Lingle
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - Philip R Adam
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma
| | - Kasra X Ramyar
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - William J McWhorter
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - Judith R Stabel
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa
| | - William D Picking
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma
| | - Brian V Geisbrecht
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
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House dust mites possess a polymorphic, single domain putative peptidoglycan d,l endopeptidase belonging to the NlpC/P60 Superfamily. FEBS Open Bio 2015; 5:813-23. [PMID: 26566476 PMCID: PMC4600878 DOI: 10.1016/j.fob.2015.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 11/23/2022] Open
Abstract
A 14 kDa protein homologous to the γ-d-glutamyl-l-diamino acid endopeptidase members of the NlpC/P60 Superfamily has been described in Dermatophagoides pteronyssinus and Dermatophagoides farinae but it is not clear whether other species produce homologues. Bioinformatics revealed homologous genes in other Sarcopteformes mite species (Psoroptes ovis and Blomia tropicalis) but not in Tetranychus urticae and Metaseiulus occidentalis. The degrees of identity (similarity) between the D. pteronyssinus mature protein and those from D. farinae, P. ovis and B. tropicalis were 82% (96%), 77% (93%) and 61% (82%), respectively. Phylogenetic studies showed the mite proteins were monophyletic and shared a common ancestor with both actinomycetes and ascomycetes. The gene encoding the D. pteronyssinus protein was polymorphic and intronless in contrast to that reported for D. farinae. Homology studies suggest that the mite, ascomycete and actinomycete proteins are involved in the catalysis of stem peptide attached to peptidoglycan. The finding of a gene encoding a P60 family member in the D. pteronyssinus genome together with the presence of a bacterial promotor suggests an evolutionary link to one or more prokaryotic endosymbionts.
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28
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Arutyunov D, Singh U, El-Hawiet A, Seckler HDS, Nikjah S, Joe M, Bai Y, Lowary TL, Klassen JS, Evoy S, Szymanski CM. Mycobacteriophage cell binding proteins for the capture of mycobacteria. BACTERIOPHAGE 2014; 4:e960346. [PMID: 26713219 DOI: 10.4161/21597073.2014.960346] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/20/2014] [Accepted: 08/28/2014] [Indexed: 12/20/2022]
Abstract
Slow growing Mycobacteriumavium subsp. paratuberculosis (MAP) causes a deadly condition in cattle known as Johne's disease where asymptomatic carriers are the major source of disease transmission. MAP was also shown to be associated with chronic Crohn's disease in humans. Mycobacterium smegmatis is a model mycobacterium that can cause opportunistic infections in a number of human tissues and, rarely, a respiratory disease. Currently, there are no rapid, culture-independent, reliable and inexpensive tests for the diagnostics of MAP or M. smegmatis infections. Bacteriophages are viruses producing a number of proteins that effectively and specifically recognize the cell envelopes of their bacterial hosts. We demonstrate that the mycobacterial phage L5 minor tail protein Gp6 and lysin Gp10 are useful tools for the rapid capture of mycobacteria. Immobilized Gp10 was able to bind both MAP and M. smegmatis cells whereas Gp6 was M. smegmatis specific. Neither of the 2 proteins was able to capture E. coli, salmonella, campylobacter or Mycobacterium marinum cells. Gp6 was detected previously as a component of the phage particle and shows no homology to proteins with known function. Therefore, electrospray ionization mass spectrometry was used to determine whether recombinant Gp6 could bind to a number of chemically synthesized fragments of mycobacterial surface glycans. These findings demonstrate that mycobacteriophage proteins could be used as a pathogen capturing platform that can potentially improve the effectiveness of existing diagnostic methods.
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Affiliation(s)
- Denis Arutyunov
- Department of Biological Sciences; University of Alberta , Edmonton, AB Canada ; Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada
| | - Upasana Singh
- Department of Electrical and Computer Engineering; University of Alberta ; Edmonton, AB Canada
| | - Amr El-Hawiet
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Henrique Dos Santos Seckler
- Department of Biological Sciences; University of Alberta , Edmonton, AB Canada ; Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada
| | - Sanaz Nikjah
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Maju Joe
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Yu Bai
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Todd L Lowary
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - John S Klassen
- Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada ; Department of Chemistry; University of Alberta ; Edmonton, AB Canada
| | - Stephane Evoy
- Department of Electrical and Computer Engineering; University of Alberta ; Edmonton, AB Canada
| | - Christine M Szymanski
- Department of Biological Sciences; University of Alberta , Edmonton, AB Canada ; Alberta Glycomics Center; University of Alberta ; Edmonton, AB Canada
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29
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Angala SK, Belardinelli JM, Huc-Claustre E, Wheat WH, Jackson M. The cell envelope glycoconjugates of Mycobacterium tuberculosis. Crit Rev Biochem Mol Biol 2014; 49:361-99. [PMID: 24915502 PMCID: PMC4436706 DOI: 10.3109/10409238.2014.925420] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Tuberculosis (TB) remains the second most common cause of death due to a single infectious agent. The cell envelope of Mycobacterium tuberculosis (Mtb), the causative agent of the disease in humans, is a source of unique glycoconjugates and the most distinctive feature of the biology of this organism. It is the basis of much of Mtb pathogenesis and one of the major causes of its intrinsic resistance to chemotherapeutic agents. At the same time, the unique structures of Mtb cell envelope glycoconjugates, their antigenicity and essentiality for mycobacterial growth provide opportunities for drug, vaccine, diagnostic and biomarker development, as clearly illustrated by recent advances in all of these translational aspects. This review focuses on our current understanding of the structure and biogenesis of Mtb glycoconjugates with particular emphasis on one of the most intriguing and least understood aspect of the physiology of mycobacteria: the translocation of these complex macromolecules across the different layers of the cell envelope. It further reviews the rather impressive progress made in the last 10 years in the discovery and development of novel inhibitors targeting their biogenesis.
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Affiliation(s)
- Shiva Kumar Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, CO , USA
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30
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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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31
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Hernández SB, Cava F, Pucciarelli MG, García-Del Portillo F, de Pedro MA, Casadesús J. Bile-induced peptidoglycan remodelling in Salmonella enterica. Environ Microbiol 2014; 17:1081-9. [PMID: 24762004 DOI: 10.1111/1462-2920.12491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/11/2014] [Accepted: 04/20/2014] [Indexed: 02/02/2023]
Abstract
Changes in the peptidoglycan (PG) structure of Salmonella enterica are detected in the presence of a sublethal concentration of sodium deoxycholate (DOC): (i) lower proportions of Braun lipoprotein (Lpp)-bound muropeptides; (ii) reduced levels of muropeptides cross-linked by L(meso)-diaminopimelyl-D(meso)-diaminopimelic acid (L-D) peptide bridges (3-3 cross-links). Similar structural changes are found in S. enterica cultures adapted to grow in the presence of a lethal concentration of DOC, suggesting that reduced anchoring of Braun protein to PG and low occurrence of 3-3 cross-links may increase S. enterica resistance to bile. This view is further supported by additional observations: (i) A triple mutant lacking L,D-transpeptidases YbiS, ErfK, and YcfS, which does not contain Lpp anchored to PG, is hyper-resistant to bile; (ii) enhanced 3-3 cross-linking upon overexpression of YnhG transpeptidase causes a decrease in bile resistance. These observations suggest that remodelling of the cell wall may be added to the list of adaptive responses that permit survival of S. enterica in the presence of bile.
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Affiliation(s)
- Sara B Hernández
- Facultad de Biología, Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain
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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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35
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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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36
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Prokaryotic expression and functional analysis of the Mb1514 gene in Mycobacterium bovis. Mol Cell Biochem 2013; 385:43-52. [PMID: 24141863 DOI: 10.1007/s11010-013-1813-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 09/13/2013] [Indexed: 12/11/2022]
Abstract
The ability of mycobacteria to grow and invade target tissues is the key component in the process of Mycobacterium bovis infection. Therefore, analysis of the proteins responsible for cell invasion will assist clinicians in combating bovine tuberculosis. The Mb1514 gene of M. bovis encodes a hypothetical invasion protein (designated here as MbINV protein), whose function has not yet been directly identified. In this study, the Mb1514 gene from M. bovis was cloned, and expressed in E. coli. The recombinant MbINV protein (a single band of approximately 28 kDa) was purified for biological analysis. Our data demonstrated that recombinant MbINV protein significantly inhibited the viability of RAW264.7 macrophages in a dose-dependent manner (P < 0.05), and induced cell necrosis, indicating that the protein is toxic. MbINV protein infection significantly enhanced the mRNA expression levels of TNF-α, IL-1β, and NOS2 (P < 0.01), suggesting that MbINV protein may be one of the virulence factors which directly interact with macrophages and modulate the host immune response to M. bovis. An invasion inhibition assay showed that MbINV-inhibited M. bovis invasion of RAW264.7 cells in a concentration-dependant manner, demonstrating it is an invasion protein.
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37
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Prigozhin DM, Mavrici D, Huizar JP, Vansell HJ, Alber T. Structural and biochemical analyses of Mycobacterium tuberculosis N-acetylmuramyl-L-alanine amidase Rv3717 point to a role in peptidoglycan fragment recycling. J Biol Chem 2013; 288:31549-55. [PMID: 24019530 DOI: 10.1074/jbc.m113.510792] [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: 02/05/2023] Open
Abstract
Peptidoglycan hydrolases are key enzymes in bacterial cell wall homeostasis. Understanding the substrate specificity and biochemical activity of peptidoglycan hydrolases in Mycobacterium tuberculosis is of special interest as it can aid in the development of new cell wall targeting therapeutics. In this study, we report biochemical and structural characterization of the mycobacterial N-acetylmuramyl-L-alanine amidase, Rv3717. The crystal structure of Rv3717 in complex with a dipeptide product shows that, compared with previously characterized peptidoglycan amidases, the enzyme contains an extra disulfide-bonded β-hairpin adjacent to the active site. The structure of two intermediates in assembly reveal that Zn(2+) binding rearranges active site residues, and disulfide formation promotes folding of the β-hairpin. Although Zn(2+) is required for hydrolysis of muramyl dipeptide, disulfide oxidation is not required for activity on this substrate. The orientation of the product in the active site suggests a role for a conserved glutamate (Glu-200) in catalysis; mutation of this residue abolishes activity. The product binds at the head of a closed tunnel, and the enzyme showed no activity on polymerized peptidoglycan. These results point to a potential role for Rv3717 in peptidoglycan fragment recycling.
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Affiliation(s)
- Daniil M Prigozhin
- From the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
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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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Chao MC, Kieser KJ, Minami S, Mavrici D, Aldridge BB, Fortune SM, Alber T, Rubin EJ. Protein complexes and proteolytic activation of the cell wall hydrolase RipA regulate septal resolution in mycobacteria. PLoS Pathog 2013; 9:e1003197. [PMID: 23468634 PMCID: PMC3585148 DOI: 10.1371/journal.ppat.1003197] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 01/03/2013] [Indexed: 01/08/2023] Open
Abstract
Peptidoglycan hydrolases are a double-edged sword. They are required for normal cell division, but when dysregulated can become autolysins lethal to bacteria. How bacteria ensure that peptidoglycan hydrolases function only in the correct spatial and temporal context remains largely unknown. Here, we demonstrate that dysregulation converts the essential mycobacterial peptidoglycan hydrolase RipA to an autolysin that compromises cellular structural integrity. We find that mycobacteria control RipA activity through two interconnected levels of regulation in vivo—protein interactions coordinate PG hydrolysis, while proteolysis is necessary for RipA enzymatic activity. Dysregulation of RipA protein complexes by treatment with a peptidoglycan synthase inhibitor leads to excessive RipA activity and impairment of correct morphology. Furthermore, expression of a RipA dominant negative mutant or of differentially processed RipA homologues reveals that RipA is produced as a zymogen, requiring proteolytic processing for activity. The amount of RipA processing differs between fast-growing and slow-growing mycobacteria and correlates with the requirement for peptidoglycan hydrolase activity in these species. Together, the complex picture of RipA regulation is a part of a growing paradigm for careful control of cell wall hydrolysis by bacteria during growth, and may represent a novel target for chemotherapy development. Peptidoglycan (PG) is a major component of the bacterial cell wall, which forms a flexible, but strong mesh around the cell to oppose osmotic pressure and prevent lysis. PG is also dynamically modified, continually being disassembled and polymerized as the cell elongates and divides. It remains poorly understood how cells can titrate enough hydrolysis of the PG to allow bacterial growth without leading to excessive digestion and disruption of cellular integrity. In our work, we have identified two methods by which a critical PG hydrolase, RipA, is carefully controlled in Mycobacterium tuberculosis—protein interactions help prevent lethal RipA dysregulation, while proteolytic cleavage is used as a second step to activate the enzyme in order to separate daughter cells. Our work elaborates multiple post-transcriptional mechanisms for preventing PG hydrolases from becoming lethal autolysins. These different levels of regulation may serve as a more general paradigm for PG remodeling in other bacterial species.
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Affiliation(s)
- Michael C. Chao
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Karen J. Kieser
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Shoko Minami
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Daniela Mavrici
- Department of Molecular and Cell Biology, QB3 Institute, University of California-Berkeley, Berkeley, California, United States of America
| | - Bree B. Aldridge
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Tom Alber
- Department of Molecular and Cell Biology, QB3 Institute, University of California-Berkeley, Berkeley, California, United States of America
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Use of a mariner-based transposon mutagenesis system to isolate Clostridium perfringens mutants deficient in gliding motility. J Bacteriol 2012. [PMID: 23204460 DOI: 10.1128/jb.01288-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium perfringens is an anaerobic Gram-positive pathogen that causes many human and animal diseases, including food poisoning and gas gangrene. C. perfringens lacks flagella but possesses type IV pili (TFP). We have previously shown that C. perfringens can glide across an agar surface in long filaments composed of individual bacteria attached end to end and that two TFP-associated proteins, PilT and PilC, are needed for this. To discover additional gene products that play a role in gliding, we developed a plasmid-based mariner transposon mutagenesis system that works effectively in C. perfringens. More than 10,000 clones were screened for mutants that lacked the ability to move away from the edge of a colony. Twenty-four mutants (0.24%) were identified that fit the criteria. The genes containing insertions that affected gliding motility fell into nine different categories. One gene, CPE0278, which encodes a homolog of the SagA cell wall-dependent endopeptidase, acquired distinct transposon insertions in two independent mutants. sagA mutants were unable to form filaments due to a complete lack of end-to-end connections essential for gliding motility. Complementation of the sagA mutants with a wild-type copy of the gene restored gliding motility. We constructed an in-frame deletion mutation in the sagA gene and found that this mutant had a phenotype similar to those of the transposon mutants. We hypothesize that the sagA mutant strains are unable to form the molecular complexes which are needed to keep the cells in an end-to-end orientation, leading to separation of daughter cells and the inability to carry out gliding motility.
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Yang DC, Tan K, Joachimiak A, Bernhardt TG. A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division. Mol Microbiol 2012; 85:768-81. [PMID: 22715947 DOI: 10.1111/j.1365-2958.2012.08138.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Remodelling of the peptidoglycan (PG) exoskeleton is intimately tied to the growth and division of bacteria. Enzymes that hydrolyse PG are critical for these processes, but their activities must be tightly regulated to prevent the generation of lethal breaches in the PG matrix. Despite their importance, the mechanisms regulating PG hydrolase activity have remained elusive. Here we investigate the control of cell division hydrolases called amidases (AmiA, AmiB and AmiC) required for Escherichia coli cell division. Poorly regulated amiB mutants were isolated encoding lytic AmiB variants with elevated basal PG hydrolase activities in vitro. The structure of an AmiB orthologue was also solved, revealing that the active site of AmiB is occluded by a conserved alpha helix. Strikingly, most of the amino acid substitutions in the lytic AmiB variants mapped to this domain and are predicted to disrupt its interaction with the active site. Our results therefore support a model in which cell separation is stimulated by the reversible relief of amidase autoinhibition governed by conserved subcomplexes within the cytokinetic ring. Analogous conformational control mechanisms are likely to be part of a general strategy used to control PG hydrolases present within multienzyme PG-remodelling machines.
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Affiliation(s)
- Desirée C Yang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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Zhang H, Gao ZQ, Su XD, Dong YH. Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa. FEBS Lett 2012; 586:3193-9. [DOI: 10.1016/j.febslet.2012.06.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 05/30/2012] [Accepted: 06/20/2012] [Indexed: 11/27/2022]
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Ding J, Wang W, Feng H, Zhang Y, Wang DC. Structural insights into the Pseudomonas aeruginosa type VI virulence effector Tse1 bacteriolysis and self-protection mechanisms. J Biol Chem 2012; 287:26911-20. [PMID: 22700987 DOI: 10.1074/jbc.m112.368043] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, it was identified that Pseudomonas aeruginosa competes with rival cells to gain a growth advantage using a novel mechanism that includes two interrelated processes as follows: employing type VI secretion system (T6SS) virulence effectors to lyse other bacteria, and at the same time producing specialized immunity proteins to inactivate their cognate effectors for self-protection against mutual toxicity. To explore the structural basis of these processes in the context of functional performance, the crystal structures of the T6SS virulence effector Tse1 and its complex with the corresponding immunity protein Tsi1 were determined, which, in association with mutagenesis and Biacore analyses, provided a molecular platform to resolve the relevant structural questions. The results indicated that Tse1 features a papain-like structure and conserved catalytic site with distinct substrate-binding sites to hydrolyze its murein peptide substrate. The immunity protein Tsi1 interacts with Tse1 via a unique interactive recognition mode to shield Tse1 from its physiological substrate. These findings reveal both the structural mechanisms for bacteriolysis and the self-protection against the T6SS effector Tse1. These mechanisms are significant not only by contributing to a novel understanding of niche competition among bacteria but also in providing a structural basis for antibacterial agent design and the development of new strategies to fight P. aeruginosa.
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Affiliation(s)
- Jingjin Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 10010, China
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Chou S, Bui NK, Russell AB, Lexa KW, Gardiner TE, LeRoux M, Vollmer W, Mougous JD. Structure of a peptidoglycan amidase effector targeted to Gram-negative bacteria by the type VI secretion system. Cell Rep 2012; 1:656-64. [PMID: 22813741 DOI: 10.1016/j.celrep.2012.05.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 05/11/2012] [Accepted: 05/21/2012] [Indexed: 12/21/2022] Open
Abstract
The target range of a bacterial secretion system can be defined by effector substrate specificity or by the efficacy of effector delivery. Here, we report the crystal structure of Tse1, a type VI secretion (T6S) bacteriolytic amidase effector from Pseudomonas aeruginosa. Consistent with its role as a toxin, Tse1 has a more accessible active site than related housekeeping enzymes. The activity of Tse1 against isolated peptidoglycan shows its capacity to act broadly against Gram-negative bacteria and even certain Gram-positive species. Studies with intact cells indicate that Gram-positive bacteria can remain vulnerable to Tse1 despite cell wall modifications. However, interbacterial competition studies demonstrate that Tse1-dependent lysis is restricted to Gram-negative targets. We propose that the previously observed specificity for T6S against Gram-negative bacteria is a consequence of high local effector concentration achieved by T6S-dependent targeting to its site of action rather than inherent effector substrate specificity.
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Affiliation(s)
- Seemay Chou
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
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Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PLoS One 2012; 7:e34052. [PMID: 22470512 PMCID: PMC3314691 DOI: 10.1371/journal.pone.0034052] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/27/2012] [Indexed: 11/28/2022] Open
Abstract
The mycobacterial cell wall presents significant challenges to mycobacteriophages – viruses that infect mycobacterial hosts – because of its unusual structure containing a mycolic acid-rich mycobacterial outer membrane attached to an arabinogalactan layer that is in turn linked to the peptidoglycan. Although little is known about how mycobacteriophages circumvent these barriers during the process of infection, destroying it for lysis at the end of their lytic cycles requires an unusual set of functions. These include Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, chaperones required for endolysin delivery to peptidoglycan, holins that regulate lysis timing, and the endolysins (Lysin As) that hydrolyze peptidoglycan. Because mycobacterial peptidoglycan contains atypical features including 3→3 interpeptide linkages, it is not surprising that the mycobacteriophage endolysins also have non-canonical features. We present here a bioinformatic dissection of these lysins and show that they are highly diverse and extensively modular, with an impressive number of domain organizations. Most contain three domains with a novel N-terminal predicted peptidase, a centrally located amidase, muramidase, or transglycosylase, and a C-terminal putative cell wall binding domain.
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