1
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Franklin A, Salgueiro VC, Layton AJ, Sullivan R, Mize T, Vázquez-Iniesta L, Benedict ST, Gurcha SS, Anso I, Besra GS, Banzhaf M, Lovering AL, Williams SJ, Guerin ME, Scott NE, Prados-Rosales R, Lowe EC, Moynihan PJ. The mycobacterial glycoside hydrolase LamH enables capsular arabinomannan release and stimulates growth. Nat Commun 2024; 15:5740. [PMID: 38982040 PMCID: PMC11233589 DOI: 10.1038/s41467-024-50051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
Mycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important are lipoarabinomannan (LAM) and its precursor, lipomannan (LM), which are trafficked from the bacterium to the host via unknown mechanisms. Arabinomannan is thought to be a capsular derivative of these molecules, lacking a lipid anchor. However, the mechanism by which this material is generated has yet to be elucidated. Here, we describe the identification of a glycoside hydrolase family 76 enzyme that we term LamH (Rv0365c in Mycobacterium tuberculosis) which specifically cleaves α-1,6-mannoside linkages within LM and LAM, driving its export to the capsule releasing its phosphatidyl-myo-inositol mannoside lipid anchor. Unexpectedly, we found that the catalytic activity of this enzyme is important for efficient exit from stationary phase cultures, potentially implicating arabinomannan as a signal for growth phase transition. Finally, we demonstrate that LamH is important for M. tuberculosis survival in macrophages.
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Affiliation(s)
- Aaron Franklin
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Vivian C Salgueiro
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | | | - Rudi Sullivan
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Todd Mize
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Lucía Vázquez-Iniesta
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | | | | | - Itxaso Anso
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona, Spanish National Research Council, Barcelona Science Park, c/Baldiri Reixac 10-12, Tower R, 08028, Barcelona, Catalonia, Spain
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Rafael Prados-Rosales
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | - Elisabeth C Lowe
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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2
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Kelly SD, Duong NH, Nothof JT, Lowary TL, Whitfield C. Three-component systems represent a common pathway for extracytoplasmic addition of pentofuranose sugars into bacterial glycans. Proc Natl Acad Sci U S A 2024; 121:e2402554121. [PMID: 38748580 PMCID: PMC11127046 DOI: 10.1073/pnas.2402554121] [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: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 05/27/2024] Open
Abstract
Cell surface glycans are major drivers of antigenic diversity in bacteria. The biochemistry and molecular biology underpinning their synthesis are important in understanding host-pathogen interactions and for vaccine development with emerging chemoenzymatic and glycoengineering approaches. Structural diversity in glycostructures arises from the action of glycosyltransferases (GTs) that use an immense catalog of activated sugar donors to build the repeating unit and modifying enzymes that add further heterogeneity. Classical Leloir GTs incorporate α- or β-linked sugars by inverting or retaining mechanisms, depending on the nucleotide sugar donor. In contrast, the mechanism of known ribofuranosyltransferases is confined to β-linkages, so the existence of α-linked ribofuranose in some glycans dictates an alternative strategy. Here, we use Citrobacter youngae O1 and O2 lipopolysaccharide O antigens as prototypes to describe a widespread, versatile pathway for incorporating side-chain α-linked pentofuranoses by extracytoplasmic postpolymerization glycosylation. The pathway requires a polyprenyl phosphoribose synthase to generate a lipid-linked donor, a MATE-family flippase to transport the donor to the periplasm, and a GT-C type GT (founding the GT136 family) that performs the final glycosylation reaction. The characterized system shares similarities, but also fundamental differences, with both cell wall arabinan biosynthesis in mycobacteria, and periplasmic glucosylation of O antigens first discovered in Salmonella and Shigella. The participation of auxiliary epimerases allows the diversification of incorporated pentofuranoses. The results offer insight into a broad concept in microbial glycobiology and provide prototype systems and bioinformatic guides that facilitate discovery of further examples from diverse species, some in currently unknown glycans.
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Affiliation(s)
- Steven D. Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | - Nam Ha Duong
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Nangang, Taipei11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Jeremy T. Nothof
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
| | - Todd L. Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
- Institute of Biochemical Sciences, National Taiwan University, Taipei10617, Taiwan
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
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3
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De K, Belardinelli JM, Pandurangan AP, Ehianeta T, Lian E, Palčeková Z, Lam H, Gonzalez-Juarrero M, Bryant JM, Blundell TL, Parkhill J, Floto RA, Lowary TL, Wheat WH, Jackson M. Lipoarabinomannan modification as a source of phenotypic heterogeneity in host-adapted Mycobacterium abscessus isolates. Proc Natl Acad Sci U S A 2024; 121:e2403206121. [PMID: 38630725 PMCID: PMC11046677 DOI: 10.1073/pnas.2403206121] [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: 02/20/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Mycobacterium abscessus is increasingly recognized as the causative agent of chronic pulmonary infections in humans. One of the genes found to be under strong evolutionary pressure during adaptation of M. abscessus to the human lung is embC which encodes an arabinosyltransferase required for the biosynthesis of the cell envelope lipoglycan, lipoarabinomannan (LAM). To assess the impact of patient-derived embC mutations on the physiology and virulence of M. abscessus, mutations were introduced in the isogenic background of M. abscessus ATCC 19977 and the resulting strains probed for phenotypic changes in a variety of in vitro and host cell-based assays relevant to infection. We show that patient-derived mutational variations in EmbC result in an unexpectedly large number of changes in the physiology of M. abscessus, and its interactions with innate immune cells. Not only did the mutants produce previously unknown forms of LAM with a truncated arabinan domain and 3-linked oligomannoside chains, they also displayed significantly altered cording, sliding motility, and biofilm-forming capacities. The mutants further differed from wild-type M. abscessus in their ability to replicate and induce inflammatory responses in human monocyte-derived macrophages and epithelial cells. The fact that different embC mutations were associated with distinct physiologic and pathogenic outcomes indicates that structural alterations in LAM caused by nonsynonymous nucleotide polymorphisms in embC may be a rapid, one-step, way for M. abscessus to generate broad-spectrum diversity beneficial to survival within the heterogeneous and constantly evolving environment of the infected human airway.
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Affiliation(s)
- Kavita De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Juan M. Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Arun Prasad Pandurangan
- Victor Phillip Dahdaleh Heart and Lung Research Institute, Biomedical Campus, Trumpington, CambridgeCB2 OBB, United Kingdom
| | - Teddy Ehianeta
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
| | - Elena Lian
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Zuzana Palčeková
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Ha Lam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Josephine M. Bryant
- Parasites and Microbes Programme, Wellcome Sanger Institute, HinxtonCB10 1SA, United Kingdom
| | - Tom L. Blundell
- Victor Phillip Dahdaleh Heart and Lung Research Institute, Biomedical Campus, Trumpington, CambridgeCB2 OBB, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - R. Andres Floto
- Victor Phillip Dahdaleh Heart and Lung Research Institute, Biomedical Campus, Trumpington, CambridgeCB2 OBB, United Kingdom
- Molecular Immunity Unit, Department of Medicine, Medical Research Council-Laboratory of Molecular Biology, University of Cambridge, Trumpington, CambridgeCB2 0QH, United Kingdom
- University of Cambridge Centre for AI in Medicine, Cambridge CB3 0WA, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, CambridgeCB2 0AY, United Kingdom
| | - Todd L. Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei106, Taiwan
| | - William H. Wheat
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO80523-1682
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4
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Primo LMDG, Roque-Borda CA, Carnero Canales CS, Caruso IP, de Lourenço IO, Colturato VMM, Sábio RM, de Melo FA, Vicente EF, Chorilli M, da Silva Barud H, Barbugli PA, Franzyk H, Hansen PR, Pavan FR. Antimicrobial peptides grafted onto the surface of N-acetylcysteine-chitosan nanoparticles can revitalize drugs against clinical isolates of Mycobacterium tuberculosis. Carbohydr Polym 2024; 323:121449. [PMID: 37940311 DOI: 10.1016/j.carbpol.2023.121449] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023]
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (MTB) and is the leading cause of death from infectious diseases in the World. The search for new antituberculosis drugs is a high priority, since several drug-resistant TB-strains have emerged. Many nanotechnology strategies are being explored to repurpose or revive drugs. An interesting approach is to graft antimicrobial peptides (AMPs) to antibiotic-loaded nanoparticles. The objective of the present work was to determine the anti-MTB activity of rifampicin-loaded N-acetylcysteine-chitosan-based nanoparticles (NPs), conjugated with the AMP Ctx(Ile21)-Ha; against clinical isolates (multi- and extensively-drug resistant) and the H37Rv strain. The modified chitosan and drug-loaded NPs were characterized with respect to their physicochemical stability and their antimycobacterial profile, which showed potent inhibition (MIC values <0.977 μg/mL) by the latter. Furthermore, their accumulation within macrophages and cytotoxicity were determined. To understand the possible mechanisms of action, an in silico study of the peptide against MTB membrane receptors was performed. The results presented herein demonstrate that antibiotic-loaded NPs grafted with an AMP can be a powerful tool for revitalizing drugs against multidrug-resistant M. tuberculosis strains, by launching multiple attacks against MTB. This approach could potentially serve as a novel treatment strategy for various long-term diseases requiring extended treatment periods.
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Affiliation(s)
- Laura Maria Duran Gleriani Primo
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Cesar Augusto Roque-Borda
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Christian Shleider Carnero Canales
- Vicerrectorado de Investigación, Facultad de Ciencias Farmacéuticas bioquímicas y biotecnológicas, Universidad Católica de Santa María, Arequipa, Peru
| | - Icaro Putinhon Caruso
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000 São José do Rio Preto, São Paulo, Brazil
| | - Isabella Ottenio de Lourenço
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000 São José do Rio Preto, São Paulo, Brazil
| | - Vitória Maria Medalha Colturato
- Department of Biotechnology, Laboratory of Polymers and Biomaterials, University of Araraquara (UNIARA), Araraquara, São Paulo, Brazil
| | - Rafael Miguel Sábio
- São Paulo State University (UNESP), Department of Drug and Medicines, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Fernando Alves de Melo
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000 São José do Rio Preto, São Paulo, Brazil
| | - Eduardo Festozo Vicente
- School of Sciences and Engineering, São Paulo State University (UNESP), Tupã, São Paulo, Brazil
| | - Marlus Chorilli
- São Paulo State University (UNESP), Department of Drug and Medicines, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Hernane da Silva Barud
- Department of Biotechnology, Laboratory of Polymers and Biomaterials, University of Araraquara (UNIARA), Araraquara, São Paulo, Brazil
| | - Paula Aboud Barbugli
- Department of Dental Materials and Prosthodontics, School of Dentistry, Sao Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil.
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5
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Krishnan A, Khan FI, Sukumar S, Khan MKA. Identification of potential molecular targets and repurposed drugs for tuberculosis using network-based screening approach, molecular docking, and simulation. J Biomol Struct Dyn 2023:1-19. [PMID: 37948198 DOI: 10.1080/07391102.2023.2279699] [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: 08/22/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023]
Abstract
The spread of drug-resistant strains of tuberculosis has hampered efforts to control the disease worldwide. The Mycobacterium tuberculosis cell wall envelope is dynamic, with complex features that protect it from the host immunological response. As a result, the bacterial cell wall components represent a potential target for drug discovery. Protein-protein interaction networks (PPIN) are critical for understanding disease conditions and identifying precise therapeutic targets. We used a rational theoretical approach by constructing a PPIN with the proteins involved in cell wall biosynthesis. The PPIN was constructed through the STRING database and embB was identified as a key protein by using four topological measures, betweenness, closeness, degree, and eigenvector, in the CytoNCA tool in Cytoscape. The 'Drug repurposing' approach was employed to find suitable inhibitors against embB. We used the Schrödinger suites for molecular docking, molecular dynamics simulation, and binding free energy calculations to validate the binding of protein with the ligand. FDA-approved drugs from the ZINC database and DrugBank were screened against embB (PDB ID: 7BVF) using high-throughput virtual screening, standard precision, and extra precision docking. The drugs were screened based on the XP docking score of the standard drug ethambutol. Accordingly, from the top five hits, azilsartan and dihydroergotamine were selected based on the binding free energy values and were further subjected to Molecular Dynamics Simulation studies for 100 ns. Our study confirms that Azilsartan and Dihydroergotamine form stable complexes with embB and can be used as potential lead molecules based on further in vitro and in vivo experimental validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arunika Krishnan
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Faez Iqbal Khan
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Sudarkodi Sukumar
- Lakshmikumaran and Sridharan Attorneys, Wallace Garden, Nungambakkam, Chennai, India
| | - Md Khurshid Alam Khan
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
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6
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Franklin A, Layton AJ, Mize T, Salgueiro VC, Sullivan R, Benedict ST, Gurcha SS, Anso I, Besra GS, Banzhaf M, Lovering AL, Williams SJ, Guerin ME, Scott NE, Prados-Rosales R, Lowe EC, Moynihan PJ. The mycobacterial glycoside hydrolase LamH enables capsular arabinomannan release and stimulates growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563968. [PMID: 37961452 PMCID: PMC10634837 DOI: 10.1101/2023.10.26.563968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Mycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important amongst these are lipoarabinomannan (LAM) and its precursor, lipomannan (LM), which are both trafficked out of the bacterium to the host via unknown mechanisms. An important class of exported LM/LAM is the capsular derivative of these molecules which is devoid of its lipid anchor. Here, we describe the identification of a glycoside hydrolase family 76 enzyme that we term LamH which specifically cleaves α-1,6-mannoside linkages within LM and LAM, driving its export to the capsule releasing its phosphatidyl-myo-inositol mannoside lipid anchor. Unexpectedly, we found that the catalytic activity of this enzyme is important for efficient exit from stationary phase cultures where arabinomannan acts as a signal for growth phase transition. Finally, we demonstrate that LamH is important for Mycobacterium tuberculosis survival in macrophages. These data provide a new framework for understanding the biological role of LAM in mycobacteria.
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Affiliation(s)
- Aaron Franklin
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Abigail J. Layton
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Todd Mize
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Vivian C. Salgueiro
- Department of Preventive Medicine, Public Health and Microbiology. School of Medicine. Universidad Autonoma de Madrid, 28029 Madrid, Spain
| | - Rudi Sullivan
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Samuel T. Benedict
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Sudagar S. Gurcha
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Itxaso Anso
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Andrew L. Lovering
- School of Biosciences, University of Birmingham, Birmingham, U.K., B15 2TT
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marcelo E. Guerin
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Rafael Prados-Rosales
- Department of Preventive Medicine, Public Health and Microbiology. School of Medicine. Universidad Autonoma de Madrid, 28029 Madrid, Spain
| | - Elisabeth C. Lowe
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, U.K., NE2 4HH
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7
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Mahajan PS, Girigosavi P, Chauware V, Mokashi ND, Nema V. Issues with the current drugs for Mycobacterium tuberculosis cure and potential of cell envelope proteins for new drug discovery. Indian J Tuberc 2023; 70:286-296. [PMID: 37562902 DOI: 10.1016/j.ijtb.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 08/12/2023]
Abstract
Mycobacterium tuberculosis has been the smartest pathogen ever and a challenge to drug development. Its replicative machinery is unique, so targeting the same for killing the pathogen remains a challenge. Our body typically throws out the drugs before they see the bacterium multiply. The pathogen has also learned how to remove drugs from its internal chambers and not allow them to reach their targets. Another strategy for Mtb is the mutation of the targets to reject drug binding and bypass the drug's inhibitory actions. In this review, we tried to explore possible targets on the outer side of the bacterial cell. We have also explored if those targets are promising enough and if there are drugs or inhibitors available. We also discuss the essential proteins and why they remain to be a good target. We concluded that the cell envelope has got a few proteins that can be targeted in isolation or maybe along with other machinery while making the outer environment more conducive for penetration of current drugs or newly proposed drugs.
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Affiliation(s)
- Pratik S Mahajan
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Payal Girigosavi
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Vijay Chauware
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Nitin D Mokashi
- Postgraduate Institute, Yashwantrao Chavan Memorial Hospital, Pune, 411018, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India.
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8
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Patel O, Brammananth R, Dai W, Panjikar S, Coppel RL, Lucet IS, Crellin PK. Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis. Acta Crystallogr D Struct Biol 2022; 78:494-508. [PMID: 35362472 PMCID: PMC8972800 DOI: 10.1107/s2059798322001772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
The bacterial genus Mycobacterium includes important pathogens, most notably M. tuberculosis, which infects one-quarter of the entire human population, resulting in around 1.4 million deaths from tuberculosis each year. Mycobacteria, and the closely related corynebacteria, synthesize a class of abundant glycolipids, the phosphatidyl-myo-inositol mannosides (PIMs). PIMs serve as membrane anchors for hyperglycosylated species, lipomannan (LM) and lipoarabinomannan (LAM), which are surface-exposed and modulate the host immune response. Previously, in studies using the model species Corynebacterium glutamicum, NCgl2760 was identified as a novel membrane protein that is required for the synthesis of full-length LM and LAM. Here, the first crystal structure of its ortholog in Mycobacterium smegmatis, MSMEG_0317, is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities and one α-helix extending away from the β-barrel core, resembling a `cone with a flake' arrangement. Through xenon derivatization and structural comparison with AlphaFold2-derived predictions of the M. tuberculosis homolog Rv0227c, structural elements were identified that may undergo conformational changes to switch from `closed' to `open' conformations, allowing cavity access. An AlphaFold2-derived NCgl2760 model predicted a smaller β-barrel core with an enclosed central cavity, suggesting that all three proteins, which were collectively termed LmcA, may have a common mechanism of ligand binding through these cavities. These findings provide new structural insights into the biosynthetic pathway for a family of surface lipoglycans with important roles in mycobacterial pathogenesis.
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Affiliation(s)
- Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Rajini Brammananth
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Weiwen Dai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Victoria 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Victoria 3800, Australia
| | - Ross L. Coppel
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Isabelle S. Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Paul K. Crellin
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria 3800, Australia
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9
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Yalcin-Ozkat G, Ersan RH, Ulger M, Ulger ST, Burmaoglu S, Yildiz I, Algul O. Design, synthesis, and computational studies of benzimidazole derivatives as new antitubercular agents. J Biomol Struct Dyn 2022; 41:2667-2686. [PMID: 35132948 DOI: 10.1080/07391102.2022.2036241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The increase in the drug-resistant strains of Mycobacterium tuberculosis has led researchers to new drug targets. The development of new compounds that have effective inhibitory properties with the selective vital structure of Mycobacterium tuberculosis is required in new scientific approaches. The most important of these approaches is the development of inhibitor molecules for Mycobacterium cell wall targets. In this study, first of all, the antitubercular activity of 23 benzimidazole derivatives was experimentally determined. And then molecular docking studies were carried out with 4 different targets: Arabinosyltransferase C (EmbC), Filamentous Temperature Sensitive Mutant Z (FtsZ), Protein Tyrosine Phosphatase B (PtpB), and Decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). It has been determined that benzimidazole derivatives show activity through the DprE1 enzyme. It is known that DprE1, which has an important role in the synthesis of the cell envelope from Arabinogalactan, is also effective in the formation of drug resistance. Due to this feature, the DprE1 enzyme has become an important target for drug development studies. Also, it was chosen as a target for this study. This study aims to identify molecules that inhibit DprE1 for the development of more potent and selective antitubercular drugs. For this purpose, molecular docking studies by AutoDock Vina, and CDOCKER and molecular dynamics (MD) simulations and in silico ADME/Tox analysis were implemented for 23 molecules. The molecules exhibited binding affinity values of less than -8.0 kcal/mol. After determining the compound's anti-TB activities by a screening test, the best-docked results were detected using compounds 20, 21, and 30. It was found that 21, was the best molecule with its binding affinity value, which was supported by MD simulations and in silico ADME modeling results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gozde Yalcin-Ozkat
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Magdeburg, Germany
- Faculty of Engineering, Bioengineering Department, Recep Tayyip Erdogan University, Rize, Turkey
| | - Ronak H. Ersan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
- Department of Medical Laboratory, Cihan University, Duhok, Iraq
| | - Mahmut Ulger
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Mersin University, Mersin, Turkey
| | - Seda T. Ulger
- Department of Medical Microbiology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Serdar Burmaoglu
- Department of Chemistry, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Ilkay Yildiz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Oztekin Algul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
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10
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Tan YZ, Mancia F. Structure and Function of Mycobacterial Arabinofuranosyltransferases. Subcell Biochem 2022; 99:379-391. [PMID: 36151383 DOI: 10.1007/978-3-031-00793-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The mycobacteria genus is responsible for numerous infectious diseases that have afflicted the human race since antiquity-tuberculosis and leprosy in particular. An important contributor to their evolutionary success is their unique cell envelope, which constitutes a quasi-impermeable barrier, protecting the microorganism from external threats, antibiotics included. The arabinofuranosyltransferases are a family of enzymes, unique to the Actinobacteria family that mycobacteria genus belongs to, that are critical to building of this cell envelope. In this chapter, we will analyze available structures of members of the mycobacterial arabinofuranosyltransferase, clarify their function, as well as explore the common themes present amongst this family of enzymes, as revealed by recent research.
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Affiliation(s)
- Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Disease Intervention Technology Laboratory (DITL), Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, NY, USA
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11
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Batt SM, Burke CE, Moorey AR, Besra GS. Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall. Cell Surf 2020; 6:100044. [PMID: 32995684 PMCID: PMC7502851 DOI: 10.1016/j.tcsw.2020.100044] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is the global leading cause of mortality from an infectious agent. Part of this success relies on the unique cell wall, which consists of a thick waxy coat with tightly packed layers of complexed sugars, lipids and peptides. This coat provides a protective hydrophobic barrier to antibiotics and the host's defences, while enabling the bacterium to spread efficiently through sputum to infect and survive within the macrophages of new hosts. However, part of this success comes at a cost, with many of the current first- and second-line drugs targeting the enzymes involved in cell wall biosynthesis. The flip side of this coin is that resistance to these drugs develops either in the target enzymes or the activation pathways of the drugs, paving the way for new resistant clinical strains. This review provides a synopsis of the structure and synthesis of the cell wall and the major current drugs and targets, along with any mechanisms of resistance.
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Affiliation(s)
- Sarah M. Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher E. Burke
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alice R. Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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12
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Tan YZ, Rodrigues J, Keener JE, Zheng RB, Brunton R, Kloss B, Giacometti SI, Rosário AL, Zhang L, Niederweis M, Clarke OB, Lowary TL, Marty MT, Archer M, Potter CS, Carragher B, Mancia F. Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Nat Commun 2020; 11:3396. [PMID: 32636380 PMCID: PMC7341804 DOI: 10.1038/s41467-020-17202-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023] Open
Abstract
Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Ruixiang Blake Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY, 10027, USA
| | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- Department of Anesthesiology, Columbia University, New York, NY, 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei, 11529, Taiwan
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA.
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13
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Cryo-EM snapshots of mycobacterial arabinosyltransferase complex EmbB 2-AcpM 2. Protein Cell 2020; 11:505-517. [PMID: 32363534 PMCID: PMC7305291 DOI: 10.1007/s13238-020-00726-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 01/26/2023] Open
Abstract
Inhibition of Mycobacterium tuberculosis (Mtb) cell wall assembly is an established strategy for anti-TB chemotherapy. Arabinosyltransferase EmbB, which catalyzes the transfer of arabinose from the donor decaprenyl-phosphate-arabinose (DPA) to its arabinosyl acceptor is an essential enzyme for Mtb cell wall synthesis. Analysis of drug resistance mutations suggests that EmbB is the main target of the front-line anti-TB drug, ethambutol. Herein, we report the cryo-EM structures of Mycobacterium smegmatis EmbB in its “resting state” and DPA-bound “active state”. EmbB is a fifteen-transmembrane-spanning protein, assembled as a dimer. Each protomer has an associated acyl-carrier-protein (AcpM) on their cytoplasmic surface. Conformational changes upon DPA binding indicate an asymmetric movement within the EmbB dimer during catalysis. Functional studies have identified critical residues in substrate recognition and catalysis, and demonstrated that ethambutol inhibits transferase activity of EmbB by competing with DPA. The structures represent the first step directed towards a rational approach for anti-TB drug discovery.
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14
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Zhang L, Zhao Y, Gao Y, Wu L, Gao R, Zhang Q, Wang Y, Wu C, Wu F, Gurcha SS, Veerapen N, Batt SM, Zhao W, Qin L, Yang X, Wang M, Zhu Y, Zhang B, Bi L, Zhang X, Yang H, Guddat LW, Xu W, Wang Q, Li J, Besra GS, Rao Z. Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol. Science 2020; 368:1211-1219. [PMID: 32327601 DOI: 10.1126/science.aba9102] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/06/2020] [Accepted: 04/14/2020] [Indexed: 11/02/2022]
Abstract
The arabinosyltransferases EmbA, EmbB, and EmbC are involved in Mycobacterium tuberculosis cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents.
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Affiliation(s)
- Lu Zhang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Yao Zhao
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Gao
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Lijie Wu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruogu Gao
- University of Chinese Academy of Sciences, Beijing 100101, China.,National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Qi Zhang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yinan Wang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Chengyao Wu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fangyu Wu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Sudagar S Gurcha
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Wei Zhao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Ling Qin
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Manfu Wang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lijun Bi
- National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Xian'en Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wenqing Xu
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quan Wang
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. .,National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Jun Li
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies, iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. .,State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, College of Pharmacy, Nankai University, Tianjin 300353, China.,Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.,National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
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15
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Kumar R, Harilal S, Gupta SV, Jose J, Thomas Parambi DG, Uddin MS, Shah MA, Mathew B. Exploring the new horizons of drug repurposing: A vital tool for turning hard work into smart work. Eur J Med Chem 2019; 182:111602. [PMID: 31421629 PMCID: PMC7127402 DOI: 10.1016/j.ejmech.2019.111602] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023]
Abstract
Drug discovery and development are long and financially taxing processes. On an average it takes 12-15 years and costs 1.2 billion USD for successful drug discovery and approval for clinical use. Many lead molecules are not developed further and their potential is not tapped to the fullest due to lack of resources or time constraints. In order for a drug to be approved by FDA for clinical use, it must have excellent therapeutic potential in the desired area of target with minimal toxicities as supported by both pre-clinical and clinical studies. The targeted clinical evaluations fail to explore other potential therapeutic applications of the candidate drug. Drug repurposing or repositioning is a fast and relatively cheap alternative to the lengthy and expensive de novo drug discovery and development. Drug repositioning utilizes the already available clinical trials data for toxicity and adverse effects, at the same time explores the drug's therapeutic potential for a different disease. This review addresses recent developments and future scope of drug repositioning strategy.
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Affiliation(s)
- Rajesh Kumar
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Seetha Harilal
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Sheeba Varghese Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
| | - Jobin Jose
- Department of Pharmaceutics, NGSM Institute of Pharmaceutical Science, NITTE Deemed to be University, Manglore, 575018, India
| | - Della Grace Thomas Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf, 2014, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh; Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Muhammad Ajmal Shah
- Department of Pharmacogonosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Bijo Mathew
- Division of Drug Design and Medicinal Chemistry Research Lab, Department of Pharmaceutical Chemistry, Ahalia School of Pharmacy, Palakkad, 678557, Kerala, India.
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16
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Characterization of Arabinosyl Transfer Reactions in the Biosynthesis of Mycobacterial Cell Envelope (Lipo)Polysaccharides. Methods Mol Biol 2019. [PMID: 30864132 DOI: 10.1007/978-1-4939-9154-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
D-Arabinofuranose is a major glycosyl constituent of mycobacteria found in two essential cell envelope heteropolysaccharides, arabinogalactan and lipoarabinomannan. Seven different arabinosyltransferases at least are required to synthesize the arabinan domain of these two major glycans. Because of their interest from the perspective of drug development, these enzymes have been the object of intense investigations. In this chapter, we describe the protocols used to perform nonradioactive arabinosyltransferase assays with synthetic acceptor and donor substrates and characterize the enzymatic products of the reactions by mass spectrometry.
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17
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Vats S, Shanker A. Groups of coevolving positions provide drug resistance to Mycobacterium tuberculosis: A study using targets of first-line antituberculosis drugs. Int J Antimicrob Agents 2019; 53:197-202. [DOI: 10.1016/j.ijantimicag.2018.10.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/13/2018] [Accepted: 10/20/2018] [Indexed: 01/19/2023]
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18
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Singh A, Somvanshi P, Grover A. Drug repurposing against arabinosyl transferase (EmbC) of Mycobacterium tuberculosis: Essential dynamics and free energy minima based binding mechanics analysis. Gene 2019; 693:114-126. [PMID: 30716439 DOI: 10.1016/j.gene.2019.01.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 01/10/2023]
Abstract
Arabinosyl tranferases (embA, embB, embC) are the key enzymes responsible for biogenesis of arabinan domain of arabinogalactan (AG) and lipoarabinomannan (LAM), two major heteropolysaccharide constituents of the peculiar mycobacterial cell envelope. EmbC is predominantly responsible for LAM synthesis and has been commonly associated with Ethambutol resistance. We have screened the FDA library against EmbC to reposition a drug better than Ethambutol with higher binding affinity to Embc. High throughput virtual screening followed by extra precision docking using Glide gave two best leads i.e. Terlipressin and Amikacin with docking score of -11.39 kcal/mol and -10.71 kcal/mol, respectively. Binding mechanics of the selected drugs was elucidated through long range molecular dynamics simulations (100 ns) using binding free energy rescoring, essential dynamics and free energy minima based approaches, thus revealing the most stable binding modes of Terlipressin with EmbC. Our study establishes the EmbC binding potential of the repurposed drugs Terlipressin and Amikacin.
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Affiliation(s)
- Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, TERI School of Advanced Studies, Plot No. 10, Vasant Kunj Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, Plot No. 10, Vasant Kunj Institutional Area, Vasant Kunj, New Delhi, 110070, India.
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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19
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Kolbe K, Veleti SK, Reiling N, Lindhorst TK. Lectins of Mycobacterium tuberculosis - rarely studied proteins. Beilstein J Org Chem 2019; 15:1-15. [PMID: 30680034 PMCID: PMC6334816 DOI: 10.3762/bjoc.15.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
The importance of bacterial lectins for adhesion, pathogenicity, and biofilm formation is well established for many Gram-positive and Gram-negative bacteria. However, there is very little information available about lectins of the tuberculosis-causing bacterium, Mycobacterium tuberculosis (Mtb). In this paper we review previous studies on the carbohydrate-binding characteristics of mycobacteria and related Mtb proteins, discussing their potential relevance to Mtb infection and pathogenesis.
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Affiliation(s)
- Katharina Kolbe
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, 33 North Drive, Bethesda, 20892, MD, United States
| | - Sri Kumar Veleti
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, 33 North Drive, Bethesda, 20892, MD, United States
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, 23845 Borstel, Germany.,German Center for Infection Research (DZIF), Borstel Site, 23845 Borstel, Germany
| | - Thisbe K Lindhorst
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3-4, 24118 Kiel, Germany
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20
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Klatt S, Brammananth R, O'Callaghan S, Kouremenos KA, Tull D, Crellin PK, Coppel RL, McConville MJ. Identification of novel lipid modifications and intermembrane dynamics in Corynebacterium glutamicum using high-resolution mass spectrometry. J Lipid Res 2018; 59:1190-1204. [PMID: 29724782 PMCID: PMC6027913 DOI: 10.1194/jlr.m082784] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/25/2018] [Indexed: 02/06/2023] Open
Abstract
The complex cell envelopes of Corynebacterineae contribute to the virulence of pathogenic species (such as Mycobacterium tuberculosis and Corynebacterium diphtheriae) and capacity of nonpathogenic species (such as Corynebacterium glutamicum) to grow in diverse niches. The Corynebacterineae cell envelope comprises an asymmetric outer membrane that overlays the arabinogalactan-peptidoglycan complex and the inner cell membrane. Dissection of the lipid composition of the inner and outer membrane fractions is important for understanding the biogenesis of this multilaminate wall structure. Here, we have undertaken the first high-resolution analysis of C. glutamicum inner and outer membrane lipids. We identified 28 lipid (sub)classes (>233 molecular species), including new subclasses of acylated/acetylated trehalose mono/dicorynomycolic acids, using high-resolution LC/MS/MS coupled with mass spectral library searches in MS-DIAL. All lipid subclasses exhibited polarized distributions across the inner and outer membrane fractions generated by differential solvent extraction. Strikingly, deletion of the TmaT protein, which is required for transport of trehalose corynomycolates across the inner membrane, led to the accumulation of triacylglycerols in the inner membrane and to suppressed synthesis of phosphatidylglycerol and alanylated lipids. These analyses indicate unanticipated connectivity in the synthesis and/or transport of different lipid classes in C. glutamicum.
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Affiliation(s)
- Stephan Klatt
- Department of Biochemistry and Molecular Biology University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rajini Brammananth
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, 3800 Australia
| | - Sean O'Callaghan
- Metabolomics Australia, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul K Crellin
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, 3800 Australia
| | - Ross L Coppel
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, 3800 Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology University of Melbourne, Parkville, Victoria 3010, Australia
- Metabolomics Australia, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
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AftD functions as an α1 → 5 arabinofuranosyltransferase involved in the biosynthesis of the mycobacterial cell wall core. ACTA ACUST UNITED AC 2018; 1:2-14. [PMID: 29998212 PMCID: PMC6034362 DOI: 10.1016/j.tcsw.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 11/23/2022]
Abstract
Generation of a single aftD and double aftB/aftD mutants in C. glutamicum. Phenotypic analysis of purified cell wall material indicates a cell wall lesion. Cell free biochemical assays indicate AftD functions as an α(1 → 5) AraT.
Arabinogalactan (AG) is an essential structural macromolecule present in the cell wall of Mycobacterium tuberculosis, serving to connect peptidoglycan with the outer mycolic acid layer. The D-arabinan segment is a highly branched component of AG and is assembled in a step-wise fashion by a variety of arabinofuranosyltransferases (AraT). We have previously used Corynebacterium glutamicum as a model organism to study these complex processes which are otherwise essential in mycobacteria. In order to further our understanding of the molecular basis of AG assembly, we investigated the role of a fourth AraT, now termed AftD by generating single (ΔaftD) and double deletion (ΔaftB ΔaftD) mutants of C. glutamicum. We demonstrate that AftD functions as an α(1 → 5) AraT and reveal the point at which it exerts its activity in the AG biosynthetic pathway.
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22
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Jiang P, Wei WF, Zhong GW, Zhou XG, Qiao WR, Fisher R, Lu L. The function of the three phosphoribosyl pyrophosphate synthetase (Prs) genes in hyphal growth and conidiation in Aspergillus nidulans. MICROBIOLOGY-SGM 2017; 163:218-232. [PMID: 28277197 DOI: 10.1099/mic.0.000427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphoribosyl pyrophosphate synthetase, which is encoded by the Prs gene, catalyses the reaction of ribose-5-phosphate and adenine ribonucleotide triphosphate (ATP) and has central importance in cellular metabolism. However, knowledge about how Prs family members function and contribute to total 5-phosphoribosyl-α-1-pyrophosphate (PRPP) synthetase activity is limited. In this study, we identified that the filamentous fungus Aspergillus nidulans genome contains three PRPP synthase-homologous genes (AnprsA, AnprsB and AnprsC), among which AnprsB and AnprsC but not AnprsA are auxotrophic genes. Transcriptional expression profiles revealed that the mRNA levels of AnprsA, AnprsB and AnprsC are dynamic during germination, hyphal growth and sporulation and that they all showed abundant expression during the vigorous hyphal growth time point. Inhibiting the expression of AnprsB or AnprsC in conditional strains produced more effects on the total PRPP synthetase activity than did inhibiting AnprsA, thus indicating that different AnPrs proteins are unequal in their contributions to Prs enzyme activity. In addition, the constitutive overexpression of AnprsA or AnprsC could significantly rescue the defective phenotype of the AnprsB-absent strain, suggesting that the function of AnprsB is not a specific consequence of this auxotrophic gene but instead comes from the contribution of Prs proteins to PRPP synthetase activity.
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Affiliation(s)
- Ping Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Wen-Fan Wei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Guo-Wei Zhong
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, Nanjing 211166, PR China
| | - Xiao-Gang Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Wei-Ran Qiao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Reinhard Fisher
- Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus Institute for Applied Biosciences, Karlsruhe, Germany
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
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23
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Identification and evolution of a plant cell wall specific glycoprotein glycosyl transferase, ExAD. Sci Rep 2017; 7:45341. [PMID: 28358137 PMCID: PMC5371791 DOI: 10.1038/srep45341] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022] Open
Abstract
Extensins are plant cell wall glycoproteins that act as scaffolds for the deposition of the main wall carbohydrate polymers, which are interlocked into the supramolecular wall structure through intra- and inter-molecular iso-di-tyrosine crosslinks within the extensin backbone. In the conserved canonical extensin repeat, Ser-Hyp4, serine and the consecutive C4-hydroxyprolines (Hyps) are substituted with an α-galactose and 1–5 β- or α-linked arabinofuranoses (Arafs), respectively. These modifications are required for correct extended structure and function of the extensin network. Here, we identified a single Arabidopsis thaliana gene, At3g57630, in clade E of the inverting Glycosyltransferase family GT47 as a candidate for the transfer of Araf to Hyp-arabinofuranotriose (Hyp-β1,4Araf-β1,2Araf-β1,2Araf) side chains in an α-linkage, to yield Hyp-Araf4 which is exclusively found in extensins. T-DNA knock-out mutants of At3g57630 showed a truncated root hair phenotype, as seen for mutants of all hitherto characterized extensin glycosylation enzymes; both root hair and glycan phenotypes were restored upon reintroduction of At3g57630. At3g57630 was named Extensin Arabinose Deficient transferase, ExAD, accordingly. The occurrence of ExAD orthologs within the Viridiplantae along with its’ product, Hyp-Araf4, point to ExAD being an evolutionary hallmark of terrestrial plants and charophyte green algae.
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Cashmore TJ, Klatt S, Yamaryo-Botte Y, Brammananth R, Rainczuk AK, McConville MJ, Crellin PK, Coppel RL. Identification of a Membrane Protein Required for Lipomannan Maturation and Lipoarabinomannan Synthesis in Corynebacterineae. J Biol Chem 2017; 292:4976-4986. [PMID: 28167532 DOI: 10.1074/jbc.m116.772202] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/26/2017] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis and related Corynebacterineae synthesize a family of lipomannans (LM) and lipoarabinomannans (LAM) that are abundant components of the multilaminate cell wall and essential virulence factors in pathogenic species. Here we describe a new membrane protein, highly conserved in all Corynebacterineae, that is required for synthesis of full-length LM and LAM. Deletion of the Corynebacterium glutamicum NCgl2760 gene resulted in a complete loss of mature LM/LAM and the appearance of a truncated LM (t-LM). Complementation of the mutant with the NCgl2760 gene fully restored LM/LAM synthesis. Structural studies, including monosaccharide analysis, methylation linkage analysis, and mass spectrometry of native LM species, indicated that the ΔNCgl2760 t-LM comprised a series of short LM species (8-27 residues long) containing an α1-6-linked mannose backbone with greatly reduced α1-2-mannose side chains and no arabinose caps. The structure of the ΔNCgl2760 t-LM was similar to that of the t-LM produced by a C. glutamicum mutant lacking the mptA gene, encoding a membrane α1-6-mannosyltransferase involved in extending the α1-6-mannan backbone of LM intermediates. Interestingly, NCgl2760 lacks any motifs or homology to other proteins of known function. Attempts to delete the NCgl2760 orthologue in Mycobacterium smegmatis were unsuccessful, consistent with previous studies indicating that the M. tuberculosis orthologue, Rv0227c, is an essential gene. Together, these data suggest that NCgl2760/Rv0227c plays a critical role in the elongation of the mannan backbone of mycobacterial and corynebacterial LM, further highlighting the complexity of lipoglycan pathways of Corynebacterineae.
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Affiliation(s)
- Tamaryn J Cashmore
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800 and
| | - Stephan Klatt
- the Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yoshiki Yamaryo-Botte
- the Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rajini Brammananth
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800 and
| | - Arek K Rainczuk
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800 and
| | - Malcolm J McConville
- the Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Sciences and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul K Crellin
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800 and
| | - Ross L Coppel
- From the Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800 and
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Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB), is recognized as a global health emergency as promoted by the World Health Organization. Over 1 million deaths per year, along with the emergence of multi- and extensively-drug resistant strains of Mtb, have triggered intensive research into the pathogenicity and biochemistry of this microorganism, guiding the development of anti-TB chemotherapeutic agents. The essential mycobacterial cell wall, sharing some common features with all bacteria, represents an apparent ‘Achilles heel’ that has been targeted by TB chemotherapy since the advent of TB treatment. This complex structure composed of three distinct layers, peptidoglycan, arabinogalactan and mycolic acids, is vital in supporting cell growth, virulence and providing a barrier to antibiotics. The fundamental nature of cell wall synthesis and assembly has rendered the mycobacterial cell wall as the most widely exploited target of anti-TB drugs. This review provides an overview of the biosynthesis of the prominent cell wall components, highlighting the inhibitory mechanisms of existing clinical drugs and illustrating the potential of other unexploited enzymes as future drug targets.
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26
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Mann E, Whitfield C. A widespread three-component mechanism for the periplasmic modification of bacterial glycoconjugates. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0594] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The diverse structures of bacterial glycoconjugates are generally established during the early stages of synthesis by the activities of nucleotide sugar-dependent glycosyltransferases active in the cytoplasm. However, in some cases, further modifications of varying complexity occur after the glycoconjugate is exported to the periplasm. These processes are distinguished by the involvement of polyprenyl monosphosphoryl donors and require glycosyltransferases possessing GT-C folds. Established prototypes are found in modifications of some bacterial lipopolysaccharides, where 4-amino-4-deoxy-l-arabinose is added to lipid A and glucose side branches are used to modify O-antigens. Here we review the current understanding of these systems and describe similarities to other periplasmic glycan modifications in bacteria and the N-glycosylation pathway for assembly of eukaryotic glycoproteins.
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Affiliation(s)
- Evan Mann
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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27
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Albesa-Jové D, Guerin ME. The conformational plasticity of glycosyltransferases. Curr Opin Struct Biol 2016; 40:23-32. [DOI: 10.1016/j.sbi.2016.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 07/08/2016] [Indexed: 12/22/2022]
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28
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Lcp1 Is a Phosphotransferase Responsible for Ligating Arabinogalactan to Peptidoglycan in Mycobacterium tuberculosis. mBio 2016; 7:mBio.00972-16. [PMID: 27486192 PMCID: PMC4981717 DOI: 10.1128/mbio.00972-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
UNLABELLED Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), has a unique cell envelope which accounts for its unusual low permeability and contributes to resistance against common antibiotics. The main structural elements of the cell wall consist of a cross-linked network of peptidoglycan (PG) in which some of the muramic acid residues are covalently attached to a complex polysaccharide, arabinogalactan (AG), via a unique α-l-rhamnopyranose-(1→3)-α-d-GlcNAc-(1→P) linker unit. While the molecular genetics associated with PG and AG biosynthetic pathways have been largely delineated, the mechanism by which these two major pathways converge has remained elusive. In Gram-positive organisms, the LytR-CpsA-Psr (LCP) family of proteins are responsible for ligating cell wall teichoic acids to peptidoglycan, through a linker unit that bears a striking resemblance to that found in mycobacterial arabinogalactan. In this study, we have identified Rv3267 as a mycobacterial LCP homolog gene that encodes a phosphotransferase which we have named Lcp1. We demonstrate that lcp1 is an essential gene required for cell viability and show that recombinant Lcp1 is capable of ligating AG to PG in a cell-free radiolabeling assay. IMPORTANCE Tuberculosis is an infectious disease caused by the bacterial organism Mycobacterium tuberculosis Survival of M. tuberculosis rests critically on the integrity of its unique cell wall; therefore, a better understanding of how the genes and enzymes involved in cell wall assembly work is fundamental for us to develop new drugs to treat this disease. In this study, we have identified Lcp1 as an essential phosphotransferase that ligates together arabinogalactan and peptidoglycan, two crucial cell wall macromolecules found within the mycobacterial cell wall. The discovery of Lcp1 sheds new light on the final stages of mycobacterial cell wall assembly and represents a key biosynthetic step that could be exploited for new anti-TB drug discovery.
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29
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Identification of a Lipoteichoic Acid Glycosyltransferase Enzyme Reveals that GW-Domain-Containing Proteins Can Be Retained in the Cell Wall of Listeria monocytogenes in the Absence of Lipoteichoic Acid or Its Modifications. J Bacteriol 2016; 198:2029-42. [PMID: 27185829 PMCID: PMC4944223 DOI: 10.1128/jb.00116-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/10/2016] [Indexed: 12/04/2022] Open
Abstract
Listeria monocytogenes is a foodborne Gram-positive bacterial pathogen, and many of its virulence factors are either secreted proteins or proteins covalently or noncovalently attached to the cell wall. Previous work has indicated that noncovalently attached proteins with GW (glycine-tryptophan) domains are retained in the cell wall by binding to the cell wall polymer lipoteichoic acid (LTA). LTA is a glycerol phosphate polymer, which is modified in L. monocytogenes with galactose and d-alanine residues. We identified Lmo0933 as the cytoplasmic glycosyltransferase required for the LTA glycosylation process and renamed the protein GtlA, for glycosyltransferase LTA A. Using L. monocytogenes mutants lacking galactose or d-alanine modifications or the complete LTA polymer, we show that GW domain proteins are retained within the cell wall, indicating that other cell wall polymers are involved in the retention of GW domain proteins. Further experiments revealed peptidoglycan as the binding receptor as a purified GW domain fusion protein can bind to L. monocytogenes cells lacking wall teichoic acid (WTA) as well as purified peptidoglycan derived from a wild-type or WTA-negative strain. With this, we not only identify the first enzyme involved in the LTA glycosylation process, but we also provide new insight into the binding mechanism of noncovalently attached cell wall proteins.
IMPORTANCE Over the past 20 years, a large number of bacterial genome sequences have become available. Computational approaches are used for the genome annotation and identification of genes and encoded proteins. However, the function of many proteins is still unknown and often cannot be predicted bioinformatically. Here, we show that the previously uncharacterized Listeria monocytogenes gene lmo0933 likely codes for a glycosyltransferase required for the decoration of the cell wall polymer lipoteichoic acid (LTA) with galactose residues. Using L. monocytogenes mutants lacking LTA modifications or the complete polymer, we show that specific cell wall proteins, often associated with virulence, are retained within the cell wall, indicating that additional cell wall polymers are involved in their retention.
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30
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Angala SK, McNeil MR, Zou L, Liav A, Zhang J, Lowary TL, Jackson M. Identification of a Novel Mycobacterial Arabinosyltransferase Activity Which Adds an Arabinosyl Residue to α-d-Mannosyl Residues. ACS Chem Biol 2016; 11:1518-24. [PMID: 27045860 DOI: 10.1021/acschembio.6b00093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The arabinosyltransferases responsible for the biosynthesis of the arabinan domains of two abundant heteropolysaccharides of the cell envelope of all mycobacterial species, lipoarabinomannan and arabinogalactan, are validated drug targets. Using a cell envelope preparation from Mycobacterium smegmatis as the enzyme source and di- and trimannoside synthetic acceptors, we uncovered a previously undetected arabinosyltransferase activity. Thin layer chromatography, GC/MS, and LC/MS/MS analyses of the major enzymatic product are consistent with the transfer of an arabinose residue to the 6 position of the terminal mannosyl residue at the nonreducing end of the acceptors. The newly identified enzymatic activity is resistant to ethambutol and could correspond to the priming arabinosyl transfer reaction that occurs during lipoarabinomannan biosynthesis.
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Affiliation(s)
- Shiva kumar Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Michael R. McNeil
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Lu Zou
- Alberta
Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Avraham Liav
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Junfeng Zhang
- Alberta
Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Todd L. Lowary
- Alberta
Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
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Mann E, Mallette E, Clarke BR, Kimber MS, Whitfield C. The Klebsiella pneumoniae O12 ATP-binding Cassette (ABC) Transporter Recognizes the Terminal Residue of Its O-antigen Polysaccharide Substrate. J Biol Chem 2016; 291:9748-61. [PMID: 26934919 DOI: 10.1074/jbc.m116.719344] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 11/06/2022] Open
Abstract
Export of the Escherichia coli serotype O9a O-antigenic polysaccharides (O-PS) involves an ATP-binding cassette (ABC) transporter. The process requires a non-reducing terminal residue, which is recognized by a carbohydrate-binding module (CBM) appended to the C terminus of the nucleotide-binding domain of the transporter. Here, we investigate the process in Klebsiella pneumoniae serotype O12 (and Raoultella terrigena ATCC 33257). The O12 polysaccharide is terminated at the non-reducing end by a β-linked 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) residue. The O12 ABC transporter also binds its cognate O-PS via a CBM, and export is dependent on the presence of the terminal β-Kdo residue. The overall structural architecture of the O12 CBM resembles the O9a prototype, but they share only weak sequence similarity, and the putative binding pocket for the O12 glycan is different. Removal of the CBM abrogated O-PS transport, but export was restored when the CBM was expressed in trans with the mutant CBM-deficient ABC transporter. These results demonstrate that the CBM-mediated substrate-recognition mechanism is evolutionarily conserved and can operate with glycans of widely differing structures.
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Affiliation(s)
- Evan Mann
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Evan Mallette
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Bradley R Clarke
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chris Whitfield
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Abstract
The cell wall of Mycobacterium tuberculosis is unique in that it differs significantly from those of both Gram-negative and Gram-positive bacteria. The thick, carbohydrate- and lipid-rich cell wall with distinct lipoglycans enables mycobacteria to survive under hostile conditions such as shortage of nutrients and antimicrobial exposure. The key features of this highly complex cell wall are the mycolyl-arabinogalactan-peptidoglycan (mAGP)-based and phosphatidyl-myo-inositol-based macromolecular structures, with the latter possessing potent immunomodulatory properties. These structures are crucial for the growth, viability, and virulence of M. tuberculosis and therefore are often the targets of effective chemotherapeutic agents against tuberculosis. Over the past decade, sophisticated genomic and molecular tools have advanced our understanding of the primary structure and biosynthesis of these macromolecules. The availability of the full genome sequences of various mycobacterial species, including M. tuberculosis, Mycobacterium marinum, and Mycobacterium bovis BCG, have greatly facilitated the identification of large numbers of drug targets and antigens specific to tuberculosis. Techniques to manipulate mycobacteria have also improved extensively; the conditional expression-specialized transduction essentiality test (CESTET) is currently used to determine the essentiality of individual genes. Finally, various biosynthetic assays using either purified proteins or synthetic cell wall acceptors have been developed to study enzyme function. This article focuses on the recent advances in determining the structural details and biosynthesis of arabinogalactan, lipoarabinomannan, and related glycoconjugates.
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Suthagar K, Fairbanks AJ. Synthesis and anti-mycobacterial activity of glycosyl sulfamides of arabinofuranose. Org Biomol Chem 2016; 14:1748-54. [DOI: 10.1039/c5ob02317c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series ofarabino N-glycosyl sulfamides, forced to adopt the furanose form by removal of the 5-hydroxyl group, were synthesised as putative isosteric mimics of decaprenolphosphoarabinose, the donor processed by arabinosyltransferases during mycobacterial cell wall assembly.
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Affiliation(s)
- Kajitha Suthagar
- Department of Chemistry
- University of Canterbury
- Christchurch 8140
- New Zealand
| | - Antony J. Fairbanks
- Department of Chemistry
- University of Canterbury
- Christchurch 8140
- New Zealand
- Biomolecular Interaction Centre
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34
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Tavares-Carreón F, Fathy Mohamed Y, Andrade A, Valvano MA. ArnT proteins that catalyze the glycosylation of lipopolysaccharide share common features with bacterial N-oligosaccharyltransferases. Glycobiology 2015; 26:286-300. [PMID: 26515403 DOI: 10.1093/glycob/cwv095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/26/2015] [Indexed: 02/07/2023] Open
Abstract
ArnT is a glycosyltransferase that catalyzes the addition of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of the lipopolysaccharide. This is a critical modification enabling bacteria to resist killing by antimicrobial peptides. ArnT is an integral inner membrane protein consisting of 13 predicted transmembrane helices and a large periplasmic C-terminal domain. We report here the identification of a functional motif with a canonical consensus sequence DEXRYAX(5)MX(3)GXWX(9)YFEKPX(4)W spanning the first periplasmic loop, which is highly conserved in all ArnT proteins examined. Site-directed mutagenesis demonstrated the contribution of this motif in ArnT function, suggesting that these proteins have a common mechanism. We also demonstrate that the Burkholderia cenocepacia and Salmonella enterica serovar Typhimurium ArnT C-terminal domain is required for polymyxin B resistance in vivo. Deletion of the C-terminal domain in B. cenocepacia ArnT resulted in a protein with significantly reduced in vitro binding to a lipid A fluorescent substrate and unable to catalyze lipid A modification with l-Ara4N. An in silico predicted structural model of ArnT strongly resembled the tertiary structure of Campylobacter lari PglB, a bacterial oligosaccharyltransferase involved in protein N-glycosylation. Therefore, distantly related oligosaccharyltransferases from ArnT and PglB families operating on lipid and polypeptide substrates, respectively, share unexpected structural similarity that could not be predicted from direct amino acid sequence comparisons. We propose that lipid A and protein glycosylation enzymes share a conserved catalytic mechanism despite their evolutionary divergence.
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Affiliation(s)
- Faviola Tavares-Carreón
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada N6A 5C1 Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León. Nuevo León, Mexico
| | - Yasmine Fathy Mohamed
- Centre for Infection and Immunity, Queen's University Belfast, Belfast BT9 5GZ, UK Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Angel Andrade
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada N6A 5C1 Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Miguel A Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada N6A 5C1 Centre for Infection and Immunity, Queen's University Belfast, Belfast BT9 5GZ, UK
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35
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Affiliation(s)
- Monika Jankute
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
| | - Jonathan A.G. Cox
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
| | - James Harrison
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
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Suthagar K, Watson AJ, Wilkinson BL, Fairbanks AJ. Synthesis of arabinose glycosyl sulfamides as potential inhibitors of mycobacterial cell wall biosynthesis. Eur J Med Chem 2015; 102:153-66. [DOI: 10.1016/j.ejmech.2015.07.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/17/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
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Assessing the progress of Mycobacterium tuberculosis H37Rv structural genomics. Tuberculosis (Edinb) 2015; 95:131-6. [DOI: 10.1016/j.tube.2014.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/05/2014] [Accepted: 12/17/2014] [Indexed: 11/19/2022]
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Suthagar K, Polson MIJ, Fairbanks AJ. Unexpected furanose/pyranose equilibration of N-glycosyl sulfonamides, sulfamides and sulfamates. Org Biomol Chem 2015; 13:6573-9. [DOI: 10.1039/c5ob00851d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arabino N-glycosyl sulfamides, sulfonamides and sulfamates convert from the furanose to the thermodynamically preferred pyranose form in aqueous solution.
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Affiliation(s)
- Kajitha Suthagar
- Department of Chemistry
- University of Canterbury
- Christchurch 8140
- New Zealand
| | | | - Antony J. Fairbanks
- Department of Chemistry
- University of Canterbury
- Christchurch 8140
- New Zealand
- Biomolecular Interaction Centre
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Korkegian A, Roberts DM, Blair R, Parish T. Mutations in the essential arabinosyltransferase EmbC lead to alterations in Mycobacterium tuberculosis lipoarabinomannan. J Biol Chem 2014; 289:35172-81. [PMID: 25352598 DOI: 10.1074/jbc.m114.583112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mycobacterium tuberculosis cell wall is a complex structure essential for the viability of the organism and its interaction with the host. The glycolipid lipoarabinomannan (LAM) plays an important role in mediating host-bacteria interactions and is involved in modulation of the immune response. The arabinosyltransferase EmbC required for LAM biosynthesis is essential. We constructed recombinant strains of M. tuberculosis expressing a variety of alleles of EmbC. We demonstrated that EmbC has a functional signal peptide in M. tuberculosis. Over- or underexpression of EmbC resulted in reduced or increased sensitivity to ethambutol, respectively. The C-terminal domain of EmbC was essential for activity because truncated alleles were unable to mediate LAM production in Mycobacterium smegmatis and were unable to complement an embC deletion in M. tuberculosis. The C-terminal domain of the closely related arabinosyltransferase EmbB was unable to complement the function of the EmbC C-terminal domain. Two functional motifs were identified. The GT-C motif contains two aspartate residues essential for function in the DDX motif. The proline-rich region contains two highly conserved asparagines (Asn-638 and Asn-652). Mutation of these residues was tolerated, but loss of Asn-638 resulted in the synthesis of truncated LAM, which appeared to lack arabinose branching. All embC alleles that were incapable of complementing LAM production in M. smegmatis were not viable in M. tuberculosis, supporting the hypothesis that LAM itself is essential in M. tuberculosis.
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Affiliation(s)
- Aaron Korkegian
- From TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102
| | - David M Roberts
- From TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102
| | - Rachel Blair
- From TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102
| | - Tanya Parish
- From TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102
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40
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Percy MG, Gründling A. Lipoteichoic Acid Synthesis and Function in Gram-Positive Bacteria. Annu Rev Microbiol 2014; 68:81-100. [DOI: 10.1146/annurev-micro-091213-112949] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew G. Percy
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ UK; ,
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ UK; ,
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41
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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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42
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Non-replicating Mycobacterium tuberculosis elicits a reduced infectivity profile with corresponding modifications to the cell wall and extracellular matrix. PLoS One 2014; 9:e87329. [PMID: 24516549 PMCID: PMC3916317 DOI: 10.1371/journal.pone.0087329] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 12/20/2013] [Indexed: 12/21/2022] Open
Abstract
A key feature of Mycobacterium tuberculosis is its ability to become dormant in the host. Little is known of the mechanisms by which these bacilli are able to persist in this state. Therefore, the focus of this study was to emulate environmental conditions encountered by M. tuberculosis in the granuloma, and determine the effect of such conditions on the physiology and infectivity of the organism. Non-replicating persistent (NRP) M. tuberculosis was established by the gradual depletion of nutrients in an oxygen-replete and controlled environment. In contrast to rapidly dividing bacilli, NRP bacteria exhibited a distinct phenotype by accumulating an extracellular matrix rich in free mycolate and lipoglycans, with increased arabinosylation. Microarray studies demonstrated a substantial down-regulation of genes involved in energy metabolism in NRP bacteria. Despite this reduction in metabolic activity, cells were still able to infect guinea pigs, but with a delay in the development of disease when compared to exponential phase bacilli. Using these approaches to investigate the interplay between the changing environment of the host and altered physiology of NRP bacteria, this study sheds new light on the conditions that are pertinent to M. tuberculosis dormancy and how this organism could be establishing latent disease.
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Rísquez‐Cuadro R, García Fernández JM, Nierengarten J, Ortiz Mellet C. Fullerene‐sp
2
‐Iminosugar Balls as Multimodal Ligands for Lectins and Glycosidases: A Mechanistic Hypothesis for the Inhibitory Multivalent Effect. Chemistry 2013; 19:16791-803. [DOI: 10.1002/chem.201303158] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Rocío Rísquez‐Cuadro
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012 Sevilla (Spain)
| | - José M. García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC ‐ Universidad de Sevilla, Av. Américo Vespucio 49, Isla de la Cartuja, 41092 Sevilla (Spain)
| | - Jean‐François Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087 Strasbourg (France)
| | - Carmen Ortiz Mellet
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012 Sevilla (Spain)
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44
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Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes. Nat Genet 2013; 45:1190-7. [PMID: 23995136 DOI: 10.1038/ng.2743] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/01/2013] [Indexed: 11/08/2022]
Abstract
To study the evolution of drug resistance, we genetically and biochemically characterized Mycobacterium tuberculosis strains selected in vitro for ethambutol resistance. Mutations in decaprenylphosphoryl-β-D-arabinose (DPA) biosynthetic and utilization pathway genes Rv3806c, Rv3792, embB and embC accumulated to produce a wide range of ethambutol minimal inhibitory concentrations (MICs) that depended on mutation type and number. Rv3806c mutations increased DPA synthesis, causing MICs to double from 2 to 4 μg/ml in a wild-type background and to increase from 16 to 32 μg/ml in an embB codon 306 mutant background. Synonymous mutations in Rv3792 increased the expression of downstream embC, an ethambutol target, resulting in MICs of 8 μg/ml. Multistep selection was required for high-level resistance. Mutations in embC or very high embC expression were observed at the highest resistance level. In clinical isolates, Rv3806c mutations were associated with high-level resistance and had multiplicative effects with embB mutations on MICs. Ethambutol resistance is acquired through the acquisition of mutations that interact in complex ways to produce a range of MICs, from those falling below breakpoint values to ones representing high-level resistance.
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45
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Stoop EJM, Mishra AK, Driessen NN, van Stempvoort G, Bouchier P, Verboom T, van Leeuwen LM, Sparrius M, Raadsen SA, van Zon M, van der Wel NN, Besra GS, Geurtsen J, Bitter W, Appelmelk BJ, van der Sar AM. Mannan core branching of lipo(arabino)mannan is required for mycobacterial virulence in the context of innate immunity. Cell Microbiol 2013; 15:2093-108. [PMID: 23902464 PMCID: PMC3963455 DOI: 10.1111/cmi.12175] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 07/03/2013] [Accepted: 07/17/2013] [Indexed: 11/28/2022]
Abstract
The causative agent of tuberculosis (TB), Mycobacterium tuberculosis, remains an important worldwide health threat. Although TB is one of the oldest infectious diseases of man, a detailed understanding of the mycobacterial mechanisms underlying pathogenesis remains elusive. Here, we studied the role of the α(1→2) mannosyltransferase MptC in mycobacterial virulence, using the Mycobacterium marinum zebrafish infection model. Like its M. tuberculosis orthologue, disruption of M. marinum mptC (mmar_3225) results in defective elongation of mannose caps of lipoarabinomannan (LAM) and absence of α(1→2)mannose branches on the lipomannan (LM) and LAM mannan core, as determined by biochemical analysis (NMR and GC-MS) and immunoblotting. We found that the M. marinum mptC mutant is strongly attenuated in embryonic zebrafish, which rely solely on innate immunity, whereas minor virulence defects were observed in adult zebrafish. Strikingly, complementation with the Mycobacterium smegmatis mptC orthologue, which restored mannan core branching but not cap elongation, was sufficient to fully complement the virulence defect of the mptC mutant in embryos. Altogether our data demonstrate that not LAM capping, but mannan core branching of LM/LAM plays an important role in mycobacterial pathogenesis in the context of innate immunity.
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Affiliation(s)
- Esther J M Stoop
- Department of Medical Microbiology and Infection Control, VU University Medical Center, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands
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46
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Espinoza-Moraga M, Njuguna NM, Mugumbate G, Caballero J, Chibale K. In silico comparison of antimycobacterial natural products with known antituberculosis drugs. J Chem Inf Model 2013; 53:649-60. [PMID: 23410241 DOI: 10.1021/ci300467b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The chemical space based on physicochemical properties and structural features of a diverse group of natural products with reported in vitro activity against different Mycobacterium tuberculosis strains is investigated using in silico tools. This is compared to the chemical space occupied by drugs currently recommended for the treatment of various forms of tuberculosis as well as compounds in preclinical and clinical development. Docking studies exploring possible binding affinities and modes of two main clusters of natural products on two different mycobacterial targets are also reported. Our docking results suggest that scytoscalarol, an antibacterial and antifungal guanidine-bearing sesterterpene, can inhibit arabinosyltransferase Mtb EmbC, and the β-carboline alkaloids 8-hydroxymanzamine A and manzamine A can bind to the oxidoreductase of Mtb INHA. On this basis, these products showing high binding affinities to the two targets in silico could be rationally selected for in vitro testing against these targets and/or semisynthetic modification.
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47
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Docking Studies of Binding of Ethambutol to the C-Terminal Domain of the Arabinosyltransferase fromMycobacterium tuberculosis. J CHEM-NY 2013. [DOI: 10.1155/2013/601270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The binding of ethambutol to the C-terminal domain of the arabinosyltransferase fromMycobacterium tuberculosiswas studied. The analysis was performed using anin silicoapproach in order to find out, by docking calculations and energy descriptors, the conformer of Ethambutol that forms the most stable complex with the C-terminal domain of arabinosyltransferase. The complex shows that location of the Ethambutol coincides with the cocrystallization ligand position and that amino acid residues ASH1051, ASN740, ASP1052, and ARG1055 should be critical in the binding of Ethambutol to C-terminal domain EmbC.
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48
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Rainczuk AK, Yamaryo-Botte Y, Brammananth R, Stinear TP, Seemann T, Coppel RL, McConville MJ, Crellin PK. The lipoprotein LpqW is essential for the mannosylation of periplasmic glycolipids in Corynebacteria. J Biol Chem 2012; 287:42726-38. [PMID: 23091062 DOI: 10.1074/jbc.m112.373415] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylinositol mannosides (PIM), lipomannan (LM), and lipoarabinomannan (LAM) are essential components of the cell wall and plasma membrane of mycobacteria, including the human pathogen Mycobacterium tuberculosis, as well as the related Corynebacterineae. We have previously shown that the lipoprotein, LpqW, regulates PIM and LM/LAM biosynthesis in mycobacteria. Here, we provide direct evidence that LpqW regulates the activity of key mannosyltransferases in the periplasmic leaflet of the cell membrane. Inactivation of the Corynebacterium glutamicum lpqW ortholog, NCgl1054, resulted in a slow growth phenotype and a global defect in lipoglycan biosynthesis. The NCgl1054 mutant lacked LAMs and was defective in the elongation of the major PIM species, AcPIM2, as well as a second glycolipid, termed Gl-X (mannose-α1-4-glucuronic acid-α1-diacylglycerol), which function as membrane anchors for LM-A and LM-B, respectively. Elongation of AcPIM2 and Gl-X was found to be dependent on expression of polyprenol phosphomannose (ppMan) synthase. However, the ΔNCgl1054 mutant synthesized normal levels of ppMan, indicating that LpqW is not required for synthesis of this donor. A spontaneous suppressor strain was isolated in which lipoglycan synthesis in the ΔNCgl1054 mutant was partially restored. Genome-wide sequencing indicated that a single amino acid substitution within the ppMan-dependent mannosyltransferase MptB could bypass the need for LpqW. Further evidence of an interaction is provided by the observation that MptB activity in cell-free extracts was significantly reduced in the absence of LpqW. Collectively, our results suggest that LpqW may directly activate MptB, highlighting the role of lipoproteins in regulating key cell wall biosynthetic pathways in these bacteria.
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Affiliation(s)
- Arek K Rainczuk
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria 3800, Australia
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49
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Jankute M, Grover S, Rana AK, Besra GS. Arabinogalactan and lipoarabinomannan biosynthesis: structure, biogenesis and their potential as drug targets. Future Microbiol 2012; 7:129-47. [PMID: 22191451 DOI: 10.2217/fmb.11.123] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of TB, remains the leading cause of mortality from a single infectious organism. The persistence of this human pathogen is associated with its distinctive lipid-rich cell wall structure that is highly impermeable to hydrophilic chemical drugs. This highly complex and unique structure is crucial for the growth, viability and virulence of M. tuberculosis, thus representing an attractive target for vaccine and drug development. It contains a large macromolecular structure known as the mycolyl-arabinogalactan-peptidoglycan complex, as well as phosphatidyl-myo-inositol derived glycolipids with potent immunomodulatory activity, notably lipomannan and lipoarabinomannan. These cell wall components are often the targets of effective chemotherapeutic agents against TB, such as ethambutol. This review focuses on the structural details and biosynthetic pathways of both arabinogalactan and lipoarabinomannan, as well as the effects of potent drugs on these important (lipo)polysaccharides.
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Affiliation(s)
- Monika Jankute
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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50
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Lai JS, Cheng CW, Sung TY, Hsu WL. Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures. PLoS One 2012; 7:e35018. [PMID: 22496884 PMCID: PMC3322152 DOI: 10.1371/journal.pone.0035018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 03/08/2012] [Indexed: 12/19/2022] Open
Abstract
Secretome analysis is important in pathogen studies. A fundamental and convenient way to identify secreted proteins is to first predict signal peptides, which are essential for protein secretion. However, signal peptides are highly complex functional sequences that are easily confused with transmembrane domains. Such confusion would obviously affect the discovery of secreted proteins. Transmembrane proteins are important drug targets, but very few transmembrane protein structures have been determined experimentally; hence, prediction of the structures is essential. In the field of structure prediction, researchers do not make assumptions about organisms, so there is a need for a general signal peptide predictor.To improve signal peptide prediction without prior knowledge of the associated organisms, we present a machine-learning method, called SVMSignal, which uses biochemical properties as features, as well as features acquired from a novel encoding, to capture biochemical profile patterns for learning the structures of signal peptides directly.We tested SVMSignal and five popular methods on two benchmark datasets from the SPdb and UniProt/Swiss-Prot databases, respectively. Although SVMSignal was trained on an old dataset, it performed well, and the results demonstrate that learning the structures of signal peptides directly is a promising approach. We also utilized SVMSignal to analyze proteomes in the entire HAMAP microbial database. Finally, we conducted a comparative study of secretome analysis on seven tuberculosis-related strains selected from the HAMAP database. We identified ten potential secreted proteins, two of which are drug resistant and four are potential transmembrane proteins.SVMSignal is publicly available at http://bio-cluster.iis.sinica.edu.tw/SVMSignal. It provides user-friendly interfaces and visualizations, and the prediction results are available for download.
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Affiliation(s)
- Jhih-Siang Lai
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
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