1
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Berkowitz N, MacMillan A, Simmons MB, Shinde U, Purdy GE. Structural modeling and characterization of the Mycobacterium tuberculosis MmpL3 C-terminal domain. FEBS Lett 2024. [PMID: 39198717 DOI: 10.1002/1873-3468.15007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024]
Abstract
The Mycobacterium tuberculosis (Mtb) cell envelope provides a protective barrier against the immune response and antibiotics. The mycobacterial membrane protein large (MmpL) family of proteins export cell envelope lipids and siderophores; therefore, these proteins are important for the basic biology and pathogenicity of Mtb. In particular, MmpL3 is essential and a known drug target. Despite interest in MmpL3, the structural data in the field are incomplete. Utilizing homology modeling, AlphaFold, and biophysical techniques, we characterized the cytoplasmic C-terminal domain (CTD) of MmpL3 to better understand its structure and function. Our in silico models of the MmpL11TB and MmpL3TB CTD reveal notable features including a long unstructured linker that connects the globular domain to the last transmembrane (TM) in each transporter, charged lysine and arginine residues facing the membrane, and a C-terminal alpha helix. Our predicted overall structure enables a better understanding of these transporters.
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Affiliation(s)
- Naomi Berkowitz
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Allison MacMillan
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Marit B Simmons
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Ujwal Shinde
- Biophysics Core Facility, Oregon Health & Science University, Portland, OR, USA
| | - Georgiana E Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
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2
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van der Klugt T, van den Biggelaar RHGA, Saris A. Host and bacterial lipid metabolism during tuberculosis infections: possibilities to synergise host- and bacteria-directed therapies. Crit Rev Microbiol 2024:1-21. [PMID: 38916142 DOI: 10.1080/1040841x.2024.2370979] [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: 04/21/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative pathogen of tuberculosis, the most lethal infectious disease resulting in 1.3 million deaths annually. Treatments against Mtb are increasingly impaired by the growing prevalence of antimicrobial drug resistance, which necessitates the development of new antibiotics or alternative therapeutic approaches. Upon infecting host cells, predominantly macrophages, Mtb becomes critically dependent on lipids as a source of nutrients. Additionally, Mtb produces numerous lipid-based virulence factors that contribute to the pathogen's ability to interfere with the host's immune responses and to create a lipid rich environment for itself. As lipids, lipid metabolism and manipulating host lipid metabolism play an important role for the virulence of Mtb, this review provides a state-of-the-art overview of mycobacterial lipid metabolism and concomitant role of host metabolism and host-pathogen interaction therein. While doing so, we will emphasize unexploited bacteria-directed and host-directed drug targets, and highlight potential synergistic drug combinations that hold promise for the development of new therapeutic interventions.
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Affiliation(s)
- Teun van der Klugt
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Anno Saris
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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3
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Jones BS, Hu DD, Nicholson KR, Cronin RM, Weaver SD, Champion MM, Champion PA. The loss of the PDIM/PGL virulence lipids causes differential secretion of ESX-1 substrates in Mycobacterium marinum. mSphere 2024; 9:e0000524. [PMID: 38661343 PMCID: PMC11237470 DOI: 10.1128/msphere.00005-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
The mycobacterial cell envelope is a major virulence determinant in pathogenic mycobacteria. Specific outer lipids play roles in pathogenesis, modulating the immune system and promoting the secretion of virulence factors. ESX-1 (ESAT-6 system-1) is a conserved protein secretion system required for mycobacterial pathogenesis. Previous studies revealed that mycobacterial strains lacking the outer lipid PDIM have impaired ESX-1 function during laboratory growth and infection. The mechanisms underlying changes in ESX-1 function are unknown. We used a proteo-genetic approach to measure phthiocerol dimycocerosate (PDIM)- and phenolic glycolipid (PGL)-dependent protein secretion in M. marinum, a non-tubercular mycobacterial pathogen that causes tuberculosis-like disease in ectothermic animals. Importantly, M. marinum is a well-established model for mycobacterial pathogenesis. Our findings showed that M. marinum strains without PDIM and PGL showed specific, significant reductions in protein secretion compared to the WT and complemented strains. We recently established a hierarchy for the secretion of ESX-1 substrates in four (I-IV) groups. Loss of PDIM differentially impacted secretion of Group III and IV ESX-1 substrates, which are likely the effectors of pathogenesis. Our data suggest that the altered secretion of specific ESX-1 substrates is responsible for the observed ESX-1-related effects in PDIM-deficient strains.IMPORTANCEMycobacterium tuberculosis, the cause of human tuberculosis, killed an estimated 1.3 million people in 2022. Non-tubercular mycobacterial species cause acute and chronic human infections. Understanding how these bacteria cause disease is critical. Lipids in the cell envelope are essential for mycobacteria to interact with the host and promote disease. Strains lacking outer lipids are attenuated for infection, but the reasons are unclear. Our research aims to identify a mechanism for attenuation of mycobacterial strains without the PDIM and PGL outer lipids in M. marinum. These findings will enhance our understanding of the importance of lipids in pathogenesis and how these lipids contribute to other established virulence mechanisms.
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Affiliation(s)
- Bradley S. Jones
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Daniel D. Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rachel M. Cronin
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Simon D. Weaver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew M. Champion
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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4
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Shyam M, Kumar S, Singh V. Unlocking Opportunities for Mycobacterium leprae and Mycobacterium ulcerans. ACS Infect Dis 2024; 10:251-269. [PMID: 38295025 PMCID: PMC10862552 DOI: 10.1021/acsinfecdis.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
In the recent decade, scientific communities have toiled to tackle the emerging burden of drug-resistant tuberculosis (DR-TB) and rapidly growing opportunistic nontuberculous mycobacteria (NTM). Among these, two neglected mycobacteria species of the Acinetobacter family, Mycobacterium leprae and Mycobacterium ulcerans, are the etiological agents of leprosy and Buruli ulcer infections, respectively, and fall under the broad umbrella of neglected tropical diseases (NTDs). Unfortunately, lackluster drug discovery efforts have been made against these pathogenic bacteria in the recent decade, resulting in the discovery of only a few countable hits and majorly repurposing anti-TB drug candidates such as telacebec (Q203), P218, and TB47 for current therapeutic interventions. Major ignorance in drug candidate identification might aggravate the dramatic consequences of rapidly spreading mycobacterial NTDs in the coming days. Therefore, this Review focuses on an up-to-date account of drug discovery efforts targeting selected druggable targets from both bacilli, including the accompanying challenges that have been identified and are responsible for the slow drug discovery. Furthermore, a succinct discussion of the all-new possibilities that could be alternative solutions to mitigate the neglected mycobacterial NTD burden and subsequently accelerate the drug discovery effort is also included. We anticipate that the state-of-the-art strategies discussed here may attract major attention from the scientific community to navigate and expand the roadmap for the discovery of next-generation therapeutics against these NTDs.
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Affiliation(s)
- Mousumi Shyam
- Department
of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mersa, Ranchi, Jharkhand 835215, India
| | - Sumit Kumar
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, University of Cape Town, Rondebosch 7701, South Africa
- Institute
of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Observatory 7925, Cape Town, South Africa
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5
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Meikle V, Zhang L, Niederweis M. Intricate link between siderophore secretion and drug efflux in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2023; 67:e0162922. [PMID: 37676015 PMCID: PMC10583673 DOI: 10.1128/aac.01629-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/30/2023] [Indexed: 09/08/2023] Open
Abstract
Drug-resistant Mycobacterium tuberculosis is a worldwide health-care problem rendering current tuberculosis (TB) drugs ineffective. Drug efflux is an important mechanism in bacterial drug resistance. The MmpL4 and MmpL5 transporters form functionally redundant complexes with their associated MmpS4 and MmpS5 proteins and constitute the inner membrane components of an essential siderophore secretion system of M. tuberculosis. Inactivating siderophore secretion is toxic for M. tuberculosis due to self-poisoning at low-iron conditions and leads to a strong virulence defect in mice. In this study, we show that M. tuberculosis mutants lacking components of the MmpS4-MmpL4 and MmpS5-MmpL5 systems are more susceptible to bedaquiline, clofazimine, and rifabutin, important drugs for treatment of drug-resistant TB. While genetic deletion experiments revealed similar functions of the MmpL4 and MmpL5 transporters in siderophore and drug secretion, complementation experiments indicated that the MmpS4-MmpL4 proteins alone are not sufficient to restore drug efflux in an M. tuberculosis mutant lacking both operons, in contrast to MmpS5-MmpL5. Importantly, an M. tuberculosis mutant lacking the recently discovered periplasmic Rv0455c protein, which is also essential for siderophore secretion, is more susceptible to the same drugs. These results reveal a promising target for the development of dual-function TB drugs, which might poison M. tuberculosis by blocking siderophore secretion and synergize with other drugs by impairing drug efflux.
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Affiliation(s)
- Virginia Meikle
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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6
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Kim H, Shin SJ. Revolutionizing control strategies against Mycobacterium tuberculosis infection through selected targeting of lipid metabolism. Cell Mol Life Sci 2023; 80:291. [PMID: 37704889 PMCID: PMC11072447 DOI: 10.1007/s00018-023-04914-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
Lipid species play a critical role in the growth and virulence expression of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). During Mtb infection, foamy macrophages accumulate lipids in granulomas, providing metabolic adaptation and survival strategies for Mtb against multiple stresses. Host-derived lipid species, including triacylglycerol and cholesterol, can also contribute to the development of drug-tolerant Mtb, leading to reduced efficacy of antibiotics targeting the bacterial cell wall or transcription. Transcriptional and metabolic analyses indicate that lipid metabolism-associated factors of Mtb are highly regulated by antibiotics and ultimately affect treatment outcomes. Despite the well-known association between major antibiotics and lipid metabolites in TB treatment, a comprehensive understanding of how altered lipid metabolites in both host and Mtb influence treatment outcomes in a drug-specific manner is necessary to overcome drug tolerance. The current review explores the controversies and correlations between lipids and drug efficacy in various Mtb infection models and proposes novel approaches to enhance the efficacy of anti-TB drugs. Moreover, the review provides insights into the efficacious control of Mtb infection by elucidating the impact of lipids on drug efficacy. This review aims to improve the effectiveness of current anti-TB drugs and facilitate the development of innovative therapeutic strategies against Mtb infection by making reverse use of Mtb-favoring lipid species.
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Affiliation(s)
- Hagyu Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea.
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7
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Moolla N, Bailo R, Marshall R, Bavro VN, Bhatt A. Structure-function analysis of MmpL7-mediated lipid transport in mycobacteria. Cell Surf 2021; 7:100062. [PMID: 34522829 PMCID: PMC8427324 DOI: 10.1016/j.tcsw.2021.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
Mycobacterial membrane protein Large (MmpL7) is a Resistance-Nodulation-Division (RND) family transporter required for the export of the virulence lipid, phthiocerol dimycocerosate (PDIM), in Mycobacterium tuberculosis. Using a null mutant of the related, vaccine strain Mycobacterium bovis BCG, we show that MmpL7 is also involved in the transport of the structurally related phenolic glycolipid (PGL), which is also produced by the hypervirulent M. tuberculosis strain HN878, but absent in M. tuberculosis H37Rv. Furthermore, we generated an in silico model of M. tuberculosis MmpL7 that revealed MmpL7 as a functional outlier within the MmpL-family, missing a canonical proton-relay signature sequence, suggesting that it employs a yet-unidentified mechanism for energy coupling for transport. In addition, our analysis demonstrates that the periplasmic porter domain 2 insert (PD2-insert), which doesn't share any recognisable homology, is highly alpha-helical in nature, suggesting an organisation similar to that seen in the hopanoid PD3/4 domains. Using the M. bovis BCG mmpL7 mutant for functional complementation with mutated alleles of mmpL7, we were able to identify residues present in the transmembrane domains TM4 and TM10, and the PD2 domain insert that play a crucial role in PDIM transport, and in certain cases, biosynthesis of PDIM.
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Affiliation(s)
- Nabiela Moolla
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Rebeca Bailo
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert Marshall
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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8
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Kumari R, Katara P. Up regulated virulence genes in M. tuberculosis H37Rv gleaned from genome wide expression profiles. Bioinformation 2021; 17:608-615. [PMID: 35173382 PMCID: PMC8819794 DOI: 10.6026/97320630017608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 11/23/2022] Open
Abstract
Identification of up regulated virulence genes in M. tuberculosis H37Rv using genome wide expression profiles is of interest in drug discovery for the disease. Hence, we report 17 up-regulated PPIN (Protein-Protein Interaction Network) enriched potential virulence linked genes using expression data available at the Gene Expression Omnibus (GEO) database for further consideration.
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Affiliation(s)
- Rohini Kumari
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, Uttar Pradesh - 211002 India
| | - Pramod Katara
- Computational Omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, Uttar Pradesh - 211002 India
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9
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Rens C, Chao JD, Sexton DL, Tocheva EI, Av-Gay Y. Roles for phthiocerol dimycocerosate lipids in Mycobacterium tuberculosis pathogenesis. MICROBIOLOGY-SGM 2021; 167. [PMID: 33629944 DOI: 10.1099/mic.0.001042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The success of Mycobacterium tuberculosis as a pathogen is well established: tuberculosis is the leading cause of death by a single infectious agent worldwide. The threat of multi- and extensively drug-resistant bacteria has renewed global concerns about this pathogen and understanding its virulence strategies will be essential in the fight against tuberculosis. The current review will focus on phthiocerol dimycocerosates (PDIMs), a long-known and well-studied group of complex lipids found in the M. tuberculosis cell envelope. Numerous studies show a role for PDIMs in several key steps of M. tuberculosis pathogenesis, with recent studies highlighting its involvement in bacterial virulence, in association with the ESX-1 secretion system. Yet, the mechanisms by which PDIMs help M. tuberculosis to control macrophage phagocytosis, inhibit phagosome acidification and modulate host innate immunity, remain to be fully elucidated.
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Affiliation(s)
- Céline Rens
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Joseph D Chao
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Danielle L Sexton
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Elitza I Tocheva
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada.,Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
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10
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Melly GC, Stokas H, Davidson PM, Roma JS, Rhodes HL, Purdy GE. Identification of residues important for M. tuberculosis MmpL11 function reveals that function is modulated by phosphorylation in the C-terminal domain. Mol Microbiol 2021; 115:208-221. [PMID: 32985735 DOI: 10.1111/mmi.14611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 11/26/2022]
Abstract
The Mycobacterium tuberculosis cell envelope is a critical interface between the host and pathogen and provides a protective barrier against the immune response and antibiotics. Cell envelope lipids are also mycobacterial virulence factors that influence the host immune response. The mycobacterial membrane protein large (MmpL) proteins transport cell envelope lipids and siderophores that are important for the basic physiology and pathogenesis of M. tuberculosis. We recently identified MmpL11 as a conserved transporter of mycolic acid-containing lipids including monomeromycolyl diacylglycerol (MMDAG), mycolate wax ester (MWE), and long-chain triacylglycerols (LC-TAGs). These lipids contribute to biofilm formation in M. tuberculosis and M. smegmatis, and non-replicating persistence in M. tuberculosis. In this report, we identified domains and residues that are essential for MmpL11TB lipid transporter activity. Specifically, we show that the D1 periplasmic loop and a conserved tyrosine are essential for the MmpL11 function. Intriguingly, we found that MmpL11 levels are regulated by the phosphorylation of threonine in the cytoplasmic C-terminal domain, providing the first direct evidence of the phospho-regulation of MmpL11 transporter activity in M. tuberculosis and M. smegmatis. Our results offer further insight into the function of MmpL transporters and regulation of mycobacterial cell envelope biogenesis.
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Affiliation(s)
- Geoff C Melly
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Haley Stokas
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Patrick M Davidson
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - José Santinni Roma
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Heather L Rhodes
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Georgiana E Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
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11
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Nicholson KR, Mousseau CB, Champion MM, Champion PA. The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens. PLoS Pathog 2021; 17:e1009124. [PMID: 33411813 PMCID: PMC7790235 DOI: 10.1371/journal.ppat.1009124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
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Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - C. Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
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12
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Beyond Toxin Transport: Novel Role of ABC Transporter for Enzymatic Machinery of Cereulide NRPS Assembly Line. mBio 2020; 11:mBio.01577-20. [PMID: 32994334 PMCID: PMC7527721 DOI: 10.1128/mbio.01577-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
This study revealed a novel, potentially conserved mechanism involved in the biosynthesis of microbial natural products, exemplified by the mitochondrial active depsipeptide cereulide. Similar to other bioactive substances, such as the last-resort antibiotics vancomycin and daptomycin, the antitumor drug cryptophycin or the cholesterol-lowering agent lovastatin, cereulide is synthesized nonribosomally by multienzyme machinery, requiring the concerted actions of multiple proteins to ensure correct product assembly. Given the importance of microbial secondary metabolites in human and veterinary medicine, it is critical to understand how these processes are orchestrated within the host cells. By revealing that tethering of a biosynthetic enzyme to the cell membrane by an ABC transporter is essential for nonribosomal peptide production, our study provides novel insights into synthesis of microbial secondary metabolites, which could contribute to isolation of novel compounds from cryptic secondary metabolite clusters or improve the yield of produced pharmaceuticals. Nonribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs) play a pivotal role in the production of bioactive natural products, such as antibiotics and cytotoxins. Despite biomedical and pharmaceutical importance, the molecular mechanisms and architectures of these multimodular enzyme complexes are not fully understood. Here, we report on an ABC transporter that forms a vital part of the nonribosomal peptide biosynthetic machinery. Emetic Bacillus cereus produces the highly potent, mitochondrial active nonribosomal depsipeptide cereulide, synthesized by the NRPS Ces. The ces gene locus includes, next to the structural cesAB genes, a putative ABC transporter, designated cesCD. Our study demonstrates that tethering of CesAB synthetase to the cell membrane by CesCD is critical for peptide assembly. In vivo studies revealed that CesAB colocalizes with CesCD on the cell membrane, suggesting direct involvement of this ABC transporter in the biosynthesis of a nonribosomal peptide. Mutation of cesCD, disrupting the assembly of the CesCD complex, resulted in decreased interaction with CesAB and, as a consequence, negatively affected cereulide biosynthesis. Specific domains within CesAB synthetase interacting with CesC were identified. Furthermore, we demonstrated that the structurally similar BerAB transporter from Bacillus thuringiensis complements CesCD function in cereulide biosynthesis, suggesting that the direct involvement of ABC transporter in secondary metabolite biosynthesis could be a widespread mechanism. In summary, our study revealed a novel, noncanonical function for ABC transporter, which is essential for megaenzyme functionality of NRPS. The new insights into natural product biosynthesis gained may facilitate the discovery of new metabolites with bioactive potential.
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13
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Dunlap MD, Prince OA, Rangel-Moreno J, Thomas KA, Scordo JM, Torrelles JB, Cox J, Steyn AJC, Zúñiga J, Kaushal D, Khader SA. Formation of Lung Inducible Bronchus Associated Lymphoid Tissue Is Regulated by Mycobacterium tuberculosis Expressed Determinants. Front Immunol 2020; 11:1325. [PMID: 32695111 PMCID: PMC7338767 DOI: 10.3389/fimmu.2020.01325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of the infectious disease tuberculosis (TB), which is a leading cause of death worldwide. Approximately one fourth of the world's population is infected with Mtb. A major unresolved question is delineating the inducers of protective long-lasting immune response without inducing overt, lung inflammation. Previous studies have shown that the presence of inducible Bronchus-Associated Lymphoid Tissue (iBALT) correlate with protection from Mtb infection. In this study, we hypothesized that specific Mtb factors could influence the formation of iBALT, thus skewing the outcome of TB disease. We infected non-human primates (NHPs) with a transposon mutant library of Mtb, and identified specific Mtb mutants that were over-represented within iBALT-containing granulomas. A major pathway reflected in these mutants was Mtb cell wall lipid transport and metabolism. We mechanistically addressed the function of one such Mtb mutant lacking mycobacteria membrane protein large 7 (MmpL7), which transports phthiocerol dimycocerosate (PDIM) to the mycobacterial outer membrane (MOM). Accordingly, murine aerosol infection with the Mtb mutant Δmmpl7 correlated with increased iBALT-containing granulomas. Our studies showed that the Δmmpl7 mutant lacking PDIMs on the surface overexpressed diacyl trehaloses (DATs) in the cell wall, which altered the cytokine/chemokine production of epithelial and myeloid cells, thus leading to a dampened inflammatory response. Thus, this study describes an Mtb specific factor that participates in the induction of iBALT formation during TB by directly modulating cytokine and chemokine production in host cells.
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Affiliation(s)
- Micah D Dunlap
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Oliver A Prince
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | | | - Kimberly A Thomas
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Julia M Scordo
- Texas Biomedical Research Institute, San Antonio, TX, United States
| | | | - Jeffery Cox
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Adrie J C Steyn
- Department of Microbiology, Centers for AIDS Research and Free Radical Biology, University of Alabama at Alabama, Birmingham, AL, United States.,African Health Research Institute (AHRI), Durban, South Africa
| | - Joaquín Zúñiga
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Deepak Kaushal
- Texas Biomedical Research Institute, San Antonio, TX, United States.,Division of Bacteriology, Tulane National Primate Research Center, Covington, LA, United States.,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Shabaana A Khader
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
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14
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Ma S, Huang Y, Xie F, Gong Z, Zhang Y, Stojkoska A, Xie J. Transport mechanism of Mycobacterium tuberculosis MmpL/S family proteins and implications in pharmaceutical targeting. Biol Chem 2020; 401:331-348. [DOI: 10.1515/hsz-2019-0326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022]
Abstract
AbstractTuberculosis caused by Mycobacterium tuberculosis remains a serious threat to public health. The M. tuberculosis cell envelope is closely related to its virulence and drug resistance. Mycobacterial membrane large proteins (MmpL) are lipid-transporting proteins of the efflux pump resistance nodulation cell division (RND) superfamily with lipid substrate specificity and non-transport lipid function. Mycobacterial membrane small proteins (MmpS) are small regulatory proteins, and they are also responsible for some virulence-related effects as accessory proteins of MmpL. The MmpL transporters are the candidate targets for the development of anti-tuberculosis drugs. This article summarizes the structure, function, phylogenetics of M. tuberculosis MmpL/S proteins and their roles in host immune response, inhibitors and regulatory system.
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Affiliation(s)
- Shuang Ma
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Yu Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Fuling Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Yuan Zhang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Andrea Stojkoska
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
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15
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2019; 113:336-351. [PMID: 31903874 PMCID: PMC7006823 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- MI Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - JG Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - MI Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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16
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Yang D, Vandenbussche G, Vertommen D, Evrard D, Abskharon R, Cavalier JF, Berger G, Canaan S, Khan MS, Zeng S, Wohlkönig A, Prévost M, Soumillion P, Fontaine V. Methyl arachidonyl fluorophosphonate inhibits Mycobacterium tuberculosis thioesterase TesA and globally affects vancomycin susceptibility. FEBS Lett 2019; 594:79-93. [PMID: 31388991 DOI: 10.1002/1873-3468.13555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 11/11/2022]
Abstract
Phthiocerol dimycocerosates and phenolic glycolipids (PGL) are considered as major virulence elements of Mycobacterium tuberculosis, in particular because of their involvement in cell wall impermeability and drug resistance. The biosynthesis of these waxy lipids involves multiple enzymes, including thioesterase A (TesA). We observed that purified recombinant M. tuberculosis TesA is able to dimerize in the presence of palmitoyl-CoA and our 3D structure model of TesA with this acyl-CoA suggests hydrophobic interaction requirement for dimerization. Furthermore, we identified that methyl arachidonyl fluorophosphonate, which inhibits TesA by covalently modifying the catalytic serine, also displays a synergistic antimicrobial activity with vancomycin further warranting the development of TesA inhibitors as valuable antituberculous drug candidates.
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Affiliation(s)
- Dong Yang
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Belgium
| | - Guy Vandenbussche
- Laboratory for the Structure and Function of Biological Membranes, Faculty of Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain (UCL), Brussels, Belgium
| | - Damien Evrard
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Romany Abskharon
- National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt.,VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Gilles Berger
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Belgium
| | | | - Mohammad Shahneawz Khan
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Sheng Zeng
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Belgium
| | - Alexandre Wohlkönig
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Martine Prévost
- Laboratory for the Structure and Function of Biological Membranes, Faculty of Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Patrice Soumillion
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Véronique Fontaine
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Belgium
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17
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Abstract
Mycolic acids are the signature lipid of mycobacteria and constitute an important physical component of the cell wall, a target of mycobacterium-specific antibiotics and a mediator of Mycobacterium tuberculosis pathogenesis. Mycolic acids are synthesized in the cytoplasm and are thought to be transported to the cell wall as a trehalose ester by the MmpL3 transporter, an antibiotic target for M. tuberculosis However, the mechanism by which mycolate synthesis is coupled to transport, and the full MmpL3 transport machinery, is unknown. Here, we identify two new components of the MmpL3 transport machinery in mycobacteria. The protein encoded by MSMEG_0736/Rv0383c is essential for growth of Mycobacterium smegmatis and M. tuberculosis and is anchored to the cytoplasmic membrane, physically interacts with and colocalizes with MmpL3 in growing cells, and is required for trehalose monomycolate (TMM) transport to the cell wall. In light of these findings, we propose MSMEG_0736/Rv0383c be named "TMM transport factor A", TtfA. The protein encoded by MSMEG_5308 also interacts with the MmpL3 complex but is nonessential for growth or TMM transport. However, MSMEG_5308 accumulates with inhibition of MmpL3-mediated TMM transport and stabilizes the MmpL3/TtfA complex, indicating that it may stabilize the transport system during stress. These studies identify two new components of the mycobacterial mycolate transport machinery, an emerging antibiotic target in M. tuberculosis IMPORTANCE The cell envelope of Mycobacterium tuberculosis, the bacterium that causes the disease tuberculosis, is a complex structure composed of abundant lipids and glycolipids, including the signature lipid of these bacteria, mycolic acids. In this study, we identified two new components of the transport machinery that constructs this complex cell wall. These two accessory proteins are in a complex with the MmpL3 transporter. One of these proteins, TtfA, is required for mycolic acid transport and cell viability, whereas the other stabilizes the MmpL3 complex. These studies identify two new components of the essential cell envelope biosynthetic machinery in mycobacteria.
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18
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Melly G, Purdy GE. MmpL Proteins in Physiology and Pathogenesis of M. tuberculosis. Microorganisms 2019; 7:microorganisms7030070. [PMID: 30841535 PMCID: PMC6463170 DOI: 10.3390/microorganisms7030070] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains an important human pathogen. The Mtb cell envelope is a critical bacterial structure that contributes to virulence and pathogenicity. Mycobacterial membrane protein large (MmpL) proteins export bulky, hydrophobic substrates that are essential for the unique structure of the cell envelope and directly support the ability of Mtb to infect and persist in the host. This review summarizes recent investigations that have enabled insight into the molecular mechanisms underlying MmpL substrate export and the role that these substrates play during Mtb infection.
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Affiliation(s)
- Geoff Melly
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Georgiana E Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
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19
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Abstract
Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA.
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20
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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21
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Dubois V, Viljoen A, Laencina L, Le Moigne V, Bernut A, Dubar F, Blaise M, Gaillard JL, Guérardel Y, Kremer L, Herrmann JL, Girard-Misguich F. MmpL8 MAB controls Mycobacterium abscessus virulence and production of a previously unknown glycolipid family. Proc Natl Acad Sci U S A 2018; 115:E10147-E10156. [PMID: 30301802 PMCID: PMC6205491 DOI: 10.1073/pnas.1812984115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium abscessus is a peculiar rapid-growing Mycobacterium (RGM) capable of surviving within eukaryotic cells thanks to an arsenal of virulence genes also found in slow-growing mycobacteria (SGM), such as Mycobacterium tuberculosis A screen based on the intracellular survival in amoebae and macrophages (MΦ) of an M. abscessus transposon mutant library revealed the important role of MAB_0855, a yet uncharacterized Mycobacterial membrane protein Large (MmpL). Large-scale comparisons with SGM and RGM genomes uncovered MmpL12 proteins as putative orthologs of MAB_0855 and a locus-scale synteny between the MAB_0855 and Mycobacterium chelonae mmpL8 loci. A KO mutant of the MAB_0855 gene, designated herein as mmpL8MAB , had impaired adhesion to MΦ and displayed a decreased intracellular viability. Despite retaining the ability to block phagosomal acidification, like the WT strain, the mmpL8MAB mutant was delayed in damaging the phagosomal membrane and in making contact with the cytosol. Virulence attenuation of the mutant was confirmed in vivo by impaired zebrafish killing and a diminished propensity to induce granuloma formation. The previously shown role of MmpL in lipid transport prompted us to investigate the potential lipid substrates of MmpL8MAB Systematic lipid analysis revealed that MmpL8MAB was required for the proper expression of a glycolipid entity, a glycosyl diacylated nonadecyl diol (GDND) alcohol comprising different combinations of oleic and stearic acids. This study shows the importance of MmpL8MAB in modifying interactions between the bacteria and phagocytic cells and in the production of a previously unknown glycolipid family.
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Affiliation(s)
- Violaine Dubois
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Albertus Viljoen
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
| | - Laura Laencina
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Vincent Le Moigne
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Audrey Bernut
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
| | - Faustine Dubar
- Université de Lille, CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Mickaël Blaise
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
| | - Jean-Louis Gaillard
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
- Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Universitaire Paris Ile de France Ouest, Hôpital Raymond Poincaré, Hôpital Ambroise Paré, 92380 Garches, Boulogne Billancourt, France
| | - Yann Guérardel
- Université de Lille, CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Laurent Kremer
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
- INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Jean-Louis Herrmann
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France;
- Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Universitaire Paris Ile de France Ouest, Hôpital Raymond Poincaré, Hôpital Ambroise Paré, 92380 Garches, Boulogne Billancourt, France
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22
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The transcriptional regulator LysG (Rv1985c) of Mycobacterium tuberculosis activates lysE (Rv1986) in a lysine-dependent manner. PLoS One 2017; 12:e0186505. [PMID: 29049397 PMCID: PMC5648196 DOI: 10.1371/journal.pone.0186505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022] Open
Abstract
The Mycobacterium tuberculosis protein encoded by the Rv1986 gene is a target for memory T cells in patients with tuberculosis, and shows strong similarities to a lysine exporter LysE of Corynebacterium glutamicum. During infection, the pathogen Mycobacterium tuberculosis adapts its metabolism to environmental changes. In this study, we found that the expression of Rv1986 is controlled by Rv1985c. Rv1985c is located directly upstream of Rv1986 with an overlapping promoter region between both genes. Semiquantitative reverse transcription PCR using an isogenic mutant of Mycobacterium tuberculosis lacking Rv1985c showed that in the presence of lysine, Rv1985c protein positively upregulated the expression of Rv1986. RNA sequencing revealed the transcription start points for both transcripts and overlapping promoters. An inverted repeat in the center of the intergenic region was identified, and binding of Rv1985c protein to the intergenic region was confirmed by electrophoretic mobility shift assays. Whole transcriptome expression analysis and RNAsequencing showed downregulated transcription of ppsBCD in the Rv1985c-mutant compared to the wild type strain. Taken together, our findings characterize the regulatory network of Rv1985c in Mycobacterium tuberculosis. Due to their similarity of an orthologous gene pair in Corynebacterium glutamicum, we suggest to rename Rv1985c to lysG(Mt), and Rv1986 to lysE(Mt).
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23
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Sandhu P, Akhter Y. Evolution of structural fitness and multifunctional aspects of mycobacterial RND family transporters. Arch Microbiol 2017; 200:19-31. [PMID: 28951954 DOI: 10.1007/s00203-017-1434-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/07/2017] [Accepted: 09/20/2017] [Indexed: 12/11/2022]
Abstract
Drug resistance is a major concern due to the evolution and emergence of pathogenic bacterial strains with novel strategies to resist the antibiotics in use. Mycobacterium tuberculosis (Mtb) is one of such pathogens with reported strains, which are not treatable with any of the available anti-TB drugs. This scenario has led to the need to look for some novel drug targets in Mtb, which may be exploited to design effective treatment strategies against the infection. The goal of this review is to discuss one such class of emerging drug targets in Mtb. MmpL (mycobacterial membrane protein large) proteins from Mtb are reported to be involved in multi-substrate transport including drug efflux and considered as one of the contributing factors for the emergence of multidrug-resistant strains. MmpL proteins belong to resistance nodulation division permeases superfamily of membrane transporters, which are viably and pathogenetically important and their inhibition could be lethal for the bacteria.
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Affiliation(s)
- Padmani Sandhu
- Structural Bioinformatics Group, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Shahpur District, Kangra, Himachal Pradesh, 176206, India
| | - Yusuf Akhter
- Structural Bioinformatics Group, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Shahpur District, Kangra, Himachal Pradesh, 176206, India.
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24
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Barnes DD, Lundahl MLE, Lavelle EC, Scanlan EM. The Emergence of Phenolic Glycans as Virulence Factors in Mycobacterium tuberculosis. ACS Chem Biol 2017; 12:1969-1979. [PMID: 28692249 DOI: 10.1021/acschembio.7b00394] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tuberculosis is the leading infectious cause of mortality worldwide. The global epidemic, caused by Mycobacterium tuberculosis, has prompted renewed interest in the development of novel vaccines for disease prevention and control. The cell envelope of M. tuberculosis is decorated with an assortment of glycan structures, including glycolipids, that are involved in disease pathogenesis. Phenolic glycolipids and the structurally related para-hydroxybenzoic acid derivatives display potent immunomodulatory activities and have particular relevance for both understanding the interaction of the bacterium with the host immune system and also in the design of new vaccine and therapeutic candidates. Interest in glycobiology has grown exponentially over the past decade, with advancements paving the way for effective carbohydrate based vaccines. This review highlights recent advances in our understanding of phenolic glycans, including their biosynthesis and role as virulence factors in M. tuberculosis. Recent chemical synthesis approaches and biochemical analysis of synthetic glycans and their conjugates have led to fundamental insights into their roles in host-pathogen interactions. The applications of these synthetic glycans as potential vaccine candidates are discussed.
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Affiliation(s)
- Danielle D. Barnes
- School of Chemistry
and Trinity Biomedical Sciences Institute, Trinity College, Pearse
St., Dublin 2, Ireland
| | - Mimmi L. E. Lundahl
- School of Chemistry
and Trinity Biomedical Sciences Institute, Trinity College, Pearse
St., Dublin 2, Ireland
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity
Biomedical Sciences Institute, Trinity College Dublin, D02 R590, Dublin 2, Ireland
| | - Ed C. Lavelle
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity
Biomedical Sciences Institute, Trinity College Dublin, D02 R590, Dublin 2, Ireland
| | - Eoin M. Scanlan
- School of Chemistry
and Trinity Biomedical Sciences Institute, Trinity College, Pearse
St., Dublin 2, Ireland
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25
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Abstract
The defining feature of the mycobacterial outer membrane (OM) is the presence of mycolic acids (MAs), which, in part, render the bilayer extremely hydrophobic and impermeable to external insults, including many antibiotics. Although the biosynthetic pathway of MAs is well studied, the mechanism(s) by which these lipids are transported across the cell envelope is(are) much less known. Mycobacterial membrane protein Large 3 (MmpL3), an essential inner membrane (IM) protein, is implicated in MA transport, but its exact function has not been elucidated. It is believed to be the cellular target of several antimycobacterial compounds; however, evidence for direct inhibition of MmpL3 activity is also lacking. Here, we establish that MmpL3 is the MA flippase at the IM of mycobacteria and is the molecular target of BM212, a 1,5-diarylpyrrole compound. We develop assays that selectively access mycolates on the surface of Mycobacterium smegmatis spheroplasts, allowing us to monitor flipping of MAs across the IM. Using these assays, we establish the mechanism of action of BM212 as a potent MmpL3 inhibitor, and use it as a molecular probe to demonstrate the requirement for functional MmpL3 in the transport of MAs across the IM. Finally, we show that BM212 binds MmpL3 directly and inhibits its activity. Our work provides fundamental insights into OM biogenesis and MA transport in mycobacteria. Furthermore, our assays serve as an important platform for accelerating the validation of small molecules that target MmpL3, and their development as future antituberculosis drugs.
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Sandhu P, Akhter Y. Siderophore transport by MmpL5-MmpS5 protein complex in Mycobacterium tuberculosis. J Inorg Biochem 2017; 170:75-84. [DOI: 10.1016/j.jinorgbio.2017.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/27/2016] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
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Viljoen A, Dubois V, Girard-Misguich F, Blaise M, Herrmann JL, Kremer L. The diverse family of MmpL transporters in mycobacteria: from regulation to antimicrobial developments. Mol Microbiol 2017; 104:889-904. [DOI: 10.1111/mmi.13675] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier (IRIM); CNRS, UMR 9004, Université de Montpellier, France
| | - Violaine Dubois
- INSERM, UMR1173; Université de Versailles Saint-Quentin-en-Yvelines; Montigny-le-Bretonneux 78180 France
| | - Fabienne Girard-Misguich
- INSERM, UMR1173; Université de Versailles Saint-Quentin-en-Yvelines; Montigny-le-Bretonneux 78180 France
| | - Mickaël Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM); CNRS, UMR 9004, Université de Montpellier, France
| | - Jean-Louis Herrmann
- INSERM, UMR1173; Université de Versailles Saint-Quentin-en-Yvelines; Montigny-le-Bretonneux 78180 France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM); CNRS, UMR 9004, Université de Montpellier, France
- IRIM; INSERM; 34293 Montpellier France
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Touchette MH, Seeliger JC. Transport of outer membrane lipids in mycobacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:1340-1354. [PMID: 28110100 DOI: 10.1016/j.bbalip.2017.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 12/24/2022]
Abstract
The complex organization of the mycobacterial cell wall poses unique challenges for the study of its assembly. Although mycobacteria are classified evolutionarily as Gram-positive bacteria, their cell wall architecture more closely resembles that of Gram-negative organisms. They possess not only an inner cytoplasmic membrane, but also a bilayer outer membrane that encloses an aqueous periplasm and includes diverse lipids that are required for the survival and virulence of pathogenic species. Questions surrounding how mycobacterial outer membrane lipids are transported from where they are made in the cytoplasm to where they function at the cell exterior are thus similar, and similarly compelling, to those that have driven the study of Gram-negative outer membrane transport pathways. However, little is understood about these processes in mycobacteria. Here we contextualize these questions by comparing our current knowledge of mycobacteria with better-defined systems in other organisms. Based on this analysis, we propose possible models and highlight continuing challenges to improving our understanding of outer membrane assembly in these medically and environmentally important bacteria. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Megan H Touchette
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, United States
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, United States.
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Chalut C. MmpL transporter-mediated export of cell-wall associated lipids and siderophores in mycobacteria. Tuberculosis (Edinb) 2016; 100:32-45. [DOI: 10.1016/j.tube.2016.06.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/23/2016] [Indexed: 10/21/2022]
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Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress. Infect Immun 2016; 84:2505-23. [PMID: 27324481 DOI: 10.1128/iai.00072-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/10/2016] [Indexed: 12/27/2022] Open
Abstract
Increasing experimental evidence supports the idea that Mycobacterium tuberculosis has evolved strategies to survive within lysosomes of activated macrophages. To further our knowledge of M. tuberculosis response to the hostile lysosomal environment, we profiled the global transcriptional activity of M. tuberculosis when exposed to the lysosomal soluble fraction (SF) prepared from activated macrophages. Transcriptome sequencing (RNA-seq) analysis was performed using various incubation conditions, ranging from noninhibitory to cidal based on the mycobacterial replication or killing profile. Under inhibitory conditions that led to the absence of apparent mycobacterial replication, M. tuberculosis expressed a unique transcriptome with modulation of genes involved in general stress response, metabolic reprogramming, respiration, oxidative stress, dormancy response, and virulence. The transcription pattern also indicates characteristic cell wall remodeling with the possible outcomes of increased infectivity, intrinsic resistance to antibiotics, and subversion of the host immune system. Among the lysosome-specific responses, we identified the glgE-mediated 1,4 α-glucan synthesis pathway and a defined group of VapBC toxin/anti-toxin systems, both of which represent toxicity mechanisms that potentially can be exploited for killing intracellular mycobacteria. A meta-analysis including previously reported transcriptomic studies in macrophage infection and in vitro stress models was conducted to identify overlapping and nonoverlapping pathways. Finally, the Tap efflux pump-encoding gene Rv1258c was selected for validation. An M. tuberculosis ΔRv1258c mutant was constructed and displayed increased susceptibility to killing by lysosomal SF and the antimicrobial peptide LL-37, as well as attenuated survival in primary murine macrophages and human macrophage cell line THP-1.
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31
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Ganji R, Dhali S, Rizvi A, Rapole S, Banerjee S. Understanding HIV-Mycobacteria synergism through comparative proteomics of intra-phagosomal mycobacteria during mono- and HIV co-infection. Sci Rep 2016; 6:22060. [PMID: 26916387 PMCID: PMC4768096 DOI: 10.1038/srep22060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/04/2016] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the most common co-infection in HIV patients and a serious co-epidemic. Apart from increasing the risk of reactivation of latent tuberculosis (TB), HIV infection also permits opportunistic infection of environmental non-pathogenic mycobacteria. To gain insights into mycobacterial survival inside host macrophages and identify mycobacterial proteins or processes that influence HIV propagation during co-infection, we employed proteomics approach to identify differentially expressed intracellular mycobacterial proteins during mono- and HIV co-infection of human THP-1 derived macrophage cell lines. Of the 92 proteins identified, 30 proteins were upregulated during mycobacterial mono-infection and 40 proteins during HIV-mycobacteria co-infection. We observed down-regulation of toxin-antitoxin (TA) modules, up-regulation of cation transporters, Type VII (Esx) secretion systems, proteins involved in cell wall lipid or protein metabolism, glyoxalate pathway and branched chain amino-acid synthesis during co-infection. The bearings of these mycobacterial factors or processes on HIV propagation during co-infection, as inferred from the proteomics data, were validated using deletion mutants of mycobacteria. The analyses revealed mycobacterial factors that possibly via modulating the host environment, increased viral titers during co-infection. The study provides new leads for investigations towards hitherto unknown molecular mechanisms explaining HIV-mycobacteria synergism, helping address diagnostics and treatment challenges for effective co-epidemic management.
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Affiliation(s)
- Rakesh Ganji
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, India
| | - Snigdha Dhali
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Arshad Rizvi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, India
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32
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Abstract
This article summarizes what is currently known of the structures, physiological roles, involvement in pathogenicity, and biogenesis of a variety of noncovalently bound cell envelope lipids and glycoconjugates of Mycobacterium tuberculosis and other Mycobacterium species. Topics addressed in this article include phospholipids; phosphatidylinositol mannosides; triglycerides; isoprenoids and related compounds (polyprenyl phosphate, menaquinones, carotenoids, noncarotenoid cyclic isoprenoids); acyltrehaloses (lipooligosaccharides, trehalose mono- and di-mycolates, sulfolipids, di- and poly-acyltrehaloses); mannosyl-beta-1-phosphomycoketides; glycopeptidolipids; phthiocerol dimycocerosates, para-hydroxybenzoic acids, and phenolic glycolipids; mycobactins; mycolactones; and capsular polysaccharides.
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33
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Trehalose Polyphleates Are Produced by a Glycolipid Biosynthetic Pathway Conserved across Phylogenetically Distant Mycobacteria. Cell Chem Biol 2016; 23:278-289. [PMID: 27028886 DOI: 10.1016/j.chembiol.2015.11.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 11/02/2015] [Accepted: 11/26/2015] [Indexed: 11/22/2022]
Abstract
Mycobacteria synthesize a variety of structurally related glycolipids with major biological functions. Common themes have emerged for the biosynthesis of these glycolipids, including several families of proteins. Genes encoding these proteins are usually clustered on bacterial chromosomal islets dedicated to the synthesis of one glycolipid family. Here, we investigated the function of a cluster of five genes widely distributed across non-tuberculous mycobacteria. Using defined mutant analysis and in-depth structural characterization of glycolipids from wild-type or mutant strains of Mycobacterium smegmatis and Mycobacterium abscessus, we established that they are involved in the formation of trehalose polyphleates (TPP), a family of compounds originally described in Mycobacterium phlei. Comparative genomics and lipid analysis of strains distributed along the mycobacterial phylogenetic tree revealed that TPP is synthesized by a large number of non-tuberculous mycobacteria. This work unravels a novel glycolipid biosynthetic pathway in mycobacteria and extends the spectrum of bacteria that produce TPP.
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34
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Székely R, Cole ST. Mechanistic insight into mycobacterial MmpL protein function. Mol Microbiol 2016; 99:831-4. [DOI: 10.1111/mmi.13306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2015] [Indexed: 01/05/2023]
Affiliation(s)
- R. Székely
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute; CH1015 Lausanne Switzerland
| | - S. T. Cole
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute; CH1015 Lausanne Switzerland
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35
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Stamm CE, Collins AC, Shiloh MU. Sensing of Mycobacterium tuberculosis and consequences to both host and bacillus. Immunol Rev 2015; 264:204-19. [PMID: 25703561 DOI: 10.1111/imr.12263] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the primary causative agent of human tuberculosis, has killed more people than any other bacterial pathogen in human history and remains one of the most important transmissible diseases worldwide. Because of the long-standing interaction of Mtb with humans, it is no surprise that human mucosal and innate immune cells have evolved multiple mechanisms to detect Mtb during initial contact. To that end, the cell surface of human cells is decorated with numerous pattern recognition receptors for a variety of mycobacterial ligands. Furthermore, once Mtb is ingested into professional phagocytes, other host molecules are engaged to report on the presence of an intracellular pathogen. In this review, we discuss the role of specific mycobacterial products in modulating the host's ability to detect Mtb. In addition, we describe the specific host receptors that mediate the detection of mycobacterial infection and the role of individual receptors in mycobacterial pathogenesis in humans and model organisms.
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Affiliation(s)
- Chelsea E Stamm
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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36
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Delmar JA, Chou TH, Wright CC, Licon MH, Doh JK, Radhakrishnan A, Kumar N, Lei HT, Bolla JR, Rajashankar KR, Su CC, Purdy GE, Yu EW. Structural Basis for the Regulation of the MmpL Transporters of Mycobacterium tuberculosis. J Biol Chem 2015; 290:28559-28574. [PMID: 26396194 DOI: 10.1074/jbc.m115.683797] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 11/06/2022] Open
Abstract
The mycobacterial cell wall is critical to the virulence of these pathogens. Recent work shows that the MmpL (mycobacterial membrane protein large) family of transporters contributes to cell wall biosynthesis by exporting fatty acids and lipidic elements of the cell wall. The expression of the Mycobacterium tuberculosis MmpL proteins is controlled by a complex regulatory network, including the TetR family transcriptional regulators Rv3249c and Rv1816. Here we report the crystal structures of these two regulators, revealing dimeric, two-domain molecules with architecture consistent with the TetR family of regulators. Buried extensively within the C-terminal regulatory domains of Rv3249c and Rv1816, we found fortuitous bound ligands, which were identified as palmitic acid (a fatty acid) and isopropyl laurate (a fatty acid ester), respectively. Our results suggest that fatty acids may be the natural ligands of these regulatory proteins. Using fluorescence polarization and electrophoretic mobility shift assays, we demonstrate the recognition of promoter and intragenic regions of multiple mmpL genes by these proteins. Binding of palmitic acid renders these regulators incapable of interacting with their respective operator DNAs, which will result in derepression of the corresponding mmpL genes. Taken together, these experiments provide new perspectives on the regulation of the MmpL family of transporters.
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Affiliation(s)
- Jared A Delmar
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Tsung-Han Chou
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Catherine C Wright
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | - Meredith H Licon
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | - Julia K Doh
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | | | - Nitin Kumar
- Departments of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Hsiang-Ting Lei
- Departments of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Jani Reddy Bolla
- Departments of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Kanagalaghatta R Rajashankar
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439
| | - Chih-Chia Su
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Georgiana E Purdy
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | - Edward W Yu
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011; Departments of Chemistry, Iowa State University, Ames, Iowa 50011.
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37
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Touchette MH, Bommineni GR, Delle Bovi RJ, Gadbery JE, Nicora CD, Shukla AK, Kyle JE, Metz TO, Martin DW, Sampson NS, Miller WT, Tonge PJ, Seeliger JC. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids. Biochemistry 2015; 54:5457-68. [PMID: 26271001 DOI: 10.1021/acs.biochem.5b00455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although they are classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl β-diol, phthiocerol, with branched-chain fatty acids known as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. Here, we show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl β-diol substrate analogues. By applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinases PknB and PknE modify PapA5 on three overlapping Thr residues and that a fourth Thr is unique to PknE phosphorylation. These results clarify the DIM biosynthetic pathway and indicate post-translational modifications that warrant further elucidation for their roles in the regulation of DIM biosynthesis.
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Affiliation(s)
| | | | | | | | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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38
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Chim N, Torres R, Liu Y, Capri J, Batot G, Whitelegge JP, Goulding CW. The Structure and Interactions of Periplasmic Domains of Crucial MmpL Membrane Proteins from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2015; 22:1098-107. [PMID: 26278184 DOI: 10.1016/j.chembiol.2015.07.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/25/2015] [Accepted: 07/13/2015] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis mycobacterial membrane protein large (MmpL) proteins are important in substrate transport across the inner membrane. Here, we show that MmpL proteins are classified into two phylogenetic clusters, where MmpL cluster II contains three soluble domains (D1, D2, and D3) and has two full-length members, MmpL3 and MmpL11. Significantly, MmpL3 is currently the most druggable M. tuberculosis target. We have solved the 2.4-Å MmpL11-D2 crystal structure, revealing structural homology to periplasmic porter subdomains of RND (multidrug) transporters. The resulting predicted cluster II MmpL membrane topology has D1 and D2 residing, and possibly interacting, within the periplasm. Crosslinking and biolayer interferometry experiments confirm that cluster II D1 and D2 bind with weak affinities, and guided D1-D2 heterodimeric model assemblies. The predicted full-length MmpL3 and MmpL11 structural models reveal key substrate binding and transport residues, and may serve as templates to set the stage for in silico anti-tuberculosis drug development.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Rodrigo Torres
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Yuqi Liu
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Joe Capri
- The Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA 90024, USA
| | - Gaëlle Batot
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA 90024, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, UCI, Irvine, CA 92697, USA.
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39
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Bailo R, Bhatt A, Aínsa JA. Lipid transport in Mycobacterium tuberculosis and its implications in virulence and drug development. Biochem Pharmacol 2015; 96:159-67. [DOI: 10.1016/j.bcp.2015.05.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/05/2015] [Indexed: 11/26/2022]
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40
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster. J Proteomics 2015; 125:1-16. [DOI: 10.1016/j.jprot.2015.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 01/05/2023]
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41
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Yu G, Cui Z, Sun X, Peng J, Jiang J, Wu W, Huang W, Chu K, Zhang L, Ge B, Li Y. Gene expression analysis of two extensively drug-resistant tuberculosis isolates show that two-component response systems enhance drug resistance. Tuberculosis (Edinb) 2015; 95:303-14. [PMID: 25869645 DOI: 10.1016/j.tube.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/21/2015] [Indexed: 10/23/2022]
Abstract
Global analysis of expression profiles using DNA microarrays was performed between a reference strain H37Rv and two clinical extensively drug-resistant isolates in response to three anti-tuberculosis drug exposures (isoniazid, capreomycin, and rifampicin). A deep analysis was then conducted using a combination of genome sequences of the resistant isolates, resistance information, and related public microarray data. Certain known resistance-associated gene sets were significantly overrepresented in upregulated genes in the resistant isolates relative to that observed in H37Rv, which suggested a link between resistance and expression levels of particular genes. In addition, isoniazid and capreomycin response genes, but not rifampicin, either obtained from published works or our data, were highly consistent with the differentially expressed genes of resistant isolates compared to those of H37Rv, indicating a strong association between drug resistance of the isolates and genes differentially regulated by isoniazid and capreomycin exposures. Based on these results, 92 genes of the studied isolates were identified as candidate resistance genes, 10 of which are known resistance-related genes. Regulatory network analysis of candidate resistance genes using published networks and literature mining showed that three two-component regulatory systems and regulator CRP play significant roles in the resistance of the isolates by mediating the production of essential envelope components. Finally, drug sensitivity testing indicated strong correlations between expression levels of these regulatory genes and sensitivity to multiple anti-tuberculosis drugs in Mycobacterium tuberculosis. These findings may provide novel insights into the mechanism underlying the emergence and development of drug resistance in resistant tuberculosis isolates and useful clues for further studies on this issue.
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Affiliation(s)
- Guohua Yu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Zhenling Cui
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai 200433, PR China
| | - Xian Sun
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Jinfu Peng
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Jun Jiang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Wei Wu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Wenhua Huang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Kaili Chu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Lu Zhang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai 200433, PR China.
| | - Yao Li
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai 200433, PR China.
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42
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Yamaryo-Botte Y, Rainczuk AK, Lea-Smith DJ, Brammananth R, van der Peet PL, Meikle P, Ralton JE, Rupasinghe TWT, Williams SJ, Coppel RL, Crellin PK, McConville MJ. Acetylation of trehalose mycolates is required for efficient MmpL-mediated membrane transport in Corynebacterineae. ACS Chem Biol 2015; 10:734-46. [PMID: 25427102 DOI: 10.1021/cb5007689] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogenic species of Mycobacteria and Corynebacteria, including Mycobacterium tuberculosis and Corynebacterium diphtheriae, synthesize complex cell walls that are rich in very long-chain mycolic acids. These fatty acids are synthesized on the inner leaflet of the cell membrane and are subsequently transported to the periplasmic space as trehalose monomycolates (TMM), where they are conjugated to other cell wall components and to TMM to form trehalose dimycolates (TDM). Mycobacterial TMM, and the equivalent Corynebacterium glutamicum trehalose corynomycolates (TMCM), are transported across the inner membrane by MmpL3, or NCgl0228 and NCgl2769, respectively, although little is known about how this process is regulated. Here, we show that transient acetylation of the mycolyl moiety of TMCM is required for periplasmic export. A bioinformatic search identified a gene in a cell wall biosynthesis locus encoding a putative acetyltransferase (M. tuberculosis Rv0228/C. glutamicum NCgl2759) that was highly conserved in all sequenced Corynebacterineae. Deletion of C. glutamicum NCgl2759 resulted in the accumulation of TMCM, with a concomitant reduction in surface transport of this glycolipid and syntheses of cell wall trehalose dicorynomycolates. Strikingly, loss of NCgl2759 was associated with a defect in the synthesis of a minor, and previously uncharacterized, glycolipid species. This lipid was identified as trehalose monoacetylcorynomycolate (AcTMCM) by mass spectrometry and chemical synthesis of the authentic standard. The in vitro synthesis of AcTMCM was dependent on acetyl-CoA, whereas in vivo [(14)C]-acetate pulse-chase labeling showed that this lipid was rapidly synthesized and turned over in wild-type and genetically complemented bacterial strains. Significantly, the biochemical and TMCM/TDCM transport phenotype observed in the ΔNCgl2759 mutant was phenocopied by inhibition of the activities of the two C. glutamicum MmpL3 homologues. Collectively, these data suggest that NCgl2759 is a novel TMCM mycolyl acetyltransferase (TmaT) that regulates transport of TMCM and is a potential drug target in pathogenic species.
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Affiliation(s)
| | | | | | | | | | - Peter Meikle
- Metabolomics
Laboratory, Baker IDI Heart and Diabetes Institute, 75 Commercial
Road, Melbourne, Victoria 3004, Australia
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43
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Sandhu P, Akhter Y. The internal gene duplication and interrupted coding sequences in the MmpL genes of Mycobacterium tuberculosis: Towards understanding the multidrug transport in an evolutionary perspective. Int J Med Microbiol 2015; 305:413-23. [PMID: 25841626 DOI: 10.1016/j.ijmm.2015.03.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/18/2014] [Accepted: 03/10/2015] [Indexed: 11/25/2022] Open
Abstract
The multidrug resistance has emerged as a major problem in the treatment of many of the infectious diseases. Tuberculosis (TB) is one of such disease caused by Mycobacterium tuberculosis. There is short term chemotherapy to treat the infection, but the main hurdle is the development of the resistance to antibiotics. This resistance is primarily due to the impermeable mycolic acid rich cell wall of the bacteria and other factors such as efflux of antibiotics from the bacterial cell. The MmpL (Mycobacterial Membrane Protein Large) proteins of mycobacteria are involved in the lipid transport and antibiotic efflux as indicated by the preliminary reports. We present here, comprehensive comparative sequence and structural analysis, which revealed topological signatures shared by the MmpL proteins and RND (Resistance Nodulation Division) multidrug efflux transporters. This provides evidence in support of the notion that they belong to the extended RND permeases superfamily. In silico modelled tertiary structures are in homology with an integral membrane component present in all of the RND efflux pumps. We document internal gene duplication and gene splitting events happened in the MmpL genes, which further elucidate the molecular functions of these putative transporters in an evolutionary perspective.
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Affiliation(s)
- Padmani Sandhu
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Shahpur District, Kangra 176206, Himachal Pradesh, India
| | - Yusuf Akhter
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Shahpur District, Kangra 176206, Himachal Pradesh, India.
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Mdluli K, Kaneko T, Upton A. The tuberculosis drug discovery and development pipeline and emerging drug targets. Cold Spring Harb Perspect Med 2015; 5:a021154. [PMID: 25635061 PMCID: PMC4448709 DOI: 10.1101/cshperspect.a021154] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Anna Upton
- Global Alliance for TB Drug Development, New York, New York 10005
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Hojo M, Omi A, Hamanaka G, Shindo K, Shimada A, Kondo M, Narita T, Kiyomoto M, Katsuyama Y, Ohnishi Y, Irie N, Takeda H. Unexpected link between polyketide synthase and calcium carbonate biomineralization. ZOOLOGICAL LETTERS 2015; 1:3. [PMID: 26605048 PMCID: PMC4604110 DOI: 10.1186/s40851-014-0001-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/15/2014] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms. RESULTS We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates. CONCLUSION The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.
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Affiliation(s)
- Motoki Hojo
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24–1, Hyakunincho, Shinju-ku, Tokyo 169-0073 Japan
| | - Ai Omi
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022 Japan
| | - Gen Hamanaka
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Kazutoshi Shindo
- />Department of Food and Nutrition, Japan Women’s University, 2-8-1, Mejirodai, Bunkyo-ku, Tokyo 112-8681 Japan
| | - Atsuko Shimada
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Mariko Kondo
- />Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225 Japan
| | - Takanori Narita
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Laboratory of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa 252-0880 Japan
| | - Masato Kiyomoto
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Yohei Katsuyama
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Naoki Irie
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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Belardinelli JM, Larrouy-Maumus G, Jones V, Sorio de Carvalho LP, McNeil MR, Jackson M. Biosynthesis and translocation of unsulfated acyltrehaloses in Mycobacterium tuberculosis. J Biol Chem 2014; 289:27952-65. [PMID: 25124040 PMCID: PMC4183827 DOI: 10.1074/jbc.m114.581199] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
A number of species-specific polymethyl-branched fatty acid-containing trehalose esters populate the outer membrane of Mycobacterium tuberculosis. Among them, 2,3-diacyltrehaloses (DAT) and penta-acyltrehaloses (PAT) not only play a structural role in the cell envelope but also contribute to the ability of M. tuberculosis to multiply and persist in the infected host, promoting the intracellular survival of the bacterium and modulating host immune responses. The nature of the machinery, topology, and sequential order of the reactions leading to the biosynthesis, assembly, and export of these complex glycolipids to the cell surface are the object of the present study. Our genetic and biochemical evidence corroborates a model wherein the biosynthesis and translocation of DAT and PAT to the periplasmic space are coupled and topologically split across the plasma membrane. The formation of DAT occurs on the cytosolic face of the plasma membrane through the action of PapA3, FadD21, and Pks3/4; that of PAT occurs on the periplasmic face via transesterification reactions between DAT substrates catalyzed by the acyltransferase Chp2 (Rv1184c). The integral membrane transporter MmpL10 is essential for DAT to reach the cell surface, and its presence in the membrane is required for Chp2 to be active. Disruption of mmpL10 or chp2 leads to an important build-up of DAT inside the cells and to the formation of a novel form of unsulfated acyltrehalose esterified with polymethyl-branched fatty acids normally found in sulfolipids that is translocated to the cell surface.
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Affiliation(s)
- Juan Manuel Belardinelli
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682 and
| | - Gérald Larrouy-Maumus
- the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Victoria Jones
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682 and
| | - Luiz Pedro Sorio de Carvalho
- the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Michael R McNeil
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682 and
| | - Mary Jackson
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682 and
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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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48
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Yang L, Lu S, Belardinelli J, Huc-Claustre E, Jones V, Jackson M, Zgurskaya HI. RND transporters protect Corynebacterium glutamicum from antibiotics by assembling the outer membrane. Microbiologyopen 2014; 3:484-96. [PMID: 24942069 PMCID: PMC4287177 DOI: 10.1002/mbo3.182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/28/2014] [Accepted: 05/09/2014] [Indexed: 01/28/2023] Open
Abstract
Corynebacterium-Mycobacterium-Nocardia (CMN) group are the causative agents of a broad spectrum of diseases in humans. A distinctive feature of these Gram-positive bacteria is the presence of an outer membrane of unique structure and composition. Recently, resistance-nodulation-division (RND) transporters (nicknamed MmpLs, Mycobacterial membrane protein Large) have emerged as major contributors to the biogenesis of the outer membranes in mycobacteria and as promising drug targets. In this study, we investigated the role of RND transporters in the physiology of Corynebacterium glutamicum and analyzed properties of these proteins. Our results show that in contrast to Gram-negative species, in which RND transporters actively extrude antibiotics from cells, in C. glutamicum and relatives these transporters protect cells from antibiotics by playing essential roles in the biogenesis of the low-permeability barrier of the outer membrane. Conditional C. glutamicum mutants lacking RND proteins and with the controlled expression of either NCgl2769 (CmpL1) or NCgl0228 (CmpL4) are hypersusceptible to multiple antibiotics, have growth deficiencies in minimal medium and accumulate intracellularly trehalose monocorynomycolates, free corynomycolates, and the previously uncharacterized corynomycolate-containing lipid. Our results also suggest that similar to other RND transporters, Corynebacterial membrane proteins Large (CmpLs) functions are dependent on a proton-motive force.
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Affiliation(s)
- Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019
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49
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Abstract
Current tuberculosis (TB) therapies take too long and the regimens are complex and subject to adverse effects and drug-drug interactions with concomitant medications. The emergence of drug-resistant TB strains exacerbates the situation. Drug discovery for TB has resurged in recent years, generating compounds (hits) with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review proposes strategies for generating improved hits and leads that could help achieve this goal.
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50
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Radhakrishnan A, Kumar N, Wright CC, Chou TH, Tringides ML, Bolla JR, Lei HT, Rajashankar KR, Su CC, Purdy GE, Yu EW. Crystal structure of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis. J Biol Chem 2014; 289:16526-40. [PMID: 24737322 DOI: 10.1074/jbc.m113.538959] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recent work demonstrates that the MmpL (mycobacterial membrane protein large) transporters are dedicated to the export of mycobacterial lipids for cell wall biosynthesis. An MmpL transporter frequently works with an accessory protein, belonging to the MmpS (mycobacterial membrane protein small) family, to transport these key virulence factors. One such efflux system in Mycobacterium tuberculosis is the MmpS5-MmpL5 transporter. The expression of MmpS5-MmpL5 is controlled by the MarR-like transcriptional regulator Rv0678, whose open reading frame is located downstream of the mmpS5-mmpL5 operon. To elucidate the structural basis of Rv0678 regulation, we have determined the crystal structure of this regulator, to 1.64 Å resolution, revealing a dimeric two-domain molecule with an architecture similar to members of the MarR family of transcriptional regulators. Rv0678 is distinct from other MarR regulators in that its DNA-binding and dimerization domains are clustered together. These two domains seemingly cooperate to bind an inducing ligand that we identified as 2-stearoylglycerol, which is a fatty acid glycerol ester. The structure also suggests that the conformational change leading to substrate-mediated derepression is primarily caused by a rigid body rotational motion of the entire DNA-binding domain of the regulator toward the dimerization domain. This movement results in a conformational state that is incompatible with DNA binding. We demonstrate using electrophoretic mobility shift assays that Rv0678 binds to the mmpS5-mmpL5, mmpS4-mmpL4, and the mmpS2-mmpL2 promoters. Binding by Rv0678 was reversed upon the addition of the ligand. These findings provide new insight into the mechanisms of gene regulation in the MarR family of regulators.
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Affiliation(s)
| | | | - Catherine C Wright
- the Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239, and
| | - Tsung-Han Chou
- the Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | | | | | | | - Kanagalaghatta R Rajashankar
- the Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439
| | - Chih-Chia Su
- the Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Georgiana E Purdy
- the Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239, and
| | - Edward W Yu
- From the Department of Chemistry and the Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011,
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