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Cooper BF, Ratkevičiūtė G, Clifton LA, Johnston H, Holyfield R, Hardy DJ, Caulton SG, Chatterton W, Sridhar P, Wotherspoon P, Hughes GW, Hall SC, Lovering AL, Knowles TJ. An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system. EMBO Rep 2024; 25:82-101. [PMID: 38228789 PMCID: PMC10897342 DOI: 10.1038/s44319-023-00014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. The pathway comprises three components: an integral inner membrane protein (PqiA), a periplasmic spanning MCE family protein (PqiB) and an outer membrane lipoprotein (PqiC). Interactions between all complex components, including stoichiometry, remain uncharacterised; nevertheless, once assembled into their quaternary complex, the trio of Pqi proteins are anticipated to provide a continuous channel between the inner and outer membranes of diderms. Here, we present X-ray structures of both the native and a truncated, soluble construct of the PqiC lipoprotein, providing insight into its biological assembly, and utilise neutron reflectometry to characterise the nature of the PqiB-PqiC-membrane interaction. Finally, we employ phenotypic complementation assays to probe specific PqiC residues, which imply the interaction between PqiB and PqiC is less intimate than previously anticipated.
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Affiliation(s)
- Benjamin F Cooper
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | | | - Luke A Clifton
- ISIS Pulsed Neutron & Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Harwell Oxford Campus, OX11 OQX, Didcot, UK
| | - Hannah Johnston
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Rachel Holyfield
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - David J Hardy
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Simon G Caulton
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - William Chatterton
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Peter Wotherspoon
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Gareth W Hughes
- Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Stephen Cl Hall
- ISIS Pulsed Neutron & Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Harwell Oxford Campus, OX11 OQX, Didcot, UK
| | - Andrew L Lovering
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK.
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Chen Y, MacGilvary NJ, Tan S. Mycobacterium tuberculosis response to cholesterol is integrated with environmental pH and potassium levels via a lipid metabolism regulator. PLoS Genet 2024; 20:e1011143. [PMID: 38266039 PMCID: PMC10843139 DOI: 10.1371/journal.pgen.1011143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/05/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024] Open
Abstract
Successful colonization of the host requires Mycobacterium tuberculosis (Mtb) to sense and respond coordinately to disparate environmental cues during infection and adapt its physiology. However, how Mtb response to environmental cues and the availability of key carbon sources may be integrated is poorly understood. Here, by exploiting a reporter-based genetic screen, we have unexpectedly found that overexpression of transcription factors involved in Mtb lipid metabolism altered the dampening effect of low environmental potassium concentrations ([K+]) on the pH response of Mtb. Cholesterol is a major carbon source for Mtb during infection, and transcriptional analyses revealed that Mtb response to acidic pH was augmented in the presence of cholesterol and vice versa. Strikingly, deletion of the putative lipid regulator mce3R had little effect on Mtb transcriptional response to acidic pH or cholesterol individually, but resulted specifically in loss of cholesterol response augmentation in the simultaneous presence of acidic pH. Similarly, while mce3R deletion had little effect on Mtb response to low environmental [K+] alone, augmentation of the low [K+] response by the simultaneous presence of cholesterol was lost in the mutant. Finally, a mce3R deletion mutant was attenuated for growth in foamy macrophages and for colonization in a murine infection model that recapitulates caseous necrotic lesions and the presence of foamy macrophages. These findings reveal the critical coordination between Mtb response to environmental cues and cholesterol, a vital carbon source, and establishes Mce3R as a transcription factor that crucially serves to integrate these signals.
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Affiliation(s)
- Yue Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Nathan J. MacGilvary
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Current affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
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3
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Maity D, Singh D, Bandhu A. Mce1R of Mycobacterium tuberculosis prefers long-chain fatty acids as specific ligands: a computational study. Mol Divers 2023; 27:2523-2543. [PMID: 36385433 DOI: 10.1007/s11030-022-10566-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 11/04/2022] [Indexed: 11/17/2022]
Abstract
The mce1 operon of Mycobacterium tuberculosis, which codes the Mce1 transporter, facilitates the transport of fatty acids. Fatty acids are one of the major sources for carbon and energy for the pathogen during its intracellular survival and pathogenicity. The mce1 operon is transcriptionally regulated by Mce1R, a VanR-type regulator, which could bind specific ligands and control the expression of the mce1 operon accordingly. This work reports computational identification of Mce1R-specific ligands. Initially by employing cavity similarity search algorithm by the ProBis server, the cavities of the proteins similar to that of Mce1R and the bound ligands were identified from which fatty acids were selected as the potential ligands. From the earlier-generated monomeric structure, the dimeric structure of Mce1R was then modeled by the GalaxyHomomer server and validated computationally to use in molecular docking and molecular dynamics simulation analysis. The fatty acid ligands were found to dock within the cavity of Mce1R and the docked complexes were subjected to molecular dynamics simulation to explore their stabilities and other dynamic properties. The data suggest that Mce1R preferably binds to long-chain fatty acids and undergoes distinct structural changes upon binding.
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Affiliation(s)
- Dipanwita Maity
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Dheeraj Singh
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Amitava Bandhu
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India.
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4
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Chen Y, Wang Y, Chng SS. A conserved membrane protein negatively regulates Mce1 complexes in mycobacteria. Nat Commun 2023; 14:5897. [PMID: 37736771 PMCID: PMC10517005 DOI: 10.1038/s41467-023-41578-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Tuberculosis continues to pose a serious threat to global health. Mycobacterium tuberculosis, the causative agent of tuberculosis, is an intracellular pathogen that relies on various mechanisms to survive and persist within the host. Among their many virulence factors, mycobacteria encode Mce systems. Some of these systems are implicated in lipid uptake, but the molecular basis for Mce function(s) is poorly understood. To gain insights into the composition and architecture of Mce systems, we characterized the putative Mce1 complex involved in fatty acid transport. We show that the Mce1 system in Mycobacterium smegmatis comprises a canonical ATP-binding cassette transporter associated with distinct heterohexameric assemblies of substrate-binding proteins. Furthermore, we establish that the conserved membrane protein Mce1N negatively regulates Mce1 function via a unique mechanism involving blocking transporter assembly. Our work offers a molecular understanding of Mce complexes, sheds light on mycobacterial lipid metabolism and its regulation, and informs future anti-mycobacterial strategies.
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Affiliation(s)
- Yushu Chen
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Yuchun Wang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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5
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Chen Y, MacGilvary NJ, Tan S. Mycobacterium tuberculosis response to cholesterol is integrated with environmental pH and potassium levels via a lipid utilization regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554309. [PMID: 37662244 PMCID: PMC10473576 DOI: 10.1101/2023.08.22.554309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
How bacterial response to environmental cues and nutritional sources may be integrated in enabling host colonization is poorly understood. Exploiting a reporter-based screen, we discovered that overexpression of Mycobacterium tuberculosis (Mtb) lipid utilization regulators altered Mtb acidic pH response dampening by low environmental potassium (K+). Transcriptional analyses unveiled amplification of Mtb response to acidic pH in the presence of cholesterol, a major carbon source for Mtb during infection, and vice versa. Strikingly, deletion of the putative lipid regulator mce3R resulted in loss of augmentation of (i) cholesterol response at acidic pH, and (ii) low [K+] response by cholesterol, with minimal effect on Mtb response to each signal individually. Finally, the ∆mce3R mutant was attenuated for colonization in a murine model that recapitulates lesions with lipid-rich foamy macrophages. These findings reveal critical coordination between bacterial response to environmental and nutritional cues, and establish Mce3R as a crucial integrator of this process.
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Affiliation(s)
- Yue Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Nathan J. MacGilvary
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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Ji L, Jiang T, Zhao X, Cai D, Hua K, Du P, Chen Y, Xie J. Mycobacterium tuberculosis Rv0494 Protein Contributes to Mycobacterial Persistence. Infect Drug Resist 2023; 16:4755-4762. [PMID: 37501888 PMCID: PMC10370413 DOI: 10.2147/idr.s419914] [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: 05/06/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Purpose Fatty acid metabolism plays an important role in the survival and pathogenesis of Mycobacterium tuberculosis. During dormancy, lipids are considered to be the main source of energy. A previous study found that Rv0494 is a starvation-inducible, lipid-responsive transcriptional regulator. However, the role of Rv0494 in bacterial persister survival has not been studied. Methods We constructed a Rv0494 deletion mutant strain of Mycobacterium tuberculosis H37Rv and evaluated the susceptibility of the mutant strain to antibiotics using a persistence test. Results We found that mutations in Rv0494 lead to survival defects of persisters, which reflected in increased sensitivity to isoniazid. Conclusion We conclude that Rv0494 is important for persister survival and may serve as a good target for developing new antibiotics that kill persister bacteria for improved treatment of persistent bacterial infections.
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Affiliation(s)
- Lei Ji
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Tingting Jiang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Xin Zhao
- Department of International Registration, Ustar Biotechnologies (Hangzhou) Ltd, Hangzhou, Zhejiang, People’s Republic of China
| | - Damin Cai
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Kouzhen Hua
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yuanyuan Chen
- Tuberculosis Diagnosis and Treatment Center, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, People’s Republic of 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 Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Chongqing, People’s Republic of China
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Chauhan NK, Anand A, Sharma A, Dhiman K, Gosain TP, Singh P, Singh P, Khan E, Chattopadhyay G, Kumar A, Sharma D, Ashish, Sharma TK, Singh R. Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein. Microbiol Spectr 2023; 11:e0197322. [PMID: 36507689 PMCID: PMC9927256 DOI: 10.1128/spectrum.01973-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.
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Affiliation(s)
- Neeraj Kumar Chauhan
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Anjali Anand
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Arun Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Kanika Dhiman
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Prashant Singh
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Padam Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Eshan Khan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | - Deepak Sharma
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ashish
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
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Rajwani R, Galata C, Lee AWT, So PK, Leung KSS, Tam KKG, Shehzad S, Ng TTL, Zhu L, Lao HY, Chan CTM, Leung JSL, Lee LK, Wong KC, Yam WC, Siu GKH. A multi-omics investigation into the mechanisms of hyper-virulence in Mycobacterium tuberculosis. Virulence 2022; 13:1088-1100. [PMID: 35791449 PMCID: PMC9262360 DOI: 10.1080/21505594.2022.2087304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical manifestations of tuberculosis range from asymptomatic infection to a life-threatening disease such as tuberculous meningitis (TBM). Recent studies showed that the spectrum of disease severity could be related to genetic diversity among clinical strains of Mycobacterium tuberculosis (Mtb). Certain strains are reported to preferentially invade the central nervous system, thus earning the label “hypervirulent strains”.However, specific genetic mutations that accounted for enhanced mycobacterial virulence are still unknown. We previously identified a set of 17 mutations in a hypervirulent Mtb strain that was from TBM patient and exhibited significantly better intracellular survivability. These mutations were also commonly shared by a cluster of globally circulating hyper-virulent strains. Here, we aimed to validate the impact of these hypervirulent-specific mutations on the dysregulation of gene networks associated with virulence in Mtb via multi-omic analysis. We surveyed transcriptomic and proteomic differences between the hyper-virulent and low-virulent strains using RNA-sequencing and label-free quantitative LC-MS/MS approach, respectively. We identified 25 genes consistently differentially expressed between the strains at both transcript and protein level, regardless the strains were growing in a nutrient-rich or a physiologically relevant multi-stress condition (acidic pH, limited nutrients, nitrosative stress, and hypoxia). Based on integrated genomic-transcriptomic and proteomic comparisons, the hypervirulent-specific mutations in FadE5 (g. 295,746 C >T), Rv0178 (p. asp150glu), higB (p. asp30glu), and pip (IS6110-insertion) were linked to deregulated expression of the respective genes and their functionally downstream regulons. The result validated the connections between mutations, gene expression, and mycobacterial pathogenicity, and identified new possible virulence-associated pathways in Mtb.
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Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chala Galata
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Annie Wing Tung Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Pui-Kin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kenneth Siu Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kingsley King Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Timothy Ting Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Li Zhu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kin Chung Wong
- Department of Clinical Pathology, United Christian Hospital, Hong Kong Special Administrative Region, China
| | - Wing Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
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Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. mSphere 2022; 7:e0003322. [PMID: 35306876 PMCID: PMC9044949 DOI: 10.1128/msphere.00033-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, and some studies have performed system-level analysis, few have been able to provide a network-based model of the TRN that also provides the relative shifts in transcriptional regulator activity triggered by changing environments. Here, we compiled a compendium of nearly 650 publicly available, high quality M. tuberculosis RNA-sequencing data sets and applied an unsupervised machine learning method to obtain a quantitative, top-down TRN. It consists of 80 independently modulated gene sets known as “iModulons,” 41 of which correspond to known regulons. These iModulons explain 61% of the variance in the organism’s transcriptional response. We show that iModulons (i) reveal the function of poorly characterized regulons, (ii) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and infection events, and (iii) identify intrinsic clusters of regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date. IMPORTANCEMycobacterium tuberculosis H37Rv is one of the world's most impactful pathogens, and a large part of the success of the organism relies on the differential expression of its genes to adapt to its environment. The expression of the organism's genes is driven primarily by its transcriptional regulatory network, and most research on the TRN focuses on identifying and quantifying clusters of coregulated genes known as regulons. While previous studies have relied on molecular measurements, in the manuscript we utilized an alternative technique that performs machine learning to a large data set of transcriptomic data. This approach is less reliant on hypotheses about the role of specific regulatory systems and allows for the discovery of new biological findings for already collected data. A better understanding of the structure of the M. tuberculosis TRN will have important implications in the design of improved therapeutic approaches.
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López-Agudelo VA, Baena A, Barrera V, Cabarcas F, Alzate JF, Beste DJV, Ríos-Estepa R, Barrera LF. Dual RNA Sequencing of Mycobacterium tuberculosis-Infected Human Splenic Macrophages Reveals a Strain-Dependent Host-Pathogen Response to Infection. Int J Mol Sci 2022; 23:ijms23031803. [PMID: 35163725 PMCID: PMC8836425 DOI: 10.3390/ijms23031803] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), leading to pulmonary and extrapulmonary TB, whereby Mtb is disseminated to many other organs and tissues. Dissemination occurs early during the disease, and bacteria can be found first in the lymph nodes adjacent to the lungs and then later in the extrapulmonary organs, including the spleen. The early global gene expression response of human tissue macrophages and intracellular clinical isolates of Mtb has been poorly studied. Using dual RNA-seq, we have explored the mRNA profiles of two closely related clinical strains of the Latin American and Mediterranean (LAM) family of Mtb in infected human splenic macrophages (hSMs). This work shows that these pathogens mediate a distinct host response despite their genetic similarity. Using a genome-scale host–pathogen metabolic reconstruction to analyze the data further, we highlight that the infecting Mtb strain also determines the metabolic response of both the host and pathogen. Thus, macrophage ontogeny and the genetic-derived program of Mtb direct the host–pathogen interaction.
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Affiliation(s)
- Víctor A. López-Agudelo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
- Grupo de Bioprocesos, Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
| | - Vianey Barrera
- Programa de Ingeniería Biológica, Universidad Nacional de Colombia, Sede Medellín, Medellín 050010, Colombia;
| | - Felipe Cabarcas
- Grupo Sistemas Embebidos e Inteligencia Computacional (SISTEMIC), Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica (CNSG), Sede de Investigación Universitaria (SIU), Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Dany J. V. Beste
- Department of Microbial Sciences, Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7XH, UK;
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
- Correspondence:
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Vilchèze C, Yan B, Casey R, Hingley-Wilson S, Ettwiller L, Jacobs WR. Commonalities of Mycobacterium tuberculosis Transcriptomes in Response to Defined Persisting Macrophage Stresses. Front Immunol 2022; 13:909904. [PMID: 35844560 PMCID: PMC9283954 DOI: 10.3389/fimmu.2022.909904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
As the goal of a bacterium is to become bacteria, evolution has imposed continued selections for gene expression. The intracellular pathogen Mycobacterium tuberculosis, the causative agent of tuberculosis, has adopted a fine-tuned response to survive its host's methods to aggressively eradicate invaders. The development of microarrays and later RNA sequencing has led to a better understanding of biological processes controlling the relationship between host and pathogens. In this study, RNA-seq was performed to detail the transcriptomes of M. tuberculosis grown in various conditions related to stresses endured by M. tuberculosis during host infection and to delineate a general stress response incurring during persisting macrophage stresses. M. tuberculosis was subjected to long-term growth, nutrient starvation, hypoxic and acidic environments. The commonalities between these stresses point to M. tuberculosis maneuvering to exploit propionate metabolism for lipid synthesis or to withstand propionate toxicity whilst in the intracellular environment. While nearly all stresses led to a general shutdown of most biological processes, up-regulation of pathways involved in the synthesis of amino acids, cofactors, and lipids were observed only in hypoxic M. tuberculosis. This data reveals genes and gene cohorts that are specifically or exclusively induced during all of these persisting stresses. Such knowledge could be used to design novel drug targets or to define possible M. tuberculosis vulnerabilities for vaccine development. Furthermore, the disruption of specific functions from this gene set will enhance our understanding of the evolutionary forces that have caused the tubercle bacillus to be a highly successful pathogen.
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Affiliation(s)
- Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Bo Yan
- Research Department, Genome Biology Division, New England Biolabs Inc., Ipswich, MA, United States
| | - Rosalyn Casey
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzie Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Laurence Ettwiller
- Research Department, Genome Biology Division, New England Biolabs Inc., Ipswich, MA, United States
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- *Correspondence: William R. Jacobs Jr,
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12
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Mycobacterial MCE proteins as transporters that control lipid homeostasis of the cell wall. Tuberculosis (Edinb) 2021; 132:102162. [PMID: 34952299 DOI: 10.1016/j.tube.2021.102162] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 01/05/2023]
Abstract
Mammalian cell entry (mce) genes are not only present in genomes of pathogenic mycobacteria, including Mycobacterium tuberculosis (the causative agent of tuberculosis), but also in saprophytic and opportunistic mycobacterial species. MCE are conserved cell-wall proteins encoded by mce operons, which maintain an identical structure in all mycobacteria: two yrbE genes (A and B) followed by six mce genes (A, B, C, D, E and F). Although these proteins are known to participate in the virulence of pathogenic mycobacteria, the presence of the operons in nonpathogenic mycobacteria and other bacteria indicates that they play another role apart from host cell invasion. In this respect, more recent studies suggest that they are functionally similar to ABC transporters and form part of lipid transporters in Actinobacteria. To date, most reviews on mce operons in the literature discuss their role in virulence. However, according to data from transcriptional studies, mce genes, particularly the mce1 and mce4 operons, modify their expression according to the carbon source and upon hypoxia, starvation, surface stress and oxidative stress; which suggests a role of MCE proteins in the response of Mycobacteria to external stressors. In addition to these data, this review also summarizes the studies demonstrating the role of MCE proteins as lipid transporters as well as the relevance of their transport function in the interaction of pathogenic Mycobacteria with the hosts. Altogether, the evidence to date would indicate that MCE proteins participate in the response to the stress conditions that mycobacteria encounter during infection, by participating in the cell wall remodelling and possibly contributing to lipid homeostasis.
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13
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Abeywickrama TD, Perera IC. In Silico Characterization and Virtual Screening of GntR/HutC Family Transcriptional Regulator MoyR: A Potential Monooxygenase Regulator in Mycobacterium tuberculosis. BIOLOGY 2021; 10:biology10121241. [PMID: 34943156 PMCID: PMC8698889 DOI: 10.3390/biology10121241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022]
Abstract
Simple Summary In an era where the world faces new diseases and pathogens, another emerging challenge is neglected pathogens becoming more notorious. Transcriptional regulators play a vital role in the pathogenesis and survival of these pathogens. Hence, characterizing transcriptional regulators, either in vitro or in silico, is of great importance. Here, we present the first structural characterization of a GntR/HutC regulator in Mycobacterium tuberculosis via in silico methods. We have suggested its possible role and potential as a drug target as well as identified possible drug leads that can be used for further improvements. Abstract Mycobacterium tuberculosis is a well-known pathogen due to the emergence of drug resistance associated with it, where transcriptional regulators play a key role in infection, colonization and persistence. The genome of M. tuberculosis encodes many transcriptional regulators, and here we report an in-depth in silico characterization of a GntR regulator: MoyR, a possible monooxygenase regulator. Homology modelling provided a reliable structure for MoyR, showing homology with a HutC regulator DasR from Streptomyces coelicolor. In silico physicochemical analysis revealed that MoyR is a cytoplasmic protein with higher thermal stability and higher pI. Four highly probable binding pockets were determined in MoyR and the druggability was higher in the orthosteric binding site consisting of three conserved critical residues: TYR179, ARG223 and GLU234. Two highly conserved leucine residues were identified in the effector-binding region of MoyR and other HutC homologues, suggesting that these two residues can be crucial for structure stability and oligomerization. Virtual screening of drug leads resulted in four drug-like compounds with greater affinity to MoyR with potential inhibitory effects for MoyR. Our findings support that this regulator protein can be valuable as a therapeutic target that can be used for developing drug leads.
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14
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Sundararajan S, Muniyan R. Latent tuberculosis: interaction of virulence factors in Mycobacterium tuberculosis. Mol Biol Rep 2021; 48:6181-6196. [PMID: 34351540 DOI: 10.1007/s11033-021-06611-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains a prominent health concern worldwide. Besides extensive research and vaccinations available, attempts to control the pandemic are cumbersome due to the complex physiology of Mycobacterium tuberculosis (Mtb). Alongside the emergence of drug-resistant TB, latent TB has worsened the condition. The tubercle bacilli are unusually behaved and successful with its strategies to modulate genes to evade host immune system and persist within macrophages. Under latent/unfavorable conditions, Mtb conceals itself from immune system and modulates its genes. Among many intracellular modulated genes, important are those involved in cell entry, fatty acid degradation, mycolic acid synthesis, phagosome acidification inhibition, inhibition of phagosome-lysosome complex and chaperon protein modulation. Though the study on these genes date back to early times of TB, an insight on their inter-relation within and to newly evolved genes are still required. This review focuses on the findings and discussions on these genes, possible mechanism, credibility as target for novel drugs and repurposed drugs and their interaction that enables Mtb in survival, pathogenesis, resistance and latency.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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15
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Madan R, Pandit K, Bhati L, Kumar H, Kumari N, Singh S. Mining the Mycobacterium tuberculosis proteome for identification of potential T-cell epitope based vaccine candidates. Microb Pathog 2021; 157:104996. [PMID: 34044044 DOI: 10.1016/j.micpath.2021.104996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/22/2022]
Abstract
Identification of protective antigens for designing a high-efficacy tuberculosis vaccine is the need of the hour. Till date only 7% of the Mycobacterium tuberculosis proteome has been explored for discovering antigens capable of activating T-cell responses. Therefore, it becomes crucial to screen the remaining Mycobacterium tuberculosis proteome for more immunodominant T-cell epitopes. An extensive knowledge of the epitopes recognized by our immune system can aid this process of finding potential T cell antigens for development of a better TB vaccine. In the present in-silico study, 237 proteins belonging to the 'virulence, detoxification, and adaptation' category of Mycobacterium tuberculosis proteome were targeted for T-cell epitope screening. 50825 MHC Class I and 49357 MHC Class II epitopes were generated using NetMHC3.4 and IEDB servers respectively and tested for their antigenicity and cytokine stimulation. The highest antigenic epitopes were analyzed for their world population coverage and epitope conservancy. Molecular docking and molecular dynamics simulation studies were performed to corroborate the binding affinities and structural stability of the peptide-MHC complexes. We predicted a total of 3 MHC Class I (ILLKMCWPA, FAVGMNVYV, and SLAGNSAKV) and 7 MHC Class II (DLTIGFFLHIPFPPV, RPDLTIGFFLHIPFP, LTIGFFLHIPFPPVE, VLVFALVVALVYLQF, LVFALVVALVYLQFR, PNLVAARFIQLTPVY, and LVLVFALVVALVYLQ) epitopes that can be promising vaccine candidates. These predicted epitopes belong to 6 distinct proteins: Rv0169 (mce1a), Rv3490 (ostA), Rv3496 (mce4D), Rv1085c, Rv0563 (HtpX), Rv3497c (mce4C). All these proteins are expressed at different stages in the life cycle of Mycobacterium tuberculosis and thus, the predicted epitopes could be employed as candidates for designing a multistage-multiepitopic vaccine.
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Affiliation(s)
- Riya Madan
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Kushankur Pandit
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Lavi Bhati
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Hindesh Kumar
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Neha Kumari
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Swati Singh
- Department of Zoology, Hansraj College, University of Delhi, India.
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16
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Almeida BC, Kaczmarek JA, Figueiredo PR, Prather KLJ, Carvalho ATP. Transcription factor allosteric regulation through substrate coordination to zinc. NAR Genom Bioinform 2021; 3:lqab033. [PMID: 33987533 PMCID: PMC8092373 DOI: 10.1093/nargab/lqab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/30/2021] [Accepted: 04/08/2021] [Indexed: 11/14/2022] Open
Abstract
The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight into allosteric transcription factors (aTFs). Here we studied the aTF UxuR, a homodimer of two domains connected by a highly flexible linker region. To explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein, the aTF bound to the inducer D-fructuronate or the structural isomer D-glucuronate. We then validated our results by constructing a sensor plasmid for D-fructuronate in Escherichia coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function since mutation to alanines prevents expression de-repression by D-fructuronate. Analyzing the different complexes, we found that the disordered linker regions allow the N-terminal domains to display fast and large movements. When the inducer is bound, UxuR can sample an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein samples closed conformations, with a more positive character at the surface of the DNA binding regions. These molecular insights provide a new basis to harness these systems for biological systems engineering.
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Affiliation(s)
- Beatriz C Almeida
- CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jennifer A Kaczmarek
- MIT-Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pedro R Figueiredo
- CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Kristala L J Prather
- MIT-Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra T P Carvalho
- CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal
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17
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Molecular Cloning, Purification and Characterization of Mce1R of Mycobacterium tuberculosis. Mol Biotechnol 2021; 63:200-220. [PMID: 33423211 DOI: 10.1007/s12033-020-00293-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The mce1 operon of Mycobacterium tuberculosis, important for lipid metabolism/transport, host cell invasion, modulation of host immune response and pathogenicity, is under the transcriptional control of Mce1R. Hence characterizing Mce1R is an important step for novel anti-tuberculosis drug discovery. The present study reports functional and in silico characterization of Mce1R. In this work, we have computationally modeled the structure of Mce1R and have validated the structure by computational and experimental methods. Mce1R has been shown to harbor the canonical VanR-like structure with a flexible N-terminal 'arm', carrying conserved positively charged residues, most likely involved in the operator DNA binding. The mce1R gene has been cloned, expressed, purified and its DNA-binding activity has been measured in vitro. The Kd value for Mce1R-operator DNA interaction has been determined to be 0.35 ± 0.02 µM which implies that Mce1R binds to DNA with moderate affinity compared to the other FCD family of regulators. So far, this is the first report for measuring the DNA-binding affinity of any VanR-type protein. Despite significant sequence similarity at the N-terminal domain, the wHTH motif of Mce1R exhibits poor conservancy of amino acid residues, critical for DNA-binding, thus results in moderate DNA-binding affinity. The N-terminal DNA-binding domain is structurally dynamic while the C-terminal domain showed significant stability and such profile of structural dynamics is most likely to be preserved in the structural orthologs of Mce1R. In addition to this, a cavity has been detected in the C-terminal domain of Mce1R which contains a few conserved residues. Comparison with other FCD family of regulators suggests that most of the conserved residues might be critical for binding to specific ligand. The max pKd value and drug score for the cavity are estimated to be 9.04 and 109 respectively suggesting that the cavity represents a suitable target site for novel anti-tuberculosis drug discovery approaches.
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18
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Lin Z, Sun Y, Liu Y, Tong S, Shang Z, Cai Y, Lin W. Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket. Front Microbiol 2020; 11:590330. [PMID: 33224125 PMCID: PMC7674646 DOI: 10.3389/fmicb.2020.590330] [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: 08/01/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
The transcription repressor of D-galactonate metabolism, DgoR, from Escherichia coli belongs to the FadR family of the GntR superfamily. In the presence of D-galactonate, DgoR binds to two inverted repeats overlapping the dgo cis-acting promoter repressing the expression of genes involved in D-galactonate metabolism. To further understand the structural and molecular details of ligand and effector interactions between D-galactonate and this FadR family member, herein we solved the crystal structure of C-terminal domain of DgoR (DgoR_C), which revealed a unique divalent metal-containing substrate binding pocket. The metal ion is required for D-galactonate binding, as evidenced by the dramatically decreased affinity between D-galactonate and DgoR in the presence of EDTA, which can be reverted by the addition of Zn2+, Mg2+, and Ca2+. The key amino acid residues involved in the interactions between D-galactonate and DgoR were revealed by molecular docking studies and further validated with biochemical studies by site-directed mutagenesis. It was found that changes to alanine in residues R102, W181, T191, and R224 resulted in significantly decreased binding affinities for D-galactonate, as determined by EMSA and MST assays. These results suggest that the molecular modifications induced by a D-galactonate and a metal binding in the DgoR are required for DNA binding activity and consequently, transcriptional inhibition.
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Affiliation(s)
- Zhaozhu Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Sun
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Liu
- Department of Chemistry, Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Shujuan Tong
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanheng Cai
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY, United States
| | - Wei Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
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19
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Petrilli JD, Müller I, Araújo LE, Cardoso TM, Carvalho LP, Barros BC, Teixeira M, Arruda S, Riley LW, Queiroz A. Differential Host Pro-Inflammatory Response to Mycobacterial Cell Wall Lipids Regulated by the Mce1 Operon. Front Immunol 2020; 11:1848. [PMID: 32973761 PMCID: PMC7461851 DOI: 10.3389/fimmu.2020.01848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/09/2020] [Indexed: 11/17/2022] Open
Abstract
The cell wall of wild-type (WT) Mycobacterium tuberculosis (Mtb), an etiologic agent of tuberculosis (TB) and a Mtb strain disrupted in a 13-gene operon mce1 (Δmce1) varies by more than 400 lipid species. Here, we examined Mtb lipid-induced response in murine macrophage, as well as in human T-cell subpopulations in order to gain an insight into how changes in cell wall lipid composition may modulate host immune response. Relative to WT Mtb cell wall lipids, the non-polar lipid extracts from Δmce1 enhanced the mRNA expression of lipid-sense nuclear receptors TR4 and PPAR-γ and dampened the macrophage expression of genes encoding TNF-α, IL-6, and IL-1β. Relative to untreated control, WT lipid-pre-stimulated macrophages from healthy individuals induced a higher level of CD4−CD8− double negative T-cells (DN T-cells) producing TNF-α. Conversely, compared to WT, stimulation with Δmce1 lipids induced higher mean fluorescence intensity (MFI) in IL-10-producing DN T cells. Mononuclear cells from TB patients stimulated with WT Mtb lipids induced an increased production of TNF-α by CD8+ lymphocytes. Taken together, these observations suggest that changes in mce1 operon expression during a course of infection may serve as a strategy by Mtb to evade the host pro-inflammatory responses.
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Affiliation(s)
- Jéssica D Petrilli
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Igor Müller
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Luana E Araújo
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Thiago M Cardoso
- Laboratório de Pesquisa Clínica, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Lucas P Carvalho
- Laboratório de Pesquisa Clínica, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Bruna C Barros
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Maurício Teixeira
- Laboratório de Pesquisa Clínica, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Sérgio Arruda
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Adriano Queiroz
- Laboratorio Avançado de Saúde Pública, Instituto Gonçalo Moniz, Salvador, Brazil
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20
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A safe non-toxic Brucella abortus ghosts induce immune responses and confer protection in BALB/c mice. Mol Immunol 2020; 124:117-124. [PMID: 32559678 DOI: 10.1016/j.molimm.2020.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Accepted: 06/01/2020] [Indexed: 11/23/2022]
Abstract
Brucellosis, which is caused by Brucella spp., is an important zoonotic infectious disease that can cause great hazard to public health and safety. However, the current vaccines have several drawbacks, including residual virulence for animals and humans. Bacterial ghost is the empty envelopes of bacteria, which emerge as a proper vaccine candidate. With the purpose of generating B. abortus ghosts and investigating the immunogenicity of bacterial ghosts as vaccine candidate, we used homologous recombination and bacterial ghost technologies to construct 2308ΔgntR ghost strain. Mice were injected with 2308ΔgntR ghost and the safety and immunogenicity of ghost were further evaluated. The mice inoculated with ghost showed no splenomegaly. The 2308ΔgntR ghost induced high protective immunity in BALB/c mice against challenge with S2308, and elicited an anti-Brucella-specific immunoglobulin G (IgG) response and induced the secretion of interferon gamma (IFN-γ) and interleukin-4 (IL-4). Additionally, 2308ΔgntR ghost demonstrated strong spleen CD4+ and CD8+ T cell responses. These results suggest that 2308ΔgntR ghost is a potential vaccine candidate and may represent a promising new approach for vaccination against Brucella infection.
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21
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Chiner-Oms Á, Sánchez-Busó L, Corander J, Gagneux S, Harris SR, Young D, González-Candelas F, Comas I. Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. SCIENCE ADVANCES 2019; 5:eaaw3307. [PMID: 31448322 PMCID: PMC6691555 DOI: 10.1126/sciadv.aaw3307] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/10/2019] [Indexed: 06/10/2023]
Abstract
Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.
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Affiliation(s)
- Á. Chiner-Oms
- Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (ISysBio), Valencia, Spain
| | - L. Sánchez-Busó
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - J. Corander
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
- Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
- Helsinki Institute of Information Technology (HIIT), Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
| | - S. Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - S. R. Harris
- Microbiotica, BioData Innovation Centre, Wellcome Genome Campus, Cambridge CB10 1DR, UK
| | - D. Young
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - F. González-Candelas
- Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (ISysBio), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | - I. Comas
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
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22
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Yan S, Zhen J, Li Y, Zhang C, Stojkoska A, Lambert N, Li Q, Li P, Xie J. Mce-associated protein Rv0177 alters the cell wall structure of Mycobacterium smegmatis and promotes macrophage apoptosis via regulating the cytokines. Int Immunopharmacol 2019; 66:205-214. [DOI: 10.1016/j.intimp.2018.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/26/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
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23
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Shur KV, Bekker OB, Zaichikova MV, Maslov DA, Akimova NI, Zakharevich NV, Chekalina MS, Danilenko VN. Genetic Aspects of Drug Resistance and Virulence in Mycobacterium tuberculosis. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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24
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Yousuf S, Angara RK, Roy A, Gupta SK, Misra R, Ranjan A. Mce2R/Rv0586 of Mycobacterium tuberculosis is the functional homologue of FadR E. coli. MICROBIOLOGY-SGM 2018; 164:1133-1145. [PMID: 29993358 DOI: 10.1099/mic.0.000686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lipid metabolism is critical to Mycobacterium tuberculosis survival and infection. Unlike Escherichia coli, which has a single FadR, the M. tuberculosis genome encodes five proteins of the FadR sub-family. While the role of E. coli FadR as a regulator of fatty acid metabolism is well known, the definitive functions of M. tuberculosis FadR proteins are still under investigation. An interesting question about the M. tuberculosis FadRs remains open: which one of these proteins is the functional homologue of E. coli FadR? To address this, we have applied two different approaches. The first one was the bioinformatics approach and the second one was the classical molecular genetic approach involving complementation studies. Surprisingly, the results of these two approaches did not agree. Among the five M. tuberculosis FadRs, Rv0494 shared the highest sequence similarity with FadRE. coli and Rv0586 was the second best match. However, only Rv0586, but not Rv0494, could complement E. coli ∆fadR, indicating that Rv0586 is the M. tuberculosis functional homologue of FadRE. coli. Further studies showed that both regulators, Rv0494 and Rv0586, show similar responsiveness to LCFA, and have conserved critical residues for DNA binding. However, analysis of the operator site indicated that the inter-palindromic distance required for DNA binding differs for the two regulators. The differences in the binding site selection helped in the success of Rv0586 binding to fadB upstream over Rv0494 and may have played a critical role in complementing E. coli ∆fadR. Further, for the first time, we report the lipid-responsive nature of Rv0586.
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Affiliation(s)
- Suhail Yousuf
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Rajendra Kumar Angara
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ajit Roy
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shailesh Kumar Gupta
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Rohan Misra
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akash Ranjan
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
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Li Z, Wang S, Zhang H, Xi L, Zhang J, Zhang X, Han J, Zhang J. Immunization with recombinant GntR plasmid confers protection against Brucella challenge in BALB/c mice. Microb Pathog 2017; 111:357-361. [PMID: 28916314 DOI: 10.1016/j.micpath.2017.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/27/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
It is essential to improve animal vaccine for brucellosis since conventional vaccines are residual virulent and poor protective effect, limit their applications. To solve these problems, the recombinant DNA vaccines were appeared, which could improve protective immunity and were attenuated to animals. In current research, the recombinant DNA vaccine (pVGntR) based on transcriptional regulator GntR of Brucella abortus (B. abortus) was constructed. The results show that pVGntR is significantly more protective than the conventional RB51 vaccine. Immunization with pVGntR increases the production of immunoglobulin G (IgG) and elicits elevated numbers of gamma interferon (IFN-γ) and interleukin-4 (IL-4). These results suggest that pVGntR is a highly efficacious vaccine candidate that confers protection against wild-type B. abortus challenge.
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Affiliation(s)
- Zhiqiang Li
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Shuli Wang
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Hui Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, Xinjiang, China.
| | - Li Xi
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Jinliang Zhang
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Xiaogen Zhang
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Jincheng Han
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Junbo Zhang
- College of Biology, Agriculture and Forestry, Tongren University, Tongren 554300, Guizhou, China
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Singh P, Katoch VM, Mohanty KK, Chauhan DS. Analysis of expression profile of mce operon genes (mce1, mce2, mce3 operon) in different Mycobacterium tuberculosis isolates at different growth phases. Indian J Med Res 2017; 143:487-94. [PMID: 27377506 PMCID: PMC4928556 DOI: 10.4103/0971-5916.184305] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background & objectives: Mycobacterium tuberculosis (M. tuberculosis) has four homologous mammalian cell entry (mce) operons (mce1-4) that encode exported proteins and have a possible role in the virulence mechanism of this pathogen. The expression of mce operon is considered to be complex and not completely understood. Although expression of mce operon at different in vitro growth phases has been studied earlier, its expression in different M. tuberculosis isolates under different growth phases is not yet studied. The present preliminary study was conducted on a limited number of isolates to know the trend of expression pattern of mce operon genes in different M. tuberculosis isolates under different growth stages. Methods: In this study, we monitored the transcriptional profile of selected mce operon genes (mce1A, mce1D, mce2A, mce2D, mce3A, mce3C) in different M. tuberculosis isolates (MDR1, MDR2, and sensitive isolate) at early exponential and stationary phases using real-time quantitative PCR. Results: The expression ratio of all selected mce operon genes in all M. tuberculosis isolates was reduced at the initial phase and increased substantially at a later phase of growth. Higher expression of mce1 operon genes was found in all M. tuberculosis isolates as compared to other mce operon genes (mce2 and mce3 operons) at stationary growth phase. Interpretation & conclusions: The higher expression of mce operon genes at stationary phase (as compared to early exponential phase) suggested growth phase dependent expression of mce operon genes. This indicated that the mce operon genes might have a role in M. tuberculosis survival and adaptation on the onset of adverse condition like stationary phase. Identification of differentially expressed genes will add to our understanding of the bacilli involved in adaptation to different growth conditions.
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Affiliation(s)
- Pratibha Singh
- Department of Microbiology & Molecular Biology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - V M Katoch
- Department of Microbiology & Molecular Biology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra; Former Secretary, Department of Health Research and Director-General, ICMR, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - K K Mohanty
- Department of Immunology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Devendra Singh Chauhan
- Department of Microbiology & Molecular Biology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
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Prados-Rosales R, Carreño L, Cheng T, Blanc C, Weinrick B, Malek A, Lowary TL, Baena A, Joe M, Bai Y, Kalscheuer R, Batista-Gonzalez A, Saavedra NA, Sampedro L, Tomás J, Anguita J, Hung SC, Tripathi A, Xu J, Glatman-Freedman A, Jacobs WR, Chan J, Porcelli SA, Achkar JM, Casadevall A. Enhanced control of Mycobacterium tuberculosis extrapulmonary dissemination in mice by an arabinomannan-protein conjugate vaccine. PLoS Pathog 2017; 13:e1006250. [PMID: 28278283 PMCID: PMC5360349 DOI: 10.1371/journal.ppat.1006250] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/21/2017] [Accepted: 02/17/2017] [Indexed: 12/22/2022] Open
Abstract
Currently there are a dozen or so of new vaccine candidates in clinical trials for prevention of tuberculosis (TB) and each formulation attempts to elicit protection by enhancement of cell-mediated immunity (CMI). In contrast, most approved vaccines against other bacterial pathogens are believed to mediate protection by eliciting antibody responses. However, it has been difficult to apply this formula to TB because of the difficulty in reliably eliciting protective antibodies. Here, we developed capsular polysaccharide conjugates by linking mycobacterial capsular arabinomannan (AM) to either Mtb Ag85b or B. anthracis protective antigen (PA). Further, we studied their immunogenicity by ELISA and AM glycan microarrays and protection efficacy in mice. Immunization with either Abg85b-AM or PA-AM conjugates elicited an AM-specific antibody response in mice. AM binding antibodies stimulated transcriptional changes in Mtb. Sera from AM conjugate immunized mice reacted against a broad spectrum of AM structural variants and specifically recognized arabinan fragments. Conjugate vaccine immunized mice infected with Mtb had lower bacterial numbers in lungs and spleen, and lived longer than control mice. These findings provide additional evidence that humoral immunity can contribute to protection against Mtb. Vaccine design in the TB field has been driven by the imperative of attempting to elicit strong cell-mediated responses. However, in recent decades evidence has accumulated that humoral immunity can protect against many intracellular pathogens through numerous mechanisms. In this work, we demonstrate that immunization with mycobacterial capsular arabinomannan (AM) conjugates elicited responses that contributed to protection against Mtb infection. We developed two different conjugates including capsular AM linked to the Mtb related protein Ag85b or the Mtb unrelated PA from B. anthracis and found that immunization with AM conjugates elicited antibody populations with different specificities. These surface-specific antibodies could directly modify the transcriptional profile and metabolism of mycobacteria. In addition, we observed a prolonged survival and a reduction in bacterial numbers in lungs and spleen in mice immunized with Ag85b-AM conjugates after infection with Mtb and that the presence of AM-binding antibodies was associated with modest prolongation in survival and a marked reduction in mycobacterial dissemination. Finally, we show that AM is antigenically variable and could potentially form the basis for a serological characterization of mycobacteria based on serotypes.
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Affiliation(s)
- Rafael Prados-Rosales
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
- * E-mail:
| | - Leandro Carreño
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Millennium Institute on Immunology and Immunotherapy, Programa Disciplinario de Inmunologia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Tingting Cheng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Caroline Blanc
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Brian Weinrick
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Adel Malek
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Center, Edmonton, Alberta, Canada
| | - Andres Baena
- Grupo de Inmunologia Celular e inmunogenetica, Universidad de Antioquia, Medellin, Colombia
| | - Maju Joe
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Center, Edmonton, Alberta, Canada
| | - Yu Bai
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Center, Edmonton, Alberta, Canada
| | - Rainer Kalscheuer
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Ana Batista-Gonzalez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Noemi A. Saavedra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
| | | | - Julen Tomás
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Shang-Cheng Hung
- Genomics Research Center, Academia Sinica, Section 2, Nankang, Taipei, Taiwan
| | - Ashish Tripathi
- Genomics Research Center, Academia Sinica, Section 2, Nankang, Taipei, Taiwan
| | - Jiayong Xu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Aharona Glatman-Freedman
- Infectious Diseases Unit, Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Israel
- Department of Pediatrics, and Department of Family and Community Medicine, New York Medical College, Valhalla, NY, United States of America
| | - Williams R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - John Chan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Steven A. Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Jacqueline M. Achkar
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Arturo Casadevall
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx NY, United States of America
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
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28
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Zeng J, Deng W, Yang W, Luo H, Duan X, Xie L, Li P, Wang R, Fu T, Abdalla AE, Xie J. Mycobacterium tuberculosis Rv1152 is a Novel GntR Family Transcriptional Regulator Involved in Intrinsic Vancomycin Resistance and is a Potential Vancomycin Adjuvant Target. Sci Rep 2016; 6:28002. [PMID: 27349953 PMCID: PMC4923875 DOI: 10.1038/srep28002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 05/27/2016] [Indexed: 12/16/2022] Open
Abstract
Novel factors involved in Mycobacteria antibiotics resistance are crucial for better targets to combat the ever-increasing drug resistant strains. Mycobacterium tuberculosis Rv1152, a novel GntR family transcriptional regulator and a promising vancomycin adjuvant target, was firstly characterized in our study. Overexpression of Rv1152 in Mycobacterium smegmatis decreased bacterial susceptibility to vancomycin. Moreover, a deficiency in MSMEG_5174, an Rv1152 homolog made M. smegmatis more sensitive to vancomycin, which was reverted by complementing the MSMEG_5174 deficiency with Rv1152 of M. tuberculosis. Rv1152 negatively regulated four vancomycin responsive genes, namely genes encoding the ribosome binding protein Hsp, small unit of sulfate adenylyltransferase CysD, L-lysine-epsilon aminotransferase Lat, and protease HtpX. Taken together, Rv1152 controls the expression of genes required for the susceptibility to vancomycin. This is the first report that links the GntR family transcriptional factor with vancomycin susceptibility. Inhibitors of Rv1152 might be ideal vancomycin adjuvants for controlling multi-drug resistant Mycobacterial infections.
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Affiliation(s)
- Jie Zeng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Wenmin Yang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Hongping Luo
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Xiangke Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Ping Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Rui Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Tiwei Fu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
| | - Abualgasim Elgaili Abdalla
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China.,Department of Clinical Microbiology, College of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Khartoum, Sudan
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment 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, Beibei, Chongqing 400715, China
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Li Q, Ge F, Tan Y, Zhang G, Li W. Genome-Wide Transcriptome Profiling of Mycobacterium smegmatis MC² 155 Cultivated in Minimal Media Supplemented with Cholesterol, Androstenedione or Glycerol. Int J Mol Sci 2016; 17:E689. [PMID: 27164097 PMCID: PMC4881515 DOI: 10.3390/ijms17050689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/12/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium smegmatis strain MC² 155 is an attractive model organism for the study of M. tuberculosis and other mycobacterial pathogens, as it can grow well using cholesterol as a carbon resource. However, its global transcriptomic response remains largely unrevealed. In this study, M. smegmatis MC² 155 cultivated in androstenedione, cholesterol and glycerol supplemented media were collected separately for a RNA-Sequencing study. The results showed that 6004, 6681 and 6348 genes were expressed in androstenedione, cholesterol and glycerol supplemented media, and 5891 genes were expressed in all three conditions, with 237 specially expressed in cholesterol added medium. A total of 1852 and 454 genes were significantly up-regulated by cholesterol compared with the other two supplements. Only occasional changes were observed in basic carbon and nitrogen metabolism, while almost all of the genes involved in cholesterol catabolism and mammalian cell entry (MCE) were up-regulated by cholesterol, but not by androstenedione. Eleven and 16 gene clusters were induced by cholesterol when compared with glycerol or androstenedione, respectively. This study provides a comprehensive analysis of the cholesterol responsive transcriptome of M. smegmatis. Our results indicated that cholesterol induced many more genes and increased the expression of the majority of genes involved in cholesterol degradation and MCE in M. smegmatis, while androstenedione did not have the same effect.
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Affiliation(s)
- Qun Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Fanglan Ge
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Yunya Tan
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Guangxiang Zhang
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Wei Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
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30
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REMap: Operon map of M. tuberculosis based on RNA sequence data. Tuberculosis (Edinb) 2016; 99:70-80. [PMID: 27450008 DOI: 10.1016/j.tube.2016.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2016] [Accepted: 04/24/2016] [Indexed: 12/18/2022]
Abstract
A map of the transcriptional organization of genes of an organism is a basic tool that is necessary to understand and facilitate a more accurate genetic manipulation of the organism. Operon maps are largely generated by computational prediction programs that rely on gene conservation and genome architecture and may not be physiologically relevant. With the widespread use of RNA sequencing (RNAseq), the prediction of operons based on actual transcriptome sequencing rather than computational genomics alone is much needed. Here, we report a validated operon map of Mycobacterium tuberculosis, developed using RNAseq data from both the exponential and stationary phases of growth. At least 58.4% of M. tuberculosis genes are organized into 749 operons. Our prediction algorithm, REMap (RNA Expression Mapping of operons), considers the many cases of transcription coverage of intergenic regions, and avoids dependencies on functional annotation and arbitrary assumptions about gene structure. As a result, we demonstrate that REMap is able to more accurately predict operons, especially those that contain long intergenic regions or functionally unrelated genes, than previous operon prediction programs. The REMap algorithm is publicly available as a user-friendly tool that can be readily modified to predict operons in other bacteria.
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31
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Blancato VS, Pagliai FA, Magni C, Gonzalez CF, Lorca GL. Functional Analysis of the Citrate Activator CitO from Enterococcus faecalis Implicates a Divalent Metal in Ligand Binding. Front Microbiol 2016; 7:101. [PMID: 26903980 PMCID: PMC4746285 DOI: 10.3389/fmicb.2016.00101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/19/2016] [Indexed: 02/04/2023] Open
Abstract
The regulator of citrate metabolism, CitO, from Enterococcus faecalis belongs to the FCD family within the GntR superfamily. In the presence of citrate, CitO binds to cis-acting sequences located upstream of the cit promoters inducing the expression of genes involved in citrate utilization. The quantification of the molecular binding affinities, performed by isothermal titration calorimetry (ITC), indicated that CitO has a high affinity for citrate (KD = 1.2 ± 0.2 μM), while it did not recognize other metabolic intermediates. Based on a structural model of CitO where a putative small molecule and a metal binding site were identified, it was hypothesized that the metal ion is required for citrate binding. In agreement with this model, citrate binding to CitO sharply decreased when the protein was incubated with EDTA. This effect was reverted by the addition of Ni2+, and Zn2+ to a lesser extent. Structure-based site-directed mutagenesis was conducted and it was found that changes to alanine in residues Arg97 and His191 resulted in decreased binding affinities for citrate, as determined by EMSA and ITC. Further assays using lacZ fusions confirmed that these residues in CitO are involved in sensing citrate in vivo. These results indicate that the molecular modifications induced by a ligand and a metal binding in the C-terminal domain of CitO are required for optimal DNA binding activity, and consequently, transcriptional activation.
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Affiliation(s)
- Víctor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y TécnicasRosario, Argentina; Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of FloridaGainesville, FL, USA
| | - Fernando A Pagliai
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
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32
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Yu L, Gao W, Li S, Pan Y, Liu G. GntR family regulator SCO6256 is involved in antibiotic production and conditionally regulates the transcription of myo-inositol catabolic genes in Streptomyces coelicolor A3(2). MICROBIOLOGY-SGM 2016; 162:537-551. [PMID: 26744083 DOI: 10.1099/mic.0.000235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SCO6256 belongs to the GntR family and shows 74% identity with SCO6974, which is the repressor of myo-inositol catabolism in Streptomyces coelicolor A3(2). Disruption of SCO6256 significantly enhanced the transcription of myo-inositol catabolic genes in R2YE medium. The purified recombinant SCO6256 directly bound to the upstream regions of SCO2727, SCO6978 and SCO6985, as well as its encoding gene. Footprinting assays demonstrated that SCO6256 bound to the same sites in the myo-inositol catabolic gene cluster as SCO6974. The expression of SCO6256 was repressed by SCO6974 in minimal medium with myo-inositol as the carbon source, but not in R2YE medium. Glutathione-S-transferase pull-down assays demonstrated that SCO6974 and SCO6256 interacted with each other; and both of the proteins controlled the transcription of myo-inositol catabolic genes in R2YE medium. These results indicated SCO6256 regulates the transcription of myo-inositol catabolic genes in coordination with SCO6974 in R2YE medium. In addition, SCO6256 negatively regulated the production of actinorhodin and calcium-dependent antibiotic via control of the transcription of actII-ORF4 and cdaR. SCO6256 bound to the upstream region of cdaR and the binding sequence was proved to be TTTCGGCACGCAGACAT, which was further confirmed through base substitution. Four putative targets (SCO2652, SCO4034, SCO4237 and SCO6377) of SCO6256 were found by screening the genome sequence of Strep. coelicolor A3(2) based on the conserved binding motif, and confirmed by transcriptional analysis and electrophoretic mobility shift assays. These results revealed that SCO6256 is involved in the regulation of myo-inositol catabolic gene transcription and antibiotic production in Strep. coelicolor A3(2).
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Affiliation(s)
- Lingjun Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wenyan Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuxian Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuanyuan Pan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Sci Rep 2015; 5:15443. [PMID: 26487098 PMCID: PMC4614345 DOI: 10.1038/srep15443] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 09/22/2015] [Indexed: 11/09/2022] Open
Abstract
Although Bacillus Calmette-Guérin (BCG) vaccines against tuberculosis have been available for more than 90 years, their effectiveness has been hindered by variable protective efficacy and a lack of lasting memory responses. One factor contributing to this variability may be the diversity of the BCG strains that are used around the world, in part from genomic changes accumulated during vaccine production and their resulting differences in gene expression. We have compared the genomes and transcriptomes of a global collection of fourteen of the most widely used BCG strains at single base-pair resolution. We have also used quantitative proteomics to identify key differences in expression of proteins across five representative BCG strains of the four tandem duplication (DU) groups. We provide a comprehensive map of single nucleotide polymorphisms (SNPs), copy number variation and insertions and deletions (indels) across fourteen BCG strains. Genome-wide SNP characterization allowed the construction of a new and robust phylogenic genealogy of BCG strains. Transcriptional and proteomic profiling revealed a metabolic remodeling in BCG strains that may be reflected by altered immunogenicity and possibly vaccine efficacy. Together, these integrated-omic data represent the most comprehensive catalogue of genetic variation across a global collection of BCG strains.
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Queiroz A, Medina-Cleghorn D, Marjanovic O, Nomura DK, Riley LW. Comparative metabolic profiling of mce1 operon mutant vs wild-type Mycobacterium tuberculosis strains. Pathog Dis 2015; 73:ftv066. [PMID: 26319139 DOI: 10.1093/femspd/ftv066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2015] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium tuberculosis disrupted in a 13-gene operon (mce1) accumulates free mycolic acids (FM) in its cell wall and causes accelerated death in mice. Here, to more comprehensively analyze differences in their cell wall lipid composition, we used an untargeted metabolomics approach to compare the lipid profiles of wild-type and mce1 operon mutant strains. By liquid chromatography-mass spectrometry, we identified >400 distinct lipids significantly altered in the mce1 mutant compared to wild type. These lipids included decreased levels of saccharolipids and glycerophospholipids, and increased levels of alpha-, methoxy- and keto mycolic acids (MA), and hydroxyphthioceranic acid. The mutant showed reduced expression of mmpL8, mmpL10, stf0, pks2 and papA2 genes involved in transport and metabolism of lipids recognized to induce proinflammatory response; these lipids were found to be decreased in the mutant. In contrast, the transcripts of mmpL3, fasI, kasA, kasB, acpM and RV3451 involved in MA transport and metabolism increased; MA inhibits inflammatory response in macrophages. Since the mce1 operon is known to be regulated in intracellular M. tuberculosis, we speculate that the differences we observed in cell wall lipid metabolism and composition may affect host response to M. tuberculosis infection and determine the clinical outcome of such an infection.
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Affiliation(s)
- Adriano Queiroz
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Daniel Medina-Cleghorn
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Olivera Marjanovic
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720, USA
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Sikri K, Kumari P, Tyagi JS, Nandi M, Taneja NK, Batra SD. The pleiotropic transcriptional response of Mycobacterium tuberculosis to vitamin C is robust and overlaps with the bacterial response to multiple intracellular stresses. Microbiology (Reading) 2015; 161:739-53. [DOI: 10.1099/mic.0.000049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022] Open
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Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infect Immun 2015; 83:1778-88. [PMID: 25690095 DOI: 10.1128/iai.03050-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/05/2015] [Indexed: 11/20/2022] Open
Abstract
The interaction of environmental bacteria with unicellular eukaryotes is generally considered a major driving force for the evolution of intracellular pathogens, allowing them to survive and replicate in phagocytic cells of vertebrate hosts. To test this hypothesis on a genome-wide level, we determined for the intracellular pathogen Mycobacterium marinum whether it uses conserved strategies to exploit host cells from both protozoan and vertebrate origin. Using transposon-directed insertion site sequencing (TraDIS), we determined differences in genetic requirements for survival and replication in phagocytic cells of organisms from different kingdoms. In line with the general hypothesis, we identified a number of general virulence mechanisms, including the type VII protein secretion system ESX-1, biosynthesis of polyketide lipids, and utilization of sterols. However, we were also able to show that M. marinum contains an even larger set of host-specific virulence determinants, including proteins involved in the modification of surface glycolipids and, surprisingly, the auxiliary proteins of the ESX-1 system. Several of these factors were in fact counterproductive in other hosts. Therefore, M. marinum contains different sets of virulence factors that are tailored for specific hosts. Our data imply that although amoebae could function as a training ground for intracellular pathogens, they do not fully prepare pathogens for crossing species barriers.
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Yousuf S, Angara R, Vindal V, Ranjan A. Rv0494 is a starvation-inducible, auto-regulatory FadR-like regulator from Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2014; 161:463-76. [PMID: 25527627 DOI: 10.1099/mic.0.000017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fatty acid metabolism plays an important role in the survival and pathogenesis of Mycobacterium tuberculosis. Lipids are assumed to be the major source of energy during dormancy. Here, we report the characterization of a starvation-inducible, lipid-responsive transcriptional regulator, Rv0494, divergently transcribed from the Rv0493c probable operon. The striking difference in the transcriptional regulatory apparatus between mycobacteria and other well-studied organisms, such as Escherichia coli, is the organization of mycobacterial promoters. Mycobacterial promoters have diverse architectures and most of these promoters function inefficiently in E. coli. In this study, we characterized the promoter elements of Rv0494 along with the sigma factors required for transcription initiation. Rv0494 promoter activity increased under nutrient starvation conditions and was transcribed via two promoters: the promoter proximal to the translational start site was active under standard growth conditions, whilst both promoters contributed to the increased activity seen during starvation, with the major contribution from the distal promoter. Furthermore, Rv0494 translation initiated at a codon located 9 bp downstream of the annotated start codon. Rv0494 bound to its upstream sequence to auto-regulate its own expression; this binding was responsive to long-chain fatty acyl-CoA molecules. We further report Rv0494-mediated transcriptional regulation of the Rv2326c gene - a probable transmembrane ATP-binding transporter encoding gene.
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Affiliation(s)
- Suhail Yousuf
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500001, India
| | - Rajendra Angara
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500001, India
| | - Vaibhav Vindal
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500001, India Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana 500046, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500001, India
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Forrellad MA, McNeil M, Santangelo MDLP, Blanco FC, García E, Klepp LI, Huff J, Niederweis M, Jackson M, Bigi F. Role of the Mce1 transporter in the lipid homeostasis of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2014; 94:170-7. [PMID: 24440549 PMCID: PMC3951760 DOI: 10.1016/j.tube.2013.12.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 12/15/2013] [Accepted: 12/18/2013] [Indexed: 12/19/2022]
Abstract
Tuberculosis is one of the leading causes of mortality throughout the world. Mycobacterium tuberculosis, the causative agent of human tuberculosis, has developed several strategies involving proteins and other compounds known collectively as virulence factors to subvert human host defences and invade the human host. The Mce proteins are among these virulence-related proteins and are encoded by the mce1, mce2, mce3 and mce4 operons in the genome of M. tuberculosis. It has been proposed that these operons encode ABC-like lipid transporters; however, the nature of their substrates has only been revealed in the case of the Mce4 proteins. Here we found that the knockout of the mce1 operon alters the lipid profile of M. tuberculosis H37Rv and the uptake of palmitic acid. Thin layer chromatography and liquid chromatography-mass spectrometry analysis showed that the mce1 mutant accumulates more mycolic acids than the wild type and complemented strains. Interestingly, this accumulation of mycolic acid is exacerbated when bacteria are cultured in the presence of palmitic acid or arachidonic acid. These results suggest that the mce1 operon may serve as a mycolic acid re-importer.
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Affiliation(s)
- Marina Andrea Forrellad
- Instituto de Biotecnología, CICVyA - INTA, N. Repetto and De los Reseros, Hurlingham 1686, Argentina
| | - Michael McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | | | - Federico Carlos Blanco
- Instituto de Biotecnología, CICVyA - INTA, N. Repetto and De los Reseros, Hurlingham 1686, Argentina
| | - Elizabeth García
- Instituto de Biotecnología, CICVyA - INTA, N. Repetto and De los Reseros, Hurlingham 1686, Argentina
| | - Laura Inés Klepp
- Instituto de Biotecnología, CICVyA - INTA, N. Repetto and De los Reseros, Hurlingham 1686, Argentina
| | - Jason Huff
- Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, AL 35294, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, AL 35294, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Fabiana Bigi
- Instituto de Biotecnología, CICVyA - INTA, N. Repetto and De los Reseros, Hurlingham 1686, Argentina.
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Sequeira PC, Senaratne RH, Riley LW. Inhibition of toll-like receptor 2 (TLR-2)-mediated response in human alveolar epithelial cells by mycolic acids and Mycobacterium tuberculosis mce1 operon mutant. Pathog Dis 2013; 70:132-40. [PMID: 24190334 DOI: 10.1111/2049-632x.12110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/16/2013] [Accepted: 10/23/2013] [Indexed: 01/12/2023] Open
Abstract
In human lungs, the earliest encounter of Mycobacterium tuberculosis, the agent of tuberculosis, involves alveolar epithelial cells. Droplets expectorated by a patient with tuberculosis are likely to contain a mixed population of M. tuberculosis cells in different physiologic and metabolic states from the lung lesions of the patient. Here, we compared the chemokine expression patterns of human epithelial cell line A549 and RAW 264.7 macrophage cells infected with wild-type M. tuberculosis H37Rv against patterns induced by a mutant that accumulates free mycolic acids in its cell wall (Δmce1). We also examined the effect of free mycolic acids on toll-like receptor-2 (TLR-2). Wild-type M. tuberculosis induced significantly higher levels of IL-8, MCP-1, RANTES, and IP-10 in both cell types than did Δmce. Free mycolic acids reduced the ability of the mammalian cells to respond to a TLR-2 agonist in a dose-dependent manner. These observations suggest that differences in mycolic acid abundance in the M. tuberculosis cell wall can affect TLR-2-mediated pro-inflammatory response in both epithelial and macrophage cells. The final fate of a new infection may be ultimately determined by the proportion of M. tuberculosis cells expressing free mycolates in the infecting inoculum population.
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40
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Lamont EA, Xu WW, Sreevatsan S. Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection. BMC Genomics 2013; 14:694. [PMID: 24112552 PMCID: PMC3832399 DOI: 10.1186/1471-2164-14-694] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 10/02/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The initial interaction between host cell and pathogen sets the stage for the ensuing infection and ultimately determine the course of disease. However, there is limited knowledge of the transcripts utilized by host and pathogen and how they may impact one another during this critical step. The purpose of this study was to create a host-Mycobacterium avium subsp. paratuberculosis (MAP) interactome for early infection in an epithelium-macrophage co-culture system using RNA-seq. RESULTS Establishment of the host-MAP interactome revealed a novel iron assimilation system for carboxymycobactin. Iron assimilation is linked to nitric oxide synthase-2 production by the host and subsequent nitric oxide buildup. Iron limitation as well as nitric oxide is a prompt for MAP to enter into an iron sequestration program. This new iron sequestration program provides an explanation for mycobactin independence in some MAP strains grown in vitro as well as during infection within the host cell. Utilization of such a pathway is likely to aid MAP establishment and long-term survival within the host. CONCLUSIONS The host-MAP interactome identified a number of metabolic, DNA repair and virulence genes worthy for consideration as novel drug targets as well as future pathogenesis studies. Reported interactome data may also be utilized to conduct focused, hypothesis-driven research. Co-culture of uninfected bovine epithelial cells (MAC-T) and primary bovine macrophages creates a tolerant genotype as demonstrated by downregulation of inflammatory pathways. This co-culture system may serve as a model to investigate other bovine enteric pathogens.
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Affiliation(s)
- Elise A Lamont
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
| | - Wayne W Xu
- Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Srinand Sreevatsan
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
- Department of Veterinary Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
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41
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Free mycolic acid accumulation in the cell wall of the mce1 operon mutant strain of Mycobacterium tuberculosis. J Microbiol 2013; 51:619-26. [PMID: 24037657 DOI: 10.1007/s12275-013-3092-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/15/2013] [Indexed: 01/29/2023]
Abstract
The lipid-rich cell wall of Mycobacterium tuberculosis, the agent of tuberculosis, serves as an effective barrier against many chemotherapeutic agents and toxic host cell effector molecules, and it may contribute to the mechanism of persistence. Mycobacterium tuberculosis strains mutated in a 13-gene operon called mce1, which encodes a putative ABC lipid transporter, induce aberrant granulomatous response in mouse lungs. Because of the postulated role of the mce1 operon in lipid importation, we compared the cell wall lipid composition of wild type and mce1 operon mutant M. tuberculosis H37Rv strains. High resolution mass spectrometric analyses of the mce1 mutant lipid extracts showed unbound mycolic acids to accumulate in the cell wall. Quantitative analysis revealed a 10.7 fold greater amount of free mycolates in the mutant compared to that of the wild type strain. The free mycolates were comprised of alpha, methoxy and keto mycolates in the ratio 1:0.9:0.6, respectively. Since the mce1 operon is regulated in vivo, the free mycolates that accumulate during infection may serve as a barrier for M. tuberculosis against toxic products and contribute to the pathogen's persistence.
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Rathor N, Chandolia A, Saini NK, Sinha R, Pathak R, Garima K, Singh S, Varma-Basil M, Bose M. An insight into the regulation of mce4 operon of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2013; 93:389-97. [PMID: 23622789 DOI: 10.1016/j.tube.2013.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/19/2013] [Accepted: 03/30/2013] [Indexed: 01/21/2023]
Abstract
The mce4 operon is reported to be involved in cholesterol utilization and intracellular survival of Mycobacterium tuberculosis (M. tuberculosis). The regulatory mechanism of this important operon was unknown so far. Here we report detection of the promoter region and regulatory factors of the mce4 operon. The in silico analyzed putative promoter region was cloned in promoter selection vector and promoter strength was measured by O-Nitrophenyl-β-D-galactopyranosidase (ONPG) assay. The transcription start site was determined by 5' Rapid amplification of C terminal end (5'RACE). Surface stress, hypoxia and presence of cholesterol, were found to be stimulatory for mce4 operon promoter induction. Pull down assay coupled with 2D gel electrophoresis resolved many proteins; few prominent spots were processed for identification. MALDI TOF-TOF identified proteins of M. tuberculosis which supported the regulatory function of the identified promoter region and cholesterol utilization of mce4 operon. Since mce4 operon is involved in cholesterol utilization and intracellular survival of M. tuberculosis in the later phase of infection, identification of the promoter sequence as reported in the present communication may facilitate development of effective inhibitors to regulate expression of mce4 operon which may prove to be a good drug target to prevent latency in tuberculosis.
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Affiliation(s)
- Nisha Rathor
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
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Singh B, Nitharwal RG, Ramesh M, Pettersson BMF, Kirsebom LA, Dasgupta S. Asymmetric growth and division inMycobacteriumspp.: compensatory mechanisms for non-medial septa. Mol Microbiol 2013; 88:64-76. [DOI: 10.1111/mmi.12169] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Bhupender Singh
- Department of Cell and Molecular Biology; Uppsala University Biomedical Center; Box 596; 751 24; Uppsala; Sweden
| | - Ram Gopal Nitharwal
- Department of Cell and Molecular Biology; Uppsala University Biomedical Center; Box 596; 751 24; Uppsala; Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology; Uppsala University Biomedical Center; Box 596; 751 24; Uppsala; Sweden
| | - B. M. Fredrik Pettersson
- Department of Cell and Molecular Biology; Uppsala University Biomedical Center; Box 596; 751 24; Uppsala; Sweden
| | - Leif A. Kirsebom
- Department of Cell and Molecular Biology; Uppsala University Biomedical Center; Box 596; 751 24; Uppsala; Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology; Uppsala University Biomedical Center; Box 596; 751 24; Uppsala; Sweden
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Uplekar S, Rougemont J, Cole ST, Sala C. High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. Nucleic Acids Res 2012; 41:961-77. [PMID: 23222129 PMCID: PMC3553938 DOI: 10.1093/nar/gks1260] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genome-wide dynamics of RNA polymerase (RNAP) and the anti-terminator NusA. Although NusA does not bind directly to DNA, but rather to RNAP and/or to the nascent transcript, we demonstrate that NusA interacts with RNAP ubiquitously throughout the chromosome, and that its profile mirrors RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the data sets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align.
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Affiliation(s)
- Swapna Uplekar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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Rao M, Liu H, Yang M, Zhao C, He ZG. A copper-responsive global repressor regulates expression of diverse membrane-associated transporters and bacterial drug resistance in mycobacteria. J Biol Chem 2012; 287:39721-31. [PMID: 23014988 DOI: 10.1074/jbc.m112.383604] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sequencing of entire bacterial genomes has led to the identification of many membrane-associated transporters, including several multidrug resistance transport proteins, in recent years. However, the regulators and signaling pathways involved in the expression of these genes remain largely unknown. In this study, we have identified Ms2173, a GntR/FadR family transcription factor, as a novel global regulator in Mycobacterium smegmatis. Ms2173 was found to specifically recognize a 15-bp palindromic motif and to broadly regulate expression of 292 genes, including 37 genes that encode membrane-associated transport proteins. Copper ions induced Ms2173 to form inactive proteins lacking DNA-binding activity. Ms2173 was shown to function as a repressor of its target genes. Interestingly, we found that the function of Ms2173 was linked to mycobacterial drug resistance. Compared with the substantially enhanced drug resistance in the Ms2173-deleted mutant strain, the strains overexpressing Ms2173 were more sensitive to anti-tuberculosis drugs than the wild-type strain. Additionally, copper ions could partially counteract the in vivo function of Ms2173. We have thus characterized the first mycobacterial GntR/Fad-like transcription factor that functions as a copper ion-responsive global repressor that we have renamed GfcR. These findings further enhance our understanding of membrane-associated transporter regulation and drug resistance in mycobacteria.
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Affiliation(s)
- Muding Rao
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Zeng J, Cui T, He ZG. A genome-wide regulator-DNA interaction network in the human pathogen Mycobacterium tuberculosis H37Rv. J Proteome Res 2012; 11:4682-92. [PMID: 22808930 DOI: 10.1021/pr3006233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcription regulation translates static genome information to dynamic cell behaviors, making it central to understand how cells interact with and adapt to their environment. However, only a limited number of transcription regulators and their target genes have been identified in the pathogen Mycobacterium tuberculosis , which has greatly impeded our understanding of its pathogenesis and virulence. In this study, we constructed a genome-wide transcription regulatory network of M. tuberculosis H37Rv using a high-throughput bacterial one-hybrid technique. A transcription factor skeleton network was derived on the basis of the identification of more than 5400 protein-DNA interactions. Our findings further highlight the regulatory mechanism of the mammalian cell entry 1 (mce1) module, which includes mce1R and the mce1 operon. Mce1R was linked to global negative regulation of cell growth, but was found to be positively regulated by the dormancy response regulator DevR. Expression of the mce1 operon was shown to be negatively regulated by the virulence regulator PhoP. These findings provide important new insights into the molecular mechanisms of several mce1 module-related hypervirulence phenotypes of the pathogen. Furthermore, a model of mce1 module-centered signal circuit for dormancy regulation in M. tuberculosis is proposed and discussed.
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Affiliation(s)
- Jumei Zeng
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Stavrum R, Valvatne H, Stavrum AK, Riley LW, Ulvestad E, Jonassen I, Doherty TM, Grewal HMS. Mycobacterium tuberculosis Mce1 protein complex initiates rapid induction of transcription of genes involved in substrate trafficking. Genes Immun 2012; 13:496-502. [PMID: 22695749 DOI: 10.1038/gene.2012.24] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mammalian cell entry (Mce)1 protein complex has an important role during the initial phase of a Mycobacterium tuberculosis (M. tuberculosis) infection. Murine macrophages were infected with M. tuberculosis H37Rv or Δ-mce1 H37Rv, and total RNA was isolated from the host cells at 15, 30 and 60 min, and 4 and 10 h post-infection. With the aim of studying the role for the Mce1 protein complex on host gene expression, the RNA was hybridized onto 44 K whole-genome microarrays. Selected genes were verified by reverse-transcriptase quantitative PCR (RT-QPCR). 'Transport' was the most overrepresented biological process during the first hour post H37Rv infection. Five genes (Abca1 (21.0-fold), Slc16a10 (3.1-fold), Slc6a12 (17.9-fold), Slc6a8 (2.3-fold) and Nr1h3, (5.5-fold)) involved in substrate trafficking were verified by RT-QPCR to be upregulated by >2-fold 1 h post H37Rv infection. By 1 h post Δ-mce1 H37Rv infection, only Abca1 and Slc6a12 were upregulated by >2-fold. A number of other genes, which may be directly involved in substrate trafficking or share the same transcription, were found to have expression profiles similar to the genes involved in substrate trafficking. The Mce1 protein complex has a significant role in the transcriptional activation of genes involved in substrate trafficking during the initial phase of an M. tuberculosis infection.
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Affiliation(s)
- R Stavrum
- Department of Microbiology and Immunology, The Gade Institute, University of Bergen, Bergen, Norway.
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Miyata T, Cheigh CI, Casali N, Goodridge A, Marjanovic O, Kendall LV, Riley LW. An adjunctive therapeutic vaccine against reactivation and post-treatment relapse tuberculosis. Vaccine 2011; 30:459-65. [PMID: 22079078 DOI: 10.1016/j.vaccine.2011.10.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/17/2011] [Accepted: 10/22/2011] [Indexed: 11/16/2022]
Abstract
Preventing latently infected or inadequately treated individuals from progressing to active disease could make a major impact on tuberculosis (TB) control worldwide. The purpose of this study was to evaluate a new approach to prevent reactivation and TB relapse that combines drug treatment and vaccination. Mycobacterium tuberculosis harbors a gene called mce1R that, in vivo, negatively regulates a 13-gene cluster called the mce1 operon. In a Cornell mouse model, BALB/c mice infected with M. tuberculosis H37Rv disrupted in mce1R consistently develop latent infection and reactivation disease. We used this new mouse model to test a recombinant M. tuberculosis cell wall protein (Mce1A), encoded by a gene in the mce1 operon, for its ability to prevent post-treatment TB. At 32 weeks of follow-up, a complete sterilizing protection was observed in lungs of the vaccinated mice. Mce1A but not phosphate-buffered saline administered intraperitoneally during the period of latent infection prevented disease progression and proliferation of M. tuberculosis mce1R mutant. The only visible lung lesions in vaccinated mice included small clusters of lymphocytes, while the unvaccinated mice showed progressively enlarging granulomas comprised of foamy macrophages surrounded by lymphocytes. The combination of anti-TB drugs and a vaccine may serve as a powerful treatment modality against TB reactivation and relapse.
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Affiliation(s)
- Toshiko Miyata
- Division of Infectious Diseases and Vaccinology, 201 Hildebrand Hall, School of Public Health, University of California, Berkeley, CA 94720, USA
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Stavrum R, Stavrum AK, Valvatne H, Riley LW, Ulvestad E, Jonassen I, Assmus J, Doherty TM, Grewal HMS. Modulation of transcriptional and inflammatory responses in murine macrophages by the Mycobacterium tuberculosis mammalian cell entry (Mce) 1 complex. PLoS One 2011; 6:e26295. [PMID: 22039457 PMCID: PMC3200323 DOI: 10.1371/journal.pone.0026295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/23/2011] [Indexed: 11/22/2022] Open
Abstract
The outcome of many infections depends on the initial interactions between agent and host. Aiming at elucidating the effect of the M. tuberculosis Mce1 protein complex on host transcriptional and immunological responses to infection with M. tuberculosis, RNA from murine macrophages at 15, 30, 60 min, 4 and 10 hrs post-infection with M. tuberculosis H37Rv or Δ-mce1 H37Rv was analyzed by whole-genome microarrays and RT-QPCR. Immunological responses were measured using a 23-plex cytokine assay. Compared to uninfected controls, 524 versus 64 genes were up-regulated by 15 min post H37Rv- and Δ-mce1 H37Rv-infection, respectively. By 15 min post-H37Rv infection, a decline of 17 cytokines combined with up-regulation of Ccl24 (26.5-fold), Clec4a2 (23.2-fold) and Pparγ (10.5-fold) indicated an anti-inflammatory response initiated by IL-13. Down-regulation of Il13ra1 combined with up-regulation of Il12b (30.2-fold), suggested switch to a pro-inflammatory response by 4 hrs post H37Rv-infection. Whereas no significant change in cytokine concentration or transcription was observed during the first hour post Δ-mce1 H37Rv-infection, a significant decline of IL-1b, IL-9, IL-13, Eotaxin and GM-CSF combined with increased transcription of Il12b (25.1-fold) and Inb1 (17.9-fold) by 4 hrs, indicated a pro-inflammatory response. The balance between pro-and anti-inflammatory responses during the early stages of infection may have significant bearing on outcome.
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Affiliation(s)
- Ruth Stavrum
- Section of Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway.
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An SQ, Lu GT, Su HZ, Li RF, He YQ, Jiang BL, Tang DJ, Tang JL. Systematic mutagenesis of all predicted gntR genes in Xanthomonas campestris pv. campestris reveals a GntR family transcriptional regulator controlling hypersensitive response and virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1027-1039. [PMID: 21615202 DOI: 10.1094/mpmi-08-10-0180] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The GntR family is one of the most abundant and widely distributed groups of helix-turn-helix transcriptional regulators in bacteria. Six open reading frames in the genome of the plant pathogen Xanthomonas campestris pv. campestris were predicted to encode GntR regulators. All six of the predicted GntR-encoding genes were individually mutagenized and mutants from five of them were successfully obtained. Plant disease response assays revealed that one, whose product belongs to the YtrA subfamily and has been named HpaR1, is involved in the hypersensitive response (HR) and virulence. Electrophoretic mobility shift assays and in vitro transcription assays revealed that HpaR1 could repress its own transcription level through binding to its promoter sequence, indicating an autoregulatory feedback inhibition mechanism for HpaR1 expression. Promoter-gusA reporter and reverse-transcription polymerase chain reaction analyses revealed that HpaR1 positively and negatively affects the expression of HR and pathogenicity (hrp) genes in host plant and standard media, respectively. Constitutive expression of the key hrp regulator, hrpG, in the hpaR1 mutant could bypass the requirement of HpaR1 for the induction of wild-type HR, suggesting that HpaR1 regulates the expression of hrp genes that encode the type III secretion system via hrpG.
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