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Brezovská B, Narasimhan S, Šiková M, Šanderová H, Kovaľ T, Borah N, Shoman M, Pospíšilová D, Vaňková Hausnerová V, Tužinčin D, Černý M, Komárek J, Janoušková M, Kambová M, Halada P, Křenková A, Hubálek M, Trundová M, Dohnálek J, Hnilicová J, Žídek L, Krásný L. MoaB2, a newly identified transcription factor, binds to σ A in Mycobacterium smegmatis. J Bacteriol 2024; 206:e0006624. [PMID: 39499088 PMCID: PMC11656743 DOI: 10.1128/jb.00066-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 09/18/2024] [Indexed: 11/07/2024] Open
Abstract
In mycobacteria, σA is the primary sigma factor. This essential protein binds to RNA polymerase (RNAP) and mediates transcription initiation of housekeeping genes. Our knowledge about this factor in mycobacteria is limited. Here, we performed an unbiased search for interacting partners of Mycobacterium smegmatis σA. The search revealed a number of proteins; prominent among them was MoaB2. The σA-MoaB2 interaction was validated and characterized by several approaches, revealing that it likely does not require RNAP and is specific, as alternative σ factors (e.g., closely related σB) do not interact with MoaB2. The structure of MoaB2 was solved by X-ray crystallography. By immunoprecipitation and nuclear magnetic resonance, the unique, unstructured N-terminal domain of σA was identified to play a role in the σA-MoaB2 interaction. Functional experiments then showed that MoaB2 inhibits σA-dependent (but not σB-dependent) transcription and may increase the stability of σA in the cell. We propose that MoaB2, by sequestering σA, has a potential to modulate gene expression. In summary, this study has uncovered a new binding partner of mycobacterial σA, paving the way for future investigation of this phenomenon.IMPORTANCEMycobacteria cause serious human diseases such as tuberculosis and leprosy. The mycobacterial transcription machinery is unique, containing transcription factors such as RbpA, CarD, and the RNA polymerase (RNAP) core-interacting small RNA Ms1. Here, we extend our knowledge of the mycobacterial transcription apparatus by identifying MoaB2 as an interacting partner of σA, the primary sigma factor, and characterize its effects on transcription and σA stability. This information expands our knowledge of interacting partners of subunits of mycobacterial RNAP, providing opportunities for future development of antimycobacterial compounds.
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Affiliation(s)
- Barbora Brezovská
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Subhash Narasimhan
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Michaela Šiková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Tomáš Kovaľ
- Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Nabajyoti Borah
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Mahmoud Shoman
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Debora Pospíšilová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague, Czechia
| | - Dávid Tužinčin
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Martin Černý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Jan Komárek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Martina Janoušková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Milada Kambová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Alena Křenková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Mária Trundová
- Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Jan Dohnálek
- Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague, Czechia
| | - Lukáš Žídek
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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Oh Y, Oh JI. The RsfSR two-component system regulates SigF function by monitoring the state of the respiratory electron transport chain in Mycobacterium smegmatis. J Biol Chem 2024; 300:105764. [PMID: 38367670 PMCID: PMC10950880 DOI: 10.1016/j.jbc.2024.105764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
In Mycobacterium smegmatis, the transcriptional activity of the alternative sigma factor SigF is posttranslationally regulated by the partner switching system consisting of SigF, the anti-SigF RsbW1, and three anti-SigF antagonists (RsfA, RsfB, and RsbW3). We previously demonstrated that expression of the SigF regulon is strongly induced in the Δaa3 mutant of M. smegmatis lacking the aa3 cytochrome c oxidase, the major terminal oxidase in the respiratory electron transport chain. Here, we identified and characterized the RsfSR two-component system involved in regulating the phosphorylation state of the major anti-SigF antagonist RsfB. RsfS (MSMEG_6130) is a histidine kinase with the cyclase/histidine kinase-associated sensing extracellular 3 domain at its N terminus, and RsfR (MSMEG_6131) is a receiver domain-containing protein phosphatase 2C-type phosphatase that can dephosphorylate phosphorylated RsfB. We demonstrated that phosphorylation of RsfR on Asp74 by RsfS reduces the phosphatase activity of RsfR toward phosphorylated RsfB and that the cellular abundance of the active unphosphorylated RsfB is increased in the Δaa3 mutant relative to the WT strain. We also demonstrated that the RsfSR two-component system is required for induction of the SigF regulon under respiration-inhibitory conditions such as inactivation of the cytochrome bcc1 complex and aa3 cytochrome c oxidase, as well as hypoxia, electron donor-limiting, high ionic strength, and low pH conditions. Collectively, our results reveal a key regulatory element involved in regulating the SigF signaling system by monitoring the state of the respiratory electron transport chain.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Korea; Microbiological Resource Research Institute, Pusan National University, Busan, Korea.
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3
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Wani SR, Jain V. Deciphering the molecular mechanism and regulation of formaldehyde detoxification in Mycobacterium smegmatis. Appl Environ Microbiol 2024; 90:e0203923. [PMID: 38259108 PMCID: PMC10880627 DOI: 10.1128/aem.02039-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
The build-up of formaldehyde, a highly reactive molecule is cytotoxic and must be eliminated for the organism's survival. Formaldehyde detoxification system is found in nearly all organisms including both pathogenic and non-pathogenic mycobacteria. MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis (Msm), is an indispensable part of this system and forms a bicistronic operon with its downstream uncharacterized gene, fmh. We here show that Fmh, a putative metallo-beta-lactamase, is essential in tolerating higher amounts of formaldehyde when co-overexpressed with mscR in vivo. Our NMR studies indicate that MscR, along with Fmh, enhances formate production through a mycothiol (MSH)-dependent pathway, emphasizing the importance of Fmh in detoxifying formaldehyde. Although another aldehyde dehydrogenase, MSMEG_1543, induces upon formaldehyde addition, it is not involved in its detoxification. We also show that the expression of the mscR operon is constitutive and remains unchanged upon formaldehyde addition, as displayed by the promoter activity of PmscR and by the transcript and protein levels of MscR. Furthermore, we establish the role of a thiol-responsive sigma factor SigH in formaldehyde detoxification. We show that SigH, and not SigE, is crucial for formaldehyde detoxification, even though it does not directly regulate mscR operon expression. In addition, sensitivity to formaldehyde in sigH-knockout could be alleviated by overexpression of mscR. Taken together, our data demonstrate the importance of MSH-dependent pathways in detoxifying formaldehyde in a mycobacterial system. An absence of such MSH-dependent proteins in eukaryotes and its complete conservation in M. tuberculosis, the causative agent of tuberculosis, further unravel new drug targets for this pathogen.IMPORTANCEExtensive research has been done on formaldehyde detoxification in different bacteria. However, our current understanding of the mechanisms underlying this process in mycobacteria remains exceedingly little. We previously showed that MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis, plays a pivotal role in this detoxification pathway. Here, we present a potential S-formyl-mycothiol hydrolase named Fmh, thought to be a metallo-beta-lactamase, which functions along with mycothiol (MSH) and MscR to enhance formate production within this detoxification pathway. Co-expression of Fmh with MscR significantly enhances the efficiency of formaldehyde detoxification in M. smegmatis. Our experiments establish that Fmh catalyzes the final step of this detoxification pathway. Although an alternative sigma factor SigH was found to be involved in formaldehyde detoxification, it did not directly regulate the expression of mscR. Since formaldehyde detoxification is essential for bacterial survival, we envisage this process to be a potential drug target for M. tuberculosis eradication.
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Affiliation(s)
- Saloni Rajesh Wani
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
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4
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Oh Y, Lee HN, Ko EM, Jeong JA, Park SW, Oh JI. Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions. J Microbiol 2023; 61:297-315. [PMID: 36847970 DOI: 10.1007/s12275-023-00026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Eon-Min Ko
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Ji-A Jeong
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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5
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Activation of the SigE-SigB signaling pathway by inhibition of the respiratory electron transport chain and its effect on rifampicin resistance in Mycobacterium smegmatis. J Microbiol 2022; 60:935-947. [DOI: 10.1007/s12275-022-2202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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Sengupta S, Bhawsinghka N, Shaw R, Patra MM, Das Gupta SK. Mycobacteriophage D29 induced association of Mycobacterial RNA polymerase with ancillary factors leads to increased transcriptional activity. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35353035 DOI: 10.1099/mic.0.001158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mycobacteriophage D29 infects species belonging to the genus Mycobacterium including the deadly pathogen Mycobacterium tuberculosis. D29 is a lytic phage, although, related to the lysogenic mycobacteriophage L5. This phage is unable to lysogenize in mycobacteria as it lacks the gene encoding the phage repressor. Infection by many mycobacteriophages cause various changes in the host that ultimately leads to inactivation of the latter. One of the host targets often modified in the process is RNA polymerase. During our investigations with phage D29 infected Mycobacterium smegmatis (Msm) we observed that the promoters from both phage, and to a lesser extent those of the host were found to be more active in cells that were exposed to D29, as compared to the unexposed. Further experiments indicate that the RNA polymerase purified from phage infected cells possessed higher affinity for promoters particularly those that were phage derived. Comparison of the purified RNA polymerase preparations from infected and uninfected cells showed that several ancillary transcription factors, Sigma factor F, Sigma factor H, CarD and RbpA are prominently associated with the RNA polymerase from infected cells. Based on our observations we conclude that the higher activity of RNA polymerase observed in D29 infected cells is due to its increased association with ancillary transcription factors.
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Affiliation(s)
- Shreya Sengupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Niketa Bhawsinghka
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India.,Present address: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Rahul Shaw
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Madhu Manti Patra
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Sujoy K Das Gupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
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Giddey AD, Ganief TA, Ganief N, Koch A, Warner DF, Soares NC, Blackburn JM. Cell Wall Proteomics Reveal Phenotypic Adaption of Drug-Resistant Mycobacterium smegmatis to Subinhibitory Rifampicin Exposure. Front Med (Lausanne) 2021; 8:723667. [PMID: 34676224 PMCID: PMC8525676 DOI: 10.3389/fmed.2021.723667] [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: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 01/01/2023] Open
Abstract
Despite the availability of effective drug treatment, Mycobacterium tuberculosis (Mtb), the causative agent of TB disease, kills ~1. 5 million people annually, and the rising prevalence of drug resistance increasingly threatens to worsen this plight. We previously showed that sublethal exposure to the frontline anti-TB drug, rifampicin, resulted in substantial adaptive remodeling of the proteome of the model organism, Mycobacterium smegmatis, in the drug-sensitive mc2155 strain [wild type (WT)]. In this study, we investigate whether these responses are conserved in an engineered, isogenic mutant harboring the clinically relevant S531L rifampicin resistance-conferring mutation (SL) and distinguish the responses that are specific to RNA polymerase β subunit- (RpoB-) binding activity of rifampicin from those that are dependent on the presence of rifampicin alone. We verified the drug resistance status of this strain and observed no phenotypic indications of rifampicin-induced stress upon treatment with the same concentration as used in WT (2.5 μg/ml). Thereafter, we used a cell wall-enrichment strategy to focus attention on the cell wall proteome and observed 253 proteins to be dysregulated in SL bacteria in comparison with 716 proteins in WT. We observed that decreased abundance of ATP-binding cassette (ABC) transporters and increased abundance of ribosomal machinery were conserved in the SL strain, whereas the upregulation of transcriptional machinery and the downregulation of numerous two-component systems were not. We conclude that the drug-resistant M. smegmatis strain displays some of the same proteomic responses observed in WT and suggest that this evidence supports the hypothesis that rifampicin exercises effects beyond RpoB-interaction alone and that mycobacteria recognise rifampicin as a signaling molecule in an RpoB-independent manner at sublethal doses. Taken together, our data indicates mixed RpoB-independent and RpoB-dependent proteomic remodeling in WT mycobacteria, with evidence for RpoB-independent ABC transporter downregulation, but drug activity-based transcriptional upregulation and two-component system downregulation.
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Affiliation(s)
- Alexander D Giddey
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tariq A Ganief
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Naadir Ganief
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anastasia Koch
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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8
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Oh Y, Song SY, Kim HJ, Han G, Hwang J, Kang HY, Oh JI. The Partner Switching System of the SigF Sigma Factor in Mycobacterium smegmatis and Induction of the SigF Regulon Under Respiration-Inhibitory Conditions. Front Microbiol 2020; 11:588487. [PMID: 33304334 PMCID: PMC7693655 DOI: 10.3389/fmicb.2020.588487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
The partner switching system (PSS) of the SigF regulatory pathway in Mycobacterium smegmatis has been previously demonstrated to include the anti-sigma factor RsbW (MSMEG_1803) and two anti-sigma factor antagonists RsfA and RsfB. In this study, we further characterized two additional RsbW homologs and revealed the distinct roles of three RsbW homologs [RsbW1 (MSMEG_1803), RsbW2 (MSMEG_6129), and RsbW3 (MSMEG_1787)] in the SigF PSS. RsbW1 and RsbW2 serve as the anti-sigma factor of SigF and the protein kinase phosphorylating RsfB, respectively, while RsbW3 functions as an anti-SigF antagonist through its protein interaction with RsbW1. Using relevant mutant strains, RsfB was demonstrated to be the major anti-SigF antagonist in M. smegmatis. The phosphorylation state of Ser-63 was shown to determine the functionality of RsfB as an anti-SigF antagonist. RsbW2 was demonstrated to be the only protein kinase that phosphorylates RsfB in M. smegmatis. Phosphorylation of Ser-63 inactivates RsfB to render it unable to interact with RsbW1. Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic Δaa3 mutant strain lacking the aa3 cytochrome c oxidase of the respiratory electron transport chain revealed that expression of the SigF regulon is strongly induced under respiration-inhibitory conditions in an RsfB-dependent way.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Su-Yeon Song
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Hye-Jun Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Jihwan Hwang
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Ho-Young Kang
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
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9
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Pereira AC, Ramos B, Reis AC, Cunha MV. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 2020; 8:microorganisms8091380. [PMID: 32916931 PMCID: PMC7563442 DOI: 10.3390/microorganisms8091380] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-500-000 (ext. 22461)
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10
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Multi-Stress Induction of the Mycobacterium tuberculosis MbcTA Bactericidal Toxin-Antitoxin System. Toxins (Basel) 2020; 12:toxins12050329. [PMID: 32429486 PMCID: PMC7291234 DOI: 10.3390/toxins12050329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/16/2022] Open
Abstract
MbcTA is a type II toxin/antitoxin (TA) system of Mycobacterium tuberculosis. The MbcT toxin triggers mycobacterial cell death in vitro and in vivo through the phosphorolysis of the essential metabolite NAD+ and its bactericidal activity is neutralized by physical interaction with its cognate antitoxin MbcA. Therefore, the MbcTA system appears as a promising target for the development of novel therapies against tuberculosis, through the identification of compounds able to antagonize or destabilize the MbcA antitoxin. Here, the expression of the mbcAT operon and its regulation were investigated. A dual fluorescent reporter system was developed, based on an integrative mycobacterial plasmid that encodes a constitutively expressed reporter, serving as an internal standard for monitoring mycobacterial gene expression, and an additional reporter, dependent on the promoter under investigation. This system was used both in M. tuberculosis and in the fast growing model species Mycobacterium smegmatis to: (i) assess the autoregulation of mbcAT; (ii) perform a genetic dissection of the mbcA promoter/operator region; and (iii) explore the regulation of mbcAT transcription from the mbcA promoter (PmbcA) in a variety of stress conditions, including in vivo in mice and in macrophages.
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11
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Dutta D, Srivastava V, Tripathi A, Singh V, Ansari MM, Pant G, Mishra M, Sharma S, Thota JR, Singh PK, Singh BN. Mycobacterium bovis sigF mutant exhibits altered surface phenotype and compromised pathogenesis. Tuberculosis (Edinb) 2019; 118:101855. [PMID: 31430695 DOI: 10.1016/j.tube.2019.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Debashis Dutta
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, 3C1, FL33458, USA; Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Vishal Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Ashutosh Tripathi
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Vandana Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Mohd Mustkim Ansari
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Garima Pant
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Manisha Mishra
- CSIR-National Botanical Research Institute, Lucknow, 226001, India.
| | - Sharad Sharma
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Jagadehswar Reddy Thota
- Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | | | - Bhupendra N Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
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12
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Yang P, Song Y, Xia X, Zhang AM. Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR. PeerJ 2019; 7:e6696. [PMID: 30972260 PMCID: PMC6448557 DOI: 10.7717/peerj.6696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis (TB) is a worldwide health, economic, and social burden, especially in developing countries. Drug-resistant TB is the most serious type of this burden. Thus, it is necessary to screen drug-resistant mutations by using a simple and rapid detection method. A total of 32 pairs of allele-specific PCR (AS-PCR) primers were designed to screen mutation and/or wild-type alleles of 16 variations in four first-line drug-resistant genes (katG, rpoB, rpsL, and embB) of TB strains. A pair of primers was designed to amplify 16S rRNA gene and to verify successful amplification. Subsequently, we tested the specificity and sensitivity of these AS-PCR primers. The optimized condition of these AS-PCR primers was first confirmed. All mutations could be screened in general AS-PCR, but only 13 of 16 variations were intuitively investigated by using real-time quantitative PCR (qPCR) and AS-PCR primers. The results of specificity assay suggested that the AS-PCR primers with mutation and/or wildtype alleles could successfully amplify the corresponding allele under optimized PCR conditions. The sensitivity of nine pairs of primers was 500 copy numbers, and the other seven pairs of primers could successfully amplify correct fragments with a template comprising 103 or 104 copy numbers template. An optimized AS-qPCR was established to screen drug-resistant mutations in TB strains with high specificity and sensitivity.
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Affiliation(s)
- Pengpeng Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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13
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Owens NA, Laurentius LB, Porter MD, Li Q, Wang S, Chatterjee D. Handheld Raman Spectrometer Instrumentation for Quantitative Tuberculosis Biomarker Detection: A Performance Assessment for Point-of-Need Infectious Disease Diagnostics. APPLIED SPECTROSCOPY 2018; 72:1104-1115. [PMID: 29664331 DOI: 10.1177/0003702818770666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Techniques for the detection of disease biomarkers are key components in the protection of human health. While work over the last few decades has redefined the low-level measurement of disease biomarkers, the translation of these capabilities from the formal clinical setting to point-of-need (PON) usage has been much more limited. This paper presents the results of experiments designed to examine the potential utility of a handheld Raman spectrometer as a PON electronic reader for a sandwich immunoassay based on surface-enhanced Raman scattering (SERS). In so doing, the study herein used a recently developed procedure for the SERS detection of phospho-myo-inositol-capped lipoarabinomannan (PILAM) as a means to compare the performance of laboratory-grade and handheld instrumentation and, therefore, gauge the utility of the handheld instrument for PON deployment. Phospho-myo-inositol-capped lipoarabinomannan is a non-pathogenic simulant for mannose-capped lipoarabinomannan (ManLAM), which is an antigenic marker found in serum and other body fluids of individuals infected with tuberculosis (TB). The results of the measurements with the field-portable spectrometer were then compared to those obtained for the same samples when using a much more sensitive benchtop Raman spectrometer. The results, albeit under different operational settings for the two spectrometers (e.g., signal integration time), are promising in that the limit of detection found for PILAM spiked in human serum when using the handheld system (0.18 ng/mL) approached that of the benchtop instrument (0.032 ng/mL). This work also: (1) identified potential adaptations (e.g., optimization of the plasmonically enhanced response for measurement by the handheld unit through a change in the excitation wavelength) to tighten the gap in performance; and (2) briefly examined the next steps and potential processes required to move this immunoassay platform closer to PON utility.
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Affiliation(s)
- Nicholas A Owens
- 1 Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Lars B Laurentius
- 2 Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
| | - Marc D Porter
- 1 Department of Chemistry, University of Utah, Salt Lake City, UT, USA
- 2 Nano Institute of Utah, University of Utah, Salt Lake City, UT, USA
- 3 Department of Chemical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Qun Li
- 4 B&W Tek, Inc., Newark, DE, USA
| | | | - Delphi Chatterjee
- 5 Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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14
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Laurentius LB, Crawford AC, Mulvihill TS, Granger JH, Robinson R, Spencer JS, Chatterjee D, Hanson KE, Porter MD. Importance of specimen pretreatment for the low-level detection of mycobacterial lipoarabinomannan in human serum. Analyst 2018; 142:177-185. [PMID: 27934985 DOI: 10.1039/c6an02109c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Patient care and prevention of disease outbreaks rely heavily on the performance of diagnostic tests. These tests are typically carried out in serum, urine, and other complex sample matrices, but are often plagued by a number of matrix effects such as nonspecific adsorption and complexation with circulating proteins. This paper demonstrates the importance of sample pretreatment to overcome matrix effects, enabling the low-level detection of a disease marker for tuberculosis (TB). The impact of pretreatment is illustrated by detecting a cell wall component unique to mycobacteria, lipoarabinomannan (LAM). LAM is a major virulence factor in the infectious pathology of Mycobacterium tuberculosis (Mtb) and has been successfully detected in the body fluids of TB-infected individuals; however, its clinical sensitivity - identifying patients with active infection - remains problematic. This and the companion paper show that the detection of LAM in an immunoassay is plagued by its complexation with proteins and other components in serum. Herein, we present the procedures and results from an investigation of several different pretreatment schemes designed to disrupt complexation and thereby improve detection. These sample pretreatment studies, aimed at determining the optimal conditions for complex disruption, were carried out by using a LAM simulant derived from the nonpathogenic M. smegmatis, a mycobacterium often used as a model for Mtb. We have found that a perchloric acid-based pretreatment step improves the ability to detect this simulant by ∼1500× with respect to that in untreated serum. This paper describes the approach to pretreatment, how pretreatment improves the detection of the LAM simulant in human serum, and the results from a preliminary investigation to identify possible contributors to complexation by fractionating serum according to molecular weight. The companion paper applies this pretreatment approach to assays of TB patient samples.
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Affiliation(s)
- Lars B Laurentius
- The Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA.
| | - Alexis C Crawford
- The Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA. and Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Jennifer H Granger
- The Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA.
| | - Ryan Robinson
- The Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA. and Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | - John S Spencer
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Delphi Chatterjee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kimberly E Hanson
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA and Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Marc D Porter
- The Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA. and Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA and Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA and Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA and Department of Chemical Engineering, University of Utah, Salt Lake City, UT 84112, USA
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15
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Li H, Cowie A, Johnson JA, Webster D, Martyniuk CJ, Gray CA. Determining the mode of action of anti-mycobacterial C17 diyne natural products using expression profiling: evidence for fatty acid biosynthesis inhibition. BMC Genomics 2016; 17:621. [PMID: 27514659 PMCID: PMC4981992 DOI: 10.1186/s12864-016-2949-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background The treatment of microbial infections is becoming increasingly challenging because of limited therapeutic options and the growing number of pathogenic strains that are resistant to current antibiotics. There is an urgent need to identify molecules with novel modes of action to facilitate the development of new and more effective therapeutic agents. The anti-mycobacterial activity of the C17 diyne natural products falcarinol and panaxydol has been described previously; however, their mode of action remains largely undetermined in microbes. Gene expression profiling was therefore used to determine the transcriptomic response of Mycobacterium smegmatis upon treatment with falcarinol and panaxydol to better characterize the mode of action of these C17 diynes. Results Our analyses identified 704 and 907 transcripts that were differentially expressed in M. smegmatis after treatment with falcarinol and panaxydol respectively. Principal component analysis suggested that the C17 diynes exhibit a mode of action that is distinct to commonly used antimycobacterial drugs. Functional enrichment analysis and pathway enrichment analysis revealed that cell processes such as ectoine biosynthesis and cyclopropane-fatty-acyl-phospholipid synthesis were responsive to falcarinol and panaxydol treatment at the transcriptome level in M. smegmatis. The modes of action of the two C17 diynes were also predicted through Prediction of Activity Spectra of Substances (PASS). Based upon convergence of these three independent analyses, we hypothesize that the C17 diynes inhibit fatty acid biosynthesis, specifically phospholipid synthesis, in mycobacteria. Conclusion Based on transcriptomic responses, it is suggested that the C17 diynes act differently than other anti-mycobacterial compounds in M. smegmatis, and do so by inhibiting phospholipid biosynthesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2949-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haoxin Li
- Department of Biological Sciences, University of New Brunswick, PO Box 5050, 100 Tucker Park Road, E2L 4L5, Saint John, NB, Canada
| | - Andrew Cowie
- Department of Biological Sciences, University of New Brunswick, PO Box 5050, 100 Tucker Park Road, E2L 4L5, Saint John, NB, Canada
| | - John A Johnson
- Department of Biological Sciences, University of New Brunswick, PO Box 5050, 100 Tucker Park Road, E2L 4L5, Saint John, NB, Canada
| | - Duncan Webster
- Department of Medicine, Division of Infectious Diseases, Saint John Regional Hospital, 400 University Ave, E2L 4L4, Saint John, NB, Canada
| | - Christopher J Martyniuk
- Department of Biological Sciences, University of New Brunswick, PO Box 5050, 100 Tucker Park Road, E2L 4L5, Saint John, NB, Canada.,Present address: Center for Environmental and Human Toxicology & Department of Physiological Sciences, UF Genetics Institute, College of Veterinary Medicine, University of Florida, 1333 Center Drive, 32610-0144, Gainesville, FL, USA
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick, PO Box 5050, 100 Tucker Park Road, E2L 4L5, Saint John, NB, Canada. .,Department of Chemistry, University of New Brunswick, PO Box 4400, 30 Dineen Drive, E3B 5A3, Fredericton, NB, Canada.
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16
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Toyoda K, Inui M. The extracytoplasmic function σ factor σ(C) regulates expression of a branched quinol oxidation pathway in Corynebacterium glutamicum. Mol Microbiol 2016; 100:486-509. [PMID: 26789738 DOI: 10.1111/mmi.13330] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2016] [Indexed: 11/30/2022]
Abstract
Bacteria modify their expression of different terminal oxidases in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium of the phylum Actinobacteria, possesses aa3 -type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced by oxygen limitation. We report that an extracytoplasmic function σ factor, σ(C) , is responsible for the regulation of this process. Chromatin immunoprecipitation with microarray analysis detected eight σ(C) -binding regions in the genome, facilitating the identification of a consensus promoter sequence for σ(C) recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. However, one consensus promoter sequence found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a σ(C) -dependent negative effect on expression of the operon. The σ(C) regulon was induced by cytochrome aa3 deficiency without modifying sigC expression, but not by bc1 complex deficiency. These findings suggest that σ(C) is activated in response to impaired electron transfer via cytochrome aa3 and not directly to a shift in oxygen levels. Our results reveal a new paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.
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Affiliation(s)
- Koichi Toyoda
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0101, Japan
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17
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Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence. Microbiol Spectr 2015; 2:MGM2-0007-2013. [PMID: 26082107 DOI: 10.1128/microbiolspec.mgm2-0007-2013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid adaptation to changing environments is one of the keys to the success of microorganisms. Since infection is a dynamic process, it is possible to predict that Mycobacterium tuberculosis adaptation involves continuous modulation of its global transcriptional profile in response to the changing environment found in the human body. In the last 18 years several studies have stressed the role of sigma (σ) factors in this process. These are small interchangeable subunits of the RNA polymerase holoenzyme that are required for transcriptional initiation and that determine promoter specificity. The M. tuberculosis genome encodes 13 of these proteins, one of which--the principal σ factor σA--is essential. Of the other 12 σ factors, at least 6 are required for virulence. In this article we review our current knowledge of mycobacterial σ factors, their regulons, the complex mechanisms determining their regulation, and their roles in M. tuberculosis physiology and virulence.
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18
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Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection. PLoS One 2015; 10:e0139823. [PMID: 26445268 PMCID: PMC4596819 DOI: 10.1371/journal.pone.0139823] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/14/2015] [Indexed: 11/28/2022] Open
Abstract
We have used RNASeq and qRT-PCR to study mRNA levels for all σ-factors in different Mycobacterium marinum strains under various growth and stress conditions. We also studied their levels in M. marinum from infected fish and mosquito larvae. The annotated σ-factors were expressed and transcripts varied in relation to growth and stress conditions. Some were highly abundant such as sigA, sigB, sigC, sigD, sigE and sigH while others were not. The σ-factor mRNA profiles were similar after heat stress, during infection of fish and mosquito larvae. The similarity also applies to some of the known heat shock genes such as the α-crystallin gene. Therefore, it seems probable that the physiological state of M. marinum is similar when exposed to these different conditions. Moreover, the mosquito larvae data suggest that this is the state that the fish encounter when infected, at least with respect to σ-factor mRNA levels. Comparative genomic analysis of σ-factor gene localizations in three M. marinum strains and Mycobacterium tuberculosis H37Rv revealed chromosomal rearrangements that changed the localization of especially sigA, sigB, sigD, sigE, sigF and sigJ after the divergence of these two species. This may explain the variation in species-specific expression upon exposure to different growth conditions.
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19
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Singh AK, Dutta D, Singh V, Srivastava V, Biswas RK, Singh BN. Characterization of Mycobacterium smegmatis sigF mutant and its regulon: overexpression of SigF antagonist (MSMEG_1803) in M. smegmatis mimics sigF mutant phenotype, loss of pigmentation, and sensitivity to oxidative stress. Microbiologyopen 2015; 4:896-916. [PMID: 26434659 PMCID: PMC4694148 DOI: 10.1002/mbo3.288] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 12/22/2022] Open
Abstract
In Mycobacterium smegmatis, sigF is widely expressed during different growth stages and plays role in adaptation to stationary phase and oxidative stress. Using a sigF deletion mutant of M. smegmatis mc2155, we demonstrate that SigF is not essential for growth of bacterium. Deletion of sigF results in loss of carotenoid pigmentation which rendered increased susceptibility to H2O2 induced oxidative stress in M. smegmatis. SigF modulates the cell surface architecture and lipid biosynthesis extending the repertoire of SigF function in this species. M. smegmatis SigF regulon included variety of genes expressed during exponential and stationary phases of growth and those responsible for oxidative stress, lipid biosynthesis, energy, and central intermediary metabolism. Furthermore, we report the identification of a SigF antagonist, an anti‐sigma factor (RsbW), which upon overexpression in M. smegmatis wild type strain produced a phenotype similar to M. smegmatis mc2155 ΔsigF strain. The SigF‐anti‐SigF interaction is duly validated using bacterial two‐hybrid and pull down assays. In addition, anti‐sigma factor antagonists, RsfA and RsfB were identified and their interactions with anti‐sigma factor were experimentally validated. Identification of these proteins will help decode regulatory circuit of this alternate sigma factor.
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Affiliation(s)
- Anirudh K Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Debashis Dutta
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Vandana Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Vishal Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Rajesh K Biswas
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Bhupendra N Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
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20
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Hnilicová J, Jirát Matějčková J, Šiková M, Pospíšil J, Halada P, Pánek J, Krásný L. Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria. Nucleic Acids Res 2014; 42:11763-76. [PMID: 25217589 PMCID: PMC4191392 DOI: 10.1093/nar/gku793] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/12/2022] Open
Abstract
Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, a sRNA that is highly expressed in Mycobacterium smegmatis during stationary phase of growth. By glycerol gradient ultracentrifugation, RNA binding assay, and RNA co-immunoprecipitation, we show that Ms1 interacts with the RNA polymerase (RNAP) core that is free of the primary sigma factor (σA) or any other σ factor. This contrasts with the situation in most other species where it is 6S RNA that interacts with RNAP and this interaction requires the presence of σA. The difference in the interaction of the two types of sRNAs (Ms1 or 6S RNA) with RNAP possibly reflects the difference in the composition of the transcriptional machinery between mycobacteria and other species. Unlike Escherichia coli, stationary phase M. smegmatis cells contain relatively few RNAP molecules in complex with σA. Thus, Ms1 represents a novel type of small RNAs interacting with RNAP.
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Affiliation(s)
- Jarmila Hnilicová
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jitka Jirát Matějčková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Michaela Šiková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jiří Pospíšil
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Petr Halada
- Department of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Josef Pánek
- Department of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Libor Krásný
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
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21
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Prasanna AN, Mehra S. Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium. PLoS One 2013; 8:e71248. [PMID: 24015186 PMCID: PMC3756022 DOI: 10.1371/journal.pone.0071248] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/26/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.
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Affiliation(s)
- Arun N. Prasanna
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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22
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Bharati BK, Swetha RK, Chatterji D. Identification and characterization of starvation induced msdgc-1 promoter involved in the c-di-GMP turnover. Gene 2013; 528:99-108. [PMID: 23932989 DOI: 10.1016/j.gene.2013.07.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/25/2013] [Accepted: 07/09/2013] [Indexed: 11/17/2022]
Abstract
C-di-GMP [Bis-(3'-5')-cyclic-dimeric-guanosine monophosphate], a second messenger is involved in intracellular communication in the bacterial species. As a result several multi-cellular behaviors in both Gram-positive and Gram-negative bacteria are directly linked to the intracellular level of c-di-GMP. The cellular concentration of c-di-GMP is maintained by two opposing activities, diguanylate cyclase (DGC) and phosphodiesterase (PDE-A). In Mycobacterium smegmatis, a single bifunctional protein MSDGC-1 is responsible for the cellular concentration of c-di-GMP. A better understanding of the regulation of c-di-GMP at the genetic level is necessary to control the function of above two activities. In this work, we have characterized the promoter element present in msdgc-1 along with the +1 transcription start site and identified the sigma factors that regulate the transcription of msdgc-1. Interestingly, msdgc-1 utilizes SigA during the initial phase of growth, whereas near the stationary phase SigB containing RNA polymerase takes over the expression of msdgc-1. We report here that the promoter activity of msdgc-1 increases during starvation or depletion of carbon source like glucose or glycerol. When msdgc-1 is deleted, the numbers of viable cells are ~10 times higher in the stationary phase in comparison to that of the wild type. We propose here that msdgc-1 is involved in the regulation of cell population density.
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Affiliation(s)
- Binod K Bharati
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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23
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Chang A, Smollett KL, Gopaul KK, Chan BHY, Davis EO. Mycobacterium tuberculosis H37Rv sigC is expressed from two promoters but is not auto-regulatory. Tuberculosis (Edinb) 2011; 92:48-55. [PMID: 22015173 DOI: 10.1016/j.tube.2011.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 09/15/2011] [Accepted: 09/20/2011] [Indexed: 11/29/2022]
Abstract
The extracytoplasmic function (ECF) sigma factor SigC has been implicated in the pathogenesis of Mycobacterium tuberculosis but control of its expression and activity is poorly understood. No proteins that interact with SigC have been detected leading to the suggestion that this sigma factor may be primarily controlled at the level of transcription. It has been suggested that SigC may be autoregulatory and a role has also been proposed for SigF in the expression of sigC. In this study we identified two promoters that were active under standard growth conditions by a combination of transcript start site mapping and promoter-lacZ fusion assays. The dominant promoter, P1, closely resembled mycobacterial SigA-dependent promoters, and introduction of a single base change at the conserved A of the -10 region eliminated promoter activity. Although the sequence of the other, P2, closely resembled the reported SigC consensus motifs, expression directed by this promoter was unaltered in a ΔsigC mutant strain, or in strains defective in other ECF sigma factors for which some similarity in consensus sequences was apparent. Comparison of the effects of different changes in the -10 region suggested that the P2 promoter was most likely recognised by SigA.
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Affiliation(s)
- Anchi Chang
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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Mukhopadhyay S, Nair S, Ghosh S. Pathogenesis in tuberculosis: transcriptomic approaches to unraveling virulence mechanisms and finding new drug targets. FEMS Microbiol Rev 2011; 36:463-85. [PMID: 22092372 DOI: 10.1111/j.1574-6976.2011.00302.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 07/31/2011] [Accepted: 08/05/2011] [Indexed: 01/12/2023] Open
Abstract
Tuberculosis (TB) remains a major health problem worldwide. Attempts to control this disease have proved difficult owing to our poor understanding of the pathobiology of Mycobacterium tuberculosis and the emergence of strains that are resistant to multiple drugs currently available for treatment. Genome-wide expression profiling has provided new insight into the transcriptome signatures of the bacterium during infection, notably of macrophages and dendritic cells. These data indicate that M. tuberculosis expresses numerous genes to evade the host immune responses, to suit its intracellular life style, and to respond to various antibiotic drugs. Among the intracellularly induced genes, several have functions in lipid metabolism, cell wall synthesis, iron uptake, oxidative stress resistance, protein secretion, or inhibition of apoptosis. Herein we review these findings and discuss possible ways to exploit the data to understand the complex etiology of TB and to find new effective drug targets.
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Affiliation(s)
- Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, India.
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Identification of the regulator gene responsible for the acetone-responsive expression of the binuclear iron monooxygenase gene cluster in mycobacteria. J Bacteriol 2011; 193:5817-23. [PMID: 21856847 DOI: 10.1128/jb.05525-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mimABCD gene cluster encodes the binuclear iron monooxygenase that oxidizes propane and phenol in Mycobacterium smegmatis strain MC2 155 and Mycobacterium goodii strain 12523. Interestingly, expression of the mimABCD gene cluster is induced by acetone. In this study, we investigated the regulator gene responsible for this acetone-responsive expression. In the genome sequence of M. smegmatis strain MC2 155, the mimABCD gene cluster is preceded by a gene designated mimR, which is divergently transcribed. Sequence analysis revealed that MimR exhibits amino acid similarity with the NtrC family of transcriptional activators, including AcxR and AcoR, which are involved in acetone and acetoin metabolism, respectively. Unexpectedly, many homologs of the mimR gene were also found in the sequenced genomes of actinomycetes. A plasmid carrying a transcriptional fusion of the intergenic region between the mimR and mimA genes with a promoterless green fluorescent protein (GFP) gene was constructed and introduced into M. smegmatis strain MC2 155. Using a GFP reporter system, we confirmed by deletion and complementation analyses that the mimR gene product is the positive regulator of the mimABCD gene cluster expression that is responsive to acetone. M. goodii strain 12523 also utilized the same regulatory system as M. smegmatis strain MC2 155. Although transcriptional activators of the NtrC family generally control transcription using the σ(54) factor, a gene encoding the σ(54) factor was absent from the genome sequence of M. smegmatis strain MC2 155. These results suggest the presence of a novel regulatory system in actinomycetes, including mycobacteria.
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Pribylova R, Kralik P, Donnelly N, Matiasovic J, Pavlik I. Mycobacterium avium subsp. Paratuberculosis and the expression of selected virulence and pathogenesis genes in response to 6°C, 65°c and ph 2.0. Braz J Microbiol 2011; 42:807-17. [PMID: 24031696 PMCID: PMC3769857 DOI: 10.1590/s1517-838220110002000049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 11/04/2010] [Indexed: 11/23/2022] Open
Abstract
The aim of this work was to study the expression of selected Mycobacterium avium subsp. paratuberculosis (MAP) genes connected with MAP virulence, adhesion and stress response. The temperature of 6°C and 65°C were chosen with regard to the food industry, storage conditions (refrigerator) and low-temperature pasteurization. A pH of 2.0, using lactic acid, was selected to mimic the natural environment of the stomach. Expression of selected genes was studied using real time reverse transcription PCR on three different MAP isolates. MAP isolates were chosen according to the number of their preceding cultivations. While isolates 8672 and 8819 were previously cultivated only once, MAP isolate 12146 went through four passages. Different expression profiles were observed in each of the three MAP isolates. However, particular similar patterns were observed. SigE, sigF and ahpC were up-regulated, while sigL was down-regulated under temperature stress. Mmp gene was found to be down-regulated under acidic conditions. Low passage isolates (8672 and 8819) showed certain level of acid resistance.
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Affiliation(s)
- Radka Pribylova
- Veterinary Research Institute , Hudcova 70, 621 00 Brno , Czech Republic
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China A, Tare P, Nagaraja V. Comparison of promoter-specific events during transcription initiation in mycobacteria. MICROBIOLOGY-SGM 2010; 156:1942-1952. [PMID: 20299402 DOI: 10.1099/mic.0.038620-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA-protein interactions that occur during transcription initiation play an important role in regulating gene expression. To initiate transcription, RNA polymerase (RNAP) binds to promoters in a sequence-specific fashion. This is followed by a series of steps governed by the equilibrium binding and kinetic rate constants, which in turn determine the overall efficiency of the transcription process. We present here the first detailed kinetic analysis of promoter-RNAP interactions during transcription initiation in the sigma(A)-dependent promoters P(rrnAPCL1), P(rrnB) and P(gyr) of Mycobacterium smegmatis. The promoters show comparable equilibrium binding affinity but differ significantly in open complex formation, kinetics of isomerization and promoter clearance. Furthermore, the two rrn promoters exhibit varied kinetic properties during transcription initiation and appear to be subjected to different modes of regulation. In addition to distinct kinetic patterns, each one of the housekeeping promoters studied has its own rate-limiting step in the initiation pathway, indicating the differences in their regulation.
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Affiliation(s)
- Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
| | - Valakunja Nagaraja
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore - 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
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The SigF regulon in Mycobacterium smegmatis reveals roles in adaptation to stationary phase, heat, and oxidative stress. J Bacteriol 2010; 192:2491-502. [PMID: 20233930 DOI: 10.1128/jb.00035-10] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SigF is an alternative sigma factor that is highly conserved among species of the genus Mycobacterium. In this study we identified the SigF regulon in Mycobacterium smegmatis using whole-genome microarray and promoter consensus analyses. In total, 64 genes in exponential phase and 124 genes in stationary phase are SigF dependent (P < 0.01, >2-fold expression change). Our experimental data reveal the SigF-dependent promoter consensus GTTT-N((15-17))-GGGTA for M. smegmatis, and we propose 130 potential genes under direct control of SigF, of which more than 50% exhibited reduced expression in a Delta sigF strain. We previously reported an increased susceptibility of the Delta sigF strain to heat and oxidative stress, and our expression data indicate a molecular basis for these phenotypes. We observed SigF-dependent expression of several genes purportedly involved in oxidative stress defense, namely, a heme-containing catalase, a manganese-containing catalase, a superoxide dismutase, the starvation-induced DNA-protecting protein MsDps1, and the biosynthesis genes for the carotenoid isorenieratene. Our data suggest that SigF regulates the biosynthesis of the thermoprotectant trehalose, as well as an uptake system for osmoregulatory compounds, and this may explain the increased heat susceptibility of the Delta sigF strain. We identified the regulatory proteins SigH3, PhoP, WhiB1, and WhiB4 as possible genes under direct control of SigF and propose four novel anti-sigma factor antagonists that could be involved in the posttranslational regulation of SigF in M. smegmatis. This study emphasizes the importance of this sigma factor for stationary-phase adaptation and stress response in mycobacteria.
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Abstract
Mycobacterium tuberculosis causes more deaths in humans than any other bacterial pathogen. The most recent data from the World Health Organization reveal that over 9million new cases of tuberculosis occur each year and that the incidence appears to be increasing with population growth. Despite the global burden of tuberculosis, we are still reliant on relatively dated measures to prevent, diagnose, and treat the disease. New, more effective tools are needed to diminish the incidence of tuberculosis. M. tuberculosis lacks a natural host beyond humans and, hence, surrogate models have been employed in the study of the pathogen. The discovery and development of new vaccines, diagnostics, or antitubercular drugs are dependent upon the validity of any experimental model used and its relevance to tuberculosis in humans. In this review, a range of experimental models, from in vitro studies with fast-growing low-pathogenic species of mycobacteria to the infection of nonhuman primates with virulent M. tuberculosis, will be discussed.
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Affiliation(s)
- Ronan O'Toole
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Malshetty V, Kurthkoti K, China A, Mallick B, Yamunadevi S, Sang PB, Srinivasan N, Nagaraja V, Varshney U. Novel insertion and deletion mutants of RpoB that render Mycobacterium smegmatis RNA polymerase resistant to rifampicin-mediated inhibition of transcription. MICROBIOLOGY-SGM 2010; 156:1565-1573. [PMID: 20150242 DOI: 10.1099/mic.0.036970-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The startling increase in the occurrence of rifampicin (Rif) resistance in the clinical isolates of Mycobacterium tuberculosis worldwide is posing a serious concern to tuberculosis management. The majority of Rif resistance in bacteria arises from mutations in the RpoB subunit of the RNA polymerase. We isolated M. smegmatis strains harbouring either an insertion (6 aa) or a deletion (10 aa) in their RpoB proteins. Although these strains showed a compromised fitness for growth in 7H9 Middlebrook medium, their resistance to Rif was remarkably high. The attenuated growth of the strains correlated with decreased specific activities of the RNA polymerases from the mutants. While the RNA polymerases from the parent or a mutant strain (harbouring a frequently occurring mutation, H442Y, in RpoB) were susceptible to Rif-mediated inhibition of transcription from calf thymus DNA, those from the insertion and deletion mutants were essentially refractory to such inhibition. Three-dimensional structure modelling revealed that the RpoB amino acids that interact with Rif are either deleted or unable to interact with Rif due to their unsuitable spatial positioning in these mutants. We discuss possible uses of the RpoB mutants in studying transcriptional regulation in mycobacteria and as potential targets for drug design.
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Affiliation(s)
- Vidyasagar Malshetty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Krishna Kurthkoti
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Arnab China
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Bratati Mallick
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Subburaj Yamunadevi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pau Biak Sang
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Valakunja Nagaraja
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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Sachdeva P, Misra R, Tyagi AK, Singh Y. The sigma factors of Mycobacterium tuberculosis: regulation of the regulators. FEBS J 2009; 277:605-26. [DOI: 10.1111/j.1742-4658.2009.07479.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Purification of RNA polymerase from mycobacteria for optimized promoter-polymerase interactions. Protein Expr Purif 2009; 69:235-42. [PMID: 19815074 DOI: 10.1016/j.pep.2009.09.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 09/29/2009] [Accepted: 09/30/2009] [Indexed: 11/20/2022]
Abstract
In vitro transcription analysis is important to understand the mechanism of transcription. Various assays for the analysis of initiation, elongation and termination form the basis for better understanding of the process. Purified RNA polymerase (RNAP) with high specific activity is necessary to carry out variety of these specific reactions. The RNAP purified from Mycobacterium smegmatis from exponential phase showed low promoter specificity in promoter-polymerase interaction studies. This is due to the presence of a large number of sigma factors during exponential phase and under-representation of sigma(A) required for house-keeping transcription. We describe an in vivo reconstitution of RNAP holoenzyme with sigma(A) and its purification, which resulted in holoenzyme with stoichiometric sigma(A) content. The reconstituted holoenzyme showed enhanced promoter-specific binding and promoter-specific-transcription activity compared to the enzyme isolated using standard procedure. Such in vivo reconstitution of stoichiometric holoenzyme could facilitate promoter-specific transcription assays, especially in organisms which encode a large number of sigma factors.
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Cook GM, Berney M, Gebhard S, Heinemann M, Cox RA, Danilchanka O, Niederweis M. Physiology of mycobacteria. Adv Microb Physiol 2009; 55:81-182, 318-9. [PMID: 19573696 DOI: 10.1016/s0065-2911(09)05502-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis is a prototrophic, metabolically flexible bacterium that has achieved a spread in the human population that is unmatched by any other bacterial pathogen. The success of M. tuberculosis as a pathogen can be attributed to its extraordinary stealth and capacity to adapt to environmental changes throughout the course of infection. These changes include: nutrient deprivation, hypoxia, various exogenous stress conditions and, in the case of the pathogenic species, the intraphagosomal environment. Knowledge of the physiology of M. tuberculosis during this process has been limited by the slow growth of the bacterium in the laboratory and other technical problems such as cell aggregation. Advances in genomics and molecular methods to analyze the M. tuberculosis genome have revealed that adaptive changes are mediated by complex regulatory networks and signals, resulting in temporal gene expression coupled to metabolic and energetic changes. An important goal for bacterial physiologists will be to elucidate the physiology of M. tuberculosis during the transition between the diverse conditions encountered by M. tuberculosis. This review covers the growth of the mycobacterial cell and how environmental stimuli are sensed by this bacterium. Adaptation to different environments is described from the viewpoint of nutrient acquisition, energy generation, and regulation. To gain quantitative understanding of mycobacterial physiology will require a systems biology approach and recent efforts in this area are discussed.
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Affiliation(s)
- Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
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Maciag A, Piazza A, Riccardi G, Milano A. Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. BMC Microbiol 2009; 9:48. [PMID: 19257911 PMCID: PMC2660348 DOI: 10.1186/1471-2180-9-48] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 03/04/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ESAT-6 (early secreted antigenic target, 6 kDa) family collects small mycobacterial proteins secreted by Mycobacterium tuberculosis, particularly in the early phase of growth. There are 23 ESAT-6 family members in M. tuberculosis H37Rv. In a previous work, we identified the Zur- dependent regulation of five proteins of the ESAT-6/CFP-10 family (esxG, esxH, esxQ, esxR, and esxS). esxG and esxH are part of ESAT-6 cluster 3, whose expression was already known to be induced by iron starvation. RESULTS In this research, we performed EMSA experiments and transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis (msmeg0615-msmeg0625) and M. tuberculosis. In contrast to what we had observed in M. tuberculosis, we found that in M. smegmatis ESAT-6 cluster 3 responds only to iron and not to zinc. In both organisms we identified an internal promoter, a finding which suggests the presence of two transcriptional units and, by consequence, a differential expression of cluster 3 genes. We compared the expression of msmeg0615 and msmeg0620 in different growth and stress conditions by means of relative quantitative PCR. The expression of msmeg0615 and msmeg0620 genes was essentially similar; they appeared to be repressed in most of the tested conditions, with the exception of acid stress (pH 4.2) where msmeg0615 was about 4-fold induced, while msmeg0620 was repressed. Analysis revealed that in acid stress conditions M. tuberculosis rv0282 gene was 3-fold induced too, while rv0287 induction was almost insignificant. CONCLUSION In contrast with what has been reported for M. tuberculosis, our results suggest that in M. smegmatis only IdeR-dependent regulation is retained, while zinc has no effect on gene expression. The role of cluster 3 in M. tuberculosis virulence is still to be defined; however, iron- and zinc-dependent expression strongly suggests that cluster 3 is highly expressed in the infective process, and that the cluster contributes to the antigenic profile during the course of infection. Moreover, cluster 3 induction in acid stress conditions strengthens the hypothesis that cluster 3 is expressed in the course of infection.In M. smegmatis, the expression of msmeg0615 and msmeg0620 genes is broadly similar in differing growth phases and in stress conditions, with the exception of acid stress (pH 4.2). Differences in expression between cluster 3 genes can be explained by the presence of internal promoters, both in M. smegmatis and M. tuberculosis.
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Affiliation(s)
- Anna Maciag
- Department of Genetics and Microbiology, University of Pavia, Pavia, Italy.
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35
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Differential expression of sigH paralogs during growth and under different stress conditions in Mycobacterium smegmatis. J Bacteriol 2009; 191:2888-93. [PMID: 19218386 DOI: 10.1128/jb.01773-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SigH regulates a transcriptional network that responds to heat and oxidative stress in mycobacteria. Seven sigH paralogs are reported to exist in the Mycobacterium smegmatis genome. A comprehensive real-time reverse transcriptase PCR analysis during different stages of growth and upon exposure to various stress conditions and antimycobacterial compounds showed differential expression of sigH paralogs during stationary phase and severalfold increases in the levels of transcription of sigH1, sigH4, sigH5, sigH6, and sigH7 under specific stress conditions.
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Smollett KL, Fivian-Hughes AS, Smith JE, Chang A, Rao T, Davis EO. Experimental determination of translational start sites resolves uncertainties in genomic open reading frame predictions - application to Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2009; 155:186-197. [PMID: 19118359 PMCID: PMC2897130 DOI: 10.1099/mic.0.022889-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/11/2008] [Accepted: 09/25/2008] [Indexed: 11/26/2022]
Abstract
Correct identification of translational start sites is important for understanding protein function and transcriptional regulation. The annotated translational start sites contained in genome databases are often predicted using bioinformatics and are rarely verified experimentally, and so are not all accurate. Therefore, we devised a simple approach for determining translational start sites using a combination of epitope tagging and frameshift mutagenesis. This assay was used to determine the start sites of three Mycobacterium tuberculosis proteins: LexA, SigC and Rv1955. We were able to show that proteins may begin before or after the predicted site. We also found that a small, non-annotated open reading frame upstream of Rv1955 was expressed as a protein, which we have designated Rv1954A. This approach is readily applicable to any bacterial species for which plasmid transformation can be achieved.
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Affiliation(s)
- Katherine L Smollett
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Amanda S Fivian-Hughes
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joanne E Smith
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Anchi Chang
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Tara Rao
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Elaine O Davis
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Gebhard S, Hümpel A, McLellan AD, Cook GM. The alternative sigma factor SigF of Mycobacterium smegmatis is required for survival of heat shock, acidic pH and oxidative stress. MICROBIOLOGY-SGM 2008; 154:2786-2795. [PMID: 18757812 DOI: 10.1099/mic.0.2008/018044-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The alternative sigma factor SigF of Mycobacterium tuberculosis has been characterized in detail as a general-stress, stationary-phase sigma factor involved in the virulence of the bacterium. While a homologous gene has been annotated in the genome of the fast-growing Mycobacterium smegmatis, little experimental evidence is available on the function of this gene. Here, we demonstrate that SigF of M. smegmatis is required for resistance to hydrogen peroxide, heat shock and acidic pH, but not for survival in human neutrophils. No difference in sensitivity to isoniazid was observed between the wild-type strain and the DeltasigF mutant, suggesting that SigF-mediated resistance to hydrogen peroxide was via a pathway independent of KatG or AhpC. RT-PCR and 5'-RACE (rapid amplification of cDNA ends) analyses showed that sigF of M. smegmatis was co-transcribed with rsbW (thought to encode an anti-sigma factor for SigF) and MSMEG_1802 (unknown function) and was expressed from two promoters, one upstream of MSMEG_1802 and the second upstream of rsbW. Analysis of transcriptional lacZ fusion constructs in the sigF-deletion background revealed that the MSMEG_1802 promoter was dependent on SigF for expression. Moreover, MSMEG_1802-lacZ was induced twofold upon entry into stationary phase, while exposure of exponentially growing cultures to various stress conditions (e.g. heat, cold, ethanol, hydrogen peroxide or different pH values) did not lead to induction of MSMEG_1802-lacZ. Expression of rsbW-lacZ was independent of SigF and remained constant throughout the growth cycle and under various stress conditions unless the bacteria were challenged with d-cycloserine.
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Affiliation(s)
- Susanne Gebhard
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Anja Hümpel
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Alexander D McLellan
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
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SigF controls carotenoid pigment production and affects transformation efficiency and hydrogen peroxide sensitivity in Mycobacterium smegmatis. J Bacteriol 2008; 190:7859-63. [PMID: 18805974 DOI: 10.1128/jb.00714-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carotenoids are complex lipids that are known for acting against photodynamic injury and free radicals. We demonstrate here that sigma(F) is required for carotenoid pigment production in Mycobacterium smegmatis. We further show that a sigF mutant exhibits a transformation efficiency 10(4)-fold higher than that of the parental strain, suggesting that sigma(F) regulates the production of components affecting cell wall permeability. In addition, a sigF mutant showed an increased sensitivity to hydrogen peroxide. An in silico search of the M. smegmatis genome identified a number of SigF consensus sites, including sites upstream of the carotenoid synthesis locus, which explains its SigF regulation.
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39
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Singh AK, Singh BN. Conservation of sigma F in mycobacteria and its expression in Mycobacterium smegmatis. Curr Microbiol 2008; 56:574-80. [PMID: 18324436 DOI: 10.1007/s00284-008-9126-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 12/11/2007] [Indexed: 11/29/2022]
Abstract
Alternate sigma factor SigF controls the expression of virulence-associated genes and is believed to contribute to the pathology of tuberculosis. It was reported to be absent in fast-growing nontuberculous mycobacteria until its orthologs were reported recently in a database. In this study, we demonstrate the presence of sigF gene in few commonly studied nonpathogenic mycobacterial species. Further, we studied the sigF expression in Mycobacterium smegmatis and observed that unlike its late-stage expression in M. tuberculosis and M. bovis, found in earlier studies, sigF is expressed throughout the growth in M. smegmatis, by and large, at the same level, but its expression varies upon exposure to different stress conditions. The presence of sigF orthologs in nontuberculous mycobacteria and its continued expression throughout the growth suggests that apart from regulating the expression of virulence factor genes in pathogenic mycobacteria, SigF is likely to have more roles in the mycobacterial physiology.
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Affiliation(s)
- Anirudh K Singh
- Division of Microbiology, Central Drug Research Institute, Post Box No. 173, M G Road, Lucknow, 226 001, India
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40
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Pimentel-Schmitt EF, Thomae AW, Amon J, Klieber MA, Roth HM, Muller YA, Jahreis K, Burkovski A, Titgemeyer F. A glucose kinase from Mycobacterium smegmatis. J Mol Microbiol Biotechnol 2007; 12:75-81. [PMID: 17183214 DOI: 10.1159/000096462] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Carbon metabolism and regulation is poorly understood in mycobacteria, a genus that includes some major pathogenic species like Mycobacterium tuberculosis and Mycobacterium leprae. Here, we report the identification of a glucose kinase from Mycobacterium smegmatis. This enzyme serves in glucose metabolism and global carbon catabolite repression in the related actinomycete Streptomyces coelicolor. The gene, msmeg1356 (glkA), was found by means of in silico screening. It was shown that it occurs in the same genetic context in all so far sequenced mycobacterial species, where it is located in a putative tricistronic operon together with a glycosyl hydrolase and a putative malonyl-CoA transacylase. Heterologous expression of glkA in an Escherichia coli glucose kinase mutant led to the restoration of glucose growth, which provided in vivo evidence for glucose kinase function. GlkA(Msm) was subsequently overproduced in order to study its enzymatic features. We found that it can form a dimer and that it efficiently phosphorylates glucose at the expense of ATP. The affinity constant for glucose was with 9 mM about eight times higher and the velocity was about tenfold slower when compared to the parallel measured glucose kinase of S. coelicolor. Both enzymes showed similar substrate specificity, which consists in an ATP-dependent phosphorylation of glucose and no, or very inefficient, phosphorylation of the glucose analogues 2-deoxyglucose and methyl alpha-glucoside. Hence, our data provide a basis for studying the role of mycobacterial glucose kinase in vivo to unravel possible catalytic and regulatory functions.
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Yukawa H, Omumasaba CA, Nonaka H, Kós P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertès AA, Inui M. Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R. Microbiology (Reading) 2007; 153:1042-1058. [PMID: 17379713 DOI: 10.1099/mic.0.2006/003657-0] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete genome sequence of Corynebacterium glutamicum strain R was determined to allow its comparative analysis with other corynebacteria. The biology of corynebacteria was explored by refining the definition of the subset of genes that constitutes the corynebacterial core as well as those characteristic of saprophytic and pathogenic ecological niches. In addition, the relative scarcity of corynebacterial sigma factors and the plasticity of their two-component system machinery reflect their relatively exacting nutritional requirements and reduced membrane-associated and secreted proteins. The conservation of key genes and pathways between corynebacteria, mycobacteria and Nocardia validates the use of C. glutamicum to study fundamental processes that are conserved in slow-growing mycobacteria, including pathogenesis-associated mechanisms. The discovery of 39 novel genes in C. glutamicum R that have not been previously reported in other corynebacteria supports the rationale for sequencing additional corynebacterial genomes to better define the corynebacterial pan-genome and identify previously undetected metabolic pathways in these organisms.
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Affiliation(s)
- Hideaki Yukawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Crispinus A Omumasaba
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Hiroshi Nonaka
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Péter Kós
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Naoko Okai
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Nobuaki Suzuki
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Masako Suda
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Yota Tsuge
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Junko Watanabe
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Yoko Ikeda
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Alain A Vertès
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
| | - Masayuki Inui
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Soraku, Kyoto 619-0292, Japan
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Wilkinson BL, Bornaghi LF, Wright AD, Houston TA, Poulsen SA. Anti-mycobacterial activity of a bis-sulfonamide. Bioorg Med Chem Lett 2007; 17:1355-7. [PMID: 17258454 DOI: 10.1016/j.bmcl.2006.11.079] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 11/24/2006] [Accepted: 11/30/2006] [Indexed: 11/22/2022]
Abstract
A bis-arylsulfonamide, 7, has been identified that exhibits growth inhibition of Mycobacterium smegmatis at less than 25 microg/mL, but has no such activity against Escherichia coli or Staphylococcus aureus. A closely related bis-arylsulfonamide (8) was much less active, but was the only other compound among 54 arylsulfonamides tested with detectable growth inhibition of M. smegmatis.
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Affiliation(s)
- Brendan L Wilkinson
- Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Qld 4111, Australia
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43
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Thakur KG, Joshi AM, Gopal B. Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(C) from Mycobacterium tuberculosis. J Biol Chem 2007; 282:4711-4718. [PMID: 17145760 PMCID: PMC1890005 DOI: 10.1074/jbc.m606283200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
sigma factors are transcriptional regulatory proteins that bind to the RNA polymerase and dictate gene expression. The extracytoplasmic function (ECF) sigma factors govern the environment dependent regulation of transcription. ECF sigma factors have two domains sigma(2) and sigma(4) that recognize the -10 and -35 promoter elements. However, unlike the primary sigma factor sigma(A), the ECF sigma factors lack sigma(3), a region that helps in the recognition of the extended -10 element and sigma(1.1), a domain involved in the autoinhibition of sigma(A) in the absence of core RNA polymerase. Mycobacterium tuberculosis sigma(C) is an ECF sigma factor that is essential for the pathogenesis and virulence of M. tuberculosis in the mouse and guinea pig models of infection. However, unlike other ECF sigma factors, sigma(C) does not appear to have a regulatory anti-sigma factor located in the same operon. We also note that M. tuberculosis sigma(C) differs from the canonical ECF sigma factors as it has an N-terminal domain comprising of 126 amino acids that precedes the sigma(C)(2) and sigma(C)(4) domains. In an effort to understand the regulatory mechanism of this protein, the crystal structures of the sigma(C)(2) and sigma(C)(4) domains of sigma(C) were determined. These promoter recognition domains are structurally similar to the corresponding domains of sigma(A) despite the low sequence similarity. Fluorescence experiments using the intrinsic tryptophan residues of sigma(C)(2) as well as surface plasmon resonance measurements reveal that the sigma(C)(2) and sigma(C)(4) domains interact with each other. Mutational analysis suggests that the Pribnow box-binding region of sigma(C)(2) is involved in this interdomain interaction. Interaction between the promoter recognition domains in M. tuberculosis sigma(C) are thus likely to regulate the activity of this protein even in the absence of an anti-sigma factor.
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MESH Headings
- Animals
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Crystallography, X-Ray
- Cytoplasm/chemistry
- Cytoplasm/genetics
- Cytoplasm/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA-Directed RNA Polymerases/chemistry
- DNA-Directed RNA Polymerases/metabolism
- Disease Models, Animal
- Gene Expression Regulation, Bacterial/physiology
- Guinea Pigs
- Humans
- Mice
- Models, Molecular
- Mutation
- Mycobacterium tuberculosis/chemistry
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/metabolism
- Mycobacterium tuberculosis/pathogenicity
- Promoter Regions, Genetic
- Protein Binding/physiology
- Protein Structure, Tertiary/physiology
- Sigma Factor/chemistry
- Sigma Factor/genetics
- Sigma Factor/metabolism
- Surface Plasmon Resonance
- Transcription, Genetic/physiology
- Tuberculosis/genetics
- Tuberculosis/metabolism
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Affiliation(s)
- Krishan Gopal Thakur
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | - B Gopal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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Sechi LA, Felis GE, Ahmed N, Paccagnini D, Usai D, Ortu S, Molicotti P, Zanetti S. Genome and transcriptome scale portrait of sigma factors in Mycobacterium avium subsp. paratuberculosis. INFECTION GENETICS AND EVOLUTION 2007; 7:424-32. [PMID: 17292677 DOI: 10.1016/j.meegid.2007.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 01/08/2007] [Indexed: 11/20/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of Johne's disease (JD), a chronic gastroenteritis of ruminants and other animals, including primates. Many evidences suggested association of MAP to Crohn's disease, a chronic granulomatous gastrointestinal disease of humans with strong similarities with JD. The present study attempts to evaluate global gene regulation in MAP, which has not been addressed previously, despite the availability of MAP genome sequence. For this purpose, we investigated: (i) the presence of sigma factors and their relationship to sigma factors of other mycobacteria (M. avium subsp.avium, M. tuberculosis, M. bovis, M. leprae and M. smegmatis), and (ii) their expression during different growth conditions and in vitro infection of intestinal epithelial Caco2 cells. MAP genome contains 19 putative sigma factor, but only 12 belong to gene families common to other mycobacteria. Gene expression was evaluated with Real-Time PCR during growth in 7H9 medium and mycobactin J, in 7H9 medium plus mycobactin J and lisozyme, and during infection of Caco2 cells: very different expression patterns were observed and, on the whole, only 7 sigma factors were found to be expressed. sigJ was upregulated during the infection of Caco2 cells. Even if only few sigma factors were expressed in the three conditions tested, the overall high numbers of MAP sigma factors suggests a noteworthy flexibility of this pathogen. Thus, this first report on expression of MAP sigma factors opens the way to an extensive characterization of global gene regulation, as a key to understand strategies of survival and mechanisms of infections used by this organism.
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Affiliation(s)
- Leonardo A Sechi
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia Sperimentale e Clinica, Università degli studi di Sassari, Viale S. Pietro 43/B, 07100 Sassari, Italy.
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45
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Rodrigue S, Provvedi R, Jacques PE, Gaudreau L, Manganelli R. The sigma factors of Mycobacterium tuberculosis. FEMS Microbiol Rev 2006; 30:926-41. [PMID: 17064287 DOI: 10.1111/j.1574-6976.2006.00040.x] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis is a remarkable pathogen capable of adapting and surviving in various harsh conditions. Correct gene expression regulation is essential for the success of this process. The reversible association of different sigma factors is a common mechanism for reprogramming bacterial RNA polymerase and modulating the transcription of numerous genes. Thirteen putative sigma factors are encoded in the M. tuberculosis genome, several being important for virulence. Here, we analyse the latest information available on mycobacterial sigma factors and discuss their roles in the physiology and virulence of M. tuberculosis.
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Affiliation(s)
- Sébastien Rodrigue
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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46
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Homerova D, Surdova K, Mikusova K, Kormanec J. Identification of promoters recognized by RNA polymerase containing Mycobacterium tuberculosis stress-response sigma factor sigma(F). Arch Microbiol 2006; 187:185-97. [PMID: 17089148 DOI: 10.1007/s00203-006-0185-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 09/20/2006] [Accepted: 10/09/2006] [Indexed: 11/24/2022]
Abstract
A previously optimized Escherichia coli two-plasmid system was used to identify Mycobacterium tuberculosis promoters recognized by RNA polymerase containing the M. tuberculosis stress response sigma factor sigma(F). The method allowed the identification of five new sigma(F)-dependent promoters. Transcriptional start points of the promoters were determined by high-resolution S1-nuclease mapping using RNA prepared from E. coli containing the two-plasmid system. The promoters were confirmed by an in vitro transcription assay. The Mycobacterium smegmatis and Mycobacterium tuberculosis core RNA polymerases, after complementation with sigma(F), were able to recognize all the five promoters. All the promoters contained sequences highly similar to the sequence of the previously identified M. tuberculosis sigma(F)-dependent promoter, usfXp1. Comparison of the promoters revealed a sigma(F) consensus sequence GtTtga-N(14-18)-GGGTAT. The sigma(F)-dependent promoters may govern expression of genes encoding a transcription regulator homologous to the response regulators of bacterial two-component signal transduction systems and proteins with unknown function.
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Affiliation(s)
- Dagmar Homerova
- Institute of Molecular Biology, Center of Excellence for Molecular Medicine, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovak Republic
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Mukherjee R, Chatterji D. Evaluation of the role of sigma B in Mycobacterium smegmatis. Biochem Biophys Res Commun 2005; 338:964-72. [PMID: 16248983 DOI: 10.1016/j.bbrc.2005.10.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2005] [Accepted: 10/07/2005] [Indexed: 11/24/2022]
Abstract
The alternate sigma factor, sigB, is known to play a crucial role in maintaining the stationary phase in mycobacteria. In this communication, we have studied the proteomics of Mycobacterium smegmatis mc(2)155 and its two derivatives, one of which has a disrupted sigB gene and the other, PMVSigB, which contains a multicopy plasmid containing sigB. We have identified by two-dimensional gel analyses, several proteins that are over-expressed in PMVSigB compared to mc(2)155. These proteins are either stress proteins or participate actively in different metabolic pathways of the organisms. On the other hand, when sigB deleted mycobacteria were grown until the stationary phase and its two-dimensional protein profile was compared to that of mc(2)155, few DNA binding proteins were found to be up-regulated. We have shown recently that upon over-expressing sigB, the cell surface glycopeptidolipids of M. smegmatis are hyperglycosylated, a situation similar to what was observed for nutritionally starved bacteria. Gene expression profile through quantitative PCR presented here identified a Rhamnosyltransferase responsible for this hyperglycosylation.
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Affiliation(s)
- Raju Mukherjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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