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Schneider RF, Hallstrom K, DeMott C, McDonough KA. Conditional protein splicing of the Mycobacterium tuberculosis RecA intein in its native host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589443. [PMID: 38659745 PMCID: PMC11042385 DOI: 10.1101/2024.04.15.589443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The recA gene, encoding Recombinase A (RecA) is one of three Mycobacterium tuberculosis (Mtb) genes encoding an in-frame intervening protein sequence (intein) that must splice out of precursor host protein to produce functional protein. Ongoing debate about whether inteins function solely as selfish genetic elements or benefit their host cells requires understanding of interplay between inteins and their hosts. We measured environmental effects on native RecA intein splicing within Mtb using a combination of western blots and promoter reporter assays. RecA splicing was stimulated in bacteria exposed to DNA damaging agents or by treatment with copper in hypoxic, but not normoxic, conditions. Spliced RecA was processed by the Mtb proteasome, while free intein was degraded efficiently by other unknown mechanisms. Unspliced precursor protein was not observed within Mtb despite its accumulation during ectopic expression of Mtb recA within E. coli. Surprisingly, Mtb produced free N-extein in some conditions, and ectopic expression of Mtb N-extein activated LexA in E. coli. These results demonstrate that the bacterial environment greatly impacts RecA splicing in Mtb, underscoring the importance of studying intein splicing in native host environments and raising the exciting possibility of intein splicing as a novel regulatory mechanism in Mtb.
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Affiliation(s)
- Ryan F. Schneider
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
| | | | | | - Kathleen A. McDonough
- Biomedical Sciences Department, School of Public Health, State University of New York at Albany
- Wadsworth Center, New York Department of Health
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2
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Schwarz MGA, Corrêa PR, Mendonça-Lima L. Transcriptional Profiling of Homologous Recombination Pathway Genes in Mycobacterium bovis BCG Moreau. Microorganisms 2023; 11:2534. [PMID: 37894192 PMCID: PMC10609372 DOI: 10.3390/microorganisms11102534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/17/2023] [Accepted: 08/29/2023] [Indexed: 10/29/2023] Open
Abstract
Mycobacterium bovis BCG Moreau is the main Brazilian strain for vaccination against tuberculosis. It is considered an early strain, more like the original BCG, whereas BCG Pasteur, largely used as a reference, belongs to the late strain clade. BCG Moreau, contrary to Pasteur, is naturally deficient in homologous recombination (HR). In this work, using a UV exposure test, we aimed to detect differences in the survival of various BCG strains after DNA damage. Transcription of core and regulatory HR genes was further analyzed using RT-qPCR, aiming to identify the molecular agent responsible for this phenotype. We show that early strains share the Moreau low survival rate after UV exposure, whereas late strains mimic the Pasteur phenotype, indicating that this increase in HR efficiency is linked to the evolutionary clade history. Additionally, RT-qPCR shows that BCG Moreau has an overall lower level of these transcripts than Pasteur, indicating a correlation between this gene expression profile and HR efficiency. Further assays should be performed to fully identify the molecular mechanism that may explain this differential phenotype between early and late BCG strains.
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Affiliation(s)
- Marcos Gustavo Araujo Schwarz
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (P.R.C.); (L.M.-L.)
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3
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Adefisayo OO, Dupuy P, Nautiyal A, Bean JM, Glickman MS. Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis. Nucleic Acids Res 2021; 49:12805-12819. [PMID: 34871411 PMCID: PMC8682763 DOI: 10.1093/nar/gkab1169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/30/2021] [Accepted: 11/10/2021] [Indexed: 11/15/2022] Open
Abstract
DNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as Mycobacterium tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here, we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.
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Affiliation(s)
- Oyindamola O Adefisayo
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Pierre Dupuy
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Astha Nautiyal
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - James M Bean
- Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
| | - Michael S Glickman
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, 1300 York Avenue, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10025, USA
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4
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The Mycobacterium tuberculosis sRNA F6 Modifies Expression of Essential Chaperonins, GroEL2 and GroES. Microbiol Spectr 2021; 9:e0109521. [PMID: 34549992 PMCID: PMC8557902 DOI: 10.1128/spectrum.01095-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Almost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of posttranscriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA F6 and shown it to be dependent on SigF for expression and significantly induced in starvation conditions in vitro and in a mouse model of infection. Further exploration of F6 using an in vitro starvation model of infection indicates that F6 affects the expression of the essential chaperonins GroEL2 and GroES. Our results point toward a role for F6 during periods of low metabolic activity typically associated with long-term survival of M. tuberculosis in human granulomas. IMPORTANCE Control of gene expression via small regulatory RNAs (sRNAs) is poorly understood in one of the most successful pathogens, Mycobacterium tuberculosis. Here, we present an in-depth characterization of the sRNA F6, including its expression in different infection models and the differential gene expression observed upon deletion of the sRNA. Our results demonstrate that deletion of F6 leads to dysregulation of the two essential chaperonins GroEL2 and GroES and, moreover, indicate a role for F6 in the long-term survival and persistence of M. tuberculosis in the human host.
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Dissecting the RecA-(In)dependent Response to Mitomycin C in Mycobacterium tuberculosis Using Transcriptional Profiling and Proteomics Analyses. Cells 2021; 10:cells10051168. [PMID: 34064944 PMCID: PMC8151990 DOI: 10.3390/cells10051168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Mycobacteria exploit at least two independent global systems in response to DNA damage: the LexA/RecA-dependent SOS response and the PafBC-regulated pathway. Intracellular pathogens, such as Mycobacterium tuberculosis, are exposed to oxidative and nitrosative stress during the course of infection while residing inside host macrophages. The current understanding of RecA-independent responses to DNA damage is based on the saprophytic model of Mycobacterium smegmatis, a free-living and nonpathogenic mycobacterium. The aim of the present study was to identify elements of RecA-independent responses to DNA damage in pathogenic intracellular mycobacteria. With the help of global transcriptional profiling, we were able to dissect RecA-dependent and RecA-independent pathways. We profiled the DNA damage responses of an M. tuberculosis strain lacking the recA gene, a strain with an undetectable level of the PafBC regulatory system, and a strain with both systems tuned down simultaneously. RNA-Seq profiling was correlated with the evaluation of cell survival in response to DNA damage to estimate the relevance of each system to the overall sensitivity to genotoxic agents. We also carried out whole-cell proteomics analysis of the M. tuberculosis strains in response to mitomycin C. This approach highlighted that LexA, a well-defined key element of the SOS system, is proteolytically inactivated during RecA-dependent DNA repair, which we found to be transcriptionally repressed in response to DNA-damaging agents in the absence of RecA. Proteomics profiling revealed that AlkB was significantly overproduced in the ΔrecA pafBCCRISPRi/dCas9 strain and that Holliday junction resolvase RuvX was a DNA damage response factor that was significantly upregulated regardless of the presence of functional RecA and PafBC systems, thus falling into a third category of DNA damage factors: RecA- and PafBC-independent. While invisible to the mass spectrometer, the genes encoding alkA, dnaB, and dnaE2 were significantly overexpressed in the ΔrecA pafBCCRISPRi/dCas9 strain at the transcript level.
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The PafBC-mediated response sensitizes a bistable DNA damage response in Mycobacteria. J Theor Biol 2020; 508:110462. [PMID: 32890555 DOI: 10.1016/j.jtbi.2020.110462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/05/2020] [Accepted: 08/24/2020] [Indexed: 01/03/2023]
Abstract
Due to the genotoxically challenging environments in which they live in, Mycobacteria have a complex DNA damage repair system that is governed by two major DNA damage responses, namely, the LexA/RecA-dependent response and the newly characterized PafBC-mediated response (Müller et al., 2018). The LexA/RecA-dependent response is a well-known bistable response found in different types of bacteria, and the Mycobacteria-specific PafBC-mediated response interacts with and modifies the LexA/RecA-dependent response (Müller et al., 2018). The interaction between the LexA/RecA-dependent response and the PafBC-mediated response has not been characterized mathematically. Our analysis shows that the addition of the PafBC-mediated response sensitizes the overall DNA damage response, effectively lowering the DNA damage rate threshold for activation.
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Hans S, Purkait D, Nandan S, Bansal M, Hameed S, Fatima Z. Rec A disruption unveils cross talk between DNA repair and membrane damage, efflux pump activity, biofilm formation in Mycobacterium smegmatis. Microb Pathog 2020; 149:104262. [PMID: 32439563 DOI: 10.1016/j.micpath.2020.104262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 10/24/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) has emerged in recent decades as one of the leading causes of mortality worldwide. The burden of TB is alarmingly high, with one third affected global population as reported by WHO. Short-course treatment with an antibiotic is a powerful weapon to treat infection of susceptible MTB strain, however; MTB has developed resistance to anti-TB drugs, which is an escalating global health crisis. Thus there is urgent need to identify new drug targets. RecA is a 38 kilodalton protein required for the repair and maintenance of DNA and regulation of the SOS response. The objective of this study is to understand the effect of disruption of RecA gene (deletion mutant ΔdisA from previous study) in a surrogate model for MTB, Mycobacterium smegmatis. This study demonstrated that disruption of RecA causes enhanced susceptibility towards rifampicin and generation of ROS leading to lipid peroxidation and impaired membrane homeostasis as depicted by altered cell membrane permeability and efflux pump activity. Mass spectrometry based lipidomic analysis revealed decreased mycolic acid moieties, phosphatidylinositol mannosides (PIM), Phthiocerol dimycocerosate (DIM). Furthermore, biofilm formation was considerably reduced. Additionally, we have validated all the disrupted phenotypes by RT-PCR which showed a good correlation with the biochemical assays. Lastly, RecA mutant displayed reduced infectivity in Caenorhabditis elegans illustrating its vulnerability as antimycobacterial target. Together, present study establishes a link between DNA repair, drug efflux and biofilm formation and validates RecA as an effective drug target. Intricate studies are needed to further understand and exploit this therapeutic opportunity.
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Affiliation(s)
- Sandeep Hans
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Dyuti Purkait
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Shiv Nandan
- Amity Lipidomics Research Facility, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Maghav Bansal
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
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8
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Manina G, Griego A, Singh LK, McKinney JD, Dhar N. Preexisting variation in DNA damage response predicts the fate of single mycobacteria under stress. EMBO J 2019; 38:e101876. [PMID: 31583725 PMCID: PMC6856624 DOI: 10.15252/embj.2019101876] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/06/2019] [Accepted: 09/16/2019] [Indexed: 11/09/2022] Open
Abstract
Clonal microbial populations are inherently heterogeneous, and this diversification is often considered as an adaptation strategy. In clinical infections, phenotypic diversity is found to be associated with drug tolerance, which in turn could evolve into genetic resistance. Mycobacterium tuberculosis, which ranks among the top ten causes of mortality with high incidence of drug-resistant infections, exhibits considerable phenotypic diversity. In this study, we quantitatively analyze the cellular dynamics of DNA damage responses in mycobacteria using microfluidics and live-cell fluorescence imaging. We show that individual cells growing under optimal conditions experience sporadic DNA-damaging events manifested by RecA expression pulses. Single-cell responses to these events occur as transient pulses of fluorescence expression, which are dependent on the gene-network structure but are triggered by extrinsic signals. We demonstrate that preexisting subpopulations, with discrete levels of DNA damage response, are associated with differential susceptibility to fluoroquinolones. Our findings reveal that the extent of DNA integrity prior to drug exposure impacts the drug activity against mycobacteria, with conceivable therapeutic implications.
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Affiliation(s)
- Giulia Manina
- Microbial Individuality and Infection GroupCell Biology and Infection DepartmentInstitut PasteurParisFrance
- School of Life SciencesSwiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Anna Griego
- Microbial Individuality and Infection GroupCell Biology and Infection DepartmentInstitut PasteurParisFrance
- Université Paris DescartesSorbonne Paris CitéParisFrance
| | - Lalit Kumar Singh
- Microbial Individuality and Infection GroupCell Biology and Infection DepartmentInstitut PasteurParisFrance
| | - John D McKinney
- School of Life SciencesSwiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
| | - Neeraj Dhar
- School of Life SciencesSwiss Federal Institute of Technology in Lausanne (EPFL)LausanneSwitzerland
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9
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Prasad D, Arora D, Nandicoori VK, Muniyappa K. Elucidating the functional role of Mycobacterium smegmatis recX in stress response. Sci Rep 2019; 9:10912. [PMID: 31358794 PMCID: PMC6662834 DOI: 10.1038/s41598-019-47312-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/15/2019] [Indexed: 12/20/2022] Open
Abstract
The RecX protein has attracted considerable interest because the recX mutants exhibit multiple phenotypes associated with RecA functions. To further our understanding of the functional relationship between recA and recX, the effect of different stress treatments on their expression profiles, cell yield and viability were investigated. A significant correlation was found between the expression of Mycobacterium smegmatis recA and recX genes at different stages of growth, and in response to different stress treatments albeit recX exhibiting lower transcript and protein abundance at the mid-log and stationary phases of the bacterial growth cycle. To ascertain their roles in vivo, a targeted deletion of the recX and recArecX was performed in M. smegmatis. The growth kinetics of these mutant strains and their sensitivity patterns to different stress treatments were assessed relative to the wild-type strain. The deletion of recA affected normal cell growth and survival, while recX deletion showed no significant effect. Interestingly, deletion of both recX and recA genes results in a phenotype that is intermediate between the phenotypes of the ΔrecA mutant and the wild-type strain. Collectively, these results reveal a previously unrecognized role for M. smegmatis recX and support the notion that it may regulate a subset of the yet unknown genes involved in normal cell growth and DNA-damage repair.
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Affiliation(s)
- Deepika Prasad
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Divya Arora
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India.
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Manikandan K, Prasad D, Srivastava A, Singh N, Dabeer S, Krishnan A, Muniyappa K, Sinha KM. The second messenger cyclic di-AMP negatively regulates the expression of Mycobacterium smegmatis recA and attenuates DNA strand exchange through binding to the C-terminal motif of mycobacterial RecA proteins. Mol Microbiol 2018; 109:600-614. [PMID: 29873124 DOI: 10.1111/mmi.13991] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 12/26/2022]
Abstract
Cyclic di-GMP and cyclic di-AMP are second messengers produced by a wide variety of bacteria. They influence bacterial cell survival, biofilm formation, virulence and bacteria-host interactions. However, many of their cellular targets and biological effects are yet to be determined. A chemical proteomics approach revealed that Mycobacterium smegmatis RecA (MsRecA) possesses a high-affinity cyclic di-AMP binding activity. We further demonstrate that both cyclic di-AMP and cyclic di-GMP bind specifically to the C-terminal motif of MsRecA and Mycobacterium tuberculosis RecA (MtRecA). Escherichia coli RecA (EcRecA) was devoid of cyclic di-AMP binding but have cyclic di-GMP binding activity. Notably, cyclic di-AMP attenuates the DNA strand exchange promoted by MsRecA as well as MtRecA through the disassembly of RecA nucleoprotein filaments. However, the structure and DNA strand exchange activity of EcRecA nucleoprotein filaments remain largely unaffected. Furthermore, M. smegmatis ΔdisA cells were found to have undetectable RecA levels due to the translational repression of recA mRNA. Consequently, the ΔdisA mutant exhibited enhanced sensitivity to DNA-damaging agents. Altogether, this study points out the importance of sequence diversity among recA genes, the role(s) of cyclic di-AMP and reveals a new mode of negative regulation of recA gene expression, DNA repair and homologous recombination in mycobacteria.
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Affiliation(s)
- Kasi Manikandan
- Institute of Molecular Medicine, 254 Okhla Industrial Estate, Phase 3, New Delh, India
| | - Deepika Prasad
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ankita Srivastava
- Institute of Molecular Medicine, 254 Okhla Industrial Estate, Phase 3, New Delh, India
| | - Nirpendra Singh
- Central Instrument Facility, University of Delhi South Campus, New Delhi, India
| | - Sadaf Dabeer
- Institute of Molecular Medicine, 254 Okhla Industrial Estate, Phase 3, New Delh, India
| | - Anuja Krishnan
- Institute of Molecular Medicine, 254 Okhla Industrial Estate, Phase 3, New Delh, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishna Murari Sinha
- Institute of Molecular Medicine, 254 Okhla Industrial Estate, Phase 3, New Delh, India
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11
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Mycobacterium smegmatis PafBC is involved in regulation of DNA damage response. Sci Rep 2017; 7:13987. [PMID: 29070902 PMCID: PMC5656591 DOI: 10.1038/s41598-017-14410-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 10/11/2017] [Indexed: 01/08/2023] Open
Abstract
Two genes, pafB and pafC, are organized in an operon with the Pup-ligase gene pafA, which is part of the Pup-proteasome system (PPS) present in mycobacteria and other actinobacteria. The PPS is crucial for Mycobacterium tuberculosis resistance towards reactive nitrogen intermediates (RNI). However, pafB and pafC apparently play only a minor role in RNI resistance. To characterize their function, we generated a pafBC deletion in Mycobacterium smegmatis (Msm). Proteome analysis of the mutant strain revealed decreased cellular levels of various proteins involved in DNA damage repair, including recombinase A (RecA). In agreement with this finding, Msm ΔpafBC displayed increased sensitivity to DNA damaging agents. In mycobacteria two pathways regulate DNA repair genes: the LexA/RecA-dependent SOS response and a predominant pathway that controls gene expression via a LexA/RecA-independent promoter, termed P1. PafB and PafC feature winged helix-turn-helix DNA binding motifs and we demonstrate that together they form a stable heterodimer in vitro, implying a function as a heterodimeric transcriptional regulator. Indeed, P1-driven transcription of recA was decreased in Msm ΔpafBC under standard conditions and induction of recA expression upon DNA damage was strongly impaired. Taken together, our data indicate an important regulatory function of PafBC in the mycobacterial DNA damage response.
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Thakur Z, Saini V, Arya P, Kumar A, Mehta PK. Computational insights into promoter architecture of toxin-antitoxin systems of Mycobacterium tuberculosis. Gene 2017; 641:161-171. [PMID: 29066303 DOI: 10.1016/j.gene.2017.10.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/27/2017] [Accepted: 10/16/2017] [Indexed: 12/16/2022]
Abstract
Toxin-antitoxin (TA) systems are two component genetic modules widespread in many bacterial genomes, including Mycobacterium tuberculosis (Mtb). The TA systems play a significant role in biofilm formation, antibiotic tolerance and persistence of pathogen inside the host cells. Deciphering regulatory motifs of Mtb TA systems is the first essential step to understand their transcriptional regulation. In this study, in silico approaches, that is, the knowledge based motif discovery and de novo motif discovery were used to identify the regulatory motifs of 79 Mtb TA systems. The knowledge based motif discovery approach was used to design a Perl based bio-tool Mtb-sig-miner available at (https://github.com/zoozeal/Mtb-sig-miner), which could successfully detect sigma (σ) factor specific regulatory motifs in the promoter region of Mtb TA modules. The manual curation of Mtb-sig-miner output hits revealed that the majority of them possessed σB regulatory motif in their promoter region. On the other hand, de novo approach resulted in the identification of a novel conserved motif [(T/A)(G/T)NTA(G/C)(C/A)AT(C/A)] within the promoter region of 14 Mtb TA systems. The identified conserved motif was also validated for its activity as conserved core region of operator sequence of corresponding TA system by molecular docking studies. The strong binding of respective antitoxin/toxin with the identified novel conserved motif reflected the validation of identified motif as the core region of operator sequence of respective TA systems. These findings provide computational insight to understand the transcriptional regulation of Mtb TA systems.
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Affiliation(s)
- Zoozeal Thakur
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Vandana Saini
- Toxicology & Computational Biology Group, Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Preeti Arya
- National Agri-Food Biotechnology Institute, Sector 81, S.A.S Nagar, Mohali, Punjab 140306, India
| | - Ajit Kumar
- Toxicology & Computational Biology Group, Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
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13
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Dogra N, Arya S, Singh K, Kaur J. Differential expression of two members of Rv1922-LipD operon in Mycobacterium tuberculosis: Does rv1923 qualify for membership? Pathog Dis 2015; 73:ftv029. [PMID: 25877878 DOI: 10.1093/femspd/ftv029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2015] [Indexed: 11/13/2022] Open
Abstract
rv1922 and rv1923 (lipD) are members of Rv1922-LipD operon in the genome of Mycobacterium tuberculosis. rv1922 was expressed under aerobic and stress conditions, whereas rv1923 was not expressed in aerobically grown bacteria but expressed moderately under oxidative stress conditions. Different expression of both the operonic genes under normal and stress conditions posed apprehensions for the inclusion of rv1922 and rv1923 in the same operon. The results from this study indicated that although the genes were expressed in an operonic manner, there existed the possibility of differential regulation for rv1923 which has been supported by in silico analysis for the presence of putative internal regulatory sites in the operon.
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Affiliation(s)
- Nandita Dogra
- Department of Biotechnology, Panjab University, BMS Block, Sec-25, Chandigarh, UT 160014, India
| | - Stuti Arya
- Department of Biotechnology, Panjab University, BMS Block, Sec-25, Chandigarh, UT 160014, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, BMS Block, Sec-25, Chandigarh, UT 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, BMS Block, Sec-25, Chandigarh, UT 160014, India
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14
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Bhatter P, Chatterjee A, Mistry N. Kinetics of recA and recX induction in drug-susceptible and MDR clinical strains of Mycobacterium tuberculosis. J Antimicrob Chemother 2014; 69:3199-202. [DOI: 10.1093/jac/dku319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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15
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Gaudion A, Dawson L, Davis E, Smollett K. Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: its operon and regulon. Tuberculosis (Edinb) 2013; 93:482-91. [PMID: 23871545 PMCID: PMC3776920 DOI: 10.1016/j.tube.2013.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/15/2013] [Accepted: 05/19/2013] [Indexed: 01/21/2023]
Abstract
A major step in the pathogenesis of Mycobacterium tuberculosis is the ability to survive inside macrophages, where it is exposed to a number of DNA damaging agents. The alternative sigma factor SigG has been shown to be upregulated by DNA damaging agents and by macrophage infection, but not to regulate genes of the DNA repair pathway. Here we show that SigG is expressed from at least two promoters, the most dominant of these being the DNA damage inducible RecA_Ndp promoter. This promoter is located within the annotated coding region of SigG and so the correct translational start site was determined experimentally and found to be 114 bp downstream of the annotated start site. Examining the gene expression profile of a SigG over-expression strain found a small number of genes to up-regulated, two of these encoded proteins containing glyoxylase-like domains.
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Affiliation(s)
- Alison Gaudion
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Newton-Foot M, Gey van Pittius NC. The complex architecture of mycobacterial promoters. Tuberculosis (Edinb) 2012; 93:60-74. [PMID: 23017770 DOI: 10.1016/j.tube.2012.08.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 01/02/2023]
Abstract
The genus Mycobacterium includes a variety of species with differing phenotypic properties, including growth rate, pathogenicity and environment- and host-specificity. Although many mycobacterial species have been extensively studied and their genomes sequenced, the reasons for phenotypic variation between closely related species remain unclear. Variation in gene expression may contribute to these characteristics and enable the bacteria to respond to changing environmental conditions. Gene expression is controlled primarily at the level of transcription, where the main element of regulation is the promoter. Transcriptional regulation and associated promoter sequences have been studied extensively in E. coli. This review describes the complex structure and characteristics of mycobacterial promoters, in comparison to the classical E. coli prokaryotic promoter structure. Some components of mycobacterial promoters are similar to those of E. coli. These include the predominant guanine residue at the transcriptional start point, conserved -10 hexamer, similar interhexameric distances, the use of ATG as a start codon, the guanine- and adenine-rich ribosome binding site and the presence of extended -10 (TGn) motifs in strong promoters. However, these components are much more variable in sequence in mycobacterial promoters and no conserved -35 hexamer sequence (clearly defined in E. coli) can be identified. This may be a result of the high G+C content of mycobacterial genomes, as well as the large number of sigma factors present in mycobacteria, which may recognise different promoter sequences. Mycobacteria possess a complex transcriptional regulatory network. Numerous regulatory motifs have been identified in mycobacterial promoters, predominantly in the interhexameric region. These are bound by specific transcriptional regulators in response to environmental changes. The combination of specific promoter sequences, transcriptional regulators and a variety of sigma factors enables rapid and specific responses to diverse conditions and different stages of infection. This review aims to provide an overview of the complex architecture of mycobacterial transcriptional regulation.
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Affiliation(s)
- Mae Newton-Foot
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Francie van Zijl Drive, Tygerberg 7505, South Africa.
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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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18
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Forse LN, Houghton J, Davis EO. Enhanced expression of recX in Mycobacterium tuberculosis owing to a promoter internal to recA. Tuberculosis (Edinb) 2011; 91:127-35. [PMID: 21251882 PMCID: PMC3062782 DOI: 10.1016/j.tube.2010.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/08/2010] [Accepted: 11/10/2010] [Indexed: 11/30/2022]
Abstract
RecX is a small protein that interacts with, and modulates the activity of, RecA protein. In mycobacteria the recX gene is located immediately downstream of the recA gene, and the coding regions overlap. It has previously been shown that these two genes are co-transcribed in Mycobacterium smegmatis. In this study we examine the expression of recX in Mycobacterium tuberculosis. In addition to being co-transcribed with recA from the DNA-damage inducible recA promoters, we identify a constitutive recX promoter located within the recA coding sequence that is strong enough to make a significant contribution to the expression level of recX in the absence of DNA damage. Intriguingly, this promoter is inactivated in M. smegmatis by a critical base change in the -10 promoter motif, which probably accounts for the lower level of expression of recX relative to recA that we observed in that species. It is possible that this difference in relative expression influences RecA functions including the response to DNA damage of LexA-regulated genes.
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Affiliation(s)
- Lorna N Forse
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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19
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Joon M, Bhatia S, Pasricha R, Bose M, Brahmachari V. Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis. BMC Microbiol 2010; 10:128. [PMID: 20420720 PMCID: PMC2867952 DOI: 10.1186/1471-2180-10-128] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/27/2010] [Indexed: 11/29/2022] Open
Abstract
Background The mce operons play an important role in the entry of M. tuberculosis into macrophages and non-phagocytic cells. Their non-redundant function as well as complex regulation is implied by the phenotype of mce mutants. Recently, mce1 operon was found to extend over 13 genes, fadD5 (Rv0166) being the first gene of the operon. The presence of a non-coding sequence of 200 base pairs between Rv0166 and Rv0167 is peculiar to mce1 among the four mce operons of M.tuberculosis. We have examined the function of this region. Results We predicted putative promoter activity of the 200 base pairs of non-coding, intergenic region between Rv0166 and Rv0167 in silico using MEME software and designate it as intergenic promoter, IGPr. We demonstrate both promoter activity and a putative negative regulatory function of this fragment by reporter assays carried out in the surrogate host M.smegmatis. We find that the repressive elements not only control the native promoter but also repress a heterologous promoter of M.smegmatis. The higher activity of the intergenic promoter in a clinical isolate in comparison with the wild type sequence from M.tuberculosis H37Rv could be correlated with a point mutation within the negative element. We have mapped two transcription start sites for mce1 operon both of which are utilized in M.tuberculosis H37Rv as well as the clinical isolate VPCI591. Our studies show that the promoter activity in the non-coding region is relevant not only in reporter gene expression but also in the expression of mce1 operon in M. tuberculosis cells grown in synthetic medium. Conclusion The mce operon of M.tuberculosis H37Rv potentially can be transcribed from two promoters P1 and P2, former mapping upstream of Rv0166 and the latter in the non-coding intergenic region between Rv0166 and Rv0167. The transcription initiation from P1 results in a transcript with Rv0166 while that from P2 will be without it. The sequences between the translation start site of Rv0167 and the promoter P2 have a negative regulatory role, as point mutation within the sequence leads to enhanced activity of P2 as well as a heterologous promoter from M.smegmatis. The mutation detected in the clinical isolate VPCI591 therefore behaves like a gain-of-function mutation.
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Affiliation(s)
- Monika Joon
- Dr B R Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
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20
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RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. J Bacteriol 2009; 192:599-603. [PMID: 19915023 DOI: 10.1128/jb.01066-09] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mycobacterium tuberculosis ruvC was induced by DNA damage in a DeltarecA strain despite having an appropriately positioned SOS box to which LexA binds in vitro. An inducible transcript start mapped within the SOS box, and transcriptional fusions identified the promoter. Disruption of the SOS box did not prevent induction, indicating that an alternative mechanism plays a significant role in the control of ruvC expression.
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Wu S, Barnes PF, Samten B, Pang X, Rodrigue S, Ghanny S, Soteropoulos P, Gaudreau L, Howard ST. Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth. MICROBIOLOGY-SGM 2009; 155:1272-1281. [PMID: 19332828 DOI: 10.1099/mic.0.024638-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
There is growing evidence that strains of Mycobacterium tuberculosis differ in pathogenicity and transmissibility, but little is understood about the contributory factors. We have previously shown that increased expression of the principal sigma factor, SigA, mediates the capacity of M. tuberculosis strain 210 to grow more rapidly in human monocytes, compared with other strains. Strain 210 is part of the widespread W-Beijing family of M. tuberculosis strains and includes clinical isolate TB294. To identify genes that respond to changes in SigA levels and that might enhance intracellular growth, we examined RNA and protein expression patterns in TB294-pSigA, a recombinant strain of TB294 that overexpresses sigA from a multicopy plasmid. Lysates from broth-grown cultures of TB294-pSigA contained high levels of Eis, a protein known to modulate host-pathogen interactions. DNA microarray analysis indicated that the eis gene, Rv2416c, was expressed at levels in TB294-pSigA 40-fold higher than in the vector control strain TB294-pCV, during growth in the human monocyte cell line MonoMac6. Other genes with elevated expression in TB294-pSigA showed much smaller changes from TB294-pCV, and the majority of genes with expression differences between the two strains had reduced expression in TB294-pSigA, including an unexpected number of genes associated with the DNA-damage response. Real-time PCR analyses confirmed that eis was expressed at very high levels in TB294-pSigA in monocytes as well as in broth culture, and further revealed that, like sigA, eis was also more highly expressed in wild-type TB294 than in the laboratory strain H37Rv, during growth in monocytes. These findings suggested an association between increased SigA levels and eis activation, and results of chromatin immunoprecipitation confirmed that SigA binds the eis promoter in live TB294 cells. Deletion of eis reduced growth of TB294 in monocytes, and complementation of eis reversed this effect. We conclude that SigA regulates eis, that there is a direct correlation between upregulation of SigA and high expression levels of eis, and that eis contributes to the enhanced capacity of a clinical isolate of M. tuberculosis strain 210 to grow in monocytes.
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Affiliation(s)
- Shiping Wu
- Department of Microbiology and Immunology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, Tyler, TX 75708-3154, USA
| | - Peter F Barnes
- Départment of Medicine, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, Tyler, TX 75708-3154, USA.,Department of Microbiology and Immunology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, Tyler, TX 75708-3154, USA
| | - Buka Samten
- Department of Microbiology and Immunology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, Tyler, TX 75708-3154, USA
| | - Xiuhua Pang
- Department of Microbiology and Immunology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, Tyler, TX 75708-3154, USA
| | - Sébastien Rodrigue
- Département de Biologie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC J1K2R1, Canada
| | - Saleena Ghanny
- Center for Applied Genomics, Public Health Research Institute, 225 Warren St, Newark, NJ 07103, USA
| | - Patricia Soteropoulos
- Center for Applied Genomics, Public Health Research Institute, 225 Warren St, Newark, NJ 07103, USA
| | - Luc Gaudreau
- Département de Biologie, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC J1K2R1, Canada
| | - Susan T Howard
- Department of Microbiology and Immunology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, Tyler, TX 75708-3154, USA
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Expression of the Mycobacterium tuberculosis acr-coregulated genes from the DevR (DosR) regulon is controlled by multiple levels of regulation. Infect Immun 2008; 76:2478-89. [PMID: 18391009 DOI: 10.1128/iai.01443-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known about how Mycobacterium tuberculosis regulates gene expression in response to its host environment, despite its importance as a pathogen. We previously characterized 10 acr-coregulated genes (ACGs), all of which belong to the DevR (DosR) "dormancy" regulon, and identified one to three copies of a conserved 18-bp palindromic DNA motif in the promoter of each ACG family member. In the present study, we used base substitution analyses to assess the importance of individual motif copies and to identify additional regulatory sequences in five ACG promoters. Regulation of acr, acg, Rv2623, narK2, and Rv1738 was examined by using single-copy M. tuberculosis promoter-lacZ reporter constructs in Mycobacterium bovis BCG under conditions of ambient air versus hypoxia, each in shaking versus standing shallow culture conditions. We found that regulation of these ACG promoters is more heterogeneous than expected and is controlled at multiple levels. In addition to the positive regulation previously associated with DevR (DosR) and the 18-bp ACG motif, we identified negative regulation associated with sequences in the 5' untranslated regions of acg and Rv2623 and positive regulation associated with far upstream regulatory regions of narK2 and Rv1738. The importance of individual ACG motifs varied among the promoters examined, and Rv1738 was exceptional in that its ACG motif copies were associated with negative, rather than positive, regulation under some conditions. Further understanding of this important regulon requires the identification of additional regulators that compete and/or collaborate with DevR (DosR) to regulate its individual gene members.
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Roback P, Beard J, Baumann D, Gille C, Henry K, Krohn S, Wiste H, Voskuil M, Rainville C, Rutherford R. A predicted operon map for Mycobacterium tuberculosis. Nucleic Acids Res 2007; 35:5085-95. [PMID: 17652327 PMCID: PMC1976454 DOI: 10.1093/nar/gkm518] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The prediction of operons in Mycobacterium tuberculosis (MTB) is a first step toward understanding the regulatory network of this pathogen. Here we apply a statistical model using logistic regression to predict operons in MTB. As predictors, our model incorporates intergenic distance and the correlation of gene expression calculated for adjacent gene pairs from over 474 microarray experiments with MTB RNA. We validate our findings with known examples from the literature and experimentation. From this model, we rank each potential operon pair by the strength of evidence for cotranscription, choose a classification threshold with a true positive rate of over 90% at a false positive rate of 9.1%, and use it to construct an operon map for the MTB genome.
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Affiliation(s)
- P. Roback
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - J. Beard
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - D. Baumann
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - C. Gille
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - K. Henry
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - S. Krohn
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - H. Wiste
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - M.I. Voskuil
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - C. Rainville
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - R. Rutherford
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
- *To whom correspondence should be addressed.+1 206 296 2501+1 206 296 5634
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Brooks PC, Dawson LF, Rand L, Davis EO. The mycobacterium-specific gene Rv2719c is DNA damage inducible independently of RecA. J Bacteriol 2006; 188:6034-8. [PMID: 16885473 PMCID: PMC1540060 DOI: 10.1128/jb.00340-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The mycobacterium-specific gene Rv2719c was found to be expressed primarily from a promoter that was clearly DNA damage inducible independently of RecA. Upstream of the transcriptional start site for this promoter, sequence motifs resembling those observed previously at the RecA-independent, DNA damage-inducible recA promoter were identified, and the -10 motif was demonstrated by mutational analysis in transcriptional fusion constructs to be important for expression of Rv2719c.
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Affiliation(s)
- Patricia C Brooks
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW71AA, United Kingdom
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Petković H, Cullum J, Hranueli D, Hunter IS, Perić-Concha N, Pigac J, Thamchaipenet A, Vujaklija D, Long PF. Genetics of Streptomyces rimosus, the oxytetracycline producer. Microbiol Mol Biol Rev 2006; 70:704-28. [PMID: 16959966 PMCID: PMC1594589 DOI: 10.1128/mmbr.00004-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
From a genetic standpoint, Streptomyces rimosus is arguably the best-characterized industrial streptomycete as the producer of oxytetracycline and other tetracycline antibiotics. Although resistance to these antibiotics has reduced their clinical use in recent years, tetracyclines have an increasing role in the treatment of emerging infections and noninfective diseases. Procedures for in vivo and in vitro genetic manipulations in S. rimosus have been developed since the 1950s and applied to study the genetic instability of S. rimosus strains and for the molecular cloning and characterization of genes involved in oxytetracycline biosynthesis. Recent advances in the methodology of genome sequencing bring the realistic prospect of obtaining the genome sequence of S. rimosus in the near term.
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Affiliation(s)
- Hrvoje Petković
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Gamulin V, Cetkovic H, Ahel I. Identification of a promoter motif regulating the major DNA damage response mechanism ofMycobacterium tuberculosis. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09737.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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