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Urtasun-Elizari JM, Ma R, Pickford H, Farrell D, Gonzalez G, Perets V, Nakajima C, Suzuki Y, MacHugh DE, Bhatt A, Gordon SV. Functional analysis of the Mycobacterium bovis AF2122/97 PhoPR system. Tuberculosis (Edinb) 2024; 148:102544. [PMID: 39018651 DOI: 10.1016/j.tube.2024.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
The PhoPR system is a master regulator in Mycobacterium tuberculosis. A key difference between M. tuberculosis and Mycobacterium bovis is a G71I substitution in the M. bovis PhoR orthologue. Functional studies of the M. bovis PhoPR system have generated conflicting findings, with some research suggesting that the M. bovis PhoPR is defective while others indicate it is functional. We sought to revisit the functionality of the M. bovis PhoPR system. To address this, we constructed a phoPR mutant in the reference strain M. bovis AF2122/97. We employed a combination of growth assays and transcriptomics analyses to assess the phenotype of the mutant vs wild type and complemented strains. We found that the M. bovis AF2122/97 ΔphoPR mutant showed a growth defect on solid and liquid media compared to the wild type and complemented strains. The transcriptome of the M. bovis AF2122/97 ΔphoPR mutant was also altered as compared to wild type, including differential expression of genes involved in lipid metabolism and secretion. Our work provides further insight into the activity of PhoPR in M. bovis and underlines the importance of the PhoPR system as a master regulator of gene expression in the Mycobacterium tuberculosis complex.
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Affiliation(s)
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Hayleah Pickford
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Gabriel Gonzalez
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan
| | - Viktor Perets
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Chie Nakajima
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - Yasuhiko Suzuki
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland; UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Dublin, Ireland.
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Martini BA, Grigorov AS, Skvortsova YV, Bychenko OS, Salina EG, Azhikina TL. Small RNA MTS1338 Configures a Stress Resistance Signature in Mycobacterium tuberculosis. Int J Mol Sci 2023; 24:ijms24097928. [PMID: 37175635 PMCID: PMC10178195 DOI: 10.3390/ijms24097928] [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: 04/02/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the course of evolution, Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, has developed sophisticated strategies to evade host immune response, including the synthesis of small non-coding RNAs (sRNAs), which regulate post-transcriptional pathways involved in the stress adaptation of mycobacteria. sRNA MTS1338 is upregulated in Mtb during its infection of cultured macrophages and in the model of chronic tuberculosis, suggesting involvement in host-pathogen interactions. Here, we analyzed the role of MTS1338 in the Mtb response to macrophage-like stresses in vitro. The Mtb strain overexpressing MTS1338 demonstrated enhanced survival ability under low pH, nitrosative, and oxidative stress conditions simulating the antimicrobial environment inside macrophages. Transcriptomic analysis revealed that in MTS1338-overexpressing Mtb, the stress factors led to the activation of a number of transcriptional regulators, toxin-antitoxin modules, and stress chaperones, about half of which coincided with the genes induced in Mtb phagocytosed by macrophages. We determined the MTS1338 "core regulon", consisting of 11 genes that were activated in all conditions under MTS1338 overexpression. Our findings indicate that MTS1338 is a stress-induced sRNA that promotes Mtb survival in macrophages by triggering adaptive transcriptional mechanisms in response to host antimicrobial defense reactions.
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Affiliation(s)
- Billy A Martini
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Artem S Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Yulia V Skvortsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Oksana S Bychenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elena G Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Tatyana L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Korycka-Machała M, Kawka M, Lach J, Płocińska R, Bekier A, Dziadek B, Brzostek A, Płociński P, Strapagiel D, Szczesio M, Gobis K, Dziadek J. 2,4-Disubstituted pyridine derivatives are effective against intracellular and biofilm-forming tubercle bacilli. Front Pharmacol 2022; 13:1004632. [DOI: 10.3389/fphar.2022.1004632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/26/2022] [Indexed: 11/12/2022] Open
Abstract
It was recently reported that 4-substituted picolinohydrazonamides carrying hydrophilic cyclic amines, such as morpholine and pyrrolidine, at the end of their thiosemicarbazide chain have potent antimycobacterial activity in vitro at concentrations below 1 μg/ml. Here, two selected compounds, 2,4-disubstituted pyridine derivatives 11 and 15, revealed significant bactericidal activity against Mycobacterium tuberculosis localized intracellularly within human macrophages, as well as against biofilm-forming tubercle bacilli. Mutants were selected that were resistant to the investigated compounds at an efficiency similar to that identified in the presence of the first line antituberculosis drug rifampicin. The resistant mutants were viable in the presence of the tested compounds exclusively on solid media. Genome-wide sequencing of the mutants selected in the presence of compound 11 revealed the accumulation of nonsynonymous mutations in the mmpR5 gene encoding a transcriptional repressor of the MmpS5-MmpL5 efflux pump, whose upregulation has been associated with bedaquiline resistance. The depletion of MmpR5 in wild-type M. tuberculosis using CRISPR–Cas9 technology increased the resistance of this strain to compound 11. Mass spectrometry-based proteomics (LC–MS/MS) of wild-type tubercle bacilli growing in subinhibitory concentrations of compounds 11 or 15 revealed 15 overproduced proteins not detectable in the control cells, including virulence-related proteins.
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Ma R, Farrell D, Gonzalez G, Browne JA, Nakajima C, Suzuki Y, Gordon SV. The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis. Front Microbiol 2022; 13:817952. [PMID: 35495699 PMCID: PMC9048740 DOI: 10.3389/fmicb.2022.817952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) contains the causative agents of tuberculosis (TB) in mammals. The archetypal members of the MTBC, Mycobacterium tuberculosis and Mycobacterium bovis, cause human tuberculosis and bovine tuberculosis, respectively. Although M. tuberculosis and M. bovis share over 99.9% genome identity, they show distinct host adaptation for humans and animals; hence, while the molecular basis of host adaptation is encoded in their genomes, the mechanistic basis of host tropism is still unclear. Exploration of the in vitro phenotypic consequences of known genetic difference between M. bovis and M. tuberculosis offers one route to explore genotype–phenotype links that may play a role in host adaptation. The TbD1 (“Mycobacterium tuberculosis deletion 1 region”) locus encompasses the mmpS6 and mmpL6 genes. TbD1 is absent in M. tuberculosis “modern” lineages (Lineages 2, 3, and 4) but present in “ancestral” M. tuberculosis (Lineages 1 and 7), Mycobacterium africanum lineages (Lineages 5 and 6), newly identified M. tuberculosis lineages (Lineages 8 and 9), and animal adapted strains, such as M. bovis. The function of TbD1 has previously been investigated in M. tuberculosis, where conflicting data has emerged on the role of TbD1 in sensitivity to oxidative stress, while the underlying mechanistic basis of such a phenotype is unclear. In this study, we aimed to shed further light on the role of the TbD1 locus by exploring its function in M. bovis. Toward this, we constructed an M. bovis TbD1 knockout (ΔTbD1) strain and conducted comparative transcriptomics to define global gene expression profiles of M. bovis wild-type (WT) and the ΔTbD1 strains under in vitro culture conditions (rolling and standing cultures). This analysis revealed differential induction of a hypoxia-driven copper response in WT and ΔTbD1 strains. In vitro phenotypic assays demonstrated that the deletion of TbD1 sensitized M. bovis to H2O2 and hypoxia-specific copper toxicity. Our study provides new information on the function of the TbD1 locus in M. bovis and its role in stress responses in the MTBC.
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Affiliation(s)
- Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - John A. Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- *Correspondence: Stephen V. Gordon,
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Willemse D, Moodley C, Mehra S, Kaushal D. Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate. Front Microbiol 2021; 12:744800. [PMID: 34721344 PMCID: PMC8554204 DOI: 10.3389/fmicb.2021.744800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Smoking is known to be an added risk factor for tuberculosis (TB), with nearly a quarter of the TB cases attributed to cigarette smokers in the 22 countries with the highest TB burden. Many studies have indicated a link between risk of active TB and cigarette smoke. Smoking is also known to significantly decrease TB cure and treatment completion rate and increase mortality rates. Cigarette smoke contains thousands of volatile compounds including carcinogens, toxins, reactive solids, and oxidants in both particulate and gaseous phase. Yet, to date, limited studies have analyzed the impact of cigarette smoke components on Mycobacterium tuberculosis (Mtb), the causative agent of TB. Here we report the impact of cigarette smoke condensate (CSC) on survival, mutation frequency, and gene expression of Mtb in vitro. We show that exposure of virulent Mtb to cigarette smoke increases the mutation frequency of the pathogen and strongly induces the expression of the regulon controlled by SigH—a global transcriptional regulator of oxidative stress. SigH has previously been shown to be required for Mtb to respond to oxidative stress, survival, and granuloma formation in vivo. A high-SigH expression phenotype is known to be associated with greater virulence of Mtb. In patients with pulmonary TB who smoke, these changes may therefore play an important, yet unexplored, role in the treatment efficacy by potentially enhancing the virulence of tubercle bacilli.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Chivonne Moodley
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Smriti Mehra
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
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Li Q, Li C, Xie L, Zhang C, Feng Y, Xie J. Characterization of a putative ArsR transcriptional regulator encoded by Rv2642 from Mycobacterium tuberculosis. J Biomol Struct Dyn 2016; 35:2031-2039. [DOI: 10.1080/07391102.2016.1206037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Qiming Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Chunyan Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Longxiang Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Chenhui Zhang
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yonghong Feng
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing 400715, China
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Furnholm TR, Tisa LS. The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. BMC Genomics 2014; 15:1092. [PMID: 25495525 PMCID: PMC4531530 DOI: 10.1186/1471-2164-15-1092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. RESULTS Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. CONCLUSIONS Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.
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Affiliation(s)
- Teal R Furnholm
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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Abstract
The ability of bacteria to survive in a variety of different niches is due, in part, to their ability to respond and adapt to the environment. Extracellular signals are recognized by bacilli, and their responses are generally conducted at the transcript level. RNA polymerases recognize specific promoter regions on the genome and initiate transcription. Therefore, the analysis of gene expression is paramount to understanding the biology of an organism. In the case of pathogens, gene expression can alter during the course of the infection, and, therefore, specific targets can be identified for drug development. Promoter activity can be determined by cloning a promoter sequence upstream of a reporter gene and assaying the reporter activity, either from whole cells or from cell lysates. This chapter describes two reporter systems (GFP and LacZ) used for determining promoter activity that have been widely used in mycobacteria.
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Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH. J Bacteriol 2009; 191:3965-80. [PMID: 19376862 DOI: 10.1128/jb.00064-09] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is one of the most successful pathogens of humankind. During infection, M. tuberculosis must cope with and survive against a variety of different environmental conditions. Sigma factors likely facilitate the modulation of the pathogen's gene expression in response to changes in its extracellular milieu during infection. sigma(H), an alternate sigma factor encoded by the M. tuberculosis genome, is induced by thiol-oxidative stress, heat shock, and phagocytosis. In response to these conditions, sigma(H) induces the expression of sigma(B), sigma(E), and the thioredoxin regulon. In order to more effectively characterize the transcriptome controlled by sigma(H), we studied the long-term effects of the induction of sigma(H) on global transcription in M. tuberculosis. The M. tuberculosis isogenic mutant of sigma(H) (Delta-sigma(H)) is more susceptible to diamide stress than wild-type M. tuberculosis. To study the long-term effects of sigma(H) induction, we exposed both strains to diamide, rapidly washed it away, and resumed culturing in diamide-free medium (post-diamide stress culturing). Analysis of the effects of sigma(H) induction in this experiment revealed a massive temporal programming of the M. tuberculosis transcriptome. Immediately after the induction of sigma(H), genes belonging to the functional categories "virulence/detoxification" and "regulatory proteins" were induced in large numbers. Fewer genes belonging to the "lipid metabolism" category were induced, while a larger number of genes belonging to this category were downregulated. sigma(H) caused the induction of the ATP-dependent clp proteolysis regulon, likely mediated by a transcription factor encoded by Rv2745c, several members of the mce1 virulence regulon, and the sulfate acquisition/transport network.
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Campbell DR, Chapman KE, Waldron KJ, Tottey S, Kendall S, Cavallaro G, Andreini C, Hinds J, Stoker NG, Robinson NJ, Cavet JS. Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J Biol Chem 2007; 282:32298-310. [PMID: 17726022 PMCID: PMC3145109 DOI: 10.1074/jbc.m703451200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A novel ArsR-SmtB family transcriptional repressor, KmtR, has been characterized from mycobacteria. Mutants of Mycobacterium tuberculosis lacking kmtR show elevated expression of Rv2025c encoding a deduced CDF-family metal exporter. KmtR-dependent repression of the cdf and kmtR operator-promoters was alleviated by nickel and cobalt in minimal medium. Electrophoretic mobility shift assays and fluorescence anisotropy show binding of purified KmtR to nucleotide sequences containing a region of dyad symmetry from the cdf and kmtR operator-promoters. Incubation of KmtR with cobalt inhibits DNA complex assembly and metal-protein binding was confirmed. KmtR is the second, to NmtR, characterized ArsR-SmtB sensor of nickel and cobalt from M. tuberculosis suggesting special significance for these ions in this pathogen. KmtR-dependent expression is elevated in complete medium with no increase in response to metals, whereas NmtR retains a response to nickel and cobalt under these conditions. KmtR has tighter affinities for nickel and cobalt than NmtR consistent with basal levels of these metals being sensed by KmtR but not NmtR in complete medium. More than a thousand genes encoding ArsR-SmtB-related proteins are listed in databases. KmtR has none of the previously defined metal-sensing sites. Substitution of His88, Glu101, His102, His110, or His111 with Gln generated KmtR variants that repress the cdf and kmtR operator-promoters even in elevated nickel and cobalt, revealing a new sensory site. Importantly, ArsR-SmtB sequence groupings do not correspond with the different sensory motifs revealing that only the latter should be used to predict metal sensing.
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Affiliation(s)
- Duncan R. Campbell
- Life Sciences, University of Manchester, 1.800 Stopford Building, Manchester M13 9PT, United Kingdom
| | - Kaye E. Chapman
- Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle NE2 4HH, United Kingdom
| | - Kevin J. Waldron
- Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle NE2 4HH, United Kingdom
| | - Stephen Tottey
- Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle NE2 4HH, United Kingdom
| | - Sharon Kendall
- The Royal Veterinary College, Royal College Street, London NW1 0TU, United Kingdom
| | - Gabriele Cavallaro
- Magnetic Resonance Centre, University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine Paramagnetiche, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudia Andreini
- Magnetic Resonance Centre, University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine Paramagnetiche, 50019 Sesto Fiorentino, Florence, Italy
| | - Jason Hinds
- Bacterial Microarray Group, St. George’s University of London, London SW17 0RE, United Kingdom
| | - Neil G. Stoker
- The Royal Veterinary College, Royal College Street, London NW1 0TU, United Kingdom
| | - Nigel J. Robinson
- Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle NE2 4HH, United Kingdom
- To whom correspondence may be addressed: Tel. 44-191-222-7695; Fax: 44-191-222-7424;
| | - Jennifer S. Cavet
- Life Sciences, University of Manchester, 1.800 Stopford Building, Manchester M13 9PT, United Kingdom
- To whom correspondence may be addressed: Tel. 44-161-275-51543; Fax: 44-161-275-5656;
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ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis. Tuberculosis (Edinb) 2005; 86:445-60. [PMID: 16376151 DOI: 10.1016/j.tube.2005.10.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 09/19/2005] [Accepted: 10/13/2005] [Indexed: 11/15/2022]
Abstract
The non-replicating persistence (NRP) phenotype of Mycobacterium tuberculosis (NRP-TB) is assumed to be responsible for the maintenance of latent infection and the requirement of a long treatment duration for active tuberculosis. Isotope coded affinity tag-based proteomic analysis was used for the determination of the relative expression of large numbers of M. tuberculosis proteins during oxygen self-depletion under controlled conditions in a multi-chambered fermentor. Expression of the alpha-crystallin homolog protein, acr, was monitored and quantified to confirm entry into NRP. Relative expression of 586 and 628 proteins was determined in log phase vs. early stage NRP (NRP-1) and log phase vs. later stage NRP (NRP-2), respectively. Relative to expression in log phase and using an abundance ratio of +/-2.0 as a cutoff, 6.5% and 20.4% of proteins were found to be upregulated in NRP-1 and NRP-2, respectively while 20.3% and 13.4% were downregulated, respectively. Functional profiling revealed that 42.1%/39.8% of upregulated proteins and 41.2%/45.2% of downregulated proteins in NRP-1/NRP-2, respectively, were involved in small molecule metabolism. Among those proteins the highest proportions of 37.5% in NRP-1 were involved with degradation and of 45.1% in NRP-2 with energy metabolism. These results suggest distinct protein expression profiles in NRP-1 and NRP-2.
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Mostowy S, Cleto C, Sherman DR, Behr MA. The Mycobacterium tuberculosis complex transcriptome of attenuation. Tuberculosis (Edinb) 2004; 84:197-204. [PMID: 15207489 DOI: 10.1016/j.tube.2004.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Although the deletion of RD1 is likely correlated to attenuation from virulence for members of the Mycobacterium tuberculosis (MTB) complex, the reasons for this phenotype remain to be fully explained. As genomic variation is responsible for at least a component of variability in gene expression, we looked to the in vitro global expression profile of the RD1 artificial knockout from M. tuberculosis H37Rv (H37Rv:deltaRD1) for clues to elucidate its phenotypic shift towards attenuation. By comparing the transcriptome of H37Rv:deltaRD1 to that of virulent H37Rv, 15 regulated genes located in nine different regions outside of RD1 have been identified, capturing an effect of RD1's deletion on the rest of the genome. To assess whether these regulations are characteristic of attenuated MTB in general, expression profiles of natural RD1 mutants (BCG Russia, BCG Pasteur, and M. microti) as well as the 'avirulent' M. tuberculosis H37Ra, whose RD1 region is genomically intact, were obtained. Results indicate that attenuated strains lack the expression of RD1 genes including cfp10 and esat6, whether through deletion or reduced expression. Furthermore, comparative transcriptomics reveals the concurrent down-regulation of several gene neighborhoods beyond RD1. The potential relevance of these other expression changes towards MTB virulence is discussed.
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Affiliation(s)
- Serge Mostowy
- McGill University Health Centre, Montreal, Canada H3G 1A4
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