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Liu Y, Li H, Dai D, He J, Liang Z. Gene Regulatory Mechanism of Mycobacterium Tuberculosis during Dormancy. Curr Issues Mol Biol 2024; 46:5825-5844. [PMID: 38921019 PMCID: PMC11203133 DOI: 10.3390/cimb46060348] [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: 04/10/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) complex, is a zoonotic disease that remains one of the leading causes of death worldwide. Latent tuberculosis infection reactivation is a challenging obstacle to eradicating TB globally. Understanding the gene regulatory network of Mtb during dormancy is important. This review discusses up-to-date information about TB gene regulatory networks during dormancy, focusing on the regulation of lipid and energy metabolism, dormancy survival regulator (DosR), White B-like (Wbl) family, Toxin-Antitoxin (TA) systems, sigma factors, and MprAB. We outline the progress in vaccine and drug development associated with Mtb dormancy.
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Affiliation(s)
- Yiduo Liu
- College of Animal Science and Technology, Guangxi University, No. 100 University West Road, Nanning 530004, China (D.D.)
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Han Li
- College of Animal Science and Technology, Guangxi University, No. 100 University West Road, Nanning 530004, China (D.D.)
| | - Dejia Dai
- College of Animal Science and Technology, Guangxi University, No. 100 University West Road, Nanning 530004, China (D.D.)
| | - Jiakang He
- College of Animal Science and Technology, Guangxi University, No. 100 University West Road, Nanning 530004, China (D.D.)
| | - Zhengmin Liang
- College of Animal Science and Technology, Guangxi University, No. 100 University West Road, Nanning 530004, China (D.D.)
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2
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Comín J, Campos E, Gonzalo-Asensio J, Samper S. Transcriptomic profile of the most successful Mycobacterium tuberculosis strain in Aragon, the MtZ strain, during exponential and stationary growth phases. Microbiol Spectr 2023; 11:e0468522. [PMID: 37882511 PMCID: PMC10714837 DOI: 10.1128/spectrum.04685-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Aragon Community suffered, during the first years of the beginning of this century, a large outbreak caused by the MtZ strain, producing more than 240 cases to date. MtZ strain and the outbreak have been previously studied from an epidemiological and molecular point of view. In this work, we analyzed the transcriptomic profile of the strain for better understanding of its success among our population. We have discovered that MtZ has some upregulated virulence pathways, such as the ESX-1 system, the cholesterol degradation pathway or the peptidoglycan biosynthesis. Interestingly, MtZ has downregulated the uptake of iron. Another special feature of MtZ strain is the interruption of desA3 gene, essential for producing oleic acid. Although the strain takes a long time to grow in the initial culture media, eventually it is able to reach normal optical densities, suggestive of the presence of another route for obtaining oleic acid in Mycobacterium tuberculosis.
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Affiliation(s)
- Jessica Comín
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | | | - Jesús Gonzalo-Asensio
- Universidad de Zaragoza, Zaragoza, Spain
- Fundación IIS Aragón, Zaragoza, Spain
- CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
- Fundación IIS Aragón, Zaragoza, Spain
- CIBER de Enfermedades Respiratorias, Madrid, Spain
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3
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Sharma A, Bansal S, Kumari N, Vashistt J, Shrivastava R. Comparative proteomic investigation unravels the pathobiology of Mycobacterium fortuitum biofilm. Appl Microbiol Biotechnol 2023; 107:6029-6046. [PMID: 37542577 DOI: 10.1007/s00253-023-12705-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/26/2023] [Accepted: 07/15/2023] [Indexed: 08/07/2023]
Abstract
Biofilm formation by Mycobacterium fortuitum causes serious threats to human health due to its increased contribution to nosocomial infections. In this study, the first comprehensive global proteome analysis of M. fortuitum was reported under planktonic and biofilm growth states. A label-free Q Exactive Quadrupole-Orbitrap tandem mass spectrometry analysis was performed on the protein lysates. The differentially abundant proteins were functionally characterized and re-annotated using Blast2GO and CELLO2GO. Comparative analysis of the proteins among two growth states provided insights into the phenotypic switch, and fundamental pathways associated with pathobiology of M. fortuitum biofilm, such as lipid biosynthesis and quorum-sensing. Interaction network generated by the STRING database revealed associations between proteins that endure M. fortuitum during biofilm growth state. Hypothetical proteins were also studied to determine their functional alliance with the biofilm phenotype. CARD, VFDB, and PATRIC analysis further showed that the proteins upregulated in M. fortuitum biofilm exhibited antibiotic resistance, pathogenesis, and virulence. Heatmap and correlation analysis provided the biomarkers associated with the planktonic and biofilm growth of M. fortuitum. Proteome data was validated by qPCR analysis. Overall, the study provides insights into previously unexplored biochemical pathways that can be targeted by novel inhibitors, either for shortened treatment duration or for eliminating biofilm of M. fortuitum and related nontuberculous mycobacterial pathogens. KEY POINTS: • Proteomic analyses of M. fortuitum reveals novel biofilm markers. • Acetyl-CoA acetyltransferase acts as the phenotype transition switch. • The study offers drug targets to combat M. fortuitum biofilm infections.
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Affiliation(s)
- Ayushi Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Saurabh Bansal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Neha Kumari
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Rahul Shrivastava
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India.
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Dhungel L, Bonner R, Cook M, Henson D, Moulder T, Benbow ME, Jordan H. Impact of Temperature and Oxygen Availability on Gene Expression Patterns of Mycobacterium ulcerans. Microbiol Spectr 2023; 11:e0496822. [PMID: 36912651 PMCID: PMC10100886 DOI: 10.1128/spectrum.04968-22] [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: 12/02/2022] [Accepted: 01/29/2023] [Indexed: 03/14/2023] Open
Abstract
Buruli ulcer disease is a neglected tropical disease caused by the environmental pathogen Mycobacterium ulcerans. The M. ulcerans major virulence factor is mycolactone, a lipid cytotoxic compound whose genes are carried on a plasmid. Although an exact reservoir and mode(s) of transmission are unknown, data provide evidence of both. First, Buruli ulcer incidence and M. ulcerans presence have been linked to slow-moving water with low oxygen. M. ulcerans has also been suggested to be sensitive to UV due to termination in crtI, encoding a phytoene dehydrogenase, required for carotenoid production. Further, M. ulcerans has been shown to cause disease following puncture but not when introduced to open abrasion sites, suggesting that puncture is necessary for transmission and pathology. Despite these findings, the function and modulation of mycolactone and other genes in response to dynamic abiotic conditions such as UV, temperature, and oxygen have not been shown. In this study, we investigated modulation of mycolactone and other genes on exposure to changing UV and oxygen microenvironmental conditions. Mycolactone expression was downregulated on exposure to the single stress high temperature and did not change significantly with exposure to UV; however, it was upregulated when exposed to microaerophilic conditions. Mycolactone expression was downregulated under combined stresses of high temperature and low oxygen, but there was upregulation of several stress response genes. Taken together, results suggest that temperature shapes M. ulcerans metabolic response more so than UV exposure or oxygen requirements. These data help to define the environmental niche of M. ulcerans and metabolic responses during initial human infection. IMPORTANCE Buruli ulcer is a debilitating skin disease caused by the environmental pathogen Mycobacterium ulcerans. M. ulcerans produces a toxic compound, mycolactone, which leads to tissue necrosis and ulceration. Barriers to preventing Buruli ulcer include an incomplete understanding of M. ulcerans reservoirs, how the pathogen is transmitted, and under what circumstances mycolactone and other M. ulcerans genes are expressed and produced in its natural environment and in the host. We conducted a study to investigate M. ulcerans gene expression under several individual or combined abiotic conditions. Our data showed that mycolactone expression was downregulated under combined stresses of high temperature and low oxygen but there was upregulation of several stress response genes. These data are among only a few studies measuring modulation of mycolactone and other M. ulcerans genes that could be involved in pathogen fitness in its natural environment and virulence while within the host.
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Affiliation(s)
- Laxmi Dhungel
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Raisa Bonner
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Meagan Cook
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Duncan Henson
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Trent Moulder
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - M. Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA
- AgBioResearch, Michigan State University, East Lansing, Michigan, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michigan, USA
| | - Heather Jordan
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
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Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis. INORGANICS 2022. [DOI: 10.3390/inorganics10100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.
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6
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Abstract
Infectious diseases pose two main compelling issues. First, the identification of the molecular factors that allow chronic infections, that is, the often completely asymptomatic coexistence of infectious agents with the human host. Second, the definition of the mechanisms that allow the switch from pathogen dormancy to pathologic (re)activation. Furthering previous studies, the present study (1) analyzed the frequency of occurrence of synonymous codons in coding DNA, that is, codon usage, as a genetic tool that rules protein expression; (2) described how human codon usage can inhibit protein expression of infectious agents during latency, so that pathogen genes the codon usage of which does not conform to the human codon usage cannot be translated; and (3) framed human codon usage among the front-line instruments of the innate immunity against infections. In parallel, it was shown that, while genetics can account for the molecular basis of pathogen latency, the changes of the quantitative relationship between codon frequencies and isoaccepting tRNAs during cell proliferation offer a biochemical mechanism that explains the pathogen switching to (re)activation. Immunologically, this study warns that using codon optimization methodologies can (re)activate, potentiate, and immortalize otherwise quiescent, asymptomatic pathogens, thus leading to uncontrollable pandemics.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
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7
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Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Mol Cell 2021; 81:2887-2900.e5. [PMID: 34171298 DOI: 10.1016/j.molcel.2021.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Huey-Xian Wong
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Li-Mei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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8
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Nasim F, Dey A, Qureshi IA. Comparative genome analysis of Corynebacterium species: The underestimated pathogens with high virulence potential. INFECTION GENETICS AND EVOLUTION 2021; 93:104928. [PMID: 34022437 DOI: 10.1016/j.meegid.2021.104928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 11/25/2022]
Abstract
Non-diphtherial Corynebacterium species or diphtheroids were previously considered as the mere contaminants of clinical samples. Of late, they have been reckoned as the formidable infection causing agents of various diseases. While the scientific database is filled with articles that document whole genome analysis of individual isolates, a comprehensive comparative genomic analysis of diphtheroids alongside Corynebacterium diphtheriae is expected to enable us in understanding their genomic as well as evolutionary divergence. Here, we have analysed the whole genome sequences of forty strains that were selected from a range of eleven Corynebacterium species (pathogenic and non-pathogenic). A statistical analysis of the pan and core genomes revealed that even though the core genome is saturated, the pan genome is yet open rendering scope for newer gene families to be accumulated in the course of evolution that might further change the pathogenic behavior of these species. Every strain had bacteriophage components integrated in its genome and some of them were intact and consisted of toxins. The presence of diversified genomic islands was observed across the dataset and most of them consisted of genes for virulence and multidrug resistance. Moreover, the phylogenetic analysis showed that a diphtheroid is the last common ancestor of all the Corynebacterium species. The current study is a compilation of genomic features of pathogenic as well as non-pathogenic Corynebacterium species which provides insights into their virulence potential in the times to come.
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Affiliation(s)
- Fouzia Nasim
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Arijit Dey
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.
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9
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Alhadlaq MA, Green J, Kudhair BK. Analysis of Kytococcus sedentarius Strain Isolated from a Dehumidifier Operating in a University Lecture Theatre: Systems for Aerobic Respiration, Resisting Osmotic Stress, and Sensing Nitric Oxide. Microb Physiol 2021; 31:135-145. [PMID: 33730718 DOI: 10.1159/000512751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/28/2020] [Indexed: 11/19/2022]
Abstract
A strain of Kytococcus sedentarius was isolated from a dehumidifier operating in a university lecture theatre. Genome analysis and phenotypic characterisation showed that this strain, K. sedentarius MBB13, was a moderately halotolerant aerobe with a branched aerobic electron transport chain and genes that could contribute to erythromycin resistance. The major compatible solute was glycine betaine, with ectoine and proline being deployed at higher osmolarities. Actinobacteria possess multiple WhiB-like (Wbl) regulatory proteins, and K. sedentarius MBB13 has four (WhiB1, WhiB2, WhiB3, and WhiB7). Wbls are iron-sulfur proteins that regulate gene expression through interactions with RNA polymerase sigma factors and/or other regulatory proteins. Bacterial two-hybrid analyses suggested that WhiB1 and WhiB2, but not WhiB3 and WhiB7, interact with the C-terminal domain of the major sigma factor, σA; no interaction was detected between any of the Wbl proteins and the only alternative sigma factors, σB, σH, or σJ. The interaction between σA and WhiB1 or WhiB2 was disrupted in a heterologous system under growth conditions that produce nitric oxide and the iron-sulfur clusters of the isolated WhiB1 and WhiB2 proteins reacted with nitric oxide. Thus, K. sedentarius strain exhibits the major phenotypic characteristics of the type strain and a comprehensive examination of the interactions between its four Wbl proteins and four sigma factors suggested that the Wbl proteins all operate through interaction with σA.
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Affiliation(s)
- Meshari Ahmed Alhadlaq
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom, .,Research and Laboratories Sector, Saudi Food and Drug Authority, Riyadh, Saudi Arabia,
| | - Jeffrey Green
- Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Bassam K Kudhair
- Department of Laboratory Investigations, Faculty of Science, University of Kufa, Najaf, Iraq
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Gupta SK, Angara RK, Yousuf S, Reddy CG, Ranjan A. Ectopic Expression of Rv0023 Mediates Isoniazid/Ethionamide Tolerance via Altering NADH/NAD + Levels in Mycobacterium smegmatis. Front Microbiol 2020; 11:3. [PMID: 32117088 PMCID: PMC7020754 DOI: 10.3389/fmicb.2020.00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/03/2020] [Indexed: 02/01/2023] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) accounts for nearly 1.2 million deaths per annum worldwide. Due to the emergence of multidrug-resistant (MDR) Mtb strains, TB, a curable and avertable disease, remains one of the leading causes of morbidity and mortality. Isoniazid (INH) is a first-line anti-TB drug while ethionamide (ETH) is used as a second-line anti-TB drug. INH and ETH resistance develop through a network of genes involved in various biosynthetic pathways. In this study, we identified Rv0023, an Mtb protein belonging to the xenobiotic response element (XRE) family of transcription regulators, which has a role in generating higher tolerance toward INH and ETH in Mycobacterium smegmatis (Msmeg). Overexpression of Rv0023 in Msmeg leads to the development of INH- and ETH-tolerant strains. The strains expressing Rv0023 have a higher ratio of NADH/NAD+, and this physiological event is known to play a crucial role in the development of INH/ETH co-resistance in Msmeg. Gene expression analysis of some target genes revealed reduction in the expression of the ndh gene, but no direct interaction was observed between Rv0023 and the ndh promoter region. Rv0023 is divergently expressed to Rv0022c (whiB5) and we observed a direct interaction between the recombinant Rv0023 protein with the upstream region of Rv0022c, confirmed using reporter constructs of Msmeg. However, we found no indication that this interaction might play a role in the development of INH/ETH drug tolerance.
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Affiliation(s)
- Shailesh Kumar Gupta
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Rajendra Kumar Angara
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Suhail Yousuf
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Chilakala Gangi Reddy
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Regional Centre for Biotechnology, Faridabad, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Shi KX, Wu YK, Tang BK, Zhao GP, Lyu LD. Housecleaning of pyrimidine nucleotide pool coordinates metabolic adaptation of nongrowing Mycobacterium tuberculosis. Emerg Microbes Infect 2019; 8:40-44. [PMID: 30866758 PMCID: PMC6455119 DOI: 10.1080/22221751.2018.1559706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adopt a slowly growing or nongrowing state within the host plays a critical role for the bacilli to persist in the face of a prolonged multidrug therapy, establish latency and sustain chronic infection. In our previous study, we revealed that genome maintenance via MazG-mediated elimination of oxidized dCTP contributes to the antibiotic tolerance of nongrowing Mtb. Here, we provide evidence that housecleaning of pyrimidine nucleotide pool via MazG coordinates metabolic adaptation of Mtb to nongrowing state. We found that the ΔmazG mutant fails to maintain a nongrowing and metabolic quiescence state under dormancy models in vitro. To investigate bacterial metabolic changes during infection, we employed RNA-seq to compare the global transcriptional response of wild-type Mtb and the ΔmazG mutant after infection of macrophages. Pathway enrichment analyses of the differentially regulated genes indicate that the deletion of mazG in Mtb not only results in DNA instability, but also perturbs pyrimidine metabolism, iron and carbon source uptake, catabolism of propionate and TCA cycle. Moreover, these transcriptional signatures reflect anticipatory metabolism and regulatory activities observed during cell cycle re-entry in the ΔmazG mutant. Taken together, these results provide evidence that pyrimidine metabolism is a metabolic checkpoint during mycobacterial adaptation to nongrowing state.
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Affiliation(s)
- Kun-Xiong Shi
- a Key Laboratory of Medical Molecular Virology of MOE/MOH , School of Basic Medical Sciences, Fudan University , Shanghai , People's Republic of China
| | - Yong-Kai Wu
- a Key Laboratory of Medical Molecular Virology of MOE/MOH , School of Basic Medical Sciences, Fudan University , Shanghai , People's Republic of China.,b Department of Microbiology , School of Life Sciences, Fudan University , Shanghai , People's Republic of China
| | - Bi-Kui Tang
- c Department of Life Science , Bengbu Medical College , Bengbu , People's Republic of China
| | - Guo-Ping Zhao
- b Department of Microbiology , School of Life Sciences, Fudan University , Shanghai , People's Republic of China.,d Department of Microbiology and Li Ka Shing Institute of Health Sciences , The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories , Hong Kong , People's Republic of China.,e CAS-Key Laboratory of Synthetic Biology , Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences , Shanghai , People's Republic of China
| | - Liang-Dong Lyu
- a Key Laboratory of Medical Molecular Virology of MOE/MOH , School of Basic Medical Sciences, Fudan University , Shanghai , People's Republic of China
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12
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Iron Supplementation Therapy, A Friend and Foe of Mycobacterial Infections? Pharmaceuticals (Basel) 2019; 12:ph12020075. [PMID: 31108902 PMCID: PMC6630247 DOI: 10.3390/ph12020075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Iron is an essential element that is required for oxygen transfer, redox, and metabolic activities in mammals and bacteria. Mycobacteria, some of the most prevalent infectious agents in the world, require iron as growth factor. Mycobacterial-infected hosts set up a series of defense mechanisms, including systemic iron restriction and cellular iron distribution, whereas mycobacteria have developed sophisticated strategies to acquire iron from their hosts and to protect themselves from iron’s harmful effects. Therefore, it is assumed that host iron and iron-binding proteins, and natural or synthetic chelators would be keys targets to inhibit mycobacterial proliferation and may have a therapeutic potential. Beyond this hypothesis, recent evidence indicates a host protective effect of iron against mycobacterial infections likely through promoting remodeled immune response. In this review, we discuss experimental procedures and clinical observations that highlight the role of the immune response against mycobacteria under various iron availability conditions. In addition, we discuss the clinical relevance of our knowledge regarding host susceptibility to mycobacteria in the context of iron availability and suggest future directions for research on the relationship between host iron and the immune response and the use of iron as a therapeutic agent.
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Miryala SK, Anbarasu A, Ramaiah S. Impact of bedaquiline and capreomycin on the gene expression patterns of multidrug‐resistant
Mycobacterium tuberculosis
H37Rv strain and understanding the molecular mechanism of antibiotic resistance. J Cell Biochem 2019; 120:14499-14509. [DOI: 10.1002/jcb.28711] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Sravan Kumar Miryala
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| | - Anand Anbarasu
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
| | - Sudha Ramaiah
- Department of Bio‐Sciences, Medical and Biological Computing Laboratory, School of Bio Sciences and Technology Vellore Institute of Technology Vellore Tamil Nadu India
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14
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Mehta M, Singh A. Mycobacterium tuberculosis WhiB3 maintains redox homeostasis and survival in response to reactive oxygen and nitrogen species. Free Radic Biol Med 2019; 131:50-58. [PMID: 30500421 PMCID: PMC6635127 DOI: 10.1016/j.freeradbiomed.2018.11.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/30/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (Mtb) survives under oxidatively and nitosatively hostile niches inside host phagocytes. In other bacteria, adaptation to these stresses is dependent upon the redox sensitive two component systems (e.g., ArcAB) and transcription factors (e.g., FNR/SoxR). However, these factors are absent in Mtb. Therefore, it is not completely understood how Mtb maintains survival and redox balance in response to reactive oxygen species (ROS) and reactive nitrogen species (RNS). Here, we present evidences that a 4Fe-4S-cofactor containing redox-sensitive transcription factor (WhiB3) is exploited by Mtb to adapt under ROS and RNS stress. We show that MtbΔwhiB3 is acutely sensitive to oxidants and to nitrosative agents. Using a genetic biosensor of cytoplasmic redox state (Mrx1-roGFP2) of Mtb, we show that WhiB3 facilitates recovery from ROS (cumene hydroperoxide and hydrogen peroxide) and RNS (acidified nitrite and peroxynitrite). Also, MtbΔwhiB3 displayed reduced survival inside RAW 264.7 macrophages. Consistent with the role of WhiB3 in modulating host-pathogen interaction, we discovered that WhiB3 coordinates the formation of early human granulomas during interaction of Mtb with human peripheral blood mononuclear cells (PBMCs). Altogether, our study provides empirical proof that WhiB3 is required to mitigate redox stress induced by ROS and RNS, which may be important to activate host/bacterial pathways required for the granuloma development and maintenance.
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Affiliation(s)
- Mansi Mehta
- Microbiology and Cell Biology, Centre for Infectious Disease Research (CIDR), Indian Institute of Science (IISc), CV Raman Av, Bangalore 12, India
| | - Amit Singh
- Microbiology and Cell Biology, Centre for Infectious Disease Research (CIDR), Indian Institute of Science (IISc), CV Raman Av, Bangalore 12, India.
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15
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out multiple functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters with small/redox-active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial reprogramming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances: Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high-resolution structural data. Although this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
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16
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Duan W, Li X, Ge Y, Yu Z, Li P, Li J, Qin L, Xie J. Mycobacterium tuberculosis Rv1473 is a novel macrolides ABC Efflux Pump regulated by WhiB7. Future Microbiol 2018; 14:47-59. [PMID: 30539658 DOI: 10.2217/fmb-2018-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM To characterize a novel macrolide ATP binding cassette efflux pump encoding gene Rv1473 which might be involved in antibiotic resistance. METHODS Mycobacterium smegmatis was used as a surrogate model for pathogenic mycobacteria, drug susceptibility assays and ethidium bromide accumulation assay were harnessed to verify drug resistance. The real-time quantitative PCR was used to evaluate the transcription levels of WhiB7 and Ms3140 upon exposure to macrolides. RESULTS Rv1473 contributes to macrolides resistance via efflux mechanisms, and was positively regulated by the transcription factor WhiB7 upon macrolides exposure. CONCLUSION Rv1473 is a novel ATP binding cassette efflux pump involved in mycobacterium intrinsic antibiotics resistance via efflux mechanism. This finding will facilitate novel antibiotic discovery and the treatment of pathogen, especially for nontuberculous mycobacteria.
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Affiliation(s)
- Wei Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Xue Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Yan Ge
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Ping Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Jiang Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai 200433, PR China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
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17
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Bush MJ. The actinobacterial WhiB-like (Wbl) family of transcription factors. Mol Microbiol 2018; 110:663-676. [PMID: 30179278 PMCID: PMC6282962 DOI: 10.1111/mmi.14117] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023]
Abstract
The WhiB‐like (Wbl) family of proteins are exclusively found in Actinobacteria. Wbls have been shown to play key roles in virulence and antibiotic resistance in Mycobacteria and Corynebacteria, reflecting their importance during infection by the human pathogens Mycobacterium tuberculosis, Mycobacterium leprae and Corynebacterium diphtheriae. In the antibiotic‐producing Streptomyces, several Wbls have important roles in the regulation of morphological differentiation, including WhiB, a protein that controls the initiation of sporulation septation and the founding member of the Wbl family. In recent years, genome sequencing has revealed the prevalence of Wbl paralogues in species throughout the Actinobacteria. Wbl proteins are small (generally ~80–140 residues) and each contains four invariant cysteine residues that bind an O2‐ and NO‐sensitive [4Fe–4S] cluster, raising the question as to how they can maintain distinct cellular functions within a given species. Despite their discovery over 25 years ago, the Wbl protein family has largely remained enigmatic. Here I summarise recent research in Mycobacteria, Corynebacteria and Streptomyces that sheds light on the biochemical function of Wbls as transcription factors and as potential sensors of O2 and NO. I suggest that Wbl evolution has created diversity in protein–protein interactions, [4Fe–4S] cluster‐sensitivity and the ability to bind DNA.
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Affiliation(s)
- Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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18
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Chawla M, Mishra S, Anand K, Parikh P, Mehta M, Vij M, Verma T, Singh P, Jakkala K, Verma HN, AjitKumar P, Ganguli M, Narain Seshasayee AS, Singh A. Redox-dependent condensation of the mycobacterial nucleoid by WhiB4. Redox Biol 2018; 19:116-133. [PMID: 30149290 PMCID: PMC6111044 DOI: 10.1016/j.redox.2018.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/02/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
Oxidative stress response in bacteria is mediated through coordination between the regulators of oxidant-remediation systems (e.g. OxyR, SoxR) and nucleoid condensation (e.g. Dps, Fis). However, these genetic factors are either absent or rendered non-functional in the human pathogen Mycobacterium tuberculosis (Mtb). Therefore, how Mtb organizes genome architecture and regulates gene expression to counterbalance oxidative imbalance is unknown. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response in Mtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNA. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findings in vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of the Mtb genome. Lastly, data indicate that WhiB4 deletion affected the expression of ~ 30% of genes preferentially bound by the protein, suggesting both direct and indirect effects on gene expression. We propose that WhiB4 structurally couples Mtb’s response to oxidative stress with genome organization and transcription. Genome condensation is involved in the management of oxidative stress in bacteria. A relation between the genome condensation and oxidative stress is unclear in Mtb. A redox sensor WhiB4 calibrates genome-condensation and antioxidants in Mtb. Over-expression of WhiB4 hyper-condensed genome and induced killing by oxidants. WhiB4 deficiency delayed genome condensation and promoted oxidative stress survival.
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Affiliation(s)
- Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Saurabh Mishra
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Kushi Anand
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Pankti Parikh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Mansi Mehta
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Manika Vij
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Taru Verma
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India; Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore 560012, India
| | - Parul Singh
- National Centre for Biological Science, Bangalore 560065, India; SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - H N Verma
- Jaipur National University, Jagatpura, Jaipur 302017, India
| | - Parthasarathi AjitKumar
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Munia Ganguli
- Department of Structural Biology, CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India.
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19
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Koster K, Largen A, Foster JT, Drees KP, Qian L, Desmond EP, Wan X, Hou S, Douglas JT. Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii. PLoS One 2018; 13:e0201146. [PMID: 30036392 PMCID: PMC6056056 DOI: 10.1371/journal.pone.0201146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/09/2018] [Indexed: 02/05/2023] Open
Abstract
While tuberculosis (TB) remains a global disease, the WHO estimates that 62% of the incident TB cases in 2016 occurred in the WHO South-East Asia and Western Pacific regions. TB in the Pacific is composed predominantly of two genetic families of Mycobacterium tuberculosis (Mtb): Beijing and Manila. The Manila family is historically under-studied relative to the families that comprise the majority of TB in Europe and North America (e.g. lineage 4), and it remains unclear why this lineage has persisted in Filipino populations despite the predominance of more globally successful Mtb lineages in most of the world. The Beijing family is of particular interest as it is increasingly associated with drug resistance throughout the world. Both of these lineages are important to the State of Hawaii, where they comprise over two-thirds of TB cases. Here, we performed whole genome sequencing on 82 Beijing family, Manila family, and outgroup clinical Mtb isolates from Hawaii to identify lineage-specific SNPs (SNPs found in all isolates from their respective families, and exclusively in those families) in established virulence factor genes. Six non-silent lineage-specific virulence factor SNPs were found in the Beijing family, including mutations in alternative sigma factor sigG and polyketide synthases pks5 and pks7. The Manila family displayed more than eleven non-silent lineage-specific and characteristic virulence factor mutations, including in genes coding for MCE-family protein Mce1B, two mutations in fatty-acid-AMP ligase FadD26, and virulence-regulating transcriptional regulator VirS. This study further identified an ancient clade that shared some virulence factor mutations with the Manila family, and investigated the relationship of those and other “Manila-like” spoligotypes to the Manila family with this SNP dataset. This work identified a set of virulence genes that are worth pursuing to determine potential differences in transmission or virulence displayed by these two Mtb families.
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Affiliation(s)
- Kent Koster
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Jeffrey T. Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Edward P. Desmond
- California Department of Public Health, Richmond, California, United States of America
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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20
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Pacl HT, Reddy VP, Saini V, Chinta KC, Steyn AJC. Host-pathogen redox dynamics modulate Mycobacterium tuberculosis pathogenesis. Pathog Dis 2018; 76:4972762. [PMID: 29873719 PMCID: PMC5989597 DOI: 10.1093/femspd/fty036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/13/2018] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, encounters variable and hostile environments within the host. A major component of these hostile conditions is reductive and oxidative stresses induced by factors modified by the host immune response, such as oxygen tension, NO or CO gases, reactive oxygen and nitrogen intermediates, the availability of different carbon sources and changes in pH. It is therefore essential for Mtb to continuously monitor and appropriately respond to the microenvironment. To this end, Mtb has developed various redox-sensitive systems capable of monitoring its intracellular redox environment and coordinating a response essential for virulence. Various aspects of Mtb physiology are regulated by these systems, including drug susceptibility, secretion systems, energy metabolism and dormancy. While great progress has been made in understanding the mechanisms and pathways that govern the response of Mtb to the host's redox environment, many questions in this area remain unanswered. The answers to these questions are promising avenues for addressing the tuberculosis crisis.
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Affiliation(s)
- Hayden T Pacl
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Vikram Saini
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Krishna C Chinta
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
| | - Adrie J C Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama 35205, USA
- Africa Health Research Institute, K-RITH Tower Building, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
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21
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Zondervan NA, van Dam JCJ, Schaap PJ, Martins Dos Santos VAP, Suarez-Diez M. Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story. Int J Mol Sci 2018; 19:E347. [PMID: 29364195 PMCID: PMC5855569 DOI: 10.3390/ijms19020347] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review recent literature to provide a systems level overview of the molecular and cellular components involved in divalent metal homeostasis and their role in regulating the three main virulence strategies of M. tuberculosis: immune modulation, dormancy and phagosomal rupture. We provide a visual and modular overview of these components and their regulation. Our analysis identified a single regulatory cascade for these three virulence strategies that respond to limited availability of divalent metals in the phagosome.
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Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Jesse C J van Dam
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
- LifeGlimmer GmbH, Markelstrasse 38, 12163 Berlin, Germany.
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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22
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out a wide range of functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters towards small/redox active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial re-programming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances. Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high resolution structural data. Though this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- School of Chemistry , University of East Anglia , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry , University plain , Norwich, United Kingdom of Great Britain and Northern Ireland , NR4 7TJ ;
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23
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Abstract
Mycobacterial 6-kDa early secreted antigenic target (ESAT-6) system (ESX) exporters transport proteins across the cytoplasmic membrane. Many proteins transported by ESX systems are then translocated across the mycobacterial cell envelope and secreted from the cell. Although the mechanism underlying protein transport across the mycolate outer membrane remains elusive, the ESX systems are closely connected with and localize to the cell envelope. Links between ESX-associated proteins, cell wall synthesis, and the maintenance of cell envelope integrity have been reported. Genes encoding the ESX systems and those required for biosynthesis of the mycobacterial envelope are coregulated. Here, we review the interplay between ESX systems and the mycobacterial cell envelope.
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24
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Wan X, Koster K, Qian L, Desmond E, Brostrom R, Hou S, Douglas JT. Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PLoS One 2017; 12:e0175330. [PMID: 28394899 PMCID: PMC5386241 DOI: 10.1371/journal.pone.0175330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/25/2017] [Indexed: 02/05/2023] Open
Abstract
With its airborne transmission and prolonged latency period, Mycobacterium tuberculosis spreads worldwide as one of the most successful bacterial pathogens and continues to kill millions of people every year. M. tuberculosis lineage 1 is inferred to originate ancestrally based on the presence of the 52-bp TbD1 sequence and analysis of single nucleotide polymorphisms. Previously, we briefly reported the complete genome sequencing of M. tuberculosis strains 96121 and 96075, which belong to the ancient Manila family and modern Beijing family respectively. Here we present the comprehensive genomic analyses of the Manila family in lineage 1 compared to complete genomes in lineages 2-4. Principal component analysis of the presence and absence of CRISPR spacers suggests that Manila isolate 96121 is distinctly distant from lineages 2-4. We further identify a truncated whiB5 gene and a putative operon consisting of genes encoding a putative serine/threonine kinase PknH and a putative ABC transporter, which are only found in the genomes of Manila family isolates. Six single nucleotide polymorphisms are uniquely conserved in 38 Manila strains. Moreover, when compared to M. tuberculosis H37Rv, 59 proteins are under positive selection in Manila family isolate 96121 but not in Beijing family isolate 96075. The unique features further serve as biomarkers for Manila strains and may shed light on the limited transmission of this ancestral lineage outside of its Filipino host population.
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Affiliation(s)
- Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Kent Koster
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Edward Desmond
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Richard Brostrom
- TB Control Program, Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
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25
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Yan L, Zhang Q, Virolle MJ, Xu D. In conditions of over-expression, WblI, a WhiB-like transcriptional regulator, has a positive impact on the weak antibiotic production of Streptomyces lividans TK24. PLoS One 2017; 12:e0174781. [PMID: 28358920 PMCID: PMC5373594 DOI: 10.1371/journal.pone.0174781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/15/2017] [Indexed: 12/28/2022] Open
Abstract
Regulators of the WhiB-like (wbl) family are playing important role in the complex regulation of metabolic and morphological differentiation in Streptomyces. In this study, we investigated the role of wblI, a member of this family, in the regulation of secondary metabolite production in Streptomyces lividans. The over-expression of wblI was correlated with an enhanced biosynthesis of undecylprodigiosin and actinorhodin and with a reduction of the biosynthesis of yCPK and of the grey spore pigment encoded by the whiE locus. Five regulatory targets of WblI were identified using in vitro formaldehyde crosslinking and confirmed by EMSA and qRT-PCR. These included the promoter regions of wblI itself, two genes of the ACT cluster (actVA3 and the intergenic region between the divergently orientated genes actII-1 and actII-2) and that of wblA, another member of the Wbl family. Quantitative RT-PCR analysis indicated that the expression of actVA3 encoding a protein of unknown function as well as that of actII-1, a TetR regulator repressing the expression of actII-2, encoding the ACT transporter, were down regulated in the WblI over-expressing strain. Consistently the expression of the transporter actII-2 was up-regulated. The expression of WblA, that is known to have a negative impact on ACT biosynthesis, was strongly down regulated in the WblI over-expressing strain. These data are consistent with the positive impact that WblI over-expression has on ACT biosynthesis. The latter might result from direct activation of ACT biosynthesis and export and from repression of the expression of WblA, a likely indirect, repressor of ACT biosynthesis.
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Affiliation(s)
- Lan Yan
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, PR China
| | - Qizhong Zhang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, PR China
| | - Marie-Joelle Virolle
- Group "Energetic Metabolism of Streptomyces ", Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, INRA, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
- * E-mail: (DLX); (MJV)
| | - Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, PR China
- * E-mail: (DLX); (MJV)
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Yan S, Xu M, Wang R, Li Q, Yu Z, Xie J. Overexpression of Rv2788 increases mycobacterium stresses survival. Microbiol Res 2016; 195:51-59. [PMID: 28024526 DOI: 10.1016/j.micres.2016.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis-one of the most devastating infectious diseases, is a successful intracellular pathogen capable of surviving diverse stresses. Unveiling the molecular mechanisms governing this superior adaptation will inspire better control measures against tuberculosis. To define the role of Rv2788, a manganese-dependent transcriptional repressor, M.smegmatis was used as the host strain for heterologous expression Rv2788. Rv2788 can significantly change the colony morphology and fatty acids and permeability of cell wall, enhance the growth of the recombinants and resistance to diverse stresses, such as hydrogen peroxide (H₂O₂), diamide exposure, surface stress, acidic condition, multiple antibiotics treatment including chloramphenicol, vancomycin and amikacin. The dysregulation of the target genes of Rv2788, such as whiB1 and lexA, might underpin such phenotypes. The results implicate important roles of Rv2788 in the survival of Mycobacterium under stresses, and might represent ideal novel antibiotics target candidate.
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Affiliation(s)
- Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengmeng Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.
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Chen Z, Hu Y, Cumming BM, Lu P, Feng L, Deng J, Steyn AJC, Chen S. Mycobacterial WhiB6 Differentially Regulates ESX-1 and the Dos Regulon to Modulate Granuloma Formation and Virulence in Zebrafish. Cell Rep 2016; 16:2512-24. [PMID: 27545883 DOI: 10.1016/j.celrep.2016.07.080] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/06/2016] [Accepted: 07/27/2016] [Indexed: 01/21/2023] Open
Abstract
During the course of infection, Mycobacterium tuberculosis (Mtb) is exposed to diverse redox stresses that trigger metabolic and physiological changes. How these stressors are sensed and relayed to the Mtb transcriptional apparatus remains unclear. Here, we provide evidence that WhiB6 differentially regulates the ESX-1 and DosR regulons through its Fe-S cluster. When challenged with NO, WhiB6 continually activates expression of the DosR regulons but regulates ESX-1 expression through initial activation followed by gradual inhibition. Comparative transcriptomic analysis of the holo- and reduced apo-WhiB6 complemented strains confirms these results and also reveals that WhiB6 controls aerobic and anaerobic metabolism, cell division, and virulence. Using the Mycobacterium marinum zebrafish infection model, we find that holo- and apo-WhiB6 modulate levels of mycobacterial infection, granuloma formation, and dissemination. These findings provide fresh insight into the role of WhiB6 in mycobacterial infection, dissemination, and disease development.
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Affiliation(s)
- Zhenkang Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 10086, China
| | - Yangbo Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Bridgette M Cumming
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban 4001, South Africa
| | - Pei Lu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lipeng Feng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiaoyu Deng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Adrie J C Steyn
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban 4001, South Africa; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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Construction and application of a co-expression network in Mycobacterium tuberculosis. Sci Rep 2016; 6:28422. [PMID: 27328747 PMCID: PMC4916473 DOI: 10.1038/srep28422] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/01/2016] [Indexed: 12/20/2022] Open
Abstract
Because of its high pathogenicity and infectivity, tuberculosis is a serious threat to human health. Some information about the functions of the genes in Mycobacterium tuberculosis genome was currently available, but it was not enough to explore transcriptional regulatory mechanisms. Here, we applied the WGCNA (Weighted Gene Correlation Network Analysis) algorithm to mine pooled microarray datasets for the M. tuberculosis H37Rv strain. We constructed a co-expression network that was subdivided into 78 co-expression gene modules. The different response to two kinds of vitro models (a constant 0.2% oxygen hypoxia model and a Wayne model) were explained based on these modules. We identified potential transcription factors based on high Pearson’s correlation coefficients between the modules and genes. Three modules that may be associated with hypoxic stimulation were identified, and their potential transcription factors were predicted. In the validation experiment, we determined the expression levels of genes in the modules under hypoxic condition and under overexpression of potential transcription factors (Rv0081, furA (Rv1909c), Rv0324, Rv3334, and Rv3833). The experimental results showed that the three identified modules related to hypoxia and that the overexpression of transcription factors could significantly change the expression levels of genes in the corresponding modules.
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Feng L, Chen Z, Wang Z, Hu Y, Chen S. Genome-wide characterization of monomeric transcriptional regulators in Mycobacterium tuberculosis. Microbiology (Reading) 2016; 162:889-897. [DOI: 10.1099/mic.0.000257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lipeng Feng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology,Chinese Academy of Sciences, Wuhan, PRChina
| | - Zhenkang Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology,Chinese Academy of Sciences, Wuhan, PRChina
| | - Zhongwei Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology,Chinese Academy of Sciences, Wuhan, PRChina
| | - Yangbo Hu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology,Chinese Academy of Sciences, Wuhan, PRChina
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology,Chinese Academy of Sciences, Wuhan, PRChina
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Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks. J Bacteriol 2016; 198:1360-73. [PMID: 26883824 DOI: 10.1128/jb.00935-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. For pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. Once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. Inappropriate responses have consequences; hence, the execution of the appropriate response is essential for survival of the bacterium in its niche. Stress responses are most often regulated at the level of gene expression and, more specifically, transcription. This minireview focuses on mechanisms of regulating transcription initiation that are required by Mycobacterium tuberculosis to respond to the arsenal of defenses imposed by the host during infection. In particular, we highlight how certain features of M. tuberculosis physiology allow this pathogen to respond swiftly and effectively to host defenses. By enacting highly integrated and coordinated gene expression changes in response to stress,M. tuberculosis is prepared for battle against the host defense and able to persist within the human population.
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Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence. Microbiol Spectr 2015; 2:MGM2-0007-2013. [PMID: 26082107 DOI: 10.1128/microbiolspec.mgm2-0007-2013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid adaptation to changing environments is one of the keys to the success of microorganisms. Since infection is a dynamic process, it is possible to predict that Mycobacterium tuberculosis adaptation involves continuous modulation of its global transcriptional profile in response to the changing environment found in the human body. In the last 18 years several studies have stressed the role of sigma (σ) factors in this process. These are small interchangeable subunits of the RNA polymerase holoenzyme that are required for transcriptional initiation and that determine promoter specificity. The M. tuberculosis genome encodes 13 of these proteins, one of which--the principal σ factor σA--is essential. Of the other 12 σ factors, at least 6 are required for virulence. In this article we review our current knowledge of mycobacterial σ factors, their regulons, the complex mechanisms determining their regulation, and their roles in M. tuberculosis physiology and virulence.
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Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR. Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol 2015; 15:502. [PMID: 25380655 DOI: 10.1186/preaccept-1701638048134699] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription factors of M. tuberculosis, we have assayed the global transcriptional consequences of overexpressing each transcription factor from an inducible promoter. RESULTS We cloned and overexpressed 206 transcription factors in M. tuberculosis to identify the regulatory signature of each. We identified 9,335 regulatory consequences of overexpressing each of 183 transcription factors, providing evidence of regulation for 70% of the M. tuberculosis genome. These transcriptional signatures agree well with previously described M. tuberculosis regulons. The number of genes differentially regulated by transcription factor overexpression varied from hundreds of genes to none, with the majority of expression changes repressing basal transcription. Exploring the global transcriptional maps of transcription factor overexpressing (TFOE) strains, we predicted and validated the phenotype of a regulator that reduces susceptibility to a first line anti-tubercular drug, isoniazid. We also combined the TFOE data with an existing model of M. tuberculosis metabolism to predict the growth rates of individual TFOE strains with high fidelity. CONCLUSION This work has led to a systems-level framework describing the transcriptome of a devastating bacterial pathogen, characterized the transcriptional influence of nearly all individual transcription factors in M. tuberculosis, and demonstrated the utility of this resource. These results will stimulate additional systems-level and hypothesis-driven efforts to understand M. tuberculosis adaptations that promote disease.
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Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR. Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol 2015. [PMID: 25380655 PMCID: PMC4249609 DOI: 10.1186/s13059-014-0502-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription factors of M. tuberculosis, we have assayed the global transcriptional consequences of overexpressing each transcription factor from an inducible promoter. Results We cloned and overexpressed 206 transcription factors in M. tuberculosis to identify the regulatory signature of each. We identified 9,335 regulatory consequences of overexpressing each of 183 transcription factors, providing evidence of regulation for 70% of the M. tuberculosis genome. These transcriptional signatures agree well with previously described M. tuberculosis regulons. The number of genes differentially regulated by transcription factor overexpression varied from hundreds of genes to none, with the majority of expression changes repressing basal transcription. Exploring the global transcriptional maps of transcription factor overexpressing (TFOE) strains, we predicted and validated the phenotype of a regulator that reduces susceptibility to a first line anti-tubercular drug, isoniazid. We also combined the TFOE data with an existing model of M. tuberculosis metabolism to predict the growth rates of individual TFOE strains with high fidelity. Conclusion This work has led to a systems-level framework describing the transcriptome of a devastating bacterial pathogen, characterized the transcriptional influence of nearly all individual transcription factors in M. tuberculosis, and demonstrated the utility of this resource. These results will stimulate additional systems-level and hypothesis-driven efforts to understand M. tuberculosis adaptations that promote disease. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0502-3) contains supplementary material, which is available to authorized users.
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Latent tuberculosis infection: myths, models, and molecular mechanisms. Microbiol Mol Biol Rev 2015; 78:343-71. [PMID: 25184558 DOI: 10.1128/mmbr.00010-14] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this review is to present the current state of knowledge on human latent tuberculosis infection (LTBI) based on clinical studies and observations, as well as experimental in vitro and animal models. Several key terms are defined, including "latency," "persistence," "dormancy," and "antibiotic tolerance." Dogmas prevalent in the field are critically examined based on available clinical and experimental data, including the long-held beliefs that infection is either latent or active, that LTBI represents a small population of nonreplicating, "dormant" bacilli, and that caseous granulomas are the haven for LTBI. The role of host factors, such as CD4(+) and CD8(+) T cells, T regulatory cells, tumor necrosis factor alpha (TNF-α), and gamma interferon (IFN-γ), in controlling TB infection is discussed. We also highlight microbial regulatory and metabolic pathways implicated in bacillary growth restriction and antibiotic tolerance under various physiologically relevant conditions. Finally, we pose several clinically important questions, which remain unanswered and will serve to stimulate future research on LTBI.
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Abstract
Bacterial secretion systems are sophisticated molecular machines that fulfil a wide range of important functions, which reach from export/secretion of essential proteins or virulence factors to the implication in conjugation processes. In contrast to the widely distributed Sec and Twin Arginine Translocation (TAT) systems, the recently identified ESX/type VII systems show a more restricted distribution and are typical for mycobacteria and other high-GC Actinobacteria. Similarly, type VII-like secretion systems have been described in low-GC Gram-positive bacteria belonging to the phylum Firmicutes. While the most complex organization of type VII secretion systems currently known is found in slow-growing mycobacteria, which harbour up to 5 chromosomal-encoded systems (ESX-1 to ESX-5), much simpler organization is reported for type VII-like systems in Firmicutes. In this chapter, we describe common and divergent features of type VII- and type VII-like secretion pathways and also comment on their biological key roles, many of which are related to species-/genus-specific host-pathogen interactions and/or virulence mechanisms.
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Mettert EL, Kiley PJ. Fe-S proteins that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1284-93. [PMID: 25450978 DOI: 10.1016/j.bbamcr.2014.11.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023]
Abstract
Iron-sulfur (Fe-S) cluster containing proteins that regulate gene expression are present in most organisms. The innate chemistry of their Fe-S cofactors makes these regulatory proteins ideal for sensing environmental signals, such as gases (e.g. O2 and NO), levels of Fe and Fe-S clusters, reactive oxygen species, and redox cycling compounds, to subsequently mediate an adaptive response. Here we review the recent findings that have provided invaluable insight into the mechanism and function of these highly significant Fe-S regulatory proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Erin L Mettert
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
| | - Patricia J Kiley
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
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WblAch, a pivotal activator of natamycin biosynthesis and morphological differentiation in Streptomyces chattanoogensis L10, is positively regulated by AdpAch. Appl Environ Microbiol 2014; 80:6879-87. [PMID: 25172865 DOI: 10.1128/aem.01849-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Detailed mechanisms of WhiB-like (Wbl) proteins involved in antibiotic biosynthesis and morphological differentiation are poorly understood. Here, we characterize the role of WblAch, a Streptomyces chattanoogensis L10 protein belonging to this superfamily. Based on DNA microarray data and verified by real-time quantitative PCR (qRT-PCR), the expression of wblAch was shown to be positively regulated by AdpAch. Gel retardation assays and DNase I footprinting experiments showed that AdpAch has specific DNA-binding activity for the promoter region of wblAch. Gene disruption and genetic complementation revealed that WblAch acts in a positive manner to regulate natamycin production. When wblAch was overexpressed in the wild-type strain, the natamycin yield was increased by ∼30%. This provides a strategy to generate improved strains for natamycin production. Moreover, transcriptional analysis showed that the expression levels of whi genes (including whiA, whiB, whiH, and whiI) were severely depressed in the ΔwblAch mutant, suggesting that WblAch plays a part in morphological differentiation by influencing the expression of the whi genes.
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Prozorov AA, Fedorova IA, Bekker OB, Danilenko VN. The virulence factors of Mycobacterium tuberculosis: Genetic control, new conceptions. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414080055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Chim N, Johnson PM, Goulding CW. Insights into redox sensing metalloproteins in Mycobacterium tuberculosis. J Inorg Biochem 2014; 133:118-26. [PMID: 24314844 PMCID: PMC3959581 DOI: 10.1016/j.jinorgbio.2013.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis, the pathogen that causes tuberculosis, has evolved sophisticated mechanisms for evading assault by the human host. This review focuses on M. tuberculosis regulatory metalloproteins that are sensitive to exogenous stresses attributed to changes in the levels of gaseous molecules (i.e., molecular oxygen, carbon monoxide and nitric oxide) to elicit an intracellular response. In particular, we highlight recent developments on the subfamily of Whi proteins, redox sensing WhiB-like proteins that contain iron-sulfur clusters, sigma factors and their cognate anti-sigma factors of which some are zinc-regulated, and the dormancy survival regulon DosS/DosT-DosR heme sensory system. Mounting experimental evidence suggests that these systems contribute to a highly complex and interrelated regulatory network that controls M. tuberculosis biology. This review concludes with a discussion of strategies that M. tuberculosis has developed to maintain redox homeostasis, including mechanisms to regulate endogenous nitric oxide and carbon monoxide levels.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Parker M Johnson
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, UCI, Irvine, CA 92697, USA.
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Burian J, Ramón-García S, Howes CG, Thompson CJ. WhiB7, a transcriptional activator that coordinates physiology with intrinsic drug resistance inMycobacterium tuberculosis. Expert Rev Anti Infect Ther 2014; 10:1037-47. [DOI: 10.1586/eri.12.90] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Serafini A, Pisu D, Palù G, Rodriguez GM, Manganelli R. The ESX-3 secretion system is necessary for iron and zinc homeostasis in Mycobacterium tuberculosis. PLoS One 2013; 8:e78351. [PMID: 24155985 PMCID: PMC3796483 DOI: 10.1371/journal.pone.0078351] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/18/2013] [Indexed: 12/25/2022] Open
Abstract
ESX-3 is one of the five type VII secretion systems encoded by the Mycobacterium tuberculosis genome. We recently showed the essentiality of ESX-3 for M. tuberculosis viability and proposed its involvement in iron and zinc metabolism. In this study we confirmed the role of ESX-3 in iron uptake and its involvement in the adaptation to low zinc environment in M. tuberculosis. Moreover, we unveiled functional differences between the ESX-3 roles in M. tuberculosis and M. smegmatis showing that in the latter ESX-3 is only involved in the adaptation to iron and not to zinc restriction. Finally, we also showed that in M. tuberculosis this secretion system is essential for iron and zinc homeostasis not only in conditions in which the concentrations of these metals are limiting but also in metal sufficient conditions.
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Affiliation(s)
- Agnese Serafini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Davide Pisu
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G. Marcela Rodriguez
- Public Health Research Institute - Rutgers, the State University of New Jersey, Newark, New Jersey, United States of America
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
- * E-mail:
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Burian J, Yim G, Hsing M, Axerio-Cilies P, Cherkasov A, Spiegelman GB, Thompson CJ. The mycobacterial antibiotic resistance determinant WhiB7 acts as a transcriptional activator by binding the primary sigma factor SigA (RpoV). Nucleic Acids Res 2013; 41:10062-76. [PMID: 23990327 PMCID: PMC3905903 DOI: 10.1093/nar/gkt751] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Tuberculosis therapeutic options are limited by the high intrinsic antibiotic resistance of Mycobacterium tuberculosis. The putative transcriptional regulator WhiB7 is crucial for the activation of systems that provide resistance to diverse antibiotic classes. Here, we used in vitro run-off, two-hybrid assays, as well as mutagenic, complementation and protein pull-down experiments, to characterize WhiB7 as an auto-regulatory, redox-sensitive transcriptional activator in Mycobacterium smegmatis. We provide the first direct biochemical proof that a WhiB protein promotes transcription and also demonstrate that this activity is sensitive to oxidation (diamide). Its partner protein for transcriptional activation was identified as SigA, the primary sigma factor subunit of RNA polymerase. Residues required for the interaction mapped to region 4 of SigA (including R515H) or adjacent domains of WhiB7 (including E63D). WhiB7's ability to provide a specific spectrum of antibiotic-resistance was dependent on these residues as well as its C-terminal AT-hook module that binds to an AT-rich motif immediately upstream of the -35 hexamer recognized by SigA. These experimentally established constrains, combined with protein structure predictions, were used to generate a working model of the WhiB7-SigA-promoter complex. Inhibitors preventing WhiB7 interactions could allow the use of previously ineffective antibiotics for treatment of mycobacterial diseases.
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Affiliation(s)
- Ján Burian
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3, Centre for Tuberculosis Research, University of British Columbia, Vancouver, Canada V6T 1Z3 and Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada V6T 1Z3
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Reprint of: Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:923-37. [PMID: 23660107 DOI: 10.1016/j.bbabio.2013.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F. Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:455-69. [PMID: 23298813 DOI: 10.1016/j.bbabio.2012.12.010] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Béatrice Roche
- Institut de Microbiologie de la Méditerranée, Marseille, France
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