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Malhotra N, Oh S, Finin P, Medrano J, Andrews J, Goodwin M, Markowitz TE, Lack J, Boshoff HIM, Barry CE. Environmental sphagnum-associated fungi target thiol homeostasis to compete with Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.23.614403. [PMID: 39372785 PMCID: PMC11451587 DOI: 10.1101/2024.09.23.614403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Mycobacterial species in nature are found in abundance in sphagnum peat bogs where they compete for nutrients with a variety of microorganisms including fungi. We screened a collection of fungi isolated from sphagnum bogs by co-culture with Mycobacterium tuberculosis (Mtb) to look for inducible expression of antitubercular agents and identified five fungi that produced cidal antitubercular agents upon exposure to live Mtb. Whole genome sequencing of these fungi followed by fungal RNAseq after Mtb exposure allowed us to identify biosynthetic gene clusters induced by co-culture. Three of these fungi induced expression of patulin, one induced citrinin expression and one induced the production of nidulalin A. The biosynthetic gene clusters for patulin and citrinin have been previously described but the genes involved in nidulalin A production have not been described before. All three of these potent electrophiles react with thiols and treatment of Mtb cells with these agents followed by Mtb RNAseq showed that these natural products all induce profound thiol stress suggesting a rapid depletion of mycothiol. The induction of thiol-reactive mycotoxins through three different systems in response to exposure to Mtb suggests that fungi have identified this as a highly vulnerable target in a similar microenvironment to that of the caseous human lesion.
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Affiliation(s)
- Neha Malhotra
- Tuberculosis Research Section, LCIM, NIAID, NIH, Bethesda, MD USA
- Current affiliation: Center for Neural Circuits and Behavior, Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Sangmi Oh
- Tuberculosis Research Section, LCIM, NIAID, NIH, Bethesda, MD USA
| | - Peter Finin
- Tuberculosis Research Section, LCIM, NIAID, NIH, Bethesda, MD USA
| | - Jessica Medrano
- Tuberculosis Research Section, LCIM, NIAID, NIH, Bethesda, MD USA
- Current affiliation: Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jenna Andrews
- Tuberculosis Research Section, LCIM, NIAID, NIH, Bethesda, MD USA
- Current affiliation: Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT
| | - Michael Goodwin
- Tuberculosis Research Section, LCIM, NIAID, NIH, Bethesda, MD USA
| | - Tovah E. Markowitz
- Integrated Data Sciences Section, Research Technologies Branch, NIAID, NIH, Bethesda, Maryland, USA
| | - Justin Lack
- Integrated Data Sciences Section, Research Technologies Branch, NIAID, NIH, Bethesda, Maryland, USA
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Wani SR, Jain V. Deciphering the molecular mechanism and regulation of formaldehyde detoxification in Mycobacterium smegmatis. Appl Environ Microbiol 2024; 90:e0203923. [PMID: 38259108 PMCID: PMC10880627 DOI: 10.1128/aem.02039-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
The build-up of formaldehyde, a highly reactive molecule is cytotoxic and must be eliminated for the organism's survival. Formaldehyde detoxification system is found in nearly all organisms including both pathogenic and non-pathogenic mycobacteria. MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis (Msm), is an indispensable part of this system and forms a bicistronic operon with its downstream uncharacterized gene, fmh. We here show that Fmh, a putative metallo-beta-lactamase, is essential in tolerating higher amounts of formaldehyde when co-overexpressed with mscR in vivo. Our NMR studies indicate that MscR, along with Fmh, enhances formate production through a mycothiol (MSH)-dependent pathway, emphasizing the importance of Fmh in detoxifying formaldehyde. Although another aldehyde dehydrogenase, MSMEG_1543, induces upon formaldehyde addition, it is not involved in its detoxification. We also show that the expression of the mscR operon is constitutive and remains unchanged upon formaldehyde addition, as displayed by the promoter activity of PmscR and by the transcript and protein levels of MscR. Furthermore, we establish the role of a thiol-responsive sigma factor SigH in formaldehyde detoxification. We show that SigH, and not SigE, is crucial for formaldehyde detoxification, even though it does not directly regulate mscR operon expression. In addition, sensitivity to formaldehyde in sigH-knockout could be alleviated by overexpression of mscR. Taken together, our data demonstrate the importance of MSH-dependent pathways in detoxifying formaldehyde in a mycobacterial system. An absence of such MSH-dependent proteins in eukaryotes and its complete conservation in M. tuberculosis, the causative agent of tuberculosis, further unravel new drug targets for this pathogen.IMPORTANCEExtensive research has been done on formaldehyde detoxification in different bacteria. However, our current understanding of the mechanisms underlying this process in mycobacteria remains exceedingly little. We previously showed that MscR, a formaldehyde dehydrogenase from Mycobacterium smegmatis, plays a pivotal role in this detoxification pathway. Here, we present a potential S-formyl-mycothiol hydrolase named Fmh, thought to be a metallo-beta-lactamase, which functions along with mycothiol (MSH) and MscR to enhance formate production within this detoxification pathway. Co-expression of Fmh with MscR significantly enhances the efficiency of formaldehyde detoxification in M. smegmatis. Our experiments establish that Fmh catalyzes the final step of this detoxification pathway. Although an alternative sigma factor SigH was found to be involved in formaldehyde detoxification, it did not directly regulate the expression of mscR. Since formaldehyde detoxification is essential for bacterial survival, we envisage this process to be a potential drug target for M. tuberculosis eradication.
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Affiliation(s)
- Saloni Rajesh Wani
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
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3
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Hurst-Hess K, McManaman C, Yang Y, Gupta S, Ghosh P. Hierarchy and interconnected networks in the WhiB7 mediated transcriptional response to antibiotic stress in Mycobacterium abscessus. PLoS Genet 2023; 19:e1011060. [PMID: 38055757 PMCID: PMC10727445 DOI: 10.1371/journal.pgen.1011060] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/18/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Mycobacterium abscessus is intrinsically resistant to antibiotics effective against other pathogenic mycobacteria largely due to the drug-induced expression of genes that confer resistance. WhiB7 is a major hub controlling the induction of resistance to ribosome-targeting antibiotics. It activates the expression of >100 genes, 7 of which are known determinants of drug resistance; the function of most genes within the regulon is however unknown, but some conceivably encode additional mechanisms of resistance. Furthermore, the hierarchy of gene expression within the regulon, if any, is poorly understood. In the present work we have identified 56 WhiB7 binding sites using chromatin immunoprecipitation sequencing (CHIP-Seq) which accounts for the WhiB7-dependent upregulation of 72 genes, and find that M. abscessus WhiB7 functions exclusively as a transcriptional activator at promoters recognized by σA/σB. We have investigated the role of 18 WhiB7 regulated genes in drug resistance. Our results suggest that while some genes within the regulon (eg. erm41, hflX, eis2 and the ABCFs) play a major role in resistance, others make smaller contributions (eg. MAB_4324c and MAB_1409c) and the observed hypersensitivity ΔMabwhiB7 is a cumulative effect of these individual contributions. Moreover, our CHIP-Seq data implicate additional roles of WhiB7 induced genes beyond antibiotic resistance. Finally, we identify a σH-dependent network in aminoglycoside and tigecycline resistance which is induced upon drug exposure and is further activated by WhiB7 demonstrating the existence of a crosstalk between components of the WhiB7-dependent and -independent circuits.
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Affiliation(s)
- Kelley Hurst-Hess
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Charity McManaman
- School of Public Health, University at Albany, Albany, New York, United States of America
| | - Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Shamba Gupta
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Pallavi Ghosh
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- School of Public Health, University at Albany, Albany, New York, United States of America
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4
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Mitermite M, Elizari JMU, Ma R, Farrell D, Gordon SV. Exploring virulence in Mycobacterium bovis: clues from comparative genomics and perspectives for the future. Ir Vet J 2023; 76:26. [PMID: 37770951 PMCID: PMC10540498 DOI: 10.1186/s13620-023-00257-6] [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: 11/06/2022] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Here we provide a summary of a plenary lecture delivered on Mycobacterium bovis, the bovine TB bacillus, at the M. bovis 2022 meeting held in Galway, Ireland, in June 2022. We focus on the analysis of genetic differences between M. bovis and the human pathogen Mycobacterium tuberculosis as a route to gain knowledge on what makes M. bovis function as an animal pathogen. We provide a brief historical background around M. bovis and comparative virulence experiments with M. tuberculosis, before moving to what we have learned from the studies of the M. bovis genome sequence. We discuss the need to translate knowledge on the molecular basis of virulence in M. bovis into improved control of bovine tuberculosis.
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Affiliation(s)
- Morgane Mitermite
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Jose Maria Urtasun Elizari
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
- UCD Conway Institute, University College Dublin, Dublin, Ireland.
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Nelson SJ, Williams JT, Buglino JA, Nambi S, Lojek LJ, Glickman MS, Ioerger TR, Sassetti CM. The Rip1 intramembrane protease contributes to iron and zinc homeostasis in Mycobacterium tuberculosis. mSphere 2023; 8:e0038922. [PMID: 37318217 PMCID: PMC10449499 DOI: 10.1128/msphere.00389-22] [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: 08/11/2022] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Mycobacterium tuberculosis is exposed to a variety of stresses during a chronic infection, as the immune system simultaneously produces bactericidal compounds and starves the pathogen of essential nutrients. The intramembrane protease, Rip1, plays an important role in the adaptation to these stresses, at least partially by the cleavage of membrane-bound transcriptional regulators. Although Rip1 is known to be critical for surviving copper intoxication and nitric oxide exposure, these stresses do not fully account for the regulatory protein's essentiality during infection. In this work, we demonstrate that Rip1 is also necessary for growth in low-iron and low-zinc conditions, similar to those imposed by the immune system. Using a newly generated library of sigma factor mutants, we show that the known regulatory target of Rip1, SigL, shares this defect. Transcriptional profiling under iron-limiting conditions supported the coordinated activity of Rip1 and SigL and demonstrated that the loss of these proteins produces an exaggerated iron starvation response. These observations demonstrate that Rip1 coordinates several aspects of metal homeostasis and suggest that a Rip1- and SigL-dependent pathway is necessary to thrive in the iron-deficient environments encountered during infection. IMPORTANCE Metal homeostasis represents a critical point of interaction between the mammalian immune system and potential pathogens. While the host attempts to intoxicate microbes with high concentrations of copper or starve the invader of iron and zinc, successful pathogens have acquired mechanisms to overcome these defenses. Our work identifies a regulatory pathway consisting of the Rip1 intramembrane protease and the sigma factor, SigL, that is essential for the important human pathogen, Mycobacterium tuberculosis, to grow in low-iron or low-zinc conditions such as those encountered during infection. In conjunction with Rip1's known role in resisting copper toxicity, our work implicates this protein as a critical integration point that coordinates the multiple metal homeostatic systems required for this pathogen to survive in host tissue.
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Affiliation(s)
- Samantha J. Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John T. Williams
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John A. Buglino
- Immunology Program, Sloan Kettering Institute, New York City, New York, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lisa J. Lojek
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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6
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Hurst-Hess K, McManaman C, Yang Y, Gupta S, Ghosh P. Hierarchy and networks in the transcriptional response of Mycobacterium abscessus to antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533064. [PMID: 36993298 PMCID: PMC10055156 DOI: 10.1101/2023.03.16.533064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mycobacterium abscessus causes acute and chronic pulmonary infection in patients with chronic lung damage. It is intrinsically resistance to antibiotics effective against other pathogenic mycobacteria largely due to the drug-induced expression of genes that confer resistance. Induction of genes upon exposure to ribosome targeting antibiotics proceeds via WhiB7-dependent and -independent pathways. WhiB7 controls the expression of >100 genes, a few of which are known determinants of drug resistance. The function of the vast majority of genes within the regulon is unknown, but some conceivably encode additional mechanisms of resistance. Furthermore, the hierarchy of gene expression within the regulon, if any, is poorly understood. In the present work we have identified 56 WhiB7 binding sites using chromatin immunoprecipitation sequencing (CHIP-Seq) which accounts for the WhiB7-dependent upregulation of 70 genes, and find that M. abscessus WhiB7 functions exclusively as a transcriptional activator at promoters recognized by σ A /σ B We have investigated the role of 18 WhiB7 regulated genes in drug resistance and demonstrated the role of MAB_1409c and MAB_4324c in aminoglycoside resistance. Further, we identify a σ H -dependent pathway in aminoglycoside and tigecycline resistance which is induced upon drug exposure and is further activated by WhiB7 demonstrating the existence of a crosstalk between components of the WhiB7-dependent and -independent circuits. Abstract Importance The induction of multiple genes that confer resistance to structurally diverse ribosome-targeting antibiotics is funneled through the induction of a single transcriptional activator, WhiB7, by antibiotic-stalled ribosomes. This poses a severe restriction in M. abscessus therapy as treatment with one ribosome-targeting antibiotic confers resistance to all other ribosome-targeting antibiotics. Here we uncover the intricacies of the WhiB7 regulatory circuit, identify three previously unknown determinants of aminoglycoside resistance and unveil a communication between WhiB7 dependent and independent components. This not only expands our understanding of the antibiotic resistance potential of M. abscessus but can also inform the development of much needed therapeutic options.
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7
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Busche T, Dostálová H, Rucká L, Holátko J, Barvík I, Štěpánek V, Pátek M, Kalinowski J. Overlapping SigH and SigE sigma factor regulons in Corynebacterium glutamicum. Front Microbiol 2023; 13:1059649. [PMID: 36925999 PMCID: PMC10012870 DOI: 10.3389/fmicb.2022.1059649] [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: 10/01/2022] [Accepted: 11/15/2022] [Indexed: 03/06/2023] Open
Abstract
The sigma H (σΗ) and sigma E (σE) subunits of Corynebacterium glutamicum RNA polymerase belong to Group 4 of sigma factors, also called extracytoplasmic function (ECF) sigma factors. Genes of the C. glutamicum σΗ regulon that are involved in heat and oxidative stress response have already been defined, whereas the genes of the σE regulon, which is involved in cell surface stress response, have not been explored until now. Using the C. glutamicum RES167 strain and its derivative C. glutamicum ΔcseE with a deletion in the anti-σΕ gene, differential gene expression was analyzed by RNA sequencing. We found 296 upregulated and 398 downregulated genes in C. glutamicum ΔcseE compared to C. glutamicum RES167. To confirm the functional link between σΕ and the corresponding promoters, we tested selected promoters using the in vivo two-plasmid system with gfpuv as a reporter gene and by in vitro transcription. Analyses with RNAP+σΗ and RNAP+σΕ, which were previously shown to recognize similar promoters, proved that the σΗ and σE regulons significantly overlap. The σE-controlled genes were found to be involved for example in protein quality control (dnaK, dnaJ2, clpB, and clpC), the regulation of Clp proteases (clgR), and membrane integrity maintenance. The single-promoter analyses with σΗ and σΕ revealed that there are two groups of promoters: those which are exclusively σΗ-specific, and the other group of promoters, which are σΗ/σE-dependent. No exclusively σE-dependent promoter was detected. We defined the consensus sequences of exclusively σΗ-regulated promotors to be -35 GGAAt and - 10 GTT and σΗ/σE-regulated promoters to be -35 GGAAC and - 10 cGTT. Fifteen genes were found to belong to the σΗ/σΕ regulon. Homology modeling showed that there is a specific interaction between Met170 in σΗ and the nucleotides -31 and - 30 within the non-coding strand (AT or CT) of the σΗ-dependent promoters. In σE, Arg185 was found to interact with the nucleotides GA at the same positions in the σE-dependent promoters.
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Affiliation(s)
- Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Bielefeld, Germany
| | - Hana Dostálová
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Lenka Rucká
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Jiří Holátko
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Prague, Czechia
| | - Václav Štěpánek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Miroslav Pátek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Cioetto-Mazzabò L, Boldrin F, Beauvineau C, Speth M, Marina A, Namouchi A, Segafreddo G, Cimino M, Favre-Rochex S, Balasingham S, Trastoy B, Munier-Lehmann H, Griffiths G, Gicquel B, Guerin M, Manganelli R, Alonso-Rodríguez N. SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression. Nucleic Acids Res 2022; 51:144-165. [PMID: 36546765 PMCID: PMC9841431 DOI: 10.1093/nar/gkac1173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of drug-resistant Mycobacterium tuberculosis strains highlights the need to discover anti-tuberculosis drugs with novel mechanisms of action. Here we discovered a mycobactericidal strategy based on the prodrug activation of selected chemical derivatives classified as nitronaphthofurans (nNFs) mediated by the coordinated action of the sigH and mrx2 genes. The transcription factor SigH is a key regulator of an extensive transcriptional network that responds to oxidative, nitrosative, and heat stresses in M. tuberculosis. The nNF action induced the SigH stress response which in turn induced the mrx2 overexpression. The nitroreductase Mrx2 was found to activate nNF prodrugs, killing replicating, non-replicating and intracellular forms of M. tuberculosis. Analysis of SigH DNA sequences obtained from spontaneous nNF-resistant M. tuberculosis mutants suggests disruption of SigH binding to the mrx2 promoter site and/or RNA polymerase core, likely promoting the observed loss of transcriptional control over Mrx2. Mutations found in mrx2 lead to structural defects in the thioredoxin fold of the Mrx2 protein, significantly impairing the activity of the Mrx2 enzyme against nNFs. Altogether, our work brings out the SigH/Mrx2 stress response pathway as a promising target for future drug discovery programs.
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Affiliation(s)
| | | | - Claire Beauvineau
- Chemical Library Institut Curie/CNRS, CNRS UMR9187, INSERM U1196 and CNRS UMR3666, INSERM U1193, Université Paris-Saclay, Orsay 91405, France
| | - Martin Speth
- Department Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0371, Norway
| | - Alberto Marina
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160 Spain
| | - Amine Namouchi
- Génétique Mycobactérienne, Institute Pasteur, Paris 75015, France,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0371, Norway
| | - Greta Segafreddo
- Department of Molecular Medicine, University of Padova, Padova 35122, Italy
| | - Mena Cimino
- Génétique Mycobactérienne, Institute Pasteur, Paris 75015, France
| | | | | | - Beatriz Trastoy
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160 Spain,Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Bizkaia 48903, Spain
| | - Hélène Munier-Lehmann
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR3523, Université de Paris, Paris 75015, France
| | - Gareth Griffiths
- Department Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0371, Norway
| | - Brigitte Gicquel
- Génétique Mycobactérienne, Institute Pasteur, Paris 75015, France,Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Centre for Chronic Disease Control, Shenzhen 518054, China
| | - Marcelo E Guerin
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160 Spain,Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Bizkaia 48903, Spain,IKERBASQUE, Basque Foundation for Science, Bilbao 48009, Spain
| | - Riccardo Manganelli
- Correspondence may also be addressed to Riccardo Manganelli. Tel: +39 049 827 2366; Fax: +39 049 827 2355;
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9
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Sawicki R, Widelski J, Okińczyc P, Truszkiewicz W, Glous J, Sieniawska E. Exposure to Nepalese Propolis Alters the Metabolic State of Mycobacterium tuberculosis. Front Microbiol 2022; 13:929476. [PMID: 35814697 PMCID: PMC9260414 DOI: 10.3389/fmicb.2022.929476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022] Open
Abstract
Propolis is a natural product proved to be efficient against Mycobacterium tuberculosis. Although it is produced by bees, its active alcoholic-aqueous fraction contains plant-derived molecules. To gain some insight into its mechanism of antimycobacterial activity, we studied the metabolic changes in bacterial cells treated with extract of Trigona sp. propolis from Nepal. The detailed metabolomic and transcriptomic analysis performed in this study indicated target points in bacterial cells under propolis extract influence. The profile of lipids forming the outer and middle layer of the mycobacterial cell envelope was not changed by propolis treatment, however, fluctuations in the profiles of amphipathic glycerophospholipids were observed. The enrichment analysis revealed bacterial metabolic pathways affected by Trigona sp. propolis treatment. The early metabolic response involved much more pathways than observed after 48 h of incubation, however, the highest enrichment ratio was observed after 48 h, indicating the long-lasting influence of propolis. The early bacterial response was related to the increased demand for energy and upregulation of molecules involved in the formation of the cell membrane. The transcriptomic analysis confirmed that bacteria also suffered from oxidative stress, which was more pronounced on the second day of exposure. This was the first attempt to explain the action of Nepalese propolis extract against mycobacteria.
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Affiliation(s)
- Rafał Sawicki
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Lublin, Poland
| | - Jarosław Widelski
- Department of Pharmacognosy, Medical University of Lublin, Lublin, Poland
| | - Piotr Okińczyc
- Department of Pharmacognosy and Herbal Medicines, Wroclaw Medical University, Wrocław, Poland
| | - Wiesław Truszkiewicz
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Lublin, Poland
| | - Joanna Glous
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Lublin, Poland
| | - Elwira Sieniawska
- Department of Natural Products Chemistry, Medical University of Lublin, Lublin, Poland
- *Correspondence: Elwira Sieniawska
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10
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Molecular Connectivity between Extracytoplasmic Sigma Factors and PhoP Accounts for Coupled Mycobacterial Stress Response. J Bacteriol 2022; 204:e0011022. [PMID: 35608366 DOI: 10.1128/jb.00110-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis encounters numerous stress conditions within the host, but how it is able to mount a coupled stress response remains unknown. Growing evidence suggests that under acidic pH, M. tuberculosis modulates redox homeostasis. In an attempt to dissect the mechanistic details of responses to multiple stress conditions, here we studied the significance of connectivity of extracytoplasmic sigma factors with PhoP. We show that PhoP impacts the mycothiol redox state, and the H37Rv ΔphoP deletion mutant strain displays a significantly higher susceptibility to redox stress than the wild-type bacilli. To probe how the two regulators PhoP and redox-active sigma factor SigH contribute to redox homeostasis, we show that SigH controls expression of redox-active thioredoxin genes, a major mycobacterial antioxidant system, and under redox stress, SigH, but not PhoP, is recruited at the target promoters. Consistent with these results, interaction between PhoP and SigH fails to impact redox-dependent gene expression. This is in striking contrast to our previous results showing PhoP-dependent SigE recruitment within acid-inducible mycobacterial promoters to maintain pH homeostasis. Our subsequent results demonstrate reduced PhoP-SigH interaction in the presence of diamide and enhanced PhoP-SigE interaction under low pH. These contrasting results uncover the underlying mechanism of the mycobacterial adaptive program, coupling low pH with maintenance of redox homeostasis. IMPORTANCE M. tuberculosis encounters reductive stress under acidic pH. To investigate the mechanism of coupled stress response, we show that PhoP plays a major role in mycobacterial redox stress response. We observed a strong correlation of phoP-dependent redox-active expression of thioredoxin genes, a major mycobacterial antioxidant system. Further probing of functioning of regulators revealed that while PhoP controls pH homeostasis via its interaction with SigE, direct recruitment of SigH, but not PhoP-SigH interaction, controls expression of thioredoxin genes. These strikingly contrasting results showing enhanced PhoP-SigE interaction under acidic pH and reduced PhoP-SigH interaction under redox conditions uncover the underlying novel mechanism of the mycobacterial adaptive program, coupling low pH with maintenance of redox homeostasis.
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Kapoor I, Shaw A, Naha A, Emam EAF, Varshney U. Role of the nucleotide excision repair pathway proteins (UvrB and UvrD2) in recycling UdgB, a base excision repair enzyme in Mycobacterium smegmatis. DNA Repair (Amst) 2022; 113:103316. [PMID: 35306347 DOI: 10.1016/j.dnarep.2022.103316] [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: 10/19/2021] [Revised: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Cross-talks between DNA repair pathways are emerging as a crucial strategy in the maintenance of the genomic integrity. A double-stranded (ds) DNA specific DNA glycosylase, UdgB is known to excise uracil, hypoxanthine and ethenocytosine. We earlier showed that Mycobacterium smegmatis (Msm) UdgB stays back on the AP-sites it generates in the DNA upon excision of the damaged bases. Here, we show that in an Msm strain deleted for a nucleotide excision repair (NER) protein, UvrB (uvrB-), UdgB expression is toxic, and its deletion from the genome (udgB-) rescues the strain from the genotoxic stress. However, UdgB bound AP-site is not a direct substrate for NER in vitro. We show that UvrD2 and UvrB, known helicases with single-stranded (ss) DNA translocase activity, facilitate recycling of UdgB from AP-DNA. Our studies reveal that the helicases play an important role in exposing the AP-sites in DNA and make them available for further repair.
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Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Abhirup Shaw
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Arindam Naha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
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12
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Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes. mSystems 2022; 7:e0011022. [PMID: 35430871 PMCID: PMC9239107 DOI: 10.1128/msystems.00110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
There is growing evidence that genetic diversity in Mycobacterium tuberculosis, the causative agent of tuberculosis, contributes to the outcomes of infection and public health interventions, such as vaccination. Epidemiological studies suggest that among the phylogeographic lineages of M. tuberculosis, strains belonging to a sublineage of Lineage 2 (mL2) are associated with concerning clinical features, including hypervirulence, treatment failure, and vaccine escape. The global expansion and increasing prevalence of this sublineage has been attributed to the selective advantage conferred by these characteristics, yet confounding host and environmental factors make it difficult to identify the bacterial determinants driving these associations in human studies. Here, we developed a molecular barcoding strategy to facilitate high-throughput, experimental phenotyping of M. tuberculosis clinical isolates. This approach allowed us to characterize growth dynamics for a panel of genetically diverse M. tuberculosis strains during infection and after vaccination in the mouse model. We found that mL2 strains exhibit distinct growth dynamics in vivo and are resistant to the immune protection conferred by Bacillus Calmette-Guerin (BCG) vaccination. The latter finding corroborates epidemiological observations and demonstrates that mycobacterial features contribute to vaccine efficacy. To investigate the genetic and biological basis of mL2 strains’ distinctive phenotypes, we performed variant analysis, transcriptional studies, and genome-wide transposon sequencing. We identified functional genetic changes across multiple stress and host response pathways in a representative mL2 strain that are associated with variants in regulatory genes. These adaptive changes may underlie the distinct clinical characteristics and epidemiological success of this lineage. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a remarkably heterogeneous disease, a feature that complicates clinical care and public health interventions. The contributions of pathogen genetic diversity to this heterogeneity are uncertain, in part due to the challenges of experimentally manipulating M. tuberculosis, a slow-growing, biosafety level 3 organism. To overcome these challenges, we applied a molecular barcoding strategy to a panel of M. tuberculosis clinical isolates. This novel application of barcoding permitted the high-throughput characterization of M. tuberculosis strain growth dynamics and vaccine resistance in the mouse model of infection. Integrating these results with genomic analyses, we uncover bacterial pathways that contribute to infection outcomes, suggesting targets for improved therapeutics and vaccines.
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13
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Shantal CJN, Juan CC, Lizbeth BUS, Carlos HGJ, Estela GPB. Candida glabrata is a successful pathogen: an artist manipulating the immune response. Microbiol Res 2022; 260:127038. [DOI: 10.1016/j.micres.2022.127038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
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14
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Buravchenko GI, Maslov DA, Alam MS, Grammatikova NE, Frolova SG, Vatlin AA, Tian X, Ivanov IV, Bekker OB, Kryakvin MA, Dontsova OA, Danilenko VN, Zhang T, Shchekotikhin AE. Synthesis and Characterization of Novel 2-Acyl-3-trifluoromethylquinoxaline 1,4-Dioxides as Potential Antimicrobial Agents. Pharmaceuticals (Basel) 2022; 15:155. [PMID: 35215268 PMCID: PMC8877263 DOI: 10.3390/ph15020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 01/25/2023] Open
Abstract
The emergence of drug resistance in pathogens leads to a loss of effectiveness of antimicrobials and complicates the treatment of bacterial infections. Quinoxaline 1,4-dioxides represent a prospective scaffold for search of new compounds with improved chemotherapeutic characteristics. Novel 2-acyl-3-trifluoromethylquinoxaline 1,4-dioxides with alteration of substituents at position 2 and 6 were synthesized via nucleophilic substitution with piperazine moiety and evaluated against a broad panel of bacteria and fungi by measuring their minimal inhibitory concentrations. Their mode of action was assessed by whole-genomic sequencing of spontaneous drug-resistant Mycobacterium smegmatis mutants, followed by comparative genomic analysis, and on an original pDualrep2 system. Most of the 2-acyl-3-trifluoromethylquinoxaline 1,4-dioxides showed high antibacterial properties against Gram-positive strains, including mycobacteria, and the introduction of a halogen atom in the position 6 of the quinoxaline ring further increased their activity, with 13c being the most active compound. The mode of action studies confirmed the DNA-damaging nature of the obtained quinoxaline 1,4-dioxides, while drug-resistance may be provided by mutations in redox homeostasis genes, encoding enzymes potentially involved in the activation of the compounds. This study extends views about the antimicrobial and antifungal activities of the quinoxaline 1,4-dioxides and can potentially lead to the discovery of new antibacterial drugs.
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Affiliation(s)
- Galina I. Buravchenko
- Gause Institute of New Antibiotics, 119021 Moscow, Russia; (G.I.B.); (N.E.G.); (I.V.I.)
| | - Dmitry A. Maslov
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (D.A.M.); (S.G.F.); (A.A.V.); (O.B.B.); (V.N.D.)
| | - Md Shah Alam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (M.S.A.); (X.T.); (T.Z.)
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Svetlana G. Frolova
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (D.A.M.); (S.G.F.); (A.A.V.); (O.B.B.); (V.N.D.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Aleksey A. Vatlin
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (D.A.M.); (S.G.F.); (A.A.V.); (O.B.B.); (V.N.D.)
- Institute of Ecology, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (M.S.A.); (X.T.); (T.Z.)
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ivan V. Ivanov
- Gause Institute of New Antibiotics, 119021 Moscow, Russia; (G.I.B.); (N.E.G.); (I.V.I.)
- Organic Chemistry Department, Faculty of Natural Sciences, Mendeleyev University of Chemical Technology, 9 Miusskaya Square, 125190 Moscow, Russia
| | - Olga B. Bekker
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (D.A.M.); (S.G.F.); (A.A.V.); (O.B.B.); (V.N.D.)
| | - Maxim A. Kryakvin
- Chemistry Department, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.A.K.); (O.A.D.)
| | - Olga A. Dontsova
- Chemistry Department, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.A.K.); (O.A.D.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143028 Skolkovo, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Valery N. Danilenko
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (D.A.M.); (S.G.F.); (A.A.V.); (O.B.B.); (V.N.D.)
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (M.S.A.); (X.T.); (T.Z.)
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Jeong H, Kim Y, Lee HS. OsnR is an autoregulatory negative transcription factor controlling redox-dependent stress responses in Corynebacterium glutamicum. Microb Cell Fact 2021; 20:203. [PMID: 34663317 PMCID: PMC8524982 DOI: 10.1186/s12934-021-01693-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/07/2021] [Indexed: 01/11/2023] Open
Abstract
Background Corynebacterium glutamicum is used in the industrial production of amino acids and nucleotides. During the course of fermentation, C. glutamicum cells face various stresses and employ multiple regulatory genes to cope with the oxidative stress. The osnR gene plays a negative regulatory role in redox-dependent oxidative-stress responses, but the underlying mechanism is not known yet. Results Overexpression of the osnR gene in C. glutamicum affected the expression of genes involved in the mycothiol metabolism. ChIP-seq analysis revealed that OsnR binds to the promoter region of multiple genes, including osnR and cg0026, which seems to function in the membrane-associated redox metabolism. Studies on the role of the osnR gene involving in vitro assays employing purified OsnR proteins and in vivo physiological analyses have identified that OsnR inhibits the transcription of its own gene. Further, oxidant diamide stimulates OsnR-binding to the promoter region of the osnR gene. The genes affected by the overexpression of osnR have been found to be under the control of σH. In the osnR-overexpressing strain, the transcription of sigH is significantly decreased and the stimulation of sigH transcription by external stress is lost, suggesting that osnR and sigH form an intimate regulatory network. Conclusions Our study suggests that OsnR not only functions as a transcriptional repressor of its own gene and of those involved in redox-dependent stress responses but also participates in the global transcriptional regulation by controlling the transcription of other master regulators, such as sigH. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01693-1.
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Affiliation(s)
- Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, Chungbuk, Republic of Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea.
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16
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Mycobacterium tuberculosis VapC4 toxin engages small ORFs to initiate an integrated oxidative and copper stress response. Proc Natl Acad Sci U S A 2021; 118:2022136118. [PMID: 34362841 DOI: 10.1073/pnas.2022136118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Mycobacterium tuberculosis (Mtb) VapBC4 toxin-antitoxin system is essential for the establishment of Mtb infection. Using a multitier, systems-level approach, we uncovered the sequential molecular events triggered by the VapC4 toxin that activate a circumscribed set of critical stress survival pathways which undoubtedly underlie Mtb virulence. VapC4 exclusively inactivated the sole transfer RNACys (tRNACys) through cleavage at a single site within the anticodon sequence. Depletion of the pool of tRNACys led to ribosome stalling at Cys codons within actively translating messenger RNAs. Genome mapping of these Cys-stalled ribosomes unexpectedly uncovered several unannotated Cys-containing open reading frames (ORFs). Four of these are small ORFs (sORFs) encoding Cys-rich proteins of fewer than 50 amino acids that function as Cys-responsive attenuators that engage ribosome stalling at tracts of Cys codons to control translation of downstream genes. Thus, VapC4 mimics a state of Cys starvation, which then activates Cys attenuation at sORFs to globally redirect metabolism toward the synthesis of free Cys. The resulting newly enriched pool of Cys feeds into the synthesis of mycothiol, the glutathione counterpart in this pathogen that is responsible for maintaining cellular redox homeostasis during oxidative stress, as well as into a circumscribed subset of cellular pathways that enable cells to defend against oxidative and copper stresses characteristically endured by Mtb within macrophages. Our ability to pinpoint activation or down-regulation of pathways that collectively align with Mtb virulence-associated stress responses and the nonreplicating persistent state brings to light a direct and vital role for the VapC4 toxin in mediating these critical pathways.
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17
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von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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18
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Khan MZ, Singha B, Ali MF, Taunk K, Rapole S, Gourinath S, Nandicoori VK. Redox homeostasis in Mycobacterium tuberculosis is modulated by a novel actinomycete-specific transcription factor. EMBO J 2021; 40:e106111. [PMID: 34018220 PMCID: PMC8280819 DOI: 10.15252/embj.2020106111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved diverse cellular processes in response to the multiple stresses it encounters within the infected host. We explored available TnSeq datasets to identify transcription factors (TFs) that are essential for Mtb survival inside the host. The analysis identified a single TF, Rv1332 (AosR), conserved across actinomycetes with a so‐far uncharacterized function. AosR mitigates phagocyte‐derived oxidative and nitrosative stress, thus promoting mycobacterial growth in the murine lungs and spleen. Oxidative stress induces formation of a single intrasubunit disulphide bond in AosR, which in turn facilitates AosR interaction with an extracytoplasmic‐function sigma factor, SigH. This leads to the specific upregulation of the CysM‐dependent non‐canonical cysteine biosynthesis pathway through an auxiliary intragenic stress‐responsive promoter, an axis critical in detoxifying host‐derived oxidative and nitrosative radicals. Failure to upregulate AosR‐dependent cysteine biosynthesis during the redox stress causes differential expression of 6% of Mtb genes. Our study shows that the AosR‐SigH pathway is critical for detoxifying host‐derived oxidative and nitrosative radicals to enhance Mtb survival in the hostile intracellular environment.
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19
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Todor H, Osadnik H, Campbell EA, Myers KS, Li H, Donohue TJ, Gross CA. Rewiring the specificity of extracytoplasmic function sigma factors. Proc Natl Acad Sci U S A 2020; 117:33496-33506. [PMID: 33318184 PMCID: PMC7776599 DOI: 10.1073/pnas.2020204117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators' DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid-nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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Affiliation(s)
- Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Kevin S Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Hao Li
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Timothy J Donohue
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158
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20
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Abstract
M. tuberculosis infections are responsible for more than 1 million deaths per year. Developing effective strategies to combat this disease requires a greater understanding of M. tuberculosis biology. As in all cells, protein quality control is essential for the viability of M. tuberculosis, which likely faces proteotoxic stress within a host. Here, we identify an M. tuberculosis protein, Ruc, that gains chaperone activity upon oxidation. Ruc represents a previously unrecognized family of redox-regulated chaperones found throughout the bacterial superkingdom. Additionally, we found that oxidized Ruc promotes the protein-folding activity of the essential M. tuberculosis Hsp70 chaperone system. This work contributes to a growing body of evidence that oxidative stress provides a particular strain on cellular protein stability. The bacterial pathogen Mycobacterium tuberculosis is the leading cause of death by an infectious disease among humans. Here, we describe a previously uncharacterized M. tuberculosis protein, Rv0991c, as a molecular chaperone that is activated by oxidation. Rv0991c has homologs in most bacterial lineages and appears to function analogously to the well-characterized Escherichia coli redox-regulated chaperone Hsp33, despite a dissimilar protein sequence. Rv0991c is transcriptionally coregulated with hsp60 and hsp70 chaperone genes in M. tuberculosis, suggesting that Rv0991c functions with these chaperones in maintaining protein quality control. Supporting this hypothesis, we found that, like oxidized Hsp33, oxidized Rv0991c prevents the aggregation of a model unfolded protein in vitro and promotes its refolding by the M. tuberculosis Hsp70 chaperone system. Furthermore, Rv0991c interacts with DnaK and can associate with many other M. tuberculosis proteins. We therefore propose that Rv0991c, which we named “Ruc” (redox-regulated protein with unstructured C terminus), represents a founding member of a new chaperone family that protects M. tuberculosis and other species from proteotoxicity during oxidative stress.
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21
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Barth VC, Woychik NA. The Sole Mycobacterium smegmatis MazF Toxin Targets tRNA Lys to Impart Highly Selective, Codon-Dependent Proteome Reprogramming. Front Genet 2020; 10:1356. [PMID: 32117414 PMCID: PMC7033543 DOI: 10.3389/fgene.2019.01356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/11/2019] [Indexed: 12/02/2022] Open
Abstract
Survival of mycobacteria, both free-living and host-dependent pathogenic species, is dependent on their ability to evade being killed by the stresses they routinely encounter. Toxin-antitoxin (TA) systems are unique to bacteria and archaea and are thought to function as stress survival proteins. Here, we study the activity of the endoribonuclease toxin derived from the MazEF TA system in Mycobacterium smegmatis, designated MazEF-ms. We first enlisted a specialized RNA-seq method, 5’ RNA-seq, to identify the primary RNA target(s) of the MazF-ms toxin. Just two tRNA species, tRNALys-UUU and tRNALys-CUU, were targeted for cleavage by MazF-ms at a single site within their anticodon sequence (UU↓U and CU↓U) to render these tRNAs nonfunctional for protein synthesis. The 5’ RNA-seq dataset also revealed hallmarks of ribosome stalling predominantly at Lys AAA codons even though both Lys tRNAs were cleaved by MazF-ms. Stalled ribosomes were then cleaved on their 5’ side by one or more RNases, resulting in very selective degradation of only those mRNAs harboring ribosomes stalled at Lys codons. This highly surgical, codon-dependent degradation of mRNA transcripts was validated using quantitative mass spectrometry of proteins that were newly synthesized during MazF-ms expression. The M. smegmatis proteome was altered as predicted, Lys AAA codon-rich proteins was downregulated while Lys AAA codon deficient proteins were upregulated. Analysis of specific subsets of proteins that were upregulated or downregulated was consistent with the growth-arrested phenotype of MazF-ms expressing cells. Curiously, the tRNA target and mechanism of action of MazF-ms paralleled that of one atypical MazF toxin in M. tuberculosis, suggesting manipulation of the levels of lysine tRNAs as the preferred conduit for reprogramming the proteomes via ribosome stalling at rare AAA codons in these GC-rich mycobacteria.
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Affiliation(s)
- Valdir Cristovao Barth
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Nancy A Woychik
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
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22
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Müller AU, Imkamp F, Weber-Ban E. The Mycobacterial LexA/RecA-Independent DNA Damage Response Is Controlled by PafBC and the Pup-Proteasome System. Cell Rep 2019; 23:3551-3564. [PMID: 29924998 DOI: 10.1016/j.celrep.2018.05.073] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/16/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
Mycobacteria exhibit two DNA damage response pathways: the LexA/RecA-dependent SOS response and a LexA/RecA-independent pathway. Using a combination of transcriptomics and genome-wide binding site analysis, we demonstrate that PafBC (proteasome accessory factor B and C), encoded in the Pup-proteasome system (PPS) gene locus, is the transcriptional regulator of the predominant LexA/RecA-independent pathway. Comparison of the resulting PafBC regulon with the DNA damage response of Mycobacterium smegmatis reveals that the majority of induced DNA repair genes are upregulated by PafBC. We further demonstrate that RecA, a member of the PafBC regulon and principal regulator of the SOS response, is degraded by the PPS when DNA damage stress has been overcome. Our results suggest a model for the regulation of the mycobacterial DNA damage response that employs the concerted action of PafBC as master transcriptional activator and the PPS for removal of DNA repair proteins to maintain a temporally controlled stress response.
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Affiliation(s)
- Andreas U Müller
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8093 Zurich, Switzerland
| | - Frank Imkamp
- University of Zurich, Institute of Medical Microbiology, 8006 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8093 Zurich, Switzerland.
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23
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Park JH, Lee JH, Roe JH. SigR, a hub of multilayered regulation of redox and antibiotic stress responses. Mol Microbiol 2019; 112:420-431. [PMID: 31269533 DOI: 10.1111/mmi.14341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2019] [Indexed: 02/01/2023]
Abstract
Signal-specific activation of alternative sigma factors redirects RNA polymerase to induce transcription of distinct sets of genes conferring protection against the damage the signal and the related stresses incur. In Streptomyces coelicolor, σR (SigR), a member of ECF12 subfamily of Group IV sigma factors, responds to thiol-perturbing signals such as oxidants and electrophiles, as well as to translation-blocking antibiotics. Oxidants and electrophiles interact with and inactivate the zinc-containing anti-sigma factor, RsrA, via disulfide bond formation or alkylation of reactive cysteines, subsequently releasing σR for target gene induction. Translation-blocking antibiotics induce the synthesis of σR , via the WhiB-like transcription factor, WblC/WhiB7. Signal transduction via RsrA produces a dramatic transient response that involves positive feedback to produce more SigR as an unstable isoform σ R ' and negative feedbacks to degrade σ R ' , and reduce oxidized RsrA that subsequently sequester σR and σ R ' . Antibiotic stress brings about a prolonged response by increasing stable σR levels. The third negative feedback, which occurs via IF3, lowers the translation efficiency of the sigRp1 transcript that utilizes a non-canonical start codon. σR is a global regulator that directly activates > 100 transcription units in S. coelicolor, including genes for thiol homeostasis, protein quality control, sulfur metabolism, ribosome modulation and DNA repair. Close homologues in Actinobacteria, such as σH in Mycobacteria and Corynebacteria, show high conservation of the signal transduction pathways and target genes, thus reflecting the robustness of this type of regulation in response to redox and antibiotic stresses.
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Affiliation(s)
- Joo-Hong Park
- School of Biological Sciences, and Institute of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Ju-Hyung Lee
- School of Biological Sciences, and Institute of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Jung-Hye Roe
- School of Biological Sciences, and Institute of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea
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Zhai W, Wu F, Zhang Y, Fu Y, Liu Z. The Immune Escape Mechanisms of Mycobacterium Tuberculosis. Int J Mol Sci 2019; 20:E340. [PMID: 30650615 PMCID: PMC6359177 DOI: 10.3390/ijms20020340] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 01/15/2023] Open
Abstract
Epidemiological data from the Center of Disease Control (CDC) and the World Health Organization (WHO) statistics in 2017 show that 10.0 million people around the world became sick with tuberculosis. Mycobacterium tuberculosis (MTB) is an intracellular parasite that mainly attacks macrophages and inhibits their apoptosis. It can become a long-term infection in humans, causing a series of pathological changes and clinical manifestations. In this review, we summarize innate immunity including the inhibition of antioxidants, the maturation and acidification of phagolysosomes and especially the apoptosis and autophagy of macrophages. Besides, we also elaborate on the adaptive immune response and the formation of granulomas. A thorough understanding of these escape mechanisms is of major importance for the prevention, diagnosis and treatment of tuberculosis.
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Affiliation(s)
- Weijie Zhai
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, China.
| | - Fengjuan Wu
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, China.
| | - Yiyuan Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang 261053, China.
| | - Yurong Fu
- Department of Medical Microbiology, Weifang Medical University, Weifang 261053, China.
| | - Zhijun Liu
- Department of Medical Microbiology, Weifang Medical University, Weifang 261053, China.
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25
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Mycobacteria and their sweet proteins: An overview of protein glycosylation and lipoglycosylation in M. tuberculosis. Tuberculosis (Edinb) 2019; 115:1-13. [PMID: 30948163 DOI: 10.1016/j.tube.2019.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications represent a key aspect of enzyme and protein regulation and function. Post-translational modifications are involved in signaling and response to stress, adaptation to changing environments, regulation of toxic and damaged proteins, proteins localization and host-pathogen interactions. Glycosylation in Mycobacterium tuberculosis (Mtb), is a post-translational modification often found in conjunction with acylation in mycobacterial proteins. Since the discovery of glycosylated proteins in the early 1980's, important advances in our understanding of the mechanisms of protein glycosylation have been made. The number of known glycosylated substrates in Mtb has grown through the years, yet many questions remain. This review will explore the current knowledge on protein glycosylation in Mtb, causative agent of Tuberculosis and number one infectious killer in the world. The mechanism and significance of this post-translational modification, as well as maturation, export and acylation of glycosylated proteins will be reviewed. We expect to provide the reader with an overall view of protein glycosylation in Mtb, as well as the significance of this post-translational modification to the physiology and host-pathogen interactions of this important pathogen. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011081 and 10.6019/PXD011081.
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Girardin RC, Bai G, He J, Sui H, McDonough KA. AbmR (Rv1265) is a novel transcription factor of Mycobacterium tuberculosis that regulates host cell association and expression of the non-coding small RNA Mcr11. Mol Microbiol 2018; 110:811-830. [PMID: 30207611 PMCID: PMC6282994 DOI: 10.1111/mmi.14126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022]
Abstract
Gene regulatory networks used by Mycobacterium tuberculosis (Mtb) during infection include many genes of unknown function, confounding efforts to determine their roles in Mtb biology. Rv1265 encodes a conserved hypothetical protein that is expressed during infection and in response to elevated levels of cyclic AMP. Here, we report that Rv1265 is a novel auto‐inhibitory ATP‐binding transcription factor that upregulates expression of the small non‐coding RNA Mcr11, and propose that Rv1265 be named ATP‐binding mcr11regulator (AbmR). AbmR directly and specifically bound DNA, as determined by electrophoretic mobility shift assays, and this DNA‐binding activity was enhanced by AbmR’s interaction with ATP. Genetic knockout of abmR in Mtb increased abmR promoter activity and eliminated growth phase‐dependent increases in mcr11 expression during hypoxia. Mutagenesis identified arginine residues in the carboxy terminus that are critical for AbmR’s DNA‐binding activity and gene regulatory function. Limited similarity to other DNA‐ or ATP‐binding domains suggests that AbmR belongs to a novel class of DNA‐ and ATP‐binding proteins. AbmR was also found to form large organized structures in solution and facilitate the serum‐dependent association of Mtb with human lung epithelial cells. These results indicate a potentially complex role for AbmR in Mtb biology.
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Affiliation(s)
- Roxie C Girardin
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Jie He
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Haixin Sui
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
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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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28
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Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress. Sci Rep 2017; 7:1195. [PMID: 28446771 PMCID: PMC5430705 DOI: 10.1038/s41598-017-01179-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/24/2017] [Indexed: 11/16/2022] Open
Abstract
Mycothiol (MSH) is the major low molecular weight (LMW) thiol in Actinomycetes. Here, we used shotgun proteomics, OxICAT and RNA-seq transcriptomics to analyse protein S-mycothiolation, reversible thiol-oxidations and their impact on gene expression in Mycobacterium smegmatis under hypochlorite stress. In total, 58 S-mycothiolated proteins were identified under NaOCl stress that are involved in energy metabolism, fatty acid and mycolic acid biosynthesis, protein translation, redox regulation and detoxification. Protein S-mycothiolation was accompanied by MSH depletion in the thiol-metabolome. Quantification of the redox state of 1098 Cys residues using OxICAT revealed that 381 Cys residues (33.6%) showed >10% increased oxidations under NaOCl stress, which overlapped with 40 S-mycothiolated Cys-peptides. The absence of MSH resulted in a higher basal oxidation level of 338 Cys residues (41.1%). The RseA and RshA anti-sigma factors and the Zur and NrdR repressors were identified as NaOCl-sensitive proteins and their oxidation resulted in an up-regulation of the SigH, SigE, Zur and NrdR regulons in the RNA-seq transcriptome. In conclusion, we show here that NaOCl stress causes widespread thiol-oxidation including protein S-mycothiolation resulting in induction of antioxidant defense mechanisms in M. smegmatis. Our results further reveal that MSH is important to maintain the reduced state of protein thiols.
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29
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Dávila Costa JS, Silva RA, Leichert L, Alvarez HM. Proteome analysis reveals differential expression of proteins involved in triacylglycerol accumulation by Rhodococcus jostii RHA1 after addition of methyl viologen. MICROBIOLOGY-SGM 2017; 163:343-354. [PMID: 28073401 DOI: 10.1099/mic.0.000424] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Rhodococcus jostii RHA1 is able to degrade toxic compounds and accumulate high amounts of triacylglycerols (TAG) upon nitrogen starvation. These NADPH-dependent processes are essential for the adaptation of rhodococci to fluctuating environmental conditions. In this study, we used an MS-based, label-free and quantitative proteomic approach to better understand the integral response of R. jostii RHA1 to the presence of methyl viologen (MV) in relation to the synthesis and accumulation of TAG. The addition of MV promoted a decrease of TAG accumulation in comparison to cells cultivated under nitrogen-limiting conditions in the absence of this pro-oxidant. Proteomic analyses revealed that the abundance of key proteins of fatty acid biosynthesis, the Kennedy pathway, glyceroneogenesis and methylmalonyl-CoA pathway, among others, decreased in the presence of MV. In contrast, some proteins involved in lipolysis and β-oxidation of fatty acids were upregulated. Some metabolic pathways linked to the synthesis of NADPH remained activated during oxidative stress as well as under nitrogen starvation conditions. Additionally, exposure to MV resulted in the activation of complete antioxidant machinery comprising superoxide dismutases, catalases, mycothiol biosynthesis, mycothione reductase and alkyl hydroperoxide reductases, among others. Our study suggests that oxidative stress response affects TAG accumulation under nitrogen-limiting conditions through programmed molecular mechanisms when both stresses occur simultaneously.
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Affiliation(s)
- José Sebastián Dávila Costa
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia (Chubut), Argentina.,Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina
| | - Roxana A Silva
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia (Chubut), Argentina
| | - Lars Leichert
- Ruhr-Universität Bochum, Medizinisches Proteom-Center, Redox Proteomics Group, Bochum, Germany
| | - Héctor M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia (Chubut), Argentina
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30
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Veatch AV, Niu T, Caskey J, McGillivray A, Gautam US, Subramanian R, Kousoulas KG, Mehra S, Kaushal D. Sequencing-relative to hybridization-based transcriptomics approaches better define Mycobacterium tuberculosis stress-response regulons. Tuberculosis (Edinb) 2016; 101S:S9-S17. [PMID: 27729257 DOI: 10.1016/j.tube.2016.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) infections cause tuberculosis (TB), an infectious disease which causes ∼1.5 million deaths annually. The ability of this pathogen to evade, escape and encounter immune surveillance is fueled by its adaptability. Thus, Mtb induces a transition in its transcriptome in response to environmental changes. Global transcriptome profiling has been key to our understanding of how Mtb responds to the different stress conditions it faces during its life cycle. While this was initially achieved using microarray technology, RNAseq is now widely employed. It is important to understand the correlation between the large amount of microarray based transcriptome data, which continues to shape our understanding of Mtb stress networks, and newer data being generated using RNAseq. We assessed how well the two platforms correlate using three well-defined stress conditions: diamide, hypoxia, and re-aeration. The data used here was generated by different individuals over time using distinct samples, providing a stringent test of platform correlation. While correlation between microarrays and sequencing was high upon diamide treatment, which causes a rapid reprogramming of the transcriptome, RNAseq allowed a better definition of the hypoxic response, characterized by subtle changes in the magnitude of gene-expression. RNAseq also allows for the best cross-platform reproducibility.
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Affiliation(s)
- Ashley V Veatch
- Divisions of Bacteriology & Parasitology, Tulane National Primate Research Center, Covington LA, USA; Department of Microbiology & Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Tianhua Niu
- Department of Biostatistics & Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans LA, USA
| | - John Caskey
- Department of Pathobiological Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, USA
| | - Amanda McGillivray
- Divisions of Bacteriology & Parasitology, Tulane National Primate Research Center, Covington LA, USA
| | - Uma Shankar Gautam
- Divisions of Bacteriology & Parasitology, Tulane National Primate Research Center, Covington LA, USA
| | - Ramesh Subramanian
- Department of Pathobiological Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, USA
| | - K Gus Kousoulas
- Department of Pathobiological Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, USA
| | - Smriti Mehra
- Divisions of Microbiology, Tulane National Primate Research Center, Covington LA, USA; Department of Pathobiological Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, USA
| | - Deepak Kaushal
- Divisions of Bacteriology & Parasitology, Tulane National Primate Research Center, Covington LA, USA; Department of Microbiology & Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
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31
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Singh AK, Carette X, Potluri LP, Sharp JD, Xu R, Prisic S, Husson RN. Investigating essential gene function in Mycobacterium tuberculosis using an efficient CRISPR interference system. Nucleic Acids Res 2016; 44:e143. [PMID: 27407107 PMCID: PMC5062980 DOI: 10.1093/nar/gkw625] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/02/2016] [Indexed: 12/23/2022] Open
Abstract
Despite many methodological advances that have facilitated investigation of Mycobacterium tuberculosis pathogenesis, analysis of essential gene function in this slow-growing pathogen remains difficult. Here, we describe an optimized CRISPR-based method to inhibit expression of essential genes based on the inducible expression of an enzymatically inactive Cas9 protein together with gene-specific guide RNAs (CRISPR interference). Using this system to target several essential genes of M. tuberculosis, we achieved marked inhibition of gene expression resulting in growth inhibition, changes in susceptibility to small molecule inhibitors and disruption of normal cell morphology. Analysis of expression of genes containing sequences similar to those targeted by individual guide RNAs did not reveal significant off-target effects. Advantages of this approach include the ability to compare inhibited gene expression to native levels of expression, lack of the need to alter the M. tuberculosis chromosome, the potential to titrate the extent of transcription inhibition, and the ability to avoid off-target effects. Based on the consistent inhibition of transcription and the simple cloning strategy described in this work, CRISPR interference provides an efficient approach to investigate essential gene function that may be particularly useful in characterizing genes of unknown function and potential targets for novel small molecule inhibitors.
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Affiliation(s)
- Atul K Singh
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xavier Carette
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lakshmi-Prasad Potluri
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jared D Sharp
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ranfei Xu
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sladjana Prisic
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Robert N Husson
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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32
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Induction of a stable sigma factor SigR by translation-inhibiting antibiotics confers resistance to antibiotics. Sci Rep 2016; 6:28628. [PMID: 27346454 PMCID: PMC4921905 DOI: 10.1038/srep28628] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
Antibiotic-producing streptomycetes are rich sources of resistance mechanisms against endogenous and exogenous antibiotics. An ECF sigma factor σR (SigR) is known to govern the thiol-oxidative stress response in Streptomyces coelicolor. Amplification of this response is achieved by producing an unstable isoform of σR called σR′. In this work, we present evidence that antibiotics induce the SigR regulon via a redox-independent pathway, leading to antibiotic resistance. The translation-inhibiting antibiotics enhanced the synthesis of stable σR, eliciting a prolonged response. WblC/WhiB7, a WhiB-like DNA-binding protein, is responsible for inducing sigRp1 transcripts encoding the stable σR. The amount of WblC protein and its binding to the sigRp1 promoter in vivo increased upon antibiotic treatment. A similar phenomenon appears to exist in Mycobacterium tuberculosis as well. These findings reveal a novel antibiotic-induced resistance mechanism conserved among actinomycetes, and also give an explicit example of overlap in cellular damage and defense mechanisms between thiol-oxidative and anti- translational stresses.
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