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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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Oh GS, Yoo JS, Park JH, Roe JH. Activity modulation of anti-sigma factor via cysteine alkylation in Actinobacteria. Mol Microbiol 2021; 117:539-550. [PMID: 34927290 DOI: 10.1111/mmi.14868] [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: 09/24/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Abstract
σR (SigR) is an alternative sigma factor that enables gene expression in Streptomyces coelicolor to cope with thiol oxidation and antibiotic stresses. Its activity is repressed by a zinc-containing anti-sigma (ZAS) factor RsrA that senses thiol oxidants and electrophiles. Inactivation of RsrA by disulfide formation has been well studied. Here we investigated another pathway of RsrA inactivation by electrophiles. Mass spectrometry revealed alkylation of RsrA in vivo by N-ethylmaleimide (NEM) at C61 and C62 located in the C-terminal loop. Substitution mutation (C61S/C62S) in RsrA decreased the induction of σR target genes by electrophiles and made cells more sensitive to electrophiles. In contrast to stable protein of oxidized RsrA, alkylated RsrA is subjected to degradation partly mediated by ClpP proteases. RsrA2, a redox-sensitive homolog of RsrA in S. coelicolor lacking cysteine in the terminal loop, did not respond to electrophiles. However, redox-sensitive RsrA homologs in other Actinobacteria also harboring terminal loop cysteines all responded to electrophiles. These results indicate that the activity of RsrA can be modulated via cysteine alkylation, apart from disulfide formation of zinc-coordinating cysteines. This pathway expands the spectrum of signals that the σR -RsrA system can sense and reveals another intricate regulatory layer for optimal survival of Actinobacteria.
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Affiliation(s)
- Gyeong-Seok Oh
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Ji-Sun Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Joo-Hong Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Jung-Hye Roe
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Korea
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3
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Beck C, Gren T, Ortiz-López FJ, Jørgensen TS, Carretero-Molina D, Martín Serrano J, Tormo JR, Oves-Costales D, Kontou EE, Mohite OS, Mingyar E, Stegmann E, Genilloud O, Weber T. Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods. Molecules 2021; 26:6580. [PMID: 34770989 PMCID: PMC8588249 DOI: 10.3390/molecules26216580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that "silent" biosynthetic gene clusters (BGCs) can be activated by heterologously expressing transcriptional regulators from other BGCs. Here, we have activated a silent BGC in Streptomyces sp. CA-256286 by overexpression of a set of SARP family transcriptional regulators. The structure of the produced compound was elucidated by NMR and found to be an N-acetyl cysteine adduct of the pyranonaphtoquinone polyketide 3'-O-α-d-forosaminyl-(+)-griseusin A. Employing a combination of multi-omics and metabolic engineering techniques, we identified the responsible BGC. These methods include genome mining, proteomics and transcriptomics analyses, in combination with CRISPR induced gene inactivations and expression of the BGC in a heterologous host strain. This work demonstrates an easy-to-implement workflow of how silent BGCs can be activated, followed by the identification and characterization of the produced compound, the responsible BGC, and hints of its biosynthetic pathway.
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Affiliation(s)
- Charlotte Beck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Jesús Martín Serrano
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Eftychia E. Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Omkar S. Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Erik Mingyar
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (E.S.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Evi Stegmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (E.S.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
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Montgomery K, Williams TJ, Brettle M, Berengut JF, Zhang E, Zaugg J, Hugenholtz P, Ferrari BC. Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environ Microbiol 2021; 23:4276-4294. [PMID: 34029441 DOI: 10.1111/1462-2920.15610] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022]
Abstract
Candidatus Dormibacterota is an uncultured bacterial phylum found predominantly in soil that is present in high abundances within cold desert soils. Here, we interrogate nine metagenome-assembled genomes (MAGs), including six new MAGs derived from soil metagenomes obtained from two eastern Antarctic sites. Phylogenomic and taxonomic analyses revealed these MAGs represent four genera and five species, representing two order-level clades within Ca. Dormibacterota. Metabolic reconstructions of these MAGs revealed the potential for aerobic metabolism, and versatile adaptations enabling persistence in the 'extreme' Antarctic environment. Primary amongst these adaptations were abilities to scavenge atmospheric H2 and CO as energy sources, as well as using the energy derived from H2 oxidation to fix atmospheric CO2 via the Calvin-Bassham-Benson cycle, using a RuBisCO type IE. We propose that these allow Ca. Dormibacterota to persist using H2 oxidation and grow using atmospheric chemosynthesis in terrestrial Antarctica. Fluorescence in situ hybridization revealed Ca. Dormibacterota to be coccoid cells, 0.3-1.4 μm in diameter, with some cells exhibiting the potential for a symbiotic or syntrophic lifestyle.
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Affiliation(s)
- Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Merryn Brettle
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Eden Zhang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
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Sánchez de la Nieta R, Antoraz S, Alzate JF, Santamaría RI, Díaz M. Antibiotic Production and Antibiotic Resistance: The Two Sides of AbrB1/B2, a Two-Component System of Streptomyces coelicolor. Front Microbiol 2020; 11:587750. [PMID: 33162964 PMCID: PMC7581861 DOI: 10.3389/fmicb.2020.587750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Antibiotic resistance currently presents one of the biggest threats to humans. The development and implementation of strategies against the spread of superbugs is a priority for public health. In addition to raising social awareness, approaches such as the discovery of new antibiotic molecules and the elucidation of resistance mechanisms are common measures. Accordingly, the two-component system (TCS) of Streptomyces coelicolor AbrB1/B2, offer amenable ways to study both antibiotic production and resistance. Global transcriptomic comparisons between the wild-type strain S. coelicolor M145 and the mutant ΔabrB, using RNA-Seq, showed that the AbrB1/B2 TCS is implicated in the regulation of different biological processes associated with stress responses, primary and secondary metabolism, and development and differentiation. The ΔabrB mutant showed the up-regulation of antibiotic biosynthetic gene clusters and the down-regulation of the vancomycin resistance gene cluster, according to the phenotypic observations of increased antibiotic production of actinorhodin and undecylprodigiosin, and greater susceptibility to vancomycin. The role of AbrB1/B2 in vancomycin resistance has also been shown by an in silico analysis, which strongly indicates that AbrB1/B2 is a homolog of VraR/S from Staphylococcus aureus and LiaR/S from Enterococcus faecium/Enterococcus faecalis, both of which are implied in vancomycin resistance in these pathogenic organisms that present a serious threat to public health. The results obtained are interesting from a biotechnological perspective since, on one hand, this TCS is a negative regulator of antibiotic production and its high degree of conservation throughout Streptomyces spp. makes it a valuable tool for improving antibiotic production and the discovery of cryptic metabolites with antibiotic action. On the other hand, AbrB1/B2 contributes to vancomycin resistance and is a homolog of VraR/S and LiaR/S, important regulators in clinically relevant antibiotic-resistant bacteria. Therefore, the study of AbrB1/B2 could provide new insight into the mechanism of this type of resistance.
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Affiliation(s)
- Ricardo Sánchez de la Nieta
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Sergio Antoraz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Ramón I Santamaría
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
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Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. Genes (Basel) 2020; 11:genes11070794. [PMID: 32674507 PMCID: PMC7397307 DOI: 10.3390/genes11070794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a Gram-positive bacterium that causes caseous lymphadenitis, a disease that predominantly affects sheep, goat, cattle, buffalo, and horses, but has also been recognized in other animals. This bacterium generates a severe economic impact on countries producing meat. Gene expression studies using RNA-Seq are one of the most commonly used techniques to perform transcriptional experiments. Computational analysis of such data through reverse-engineering algorithms leads to a better understanding of the genome-wide complexity of gene interactomes, enabling the identification of genes having the most significant functions inferred by the activated stress response pathways. In this study, we identified the influential or causal genes from four RNA-Seq datasets from different stress conditions (high iron, low iron, acid, osmosis, and PH) in C. pseudotuberculosis, using a consensus-based network inference algorithm called miRsigand next identified the causal genes in the network using the miRinfluence tool, which is based on the influence diffusion model. We found that over 50% of the genes identified as influential had some essential cellular functions in the genomes. In the strains analyzed, most of the causal genes had crucial roles or participated in processes associated with the response to extracellular stresses, pathogenicity, membrane components, and essential genes. This research brings new insight into the understanding of virulence and infection by C. pseudotuberculosis.
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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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Ludwig P, Sévin DC, Busche T, Kalinowski J, Bourdeaux F, Grininger M, Mack M. Characterization of the small flavin-binding dodecin in the roseoflavin producer Streptomyces davawensis. MICROBIOLOGY-SGM 2019; 164:908-919. [PMID: 29856311 DOI: 10.1099/mic.0.000662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genes encoding dodecin proteins are present in almost 20 % of archaeal and in more than 50 % of bacterial genomes. Archaeal dodecins bind riboflavin (vitamin B2), are thought to play a role in flavin homeostasis and possibly also help to protect cells from radical or oxygenic stress. Bacterial dodecins were found to bind riboflavin-5'-phosphate (also called flavin mononucleotide or FMN) and coenzyme A, but their physiological function remained unknown. In this study, we set out to investigate the relevance of dodecins for flavin metabolism and oxidative stress management in the phylogenetically related bacteria Streptomyces coelicolor and Streptomyces davawensis. Additionally, we explored the role of dodecins with regard to resistance against the antibiotic roseoflavin, a riboflavin analogue produced by S. davawensis. Our results show that the dodecin of S. davawensis predominantly binds FMN and is neither involved in roseoflavin biosynthesis nor in roseoflavin resistance. In contrast to S. davawensis, growth of S. coelicolor was not reduced in the presence of plumbagin, a compound, which induces oxidative stress. Plumbagin treatment stimulated expression of the dodecin gene in S. davawensis but not in S. coelicolor. Deletion of the dodecin gene in S. davawensis generated a recombinant strain which, in contrast to the wild-type, was fully resistant to plumbagin. Subsequent metabolome analyses revealed that the S. davawensis dodecin deletion strain exhibited a very different stress response when compared to the wild-type indicating that dodecins broadly affect cellular physiology.
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Affiliation(s)
- Petra Ludwig
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Florian Bourdeaux
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
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Anti-σ factor YlaD regulates transcriptional activity of σ factor YlaC and sporulation via manganese-dependent redox-sensing molecular switch in Bacillus subtilis. Biochem J 2018; 475:2127-2151. [PMID: 29760236 DOI: 10.1042/bcj20170911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/29/2018] [Accepted: 05/14/2018] [Indexed: 02/01/2023]
Abstract
YlaD, a membrane-anchored anti-sigma (σ) factor of Bacillus subtilis, contains a HX3CXXC motif that functions as a redox-sensing domain and belongs to one of the zinc (Zn)-co-ordinated anti-σ factor families. Despite previously showing that the YlaC transcription is controlled by YlaD, experimental evidence of how the YlaC-YlaD interaction is affected by active cysteines and/or metal ions is lacking. Here, we showed that the P yla promoter is autoregulated solely by YlaC. Moreover, reduced YlaD contained Zn and iron, while oxidized YlaD did not. Cysteine substitution in YlaD led to changes in its secondary structure; Cys3 had important structural functions in YlaD, and its mutation caused dissociation from YlaC, indicating the essential requirement of a HX3CXXC motif for regulating interactions of YlaC with YlaD. Analyses of the far-UV CD spectrum and metal content revealed that the addition of Mn ions to Zn-YlaD changed its secondary structure and that iron was substituted for manganese (Mn). The ylaC gene expression using βGlu activity from P yla :gusA was observed at the late-exponential and early-stationary phase, and the ylaC-overexpressing mutant constitutively expressed gene transcripts of clpP and sigH, an important alternative σ factor regulated by ClpXP. Collectively, our data demonstrated that YlaD senses redox changes and elicits increase in Mn ion concentrations and that, in turn, YlaD-mediated transcriptional activity of YlaC regulates sporulation initiation under oxidative stress and Mn-substituted conditions by regulating clpP gene transcripts. This is the first report of the involvement of oxidative stress-responsive B. subtilis extracytoplasmic function σ factors during sporulation via a Mn-dependent redox-sensing molecular switch.
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Reyes AM, Pedre B, De Armas MI, Tossounian MA, Radi R, Messens J, Trujillo M. Chemistry and Redox Biology of Mycothiol. Antioxid Redox Signal 2018; 28:487-504. [PMID: 28372502 DOI: 10.1089/ars.2017.7074] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SIGNIFICANCE Mycothiol (MSH, AcCys-GlcN-Ins) is the main low-molecular weight (LMW) thiol of most Actinomycetes, including the human pathogen Mycobacterium tuberculosis that affects millions of people worldwide. Strains with decreased MSH content show increased susceptibilities to hydroperoxides and electrophilic compounds. In M. tuberculosis, MSH modulates the response to several antituberculosis drugs. Enzymatic routes involving MSH could provide clues for specific drug design. Recent Advances: Physicochemical data argue against a rapid, nonenzymatic reaction of MSH with oxidants, disulfides, or electrophiles. Moreover, exposure of the bacteria to high concentrations of two-electron oxidants resulted in protein mycothiolation. The recently described glutaredoxin-like protein mycoredoxin-1 (Mrx-1) provides a route for catalytic reduction of mycothiolated proteins, protecting critical cysteines from irreversible oxidation. The description of MSH/Mrx-1-dependent activities of peroxidases helped to explain the higher susceptibility to oxidants observed in Actinomycetes lacking MSH. Moreover, the first mycothiol-S-transferase, member of the DinB superfamily of proteins, was described. In Corynebacterium, both the MSH/Mrx-1 and the thioredoxin pathways reduce methionine sulfoxide reductase A. A novel tool for in vivo imaging of the MSH/mycothiol disulfide (MSSM) status allows following changes in the mycothiol redox state during macrophage infection and its relationship with antibiotic sensitivity. CRITICAL ISSUES Redundancy of MSH with other LMW thiols is starting to be unraveled and could help to rationalize the differences in the reported importance of MSH synthesis observed in vitro versus in animal infection models. FUTURE DIRECTIONS Future work should be directed to establish the structural bases of the specificity of MSH-dependent enzymes, thus facilitating drug developments. Antioxid. Redox Signal. 28, 487-504.
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Affiliation(s)
- Aníbal M Reyes
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Brandán Pedre
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - María Inés De Armas
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Maria-Armineh Tossounian
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Rafael Radi
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Joris Messens
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Madia Trujillo
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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11
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Translational Control of the SigR-Directed Oxidative Stress Response in Streptomyces via IF3-Mediated Repression of a Noncanonical GTC Start Codon. mBio 2017; 8:mBio.00815-17. [PMID: 28611250 PMCID: PMC5472188 DOI: 10.1128/mbio.00815-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The major oxidative stress response in Streptomyces is controlled by the sigma factor SigR and its cognate antisigma factor RsrA, and SigR activity is tightly controlled through multiple mechanisms at both the transcriptional and posttranslational levels. Here we show that sigR has a highly unusual GTC start codon and that this leads to another level of SigR regulation, in which SigR translation is repressed by translation initiation factor 3 (IF3). Changing the GTC to a canonical start codon causes SigR to be overproduced relative to RsrA, resulting in unregulated and constitutive expression of the SigR regulon. Similarly, introducing IF3* mutations that impair its ability to repress SigR translation has the same effect. Thus, the noncanonical GTC sigR start codon and its repression by IF3 are critical for the correct and proper functioning of the oxidative stress regulatory system. sigR and rsrA are cotranscribed and translationally coupled, and it had therefore been assumed that SigR and RsrA are produced in stoichiometric amounts. Here we show that RsrA can be transcribed and translated independently of SigR, present evidence that RsrA is normally produced in excess of SigR, and describe the factors that determine SigR-RsrA stoichiometry. In all sigma factor-antisigma factor regulatory switches, the relative abundance of the two proteins is critical to the proper functioning of the system. Many sigma-antisigma operons are cotranscribed and translationally coupled, leading to a generic assumption that the sigma and antisigma factors are produced in a fixed 1:1 ratio. In the case of sigR-rsrA, we show instead that the antisigma factor is produced in excess over the sigma factor, providing a buffer to prevent spurious release of sigma activity. This excess arises in part because sigR has an extremely rare noncanonical GTC start codon, and as a result, SigR translation initiation is repressed by IF3. This finding highlights the potential significance of noncanonical start codons, very few of which have been characterized experimentally. It also emphasizes the limitations of predicting start codons using bioinformatic approaches, which rely heavily on the assumption that ATG, GTG, and TTG are the only permissible start codons.
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12
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Ang MLT, Zainul Rahim SZ, de Sessions PF, Lin W, Koh V, Pethe K, Hibberd ML, Alonso S. EthA/R-Independent Killing of Mycobacterium tuberculosis by Ethionamide. Front Microbiol 2017; 8:710. [PMID: 28487681 PMCID: PMC5403819 DOI: 10.3389/fmicb.2017.00710] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
Ethionamide (ETH) is part of the drug arsenal available to treat multi-drug resistant tuberculosis. The current paradigm of this pro-drug activation involves the mycobacterial enzyme EthA and the transcriptional repressor, EthR. However, several lines of evidence suggest the involvement of additional players. The ethA/R locus was deleted in Mycobacterium bovis BCG and three Mycobacterium tuberculosis (MTB) strains. While complete resistance to ETH was observed with BCG ethA/R KO, drug susceptibility and dose-dependent killing were retained in the ethA/R KO MTB mutants, suggesting the existence of an alternative pathway of ETH bio-activation in MTB. We further demonstrated that this alternative pathway is EthR-independent, whereby re-introduction of ethR in ethA/R KO MTB did not lead to increased resistance to ETH. Consistently, ethA KO MTB (with intact ethR expression) displayed similar ETH susceptibility profile as their ethA/R KO counterparts. To identify the alternative ETH bio-activator, spontaneous ETH-resistant mutants were obtained from ethA/R KO MTB and whole genome sequencing identified single nucleotide polymorphisms in mshA, involved in mycothiol biosynthesis and previously linked to ETH resistance. Deletion of mshA in ethA/R KO MTB led to complete ETH resistance, supporting that the role of MshA in ETH killing is EthA/R-independent. Furthermore mshA single KO MTB displayed levels of ETH resistance similar or greater than those obtained with ethA/R KO strains, supporting that mshA is as critical as ethA/R for ETH killing efficacy.
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Affiliation(s)
- Michelle L T Ang
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | - Siti Z Zainul Rahim
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | | | - Wenwei Lin
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | - Vanessa Koh
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | - Kevin Pethe
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
| | - Martin L Hibberd
- Genome Institute of SingaporeSingapore, Singapore.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical MedicineLondon, UK
| | - Sylvie Alonso
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
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13
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The Arsenic Detoxification System in Corynebacteria: Basis and Application for Bioremediation and Redox Control. ADVANCES IN APPLIED MICROBIOLOGY 2017; 99:103-137. [PMID: 28438267 DOI: 10.1016/bs.aambs.2017.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Arsenic (As) is widespread in the environment and highly toxic. It has been released by volcanic and anthropogenic activities and causes serious health problems worldwide. To survive arsenic-rich environments, soil and saprophytic microorganisms have developed molecular detoxification mechanisms to survive arsenic-rich environments, mainly by the enzymatic conversion of inorganic arsenate (AsV) to arsenite (AsIII) by arsenate reductases, which is then extruded by arsenite permeases. One of these Gram-positive bacteria, Corynebacterium glutamicum, the workhorse of biotechnological research, is also resistant to arsenic. To sanitize contaminated soils and waters, C. glutamicum strains were modified to work as arsenic "biocontainers." Two chromosomally encoded ars operons (ars1 and ars2) are responsible for As resistance. The genes within these operons encode for metalloregulatory proteins (ArsR1/R2), arsenite permeases (Acr3-1/-2), and arsenate reductases (ArsC1/C2/C1'). ArsC1/C2 arsenate reductases are coupled to the low molecular weight thiol mycothiol (MSH) and to the recently discovered mycoredoxin-1 (Mrx-1) present in most Actinobacteria. This MSH/Mrx-1 redox system protects cells against different forms of stress, including reactive oxygen species (ROS), metals, and antibiotics. ROS can modify functional sulfur cysteines by oxidizing the thiol (-SH) to a sulfenic acid (-SOH). These oxidation-sensitive protein cysteine thiols are redox regulated by the MSH/Mrx-1 couple in Corynebacterium and Mycobacterium. In summary, the molecular mechanisms involved in arsenic resistance system in C. glutamicum have paved the way for understanding the cellular response against oxidative stress in Actinobacteria.
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14
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Lee KL, Yoo JS, Oh GS, Singh AK, Roe JH. Simultaneous Activation of Iron- and Thiol-Based Sensor-Regulator Systems by Redox-Active Compounds. Front Microbiol 2017; 8:139. [PMID: 28210250 PMCID: PMC5288332 DOI: 10.3389/fmicb.2017.00139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/19/2017] [Indexed: 12/21/2022] Open
Abstract
Bacteria in natural habitats are exposed to myriad redox-active compounds (RACs), which include producers of reactive oxygen species (ROS) and reactive electrophile species (RES) that alkylate or oxidize thiols. RACs can induce oxidative stress in cells and activate response pathways by modulating the activity of sensitive regulators. However, the effect of a certain compound on the cell has been investigated primarily with respect to a specific regulatory pathway. Since a single compound can exert multiple chemical effects in the cell, its effect can be better understood by time-course monitoring of multiple sensitive regulatory pathways that the compound induces. We investigated the effect of representative RACs by monitoring the activity of three sensor-regulators in the model actinobacterium Streptomyces coelicolor; SoxR that senses reactive compounds directly through oxidation of its [2Fe–2S] cluster, CatR/PerR that senses peroxides through bound iron, and an anti-sigma factor RsrA that senses RES via disulfide formation. The time course and magnitude of induction of their target transcripts were monitored to predict the chemical activities of each compound in S. coelicolor. Phenazine methosulfate (PMS) was found to be an effective RAC that directly activated SoxR and an effective ROS-producer that induced CatR/PerR with little thiol-perturbing activity. p-Benzoquinone was an effective RAC that directly activated SoxR, with slower ROS-producing activity, and an effective RES that induced the RsrA-SigR system. Plumbagin was an effective RAC that activated SoxR, an effective ROS-producer, and a less agile but effective RES. Diamide was an RES that effectively formed disulfides and a weak RAC that activated SoxR. Monobromobimane was a moderately effective RES and a slow producer of ROS. Interestingly, benzoquinone induced the SigR system by forming adducts on cysteine thiols in RsrA, revealing a new pathway to modulate RsrA activity. Overall, this study showed that multiple chemical activities of a reactive compound can be conveniently monitored in vivo by examining the temporal response of multiple sensitive regulators in the cell to reveal novel activities of the chemicals.
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Affiliation(s)
- Kang-Lok Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University Seoul, South Korea
| | - Ji-Sun Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University Seoul, South Korea
| | - Gyeong-Seok Oh
- School of Biological Sciences and Institute of Microbiology, Seoul National University Seoul, South Korea
| | - Atul K Singh
- School of Biological Sciences and Institute of Microbiology, Seoul National University Seoul, South Korea
| | - Jung-Hye Roe
- School of Biological Sciences and Institute of Microbiology, Seoul National University Seoul, South Korea
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15
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Busche T, Winkler A, Wedderhoff I, Rückert C, Kalinowski J, Ortiz de Orué Lucana D. Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes. PLoS One 2016; 11:e0159873. [PMID: 27541358 PMCID: PMC4991794 DOI: 10.1371/journal.pone.0159873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022] Open
Abstract
The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress. Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. Amongst others, the results show an up-regulated transcription of genes for biosynthesis of cysteine and vitamin B12, transport of methionine and vitamin B12, and DNA synthesis and repair. Simultaneously, transcription of genes for degradation of an anti-oxidant compound is down-regulated in a HbpSc-SenSc-SenRc-dependent manner. It appears that HbpSc-SenSc-SenRc controls the non-enzymatic response of Streptomyces coelicolor A3(2) to counteract the hazardous effects of oxidative stress. Binding of the response regulator SenRc to regulatory regions of some of the studied genes indicates that the regulation is direct. The results additionally suggest that HbpSc-SenSc-SenRc may act in concert with other regulatory modules such as a transcriptional regulator, a two-component system and the Streptomyces B12 riboswitch. The transcriptomics data, together with our previous in vitro results, enable a profound characterization of the HbpS-SenS-SenR system from streptomycetes. Since homologues to HbpS-SenS-SenR are widespread in different actinobacteria with ecological and medical relevance, the data presented here will serve as a basis to elucidate the biological role of these homologues.
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Affiliation(s)
- Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Ina Wedderhoff
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Darío Ortiz de Orué Lucana
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
- * E-mail:
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16
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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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17
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Hillion M, Antelmann H. Thiol-based redox switches in prokaryotes. Biol Chem 2016; 396:415-44. [PMID: 25720121 DOI: 10.1515/hsz-2015-0102] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/05/2015] [Indexed: 12/12/2022]
Abstract
Bacteria encounter reactive oxygen species (ROS) as a consequence of the aerobic life or as an oxidative burst of activated neutrophils during infections. In addition, bacteria are exposed to other redox-active compounds, including hypochloric acid (HOCl) and reactive electrophilic species (RES) such as quinones and aldehydes. These reactive species often target the thiol groups of cysteines in proteins and lead to thiol-disulfide switches in redox-sensing regulators to activate specific detoxification pathways and to restore the redox balance. Here, we review bacterial thiol-based redox sensors that specifically sense ROS, RES and HOCl via thiol-based mechanisms and regulate gene transcription in Gram-positive model bacteria and in human pathogens, such as Staphylococcus aureus and Mycobacterium tuberculosis. We also pay particular attention to emerging widely conserved HOCl-specific redox regulators that have been recently characterized in Escherichia coli. Different mechanisms are used to sense and respond to ROS, RES and HOCl by 1-Cys-type and 2-Cys-type thiol-based redox sensors that include versatile thiol-disulfide switches (OxyR, OhrR, HypR, YodB, NemR, RclR, Spx, RsrA/RshA) or alternative Cys phosphorylations (SarZ, MgrA, SarA), thiol-S-alkylation (QsrR), His-oxidation (PerR) and methionine oxidation (HypT). In pathogenic bacteria, these redox-sensing regulators are often important virulence regulators and required for adapation to the host immune defense.
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18
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Netto LES, de Oliveira MA, Tairum CA, da Silva Neto JF. Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions. Free Radic Res 2016; 50:206-45. [DOI: 10.3109/10715762.2015.1120864] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Loi VV, Rossius M, Antelmann H. Redox regulation by reversible protein S-thiolation in bacteria. Front Microbiol 2015; 6:187. [PMID: 25852656 PMCID: PMC4360819 DOI: 10.3389/fmicb.2015.00187] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/20/2015] [Indexed: 12/31/2022] Open
Abstract
Low molecular weight (LMW) thiols function as thiol-redox buffers to maintain the reduced state of the cytoplasm. The best studied LMW thiol is the tripeptide glutathione (GSH) present in all eukaryotes and Gram-negative bacteria. Firmicutes bacteria, including Bacillus and Staphylococcus species utilize the redox buffer bacillithiol (BSH) while Actinomycetes produce the related redox buffer mycothiol (MSH). In eukaryotes, proteins are post-translationally modified to S-glutathionylated proteins under conditions of oxidative stress. S-glutathionylation has emerged as major redox-regulatory mechanism in eukaryotes and protects active site cysteine residues against overoxidation to sulfonic acids. First studies identified S-glutathionylated proteins also in Gram-negative bacteria. Advances in mass spectrometry have further facilitated the identification of protein S-bacillithiolations and S-mycothiolation as BSH- and MSH-mixed protein disulfides formed under oxidative stress in Firmicutes and Actinomycetes, respectively. In Bacillus subtilis, protein S-bacillithiolation controls the activities of the redox-sensing OhrR repressor and the methionine synthase MetE in vivo. In Corynebacterium glutamicum, protein S-mycothiolation was more widespread and affected the functions of the maltodextrin phosphorylase MalP and thiol peroxidase (Tpx). In addition, novel bacilliredoxins (Brx) and mycoredoxins (Mrx1) were shown to function similar to glutaredoxins in the reduction of BSH- and MSH-mixed protein disulfides. Here we review the current knowledge about the functions of the bacterial thiol-redox buffers glutathione, bacillithiol, and mycothiol and the role of protein S-thiolation in redox regulation and thiol protection in model and pathogenic bacteria.
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Affiliation(s)
- Vu Van Loi
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald Greifswald, Germany
| | - Martina Rossius
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald Greifswald, Germany
| | - Haike Antelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald Greifswald, Germany
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20
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Taguchi T, Maruyama T, Sawa R, Igarashi M, Okamoto S, Ichinose K. Structure and biosynthetic implication of 5R-(N-acetyl-L-cysteinyl)-14S-hydroxy-dihydrokalafungin from a mutant of the actVA-ORF4 gene for actinorhodin biosynthesis in Streptomyces coelicolor A3(2). J Antibiot (Tokyo) 2015; 68:481-3. [DOI: 10.1038/ja.2015.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 12/19/2014] [Accepted: 01/22/2015] [Indexed: 11/09/2022]
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21
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Si M, Long M, Chaudhry MT, Xu Y, Zhang P, Zhang L, Shen X. Functional characterization of Corynebacterium glutamicum mycothiol S-conjugate amidase. PLoS One 2014; 9:e115075. [PMID: 25514023 PMCID: PMC4267739 DOI: 10.1371/journal.pone.0115075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 11/18/2014] [Indexed: 11/18/2022] Open
Abstract
The present study focuses on the genetic and biochemical characterization of mycothiol S-conjugate amidase (Mca) of Corynebacterium glutamicum. Recombinant C. glutamicum Mca was heterologously expressed in Escherichia coli and purified to apparent homogeneity. The molecular weight of native Mca protein determined by gel filtration chromatography was 35 kDa, indicating that Mca exists as monomers in the purification condition. Mca showed amidase activity with mycothiol S-conjugate of monobromobimane (MSmB) in vivo while mca mutant lost the ability to cleave MSmB. In addition, Mca showed limited deacetylase activity with N-acetyl-D-glucosamine (GlcNAc) as substrate. Optimum pH for amidase activity was between 7.5 and 8.5, while the highest activity in the presence of Zn2+ confirmed Mca as a zinc metalloprotein. Amino acid residues conserved among Mca family members were located in C. glutamicum Mca and site-directed mutagenesis of these residues indicated that Asp14, Tyr137, His139 and Asp141 were important for activity. The mca deletion mutant showed decreased resistance to antibiotics, alkylating agents, oxidants and heavy metals, and these sensitive phenotypes were recovered in the complementary strain to a great extent. The physiological roles of Mca in resistance to various toxins were further supported by the induced expression of Mca in C. glutamicum under various stress conditions, directly under the control of the stress-responsive extracytoplasmic function-sigma (ECF-σ) factor SigH.
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Affiliation(s)
- Meiru Si
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingxiu Long
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Muhammad Tausif Chaudhry
- Environmental Analytical Laboratory, National Physical & Standards Laboratory, PCSIR, Islamabad, Pakistan
| | - Yixiang Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Pan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
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22
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Expanding the regulatory network governed by the extracytoplasmic function sigma factor σH in Corynebacterium glutamicum. J Bacteriol 2014; 197:483-96. [PMID: 25404703 DOI: 10.1128/jb.02248-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extracytoplasmic function sigma factor σ(H) is responsible for the heat and oxidative stress response in Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, previous transcriptome analyses have not been able to discriminate between direct and indirect targets of σ(H). Here, we determined the direct genome-wide targets of σ(H) using chromatin immunoprecipitation with microarray technology (ChIP-chip) for analysis of a deletion mutant of rshA, encoding an anti-σ factor of σ(H). Seventy-five σ(H)-dependent promoters, including 39 new ones, were identified. σ(H)-dependent, heat-inducible transcripts for several of the new targets, including ilvD encoding a labile Fe-S cluster enzyme, dihydroxy-acid dehydratase, were detected, and their 5' ends were mapped to the σ(H)-dependent promoters identified. Interestingly, functional internal σ(H)-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin and affected expression of Zn-responsive genes, possibly through intracellular Zn overload, indicating new physiological roles of σ(H). Furthermore, sigA encoding the primary σ factor was identified as a new target of σ(H). Reporter assays demonstrated that the σ(H)-dependent promoter upstream of sigA was highly heat inducible but much weaker than the known σ(A)-dependent one. Our ChIP-chip analysis also detected the σ(H)-dependent promoters upstream of rshA within the sigH-rshA operon and of sigB encoding a group 2 σ factor, supporting the previous findings of their σ(H)-dependent expression. Taken together, these results reveal an additional layer of the sigma factor regulatory network in C. glutamicum.
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23
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Recent advances in biochemistry and biotechnological synthesis of avermectins and their derivatives. Appl Microbiol Biotechnol 2014; 98:7747-59. [DOI: 10.1007/s00253-014-5926-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/29/2014] [Accepted: 07/01/2014] [Indexed: 10/24/2022]
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24
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Albesa-Jové D, Chiarelli LR, Makarov V, Pasca MR, Urresti S, Mori G, Salina E, Vocat A, Comino N, Mohorko E, Ryabova S, Pfieiffer B, Lopes Ribeiro ALDJ, Rodrigo-Unzueta A, Tersa M, Zanoni G, Buroni S, Altmann KH, Hartkoorn RC, Glockshuber R, Cole ST, Riccardi G, Guerin ME. Rv2466c mediates the activation of TP053 to kill replicating and non-replicating Mycobacterium tuberculosis. ACS Chem Biol 2014; 9:1567-75. [PMID: 24877756 DOI: 10.1021/cb500149m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The emergence of multidrug- and extensively drug-resistant strains of Mycobacterium tuberculosis highlights the need to discover new antitubercular agents. Here we describe the synthesis and characterization of a new series of thienopyrimidine (TP) compounds that kill both replicating and non-replicating M. tuberculosis. The strategy to determine the mechanism of action of these TP derivatives was to generate resistant mutants to the most effective compound TP053 and to isolate the genetic mutation responsible for this phenotype. The only non-synonymous mutation found was a g83c transition in the Rv2466c gene, resulting in the replacement of tryptophan 28 by a serine. The Rv2466c overexpression increased the sensitivity of M. tuberculosis wild-type and resistant mutant strains to TP053, indicating that TP053 is a prodrug activated by Rv2466c. Biochemical studies performed with purified Rv2466c demonstrated that only the reduced form of Rv2466c can activate TP053. The 1.7 Å resolution crystal structure of the reduced form of Rv2466c, a protein whose expression is transcriptionally regulated during the oxidative stress response, revealed a unique homodimer in which a β-strand is swapped between the thioredoxin domains of each subunit. A pronounced groove harboring the unusual active-site motif CPWC might account for the uncommon reactivity profile of the protein. The mutation of Trp28Ser clearly predicts structural defects in the thioredoxin fold, including the destabilization of the dimerization core and the CPWC motif, likely impairing the activity of Rv2466c against TP053. Altogether our experimental data provide insights into the molecular mechanism underlying the anti-mycobacterial activity of TP-based compounds, paving the way for future drug development programmes.
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Affiliation(s)
- David Albesa-Jové
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Laurent R. Chiarelli
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- A.
N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Maria Rosalia Pasca
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Saioa Urresti
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Giorgia Mori
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Elena Salina
- A.
N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Anthony Vocat
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Natalia Comino
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Elisabeth Mohorko
- Institute
of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Svetlana Ryabova
- A.
N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Bernhard Pfieiffer
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical
Sciences, ETH Zürich, HCI H405, Wolfgang-Pauli Str. 10, CH-8093 Zürich, Switzerland
| | | | - Ane Rodrigo-Unzueta
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Montse Tersa
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - Giuseppe Zanoni
- Department
of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Silvia Buroni
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical
Sciences, ETH Zürich, HCI H405, Wolfgang-Pauli Str. 10, CH-8093 Zürich, Switzerland
| | - Ruben C. Hartkoorn
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Rudi Glockshuber
- Institute
of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Stewart T. Cole
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
| | - Giovanna Riccardi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Marcelo E. Guerin
- Unidad
de Biofísica,
Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad
del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Leioa, Bizkaia 48940, Spain
- Departamento
de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
- IKERBASQUE, Basque
Foundation for Science, 48011 Bilbao, Spain
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Abstract
ABSTRACT
During infection,
Mycobacterium tuberculosis
is exposed to a diverse array of microenvironments in the human host, each with its own unique set of redox conditions. Imbalances in the redox environment of the bacillus or the host environment serve as stimuli, which could regulate virulence. The ability of
M. tuberculosis
to evade the host immune response and cause disease is largely owing to the capacity of the mycobacterium to sense changes in its environment, such as host-generated gases, carbon sources, and pathological conditions, and alter its metabolism and redox balance accordingly for survival. In this article we discuss the redox sensors that are, to date, known to be present in
M. tuberculosis
, such as the Dos dormancy regulon, WhiB family, anti-σ factors, and MosR, in addition to the strategies present in the bacillus to neutralize free radicals, such as superoxide dismutases, catalase-peroxidase, thioredoxins, and methionine sulfoxide reductases, among others.
M. tuberculosis
is peculiar in that it appears to have a hierarchy of redox buffers, namely, mycothiol and ergothioneine. We discuss the current knowledge of their biosynthesis, function, and regulation. Ergothioneine is still an enigma, although it appears to have distinct and overlapping functions with mycothiol, which enable it to protect against a wide range of toxic metabolites and free radicals generated by the host. Developing approaches to quantify the intracellular redox status of the mycobacterium will enable us to determine how the redox balance is altered in response to signals and environments that mimic those encountered in the host.
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Wei ZH, Chen H, Zhang C, Ye BC. FRET-based system for probing protein-protein interactions between σR and RsrA from Streptomyces coelicolor in response to the redox environment. PLoS One 2014; 9:e92330. [PMID: 24651617 PMCID: PMC3961337 DOI: 10.1371/journal.pone.0092330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 02/21/2014] [Indexed: 11/26/2022] Open
Abstract
Protein-protein interactions between sigma factor σ(R) and its corresponding zinc-binding anti-sigma (ZAS) protein RsrA trigger the thioredoxin system for maintaining cellular redox homeostasis in S. coelicolor. RsrA bound to zinc associates with σ(R), inhibiting its transcriptional activity in a reducing environment. During disulfide stress it forms intramolecular disulfide bonds, leading to zinc release and dissociation from σ(R), which initiates transcription to produce reductase and thioredoxin. We designed a fluorescence resonance energy transfer (FRET) based system for monitoring protein-protein interactions between σ(R) and RsrA to further understand how this redox switch regulates the thioredoxin system in S. coelicolor in response to its redox environment, especially various reactive oxygen species (ROS) derived from different metabolic pathways, and clarify the different response mechanisms between Zn-RsrA and apo-RsrA. By the use of the FRET approach described here, we showed that zinc protected thiols in RsrA and causes the σ(R)-RsrA complex to form a more compact structure. This system was also utilized to detect changes in redox status induced by ROS and diamide in real time in E. coli cells.
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Affiliation(s)
- Zi-Han Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huan Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Chi BK, Busche T, Van Laer K, Bäsell K, Becher D, Clermont L, Seibold GM, Persicke M, Kalinowski J, Messens J, Antelmann H. Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress. Antioxid Redox Signal 2014; 20:589-605. [PMID: 23886307 PMCID: PMC3901351 DOI: 10.1089/ars.2013.5423] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
AIMS Protein S-bacillithiolation was recently discovered as important thiol protection and redox-switch mechanism in response to hypochlorite stress in Firmicutes bacteria. Here we used transcriptomics to analyze the NaOCl stress response in the mycothiol (MSH)-producing Corynebacterium glutamicum. We further applied thiol-redox proteomics and mass spectrometry (MS) to identify protein S-mycothiolation. RESULTS Transcriptomics revealed the strong upregulation of the disulfide stress σ(H) regulon by NaOCl stress in C. glutamicum, including genes for the anti sigma factor (rshA), the thioredoxin and MSH pathways (trxB1, trxC, cg1375, trxB, mshC, mca, mtr) that maintain the redox balance. We identified 25 S-mycothiolated proteins in NaOCl-treated cells by liquid chromatography-tandem mass spectrometry (LC-MS/MS), including 16 proteins that are reversibly oxidized by NaOCl in the thiol-redox proteome. The S-mycothiolome includes the methionine synthase (MetE), the maltodextrin phosphorylase (MalP), the myoinositol-1-phosphate synthase (Ino1), enzymes for the biosynthesis of nucleotides (GuaB1, GuaB2, PurL, NadC), and thiamine (ThiD), translation proteins (TufA, PheT, RpsF, RplM, RpsM, RpsC), and antioxidant enzymes (Tpx, Gpx, MsrA). We further show that S-mycothiolation of the thiol peroxidase (Tpx) affects its peroxiredoxin activity in vitro that can be restored by mycoredoxin1. LC-MS/MS analysis further identified 8 proteins with S-cysteinylations in the mshC mutant suggesting that cysteine can be used for S-thiolations in the absence of MSH. INNOVATION AND CONCLUSION We identified widespread protein S-mycothiolations in the MSH-producing C. glutamicum and demonstrate that S-mycothiolation reversibly affects the peroxidase activity of Tpx. Interestingly, many targets are conserved S-thiolated across bacillithiol- and MSH-producing bacteria, which could become future drug targets in related pathogenic Gram-positives.
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Affiliation(s)
- Bui Khanh Chi
- 1 Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald , Greifswald, Germany
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28
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Hernick M. Mycothiol: a target for potentiation of rifampin and other antibiotics againstMycobacterium tuberculosis. Expert Rev Anti Infect Ther 2014; 11:49-67. [DOI: 10.1586/eri.12.152] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Strakova E, Zikova A, Vohradsky J. Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote. Nucleic Acids Res 2013; 42:748-63. [PMID: 24157841 PMCID: PMC3902916 DOI: 10.1093/nar/gkt917] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A computational model of gene expression was applied to a novel test set of microarray time series measurements to reveal regulatory interactions between transcriptional regulators represented by 45 sigma factors and the genes expressed during germination of a prokaryote Streptomyces coelicolor. Using microarrays, the first 5.5 h of the process was recorded in 13 time points, which provided a database of gene expression time series on genome-wide scale. The computational modeling of the kinetic relations between the sigma factors, individual genes and genes clustered according to the similarity of their expression kinetics identified kinetically plausible sigma factor-controlled networks. Using genome sequence annotations, functional groups of genes that were predominantly controlled by specific sigma factors were identified. Using external binding data complementing the modeling approach, specific genes involved in the control of the studied process were identified and their function suggested.
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Affiliation(s)
- Eva Strakova
- Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
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30
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Gaballa A, Antelmann H, Hamilton CJ, Helmann JD. Regulation of Bacillus subtilis bacillithiol biosynthesis operons by Spx. MICROBIOLOGY-SGM 2013; 159:2025-2035. [PMID: 23894131 DOI: 10.1099/mic.0.070482-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bacillithiol is the major low molecular mass thiol produced by many firmicutes bacteria, including the model organism Bacillus subtilis and pathogens such as Bacillus anthracis and Staphylococcus aureus. We have previously shown that four genes (bshA, bshB1, bshB2 and bshC) are involved in bacillithiol biosynthesis. Here, we report that these four genes are encoded within three, unlinked operons all expressed from canonical σ(A)-dependent promoters as determined by 5'RACE (rapid amplification of cDNA ends). The bshA and bshB1 genes are embedded within a seven-gene operon additionally including mgsA, encoding methylglyoxal synthase, and the essential genes cca and birA, encoding tRNA nucleotidyltransferase (CCA transferase) and biotin-protein ligase, respectively. The bshB2 gene is co-transcribed with unknown function genes, while bshC is expressed both as part of a two-gene operon (with the upstream putative pantothenate biosynthesis gene ylbQ) and from its own promoter. All three operons are expressed at a reduced level in an spx null mutant, consistent with a direct role of Spx as a transcriptional activator for these operons, and all three operons are induced by the thiol oxidant diamide. In contrast with other Spx-regulated genes characterized to date, the effects of Spx on basal expression and diamide-stimulated expression appear to be independent of Cys10 in the redox centre of Spx. Consistent with the role of Spx as an activator of bacillithiol biosynthetic genes, cellular levels of bacillithiol are reduced several-fold in an spx null mutant.
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Affiliation(s)
- Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Haike Antelmann
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487 Greifswald, Germany
| | - Chris J Hamilton
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
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31
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Comparative proteomic analysis of Streptomyces lividans Wild-Type and ppk mutant strains reveals the importance of storage lipids for antibiotic biosynthesis. Appl Environ Microbiol 2013; 79:5907-17. [PMID: 23872561 DOI: 10.1128/aem.02280-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Streptomyces lividans TK24 is a strain that naturally produces antibiotics at low levels, but dramatic overproduction of antibiotics occurs upon interruption of the ppk gene. However, the role of the Ppk enzyme in relation to the regulation of antibiotic biosynthesis remains poorly understood. In order to gain a better understanding of the phenotype of the ppk mutant, the proteomes of the wild-type (wt) and ppk mutant strains, grown for 96 h on R2YE medium limited in phosphate, were analyzed. Intracellular proteins were separated on two-dimensional (2D) gels, spots were quantified, and those showing a 3-fold variation or more were identified by mass spectrometry. The expression of 12 proteins increased and that of 29 decreased in the ppk mutant strain. Our results suggested that storage lipid degradation rather than hexose catabolism was taking place in the mutant. In order to validate this hypothesis, the triacylglycerol contents of the wt and ppk mutant strains of S. lividans as well as that of Streptomyces coelicolor M145, a strain that produces antibiotics at high levels and is closely related to S. lividans, were assessed using electron microscopy and thin-layer chromatography. These studies highlighted the large difference in triacylglycerol contents of the three strains and confirmed the hypothetical link between storage lipid metabolism and antibiotic biosynthesis in Streptomyces.
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32
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Liu YB, Long MX, Yin YJ, Si MR, Zhang L, Lu ZQ, Wang Y, Shen XH. Physiological roles of mycothiol in detoxification and tolerance to multiple poisonous chemicals in Corynebacterium glutamicum. Arch Microbiol 2013; 195:419-29. [PMID: 23615850 DOI: 10.1007/s00203-013-0889-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 03/31/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
Abstract
Mycothiol (MSH) plays important roles in maintaining cytosolic redox homeostasis and in adapting to reactive oxygen species in the high-(G + C)-content Gram-positive Actinobacteria. However, its physiological roles are ill defined compared to glutathione, the functional analog of MSH in Gram-negative bacteria and most eukaryotes. In this research, we explored the impact of intracellular MSH on cellular physiology by using MSH-deficient mutants in the model organism Corynebacterium glutamicum. We found that intracellular MSH contributes significantly to resistance to alkylating agents, glyphosate, ethanol, antibiotics, heavy metals and aromatic compounds. In addition, intracellular MSH is beneficial for withstanding oxidative stress induced by various oxidants in C. glutamicum. This study greatly expanded our current knowledge on the physiological functions of mycothiol in C. glutamicum and could be applied to improve the robustness of this scientifically and commercially important species in the future.
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Affiliation(s)
- Ying-Bao Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi, People's Republic of China
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33
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Paritala H, Carroll KS. New targets and inhibitors of mycobacterial sulfur metabolism. Infect Disord Drug Targets 2013; 13:85-115. [PMID: 23808874 PMCID: PMC4332622 DOI: 10.2174/18715265113139990022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022]
Abstract
The identification of new antibacterial targets is urgently needed to address multidrug resistant and latent tuberculosis infection. Sulfur metabolic pathways are essential for survival and the expression of virulence in many pathogenic bacteria, including Mycobacterium tuberculosis. In addition, microbial sulfur metabolic pathways are largely absent in humans and therefore, represent unique targets for therapeutic intervention. In this review, we summarize our current understanding of the enzymes associated with the production of sulfated and reduced sulfur-containing metabolites in Mycobacteria. Small molecule inhibitors of these catalysts represent valuable chemical tools that can be used to investigate the role of sulfur metabolism throughout the Mycobacterial lifecycle and may also represent new leads for drug development. In this light, we also summarize recent progress made in the development of inhibitors of sulfur metabolism enzymes.
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Affiliation(s)
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, 33458, USA
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34
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Taguchi T, Yabe M, Odaki H, Shinozaki M, Metsä-Ketelä M, Arai T, Okamoto S, Ichinose K. Biosynthetic Conclusions from the Functional Dissection of Oxygenases for Biosynthesis of Actinorhodin and Related Streptomyces Antibiotics. ACTA ACUST UNITED AC 2013; 20:510-20. [DOI: 10.1016/j.chembiol.2013.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/25/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
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35
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Otani H, Higo A, Nanamiya H, Horinouchi S, Ohnishi Y. An alternative sigma factor governs the principal sigma factor inStreptomyces griseus. Mol Microbiol 2013; 87:1223-36. [DOI: 10.1111/mmi.12160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroshi Otani
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo; 113-8657; Japan
| | - Akiyoshi Higo
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo; 113-8657; Japan
| | - Hideaki Nanamiya
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo; 113-8657; Japan
| | - Sueharu Horinouchi
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo; 113-8657; Japan
| | - Yasuo Ohnishi
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo; 113-8657; Japan
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36
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Abstract
SIGNIFICANCE The reactivity of the thiol in the side chain of cysteines is exploited by bacterial regulatory proteins that sense and respond to reactive oxygen and nitrogen species. RECENT ADVANCES Charged residues and helix dipoles diminish the pKa of redox active cysteines, resulting in a thiolate that is stabilized by neighboring polar amino acids. The reaction of peroxides with thiolates generates a sulfenic acid (-SOH) intermediate that often gives rise to a reversible disulfide bond. Peroxide-induced intramolecular and intermolecular disulfides and intermolecular mixed disulfides modulate the signaling activity of members of the LysR/OxyR, MarR/OhrR, and RsrA family of transcriptional regulators. Thiol-dependent regulators also help bacteria resist the nitrosative and nitroxidative stress. -SOHs, mixed disulfides, and S-nitrosothiols are some of the post-translational modifications induced by nitrogen oxides in the thiol groups of OxyR and SsrB bacterial regulatory proteins. Sulfenylation, disulfide bond formation, S-thiolation, and S-nitrosylation are reversible modifications amenable to feedback regulation by antioxidant and antinitrosative repair systems. The structural and functional changes engaged in the thiol-dependent sensing of reactive species have been adopted by several regulators to foster bacterial virulence during exposure to products of NADPH phagocyte oxidase and inducible nitric oxide synthase. CRITICAL ISSUES Investigations with LysR/OxyR, MarR/OhrR, and RsrA family members have helped in an understanding of the mechanisms by which thiols in regulatory proteins react with reactive species, thereby activating antioxidant and antinitrosative gene expression. FUTURE DIRECTIONS To define the determinants that provide selectivity of redox active thiolates for some reactive species but not others is an important challenge for future investigations.
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Affiliation(s)
- Andrés Vázquez-Torres
- Department of Microbiology, University of Colorado Denver School of Medicine, Aurora, Colorado, USA.
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37
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Analysis of the organic hydroperoxide response of Chromobacterium violaceum reveals that OhrR is a cys-based redox sensor regulated by thioredoxin. PLoS One 2012; 7:e47090. [PMID: 23071722 PMCID: PMC3469484 DOI: 10.1371/journal.pone.0047090] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 09/10/2012] [Indexed: 12/17/2022] Open
Abstract
Organic hydroperoxides are oxidants generated during bacterial-host interactions. Here, we demonstrate that the peroxidase OhrA and its negative regulator OhrR comprise a major pathway for sensing and detoxifying organic hydroperoxides in the opportunistic pathogen Chromobacterium violaceum. Initially, we found that an ohrA mutant was hypersensitive to organic hydroperoxides and that it displayed a low efficiency for decomposing these molecules. Expression of ohrA and ohrR was specifically induced by organic hydroperoxides. These genes were expressed as monocistronic transcripts and also as a bicistronic ohrR-ohrA mRNA, generating the abundantly detected ohrA mRNA and the barely detected ohrR transcript. The bicistronic transcript appears to be processed. OhrR repressed both the ohrA and ohrR genes by binding directly to inverted repeat sequences within their promoters in a redox-dependent manner. Site-directed mutagenesis of each of the four OhrR cysteine residues indicated that the conserved Cys21 is critical to organic hydroperoxide sensing, whereas Cys126 is required for disulfide bond formation. Taken together, these phenotypic, genetic and biochemical data indicate that the response of C. violaceum to organic hydroperoxides is mediated by OhrA and OhrR. Finally, we demonstrated that oxidized OhrR, inactivated by intermolecular disulfide bond formation, is specifically regenerated via thiol-disulfide exchange by thioredoxin (but not other thiol reducing agents such as glutaredoxin, glutathione and lipoamide), providing a physiological reducing system for this thiol-based redox switch.
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Antelmann H, Hamilton CJ. Bacterial mechanisms of reversible protein S-thiolation: structural and mechanistic insights into mycoredoxins. Mol Microbiol 2012; 86:759-64. [PMID: 22998128 DOI: 10.1111/mmi.12031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
Mycobacteria produce millimolar concentrations of mycothiol (MSH) as their major low molecular weight thiol redox buffer. MSH-deficient mutants display increased sensitivity towards reactive oxygen, nitrogen and electrophilic species as well as alkylating agents and antibiotics. MSH is maintained in its reduced thiol state by the NADPH-dependent mycothiol disulphide reductase (Mtr). However, the redoxin that uses the MSH/Mtr/NADPH pathway for reduction of MSH-mixed protein disulphides, formed during oxidative stress, has long remained unknown. In this issue, Van Laer et al. report that MSH provides the reducing power for mycoredoxin-1 (Mrx1) in reduction of synthetic MSH-mixed disulphides. The reduced (dithiol) and oxidized (disulphide) solution structures of Mrx1 have been solved by nuclear magnetic resonance (NMR) spectroscopy. NMR time course experiments have also demonstrated the transient S-mycothiolation of the active site Cys14 of oxidized Mrx1 during reduction by the MSH/Mtr/NADPH electron pathway. The paper opens a new era of research to identify S-mycothiolated Mrx1 substrates and the function of MSH in redox regulation and virulence in Mycobacterium tuberculosis.
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Affiliation(s)
- Haike Antelmann
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, D-17487, Greifswald, Germany.
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Busche T, Silar R, Pičmanová M, Pátek M, Kalinowski J. Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum. BMC Genomics 2012; 13:445. [PMID: 22943411 PMCID: PMC3489674 DOI: 10.1186/1471-2164-13-445] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 08/22/2012] [Indexed: 02/02/2023] Open
Abstract
Background The expression of genes in Corynebacterium glutamicum, a Gram-positive non-pathogenic bacterium used mainly for the industrial production of amino acids, is regulated by seven different sigma factors of RNA polymerase, including the stress-responsive ECF-sigma factor SigH. The sigH gene is located in a gene cluster together with the rshA gene, putatively encoding an anti-sigma factor. The aim of this study was to analyze the transcriptional regulation of the sigH and rshA gene cluster and the effects of RshA on the SigH regulon, in order to refine the model describing the role of SigH and RshA during stress response. Results Transcription analyses revealed that the sigH gene and rshA gene are cotranscribed from four sigH housekeeping promoters in C. glutamicum. In addition, a SigH-controlled rshA promoter was found to only drive the transcription of the rshA gene. To test the role of the putative anti-sigma factor gene rshA under normal growth conditions, a C. glutamicum rshA deletion strain was constructed and used for genome-wide transcription profiling with DNA microarrays. In total, 83 genes organized in 61 putative transcriptional units, including those previously detected using sigH mutant strains, exhibited increased transcript levels in the rshA deletion mutant compared to its parental strain. The genes encoding proteins related to disulphide stress response, heat stress proteins, components of the SOS-response to DNA damage and proteasome components were the most markedly upregulated gene groups. Altogether six SigH-dependent promoters upstream of the identified genes were determined by primer extension and a refined consensus promoter consisting of 45 original promoter sequences was constructed. Conclusions The rshA gene codes for an anti-sigma factor controlling the function of the stress-responsive sigma factor SigH in C. glutamicum. Transcription of rshA from a SigH-dependent promoter may serve to quickly shutdown the SigH-dependent stress response after the cells have overcome the stress condition. Here we propose a model of the regulation of oxidative and heat stress response including redox homeostasis by SigH, RshA and the thioredoxin system.
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Affiliation(s)
- Tobias Busche
- Centrum für Biotechnologie, Universität Bielefeld, 33594, Bielefeld, Germany
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Kim MS, Dufour YS, Yoo JS, Cho YB, Park JH, Nam GB, Kim HM, Lee KL, Donohue TJ, Roe JH. Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes. Mol Microbiol 2012; 85:326-44. [PMID: 22651816 DOI: 10.1111/j.1365-2958.2012.08115.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Numerous thiol-reactive compounds cause oxidative stress where cells counteract by activation of survival strategies regulated by thiol-based sensors. In Streptomyces coelicolor, a model actinomycete, a sigma/antisigma pair SigR/RsrA controls the response to thiol-oxidative stress. To unravel its full physiological functions, chromatin immuno-precipitation combined with sequence and transcript analyses were employed to identify 108 SigR target genes in S. coelicolor and to predict orthologous regulons across actinomycetes. In addition to reported genes for thiol homeostasis, protein degradation and ribosome modulation, 64 additional operons were identified suggesting new functions of this global regulator. We demonstrate that SigR maintains the level and activity of the housekeeping sigma factor HrdB during thiol-oxidative stress, a novel strategy for stress responses. We also found that SigR defends cells against UV and thiol-reactive damages, in which repair UvrA takes a part. Using a refined SigR-binding sequence model, SigR orthologues and their targets were predicted in 42 actinomycetes. This revealed a conserved core set of SigR targets to function for thiol homeostasis, protein quality control, possible modulation of transcription and translation, flavin-mediated redox reactions, and Fe-S delivery. The composition of the SigR regulon reveals a robust conserved physiological mechanism to deal with thiol-oxidative stress from bacteria to human.
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Affiliation(s)
- Min-Sik Kim
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
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Bibb MJ, Domonkos A, Chandra G, Buttner MJ. Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σ(BldN) and a cognate anti-sigma factor, RsbN. Mol Microbiol 2012; 84:1033-49. [PMID: 22582857 DOI: 10.1111/j.1365-2958.2012.08070.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chaplin and rodlin proteins together constitute the major components of the hydrophobic sheath that coats the aerial hyphae and spores in Streptomyces, and mutants lacking the chaplins are unable to erect aerial hyphae and differentiate on minimal media. We have gained insight into the developmental regulation of the chaplin (chp) and rodlin (rdl) genes by exploiting a new model species, Streptomyces venezuelae, which sporulates in liquid culture. Using microarrays, the chaplin and rodlin genes were found to be highly induced during submerged sporulation in a bldN-dependent manner. Using σ(BldN) ChIP-chip, we show that this dependence arises because the chaplin and rodlin genes are direct biochemical targets of σ(BldN) . sven3186 (here named rsbN for regulator of sigma BldN), the gene lying immediately downstream of bldN, was also identified as a target of σ(BldN) . Disruption of rsbN causes precocious sporulation and biochemical experiments demonstrate that RsbN functions as a σ(BldN) -specific anti-sigma factor.
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Affiliation(s)
- Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
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Zhang G, Tian Y, Hu K, Zhu Y, Chater KF, Feng C, Liu G, Tan H. Importance and regulation of inositol biosynthesis during growth and differentiation of Streptomyces. Mol Microbiol 2012; 83:1178-94. [PMID: 22329904 DOI: 10.1111/j.1365-2958.2012.08000.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Unusually among bacteria, actinobacteria possess myo-inositol 1-phosphate synthase (mIPS). In the developmentally complex Streptomyces coelicolor, the mIPS-encoding gene (inoA) is cotranscribed with a putative regulatory gene (inoR). The inoRA transcript was more abundant in an inoR in-frame deletion mutant, and InoR formed different complexes in vitro with an extensive region around the inoRA promoter. Binding was relieved by adding glucose 6-phosphate. Thus, InoR is a metabolite-sensitive autorepressor that influences inoA expression, and hence the level of inositol, by controlling transcription from P(inoRA) . Disruption of inoA resulted in inositol-dependent growth and development, with full phenotypic correction at 0.1 mM inositol: at lower inositol concentrations differentiation was arrested at intermediate stages. This pattern may partly reflect increased demand for membrane phospholipids during sporulation septation. A corresponding sharp upregulation of inoRA transcription coincident with sporulation was dependent on a developmental regulator, WhiI. A truncated form of WhiI could bind two sites downstream of P(inoRA) , and one of the WhiI-binding sites overlapped the InoR-binding site. The combined action of a metabolic regulator and a developmental regulator at the simple P(inoRA) promoter is a previously undescribed strategy for the differential provision of developmentally appropriate levels of a substance required during the formation of spore chains.
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Affiliation(s)
- Guohua Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Trivedi A, Singh N, Bhat SA, Gupta P, Kumar A. Redox biology of tuberculosis pathogenesis. Adv Microb Physiol 2012; 60:263-324. [PMID: 22633061 DOI: 10.1016/b978-0-12-398264-3.00004-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most successful human pathogens. Mtb is persistently exposed to numerous oxidoreductive stresses during its pathogenic cycle of infection and transmission. The distinctive ability of Mtb, not only to survive the redox stress manifested by the host but also to use it for synchronizing the metabolic pathways and expression of virulence factors, is central to its success as a pathogen. This review describes the paradigmatic redox and hypoxia sensors employed by Mtb to continuously monitor variations in the intracellular redox state and the surrounding microenvironment. Two component proteins, namely, DosS and DosT, are employed by Mtb to sense changes in oxygen, nitric oxide, and carbon monoxide levels, while WhiB3 and anti-sigma factor RsrA are used to monitor changes in intracellular redox state. Using these and other unidentified redox sensors, Mtb orchestrates its metabolic pathways to survive in nutrient-deficient, acidic, oxidative, nitrosative, and hypoxic environments inside granulomas or infectious lesions. A number of these metabolic pathways are unique to mycobacteria and thus represent potential drug targets. In addition, Mtb employs versatile machinery of the mycothiol and thioredoxin systems to ensure a reductive intracellular environment for optimal functioning of its proteins even upon exposure to oxidative stress. Mtb also utilizes a battery of protective enzymes, such as superoxide dismutase (SOD), catalase (KatG), alkyl hydroperoxidase (AhpC), and peroxiredoxins, to neutralize the redox stress generated by the host immune system. This chapter reviews the current understanding of mechanisms employed by Mtb to sense and neutralize redox stress and their importance in TB pathogenesis and drug development.
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Manteca A, Ye J, Sánchez J, Jensen ON. Phosphoproteome analysis of Streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation. J Proteome Res 2011; 10:5481-92. [PMID: 21999169 DOI: 10.1021/pr200762y] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomycetes are bacterial species that undergo a complex developmental cycle that includes programmed cell death (PCD) events and sporulation. They are widely used in biotechnology because they produce most clinically relevant secondary metabolites. Although Streptomyces coelicolor is one of the bacteria encoding the largest number of eukaryotic type kinases, the biological role of protein phosphorylation in this bacterium has not been extensively studied before. In this issue, the variations of the phosphoproteome of S. coelicolor were characterized. Most distinct Ser/Thr/Tyr phosphorylation events were detected during the presporulation and sporulation stages (80%). Most of these phosphorylations were not reported before in Streptomyces, and included sporulation factors, transcriptional regulators, protein kinases and other regulatory proteins. Several of the identified phosphorylated proteins, FtsZ, DivIVA, and FtsH2, were previously demonstrated to be involved in the sporulation process. We thus established for the first time the widespread occurrence and dynamic features of Ser/Thr/Tyr protein phosphorylation in a bacteria species and also revealed a previously unrecognized phosphorylation motif "x(pT)xEx".
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Affiliation(s)
- Angel Manteca
- Area de Microbiologia, Departamento de Biologia Funcional and IUBA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain.
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Abstract
Mycobacterium tuberculosis (Mtb) has evolved into a highly successful human pathogen. It deftly subverts the bactericidal mechanisms of alveolar macrophages, ultimately inducing granuloma formation and establishing long-term residence in the host. These hallmarks of Mtb infection are facilitated by the metabolic adaptation of the pathogen to its surrounding environment and the biosynthesis of molecules that mediate its interactions with host immune cells. The sulfate assimilation pathway of Mtb produces a number of sulfur-containing metabolites with important contributions to pathogenesis and survival. This pathway is regulated by diverse environmental cues and regulatory proteins that mediate sulfur transactions in the cell. Here, we discuss the transcriptional and biochemical mechanisms of sulfur metabolism regulation in Mtb and potential small molecule regulators of the sulfate assimilation pathway that are collectively poised to aid this intracellular pathogen in its expert manipulation of the host. From this global analysis, we have identified a subset of sulfur-metabolizing enzymes that are sensitive to multiple regulatory cues and may be strong candidates for therapeutic intervention.
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Affiliation(s)
- Stavroula K. Hatzios
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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Inactivation of the extracytoplasmic function sigma factor Sig6 stimulates avermectin production in Streptomyces avermitilis. Biotechnol Lett 2011; 33:1955-61. [PMID: 21691838 DOI: 10.1007/s10529-011-0673-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
The role of the extracytoplasmic function (ECF) σ factor Sig6 (SAV663) in avermectin production by Streptomyces avermitilis was investigated by gene-deletion, complementation and over-expression experiments. Inactivation of Sig6 had no major effect on growth, stress responses, or morphology. Avermectin yield was increased 2- to 2.7-fold (~680 μg/ml) relative to the wild-type strain by deletion of the sig6 gene, and was restored to the wild-type level by introduction of a single copy of sig6. Introduction of extra multi-copy or integrative sig6 vectors into the wild-type decreased avermectin yield by 56-63%. Taken together, these findings indicate that Sig6 plays a negative regulatory role in avermectin production in S. avermitilis. RT-PCR analysis demonstrated that this role of Sig6 is mediated by the pathway-specific activator gene aveR.
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Jung YG, Cho YB, Kim MS, Yoo JS, Hong SH, Roe JH. Determinants of redox sensitivity in RsrA, a zinc-containing anti-sigma factor for regulating thiol oxidative stress response. Nucleic Acids Res 2011; 39:7586-97. [PMID: 21685450 PMCID: PMC3177212 DOI: 10.1093/nar/gkr477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Various environmental oxidative stresses are sensed by redox-sensitive regulators through cysteine thiol oxidation or modification. A few zinc-containing anti-sigma (ZAS) factors in actinomycetes have been reported to respond sensitively to thiol oxidation, among which RsrA from Streptomyces coelicolor is best characterized. It forms disulfide bonds upon oxidation and releases bound SigR to activate thiol oxidative stress response genes. Even though numerous ZAS proteins exist in bacteria, features that confer redox sensitivity to a subset of these have been uncharacterized. In this study, we identified seven additional redox-sensitive ZAS factors from actinomycetes. Comparison with redox-insensitive ZAS revealed characteristic sequence patterns. Domain swapping demonstrated the significance of the region K33FEHH37FEEC41SPC44LEK47 that encompass the conserved HX3CX2C (HCC) motif. Mutational effect of each residue on diamide responsive induction of SigR target genes in vivo demonstrated that several residues, especially those that flank two cysteines (E39, E40, L45, E46), contribute to redox sensitivity. These residues are well conserved among redox-sensitive ZAS factors, and hence are proposed as redox-determinants in sensitive ZAS. H37A, C41A, C44A and F38A mutations, in contrast, compromised SigR-binding activity significantly, apparently affecting structural integrity of RsrA. The residue pattern around HCC motif could therefore serve as an indicator to predict redox-sensitive ZAS factors from sequence information.
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Affiliation(s)
- Yong-Gyun Jung
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Korea
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Sanssouci E, Lerat S, Grondin G, Shareck F, Beaulieu C. tdd8: a TerD domain-encoding gene involved in Streptomyces coelicolor differentiation. Antonie van Leeuwenhoek 2011; 100:385-98. [PMID: 21638113 DOI: 10.1007/s10482-011-9593-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/20/2011] [Indexed: 10/18/2022]
Abstract
The Streptomyces coelicolor genome contains 17 TerD domain-encoding genes (tdd genes) of unknown function. The proteins encoded by these genes have been presumed to be involved in tellurite resistance on the basis of their homology with the protein TerD of Serratia marcescens. To elucidate the role of a Tdd protein (Tdd8), both a deletion mutant for the corresponding gene tdd8 (SCO2368) and a recombinant strain over-expressing tdd8 were produced in S. coelicolor M145. The deletion mutant (Δtdd8), like the wild strain, was not resistant to potassium tellurite. The deletion was not lethal but had a marked effect on differentiation. The deletion strain showed more rapid growth in liquid medium and produced long chains of short spores with a dense and non-spherical spore wall on agar plates. The strain over-expressing tdd8 had a growth delay in liquid medium and produced very few spores of irregular shapes and sizes on solid medium. The results of this study demonstrated that Tdd proteins might have a function other than tellurite resistance and this function seems to be of crucial importance for the proper development of the actinomycete S. coelicolor.
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Affiliation(s)
- Edith Sanssouci
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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Abstract
Cysteine is notable among the universal, proteinogenic amino acids for its facile redox chemistry. Cysteine thiolates are readily modified by reactive oxygen species (ROS), reactive electrophilic species (RES), and reactive nitrogen species (RNS). Although thiol switches are commonly triggered by disulfide bond formation, they can also be controlled by S-thiolation, S-alkylation, or modification by RNS. Thiol-based switches are common in both prokaryotic and eukaryotic organisms and activate functions that detoxify reactive species and restore thiol homeostasis while repressing functions that would be deleterious if expressed under oxidizing conditions. Here, we provide an overview of the best-understood examples of thiol-based redox switches that affect gene expression. Intra- or intermolecular disulfide bond formation serves as a direct regulatory switch for several bacterial transcription factors (OxyR, OhrR/2-Cys, Spx, YodB, CrtJ, and CprK) and indirectly regulates others (the RsrA anti-σ factor and RegB sensory histidine kinase). In eukaryotes, thiol-based switches control the yeast Yap1p transcription factor, the Nrf2/Keap1 electrophile and oxidative stress response, and the Chlamydomonas NAB1 translational repressor. Collectively, these regulators reveal a remarkable range of chemical modifications exploited by Cys residues to effect changes in gene expression.
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Affiliation(s)
- Haike Antelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany.
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