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Guiza Beltran D, Wan T, Zhang L. WhiB-like proteins: Diversity of structure, function and mechanism. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119787. [PMID: 38879133 DOI: 10.1016/j.bbamcr.2024.119787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/20/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
The WhiB-Like (Wbl) proteins are a large family of iron-sulfur (Fe-S) cluster-containing transcription factors exclusively found in the phylum Actinobacteria, including the notable genera like Mycobacteria, Streptomycetes and Corynebacteria. These proteins play pivotal roles in diverse biological processes, such as cell development, redox stress response and antibiotic resistance. Members of the Wbl family exhibit remarkable diversity in their sequences, structures and functions, attracting great attention since their first discovery. This review highlights the most recent breakthroughs in understanding the structural and mechanistic aspects of Wbl-dependent transcriptional regulation.
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Affiliation(s)
- Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA
| | - Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA
| | - LiMei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA.
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2
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Bernard C, Liu Y, Larrouy-Maumus G, Guilhot C, Cam K, Chalut C. Altered serine metabolism promotes drug tolerance in Mycobacterium abscessus via a WhiB7-mediated adaptive stress response. Antimicrob Agents Chemother 2024:e0145623. [PMID: 38651855 DOI: 10.1128/aac.01456-23] [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: 11/07/2023] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Mycobacterium abscessus is an emerging opportunistic pathogen responsible for chronic lung diseases, especially in patients with cystic fibrosis. Treatment failure of M. abscessus infections is primarily associated with intrinsic or acquired antibiotic resistance. However, there is growing evidence that antibiotic tolerance, i.e., the ability of bacteria to transiently survive exposure to bactericidal antibiotics through physiological adaptations, contributes to the relapse of chronic infections and the emergence of acquired drug resistance. Yet, our understanding of the molecular mechanisms that underlie antibiotic tolerance in M. abscessus remains limited. In the present work, a mutant with increased cross-tolerance to the first- and second-line antibiotics cefoxitin and moxifloxacin, respectively, has been isolated by experimental evolution. This mutant harbors a mutation in serB2, a gene involved in L-serine biosynthesis. Metabolic changes caused by this mutation alter the intracellular redox balance to a more reduced state that induces overexpression of the transcriptional regulator WhiB7 during the stationary phase, promoting tolerance through activation of a WhiB7-dependant adaptive stress response. These findings suggest that alteration of amino acid metabolism and, more generally, conditions that trigger whiB7 overexpression, makes M. abscessus more tolerant to antibiotic treatment.
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Affiliation(s)
- Célia Bernard
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Yi Liu
- Faculty of Natural Sciences, Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Gérald Larrouy-Maumus
- Faculty of Natural Sciences, Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Kaymeuang Cam
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
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3
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Williams MT, Yee E, Larson GW, Apiche EA, Rama Damodaran A, Bhagi-Damodaran A. Metalloprotein enabled redox signal transduction in microbes. Curr Opin Chem Biol 2023; 76:102331. [PMID: 37311385 PMCID: PMC10524656 DOI: 10.1016/j.cbpa.2023.102331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
Microbes utilize numerous metal cofactor-containing proteins to recognize and respond to constantly fluctuating redox stresses in their environment. Gaining an understanding of how these metalloproteins sense redox events, and how they communicate such information downstream to DNA to modulate microbial metabolism, is a topic of great interest to both chemists and biologists. In this article, we review recently characterized examples of metalloprotein sensors, focusing on the coordination and oxidation state of the metals involved, how these metals are able to recognize redox stimuli, and how the signal is transmitted beyond the metal center. We discuss specific examples of iron, nickel, and manganese-based microbial sensors, and identify gaps in knowledge in the field of metalloprotein-based signal transduction pathways.
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Affiliation(s)
- Murphi T Williams
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Eaindra Yee
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Grant W Larson
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Elizabeth A Apiche
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota Twin Cities, 207 Pleasant St. SE, Minneapolis MN 55414, USA.
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4
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Davies-Bolorunduro OF, Jaemsai B, Ruangchai W, Phumiphanjarphak W, Aiewsakun P, Palittapongarnpim P. Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations. Sci Rep 2023; 13:13324. [PMID: 37587174 PMCID: PMC10432532 DOI: 10.1038/s41598-023-40152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023] Open
Abstract
Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding sequences of whiB7 of over 40,000 diverse Mtb isolates. Our results unveil the dominant c.191delG (Gly64delG) mutation, present in all members of the lineage L1.2.2 and its impact on WhiB7's conserved GVWGG-motif, causing conformational changes and deletion of the C-terminal AT-hook. Excitingly, we discovered six unique mutations associated with partial or total deletion of the AT-hook, specific to certain sublineages. Our findings suggest the selective pressures driving these mutations, underlining the potential of genomics to advance our understanding of Mtb's antibiotic resistance. As tuberculosis remains a global health threat, our study offers valuable insights into the diverse nature and functional consequences of whiB7 mutations, paving the way for the development of novel therapeutic interventions.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Center for Tuberculosis Research, Microbiology Department, Nigerian Institute of Medical Research, 6 Edmund Crescent, P.M.B 2013, Yaba, 101012, Lagos, Nigeria
| | - Bharkbhoom Jaemsai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
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5
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Wan T, Horová M, Khetrapal V, Li S, Jones C, Schacht A, Sun X, Zhang L. Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis. J Biol Chem 2023; 299:104777. [PMID: 37142222 PMCID: PMC10245118 DOI: 10.1016/j.jbc.2023.104777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) WhiB3 is an iron-sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σA4) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σA4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σA4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σA4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σA4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Vimmy Khetrapal
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Camden Jones
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Andrew Schacht
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - LiMei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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6
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Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA. Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB. Proc Natl Acad Sci U S A 2023; 120:e2220785120. [PMID: 36888660 PMCID: PMC10243135 DOI: 10.1073/pnas.2220785120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/26/2023] [Indexed: 03/09/2023] Open
Abstract
Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as Mycobacterium tuberculosis. The WhiA/B regulons and binding sites have been elucidated in Streptomyces venezuelae (Sven), where they coordinate to activate sporulation septation. However, how these factors cooperate at the molecular level is not understood. Here we present cryoelectron microscopy structures of Sven transcriptional regulatory complexes comprising RNA polymerase (RNAP) σA-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. These structures reveal that WhiB binds to domain 4 of σA (σA4) of the σA-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σA4 housekeeping σ-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduces or abolishes developmental cell division in Sven, confirming their significance. Finally, we compare the architecture of the WhiA/B σA-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation.
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Affiliation(s)
- Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Alexandra K. Marti
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - David A. Widdick
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, UK
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Steven Koh
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
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7
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Singha B, Behera D, Khan MZ, Singh NK, Sowpati DT, Gopal B, Nandicoori VK. The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein. J Biol Chem 2023; 299:102933. [PMID: 36690275 PMCID: PMC10011835 DOI: 10.1016/j.jbc.2023.102933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
SigA (σA) is an essential protein and the primary sigma factor in Mycobacterium tuberculosis (Mtb). However, due to the absence of genetic tools, our understanding of the role and regulation of σA activity and its molecular attributes that help modulate Mtb survival is scant. Here, we generated a conditional gene replacement of σA in Mtb and showed that its depletion results in a severe survival defect in vitro, ex vivo, and in vivo in a murine infection model. Our RNA-seq analysis suggests that σA either directly or indirectly regulates ∼57% of the Mtb transcriptome, including ∼28% of essential genes. Surprisingly, we note that despite having ∼64% similarity with σA, overexpression of the primary-like σ factor SigB (σB) fails to compensate for the absence of σA, suggesting minimal functional redundancy. RNA-seq analysis of the Mtb σB deletion mutant revealed that 433 genes are regulated by σB, of which 283 overlap with the σA transcriptome. Additionally, surface plasmon resonance, in vitro transcription, and functional complementation experiments reveal that σA residues between 132-179 that are disordered and missing from all experimentally determined σA-RNAP structural models are imperative for σA function. Moreover, phosphorylation of σA in the intrinsically disordered N-terminal region plays a regulatory role in modulating its activity. Collectively, these observations and analysis provide a rationale for the centrality of σA for the survival and pathogenicity of this bacillus.
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Affiliation(s)
- Biplab Singha
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Debashree Behera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | | | | | - Vinay Kumar Nandicoori
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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8
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Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis. INORGANICS 2022. [DOI: 10.3390/inorganics10100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.
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9
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Li H, Yuan J, Duan S, Pang Y. Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics. WIREs Mech Dis 2022; 14:e1573. [PMID: 35753313 DOI: 10.1002/wsbm.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinfeng Yuan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shujuan Duan
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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10
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A Feedback Regulatory Loop Containing McdR and WhiB2 Controls Cell Division and DNA Repair in Mycobacteria. mBio 2022; 13:e0334321. [PMID: 35357209 PMCID: PMC9040748 DOI: 10.1128/mbio.03343-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell division must be coordinated with DNA repair, which is strictly regulated in response to different drugs and environmental stresses in bacteria. However, the mechanisms by which mycobacteria orchestrate these two processes remain largely uncharacterized. Here, we report a regulatory loop between two essential mycobacterial regulators, McdR (Rv1830) and WhiB2, in coordinating the processes of cell division and DNA repair. McdR inhibits cell division-associated whiB2 expression by binding to the AATnACAnnnnTGTnATT motif in the promoter region. Furthermore, McdR overexpression simultaneously activates imuAB and dnaE2 expression to promote error-prone DNA repair, which facilitates genetic adaptation to stress conditions. Through a feedback mechanism, WhiB2 activates mcdR expression by binding to the cGACACGc motif in the promoter region. Importantly, analyses of mutations in clinical Mycobacterium tuberculosis strains indicate that disruption of this McdR-WhiB2 feedback regulatory loop influences expression of both cell growth- and DNA repair-associated genes, which further supports the contribution of McdR-WhiB2 regulatory loop in regulating mycobacterial cell growth and drug resistance. This highly conserved feedback regulatory loop provides fresh insight into the link between mycobacterial cell growth control and stress responses. IMPORTANCE Drug-resistant M. tuberculosis poses a threat to the control and prevention of tuberculosis (TB) worldwide. Thus, there is a need to identify the mechanisms enabling M. tuberculosis to adapt and grow under drug-induced stress. Rv1830 has been shown to be associated with drug resistance in M. tuberculosis, but its mechanisms have not yet been elucidated. Here, we reveal a regulatory role of Rv1830, which coordinates cell division and DNA repair in mycobacteria, and rename it McdR (mycobacterial cell division regulator). An increase in McdR levels represses the expression of cell division-associated whiB2 but activates the DNA repair-associated, error-prone enzymes ImuA/B and DnaE2, which in turn facilitates adaptation to stress responses and drug resistance. Furthermore, WhiB2 activates the transcription of mcdR to form a conserved regulatory loop. These data provide new insights into the mechanisms controlling mycobacterial cell growth and stress responses.
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11
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Boncella AE, Sabo ET, Santore RM, Carter J, Whalen J, Hudspeth JD, Morrison CN. The expanding utility of iron-sulfur clusters: Their functional roles in biology, synthetic small molecules, maquettes and artificial proteins, biomimetic materials, and therapeutic strategies. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Lee JH, Lee EJ, Roe JH. uORF-mediated riboregulation controls transcription of whiB7/wblC antibiotic resistance gene. Mol Microbiol 2021; 117:179-192. [PMID: 34687261 DOI: 10.1111/mmi.14834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022]
Abstract
WhiB7/WblC is a transcriptional factor of actinomycetes conferring intrinsic resistance to multiple translation-inhibitory antibiotics. It positively autoregulates its own transcription in response to the same antibiotics. The presence of a uORF and a potential Rho-independent transcription terminator in the 5' leader region has suggested a possibility that the whiB7/wblC gene is regulated via a uORF-mediated transcription attenuation. However, experimental evidence for the molecular mechanism to explain how antibiotic stress suppresses the attenuator, if any, and induces transcription of the whiB7/wblC gene has been lacking. Here we report that the 5' leader sequences of the whiB7/wblC genes in sub-clades of actinomycetes include conserved antiterminator RNA structures. We confirmed that the putative antiterminator in the whiB7/wblC leader sequences of both Streptomyces and Mycobacterium indeed suppresses Rho-independent transcription terminator and facilitates transcription readthrough, which is required for WhiB7/WblC-mediated antibiotic resistance. The antibiotic-mediated suppression of the attenuator can be recapitulated by amino acid starvation, indicating that translational inhibition of uORF by multiple signals is a key to induce whiB7/wblC expression. Our findings of a mechanism leading to intrinsic antibiotic resistance could provide an alternative to treat drug-resistant mycobacteria.
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Affiliation(s)
- Ju-Hyung Lee
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jung-Hye Roe
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Korea
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13
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Shi J, Li F, Wen A, Yu L, Wang L, Wang F, Jin Y, Jin S, Feng Y, Lin W. Structural basis of transcription activation by the global regulator Spx. Nucleic Acids Res 2021; 49:10756-10769. [PMID: 34530448 PMCID: PMC8501982 DOI: 10.1093/nar/gkab790] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Spx is a global transcriptional regulator in Gram-positive bacteria and has been inferred to efficiently activate transcription upon oxidative stress by engaging RNA polymerase (RNAP) and promoter DNA. However, the precise mechanism by which it interacts with RNAP and promoter DNA to initiate transcription remains obscure. Here, we report the cryo-EM structure of an intact Spx-dependent transcription activation complex (Spx-TAC) from Bacillus subtilis at 4.2 Å resolution. The structure traps Spx in an active conformation and defines key interactions accounting for Spx-dependent transcription activation. Strikingly, an oxidized Spx monomer engages RNAP by simultaneously interacting with the C-terminal domain of RNAP alpha subunit (αCTD) and σA. The interface between Spx and αCTD is distinct from those previously reported activators, indicating αCTD as a multiple target for the interaction between RNAP and various transcription activators. Notably, Spx specifically wraps the conserved -44 element of promoter DNA, thereby stabilizing Spx-TAC. Besides, Spx interacts extensively with σA through three different interfaces and promotes Spx-dependent transcription activation. Together, our structural and biochemical results provide a novel mechanistic framework for the regulation of bacterial transcription activation and shed new light on the physiological roles of the global Spx-family transcription factors.
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Affiliation(s)
- Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fangfang Li
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Libing Yu
- Institute of Materials, China Academy of Engineering Physics, Mianyang, China
| | - Lu Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanling Jin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sha Jin
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China
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