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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 PMCID: PMC11365794 DOI: 10.1016/j.bbamcr.2024.119787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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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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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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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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d’Andrea FB, Poulton NC, Froom R, Tam K, Campbell EA, Rock JM. The essential M. tuberculosis Clp protease is functionally asymmetric in vivo. SCIENCE ADVANCES 2022; 8:eabn7943. [PMID: 35507665 PMCID: PMC9067928 DOI: 10.1126/sciadv.abn7943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The Clp protease system is a promising, noncanonical drug target against Mycobacterium tuberculosis (Mtb). Unlike in Escherichia coli, the Mtb Clp protease consists of two distinct proteolytic subunits, ClpP1 and ClpP2, which hydrolyze substrates delivered by the chaperones ClpX and ClpC1. While biochemical approaches uncovered unique aspects of Mtb Clp enzymology, its essentiality complicates in vivo studies. To address this gap, we leveraged new genetic tools to mechanistically interrogate the in vivo essentiality of the Mtb Clp protease. While validating some aspects of the biochemical model, we unexpectedly found that only the proteolytic activity of ClpP1, but not of ClpP2, is essential for substrate degradation and Mtb growth and infection. Our observations not only support a revised model of Mtb Clp biology, where ClpP2 scaffolds chaperone binding while ClpP1 provides the essential proteolytic activity of the complex; they also have important implications for the ongoing development of inhibitors toward this emerging therapeutic target.
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Affiliation(s)
- Felipe B. d’Andrea
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas C. Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Ruby Froom
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Kayan Tam
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Jeremy M. Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
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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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Schneider T, Tan Y, Li H, Fisher JS, Zhang D. Photoglobin, a distinct family of non-heme binding globins, defines a potential photosensor in prokaryotic signal transduction systems. Comput Struct Biotechnol J 2022; 20:261-273. [PMID: 35024098 PMCID: PMC8717448 DOI: 10.1016/j.csbj.2021.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Globins constitute an ancient superfamily of proteins, exhibiting enormous structural and functional diversity, as demonstrated by many heme-binding families and two non-heme binding families that were discovered in bacterial stressosome component RsbR and in light-harvesting phycobiliproteins (phycocyanin) in cyanobacteria and red algae. By comprehensively exploring the globin repertoire using sensitive computational analyses of sequences, structures, and genomes, we present the identification of the third family of non-heme binding globins—the photoglobin. By conducting profile-based comparisons, clustering analyses, and structural modeling, we demonstrate that photoglobin is related to, but distinct from, the phycocyanin family. Photoglobin preserves a potential ligand-binding pocket, whose residue configuration closely resembles that of phycocyanin, indicating that photoglobin potentially binds to a comparable linear tetrapyrrole. By exploring the contextual information provided by the photoglobin’s domain architectures and gene-neighborhoods, we found that photoglobin is frequently associated with the B12-binding light sensor domain and many domains typical of prokaryotic signal transduction systems. Structural modeling using AlphaFold2 demonstrated that photoglobin and B12-binding domains form a structurally conserved hub among different domain architecture contexts. Based on these strong associations, we predict that the coupled photoglobin and B12-binding domains act as a light-sensing regulatory bundle, with each domain sensing different wavelengths of light resulting in switch-like regulation of downstream signaling effectors. Thus, based on the above lines of evidence, we present a distinct non-heme binding globin family and propose that it may define a new type of light sensor, by means of a linear tetrapyrrole, in complex prokaryotic signal transduction systems.
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Affiliation(s)
- Theresa Schneider
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Jonathan S Fisher
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States.,Program of Bioinformatics and Computational Biology, College of Arts & Sciences, Saint Louis University, MO 63103, United States
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Lilic M, Darst SA, Campbell EA. Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7. Mol Cell 2021; 81:2875-2886.e5. [PMID: 34171296 PMCID: PMC8311663 DOI: 10.1016/j.molcel.2021.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/22/2021] [Accepted: 05/12/2021] [Indexed: 01/25/2023]
Abstract
In pathogenic mycobacteria, transcriptional responses to antibiotics result in induced antibiotic resistance. WhiB7 belongs to the Actinobacteria-specific family of Fe-S-containing transcription factors and plays a crucial role in inducible antibiotic resistance in mycobacteria. Here, we present cryoelectron microscopy structures of Mycobacterium tuberculosis transcriptional regulatory complexes comprising RNA polymerase σA-holoenzyme, global regulators CarD and RbpA, and WhiB7, bound to a WhiB7-regulated promoter. The structures reveal how WhiB7 interacts with σA-holoenzyme while simultaneously interacting with an AT-rich sequence element via its AT-hook. Evidently, AT-hooks, rare elements in bacteria yet prevalent in eukaryotes, bind to target AT-rich DNA sequences similarly to the nuclear chromosome binding proteins. Unexpectedly, a subset of particles contained a WhiB7-stabilized closed promoter complex, revealing this intermediate's structure, and we apply kinetic modeling and biochemical assays to rationalize how WhiB7 activates transcription. Altogether, our work presents a comprehensive view of how WhiB7 serves to activate gene expression leading to antibiotic resistance.
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Affiliation(s)
- Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Mol Cell 2021; 81:2887-2900.e5. [PMID: 34171298 DOI: 10.1016/j.molcel.2021.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Huey-Xian Wong
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Li-Mei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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Stewart MYY, Bush MJ, Crack JC, Buttner MJ, Le Brun NE. Interaction of the Streptomyces Wbl protein WhiD with the principal sigma factor σ HrdB depends on the WhiD [4Fe-4S] cluster. J Biol Chem 2020; 295:9752-9765. [PMID: 32303639 PMCID: PMC7363131 DOI: 10.1074/jbc.ra120.012708] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/15/2020] [Indexed: 12/29/2022] Open
Abstract
The bacterial protein WhiD belongs to the Wbl family of iron-sulfur [Fe-S] proteins present only in the actinomycetes. In Streptomyces coelicolor, it is required for the late stages of sporulation, but precisely how it functions is unknown. Here, we report results from in vitro and in vivo experiments with WhiD from Streptomyces venezuelae (SvWhiD), which differs from S. coelicolor WhiD (ScWhiD) only at the C terminus. We observed that, like ScWhiD and other Wbl proteins, SvWhiD binds a [4Fe-4S] cluster that is moderately sensitive to O2 and highly sensitive to nitric oxide (NO). However, although all previous studies have reported that Wbl proteins are monomers, we found that SvWhiD exists in a monomer-dimer equilibrium associated with its unusual C-terminal extension. Several Wbl proteins of Mycobacterium tuberculosis are known to interact with its principal sigma factor SigA. Using bacterial two-hybrid, gel filtration, and MS analyses, we demonstrate that SvWhiD interacts with domain 4 of the principal sigma factor of Streptomyces, σHrdB (σHrdB 4). Using MS, we determined the dissociation constant (Kd ) for the SvWhiD-σHrdB 4 complex as ∼0.7 μm, consistent with a relatively tight binding interaction. We found that complex formation was cluster dependent and that a reaction with NO, which was complete at 8-10 NO molecules per cluster, resulted in dissociation into the separate proteins. The SvWhiD [4Fe-4S] cluster was significantly less sensitive to reaction with O2 and NO when SvWhiD was bound to σHrdB 4, consistent with protection of the cluster in the complex.
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Affiliation(s)
- Melissa Y Y Stewart
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Matthew J Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition. mBio 2020; 11:mBio.00625-20. [PMID: 32291305 PMCID: PMC7157823 DOI: 10.1128/mbio.00625-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The emergence of antibiotic-resistant bacteria is one of the top threats in human health. Therefore, we need to understand how bacteria acquire resistance to antibiotics and continue growth even in the presence of antibiotics. Streptomyces coelicolor, an antibiotic-producing soil bacterium, intrinsically develops resistance to translation-targeting antibiotics. Intrinsic resistance is controlled by the WblC/WhiB7 transcription factor that is highly conserved within Actinobacteria, including Mycobacterium tuberculosis. Here, identification of the WblC/WhiB7 regulon revealed that WblC/WhiB7 controls ribosome maintenance genes and promotes translation in the presence of antibiotics by altering the composition of ribosome-associated proteins. Also, the WblC-mediated ribosomal alteration is indeed required for resistance to translation-targeting antibiotics. This suggests that inactivation of the WblC/WhiB7 regulon could be a potential target to treat antibiotic-resistant mycobacteria. Bacteria that encounter antibiotics can efficiently change their physiology to develop resistance. This intrinsic antibiotic resistance is mediated by multiple pathways, including a regulatory system(s) that activates specific genes. In some Streptomyces and Mycobacterium spp., the WblC/WhiB7 transcription factor is required for intrinsic resistance to translation-targeting antibiotics. Wide conservation of WblC/WhiB7 within Actinobacteria indicates a critical role of WblC/WhiB7 in developing resistance to such antibiotics. Here, we identified 312 WblC target genes in Streptomyces coelicolor, a model antibiotic-producing bacterium, using a combined analysis of RNA sequencing and chromatin immunoprecipitation sequencing. Interestingly, WblC controls many genes involved in translation, in addition to previously identified antibiotic resistance genes. Moreover, WblC promotes translation rate during antibiotic stress by altering the ribosome-associated protein composition. Our genome-wide analyses highlight a previously unappreciated antibiotic resistance mechanism that modifies ribosome composition and maintains the translation rate in the presence of sub-MIC levels of antibiotics.
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