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Sudzinová P, Šanderová H, Koval' T, Skálová T, Borah N, Hnilicová J, Kouba T, Dohnálek J, Krásný L. What the Hel: recent advances in understanding rifampicin resistance in bacteria. FEMS Microbiol Rev 2023; 47:fuac051. [PMID: 36549665 PMCID: PMC10719064 DOI: 10.1093/femsre/fuac051] [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: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
Rifampicin is a clinically important antibiotic that binds to, and blocks the DNA/RNA channel of bacterial RNA polymerase (RNAP). Stalled, nonfunctional RNAPs can be removed from DNA by HelD proteins; this is important for maintenance of genome integrity. Recently, it was reported that HelD proteins from high G+C Actinobacteria, called HelR, are able to dissociate rifampicin-stalled RNAPs from DNA and provide rifampicin resistance. This is achieved by the ability of HelR proteins to dissociate rifampicin from RNAP. The HelR-mediated mechanism of rifampicin resistance is discussed here, and the roles of HelD/HelR in the transcriptional cycle are outlined. Moreover, the possibility that the structurally similar HelD proteins from low G+C Firmicutes may be also involved in rifampicin resistance is explored. Finally, the discovery of the involvement of HelR in rifampicin resistance provides a blueprint for analogous studies to reveal novel mechanisms of bacterial antibiotic resistance.
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Affiliation(s)
- Petra Sudzinová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Koval'
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Nabajyoti Borah
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
| | - Tomáš Kouba
- Cryogenic Electron Microscopy Research-Service Group, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16000 Prague, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Průmyslová 595, 25250 Vestec, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic
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Tohda M, Oinuma KI, Sakiyama A, Tsubouchi T, Niki M, Namikawa H, Yamane K, Yamada K, Watanabe T, Asai K, Kakeya H, Kaneko Y, Kawaguchi T. Rifampicin exerts anti-mucoviscous activity against hypervirulent Klebsiella pneumoniae via binding to the RNA polymerase β subunit. J Glob Antimicrob Resist 2023; 32:21-28. [PMID: 36572148 DOI: 10.1016/j.jgar.2022.11.018] [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: 01/04/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES In hypervirulent Klebsiella pneumoniae (hvKP), the hypermucoviscous capsule is known to be a major virulence determinant. We previously discovered that rifampicin (RFP), a bactericidal drug that binds to and inhibits the β subunit of RNA polymerase (RpoB), elicits anti-mucoviscous activity against hvKP by suppressing rmpA, a regulator of capsule production. Here, we aimed to determine whether RFP exerts this effect at sub-growth-inhibitory concentrations via its binding to RpoB. METHODS Five spontaneous RFP-resistant mutants (R1-R5) were prepared from an hvKP clinical isolate and subjected to whole genome sequencing and mucoviscosity analyses. Subsequently, a two-step allelic exchange procedure was used to create a rpoB mutant R6 and revertants with wild-type rpoB from R1-R5 (named R1'-R5'). Transcription levels of rmpA and the capsular polysaccharide polymerase gene magA and capsule thickness of R1-R5 and R1'-R5' grown without or with RFP were evaluated by quantitative reverse transcription polymerase chain reaction and microscopic observation using India ink staining. RESULTS R1-R5 all had non-synonymous point mutations in rpoB and were highly resistant to the bactericidal effects and anti-mucoviscous activity of RFP. While the properties of R6 were similar to those of R1-R5, the responses of R1'-R5' to RFP were identical to those of the wild type. rmpA and magA transcription levels and capsule thickness correlated well with the mucoviscosity levels. CONCLUSIONS RFP exerts anti-mucoviscous activity by binding to RpoB. The mechanism of how this causes rmpA suppression remains to be explored.
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Affiliation(s)
- Mitsunori Tohda
- Department of Respiratory Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Ken-Ichi Oinuma
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan.
| | - Arata Sakiyama
- Department of Bacteriology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Taishi Tsubouchi
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Mamiko Niki
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Hiroki Namikawa
- Department of Medical Education and General Practice, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Kenshi Yamane
- Department of Respiratory Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Koichi Yamada
- Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan; Department of Infection Control Science, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Tetsuya Watanabe
- Department of Respiratory Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Kazuhisa Asai
- Department of Respiratory Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Kakeya
- Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan; Department of Infection Control Science, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Yukihiro Kaneko
- Department of Bacteriology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan; Research Center for Infectious Disease Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Tomoya Kawaguchi
- Department of Respiratory Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
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ClpP inhibitors are produced by a widespread family of bacterial gene clusters. Nat Microbiol 2022; 7:451-462. [PMID: 35246663 DOI: 10.1038/s41564-022-01073-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/31/2022] [Indexed: 11/08/2022]
Abstract
The caseinolytic protease (ClpP) is part of a highly conserved proteolytic complex whose disruption can lead to antibacterial activity but for which few specific inhibitors have been discovered. Specialized metabolites produced by bacteria have been shaped by evolution for specific functions, making them a potential source of selective ClpP inhibitors. Here, we describe a target-directed genome mining strategy for discovering ClpP-interacting compounds by searching for biosynthetic gene clusters that contain duplicated copies of ClpP as putative antibiotic resistance genes. We identify a widespread family of ClpP-associated clusters that are known to produce pyrrolizidine alkaloids but whose connection to ClpP has never been made. We show that previously characterized molecules do not affect ClpP function but are shunt metabolites derived from the genuine product of these gene clusters, a reactive covalent ClpP inhibitor. Focusing on one such cryptic gene cluster from Streptomyces cattleya, we identify the relevant inhibitor, which we name clipibicyclene, and show that it potently and selectively inactivates ClpP. Finally, we solve the crystal structure of clipibicyclene-modified Escherichia coli ClpP. Clipibicyclene's discovery reveals the authentic function of a family of natural products whose specificity for ClpP and abundance in nature illuminate the role of eco-evolutionary forces during bacterial competition.
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Rifampicin can induce antibiotic tolerance in mycobacteria via paradoxical changes in rpoB transcription. Nat Commun 2018; 9:4218. [PMID: 30310059 PMCID: PMC6181997 DOI: 10.1038/s41467-018-06667-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/19/2018] [Indexed: 12/17/2022] Open
Abstract
Metrics commonly used to describe antibiotic efficacy rely on measurements performed on bacterial populations. However, certain cells in a bacterial population can continue to grow and divide, even at antibiotic concentrations that kill the majority of cells, in a phenomenon known as antibiotic tolerance. Here, we describe a form of semi-heritable tolerance to the key anti-mycobacterial agent rifampicin, which is known to inhibit transcription by targeting the β subunit of the RNA polymerase (RpoB). We show that rifampicin exposure results in rpoB upregulation in a sub-population of cells, followed by growth. More specifically, rifampicin preferentially inhibits one of the two rpoB promoters (promoter I), allowing increased rpoB expression from a second promoter (promoter II), and thus triggering growth. Disruption of promoter architecture leads to differences in rifampicin susceptibility of the population, confirming the contribution of rifampicin-induced rpoB expression to tolerance. The antibiotic rifampicin inhibits transcription by targeting RpoB, a bacterial RNA polymerase subunit. Here, Zhu et al. show that certain cells in mycobacterial populations can continue to grow and divide in the presence of rifampicin due, paradoxically, to rifampicin-induced upregulation of the rpoB gene.
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Traxler MF, Kolter R. Natural products in soil microbe interactions and evolution. Nat Prod Rep 2015; 32:956-70. [DOI: 10.1039/c5np00013k] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gram positive bacteria from the soil have historically been a deep source of useful natural products. This article considers how natural products may mediate microbial interactions in the soil environment.
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Affiliation(s)
- Matthew F. Traxler
- Dept. of Plant and Microbial Biology
- University of California at Berkeley
- Berkeley
- USA
| | - Roberto Kolter
- Dept. of Microbiology and Immunobiology
- Harvard Medical School
- Boston
- USA
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