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Pountain AW, Jiang P, Yao T, Homaee E, Guan Y, McDonald KJC, Podkowik M, Shopsin B, Torres VJ, Golding I, Yanai I. Transcription-replication interactions reveal bacterial genome regulation. Nature 2024; 626:661-669. [PMID: 38267581 PMCID: PMC10923101 DOI: 10.1038/s41586-023-06974-w] [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: 03/22/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024]
Abstract
Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. In bacteria, the relationship between the regulatory architecture of a gene and its expression is well understood for individual model gene circuits2,3. However, a broader perspective of these dynamics at the genome scale is lacking, in part because bacterial transcriptomics has hitherto captured only a static snapshot of expression averaged across millions of cells4. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on the transcriptional response of each gene to its own replication, which we term the transcription-replication interaction profile (TRIP). Analysing single-bacterium RNA-sequencing data, we found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal the local regulatory context of a gene. Whereas the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, and this is shaped by factors such as intra-operon position and repression state. By revealing the underlying mechanistic drivers of gene expression heterogeneity, this work provides a quantitative, biophysical framework for modelling replication-dependent expression dynamics.
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Affiliation(s)
- Andrew W Pountain
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Peien Jiang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Ehsan Homaee
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yichao Guan
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Kevin J C McDonald
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Bo Shopsin
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Victor J Torres
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ido Golding
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Itai Yanai
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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Shearer HL, Loi VV, Weiland P, Bange G, Altegoer F, Hampton MB, Antelmann H, Dickerhof N. MerA functions as a hypothiocyanous acid reductase and defense mechanism in Staphylococcus aureus. Mol Microbiol 2023; 119:456-470. [PMID: 36779383 DOI: 10.1111/mmi.15035] [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: 08/24/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/14/2023]
Abstract
The major pathogen Staphylococcus aureus has to cope with host-derived oxidative stress to cause infections in humans. Here, we report that S. aureus tolerates high concentrations of hypothiocyanous acid (HOSCN), a key antimicrobial oxidant produced in the respiratory tract. We discovered that the flavoprotein disulfide reductase (FDR) MerA protects S. aureus from this oxidant by functioning as a HOSCN reductase, with its deletion sensitizing bacteria to HOSCN. Crystal structures of homodimeric MerA (2.4 Å) with a Cys43 -Cys48 intramolecular disulfide, and reduced MerACys43 S (1.6 Å) showed the FAD cofactor close to the active site, supporting that MerA functions as a group I FDR. MerA is controlled by the redox-sensitive repressor HypR, which we show to be oxidized to intermolecular disulfides under HOSCN stress, resulting in its inactivation and derepression of merA transcription to promote HOSCN tolerance. Our study highlights the HOSCN tolerance of S. aureus and characterizes the structure and function of MerA as a major HOSCN defense mechanism. Crippling the capacity to respond to HOSCN may be a novel strategy for treating S. aureus infections.
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Affiliation(s)
- Heather L Shearer
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Vu V Loi
- Freie Universität Berlin, Institute of Biology-Microbiology, Berlin, Germany
| | - Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Center for Tumor Biology and Immunology, Department of Medicine, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Institute of Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Haike Antelmann
- Freie Universität Berlin, Institute of Biology-Microbiology, Berlin, Germany
| | - Nina Dickerhof
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
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Copley SD, Newton MS, Widney KA. How to Recruit a Promiscuous Enzyme to Serve a New Function. Biochemistry 2023; 62:300-308. [PMID: 35729117 PMCID: PMC9881647 DOI: 10.1021/acs.biochem.2c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Promiscuous enzymes can be recruited to serve new functions when a genetic or environmental change makes catalysis of a novel reaction important for fitness or even survival. Subsequently, gene duplication and divergence can lead to evolution of an efficient and specialized new enzyme. Every organism likely has thousands of promiscuous enzyme activities that provide a vast reservoir of catalytic potential. However, much of this potential may not be accessible. We compiled kinetic parameters for promiscuous reactions catalyzed by 108 enzymes. The median value of kcat/KM is a very modest 31 M-1 s-1. Based upon the fluxes through metabolic pathways in E. coli, we estimate that many, if not most, promiscuous activities are too inefficient to impact fitness. However, mutations can elevate the level of an insufficient promiscuous activity by increasing enzyme expression, improving kcat/KM, or altering concentrations of the promiscuous and native substrates and allosteric regulators. Particularly in large bacterial populations, stochastic mutations may provide a viable pathway for recruitment of even inefficient promiscuous activities.
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Fritsch VN, Loi VV, Kuropka B, Gruhlke M, Weise C, Antelmann H. The MarR/DUF24-Family QsrR Repressor Senses Quinones and Oxidants by Thiol Switch Mechanisms in Staphylococcus aureus. Antioxid Redox Signal 2022; 38:877-895. [PMID: 36242097 DOI: 10.1089/ars.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Aims: The MarR/DUF24-family QsrR and YodB repressors control quinone detoxification pathways in Staphylococcus aureus and Bacillus subtilis. In S. aureus, the QsrR regulon also confers resistance to antimicrobial compounds with quinone-like elements, such as rifampicin, ciprofloxacin, and pyocyanin. Although QsrR was shown to be inhibited by thiol-S-alkylation of its conserved Cys4 residue by 1,4-benzoquinone, YodB senses quinones and diamide by the formation of reversible intermolecular disulfides. In this study, we aimed at further investigating the redox-regulation of QsrR and the role of its Cys4, Cys29, and Cys32 residues under quinone and oxidative stress in S. aureus. Results: The QsrR regulon was strongly induced by quinones and oxidants, such as diamide, allicin, hypochlorous acid (HOCl), and AGXX® in S. aureus. Transcriptional induction of catE2 by quinones and oxidants required Cys4 and either Cys29' or Cys32' of QsrR for redox sensing in vivo. DNA-binding assays revealed that QsrR is reversibly inactivated by quinones and oxidants, depending on Cys4. Using mass spectrometry, QsrR was shown to sense diamide by an intermolecular thiol-disulfide switch, involving Cys4 and Cys29' of opposing subunits in vitro. In contrast, allicin caused S-thioallylation of all three Cys residues in QsrR, leading to its dissociation from the operator sequence. Further, the QsrR regulon confers resistance against quinones and oxidants, depending on Cys4 and either Cys29' or Cys32'. Conclusion and Innovation: QsrR was characterized as a two-Cys-type redox-sensing regulator, which senses the oxidative mode of quinones and strong oxidants, such as diamide, HOCl, and the antimicrobial compound allicin via different thiol switch mechanisms.
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Affiliation(s)
| | - Vu Van Loi
- Institute of Biology-Microbiology; Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry; Freie Universität Berlin, Berlin, Germany
| | - Martin Gruhlke
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry; Freie Universität Berlin, Berlin, Germany
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Liu X, Xiong Y, Shi Y, Deng X, Deng Q, Liu Y, Yu Z, Li D, Zheng J, Li P. In vitro activities of licochalcone A against planktonic cells and biofilm of Enterococcus faecalis. Front Microbiol 2022; 13:970901. [PMID: 36338074 PMCID: PMC9634178 DOI: 10.3389/fmicb.2022.970901] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2023] Open
Abstract
This study aims to evaluate the in vitro antibacterial and anti-biofilm activities of licochalcone A on Enterococcus faecalis and to investigate the possible target genes of licochalcone A in E. faecalis. This study found that licochalcone A had antibacterial activities against E. faecalis, with the MIC50 and MIC90 were 25 μM. Licochalcone A (at 4 × MIC) indicated a rapid bactericidal effect on E. faecalis planktonic cells, and killed more E. faecalis planktonic cells (at least 3-log10 cfu/ml) than vancomycin, linezolid, or ampicillin at the 2, 4, and 6 h of the time-killing test. Licochalcone A (at 10 × MIC) significantly reduced the production of E. faecalis persister cells (at least 2-log10 cfu/ml) than vancomycin, linezolid, or ampicillin at the 24, 48, 72, and 96 h of the time-killing test. Licochalcone A (at 1/4 × MIC) significantly inhibited the biofilm formation of E. faecalis. The RNA levels of biofilm formation-related genes, agg, esp, and srtA, markedly decreased when the E. faecalis isolates were treated with licochalcone A at 1/4 × MIC for 6 h. To explore the possible target genes of licochalcone A in E. faecalis, the licochalcone A non-sensitive E. faecalis clones were selected in vitro by induction of wildtype strains for about 140 days under the pressure of licochalcone A, and mutations in the possible target genes were detected by whole-genome sequencing. This study found that there were 11 nucleotide mutations leading to nonsynonymous mutations of 8 amino acids, and among these amino acid mutations, there were 3 mutations located in transcriptional regulator genes (MarR family transcriptional regulator, TetR family transcriptional regulator, and MerR family transcriptional regulator). In conclusion, this study found that licochalcone A had an antibacterial effect on E. faecalis, and significantly inhibited the biofilm formation of E. faecalis at subinhibitory concentrations.
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Affiliation(s)
- Xiaoju Liu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Yanpeng Xiong
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Yiyi Shi
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Xiangbin Deng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Qiwen Deng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Yansong Liu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Duoyun Li
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Jinxin Zheng
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Peiyu Li
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Department of Infectious Diseases and Shenzhen Key Lab of Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
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