1
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Hu Q, Wang J, Liu C, Feng Y, Chen H. Determinants of mer Promoter Activity from Pseudomonas aeruginosa. Genes (Basel) 2024; 15:490. [PMID: 38674424 PMCID: PMC11049809 DOI: 10.3390/genes15040490] [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: 03/18/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Since the MerR family is known for its special regulatory mechanism, we aimed to explore which factors determine the expression activity of the mer promoter. The Tn501/Tn21 mer promoter contains an abnormally long spacer (19 bp) between the -35 and -10 elements, which is essential for the unique DNA distortion mechanism. To further understand the role of base sequences in the mer promoter spacer, this study systematically engineered a series of mutant derivatives and used luminescent and fluorescent reporter genes to investigate the expression activity of these derivatives. The results reveal that the expression activity of the mer promoter is synergistically modulated by the spacer length (17 bp is optimal) and the region upstream of -10 (especially -13G). The spacing is regulated by MerR transcription factors through symmetrical sequences, and -13G presumably functions through interaction with the RNA polymerase sigma-70 subunit.
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Affiliation(s)
| | | | | | | | - Hao Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; (Q.H.); (J.W.); (C.L.); (Y.F.)
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2
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Hui CY, Ma BC, Wang YQ, Yang XQ, Cai JM. Designed bacteria based on natural pbr operons for detecting and detoxifying environmental lead: A mini-review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115662. [PMID: 37939554 DOI: 10.1016/j.ecoenv.2023.115662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/10/2023]
Abstract
Lead (Pb), a naturally occurring element, is redistributed in the environment mainly due to anthropogenic activities. Pb pollution is a crucial public health problem worldwide due to its adverse effects. Environmental bacteria have evolved various protective mechanisms against high levels of Pb. The pbr operon, first identified in Cupriavidus metallidurans CH34, encodes a unique Pb(II) resistance mechanism involving transport, efflux, sequestration, biomineralization, and precipitation. Similar pbr operons are gradually found in diverse bacterial strains. This review focuses on the pbr-encoded Pb(II) resistance system. It summarizes various whole-cell biosensors harboring artificially designed pbr operons for Pb(II) biomonitoring with fluorescent, luminescent, and colorimetric signal output. Optimization of genetic circuits, employment of pigment-based reporters, and screening of host cells are promising in improving the sensitivity, selectivity, and response range of whole-cell biosensors. Engineered bacteria displaying Pb(II) binding and sequestration proteins, including PbrR and its derivatives, PbrR2 and PbrD, for adsorption are involved. Although synthetic bacteria show great potential in determining and removing Pb at the nanomolar level for environmental protection and food safety, some challenges must be addressed to meet demanding application requirements.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China.
| | - Bing-Chan Ma
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China; School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yong-Qiang Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Xue-Qin Yang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Jin-Min Cai
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
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3
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Zhu DL, Guo Y, Ma BC, Lin YQ, Wang HJ, Gao CX, Liu MQ, Zhang NX, Luo H, Hui CY. Pb(II)-inducible proviolacein biosynthesis enables a dual-color biosensor toward environmental lead. Front Microbiol 2023; 14:1218933. [PMID: 37577420 PMCID: PMC10413148 DOI: 10.3389/fmicb.2023.1218933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
With the rapid development of synthetic biology, various whole-cell biosensors have been designed as valuable biological devices for the selective and sensitive detection of toxic heavy metals in environmental water. However, most proposed biosensors are based on fluorescent and bioluminescent signals invisible to the naked eye. The development of visible pigment-based biosensors can address this issue. The pbr operon from Klebsiella pneumoniae is selectively induced by bioavailable Pb(II). In the present study, the proviolacein biosynthetic gene cluster was transcriptionally fused to the pbr Pb(II) responsive element and introduced into Escherichia coli. The resultant biosensor responded to Pb(II) in a time- and dose-dependent manner. After a 5-h incubation with Pb(II), the brown pigment was produced, which could be extracted into n-butanol. Extra hydrogen peroxide treatment during n-butanol extract resulted in the generation of a stable green pigment. An increased brown signal was observed upon exposure to lead concentrations above 2.93 nM, and a linear regression was fitted from 2.93 to 3,000 nM. Extra oxidation significantly decreased the difference between parallel groups. The green signal responded to as low as 0.183 nM Pb(II), and a non-linear regression was fitted in a wide concentration range from 0.183 to 3,000 nM. The specific response toward Pb(II) was not interfered with by various metals except for Cd(II) and Hg(II). The PV-based biosensor was validated in monitoring bioaccessible Pb(II) spiked into environmental water. The complex matrices did not influence the regression relationship between spiked Pb(II) and the dual-color signals. Direct reading with the naked eye and colorimetric quantification enable the PV-based biosensor to be a dual-color and low-cost bioindicator for pollutant heavy metal.
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Affiliation(s)
- De-long Zhu
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yan Guo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Bing-chan Ma
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong-qin Lin
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Hai-jun Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Chao-xian Gao
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Ming-qi Liu
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Nai-xing Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Hao Luo
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Chang-ye Hui
- School of Public Health, Guangdong Medical University, Dongguan, China
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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4
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Pal P, Khan MY, Sharma S, Kumar Y, Mangla N, Kaushal PS, Agarwal N. ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis. Commun Biol 2023; 6:708. [PMID: 37433855 DOI: 10.1038/s42003-023-05059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/21/2023] [Indexed: 07/13/2023] Open
Abstract
Survival response of the human tuberculosis pathogen, Mycobacterium tuberculosis (Mtb) to a diverse environmental cues is governed through its versatile transcription regulatory mechanisms with the help of a large pool of transcription regulators (TRs). Rv1830 is one such conserved TR, which remains uncharacterized in Mtb. It was named as McdR based on an effect on cell division upon its overexpression in Mycobacterium smegmatis. Recently, it has been implicated in antibiotic resilience in Mtb and reannotated as ResR. While Rv1830 affects cell division by modulating the expression of M. smegmatis whiB2, the underlying cause of its essentiality and regulation of drug resilience in Mtb is yet to be deciphered. Here we show that ResR/McdR, encoded by ERDMAN_2020 in virulent Mtb Erdman, is pivotal for bacterial proliferation and crucial metabolic activities. Importantly, ResR/McdR directly regulates ribosomal gene expression and protein synthesis, requiring distinct disordered N-terminal sequence. Compared to control, bacteria depleted with resR/mcdR exhibit delayed recovery post-antibiotic treatment. A similar effect upon knockdown of rplN operon genes further implicates ResR/McdR-regulated protein translation machinery in attributing drug resilience in Mtb. Overall, findings from this study suggest that chemical inhibitors of ResR/McdR may be proven effective as adjunctive therapy for shortening the duration of TB treatment.
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Affiliation(s)
- Pramila Pal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, Delhi, India
| | - Mohd Younus Khan
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, Delhi, India
| | - Shivani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Nikita Mangla
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, Delhi, India
| | - Prem S Kaushal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.
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5
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Kosol S, Rostock L, Barsig J, Tabarelli T, Hommernick K, Kulike M, Eulberg T, Seidel M, Behroz I, Kleebauer L, Grätz S, Mainz A, Süssmuth RD. Transcription activation by the resistance protein AlbA as a tool to evaluate derivatives of the antibiotic albicidin. Chem Sci 2023; 14:5069-5078. [PMID: 37206387 PMCID: PMC10189885 DOI: 10.1039/d3sc00955f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/15/2023] [Indexed: 05/21/2023] Open
Abstract
The rising numbers of fatal infections with resistant pathogens emphasizes the urgent need for new antibiotics. Ideally, new antibiotics should be able to evade or overcome existing resistance mechanisms. The peptide antibiotic albicidin is a highly potent antibacterial compound with a broad activity spectrum but also with several known resistance mechanisms. In order to assess the effectiveness of novel albicidin derivatives in the presence of the binding protein and transcription regulator AlbA, a resistance mechanism against albicidin identified in Klebsiella oxytoca, we designed a transcription reporter assay. In addition, by screening shorter albicidin fragments, as well as various DNA-binders and gyrase poisons, we were able to gain insights into the AlbA target spectrum. We analysed the effect of mutations in the binding domain of AlbA on albicidin sequestration and transcription activation, and found that the signal transduction mechanism is complex but can be evaded. Further demonstrating AlbA's high level of specificity, we find clues for the logical design of molecules capable of avoiding the resistance mechanism.
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Affiliation(s)
- Simone Kosol
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Lida Rostock
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Jonas Barsig
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Theresa Tabarelli
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Tobias Eulberg
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Leonardo Kleebauer
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Stefan Grätz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
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6
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Bai S, Han X, Feng D. Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1139744. [PMID: 36890896 PMCID: PMC9987563 DOI: 10.3389/fpls.2023.1139744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.
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Affiliation(s)
- Shiyan Bai
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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7
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Ziemann M, Reimann V, Liang Y, Shi Y, Ma H, Xie Y, Li H, Zhu T, Lu X, Hess WR. CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems. Nat Commun 2023; 14:924. [PMID: 36801863 PMCID: PMC9938897 DOI: 10.1038/s41467-023-36542-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/06/2023] [Indexed: 02/20/2023] Open
Abstract
Certain CRISPR-Cas elements integrate into Tn7-like transposons, forming CRISPR-associated transposon (CAST) systems. How the activity of these systems is controlled in situ has remained largely unknown. Here we characterize the MerR-type transcriptional regulator Alr3614 that is encoded by one of the CAST (AnCAST) system genes in the genome of cyanobacterium Anabaena sp. PCC 7120. We identify a number of Alr3614 homologs across cyanobacteria and suggest naming these regulators CvkR for Cas V-K repressors. Alr3614/CvkR is translated from leaderless mRNA and represses the AnCAST core modules cas12k and tnsB directly, and indirectly the abundance of the tracr-CRISPR RNA. We identify a widely conserved CvkR binding motif 5'-AnnACATnATGTnnT-3'. Crystal structure of CvkR at 1.6 Å resolution reveals that it comprises distinct dimerization and potential effector-binding domains and that it assembles into a homodimer, representing a discrete structural subfamily of MerR regulators. CvkR repressors are at the core of a widely conserved regulatory mechanism that controls type V-K CAST systems.
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Affiliation(s)
- Marcus Ziemann
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Viktoria Reimann
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Yajing Liang
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Yue Shi
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Honglei Ma
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,Shandong Energy Institute, Qingdao, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuman Xie
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Zhu
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China. .,Shandong Energy Institute, Qingdao, 266101, China. .,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, No.189 Songling Road, Qingdao, 266101, China. .,Shandong Energy Institute, Qingdao, 266101, China. .,Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany.
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8
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Fritsch VN, Linzner N, Busche T, Said N, Weise C, Kalinowski J, Wahl MC, Antelmann H. The MerR-family regulator NmlR is involved in the defense against oxidative stress in Streptococcus pneumoniae. Mol Microbiol 2023; 119:191-207. [PMID: 36349475 DOI: 10.1111/mmi.14999] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/25/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Streptococcus pneumoniae has to cope with the strong oxidant hypochlorous acid (HOCl), during host-pathogen interactions. Thus, we analyzed the global gene expression profile of S. pneumoniae D39 towards HOCl stress. In the RNA-seq transcriptome, the NmlR, SifR, CtsR, HrcA, SczA and CopY regulons and the etrx1-ccdA1-msrAB2 operon were most strongly induced under HOCl stress, which participate in the oxidative, electrophile and metal stress response in S. pneumoniae. The MerR-family regulator NmlR harbors a conserved Cys52 and controls the alcohol dehydrogenase-encoding adhC gene under carbonyl and NO stress. We demonstrated that NmlR senses also HOCl stress to activate transcription of the nmlR-adhC operon. HOCl-induced transcription of adhC required Cys52 of NmlR in vivo. Using mass spectrometry, NmlR was shown to be oxidized to intersubunit disulfides or S-glutathionylated under oxidative stress in vitro. A broccoli-FLAP-based assay further showed that both NmlR disulfides significantly increased transcription initiation at the nmlR promoter by RNAP in vitro, which depends on Cys52. Phenotype analyses revealed that NmlR functions in the defense against oxidative stress and promotes survival of S. pneumoniae during macrophage infections. In conclusion, NmlR was characterized as HOCl-sensing transcriptional regulator, which activates transcription of adhC under oxidative stress by thiol switches in S. pneumoniae.
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Affiliation(s)
| | - Nico Linzner
- Institute of Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Tobias Busche
- Center for Biotechnology, University Bielefeld, Bielefeld, Germany.,NGS Core Facility, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Nelly Said
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, University Bielefeld, Bielefeld, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.,Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Haike Antelmann
- Institute of Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
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9
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Transcriptome analysis reveals reasons for the low tolerance of Clostridium tyrobutyricum to furan derivatives. Appl Microbiol Biotechnol 2022; 107:327-339. [DOI: 10.1007/s00253-022-12281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
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10
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Abstract
Oxidative stress causes cellular damage, including DNA mutations, protein dysfunction, and loss of membrane integrity. Here, we discovered that a TrmB (transcription regulator of mal operon) family protein (Pfam PF01978) composed of a single winged-helix DNA binding domain (InterPro IPR002831) can function as thiol-based transcriptional regulator of oxidative stress response. Using the archaeon Haloferax volcanii as a model system, we demonstrate that the TrmB-like OxsR is important for recovery of cells from hypochlorite stress. OxsR is shown to bind specific regions of genomic DNA, particularly during hypochlorite stress. OxsR-bound intergenic regions were found proximal to oxidative stress operons, including genes associated with thiol relay and low molecular weight thiol biosynthesis. Further analysis of a subset of these sites revealed OxsR to function during hypochlorite stress as a transcriptional activator and repressor. OxsR was shown to require a conserved cysteine (C24) for function and to use a CG-rich motif upstream of conserved BRE/TATA box promoter elements for transcriptional activation. Protein modeling suggested the C24 is located at a homodimer interface formed by antiparallel α helices, and that oxidation of this cysteine would result in the formation of an intersubunit disulfide bond. This covalent linkage may promote stabilization of an OxsR homodimer with the enhanced DNA binding properties observed in the presence of hypochlorite stress. The phylogenetic distribution TrmB family proteins, like OxsR, that have a single winged-helix DNA binding domain and conserved cysteine residue suggests this type of redox signaling mechanism is widespread in Archaea.
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