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Köksaldı İÇ, Avcı E, Köse S, Özkul G, Kehribar EŞ, Şafak Şeker UÖ. Genetically engineered bacterial biofilm materials enhances portable whole cell sensing. Biosens Bioelectron 2024; 264:116644. [PMID: 39137519 DOI: 10.1016/j.bios.2024.116644] [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: 03/09/2024] [Revised: 07/16/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
In recent years, whole-cell biosensors (WCBs) have emerged as a potent approach for environmental monitoring and on-site analyte detection. These biosensors harness the biological apparatus of microorganisms to identify specific analytes, offering advantages in sensitivity, specificity, and real-time monitoring capabilities. A critical hurdle in biosensor development lies in ensuring the robust attachment of cells to surfaces, a crucial step for practical utility. In this study, we present a comprehensive approach to tackle this challenge via engineering Escherichia coli cells for immobilization on paper through the Curli biofilm pathway. Furthermore, incorporating a cellulose-binding peptide domain to the CsgA biofilm protein enhances cell adhesion to paper surfaces, consequently boosting biosensor efficacy. To demonstrate the versatility of this platform, we developed a WCB for copper, optimized to exhibit a discernible response, even with the naked eye. To confirm its suitability for practical field use, we characterized our copper sensor under various environmental conditions-temperature, salinity, and pH-to mimic real-world scenarios. The biosensor-equipped paper discs can be freeze-dried for deployment in on-site applications, providing a practical method for long-term storage without loss of sensitivity paper discs demonstrate sustained functionality and viability even after months of storage with 5 μM limit of detection for copper with visible-to-naked-eye signal levels. Biofilm-mediated surface attachment and analyte sensing can be independently engineered, allowing for flexible utilization of this platform as required. With the implementation of copper sensing as a proof-of-concept study, we underscore the potential of WCBs as a promising avenue for the on-site detection of a multitude of analytes.
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Affiliation(s)
- İlkay Çisil Köksaldı
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Ece Avcı
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Sıla Köse
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Gökçe Özkul
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Ebru Şahin Kehribar
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey.
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2
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Hirsch M, Hofmann L, Yakobov I, Kahremany S, Sameach H, Shenberger Y, Gevorkyan-Airapetov L, Ruthstein S. An efficient EPR spin-labeling method enables insights into conformational changes in DNA. BIOPHYSICAL REPORTS 2024; 4:100168. [PMID: 38945453 PMCID: PMC11298882 DOI: 10.1016/j.bpr.2024.100168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Electron paramagnetic resonance (EPR) is a powerful tool for elucidating both static and dynamic conformational alterations in macromolecules. However, to effectively utilize EPR for such investigations, the presence of paramagnetic centers, known as spin labels, is required. The process of spin labeling, particularly for nucleotides, typically demands intricate organic synthesis techniques. In this study, we introduce a unique addition-elimination reaction method with a simple spin-labeling process, facilitating the monitoring of structural changes within nucleotide sequences. Our investigation focuses on three distinct labeling positions with a DNA sequence, allowing the measurement of distance between two spin labels. The experimental mean distances obtained agreed with the calculated distances, underscoring the efficacy of this straightforward spin-labeling approach in studying complex biological processes such as transcription mechanism using EPR measurements.
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Affiliation(s)
- Melanie Hirsch
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Idan Yakobov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Shirin Kahremany
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Hila Sameach
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan, Israel.
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3
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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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4
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Kompaniiets D, Wang D, Yang Y, Hu Y, Liu B. Structure and molecular mechanism of bacterial transcription activation. Trends Microbiol 2024; 32:379-397. [PMID: 37903670 DOI: 10.1016/j.tim.2023.10.001] [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: 06/23/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023]
Abstract
Transcription activation is an important checkpoint of regulation of gene expression which occurs in response to different intracellular and extracellular signals. The key elements in this signal transduction process are transcription activators, which determine when and how gene expression is activated. Recent structural studies on a considerable number of new transcription activation complexes (TACs) revealed the remarkable mechanistic diversity of transcription activation mediated by different factors, necessitating a review and re-evaluation of the transcription activation mechanisms. In this review, we present a comprehensive summary of transcription activation mechanisms and propose a new, elaborate, and systematic classification of transcription activation mechanisms, primarily based on the structural features of diverse TAC components.
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Affiliation(s)
- Dmytro Kompaniiets
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Dong Wang
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Bin Liu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
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5
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Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ. DNA looping mediates cooperative transcription activation. Nat Struct Mol Biol 2024; 31:293-299. [PMID: 38177666 DOI: 10.1038/s41594-023-01149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.
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Affiliation(s)
- Shu-Jing Han
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
| | - Lin-Lin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Qiang Shen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Feng Yang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ning Cui
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui Sun
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ke Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui-Chao Meng
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Zhi-Peng Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Cong-Zhao Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
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6
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Hu Y, Liu B. The Copper Efflux Regulator (CueR). Subcell Biochem 2024; 104:17-31. [PMID: 38963481 DOI: 10.1007/978-3-031-58843-3_2] [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] [Indexed: 07/05/2024]
Abstract
The copper efflux regulator (CueR) is a classical member of the MerR family of metalloregulators and is common in gram-negative bacteria. Through its C-terminal effector-binding domain, CueR senses cytoplasmic copper ions to regulate the transcription of genes contributing to copper homeostasis, an essential process for survival of all cells. In this chapter, we review the regulatory roles of CueR in the model organism Escherichia coli and the mechanisms for CueR in copper binding, DNA recognition, and interplay with RNA polymerase in regulating transcription. In light of biochemical and structural analyses, we provide molecular details for how CueR represses transcription in the absence of copper ions, how copper ions mediate CueR conformational change to form holo CueR, and how CueR bends and twists promoter DNA to activate transcription. We also characterize the functional domains and key residues involved in these processes. Since CueR is a representative member of the MerR family, elucidating its regulatory mechanisms could help to understand the CueR-like regulators in other organisms and facilitate the understanding of other metalloregulators in the same family.
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Affiliation(s)
- Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Bin Liu
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.
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7
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Li J, Zhang H, Li D, Liu YJ, Bayer EA, Cui Q, Feng Y, Zhu P. Structure of the transcription open complex of distinct σ I factors. Nat Commun 2023; 14:6455. [PMID: 37833284 PMCID: PMC10575876 DOI: 10.1038/s41467-023-41796-4] [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: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Bacterial σI factors of the σ70-family are widespread in Bacilli and Clostridia and are involved in the heat shock response, iron metabolism, virulence, and carbohydrate sensing. A multiplicity of σI paralogues in some cellulolytic bacteria have been shown to be responsible for the regulation of the cellulosome, a multienzyme complex that mediates efficient cellulose degradation. Here, we report two structures at 3.0 Å and 3.3 Å of two transcription open complexes formed by two σI factors, SigI1 and SigI6, respectively, from the thermophilic, cellulolytic bacterium, Clostridium thermocellum. These structures reveal a unique, hitherto-unknown recognition mode of bacterial transcriptional promoters, both with respect to domain organization and binding to promoter DNA. The key characteristics that determine the specificities of the σI paralogues were further revealed by comparison of the two structures. Consequently, the σI factors represent a distinct set of the σ70-family σ factors, thus highlighting the diversity of bacterial transcription.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Haonan Zhang
- University of Chinese Academy of Sciences, 100049, Beijing, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Dongyu Li
- University of Chinese Academy of Sciences, 100049, Beijing, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China.
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, Shandong, China.
- Shandong Energy Institute, 266101, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Ping Zhu
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
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8
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Shenberger Y, Gevorkyan-Airapetov L, Hirsch M, Hofmann L, Ruthstein S. An in-cell spin-labelling methodology provides structural information on cytoplasmic proteins in bacteria. Chem Commun (Camb) 2023; 59:10524-10527. [PMID: 37563959 DOI: 10.1039/d3cc03047d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
EPR in-cell spin-labeling was applied to CueR in E. coli. The methodology employed a Cu(II)-NTA complexed with dHis. High resolved in-cell distance distributions were obtained revealing minor differences between in vitro and in-cell data. This methodology allows study of structural changes of any protein in-cell, independent of size or cellular system.
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Affiliation(s)
- Yulia Shenberger
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Melanie Hirsch
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Lukas Hofmann
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
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9
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Yoon CK, Lee SH, Zhang J, Lee HY, Kim MK, Seok YJ. HPr prevents FruR-mediated facilitation of RNA polymerase binding to the fru promoter in Vibrio cholerae. Nucleic Acids Res 2023; 51:5432-5448. [PMID: 36987873 PMCID: PMC10287919 DOI: 10.1093/nar/gkad220] [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: 09/30/2022] [Revised: 02/17/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Phosphorylation state-dependent interactions of the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) components with transcription factors play a key role in carbon catabolite repression (CCR) by glucose in bacteria. Glucose inhibits the PTS-dependent transport of fructose and is preferred over fructose in Vibrio cholerae, but the mechanism is unknown. We have recently shown that, contrary to Escherichia coli, the fructose-dependent transcriptional regulator FruR acts as an activator of the fru operon in V. cholerae and binding of the FruR-fructose 1-phosphate (F1P) complex to an operator facilitates RNA polymerase (RNAP) binding to the fru promoter. Here we show that, in the presence of glucose, dephosphorylated HPr, a general PTS component, binds to FruR. Whereas HPr does not affect DNA-binding affinity of FruR, regardless of the presence of F1P, it prevents the FruR-F1P complex from facilitating the binding of RNAP to the fru promoter. Structural and biochemical analyses of the FruR-HPr complex identify key residues responsible for the V. cholerae-specific FruR-HPr interaction not observed in E. coli. Finally, we reveal how the dephosphorylated HPr interacts with FruR in V. cholerae, whereas the phosphorylated HPr binds to CcpA, which is a global regulator of CCR in Bacillus subtilis and shows structural similarity to FruR.
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Affiliation(s)
- Chang-Kyu Yoon
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Seung-Hwan Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
| | - Jing Zhang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Hye-Young Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Min-Kyu Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
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10
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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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11
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Lu Q, Chen T, Wang J, Wang F, Ye W, Ma L, Wu S. Structural Insight into the Mechanism of σ32-Mediated Transcription Initiation of Bacterial RNA Polymerase. Biomolecules 2023; 13:biom13050738. [PMID: 37238608 DOI: 10.3390/biom13050738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Bacterial RNA polymerases (RNAP) form distinct holoenzymes with different σ factors to initiate diverse gene expression programs. In this study, we report a cryo-EM structure at 2.49 Å of RNA polymerase transcription complex containing a temperature-sensitive bacterial σ factor, σ32 (σ32-RPo). The structure of σ32-RPo reveals key interactions essential for the assembly of E. coli σ32-RNAP holoenzyme and for promoter recognition and unwinding by σ32. Specifically, a weak interaction between σ32 and -35/-10 spacer is mediated by T128 and K130 in σ32. A histidine in σ32, rather than a tryptophan in σ70, acts as a wedge to separate the base pair at the upstream junction of the transcription bubble, highlighting the differential promoter-melting capability of different residue combinations. Structure superimposition revealed relatively different orientations between βFTH and σ4 from other σ-engaged RNAPs and biochemical data suggest that a biased σ4-βFTH configuration may be adopted to modulate binding affinity to promoter so as to orchestrate the recognition and regulation of different promoters. Collectively, these unique structural features advance our understanding of the mechanism of transcription initiation mediated by different σ factors.
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Affiliation(s)
- Qiang Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Taiyu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jiening Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Feng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenlong Ye
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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12
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Gautam P, Erill I, Cusick KD. Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria. Microorganisms 2023; 11:microorganisms11041012. [PMID: 37110435 PMCID: PMC10141476 DOI: 10.3390/microorganisms11041012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Copper is an essential trace element for living cells. However, copper can be potentially toxic for bacterial cells when it is present in excess amounts due to its redox potential. Due to its biocidal properties, copper is prevalent in marine systems due to its use in antifouling paints and as an algaecide. Thus, marine bacteria must possess means of sensing and responding to both high copper levels and those in which it is present at only typical trace metal levels. Bacteria harbor diverse regulatory mechanisms that respond to intracellular and extracellular copper and maintain copper homeostasis in cells. This review presents an overview of the copper-associated signal transduction systems in marine bacteria, including the copper efflux systems, detoxification, and chaperone mechanisms. We performed a comparative genomics study of the copper-regulatory signal transduction system on marine bacteria to examine the influence of the environment on the presence, abundance, and diversity of copper-associated signal transduction systems across representative phyla. Comparative analyses were performed among species isolated from sources, including seawater, sediment, biofilm, and marine pathogens. Overall, we observed many putative homologs of copper-associated signal transduction systems from various copper systems across marine bacteria. While the distribution of the regulatory components is mainly influenced by phylogeny, our analyses identified several intriguing trends: (1) Bacteria isolated from sediment and biofilm displayed an increased number of homolog hits to copper-associated signal transduction systems than those from seawater. (2) A large variability exists for hits to the putative alternate σ factor CorE hits across marine bacteria. (3) Species isolated from seawater and marine pathogens harbored fewer CorE homologs than those isolated from the sediment and biofilm.
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Affiliation(s)
- Pratima Gautam
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Kathleen D Cusick
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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13
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Wu X, Yu C, Mu W, Gu Z, Feng Y, Zhang Y. The structural mechanism for transcription activation by Caulobacter crescentus GcrA. Nucleic Acids Res 2023; 51:1960-1970. [PMID: 36715319 PMCID: PMC9976885 DOI: 10.1093/nar/gkad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/31/2023] Open
Abstract
Canonical bacterial transcription activators bind to their cognate cis elements at the upstream of transcription start site (TSS) in a form of dimer. Caulobacter crescentus GcrA, a non-canonical transcription activator, can activate transcription from promoters harboring its cis element at the upstream or downstream of TSS in a form of monomer. We determined two cryo-EM structures of C. crescentus GcrA-bound transcription activation complexes, GcrA TACU and GcrA TACD, which comprise GcrA, RNAP, σ70 and promoter DNA with GcrA cis elements at either the upstream or downstream of TSS at 3.6 and 3.8 Å, respectively. In the GcrA-TACU structure, GcrA makes bipartite interactions with both σ70 domain 2 (σ702) and its cis element, while in the GcrA-TACD structure, GcrA retains interaction with σ702 but loses the interaction with its cis element. Our results suggest that GcrA likely forms a functionally specialized GcrA-RNAP-σA holoenzyme, in which GcrA first locates its cis element and then facilitates RNAP to load on core promoter at its proximal region. The sequence-specific interaction of GcrA and DNA is disrupted either at the stage of RPo formation or promoter escape depending on the location of GcrA cis elements relative to TSS.
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Affiliation(s)
- Xiaoxian Wu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengzhi Yu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhui Mu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhanxi Gu
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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14
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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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15
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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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16
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Hofmann L, Ruthstein S. EPR Spectroscopy Provides New Insights into Complex Biological Reaction Mechanisms. J Phys Chem B 2022; 126:7486-7494. [PMID: 36137278 PMCID: PMC9549461 DOI: 10.1021/acs.jpcb.2c05235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In the last 20 years, the use of electron paramagnetic
resonance
(EPR) has made a pronounced and lasting impact in the field of structural
biology. The advantage of EPR spectroscopy over other structural techniques
is its ability to target even minor conformational changes in any
biomolecule or macromolecular complex, independent of its size or
complexity, or whether it is in solution or in the cell during a biological
or chemical reaction. Here, we focus on the use of EPR spectroscopy
to study transmembrane transport and transcription mechanisms. We
discuss experimental and analytical concerns when referring to studies
of two biological reaction mechanisms, namely, transfer of copper
ions by the human copper transporter hCtr1 and the mechanism of action
of the Escherichia coli copper-dependent
transcription factor CueR. Last, we elaborate on future avenues in
the field of EPR structural biology.
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Affiliation(s)
- Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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17
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Mendoza JI, Lescano J, Soncini FC, Checa SK. The protein scaffold calibrates metal specificity and activation in MerR sensors. Microb Biotechnol 2022; 15:2992-3002. [PMID: 36134649 PMCID: PMC9733647 DOI: 10.1111/1751-7915.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
MerR metalloregulators are the central components of many biosensor platforms designed to report metal contamination. However, most MerR proteins are non-specific. This makes it difficult to apply these biosensors in the analysis of real environmental samples. On-demand implementation of molecular engineering to modify the MerR metal preferences is innovative, although it does not always yield the expected results. As the metal binding loop region (MBL) of these sensors has been proposed to be the major modulator of their specificity, we surgically switched this region for that of well-characterized specific and non-specific homologues. We found that identical modifications in different MerR proteins result in synthetic sensors displaying particular metal-detection patterns that cannot be predicted from the nature of the assembled modules. For instance, the MBL from a native Hg(II) sensor provided non-specificity or specificity toward Hg(II) or Cd(II) depending on the MerR scaffold into which it was integrated. These and other evidences reveal that residues outside the MBL are required to modulate ion recognition and transduce the input signal to the target promoter. Revealing their identity and their interactions with other residues is a critical step toward the design of more efficient biosensor devices for environmental metal monitoring.
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Affiliation(s)
- Julián I. Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Julián Lescano
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Fernando C. Soncini
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
| | - Susana K. Checa
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
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18
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Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J. Structural basis of Streptomyces transcription activation by zinc uptake regulator. Nucleic Acids Res 2022; 50:8363-8376. [PMID: 35871291 PMCID: PMC9371925 DOI: 10.1093/nar/gkac627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of −35 elements. Here we deciphered the molecular mechanism by which ScZur interacts with promoter DNA and Sc RNA polymerase (RNAP) by cryo-EM structures and biochemical assays. The ScZur-DNA structures reveal a sequential and cooperative binding of three ScZur dimers surrounding a Zur-box spaced 8 nt upstream from a −35 element. The ScRNAPσHrdB-Zur-DNA structures define protein-protein and protein-DNA interactions involved in the principal housekeeping σHrdB-dependent transcription initiation from a noncanonical promoter with a −10 element lacking the critical adenine residue at position −11 and a TTGCCC −35 element deviating from the canonical TTGACA motif. ScZur interacts with the C-terminal domain of ScRNAP α subunit (αCTD) in a complex structure trapped in an active conformation. Key ScZur-αCTD interfacial residues accounting for ScZur-dependent transcription activation were confirmed by mutational studies. Together, our structural and biochemical results provide a comprehensive model for transcription activation of Zur family regulators.
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Affiliation(s)
- Xu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Yiqun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Guiyang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University , Shanghai 200240, China
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19
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He D, You L, Wu X, Shi J, Wen A, Yan Z, Mu W, Fang C, Feng Y, Zhang Y. Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. Nat Commun 2022; 13:4204. [PMID: 35859063 PMCID: PMC9300723 DOI: 10.1038/s41467-022-31871-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/07/2022] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σS (RNAP-σS). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σS holoenzyme, Pae RNAP-σS holoenzyme complexed with SutA, and Pae RNAP-σS transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σS holoenzyme. SutA is a transcription factor which increases transcription activity of an RNA polymerase (RNAP). Here, authors present cryo-EM structures of SutA-bound RNAP-σS holoenzyme and SutA-bound transcription initiation complex, which reveals SutA wedging the RNAP-β lobe open to aid unwinding.
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Affiliation(s)
- Dingwei He
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aijia Wen
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Yan
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wenhui Mu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Chengli Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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20
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Wang P, Zhang G, Xu Z, Chen Z, Liu X, Wang C, Zheng C, Wang J, Zhang H, Yan A. Whole-cell FRET monitoring of transcription factor activities enables functional annotation of signal transduction systems in living bacteria. J Biol Chem 2022; 298:102258. [PMID: 35839853 PMCID: PMC9396075 DOI: 10.1016/j.jbc.2022.102258] [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: 02/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria adapt to their constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor TF–promoter interactions in situ in living bacteria are lacking. Herein, we developed a whole-cell TF–promoter binding assay based on the intermolecular FRET between an unnatural amino acid, l-(7-hydroxycoumarin-4-yl) ethylglycine, which labels TFs with bright fluorescence through genetic encoding (donor fluorophore) and the live cell nucleic acid stain SYTO 9 (acceptor fluorophore). We show that this new FRET pair monitors the intricate TF–promoter interactions elicited by various types of signal transduction systems, including one-component (CueR) and two-component systems (BasSR and PhoPQ), in bacteria with high specificity and sensitivity. We demonstrate that robust CouA incorporation and FRET occurrence is achieved in all these regulatory systems based on either the crystal structures of TFs or their simulated structures, if 3D structures of the TFs were unavailable. Furthermore, using CueR and PhoPQ systems as models, we demonstrate that the whole-cell FRET assay is applicable for the identification and validation of complex regulatory circuit and novel modulators of regulatory systems of interest. Finally, we show that the FRET system is applicable for single-cell analysis and monitoring TF activities in Escherichia coli colonizing a Caenorhabditis elegans host. In conclusion, we established a tractable and sensitive TF–promoter binding assay, which not only complements currently available approaches for DNA–protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria–host interface.
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Affiliation(s)
- Pengchao Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Guangming Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zhe Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Chenyin Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 15 Datun Road, Chaoyang District, Beijing 100101, China.
| | - Hongmin Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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21
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Balogh RK, Gyurcsik B, Jensen M, Thulstrup PW, Köster U, Christensen NJ, Jensen ML, Hunyadi-Gulyás É, Hemmingsen L, Jancso A. Tying up a loose end: On the role of the C-terminal CCHHRAG fragment of the metalloregulator CueR. Chembiochem 2022; 23:e202200290. [PMID: 35714117 PMCID: PMC9542689 DOI: 10.1002/cbic.202200290] [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] [Received: 05/20/2022] [Indexed: 11/07/2022]
Abstract
The transcriptional regulator CueR is activated by the binding of CuI, AgI, or AuI to two cysteinates in a near‐linear fashion. The C‐terminal CCHHRAG sequence in Escherichia coli CueR present potential additional metal binding ligands and here we explore the effect of deleting this fragment on the binding of AgI to CueR. CD spectroscopic and ESI‐MS data indicate that the high AgI‐binding affinity of WT‐CueR is significantly reduced in Δ7C‐CueR.[111 Ag PAC spectroscopy demonstrates that the WT‐CueR metal site structure (AgS2) is conserved, but less populated in the truncated variant. Thus, the function of the C‐terminal fragment may be to stabilize the two‐coordinate metal site for cognate monovalent metal ions. In a broader perspective this is an example of residues beyond the second coordination sphere affecting metal site physicochemical properties while leaving the structure unperturbed.
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Affiliation(s)
- Ria K Balogh
- University of Szeged: Szegedi Tudomanyegyetem, Department of Inorganic and Analytical Chemistry, HUNGARY
| | - Béla Gyurcsik
- University of Szeged: Szegedi Tudomanyegyetem, Department of Inorganic and Analytical Chemistry, HUNGARY
| | - Mikael Jensen
- Technical University of Denmark: Danmarks Tekniske Universitet, Hevesy Laboratory, Center for Nuclear Technologies, DENMARK
| | - Peter W Thulstrup
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, DENMARK
| | - Ulli Köster
- Institut Laue-Langevin, Institut Laue-Langevin, FRANCE
| | - Niels Johan Christensen
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, Faculty of Science, DENMARK
| | - Marianne L Jensen
- Niels Bohr Instituttet: Kobenhavns Universitet Niels Bohr Instituttet, Niels Bohr Institute, DENMARK
| | - Éva Hunyadi-Gulyás
- Biological Research Centre, Szeged, Laboratory of Proteomics Research, HUNGARY
| | - Lars Hemmingsen
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, DENMARK
| | - Attila Jancso
- University of Szeged, Department of Inorganic and Analytical Chemistry, Dóm tér 7., 6720, Szeged, HUNGARY
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22
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Yakobov I, Mandato A, Hofmann L, Singewald K, Shenberger Y, Gevorkyan‐Airapetov L, Saxena S, Ruthstein S. Allostery-driven changes in dynamics regulate the activation of bacterial copper transcription factor. Protein Sci 2022; 31:e4309. [PMID: 35481642 PMCID: PMC9004249 DOI: 10.1002/pro.4309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 12/27/2022]
Abstract
Metalloregulators bind and respond to metal ions by regulating the transcription of metal homeostasis genes. Copper efflux regulator (CueR) is a copper-responsive metalloregulator that is found in numerous Gram-negative bacteria. Upon Cu(I) coordination, CueR initiates transcription by bending the bound DNA promoter regions facilitating interaction with RNA polymerase. The structure of Escherichia coli CueR in presence of DNA and metal ion has been reported using X-ray crystallography and cryo-EM, providing information about the mechanism of action. However, the specific role of copper in controlling this transcription mechanism remains elusive. Herein, we use room temperature electron paramagnetic resonance (EPR) experiments to follow allosterically driven dynamical changes in E. coli CueR induced by Cu(I) binding. We suggest that more than one Cu(I) ion binds per CueR monomer, leading to changes in site-specific dynamics at the Cu(I) binding domain and at the distant DNA binding site. Interestingly, Cu(I) binding leads to an increase in dynamics about 27 Å away at the DNA binding domain. These changes in the dynamics of the DNA binding domain are important for exact coordination with the DNA. Thus, Cu(I) binding is critical to initiate a series of conformational changes that regulate and initiate gene transcription. BROAD AUDIENCE STATEMENT: The dynamics of metal transcription factors as a function of metal and DNA binding are complex. In this study, we use EPR spectroscopy to measure dynamical changes of Escherichia coli CueR as a function of copper and DNA binding. We show that copper controls the activation of the transcription processes by initiation a series of dynamical changes over the protein.
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Affiliation(s)
- Idan Yakobov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Alysia Mandato
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Kevin Singewald
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Lada Gevorkyan‐Airapetov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Sunil Saxena
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
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23
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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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24
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Refactoring transcription factors for metabolic engineering. Biotechnol Adv 2022; 57:107935. [PMID: 35271945 DOI: 10.1016/j.biotechadv.2022.107935] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 12/19/2022]
Abstract
Due to the ability to regulate target metabolic pathways globally and dynamically, metabolic regulation systems composed of transcription factors have been widely used in metabolic engineering and synthetic biology. This review introduced the categories, action principles, prediction strategies, and related databases of transcription factors. Then, the application of global transcription machinery engineering technology and the transcription factor-based biosensors and quorum sensing systems are overviewed. In addition, strategies for optimizing the transcriptional regulatory tools' performance by refactoring transcription factors are summarized. Finally, the current limitations and prospects of constructing various regulatory tools based on transcription factors are discussed. This review will provide theoretical guidance for the rational design and construction of transcription factor-based metabolic regulation systems.
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25
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Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. Int J Mol Sci 2022; 23:ijms23042179. [PMID: 35216300 PMCID: PMC8879271 DOI: 10.3390/ijms23042179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.
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26
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Plasmids Bring Additional Capabilities to Caulobacter Isolates. Curr Microbiol 2022; 79:45. [PMID: 34982248 PMCID: PMC8812328 DOI: 10.1007/s00284-021-02742-z] [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: 02/10/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Caulobacter is a well-studied bacterial genus, but little is known about the plasmids that are found in some wild Caulobacter isolates. We used bioinformatic approaches to identify nine plasmids from seven different Caulobacter strains and grouped them based on their size and the similarity of their repABC, parAB, and mobAB genes. Protein pathway analysis of the genes on the K31p1 and K31p2 plasmids showed many metabolic pathways that would enhance the metabolic versatility of the host strain. In contrast, the CB4 plasmid contained 21 heavy metal resistance genes with the majority coding for proteins that enhance copper resistance. Growth assays of C. henricii CB4 demonstrated increased copper resistance and quantitative PCR showed an increase in the expression of eight heavy metal genes when induced with copper.
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27
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Casto J, Mandato A, Hofmann L, Yakobov I, Ghosh S, Ruthstein S, Saxena S. Cu(II)-based DNA Labeling Identifies the Structural Link Between Activation and Termination in a Metalloregulator. Chem Sci 2022; 13:1693-1697. [PMID: 35282619 PMCID: PMC8827015 DOI: 10.1039/d1sc06563g] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/16/2022] [Indexed: 11/25/2022] Open
Abstract
Understanding the structural and mechanistic details of protein-DNA interactions that lead to cellular defence against toxic metal ions in pathogenic bacteria can lead to new ways of combating their virulence. Herein, we examine the Copper Efflux Regulator (CueR) protein, a transcription factor which interacts with DNA to generate proteins that ameliorate excess free Cu(i). We exploit site directed Cu(ii) labeling to measure the conformational changes in DNA as a function of protein and Cu(i) concentration. Unexpectedly, the EPR data indicate that the protein can bend the DNA at high protein concentrations even in the Cu(i)-free state. On the other hand, the bent state of the DNA is accessed at a low protein concentration in the presence of Cu(i). Such bending enables the coordination of the DNA with RNA polymerase. Taken together, the results lead to a structural understanding of how transcription is activated in response to Cu(i) stress and how Cu(i)-free CueR can replace Cu(i)-bound CueR in the protein-DNA complex to terminate transcription. This work also highlights the utility of EPR to measure structural data under conditions that are difficult to access in order to shed light on protein function. Herein, we exploit site-directed Cu(ii)-labeling to measure the DNA conformations in each step of the transcription cycle of the Copper Efflux Regulator (CueR), in order to establish how transcription is activated and terminated.![]()
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Affiliation(s)
- Joshua Casto
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alysia Mandato
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Lukas Hofmann
- Department of Chemistry, Faculty of Exact Sciences, The Institution of Nanotechnology and Advanced Materials, Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Idan Yakobov
- Department of Chemistry, Faculty of Exact Sciences, The Institution of Nanotechnology and Advanced Materials, Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences, The Institution of Nanotechnology and Advanced Materials, Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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28
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Wood DM, Dobson RC, Horne CR. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Biochem Soc Trans 2021; 49:2711-2726. [PMID: 34854920 PMCID: PMC8786299 DOI: 10.1042/bst20210674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
Abstract
Transcription is the principal control point for bacterial gene expression, and it enables a global cellular response to an intracellular or environmental trigger. Transcriptional regulation is orchestrated by transcription factors, which activate or repress transcription of target genes by modulating the activity of RNA polymerase. Dissecting the nature and precise choreography of these interactions is essential for developing a molecular understanding of transcriptional regulation. While the contribution of X-ray crystallography has been invaluable, the 'resolution revolution' of cryo-electron microscopy has transformed our structural investigations, enabling large, dynamic and often transient transcription complexes to be resolved that in many cases had resisted crystallisation. In this review, we highlight the impact cryo-electron microscopy has had in gaining a deeper understanding of transcriptional regulation in bacteria. We also provide readers working within the field with an overview of the recent innovations available for cryo-electron microscopy sample preparation and image reconstruction of transcription complexes.
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Affiliation(s)
- David M. Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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29
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Tsai ST, Cheng WJ, Zhang QX, Yeh YC. Gold-Specific Biosensor for Monitoring Wastewater Using Genetically Engineered Cupriavidus metallidurans CH34. ACS Synth Biol 2021; 10:3576-3582. [PMID: 34860511 DOI: 10.1021/acssynbio.1c00520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Transcription factor-based whole-cell biosensors have recently become promising alternatives to conventional analytical methods due to their advantage of simplicity, cost-effectiveness, and environmental friendliness. In this study, we used genetic engineering to develop a whole-cell biosensor based on the activation of promoters by CupR via interactions with gold ions, leading to the expression of reporter genes that yield output signals. Altering the promoter sequences was shown to significantly improve the performance of the biosensor strain in terms of gold-specificity. The detection sensitivity of our engineered strains was 42-fold higher than that of wild-type strains. The linear range of the purposed sensor was 125-1000 nM with a limit of detection at 46.5 nM. The effectiveness of the sensor strain was verified in wastewater samples.
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Affiliation(s)
- Ssu-Tzu Tsai
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Wen-Jui Cheng
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Qian-Xian Zhang
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
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30
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Zhang Z, Han Z, Wu Y, Jiang S, Ma C, Zhang Y, Zhang J. Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China. Food Res Int 2021; 150:110785. [PMID: 34865800 DOI: 10.1016/j.foodres.2021.110785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/01/2021] [Accepted: 10/24/2021] [Indexed: 11/30/2022]
Abstract
Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.
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Affiliation(s)
- Zeng Zhang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Zhe Han
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Yuqing Wu
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Shuaiming Jiang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Chenchen Ma
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China
| | - Yanjun Zhang
- Chinese Academy of Tropical Agricultural Science, Spice and Beverages Research Institute, Wanning, Hainan 571533, China.
| | - Jiachao Zhang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, Hainan, China.
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31
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Fang C, Zhang Y. Bacterial MerR family transcription regulators: activationby distortion. Acta Biochim Biophys Sin (Shanghai) 2021; 54:25-36. [PMID: 35130613 PMCID: PMC9909328 DOI: 10.3724/abbs.2021003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Transcription factors (TFs) modulate gene expression by regulating the accessibility of promoter DNA to RNA polymerases (RNAPs) in bacteria. The MerR family TFs are a large class of bacterial proteins unique in their physiological functions and molecular action: they function as transcription repressors under normal circumstances, but rapidly transform to transcription activators under various cellular triggers, including oxidative stress, imbalance of cellular metal ions, and antibiotic challenge. The promoters regulated by MerR TFs typically contain an abnormal long spacer between the -35 and -10 elements, where MerR TFs bind and regulate transcription activity through unique mechanisms. In this review, we summarize the function, ligand reception, DNA recognition, and molecular mechanism of transcription regulation of MerR-family TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yu Zhang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
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32
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Foster AW, Young TR, Chivers PT, Robinson NJ. Protein metalation in biology. Curr Opin Chem Biol 2021; 66:102095. [PMID: 34763208 PMCID: PMC8867077 DOI: 10.1016/j.cbpa.2021.102095] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/08/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022]
Abstract
Inorganic metals supplement the chemical repertoire of organic molecules, especially proteins. This requires the correct metals to associate with proteins at metalation. Protein mismetalation typically occurs when excesses of unbound metals compete for a binding site ex vivo. However, in biology, excesses of metal-binding sites typically compete for limiting amounts of exchangeable metals. Here, we summarise mechanisms of metal homeostasis that sustain optimal metal availabilities in biology. We describe recent progress to understand metalation by comparing the strength of metal binding to a protein versus the strength of binding to competing sites inside cells.
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Affiliation(s)
- Andrew W Foster
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Peter T Chivers
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK; Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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33
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Transcriptional Profiling Reveals the Importance of RcrR in the Regulation of Multiple Sugar Transportation and Biofilm Formation in Streptococcus mutans. mSystems 2021; 6:e0078821. [PMID: 34427509 PMCID: PMC8407328 DOI: 10.1128/msystems.00788-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ability of Streptococcus mutans to survive and cause dental caries is dependent on its ability to metabolize various carbohydrates, accompanied by extracellular polysaccharide synthesis and biofilm formation. Here, the role of an rel competence-related regulator (RcrR) in the regulation of multiple sugar transportation and biofilm formation is reported. The deletion of the rcrR gene in S. mutans caused delayed growth, decreased biofilm formation ability, and affected the expression level of its multiple sugar transportation-related genes. Transcriptional profiling revealed 17 differentially expressed genes in the rcrR mutant. Five were downregulated and clustered with the sugar phosphotransferase (PTS) systems (mannitol- and trehalose-specific PTS systems). The conserved sites bound by the rcrR promoter were then determined by electrophoretic mobility shift assays (EMSAs) and DNase I footprinting assays. Furthermore, a potential binding motif in the promoters of the two PTS operons was predicted using MEME Suite 5.1.1. RcrR could bind to the promoter regions of the two operons in vitro, and the sugar transporter-related genes of the two operons were upregulated in an rcrR-overexpressing strain. In addition, when RcrR-binding sites were deleted, the growth rates and final yield of S. mutans were significantly decreased in tryptone-vitamin (TV) medium supplemented with different sugars, but not in absolute TV medium. These results revealed that RcrR acted as a transcription activator to regulate the two PTS systems, accompanied by multiple sugar transportation and biofilm formation. Collectively, these results indicate that RcrR is a critical transcription factor in S. mutans that regulates bacterial growth, biofilm formation, and multiple sugar transportation. IMPORTANCE The human oral cavity is a constantly changing environment. Tooth decay is a commonly prevalent chronic disease mainly caused by the cariogenic bacterium Streptococcus mutans. S. mutans is an oral pathogen that metabolizes various carbohydrates into extracellular polysaccharides (EPSs), biofilm, and tooth-destroying lactic acid. The host diet strongly influences the availability of multiple carbohydrates. Here, we showed that the RcrR transcription regulator plays a significant role in the regulation of biofilm formation and multiple sugar transportation. Further systematic evaluation of how RcrR regulates the transportation of various sugars and biofilm formation was also conducted. Notably, this study decrypts the physiological functions of RcrR as a potential target for the better prevention of dental caries.
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34
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Schwartz R, Ruthstein S, Major DT. Molecular Dynamics Simulations of the Apo and Holo States of the Copper Binding Protein CueR Reveal Principal Bending and Twisting Motions. J Phys Chem B 2021; 125:9417-9425. [PMID: 34384216 DOI: 10.1021/acs.jpcb.1c02553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper is essential for proper functioning of cells but is dangerous in unregulated concentrations. One of the members in the bacterial system responsible for facilitating copper homeostasis is the copper efflux regulator (CueR) protein. Upon copper binding, CueR induces transcription of additional copper homeostasis proteins via a cascade of events. There are some available crystal structures of CueR, in the holo (copper-bound), active (copper- and DNA-bound), and repressed (only DNA-bound) states, and these structures suggest that transcription initiation involves a distortion in the promoter DNA strand. In this work, we study the dynamic behavior of the protein, using molecular dynamics simulations, and compare with available electron paramagnetic resonance measurements for validation. We develop simple force-field parameters to describe the copper-binding motif, thus enabling the use of simplified, classical physics equations. This enabled us to access reasonable simulation times that illustrate global motions of the protein. Both in the holo and apo states of CueR, we observed large-scale helical bending motions that could be involved in the bending of a bound DNA molecule so that transcription activation can take place. Additionally, copper binding might afford increased rigidification of the active state via helix α6.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sharon Ruthstein
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B. Structural basis of copper-efflux-regulator-dependent transcription activation. iScience 2021; 24:102449. [PMID: 34113812 PMCID: PMC8169799 DOI: 10.1016/j.isci.2021.102449] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/18/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
The copper efflux regulator (CueR), a representative member of mercury resistance regulator (MerR) family metalloregulators, controls expression of copper homeostasis-regulating genes in bacteria. The mechanism of transcription activation by CueR and other MerR family regulators is bending the spacer domain of promoter DNA. Here, we report the cryo-EM structures of the intact CueR-dependent transcription activation complexes. The structures show that CueR dimer bends the 19-bp promoter spacer to realign the -35 and -10 elements for recognition by σ70-RNA polymerase holoenzyme and reveal a previously unreported interaction between the DNA-binding domain (DBD) from one CueR subunit and the σ70 nonconserved region (σNCR). Functional studies have shown that the CueR-σNCR interaction plays an auxiliary role in CueR-dependent transcription, assisting the activation mechanism of bending promoter DNA by CueR dimer. Because DBDs are highly conserved in sequence and structure, this transcription-activating mechanism could be generally used by MerR family regulators.
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Affiliation(s)
- Wei Shi
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Baoyue Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Jiang
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chang Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Wei Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bin Liu
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA
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Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation. Microorganisms 2021; 9:microorganisms9051067. [PMID: 34063365 PMCID: PMC8156234 DOI: 10.3390/microorganisms9051067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Myxobacteria are Gram-negative δ-proteobacteria found predominantly in terrestrial habitats and often brightly colored due to the biosynthesis of carotenoids. Carotenoids are lipophilic isoprenoid pigments that protect cells from damage and death by quenching highly reactive and toxic oxidative species, like singlet oxygen, generated upon growth under light. The model myxobacterium Myxococcus xanthus turns from yellow in the dark to red upon exposure to light because of the photoinduction of carotenoid biosynthesis. How light is sensed and transduced to bring about regulated carotenogenesis in order to combat photooxidative stress has been extensively investigated in M. xanthus using genetic, biochemical and high-resolution structural methods. These studies have unearthed new paradigms in bacterial light sensing, signal transduction and gene regulation, and have led to the discovery of prototypical members of widely distributed protein families with novel functions. Major advances have been made over the last decade in elucidating the molecular mechanisms underlying the light-dependent signaling and regulation of the transcriptional response leading to carotenogenesis in M. xanthus. This review aims to provide an up-to-date overview of these findings and their significance.
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Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nat Commun 2021; 12:2702. [PMID: 33976201 PMCID: PMC8113463 DOI: 10.1038/s41467-021-22990-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/08/2021] [Indexed: 01/25/2023] Open
Abstract
Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.
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Hofmann L, Hirsch M, Ruthstein S. Advances in Understanding of the Copper Homeostasis in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:2050. [PMID: 33669570 PMCID: PMC7922089 DOI: 10.3390/ijms22042050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Thirty-five thousand people die as a result of more than 2.8 million antibiotic-resistant infections in the United States of America per year. Pseudomonas aeruginosa (P. aeruginosa) is classified a serious threat, the second-highest threat category of the U.S. Department of Health and Human Services. Among others, the World Health Organization (WHO) encourages the discovery and development of novel antibiotic classes with new targets and mechanisms of action without cross-resistance to existing classes. To find potential new target sites in pathogenic bacteria, such as P. aeruginosa, it is inevitable to fully understand the molecular mechanism of homeostasis, metabolism, regulation, growth, and resistances thereof. P. aeruginosa maintains a sophisticated copper defense cascade comprising three stages, resembling those of public safety organizations. These stages include copper scavenging, first responder, and second responder. Similar mechanisms are found in numerous pathogens. Here we compare the copper-dependent transcription regulators cueR and copRS of Escherichia coli (E. coli) and P. aeruginosa. Further, phylogenetic analysis and structural modelling of mexPQ-opmE reveal that this efflux pump is unlikely to be involved in the copper export of P. aeruginosa. Altogether, we present current understandings of the copper homeostasis in P. aeruginosa and potential new target sites for antimicrobial agents or a combinatorial drug regimen in the fight against multidrug resistant pathogens.
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Affiliation(s)
| | | | - Sharon Ruthstein
- Institute of Nanotechnology and Advanced Materials & Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (L.H.); (M.H.)
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Baya G, Muhindi S, Ngendahimana V, Caguiat J. Potential Whole-Cell Biosensors for Detection of Metal Using MerR Family Proteins from Enterobacter sp. YSU and Stenotrophomonas maltophilia OR02. MICROMACHINES 2021; 12:mi12020142. [PMID: 33572806 PMCID: PMC7911910 DOI: 10.3390/mi12020142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 01/15/2023]
Abstract
Cell-based biosensors harness a cell's ability to respond to the environment by repurposing its sensing mechanisms. MerR family proteins are activator/repressor switches that regulate the expression of bacterial metal resistance genes and have been used in metal biosensors. Upon metal binding, a conformational change switches gene expression from off to on. The genomes of the multimetal resistant bacterial strains, Stenotrophomonas maltophilia Oak Ridge strain 02 (S. maltophilia 02) and Enterobacter sp. YSU, were recently sequenced. Sequence analysis and gene cloning identified three mercury resistance operons and three MerR switches in these strains. Transposon mutagenesis and sequence analysis identified Enterobacter sp. YSU zinc and copper resistance operons, which appear to be regulated by the protein switches, ZntR and CueR, respectively. Sequence analysis and reverse transcriptase polymerase chain reaction (RT-PCR) showed that a CueR switch appears to activate a S. maltophilia 02 copper transport gene in the presence of CuSO4 and HAuCl4·3H2O. In previous studies, genetic engineering replaced metal resistance genes with the reporter genes for β-galactosidase, luciferase or the green fluorescence protein (GFP). These produce a color change of a reagent, produce light, or fluoresce in the presence of ultraviolet (UV) light, respectively. Coupling these discovered operons with reporter genes has the potential to create whole-cell biosensors for HgCl2, ZnCl2, CuSO4 and HAuCl4·3H2O.
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Affiliation(s)
- Georgina Baya
- Department of Biological and Chemical Sciences, Youngstown State University, Youngstown, OH 44555, USA;
| | - Stephen Muhindi
- Department of Biological Sciences, University of Toledo, Toledo, OH 43606, USA;
| | - Valentine Ngendahimana
- Biology Department, Lone Star College-CyFair, 9191 Barker Cypress Rd, Cypress, TX 77433, USA;
| | - Jonathan Caguiat
- Department of Biological and Chemical Sciences, Youngstown State University, Youngstown, OH 44555, USA;
- Correspondence: ; Tel.: +1-330-941-2063
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Fang C, Li L, Zhao Y, Wu X, Philips SJ, You L, Zhong M, Shi X, O'Halloran TV, Li Q, Zhang Y. The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription. Nat Commun 2020; 11:6284. [PMID: 33293519 PMCID: PMC7722741 DOI: 10.1038/s41467-020-20134-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure of a B. subtilis transcription activation complex comprising B. subtilis six-subunit (2αββ'ωε) RNA Polymerase (RNAP) core enzyme, σA, a promoter DNA, and the ligand-bound B. subtilis BmrR, a prototype of MerR-family TFs. The structure reveals that RNAP and BmrR recognize the upstream promoter DNA from opposite faces and induce four significant kinks from the -35 element to the -10 element of the promoter DNA in a cooperative manner, which restores otherwise inactive promoter activity by shortening the length of promoter non-optimal -35/-10 spacer. Our structure supports a DNA-distortion and RNAP-non-contact paradigm of transcriptional activation by MerR TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linyu Li
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Yihan Zhao
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Steven J Philips
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingkang Zhong
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xiaojin Shi
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Thomas V O'Halloran
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
- The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Qunyi Li
- Clinical Pharmacy Laboratory, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
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