1
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Yang J, Xia Y, Shen W, Yang H, Chen X. Development of a gene-coded biosensor to establish a high-throughput screening platform for salidroside production. Biochem Biophys Res Commun 2024; 712-713:149942. [PMID: 38642492 DOI: 10.1016/j.bbrc.2024.149942] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Metabolic engineering reconfigures cellular networks to produce value-added compounds from renewable substrates efficiently. However, identifying strains with desired phenotypes from large libraries through rational or random mutagenesis remains challenging. To overcome this bottleneck, an effective high-throughput screening (HTS) method must be developed to detect and analyze target candidates rapidly. Salidroside is an aromatic compound with broad applications in food, healthcare, medicine, and daily chemicals. However, there currently needs to be HTS methods available to monitor salidroside levels or to screen enzyme variants and strains for high-yield salidroside biosynthesis, which severely limits the development of microbial cell factories capable of efficiently producing salidroside on an industrial scale. This study developed a gene-encoded whole-cell biosensor that is specifically responsive to salidroside. The biosensor was created by screening a site-saturated mutagenic library of uric acid response regulatory protein binding bags. This work demonstrates the feasibility of monitoring metabolic flux with whole-cell biosensors for critical metabolites. It provides a promising tool for building salidroside high-yielding strains for high-throughput screening and metabolic regulation to meet industrial needs.
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Affiliation(s)
- Jing Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Wei Shen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China
| | - Haiquan Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xianzhong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; School of Biotechnology, Jiangnan University, Wuxi, China.
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2
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Köse S, Ahan RE, Köksaldı İÇ, Olgaç A, Kasapkara ÇS, Şeker UÖŞ. Multiplexed cell-based diagnostic devices for detection of renal biomarkers. Biosens Bioelectron 2023; 223:115035. [PMID: 36571991 DOI: 10.1016/j.bios.2022.115035] [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: 09/14/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
The number of synthetic biology-based solutions employed in the medical industry is growing every year. The whole cell biosensors being one of them, have been proven valuable tools for developing low-cost, portable, personalized medicine alternatives to conventional techniques. Based on this concept, we targeted one of the major health problems in the world, Chronic Kidney Disease (CKD). To do so, we developed two novel biosensors for the detection of two important renal biomarkers: urea and uric acid. Using advanced gene expression control strategies, we improved the operational range and the response profiles of each biosensor to meet clinical specifications. We further engineered these systems to enable multiplexed detection as well as an AND-logic gate operating system. Finally, we tested the applicability of these systems and optimized their working dynamics inside complex medium human blood serum. This study could help the efforts to transition from labor-intensive and expensive laboratory techniques to widely available, portable, low-cost diagnostic options.
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Affiliation(s)
- Sıla Köse
- UNAM-Institute of Materias Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
| | - Recep Erdem Ahan
- UNAM-Institute of Materias Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
| | - İlkay Çisil Köksaldı
- UNAM-Institute of Materias Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
| | - Asburçe Olgaç
- Dr Sami Ulus Children's Training and Research Hospital, Ankara, Turkey
| | - Çiğdem Seher Kasapkara
- Ankara Yildirim Beyazit University, Department of Internal Medicine, Children's Health and Disease Section, Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM-Institute of Materias Science and Nanotechnology, National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey.
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3
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Caporaletti F, Pietras Z, Morad V, Mårtensson LG, Gabel F, Wallner B, Martel A, Sunnerhagen M. Small-angle x-ray and neutron scattering of MexR and its complex with DNA supports a conformational selection binding model. Biophys J 2023; 122:408-418. [PMID: 36474441 PMCID: PMC9892617 DOI: 10.1016/j.bpj.2022.11.2949] [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: 03/09/2022] [Revised: 09/02/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
In this work, we used small-angle x-ray and neutron scattering to reveal the shape of the protein-DNA complex of the Pseudomonas aeruginosa transcriptional regulator MexR, a member of the multiple antibiotics resistance regulator (MarR) family, when bound to one of its native DNA binding sites. Several MarR-like proteins, including MexR, repress the expression of efflux pump proteins by binding to DNA on regulatory sites overlapping with promoter regions. When expressed, efflux proteins self-assemble to form multiprotein complexes and actively expel highly toxic compounds out of the host organism. The mutational pressure on efflux-regulating MarR family proteins is high since deficient DNA binding leads to constitutive expression of efflux pumps and thereby supports acquired multidrug resistance. Understanding the functional outcome of such mutations and their effects on DNA binding has been hampered by the scarcity of structural and dynamic characterization of both free and DNA-bound MarR proteins. Here, we show how combined neutron and x-ray small-angle scattering of both states in solution support a conformational selection model that enhances MexR asymmetry in binding to one of its promoter-overlapping DNA binding sites.
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Affiliation(s)
- Francesca Caporaletti
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden; Large Scale Structure, Institute Laue Langevin, Grenoble, France
| | - Zuzanna Pietras
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden
| | - Vivian Morad
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden
| | - Lars-Göran Mårtensson
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden
| | - Frank Gabel
- University Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Björn Wallner
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden
| | - Anne Martel
- Large Scale Structure, Institute Laue Langevin, Grenoble, France
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden.
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4
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The structure of Deinococcus radiodurans transcriptional regulator HucR retold with the urate bound. Biochem Biophys Res Commun 2022; 615:63-69. [DOI: 10.1016/j.bbrc.2022.05.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022]
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5
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PicR as a MarR Family Transcriptional Repressor Multiply Controls the Transcription of Picolinic Acid Degradation Gene Cluster pic in Alcaligenes faecalis JQ135. Appl Environ Microbiol 2022; 88:e0017222. [PMID: 35604228 DOI: 10.1128/aem.00172-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene cluster, pic, that responsible for the catabolism of PA in Alcaligenes faecalis JQ135. However, the transcriptional regulation of the pic cluster remains known. This study showed that the entire pic cluster was composed of 17 genes and transcribed as four operons: picR, picCDEF, picB4B3B2B1, and picT1A1A2A3T2T3MN. Deletion of picR, encoding a putative MarR-type regulator, greatly shortened the lag phase of PA degradation. An electrophoretic mobility shift assay and DNase I footprinting showed that PicR has one binding site in the picR-picC intergenic region and two binding sites in the picB-picT1 intergenic region. The DNA sequences of the three binding sites have the palindromic characteristics of TCAG-N4-CTNN: the space consists of four nonspecific bases, and the four palindromic bases on the left and the first two palindromic bases on the right are strictly conserved, while the last two bases on the right vary among the three binding sites. An in vivo β-galactosidase activity reporter assay indicated that 6-hydroxypicolinic acid but not PA acted as a ligand of PicR, preventing PicR from binding to promoter regions and thus derepressing the transcription of the pic cluster. This study revealed the negative transcriptional regulation mechanism of PA degradation by PicR in A. faecalis JQ135 and provides new insights into the structure and function of the MarR-type regulator. IMPORTANCE The pic gene cluster was found to be responsible for PA degradation and widely distributed in Alpha-, Beta-, and Gammaproteobacteria. Thus, it is very necessary to understand the regulation mechanism of the pic cluster in these strains. This study revealed that PicR binds to three sites of the promoter regions of the pic cluster to multiply regulate the transcription of the pic cluster, which enables A. faecalis JQ135 to efficiently utilize PA. Furthermore, the study also found a unique palindrome sequence for binding of the MarR-type regulator. This study enhanced our understanding of microbial catabolism of environmental toxic pyridine derivatives.
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6
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Hemamali EH, Weerasinghe LP, Tanaka H, Kurisu G, Perera IC. LcaR: a regulatory switch from Pseudomonas aeruginosa for bioengineering alkane degrading bacteria. Biodegradation 2022; 33:117-133. [PMID: 34989928 DOI: 10.1007/s10532-021-09970-x] [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: 06/24/2021] [Accepted: 12/22/2021] [Indexed: 11/26/2022]
Abstract
Application of genetically engineered bacterial strains for biodegradation of hydrocarbons is a sustainable solution for treating pollutants as well as in industrial applications. However, the process of bioengineering should be carefully carried out to optimize the output. Investigation of regulatory genes for bioengineering is essential for developing synthetic circuits for effective biocatalysts. Here we focus on LcaR, a putative transcriptional regulator affecting the expression of alkB2 and lcaR operon that has a high potential to become a tool in designing such pathways. Four LcaR dimers bind specifically to the upstream regulatory region where divergent promoters of alkB2 and lcaR genes are located with high affinity at a Kd of 0.94 ± 0.17 nM and a Hill coefficient is 1.7 ± 0.3 demonstrating cooperativity in the association. Ligand binding alters the conformation of LcaR, which releases the regulator from its cognate DNA. Tetradecanal and hexadecanal act as natural ligands of LcaR with an IC50 values of 3.96 ± 0.59 µg/ml and 0.68 ± 0.21 µg/ml, respectively. The structure and function of transcription factors homologous to LcaR have not been characterized to date. This study provides insight into regulatory mechanisms of alkane degradation with a direction towards potential applications in bioengineering for bioremediation and industrial applications.
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Affiliation(s)
- Erandika H Hemamali
- Synthetic Biology Laboratory, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Laksiri P Weerasinghe
- Department of Chemistry, Faculty of Applied Science, University of Sri Jayewardenapura, Colombo, Sri Lanka
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Inoka C Perera
- Synthetic Biology Laboratory, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
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7
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Mauran S, Perera NT, Perera IC. MxyR of Mycobacterium tuberculosis Responds to Xylan; an Unusual Ligand for a MarR Family Transcriptional Regulator. Mol Biol 2021. [DOI: 10.1134/s0026893321050162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Lin H, Rodríguez-Serrano AF, Hsing IM. Rational design of allosterically regulated toehold mediated strand displacement circuits for sensitive and on-site detection of small molecule metabolites. Analyst 2021; 146:7144-7151. [PMID: 34734587 DOI: 10.1039/d1an01488a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Development of small molecule biosensors enables rapid and de-centralized small molecule detection that meets the demands of routine health monitoring and rapid diagnosis. Among them, allosteric transcription factor (aTF)-based biosensors have shown potential in modular design of small molecule detection platforms due to their ligand-regulated DNA binding activity. Here, we expand the capabilities of a biosensor that leverages the aTF-based regulation of toehold-mediated strand displacement (TMSD) circuits for uric acid (UA) detection in non-invasive salivary samples by utilizing the UA-responsive aTF HucR. The impact of the low ligand affinity of the native HucR was addressed by engineering a two-pass TMSD circuit with in silico rational design. This combined strategy achieved enrichment of the output signal and overcame the negative impact of the matrix effect on the sensitivity and overall response of the biosensor when using real samples, which enabled semi-quantitative detection in the normal salivary UA levels. As well, enhancements provided by the two-pass design halved the turnaround time to less than 15 minutes. To sum up, the two-cycle DNA circuit design enabled aTF-based simple, rapid and one-step non-invasive salivary UA detection, showing its potential in metabolite detection for health monitoring.
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Affiliation(s)
- Haosi Lin
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Alan F Rodríguez-Serrano
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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9
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Wang D, Xu P, Sun J, Yuan J, Zhao J. Effects of ethanol stress on epsilon-poly-l-lysine (ε-PL) biosynthesis in Streptomyces albulus X-18. Enzyme Microb Technol 2021; 153:109907. [PMID: 34670188 DOI: 10.1016/j.enzmictec.2021.109907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 01/10/2023]
Abstract
The aim of the study was to reveal the effects of ethanol stress on the production of epsilon-poly-l-lysine (ε-PL) in Streptomyces albulus X-18. The results showed that biomass and the utilization of glucose were respectively increased by ethanol stress. The ε-PL yield was increased by 41.42 % in the shake flask and 37.02 % in 10 L fermenter with 1% (v/v) ethanol. The morphology of colonies and mycelia showed significant differences. The intracellular reactive oxygen species level was increased by about 100 %. The ratio of unsaturated fatty acids to saturated fatty acids in the cell membrane was increased by ethanol stress. Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) proteomic profile showed that 265 identified proteins were differentially expressed. The differentially expressed proteins (DEPs) were mainly involved in biological processes. The up-regulated DEPs were mainly involved in the redox reaction and stress response. The metabolic flux of l-Asp was shifted to l-Lys biosynthesis, and the DAP pathway was strengthened. Protein-protein interaction analysis showed that 30 DEPs interacted with l-Lys biosynthesis. The changes of ten proteins by Parallel Reaction Monitoring (PRM) were consistent with those by iTRAQ. The study provided valuable clues to better understand the mechanism of ε-PL biosynthesis improvement by ethanol stress.
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Affiliation(s)
- Dahong Wang
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China; Henan Engineering Research Center of Food Microbiology, Luoyang, China.
| | - Peng Xu
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China
| | - Jianrui Sun
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China
| | - Jiangfeng Yuan
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, China
| | - Junfeng Zhao
- College of Food and Bioengineering, Henan University of Science & Technology, Luoyang, China
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10
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Hwang J, Park SH, Lee CW, Do H, Shin SC, Kim HW, Lee SG, Park HH, Kwon S, Lee JH. Crystal structure of a MarR family protein from the psychrophilic bacterium Paenisporosarcina sp. TG-14 in complex with a lipid-like molecule. IUCRJ 2021; 8:842-852. [PMID: 34584745 PMCID: PMC8420766 DOI: 10.1107/s2052252521005704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
MarR family proteins regulate the transcription of multiple antibiotic-resistance genes and are widely found in bacteria and archaea. Recently, a new MarR family gene was identified by genome analysis of the psychrophilic bacterium Paenisporosarcina sp. TG-14, which was isolated from sediment-laden basal ice in Antarctica. In this study, the crystal structure of the MarR protein from Paenisporosarcina sp. TG-14 (PaMarR) was determined at 1.6 Å resolution. In the crystal structure, a novel lipid-type compound (palmitic acid) was found in a deep cavity, which was assumed to be an effector-binding site. Comparative structural analysis of homologous MarR family proteins from a mesophile and a hyperthermophile showed that the DNA-binding domain of PaMarR exhibited relatively high mobility, with a disordered region between the β1 and β2 strands. In addition, structural comparison with other homologous complex structures suggests that this structure constitutes a conformer transformed by palmitic acid. Biochemical analysis also demonstrated that PaMarR binds to cognate DNA, where PaMarR is known to recognize two putative binding sites depending on its molar concentration, indicating that PaMarR binds to its cognate DNA in a stoichiometric manner. The present study provides structural information on the cold-adaptive MarR protein with an aliphatic compound as its putative effector, extending the scope of MarR family protein research.
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Affiliation(s)
- Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Sun-Ha Park
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang Woo Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Sung Gu Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk 27478, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
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11
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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12
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Yekani M, Baghi HB, Vahed SZ, Ghanbari H, Hosseinpur R, Azargun R, Azimi S, Memar MY. Tightly controlled response to oxidative stress; an important factor in the tolerance of Bacteroides fragilis. Res Microbiol 2021; 172:103798. [PMID: 33485914 DOI: 10.1016/j.resmic.2021.103798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/01/2022]
Abstract
The exposure of Bacteroides fragilis to highly oxygenated tissues induces an oxidative stress due to a shift from the reduced condition of the gastrointestinal tract to an aerobic environment of host tissues. The potent and effective responses to reactive oxygen species (ROS) make the B. fragilis tolerant to atmospheric oxygen for several days. The response to oxidative stress in B. fragilis is a complicated event that is induced and regulated by different agents. In this review, we will focus on the B. fragilis response to oxidative stress and present an overview of the regulators of responses to oxidative stress in this bacterium.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hadi Ghanbari
- Department of Pharmacognosy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rasul Hosseinpur
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Robab Azargun
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Somayeh Azimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Microbiology Department, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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13
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Jung JK, Alam KK, Verosloff MS, Capdevila DA, Desmau M, Clauer PR, Lee JW, Nguyen PQ, Pastén PA, Matiasek SJ, Gaillard JF, Giedroc DP, Collins JJ, Lucks JB. Cell-free biosensors for rapid detection of water contaminants. Nat Biotechnol 2020; 38:1451-1459. [PMID: 32632301 PMCID: PMC7718425 DOI: 10.1038/s41587-020-0571-7] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Abstract
Lack of access to safe drinking water is a global problem, and methods to reliably and easily detect contaminants could be transformative. We report the development of a cell-free in vitro transcription system that uses RNA Output Sensors Activated by Ligand Induction (ROSALIND) to detect contaminants in water. A combination of highly processive RNA polymerases, allosteric protein transcription factors and synthetic DNA transcription templates regulates the synthesis of a fluorescence-activating RNA aptamer. The presence of a target contaminant induces the transcription of the aptamer, and a fluorescent signal is produced. We apply ROSALIND to detect a range of water contaminants, including antibiotics, small molecules and metals. We also show that adding RNA circuitry can invert responses, reduce crosstalk and improve sensitivity without protein engineering. The ROSALIND system can be freeze-dried for easy storage and distribution, and we apply it in the field to test municipal water supplies, demonstrating its potential use for monitoring water quality.
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Affiliation(s)
- Jaeyoung K Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Khalid K Alam
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Matthew S Verosloff
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Center for Water Research, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | | | - Morgane Desmau
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Phillip R Clauer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Pablo A Pastén
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Desarrollo Urbano Sustentable, Santiago, Chile
| | - Sandrine J Matiasek
- Department of Geological and Environmental Sciences, California State University, Chico, Chico, CA, USA.,Center for Water and the Environment, California State University, Chico, Chico, CA, USA
| | - Jean-François Gaillard
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA. .,Center for Water Research, Northwestern University, Evanston, IL, USA. .,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA.
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14
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The evolution of MarR family transcription factors as counter-silencers in regulatory networks. Curr Opin Microbiol 2020; 55:1-8. [PMID: 32044654 DOI: 10.1016/j.mib.2020.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/29/2019] [Accepted: 01/03/2020] [Indexed: 11/21/2022]
Abstract
Gene duplication facilitates the evolution of biological complexity, as one copy of a gene retains its original function while a duplicate copy can acquire mutations that would otherwise diminish fitness. Duplication has played a particularly important role in the evolution of regulatory networks by permitting novel regulatory interactions and responses to stimuli. The diverse MarR family of transcription factors (MFTFs) illustrate this concept, ranging from highly specific repressors of single operons to pleiotropic global regulators controlling hundreds of genes. MFTFs are often genetically and functionally linked to antimicrobial efflux systems. However, the SlyA MFTF lineage in the Enterobacteriaceae plays little or no role in regulating efflux but rather functions as transcriptional counter-silencers, which alleviate xenogeneic silencing of horizontally acquired genes and facilitate bacterial evolution by horizontal gene transfer. This review will explore recent advances in our understanding of MFTF traits that have contributed to their functional evolution.
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15
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Liang C, Zhang X, Wu J, Mu S, Wu Z, Jin JM, Tang SY. Dynamic control of toxic natural product biosynthesis by an artificial regulatory circuit. Metab Eng 2020; 57:239-246. [DOI: 10.1016/j.ymben.2019.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 01/10/2023]
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16
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Wang W, Ma Y, He J, Qi H, Xiao F, He S. Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans. Gene 2019; 715:144008. [DOI: 10.1016/j.gene.2019.144008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023]
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17
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A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat Commun 2019; 10:3672. [PMID: 31413315 PMCID: PMC6694116 DOI: 10.1038/s41467-019-11648-1] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/04/2019] [Indexed: 12/26/2022] Open
Abstract
Besides genome editing, CRISPR-Cas12a has recently been used for DNA detection applications with attomolar sensitivity but, to our knowledge, it has not been used for the detection of small molecules. Bacterial allosteric transcription factors (aTFs) have evolved to sense and respond sensitively to a variety of small molecules to benefit bacterial survival. By combining the single-stranded DNA cleavage ability of CRISPR-Cas12a and the competitive binding activities of aTFs for small molecules and double-stranded DNA, here we develop a simple, supersensitive, fast and high-throughput platform for the detection of small molecules, designated CaT-SMelor (CRISPR-Cas12a- and aTF-mediated small molecule detector). CaT-SMelor is successfully evaluated by detecting nanomolar levels of various small molecules, including uric acid and p-hydroxybenzoic acid among their structurally similar analogues. We also demonstrate that our CaT-SMelor directly measured the uric acid concentration in clinical human blood samples, indicating a great potential of CaT-SMelor in the detection of small molecules. Bacterial allosteric transcription factors can sense and respond to a variety of small molecules. Here the authors present CaT-SMelor which uses Cas12a and allosteric transcription factors to detect small molecules in the nanomolar range.
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18
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Engineering the effector specificity of regulatory proteins for the in vitro detection of biomarkers and pesticide residues. Appl Microbiol Biotechnol 2019; 103:3205-3213. [PMID: 30770965 DOI: 10.1007/s00253-019-09679-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/30/2019] [Accepted: 02/02/2019] [Indexed: 02/07/2023]
Abstract
Transcriptional regulatory proteins (TRPs)-based whole-cell biosensors are promising owing to their specificity and sensitivity, but their applications are currently limited. Herein, TRPs were adapted for the extracellular detection of a disease biomarker, uric acid, and a typical pesticide residue, carbaryl. A mutant regulatory protein that specifically recognizes carbaryl as its non-natural effector and activates transcription upon carbaryl binding was developed by engineering the regulatory protein TtgR from Pseudomonas putida. The TtgR mutant responsive to carbaryl and a regulatory protein responsive to uric acid were used for in vitro detection, based on their allosteric binding of operator DNA and inducer molecules. Based on the quantitative polymerase chain reactions (qPCRs) output, the minimum detectable concentration was between 1 nM-1 μM and 1-10 nM for uric acid and carbaryl, respectively. Our results demonstrated that engineering the effector specificity of regulatory proteins is a potential technique for generating molecular recognition elements for not only in vivo but also in vitro applications.
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19
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MarR Family Transcription Factors from Burkholderia Species: Hidden Clues to Control of Virulence-Associated Genes. Microbiol Mol Biol Rev 2018; 83:83/1/e00039-18. [PMID: 30487164 DOI: 10.1128/mmbr.00039-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Species within the genus Burkholderia exhibit remarkable phenotypic diversity. Genomic plasticity, including genome reduction and horizontal gene transfer, has been correlated with virulence traits in several species. However, the conservation of virulence genes in species otherwise considered to have limited potential for infection suggests that phenotypic diversity may not be explained solely on the basis of genetic diversity. Instead, differential organization and control of gene regulatory networks may underlie many phenotypic differences. In this review, we evaluate how regulation of gene expression by members of the multiple antibiotic resistance regulator (MarR) family of transcription factors may contribute to shaping the physiological diversity of Burkholderia species, with a focus on the clinically relevant human pathogens. All Burkholderia species encode a relatively large number of MarR proteins, a feature common to bacteria that must respond to environmental changes such as those associated with host invasion. However, evolution of gene regulatory networks has likely resulted in orthologous transcription factors controlling disparate sets of genes. Adaptation to, and survival in, diverse habitats, including a human or plant host, is key to the success of Burkholderia species as (opportunistic) pathogens, and recent reports suggest that control of virulence-associated genes by MarR proteins features prominently among the survival strategies employed by these species. We suggest that identification of MarR regulons will contribute significantly to clarification of virulence determinants and phenotypic diversity.
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20
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Cross Talk between MarR-Like Transcription Factors Coordinates the Regulation of Motility in Uropathogenic Escherichia coli. Infect Immun 2018; 86:IAI.00338-18. [PMID: 30275009 PMCID: PMC6246914 DOI: 10.1128/iai.00338-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/16/2018] [Indexed: 01/19/2023] Open
Abstract
The MarR-like protein PapX represses the transcription of the flagellar master regulator genes flhDC in uropathogenic Escherichia coli (UPEC), the primary cause of uncomplicated urinary tract infections (UTIs). PapX is encoded by the pap operon, which also encodes the adherence factors termed P fimbriae. The MarR-like protein PapX represses the transcription of the flagellar master regulator genes flhDC in uropathogenic Escherichia coli (UPEC), the primary cause of uncomplicated urinary tract infections (UTIs). PapX is encoded by the pap operon, which also encodes the adherence factors termed P fimbriae. Both adherence and motility are critical for productive colonization of the urinary tract. However, the mechanisms involved in coordinating the transition between adherence and motility are not well characterized. UPEC strain CFT073 carries both papX and a homolog, focX, located in the foc operon encoding F1C fimbriae. In this study, we characterized the dose effects of “X” genes on flagellar gene expression and cross talk between focX and papX. We found that both FocX and PapX repress flhD transcription. However, we determined that the ΔpapX mutant was hypermotile, while the loss of focX did not affect motility. We further investigated this phenotype and found that FocX functions as a repressor of papX. Additionally, we identified a proximal independent promoter upstream of both focX and papX and assessed the expression of focX and papX during culture in human urine and on LB agar plates compared to LB medium. Finally, we characterized the contributions of PapX and FocX to fitness in the ascending murine model of UTI and observed a subtle, but not statistically significant, fitness defect in colonization of the kidneys. Altogether, these results expand our understanding of the impact of carrying multiple X genes on the coordinated regulation of motility and adherence in UPEC.
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21
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Murbach Teles Andrade BF, Nunes Barbosa L, Bérgamo Alves FC, Pereira Marques AF, Albano M, Mores Rall VL, Brüggemann H, Fernandes Júnior A. The impact of Cymbopogon martinii essential oil on Cutibacterium (formerly Propionibacterium) acnes strains and its interaction with keratinocytes. J Pharm Pharmacol 2018; 70:1688-1699. [PMID: 30277563 DOI: 10.1111/jphp.13011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/10/2018] [Indexed: 12/01/2022]
Abstract
OBJECTIVES The human skin microbiota is mainly composed of bacteria belonging to the genera Staphylococcus, Cutibacterium, Micrococcus and Corynebacterium, but on the skin of the face and back, ca. 50% of the total microbiota is represented by the bacterium Cutibacterium acnes. The aim of this research was to evaluate the impact of C. martini EO and its major compound, geraniol, on C. acnes. METHODS The minimum inhibitory concentration against C. acnes strains, phenotypic changes and responses of the proteome was determined. In addition, was assessed the effect of compounds in RNA-binding assay, on C. acnes-exposed keratinocytes and on the C. acnes type distribution on shoulder skin. KEY FINDINGS The range of the MIC was 0.7 to 1.6 mg/ml for the three main C. acnes types. There were no cytotoxic effects of compounds in the absence or presence of C. acnes; after 7 days of exposure to C. martini EO, we could not detect a major shift of the C. acnes types on shoulder skin that was found to be dominated by C. acnes strains of types II and IA2. CONCLUSIONS Our work gives novel insight into the skin microbiota-interacting properties of C. martini EO.
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Affiliation(s)
| | | | - Fernanda Cristina Bérgamo Alves
- Department of Microbiology and Immunology, Institute of Biosciences of Botucatu, UNESP - Campus de Botucatu, Botucatu, SP, Brazil
| | - Ana Flávia Pereira Marques
- Department of Microbiology and Immunology, Institute of Biosciences of Botucatu, UNESP - Campus de Botucatu, Botucatu, SP, Brazil
| | - Mariana Albano
- Department of Microbiology and Immunology, Institute of Biosciences of Botucatu, UNESP - Campus de Botucatu, Botucatu, SP, Brazil
| | - Vera Lúcia Mores Rall
- Department of Microbiology and Immunology, Institute of Biosciences of Botucatu, UNESP - Campus de Botucatu, Botucatu, SP, Brazil
| | | | - Ary Fernandes Júnior
- Department of Microbiology and Immunology, Institute of Biosciences of Botucatu, UNESP - Campus de Botucatu, Botucatu, SP, Brazil
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22
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Teixeira FL, Pauer H, Costa SB, Smith CJ, Domingues RMCP, Rocha ER, Lobo LA. Deletion of BmoR affects the expression of genes related to thiol/disulfide balance in Bacteroides fragilis. Sci Rep 2018; 8:14405. [PMID: 30258073 PMCID: PMC6158253 DOI: 10.1038/s41598-018-32880-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/10/2018] [Indexed: 01/03/2023] Open
Abstract
Bacteroides fragilis, an opportunistic pathogen and commensal bacterium in the gut, is one the most aerotolerant species among strict anaerobes. However, the mechanisms that control gene regulation in response to oxidative stress are not completely understood. In this study, we show that the MarR type regulator, BmoR, regulates the expression of genes involved in the homeostasis of intracellular redox state. Transcriptome analysis showed that absence of BmoR leads to altered expression in total of 167 genes. Sixteen of these genes had a 2-fold or greater change in their expression. Most of these genes are related to LPS biosynthesis and carbohydrates metabolism, but there was a significant increase in the expression of genes related to the redox balance inside the cell. A pyridine nucleotide-disulfide oxidoreductase located directly upstream of bmoR was shown to be repressed by direct binding of BmoR to the promoter region. The expression of two other genes, coding for a thiosulphate:quinone-oxidoreductase and a thioredoxin, are indirectly affected by bmoR mutation during oxygen exposure. Phenotypic assays showed that BmoR is important to maintain the thiol/disulfide balance in the cell, confirming its relevance to B. fragilis response to oxidative stress.
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Affiliation(s)
- Felipe L Teixeira
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA.
| | - Heidi Pauer
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Scarlathe B Costa
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - C Jeffrey Smith
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Regina M C P Domingues
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Edson R Rocha
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Leandro A Lobo
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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23
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Gene Regulation by Redox-Sensitive Burkholderia thailandensis OhrR and Its Role in Bacterial Killing of Caenorhabditis elegans. Infect Immun 2018; 86:IAI.00322-18. [PMID: 29967095 DOI: 10.1128/iai.00322-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/26/2018] [Indexed: 12/16/2022] Open
Abstract
Fatty acid hydroperoxides are involved in host-pathogen interactions. In both plants and mammals, polyunsaturated fatty acids are liberated during infection and enzymatically oxidized to the corresponding toxic hydroperoxides during the defensive oxidative burst that is designed to thwart the infection. The bacterial transcription factor OhrR (organic hydroperoxide reductase regulator) is oxidized by organic hydroperoxides, as a result of which the ohr gene encoding organic hydroperoxide reductase is induced. This enzyme converts the hydroperoxides to less toxic alcohols. We show here that OhrR from Burkholderia thailandensis represses expression of ohr Gene expression is induced by cumene hydroperoxide and to a lesser extent by inorganic oxidants; however, Ohr contributes to degradation only of the organic hydroperoxide. B. thailandensis OhrR, which binds specific sites in both ohr and ohrR promoters, as evidenced by DNase I footprinting, belongs to the 2-Cys subfamily of OhrR proteins, and its oxidation leads to reversible disulfide bond formation between conserved N- and C-terminal cysteines in separate monomers. Oxidation of the N-terminal Cys is sufficient for attenuation of DNA binding in vitro, with complete restoration of DNA binding occurring on addition of a reducing agent. Surprisingly, both overexpression of ohr and deletion of ohr results in enhanced survival on exposure to organic hydroperoxide in vitro While Δohr cells are more virulent in a Caenorhabditis elegans model of infection, ΔohrR cells are less so. Taken together, our data suggest that B. thailandensis OhrR has several unconventional features and that both OhrR and organic hydroperoxides may contribute to virulence.
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24
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A novel signal transduction system for development of uric acid biosensors. Appl Microbiol Biotechnol 2018; 102:7489-7497. [DOI: 10.1007/s00253-018-9056-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 10/28/2022]
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25
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Ugarte-Ruiz M, Domínguez L, Corcionivoschi N, Wren BW, Dorrell N, Gundogdu O. Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry. Res Vet Sci 2018; 119:170-175. [PMID: 29957495 DOI: 10.1016/j.rvsc.2018.06.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 04/25/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022]
Abstract
Campylobacter jejuni is the leading cause of food-borne bacterial enteritis in humans, with contaminated poultry products considered the main source of infection. To survive the food chain, C. jejuni utilizes multiple defense mechanisms that counter oxidative and aerobic stresses. In this study, we phenotypically characterised 63 C. jejuni strains with oxidative stress survival and antimicrobial susceptibility testing to investigate correlations between these two phenotypes against the source of the strains and the presence of the MarR regulators RrpA and RrpB which have a role in regulating the response to oxidative and aerobic stress. C. jejuni strains isolated from meat and neck skin displayed the highest resistance to oxidative stress. In addition, C. jejuni strains that have an rrpA+rrpB- profile exhibit increased resistance to oxidative stress and to antimicrobials. Here we establish a preliminary link between the distribution of RrpA and RrpB and the increased resistance to antimicrobials. This study provides insight into how the genotypic make up of C. jejuni can influence the ability of the bacterium to survive within areas of high oxygen stress, such as the food chain, and subsequently can have a potential negative impact on human health.
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Affiliation(s)
- Maria Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain.
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain; Facultad de Veterinaria, Universidad Complutense Madrid, Madrid, Spain.
| | | | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
| | - Nick Dorrell
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
| | - Ozan Gundogdu
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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26
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Yao Y, Li S, Cao J, Liu W, Fan K, Xiang W, Yang K, Kong D, Wang W. Development of small molecule biosensors by coupling the recognition of the bacterial allosteric transcription factor with isothermal strand displacement amplification. Chem Commun (Camb) 2018; 54:4774-4777. [PMID: 29546904 DOI: 10.1039/c8cc01764f] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here, we demonstrate an easy-to-implement and general biosensing strategy by coupling the small-molecule recognition of the bacterial allosteric transcription factor (aTF) with isothermal strand displacement amplification (SDA) in vitro. Based on this strategy, we developed two biosensors for the detection of an antiseptic, p-hydroxybenzoic acid, and a disease marker, uric acid, using bacterial aTF HosA and HucR, respectively, highlighting the great potential of this strategy for the development of small-molecule biosensors.
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Affiliation(s)
- Yongpeng Yao
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Jiaqian Cao
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Weiwei Liu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
| | - Deming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
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27
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Li H, Liang C, Chen W, Jin JM, Tang SY, Tao Y. Monitoring in vivo metabolic flux with a designed whole-cell metabolite biosensor of shikimic acid. Biosens Bioelectron 2017; 98:457-465. [DOI: 10.1016/j.bios.2017.07.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/01/2017] [Accepted: 07/08/2017] [Indexed: 01/24/2023]
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28
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Wang Y, Wang M, Dong K, Ye H. Engineering Mammalian Designer Cells for the Treatment of Metabolic Diseases. Biotechnol J 2017; 13:e1700160. [PMID: 29144600 DOI: 10.1002/biot.201700160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/03/2017] [Indexed: 12/22/2022]
Abstract
Synthetic biology applies engineering principles to biological systems and has significantly advanced the design of synthetic gene circuits that can reprogram cell activities to perform new functions. The ability to engineer mammalian designer cells with robust therapeutic behaviors has brought new opportunities for treating metabolic diseases. In this review, the authors highlight the most recent advances in the development of synthetic designer cells uploaded with open- or closed-loop gene circuits for the treatment of metabolic disorders including diabetes, hypertension, hyperuricemia, and obesity, and discuss the current technologies and future perspectives in applying these designer cells for clinical applications. In the future, more and more rationally designed cells will be constructed and revolutionized to treat a number of metabolic disorders in an intelligent manner.
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Affiliation(s)
- Yidan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Meiyan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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29
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Deochand DK, Perera IC, Crochet RB, Gilbert NC, Newcomer ME, Grove A. Histidine switch controlling pH-dependent protein folding and DNA binding in a transcription factor at the core of synthetic network devices. MOLECULAR BIOSYSTEMS 2017; 12:2417-26. [PMID: 27282811 DOI: 10.1039/c6mb00304d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Therapeutic strategies have been reported that depend on synthetic network devices in which a urate-sensing transcriptional regulator detects pathological levels of urate and triggers production or release of urate oxidase. The transcription factor involved, HucR, is a member of the multiple antibiotic resistance (MarR) protein family. We show that protonation of stacked histidine residues at the pivot point of long helices that form the scaffold of the dimer interface leads to reversible formation of a molten globule state and significantly attenuated DNA binding at physiological temperatures. We also show that binding of urate to symmetrical sites in each protein lobe is communicated via the dimer interface. This is the first demonstration of regulation of a MarR family transcription factor by pH-dependent interconversion between a molten globule and a compact folded state. Our data further suggest that HucR may be utilized in synthetic devices that depend on detection of pH changes.
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Affiliation(s)
- D K Deochand
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - I C Perera
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - R B Crochet
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - N C Gilbert
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - M E Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - A Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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30
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Deochand DK, Grove A. MarR family transcription factors: dynamic variations on a common scaffold. Crit Rev Biochem Mol Biol 2017; 52:595-613. [PMID: 28670937 DOI: 10.1080/10409238.2017.1344612] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Members of the multiple antibiotic resistance regulator (MarR) family of transcription factors are critical for bacterial cells to respond to chemical signals and to convert such signals into changes in gene activity. Obligate dimers belonging to the winged helix-turn-helix protein family, they are critical for regulation of a variety of functions, including degradation of organic compounds and control of virulence gene expression. The conventional regulatory paradigm is based on a genomic locus in which the gene encoding the MarR protein is divergently oriented from a gene under its control; MarR binding to the intergenic region controls expression of both genes by changing the interaction of RNA polymerase with gene promoters. MarR protein oxidation or binding of a small molecule ligand adversely affects DNA binding, resulting in altered expression of the divergent genes. The generality of this simple paradigm, including the regulation of Escherichia coli MarR by direct binding of antibiotics, has been challenged by reports published in recent years. In addition, structural and biochemical analyses of ligand binding to numerous MarR homologs are converging to identify a shared ligand-binding "hot-spot". This review highlights recent research advances that point to shared features, yet at the same time highlights the remarkable flexibility with which members of this protein family implement responses to inducing signals. A more comprehensive understanding of protein function will pave the way towards the development of both antibacterial agents and biosensors that are based on MarR family proteins.
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Affiliation(s)
- Dinesh K Deochand
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Anne Grove
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
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Grove A. Regulation of Metabolic Pathways by MarR Family Transcription Factors. Comput Struct Biotechnol J 2017; 15:366-371. [PMID: 28694934 PMCID: PMC5487221 DOI: 10.1016/j.csbj.2017.06.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved sophisticated mechanisms for regulation of metabolic pathways. Such regulatory circuits ensure that anabolic pathways remain repressed unless final products are in short supply and that catabolic enzymes are not produced in absence of their substrates. The precisely tuned gene activity underlying such circuits is in the purview of transcription factors that may bind pathway intermediates, which in turn modulate transcription factor function and therefore gene expression. This review focuses on the role of ligand-responsive MarR family transcription factors in controlling expression of genes encoding metabolic enzymes and the mechanisms by which such control is exerted. Prospects for exploiting these transcription factors for optimization of gene expression for metabolic engineering and for the development of biosensors are considered.
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Affiliation(s)
- Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Gupta A, Fuentes SM, Grove A. Redox-Sensitive MarR Homologue BifR from Burkholderia thailandensis Regulates Biofilm Formation. Biochemistry 2017; 56:2315-2327. [PMID: 28406615 DOI: 10.1021/acs.biochem.7b00103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biofilm formation by pathogenic Burkholderia species is a serious complication as it renders the bacteria resistant to antibiotics and host defenses. Using B. thailandensis, we report here a novel redox-sensitive member of the multiple antibiotic resistance regulator (MarR) protein family, BifR, which represses biofilm formation. BifR is encoded as part of the emrB-bifR operon; emrB-bifR is divergent to ecsC, which encodes a putative LasA protease. In Pseudomonas aeruginosa, LasA has been implicated in virulence by contributing to cleavage of elastase. BifR repressed the expression of ecsC and emrB-bifR, and expression was further repressed under oxidizing conditions. BifR bound two sites in the intergenic region between ecsC and emrB-bifR with nanomolar affinity under both reducing and oxidizing conditions; however, oxidized BifR formed a disulfide-linked dimer-of-dimers, a covalent linkage that was absent in BifR-C104A in which the redox-active cysteine was replaced with alanine. BifR also repressed an operon encoding enzymes required for synthesis of phenazine antibiotics, which function as alternate respiratory electron receptors, and inactivation of bifR resulted in enhanced biofilm formation. Taken together, our data suggest that BifR functions to control LasA production and expression of genes involved in biofilm formation, in part by regulating synthesis of alternate electron acceptors that promote survival in the oxygen-limiting environment of a biofilm. The correlation between increased repression of emrB-bifR under oxidative conditions and the formation of a covalently linked BifR dimer-of-dimers suggests that BifR may modulate gene activity in response to cellular redox state.
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Affiliation(s)
- Ashish Gupta
- Department of Biological Sciences, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Stanley M Fuentes
- Department of Biological Sciences, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Li S, Zhou L, Yao Y, Fan K, Li Z, Zhang L, Wang W, Yang K. A platform for the development of novel biosensors by configuring allosteric transcription factor recognition with amplified luminescent proximity homogeneous assays. Chem Commun (Camb) 2017; 53:99-102. [DOI: 10.1039/c6cc07244e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using isolated allosteric transcription factors as recognition elements, a versatile platform was established in vitro to develop sensitive biosensors for the detection of various chemicals.
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Affiliation(s)
- Shanshan Li
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Li Zhou
- Institute of Health Sciences
- Anhui University
- Hefei
- China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Zilong Li
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Lixin Zhang
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
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Agapov AA, Kulbachinskiy AV. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans. BIOCHEMISTRY (MOSCOW) 2016; 80:1201-16. [PMID: 26567564 DOI: 10.1134/s0006297915100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.
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Affiliation(s)
- A A Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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Randazzo P, Aubert-Frambourg A, Guillot A, Auger S. The MarR-like protein PchR (YvmB) regulates expression of genes involved in pulcherriminic acid biosynthesis and in the initiation of sporulation in Bacillus subtilis. BMC Microbiol 2016; 16:190. [PMID: 27542896 PMCID: PMC4992311 DOI: 10.1186/s12866-016-0807-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/07/2016] [Indexed: 12/27/2022] Open
Abstract
Background Cyclodipeptides and their derivatives constitute a large class of peptide natural products with noteworthy biological activities. In some yeasts and bacterial species, pulcherriminic acid derived from cyclo-L-leucyl-L-leucyl is excreted and chelates free ferric ions to form the pulcherrimin. In Bacillus subtilis, the enzymes YvmC and CypX are known to be involved in pulcherriminic acid biosynthesis. However, the mechanisms controlling the transcription of the yvmC-cypX operon are still unknown. Results In this work, we demonstrated that the B. subtilis YvmB MarR-like regulator is the major transcription factor controlling yvmC-cypX expression. A comprehensive quantitative proteomic analysis revealed a wide and prominent effect of yvmB deletion on proteins involved in cellular processes depending on iron availability. In addition, expression of yvmB depends on iron availability. Further analysis with real-time in vivo transcriptional profiling allowed us to define the YvmB regulon. We identified yvmBA, yvmC-cypX and yvnB for negative regulation and yisI for positive regulation. In combination with genetic approaches, gel mobility shift assays indicated that a 14-bp palindromic motif constitutes the YvmB binding site. It was unexpected that YvmB controls expression of yisI, whose encoding protein plays a negative role in the regulation of the sporulation initiation pathway. YvmB appears as an additional regulatory element into the cell’s decision to grow or sporulate. Conclusion Our findings reveal a possible role of the B. subtilis YvmB regulator in the regulatory networks connected to iron metabolism and to the control of proper timing of sporulation. YvmB was renamed as PchR controlling the pulcherriminic acid biosynthetic pathway of B. subtilis. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0807-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paola Randazzo
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Anne Aubert-Frambourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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Deochand DK, Meariman JK, Grove A. pH-Dependent DNA Distortion and Repression of Gene Expression by Pectobacterium atrosepticum PecS. ACS Chem Biol 2016; 11:2049-56. [PMID: 27213700 DOI: 10.1021/acschembio.6b00168] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Transcriptional activity is exquisitely sensitive to changes in promoter DNA topology. Transcription factors may therefore control gene activity by modulating the relative positioning of -10 and -35 promoter elements. The plant pathogen Pectobacterium atrosepticum, which causes soft rot in potatoes, must alter gene expression patterns to ensure growth in planta. In the related soft-rot enterobacterium Dickeya dadantii, PecS functions as a master regulator of virulence gene expression. Here, we report that P. atrosepticum PecS controls gene activity by altering promoter DNA topology in response to pH. While PecS binds the pecS promoter with high affinity regardless of pH, it induces significant DNA distortion only at neutral pH, the pH at which the pecS promoter is repressed in vivo. At pH ∼8, DNA distortions are attenuated, and PecS no longer represses the pecS promoter. A specific histidine (H142) located in a crevice between the dimerization- and DNA-binding regions is required for pH-dependent changes in DNA distortion and repression of gene activity, and mutation of this histidine renders the mutant protein incapable of repressing the pecS promoter. We propose that protonated PecS induces a DNA conformation at neutral pH in which -10 and -35 promoter elements are suboptimally positioned for RNA polymerase binding; on deprotonation of PecS, binding is no longer associated with significant changes in DNA conformation, allowing gene expression. We suggest that this mode of gene regulation leads to differential expression of the PecS regulon in response to alkalinization of the plant apoplast.
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Affiliation(s)
- Dinesh K. Deochand
- Department
of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jacob K. Meariman
- Department
of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Anne Grove
- Department
of Biological
Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Roy A, Reddi R, Sawhney B, Ghosh DK, Addlagatta A, Ranjan A. Expression, Functional Characterization and X-ray Analysis of HosA, A Member of MarR Family of Transcription Regulator from Uropathogenic Escherichia coli. Protein J 2016; 35:269-82. [DOI: 10.1007/s10930-016-9670-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.
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Sivapragasam S, Grove A. Streptomyces coelicolor XdhR is a direct target of (p)ppGpp that controls expression of genes encoding xanthine dehydrogenase to promote purine salvage. Mol Microbiol 2016; 100:701-18. [PMID: 26833627 DOI: 10.1111/mmi.13342] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2016] [Indexed: 12/20/2022]
Abstract
The gene encoding Streptomyces coelicolor xanthine dehydrogenase regulator (XdhR) is divergently oriented from xdhABC, which encodes xanthine dehydrogenase (Xdh). Xdh is required for purine salvage pathways. XdhR was previously shown to repress xdhABC expression. We show that XdhR binds the xdhABC-xdhR intergenic region with high affinity (Kd ∼ 0.5 nM). DNaseI footprinting reveals that this complex formation corresponds to XdhR binding the xdhR gene promoter at two adjacent sites; at higher protein concentrations, protection expands to a region that overlaps the transcriptional and translational start sites of xdhABC. While substrates for Xdh have little effect on DNA binding, GTP and ppGpp dissociate the DNA-XdhR complex. Progression of cells to stationary phase, a condition associated with increased (p)ppGpp production, leads to elevated xdhB expression; in contrast, inhibition of Xdh by allopurinol results in xdhB repression. We propose that XdhR is a direct target of (p)ppGpp, and that expression of xdhABC is upregulated during the stringent response to promote purine salvage pathways, maintain GTP homeostasis and ensure continued (p)ppGpp synthesis. During exponential phase growth, basal levels of xdhABC expression may be achieved by GTP serving as a lower-affinity XdhR ligand.
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Affiliation(s)
- Smitha Sivapragasam
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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Pagliai FA, Gonzalez CF, Lorca GL. Identification of a Ligand Binding Pocket in LdtR from Liberibacter asiaticus. Front Microbiol 2015; 6:1314. [PMID: 26635775 PMCID: PMC4658428 DOI: 10.3389/fmicb.2015.01314] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
LdtR is a transcriptional activator involved in the regulation of a putative L,D transpeptidase in Liberibacter asiaticus, an unculturable pathogen and one of the causative agents of Huanglongbing disease. Using small molecule screens we identified benzbromarone as an inhibitor of LdtR activity, which was confirmed using in vivo and in vitro assays. Based on these previous results, the objective of this work was to identify the LdtR ligand binding pocket and characterize its interactions with benzbromarone. A structural model of LdtR was constructed and the molecular interactions with the ligand were predicted using the SwissDock interface. Using site-directed mutagenesis, these residues were changed to alanine. Electrophoretic mobility shift assays, thermal denaturation, isothermal titration calorimetry experiments, and in vivo assays were used to identify residues T43, L61, and F64 in the Benz1 pocket of LdtR as the amino acids most likely involved in the binding to benzbromarone. These results provide new information on the binding mechanism of LdtR to a modulatory molecule and provide a blue print for the design of therapeutics for other members of the MarR family of transcriptional regulators involved in pathogenicity.
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Affiliation(s)
- Fernando A Pagliai
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville FL, USA
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville FL, USA
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville FL, USA
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Wang ZC, Liu CJ, Huang YJ, Wang YS, Peng HL. PecS regulates the urate-responsive expression of type 1 fimbriae in Klebsiella pneumoniae CG43. MICROBIOLOGY-SGM 2015; 161:2395-409. [PMID: 26385366 DOI: 10.1099/mic.0.000185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In the Klebsiella pneumoniae CG43 genome, the divergently transcribed genes coding for PecS, the MarR-type transcription factor, and PecM, the drug metabolite transporter, are located between the type 1 and type 3 fimbrial gene clusters. The intergenic sequence pecO between pecS and pecM contains three putative PecS binding sites and a CpxR box. Electrophoretic mobility shift assay revealed that the recombinant PecS and CpxR could specifically bind to the pecO sequence, and the specific interaction of PecS and pecO could be attenuated by urate. The expression of pecS and pecM was negatively regulated by CpxAR and PecS, and was inducible by exogenous urate in the absence of cpxAR. Compared with CG43S3ΔcpxAR, the derived mutants CG43S3ΔcpxARΔpecS and CG43S3ΔcpxARΔpecSΔpecM exerted similar levels of sensitivity to H2O2 or paraquat, but higher levels of mannose-sensitive yeast agglutination activity and FimA production. The promoter activity and transcript levels of fimA in CG43S3ΔcpxAR were also increased by deleting pecS. However, no binding activity between PecS and the fimA promoter could be observed. Nevertheless, PecS deletion could reduce the expression of the global regulator HNS and release the negative effect of HNS on FimA expression. In CG43S3ΔcpxAR, the expression of FimA as well as PecS was inducible by urate, whilst urate-induced FimA expression was inhibited by the deletion of pecS. Taken together, we propose that K. pneumoniae PecS indirectly and negatively regulates the expression of type 1 fimbriae, and the regulation is urate-inducible in the absence of CpxAR.
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Affiliation(s)
- Zhe-Chong Wang
- 1 Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsin Chu, ROC
| | - Chia-Jui Liu
- 1 Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsin Chu, ROC
| | - Ying-Jung Huang
- 2 Division of Hematology-Oncology, Chang Gung Memorial Hospital, Tao Yuan, ROC
| | - Yu-Seng Wang
- 1 Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsin Chu, ROC
| | - Hwei-Ling Peng
- 1 Department of Biological Science and Technology, School of Biological Science and Technology, National Chiao Tung University, Hsin Chu, ROC
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Gundogdu O, da Silva DT, Mohammad B, Elmi A, Mills DC, Wren BW, Dorrell N. The Campylobacter jejuni MarR-like transcriptional regulators RrpA and RrpB both influence bacterial responses to oxidative and aerobic stresses. Front Microbiol 2015; 6:724. [PMID: 26257713 PMCID: PMC4508579 DOI: 10.3389/fmicb.2015.00724] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/02/2015] [Indexed: 11/13/2022] Open
Abstract
The ability of the human intestinal pathogen Campylobacter jejuni to respond to oxidative stress is central to bacterial survival both in vivo during infection and in the environment. Re-annotation of the C. jejuni NCTC11168 genome revealed the presence of two MarR-type transcriptional regulators Cj1546 and Cj1556, originally annotated as hypothetical proteins, which we have designated RrpA and RrpB (regulator of response to peroxide) respectively. Previously we demonstrated a role for RrpB in both oxidative and aerobic (O2) stress and that RrpB was a DNA binding protein with auto-regulatory activity, typical of MarR-type transcriptional regulators. In this study, we show that RrpA is also a DNA binding protein and that a rrpA mutant in strain 11168H exhibits increased sensitivity to hydrogen peroxide oxidative stress. Mutation of either rrpA or rrpB reduces catalase (KatA) expression. However, a rrpAB double mutant exhibits higher levels of resistance to hydrogen peroxide oxidative stress, with levels of KatA expression similar to the wild-type strain. Mutation of either rrpA or rrpB also results in a reduction in the level of katA expression, but this reduction was not observed in the rrpAB double mutant. Neither the rrpA nor rrpB mutant exhibits any significant difference in sensitivity to either cumene hydroperoxide or menadione oxidative stresses, but both mutants exhibit a reduced ability to survive aerobic (O2) stress, enhanced biofilm formation and reduced virulence in the Galleria mellonella infection model. The rrpAB double mutant exhibits wild-type levels of biofilm formation and wild-type levels of virulence in the G mellonella infection model. Together these data indicate a role for both RrpA and RrpB in the C. jejuni peroxide oxidative and aerobic (O2) stress responses, enhancing bacterial survival in vivo and in the environment.
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Affiliation(s)
- Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
| | - Daiani T da Silva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
| | - Banaz Mohammad
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
| | - Abdi Elmi
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
| | - Dominic C Mills
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
| | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
| | - Nick Dorrell
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine , London, UK
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Zhang Y, Luo F, Wu D, Hikichi Y, Kiba A, Igarashi Y, Ding W, Ohnishi K. PrhN, a putative marR family transcriptional regulator, is involved in positive regulation of type III secretion system and full virulence of Ralstonia solanacearum. Front Microbiol 2015; 6:357. [PMID: 25972849 PMCID: PMC4412082 DOI: 10.3389/fmicb.2015.00357] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/09/2015] [Indexed: 11/13/2022] Open
Abstract
The MarR-family of transcriptional regulators are involved in various cellular processes, including resistance to multiple antibiotics and other toxic chemicals, adaptation to different environments and pathogenesis in many plant and animal pathogens. Here, we reported a new MarR regulator PrhN, which was involved in the pathogenesis of Ralstonia solanacearum. prhN mutant exhibited significantly reduced virulence and stem colonization compared to that of wild type in tomato plants. prhN mutant caused identical hypersensitive response (HR) on resistant plants to the wild type. Deletion of prhN gene substantially reduced the expression of type III secretion system (T3SS) in vitro and in planta (mainly in tomato plants), which is essential for pathogenicity of R. solanacearum, and the complemented PrhN could restore its virulence and T3SS expression to that of wild type. T3SS is directly controlled by AraC-type transcriptional regulator HrpB, and the transcription of hrpB is activated by HrpG and PrhG. HrpG and PrhG are homologs but are regulated by the PhcA positively and negatively, respectively. Deletion of prhN gene also abolished the expression of hrpB and prhG, but didn't change the expression of hrpG and phcA. Together, these results indicated that PrhN positively regulates T3SS expression through PrhG and HrpB. PrhN and PhcA should regulate prhG expression in a parallel way. This is the first report on the pathogenesis of MarR regulator in R. solanacearum, and this new finding will improve our understanding on the various biological functions of MarR regulator and the complex regulatory network on hrp regulon in R. solanacearum.
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Affiliation(s)
- Yong Zhang
- Research Center of Bioenergy and Bioremediation, Southwest University Chongqing, China
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, Southwest University Chongqing, China
| | - Dousheng Wu
- College of Plant Protection, Southwest University Chongqing, China
| | - Yasufumi Hikichi
- Laboratory of Plant Pathology and Biotechnology, Kochi University Kochi, Japan
| | - Akinori Kiba
- Laboratory of Plant Pathology and Biotechnology, Kochi University Kochi, Japan
| | - Yasuo Igarashi
- Research Center of Bioenergy and Bioremediation, Southwest University Chongqing, China
| | - Wei Ding
- College of Plant Protection, Southwest University Chongqing, China
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University Kochi, Japan
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Abstract
Trans-aconitate methyltransferase regulator (TamR) is a member of the ligand-responsive multiple antibiotic resistance regulator (MarR) family of transcription factors. In Streptomyces coelicolor, TamR regulates transcription of tamR (encoding TamR), tam (encoding trans-aconitate methyltransferase) and sacA (encoding aconitase); up-regulation of these genes promotes metabolic flux through the citric acid cycle. DNA binding by TamR is attenuated and transcriptional derepression is achieved on binding of ligands such as citrate and trans-aconitate to TamR. In the present study, we show that three additional genes are regulated by S. coelicolor TamR. Genes encoding malate synthase (aceB1; SCO6243), malate dehydrogenase (mdh; SCO4827) and isocitrate dehydrogenase (idh; SCO7000) are up-regulated in vivo when citrate and trans-aconitate accumulate, and TamR binds the corresponding gene promoters in vitro, a DNA binding that is attenuated by cognate ligands. Mutations to the TamR binding site attenuate DNA binding in vitro and result in constitutive promoter activity in vivo. The predicted TamR binding sites are highly conserved in the promoters of these genes in Streptomyces species that encode divergent tam-tamR gene pairs, suggesting evolutionary conservation. Like aconitase and trans-aconitate methyltransferase, malate dehydrogenase, isocitrate dehydrogenase and malate synthase are closely related to the citric acid cycle, either catalysing individual reaction steps or, in the case of malate synthase, participating in the glyoxylate cycle to produce malate that enters the citric acid cycle to replenish the intermediate pool. Taken together, our data suggest that TamR plays an important and conserved role in promoting metabolic flux through the citric acid cycle.
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The Bacillus subtilis tyrZ gene encodes a highly selective tyrosyl-tRNA synthetase and is regulated by a MarR regulator and T box riboswitch. J Bacteriol 2015; 197:1624-31. [PMID: 25733610 DOI: 10.1128/jb.00008-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/19/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Misincorporation of D-tyrosine (D-Tyr) into cellular proteins due to mischarging of tRNA(Tyr) with D-Tyr by tyrosyl-tRNA synthetase inhibits growth and biofilm formation of Bacillus subtilis. Furthermore, many B. subtilis strains lack a functional gene encoding D-aminoacyl-tRNA deacylase, which prevents misincorporation of D-Tyr in most organisms. B. subtilis has two genes that encode tyrosyl-tRNA synthetase: tyrS is expressed under normal growth conditions, and tyrZ is known to be expressed only when tyrS is inactivated by mutation. We hypothesized that tyrZ encodes an alternate tyrosyl-tRNA synthetase, expression of which allows the cell to grow when D-Tyr is present. We show that TyrZ is more selective for L-Tyr over D-Tyr than is TyrS; however, TyrZ is less efficient overall. We also show that expression of tyrZ is required for growth and biofilm formation in the presence of D-Tyr. Both tyrS and tyrZ are preceded by a T box riboswitch, but tyrZ is found in an operon with ywaE, which is predicted to encode a MarR family transcriptional regulator. Expression of tyrZ is repressed by YwaE and also is regulated at the level of transcription attenuation by the T box riboswitch. We conclude that expression of tyrZ may allow growth when excess D-Tyr is present. IMPORTANCE Accurate protein synthesis requires correct aminoacylation of each tRNA with the cognate amino acid and discrimination against related compounds. Bacillus subtilis produces D-Tyr, an analog of L-Tyr that is toxic when incorporated into protein, during stationary phase. Most organisms utilize a D-aminoacyl-tRNA deacylase to prevent misincorporation of D-Tyr. This work demonstrates that the increased selectivity of the TyrZ form of tyrosyl-tRNA synthetase may provide a mechanism by which B. subtilis prevents misincorporation of D-Tyr in the absence of a functional D-aminoacyl-tRNA deacylase gene.
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Affiliation(s)
- Asim K. Mandal
- Renal Divisions, Brigham and Women's Hospital and VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts 02115;
| | - David B. Mount
- Renal Divisions, Brigham and Women's Hospital and VA Boston Healthcare System, Harvard Medical School, Boston, Massachusetts 02115;
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Liang C, Xiong D, Zhang Y, Mu S, Tang SY. Development of a novel uric-acid-responsive regulatory system in Escherichia coli. Appl Microbiol Biotechnol 2014; 99:2267-75. [DOI: 10.1007/s00253-014-6290-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/14/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
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Mol M, Raj Bejugam P, Singh S. Synthetic biology at the interface of functional genomics. Brief Funct Genomics 2014; 14:180-8. [PMID: 25212484 DOI: 10.1093/bfgp/elu031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Functional genomics is considered a powerful tool that helps understand the relation between an organism's genotype and possible phenotypes. Volumes of data generated on several 'omics' platforms have revealed the network complexities underlying biological processes. Systems and synthetic biology have garnered much attention because of the ability to infer and comprehend the uncertainties associated with such complexities. Also, part-wise characterization of the network components (e.g. DNA, RNA, protein) has rendered an engineering perspective in life sciences to build modular and functional devices. This approach can be used to combat one of the many concerns of the world, i.e. in the area of biomedical translational research by designing and constructing novel therapeutic devices to intervene network perturbation in a diseased state to transform to a healthy state.
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Gupta A, Grove A. Ligand-binding pocket bridges DNA-binding and dimerization domains of the urate-responsive MarR homologue MftR from Burkholderia thailandensis. Biochemistry 2014; 53:4368-80. [PMID: 24955985 PMCID: PMC4100783 DOI: 10.1021/bi500219t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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Members of the multiple antibiotic
resistance regulator (MarR)
family often regulate gene activity by responding to a specific ligand.
In the absence of ligand, most MarR proteins function as repressors,
while ligand binding causes attenuated DNA binding and therefore increased
gene expression. Previously, we have shown that urate is a ligand
for MftR (major facilitator transport regulator), which is encoded
by the soil bacterium Burkholderia thailandensis.
We show here that both mftR and the divergently oriented
gene mftP encoding a major facilitator transport
protein are upregulated in the presence of urate. MftR binds two cognate
sites in the mftR-mftP intergenic region with equivalent
affinity and sensitivity to urate. Mutagenesis of four conserved residues
previously reported to be involved in urate binding to Deinococcus
radiodurans HucR and Rhizobium radiobacter PecS significantly reduced protein stability and DNA binding affinity
but not ligand binding. These data suggest that residues equivalent
to those implicated in ligand binding to HucR and PecS serve structural
roles and that MftR relies on distinct residues for ligand binding.
MftR exhibits a two-step melting transition suggesting independent
unfolding of the dimerization and DNA-binding regions; urate binding
or mutations in the predicted ligand-binding sites result in one-step
unfolding transitions. We suggest that MftR binds the ligand in a
cleft between the DNA-binding lobes and the dimer interface but that
the mechanism of ligand-mediated attenuation of DNA binding differs
from that proposed for other urate-responsive MarR homologues. Since
DNA binding by MftR is attenuated at 37 °C, our data also suggest
that MftR responds to both ligand and a thermal upshift by attenuated
DNA binding and upregulation of the genes under its control.
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Affiliation(s)
- Ashish Gupta
- Department of Biological Sciences, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Mustakhimov II, Reshetnikov AS, Fedorov DN, Khmelenina VN, Trotsenko YA. Role of EctR as transcriptional regulator of ectoine biosynthesis genes in Methylophaga thalassica. BIOCHEMISTRY (MOSCOW) 2013; 77:857-63. [PMID: 22860907 DOI: 10.1134/s0006297912080068] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the halophilic aerobic methylotrophic bacterium Methylophaga thalassica, the genes encoding the enzymes for biosynthesis of the osmoprotectant ectoine were shown to be located in operon ectABC-ask. Transcription of the ect-operon was started from the two promoters homologous to the σ(70)-dependent promoter of Escherichia coli and regulated by protein EctR, whose encoding gene, ectR, is transcribed from three promoters. Genes homologous to ectR of methylotrophs were found in clusters of ectoine biosynthesis genes in some non-methylotrophic halophilic bacteria. EctR proteins of methylotrophic and heterotrophic halophiles belong to the MarR-family of transcriptional regulators but form a separate branch on the phylogenetic tree of the MarR proteins.
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Affiliation(s)
- I I Mustakhimov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, 142290 Pushchino, Moscow Region, Russia
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