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Pham C, Nasr MA, Skarina T, Di Leo R, Kwan DH, Martin VJJ, Stogios PJ, Mahadevan R, Savchenko A. Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors. FEBS J 2024; 291:3481-3498. [PMID: 38696354 DOI: 10.1111/febs.17149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- The Institute of Biomedical Engineering, University of Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Canada
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Ma Z, Li Y, Lu Z, Pan J, Li M. A novel biosensor-based method for the detection of p-nitrophenol in agricultural soil. CHEMOSPHERE 2023; 313:137306. [PMID: 36410515 DOI: 10.1016/j.chemosphere.2022.137306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/19/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Directly measurement of the bioavailable concentration of soil contaminants is essential for their accurate risk assessment. In this study, we successfully modified and identified the key genetic elements (pobR1-3) for the bio-detection of p-nitrophenol and synthesized five novel whole-cell biosensors (Escherichia coli BL21/pPNP-mrfp, E. coli BL21/pPNP-CFP, E. coli BL21/pPNP-YFP, E. coli BL21/pPNP-GFP, and E. coli BL21/pPNP-amilCP) to directly detect the concentration of p-nitrophenol in soils. These biosensor methods contained a simple biosensor activation and sample extraction step, a cost-effective detection means, and a fast detection process (5 h) by using a 96-microwell plate with a low background value and high-reliability equation for p-nitrophenol detection. These biosensors had a detection limit of 6.21-25.2 μg/kg and a linear range of 10-10000 μg/kg for p-nitrophenol in four soils. All biosensors showed better detection performance in the detection of p-nitrophenol in soil samples. The biosensors method can help to quickly and directly assess the actual bioavailable fractions of p-nitrophenol in soils, thus facilitating to understand the environmental cycling of p-nitrophenol.
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Affiliation(s)
- Zhao Ma
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, 518060, PR China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
| | - Yuanbo Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, PR China.
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Clara L, David C, Laila S, Virginie R, Marie-Joelle V. Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances in S. lividans and S. coelicolor Suggests a Link between Various Stresses and Antibiotic Production. Int J Mol Sci 2022; 23:ijms232314792. [PMID: 36499130 PMCID: PMC9739823 DOI: 10.3390/ijms232314792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Streptomyces coelicolor and Streptomyces lividans constitute model strains to study the regulation of antibiotics biosynthesis in Streptomyces species since these closely related strains possess the same pathways directing the biosynthesis of various antibiotics but only S. coelicolor produces them. To get a better understanding of the origin of the contrasted abilities of these strains to produce bioactive specialized metabolites, these strains were grown in conditions of phosphate limitation or proficiency and a comparative analysis of their transcriptional/regulatory proteins was carried out. The abundance of the vast majority of the 355 proteins detected greatly differed between these two strains and responded differently to phosphate availability. This study confirmed, consistently with previous studies, that S. coelicolor suffers from nitrogen stress. This stress likely triggers the degradation of the nitrogen-rich peptidoglycan cell wall in order to recycle nitrogen present in its constituents, resulting in cell wall stress. When an altered cell wall is unable to fulfill its osmo-protective function, the bacteria also suffer from osmotic stress. This study thus revealed that these three stresses are intimately linked in S. coelicolor. The aggravation of these stresses leading to an increase of antibiotic biosynthesis, the connection between these stresses, and antibiotic production are discussed.
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Affiliation(s)
- Lejeune Clara
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Cornu David
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Sago Laila
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Redeker Virginie
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Laboratory of Neurodegenerative Diseases, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) and Centre National de la Recherche Scientifique (CNRS), Molecular Imaging Center (MIRCen), Institut François Jacob, Université Paris-Saclay, 92260 Fontenay-aux-Roses, France
| | - Virolle Marie-Joelle
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Correspondence:
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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Ghimire N, Kim B, Lee CM, Oh TJ. Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660. BMC Genomics 2022; 23:375. [PMID: 35585492 PMCID: PMC9115942 DOI: 10.1186/s12864-022-08589-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Background While the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 is a lichen-associated bacterium isolated from Antarctica. The work presents the genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp. PAMC26660. Additionally, the accessory, core and unique genes were identified among Variovorax species using the pan genome analysis tool. A detailed analysis of the genes related to xenobiotic metabolism revealed the potential roles of Variovorax sp. PAMC26660 and other species in bioremediation. Results TYGS analysis, dDDH, phylogenetic placement and average nucleotide identity (ANI) analysis identified the strain as Variovorax sp. Cell morphology was assessed using scanning electron microscopy (SEM). On analysis of the core, accessory, and unique genes, xenobiotic metabolism accounted only for the accessory and unique genes. On detailed analysis of the aromatic compound catabolic genes, peripheral pathway related to 4-hydroxybenzoate (4-HB) degradation was found among all species while phenylacetate and tyrosine degradation pathways were present in most of the species including PAMC26660. Likewise, central catabolic pathways, like protocatechuate, gentisate, homogentisate, and phenylacetyl-CoA, were also present. The peripheral pathway for 4-HB degradation was functionally tested using PAMC26660, which resulted in the growth using it as a sole source of carbon. Conclusions Computational tools for genome and pan genome analysis are important to understand the behavior of an organism. Xenobiotic metabolism-related genes, that only account for the accessory and unique genes infer evolution through events like lateral gene transfer, mutation and gene rearrangement. 4-HB, an aromatic compound present among lichen species is utilized by lichen-associated Variovorax sp. PAMC26660 as the sole source of carbon. The strain holds genes and pathways for its utilization. Overall, this study outlines the importance of Variovorax in bioremediation and presents the genomic information of the species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08589-3.
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Affiliation(s)
- Nisha Ghimire
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea
| | - Chang-Muk Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 55365, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Korea. .,Genome-based BioIT Convergence Institute, Asan, 31460, Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, South Korea.
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Akiyama T, Sasaki Y, Ito S, Yajima S. Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140644. [PMID: 33716191 DOI: 10.1016/j.bbapap.2021.140644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
Microbacterium hydrocarbonoxydans has been isolated using an unnatural acylhydrazide compound as the sole carbon source. The compound is hydrolyzed by bacterial hydrazidase, and the gene expression of the enzyme is considered to be controlled by a transcription factor of the Isocitrate lyase Regulator (IclR) family, belonging to the one-component signaling systems. Recently, we reported the crystal structure of an unliganded IclR homolog from M. hydrocarbonoxydans, named putative 4-hydroxybenzoate response regulator (pHbrR), which has a unique homotetramer conformation. In this study, we report the crystal structure of pHbrR complexed with 4-hydroxybenzoic acid, the catalytic product of hydrazidase, at 2.0 Å resolution. pHbrR forms a homodimer with multimeric rearrangement in the unliganded state. Gel filtration column chromatography results suggested dimer-tetramer rearrangement. We observed conformational change in the loop region covering the ligand-binding site, and domain rearrangements in the monomer. This study reports the first liganded IclR family protein structure that demonstrates large structural rearrangements between liganded and unliganded proteins, which may represent a general model for IclRs.
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Affiliation(s)
- Tomonori Akiyama
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinsaku Ito
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan.
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Chen B, Li RF, Zhou L, Qiu JH, Song K, Tang JL, He YW. The phytopathogen Xanthomonas campestris utilizes the divergently transcribed pobA/pobR locus for 4-hydroxybenzoic acid recognition and degradation to promote virulence. Mol Microbiol 2020; 114:870-886. [PMID: 32757400 DOI: 10.1111/mmi.14585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/29/2020] [Indexed: 01/26/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot in crucifers. Our previous findings revealed that Xcc can degrade 4-hydroxybenzoic acid (4-HBA) via the β-ketoadipate pathway. This present study expands on this knowledge in several ways. First, we show that infective Xcc cells induce in situ biosynthesis of 4-HBA in host plants, and Xcc can efficiently degrade 4-HBA via the pobA/pobR locus, which encodes a 4-hydroxybenzoate hydroxylase and an AraC-family transcription factor respectively. Next, the transcription of pobA is specifically induced by 4-HBA and is positively regulated by PobR, which is constitutively expressed in Xcc. 4-HBA directly binds to PobR dimers, resulting in activation of pobA expression. Point mutation and subsequent isothermal titration calorimetry and size exclusion chromatography analysis identified nine key conserved residues required for 4-HBA binding and/or dimerization of PobR. Furthermore, overlapping promoters harboring fully overlapping -35 elements were identified between the divergently transcribed pobA and pobR. The 4-HBA/PobR dimer complex specifically binds to a 25-bp site, which encompasses the -35 elements shared by the overlapping promoters. Finally, GUS histochemical staining and subsequent quantitative assay showed that both pobA and pobR genes are transcribed during Xcc infection of Chinese radish, and the strain ΔpobR exhibited compromised virulence in Chinese radish. These findings suggest that the ability of Xcc to survive the 4-HBA stress might be important for its successful colonization of host plants.
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Affiliation(s)
- Bo Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Fang Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lian Zhou
- Zhiyuan Innovation Research Centre, Student Innovation Institute, Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Hui Qiu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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