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Kan J, Peng T, Huang T, Xiong G, Hu Z. NarL, a Novel Repressor for CYP108j1 Expression during PAHs Degradation in Rhodococcus sp. P14. Int J Mol Sci 2020; 21:ijms21030983. [PMID: 32024188 PMCID: PMC7037279 DOI: 10.3390/ijms21030983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
Rhodococcus sp. P14 was isolated from crude-oil-contaminated sediments, and a wide range of polycyclic aromatic hydrocarbons (PAHs) could be used as the sole source of carbon and energy. A key CYP450 gene, designated as cyp108j1 and involved in the degradation of PAHs, was identified and was able to hydroxylate various PAHs. However, the regulatory mechanism of the expression of cyp108j1 remains unknown. In this study, we found that the expression of cyp108j1 is negatively regulated by a LuxR (helix-turn-helix transcription factors in acyl-homoserine lactones-mediated quorum sensing) family regulator, NarL (nitrate-dependent two-component regulatory factor), which is located upstream of cyp108j1. Further analysis revealed that NarL can directly bind to the promoter region of cyp108j1. Mutational experiments demonstrated that the binding site between NarL and the cyp108j1 promoter was the palindromic sequence GAAAGTTG-CAACTTTC. Together, the finding reveal that NarL is a novel repressor for the expression of cyp108j1 during PAHs degradation.
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Affiliation(s)
- Jie Kan
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
| | - Tao Peng
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
| | - Guangming Xiong
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, 24103 Kiel, Germany;
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
- Correspondence:
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Stanislauskienė R, Kutanovas S, Kalinienė L, Bratchikov M, Meškys R. Tetramethylpyrazine-Inducible Promoter Region from Rhodococcus jostii TMP1. Molecules 2018; 23:molecules23071530. [PMID: 29941849 PMCID: PMC6099782 DOI: 10.3390/molecules23071530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 11/17/2022] Open
Abstract
An inducible promoter region, PTTMP (tetramethylpyrazine [TTMP]), has been identified upstream of the tpdABC operon, which contains the genes required for the initial degradation of 2,3,5,6-tetramethylpyrazine in Rhodococcus jostii TMP1 bacteria. In this work, the promoter region was fused with the gene for the enhanced green fluorescent protein (EGFP) to investigate the activity of PTTMP by measuring the fluorescence of bacteria. The highest promoter activity was observed when bacteria were grown in a nutrient broth (NB) medium supplemented with 5 mM 2,3,5,6-tetramethylpyrazine for 48 h. Using a primer extension reaction, two transcriptional start sites for tpdA were identified, and the putative −35 and −10 promoter motifs were determined. The minimal promoter along with two 15 bp long direct repeats and two 7 bp inverted sequences were identified. Also, the influence of the promoter elements on the activity of PTTMP were determined using site-directed mutagenesis. Furthermore, PTTMP was shown to be induced by pyrazine derivatives containing methyl groups in the 2- and 5-positions of the heterocyclic ring, in the presence of the LuxR family transcriptional activator TpdR.
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Affiliation(s)
- Rūta Stanislauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Simonas Kutanovas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Laura Kalinienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Maksim Bratchikov
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio 21, LT-03101 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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Goutam K, Gupta AK, Gopal B. The fused SnoaL_2 domain in the Mycobacterium tuberculosis sigma factor σJ modulates promoter recognition. Nucleic Acids Res 2017; 45:9760-9772. [PMID: 28934483 PMCID: PMC5766207 DOI: 10.1093/nar/gkx609] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022] Open
Abstract
Extra-cytoplasmic function (ECF) σ-factors are widespread in bacteria, linking environmental stimuli with changes in gene expression. These transcription factors span several phylogenetically distinct groups and are remarkably diverse in their activation and regulatory mechanisms. Here, we describe the structural and biochemical features of a Mycobacterium tuberculosis ECF factor σJ that suggests that the SnoaL_2 domain at the C-terminus can modulate the activity of this initiation factor in the absence of a cognate regulatory anti-σ factor. M. tuberculosis σJ can bind promoter DNA in vitro; this interaction is substantially impaired by the removal of the SnoaL_2 domain. This finding is consistent with assays to evaluate σJ-mediated gene expression. Structural similarity of the SnoaL_2 domain with epoxide hydrolases also suggests a novel functional role for this domain. The conserved sequence features between M. tuberculosis σJ and other members of the ECF41 family of σ-factors suggest that the regulatory mechanism involving the C-terminal SnoaL_2 domain is likely to be retained in this family of proteins. These studies suggest that the ECF41 family of σ-factors incorporate features of both-the σ70 family and bacterial one-component systems thereby providing a direct mechanism to implement environment-mediated transcription changes.
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Affiliation(s)
- Kapil Goutam
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Arvind K Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balasubramanian Gopal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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Singh J, Thakur IS. Evaluation of cyanobacterial endolith Leptolyngbya sp. ISTCY101, for integrated wastewater treatment and biodiesel production: A toxicological perspective. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.07.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Batchelor JD, Lee PS, Wang AC, Doucleff M, Wemmer DE. Structural mechanism of GAF-regulated σ(54) activators from Aquifex aeolicus. J Mol Biol 2013; 425:156-70. [PMID: 23123379 PMCID: PMC3544215 DOI: 10.1016/j.jmb.2012.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/26/2012] [Accepted: 10/26/2012] [Indexed: 11/22/2022]
Abstract
The σ subunits of bacterial RNA polymerase occur in many variant forms and confer promoter specificity to the holopolymerase. Members of the σ(54) family of σ subunits require the action of a 'transcriptional activator' protein to open the promoter and initiate transcription. The activator proteins undergo regulated assembly from inactive dimers to hexamers that are active ATPases. These contact σ(54) directly and, through ATP hydrolysis, drive a conformational change that enables promoter opening. σ(54) activators use several different kinds of regulatory domains to respond to a wide variety of intracellular signals. One common regulatory module, the GAF domain, is used by σ(54) activators to sense small-molecule ligands. The structural basis for GAF domain regulation in σ(54) activators has not previously been reported. Here, we present crystal structures of GAF regulatory domains for Aquifex aeolicus σ(54) activators NifA-like homolog (Nlh)2 and Nlh1 in three functional states-an 'open', ATPase-inactive state; a 'closed', ATPase-inactive state; and a 'closed', ligand-bound, ATPase-active state. We also present small-angle X-ray scattering data for Nlh2-linked GAF-ATPase domains in the inactive state. These GAF domain dimers regulate σ(54) activator proteins by holding the ATPase domains in an inactive dimer conformation. Ligand binding of Nlh1 dramatically remodels the GAF domain dimer interface, disrupting the contacts with the ATPase domains. This mechanism has strong parallels to the response to phosphorylation in some two-component regulated σ(54) activators. We describe a structural mechanism of GAF-mediated enzyme regulation that appears to be conserved among humans, plants, and bacteria.
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Affiliation(s)
- Joseph D. Batchelor
- Graduate Group in Biophysics and Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720
| | - Peter S. Lee
- Graduate Group in Biophysics and Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720
| | - Andrew C. Wang
- Graduate Group in Biophysics and Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720
| | - Michaeleen Doucleff
- Graduate Group in Biophysics and Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720
| | - David E. Wemmer
- Graduate Group in Biophysics and Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720
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Cloning of dfdA genes from Terrabacter sp. strain DBF63 encoding dibenzofuran 4,4a-dioxygenase and heterologous expression in Streptomyces lividans. Appl Microbiol Biotechnol 2012. [DOI: 10.1007/s00253-012-4565-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Peng P, Yang H, Jia R, Li L. Biodegradation of dioxin by a newly isolated Rhodococcus sp. with the involvement of self-transmissible plasmids. Appl Microbiol Biotechnol 2012; 97:5585-95. [DOI: 10.1007/s00253-012-4363-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 10/27/2022]
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Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries N,N-dimethylformamide degradation-related genes whose expression is activated by a LuxR family regulator. Appl Environ Microbiol 2010; 76:1861-9. [PMID: 20118371 DOI: 10.1128/aem.01926-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N,N-Dimethylformamide (DMF), a toxic solvent used in the chemical industry, is frequently present in industrial wastes. Plasmid pAMI2 (18.6 kb) of Paracoccus aminophilus JCM 7686 carries genetic information which is crucial for methylotrophic growth of this bacterium, using DMF as the sole source of carbon and energy. Besides a conserved backbone related to pAgK84 of Agrobacterium radiobacter K84, pAMI2 carries a three-gene cluster coding for the protein DmfR, which has sequence similarities to members of the LuxR family of transcription regulators, and two subunits (DmfA1 and DmfA2) of N,N-dimethylformamidase, an enzyme of high substrate specificity that catalyzes the first step in the degradation of DMF. Genetic analysis revealed that these genes, which are all placed in the same orientation, constitute an inducible operon whose expression is activated in the presence of DMF by the positive transcription regulator DmfR. This operon was used to construct a strain able to degrade DMF at high concentrations that might be used in the biotreatment of DMF-containing industrial wastewaters. To our knowledge, this is the first study to provide insights into the genetic organization and regulation as well as the dissemination in bacteria of genes involved in the enzymatic breakdown of DMF.
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Yam KC, van der Geize R, Eltis LD. Catabolism of Aromatic Compounds and Steroids by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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