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Liu M, Wang K, Wei J, Liu N, Niu G, Tan H, Huang Y. Comparative and Functional Analyses Reveal Conserved and Variable Regulatory Systems That Control Lasalocid Biosynthesis in Different Streptomyces Species. Microbiol Spectr 2023; 11:e0385222. [PMID: 36847561 PMCID: PMC10100954 DOI: 10.1128/spectrum.03852-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
Lasalocid, a representative polyether ionophore, has been successfully applied in veterinary medicine and animal husbandry and also displays promising potential for cancer therapy. Nevertheless, the regulatory system governing lasalocid biosynthesis remains obscure. Here, we identified two conserved (lodR2 and lodR3) and one variable (lodR1, found only in Streptomyces sp. strain FXJ1.172) putative regulatory genes through a comparison of the lasalocid biosynthetic gene cluster (lod) from Streptomyces sp. FXJ1.172 with those (las and lsd) from Streptomyces lasalocidi. Gene disruption experiments demonstrated that both lodR1 and lodR3 positively regulate lasalocid biosynthesis in Streptomyces sp. FXJ1.172, while lodR2 plays a negative regulatory role. To unravel the regulatory mechanism, transcriptional analysis and electrophoretic mobility shift assays (EMSAs) along with footprinting experiments were performed. The results revealed that LodR1 and LodR2 could bind to the intergenic regions of lodR1-lodAB and lodR2-lodED, respectively, thereby repressing the transcription of the lodAB and lodED operons, respectively. The repression of lodAB-lodC by LodR1 likely boosts lasalocid biosynthesis. Furthermore, LodR2 and LodE constitute a repressor-activator system that senses changes in intracellular lasalocid concentrations and coordinates its biosynthesis. LodR3 could directly activate the transcription of key structural genes. Comparative and parallel functional analyses of the homologous genes in S. lasalocidi ATCC 31180T confirmed the conserved roles of lodR2, lodE, and lodR3 in controlling lasalocid biosynthesis. Intriguingly, the variable gene locus lodR1-lodC from Streptomyces sp. FXJ1.172 seems functionally conserved when introduced into S. lasalocidi ATCC 31180T. Overall, our findings demonstrate that lasalocid biosynthesis is tightly controlled by both conserved and variable regulators, providing valuable guidance for further improving lasalocid production. IMPORTANCE Compared to its elaborated biosynthetic pathway, the regulation of lasalocid biosynthesis remains obscure. Here, we characterize the roles of regulatory genes in lasalocid biosynthetic gene clusters of two distinct Streptomyces species and identify a conserved repressor-activator system, LodR2-LodE, which could sense changes in the concentration of lasalocid and coordinate its biosynthesis with self-resistance. Furthermore, in parallel, we verify that the regulatory system identified in a new Streptomyces isolate is valid in the industrial lasalocid producer and thus applicable for the construction of high-yield strains. These findings deepen our understanding of regulatory mechanisms involved in the production of polyether ionophores and provide novel clues for the rational design of industrial strains for scaled-up production.
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Affiliation(s)
- Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kairui Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junhong Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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2
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Liu J, Li L, Wang Y, Li B, Cai X, Tang L, Dong S, Yang E, Wu H, Zhang B. Joint engineering of SACE_Lrp and its target MarR enhances the biosynthesis and export of erythromycin in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2021; 105:2911-2924. [PMID: 33760930 DOI: 10.1007/s00253-021-11228-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 11/24/2022]
Abstract
The Lrp and MarR families are two groups of transcriptional regulators widely distributed among prokaryotes. However, the hierarchical-regulatory relationship between the Lrp family and the MarR family remains unknown. Our previous study found that an Lrp (SACE_Lrp) from Saccharopolyspora erythraea indirectly repressed the biosynthesis of erythromycin. In this study, we characterized a novel MarR family protein (SACE_6745) from S. erythraea, which is controlled by SACE_Lrp and plays a direct regulatory role in erythromycin biosynthesis and export. SACE_Lrp directly regulated the expression of marR by specifically binding a precise site OM (5'-CTCCGGGAACCATT-3'). Gene disruption of marR increased the production of erythromycin by 45% in S. erythraea A226. We found that MarR has direct DNA-binding activity for the promoter regions of the erythromycin biosynthetic genes, as well as an ABC exporter SACE_2701-2702 which was genetically proved to be responsible for erythromycin efflux. Disruption of SACE_Lrp in industrial S. erythraea WB was an efficient strategy to enhance erythromycin production. Herein, we jointly engineered SACE_Lrp and its target MarR by deleting marR in WBΔSACE_Lrp, resulting in 20% increase in erythromycin yield in mutant WBΔLrpΔmarR compared to WBΔSACE_Lrp, and 39% to WB. Overall, our findings provide new insights into the hierarchical-regulatory relationship of Lrp and MarR proteins and new avenues for coordinating antibiotic biosynthesis and export by joint engineering regulators in actinomycetes. KEY POINTS: • The hierarchical-regulatory relationship between SACE_Lrp and MarR was identified. • MarR directly controlled the expression of erythromycin biosynthesis and export genes. • Joint engineering of SACE_Lrp-MarR regulatory element enhanced erythromycin production.
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Affiliation(s)
- Jing Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Long Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Bowen Li
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Xinlu Cai
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Lijuan Tang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shengnan Dong
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Endong Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hang Wu
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life Sciences, Anhui University, Hefei, 230601, China.
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3
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Noël A, Garnier A, Clément M, Rouaud I, Sauvager A, Bousarghin L, Vásquez-Ocmín P, Maciuk A, Tomasi S. Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity. PHYTOCHEMISTRY 2021; 181:112535. [PMID: 33099225 DOI: 10.1016/j.phytochem.2020.112535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Lichens are specific symbiotic organisms harboring various microorganisms in addition to the two classic partners (algae or cyanobacterium and fungus). Although lichens produce many antibiotic compounds such as (+)-usnic acid, their associated microorganisms possess the ability to colonize an environment where antibiosis exists. Here, we have studied the behavior of several lichen-associated bacterial strains in the presence of (+)-usnic acid, a known antibiotic lichen compound. The effect of this compound was firstly evaluated on the growth and metabolism of three bacteria, thus showing its ability to inhibit Gram-positive bacteria. This inhibition was not thwarted with the usnic acid producer strain Streptomyces cyaneofuscatus. The biotransformation of this lichen metabolite was also studied. An ethanolamine derivative of (+)-usnic acid with low antibiotic activity was highlighted with chemical profiling, using HPLC-UV combined with low resolution mass spectrometry. These findings highlight the way in which some strains develop resistance mechanisms. A methylated derivative of (+)-usnic acid was annotated using the molecular networking method, thus showing the interest of this computer-based approach in biotransformation studies.
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Affiliation(s)
- Alba Noël
- Univ Rennes, CNRS, ISCR - UMR 6226, F-35000, Rennes, France
| | | | | | | | | | - Latifa Bousarghin
- INSERM, Univ. Rennes, INRA, CHU Rennes, Nutrition Metabolisms and Cancer (NuMeCan), UMR-1241, Biosit, MRic/ISFR, Rennes, France
| | | | - Alexandre Maciuk
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Sophie Tomasi
- Univ Rennes, CNRS, ISCR - UMR 6226, F-35000, Rennes, France.
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4
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Murarka P, Srivastava P. Characterization of DNA binding and ligand binding properties of the TetR family protein involved in regulation of dsz operon in Gordonia sp. IITR100. Int J Biol Macromol 2019; 141:671-679. [PMID: 31493456 DOI: 10.1016/j.ijbiomac.2019.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/13/2019] [Accepted: 09/03/2019] [Indexed: 01/03/2023]
Abstract
Gordonia sp. IITR100 is a biodesulfurizing bacterium which can metabolize dibenzothiophene (DBT) to 2 hydroxybiphenyl in four steps via the 4S pathway. The genes involved in the metabolism are present in the form of an operon, dszABC, which gets activated by a TetR family protein. Here, we report the detailed characterization of the DNA binding and ligand binding property of the TetR family protein. The protein was found to be conserved across other desulfurizing organisms. The protein was purified and was found to exist as dimer. The presence of ligand binding site was identified by docking studies and the structural changes in the protein upon ligand binding were determined by CD spectroscopy and tryptophan fluorescence. Further, it was determined that this protein binds to an imperfect palindromic DNA sequence present in the dsz promoter DNA. Binding to the DNA also changes conformation of the protein.
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Affiliation(s)
- Pooja Murarka
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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5
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Hou B, Zhu X, Kang Y, Wang R, Wu H, Ye J, Zhang H. LmbU, a Cluster-Situated Regulator for Lincomycin, Consists of a DNA-Binding Domain, an Auto-Inhibitory Domain, and Forms Homodimer. Front Microbiol 2019; 10. [DOI: doi.org/10.3389/fmicb.2019.00989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023] Open
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6
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Hou B, Zhu X, Kang Y, Wang R, Wu H, Ye J, Zhang H. LmbU, a Cluster-Situated Regulator for Lincomycin, Consists of a DNA-Binding Domain, an Auto-Inhibitory Domain, and Forms Homodimer. Front Microbiol 2019; 10:989. [PMID: 31130942 PMCID: PMC6510168 DOI: 10.3389/fmicb.2019.00989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/18/2019] [Indexed: 12/17/2022] Open
Abstract
Few studies were reported about the regulatory mechanism of lincomycin biosynthesis since it was found in 1962. Although we have proved that a cluster-situated regulator (CSR) LmbU (GenBank Accession No. ABX00623.1) positively modulates lincomycin biosynthesis in Streptomyces lincolnensis NRRL 2936, the molecular mechanism of LmbU regulation is still unclear. In this study, we demonstrated that LmbU binds to the target lmbAp by a central DNA-binding domain (DBD), which interacts with the binding sites through the helix-turn-helix (HTH) motif. N-terminal of LmbU includes an auto-inhibitory domain (AID), inhibiting the DNA-binding activity of LmbU. Without the AID, LmbU variant can bind to its own promoter. Interestingly, compared to other LmbU homologs, the homologs within the biosynthetic gene clusters (BGCs) of known antibiotics generally contain N-terminal AIDs, which offer them the abilities to play complex regulatory functions. In addition, cysteine 12 (C12) has been proved to be mainly responsible for LmbU homodimer formation in vitro. In conclusion, LmbU homologs naturally exist in hundreds of actinomycetes, and belong to a new regulatory family, LmbU family. The present study reveals the DBD, AID and dimerization of LmbU, and sheds new light on the regulatory mechanism of LmbU and its homologs.
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Affiliation(s)
- Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaoyu Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
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7
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Srivastava SK, King KS, AbuSara NF, Malayny CJ, Piercey BM, Wilson JA, Tahlan K. In vivo functional analysis of a class A β-lactamase-related protein essential for clavulanic acid biosynthesis in Streptomyces clavuligerus. PLoS One 2019; 14:e0215960. [PMID: 31013337 PMCID: PMC6478378 DOI: 10.1371/journal.pone.0215960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/12/2019] [Indexed: 11/23/2022] Open
Abstract
In Streptomyces clavuligerus, the gene cluster involved in the biosynthesis of the clinically used β-lactamase inhibitor clavulanic acid contains a gene (orf12 or cpe) encoding a protein with a C-terminal class A β-lactamase-like domain. The cpe gene is essential for clavulanic acid production, and the recent crystal structure of its product (Cpe) was shown to also contain an N-terminal isomerase/cyclase-like domain, but the function of the protein remains unknown. In the current study, we show that Cpe is a cytoplasmic protein and that both its N- and C-terminal domains are required for in vivo clavulanic acid production in S. clavuligerus. Our results along with those from previous studies allude towards a biosynthetic role for Cpe during the later stages of clavulanic acid production in S. clavuligerus. Amino acids from Cpe essential for biosynthesis were also identified, including one (Lys89) from the recently described N-terminal isomerase-like domain of unknown function. Homologues of Cpe from other clavulanic acid-producing Streptomyces spp. were shown to be functionally equivalent to the S. clavuligerus protein, whereas those from non-producers containing clavulanic acid-like gene clusters were not. The suggested in vivo involvement of an isomerase-like domain recruited by an ancestral β-lactamase related protein, supports a previous hypothesis that Cpe could be involved in a step requiring the opening and modification of the clavulanic acid core during its biosynthesis from 5S precursors.
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Affiliation(s)
| | - Kelcey S. King
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Nader F. AbuSara
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Chelsea J. Malayny
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Brandon M. Piercey
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Jaime A. Wilson
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
- * E-mail:
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8
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Rebets Y, Schmelz S, Gromyko O, Tistechok S, Petzke L, Scrima A, Luzhetskyy A. Design, development and application of whole-cell based antibiotic-specific biosensor. Metab Eng 2018; 47:263-270. [DOI: 10.1016/j.ymben.2018.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 01/25/2023]
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9
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Van Dyke AR, Gatazka DH, Hanania MM. Innovations in Undergraduate Chemical Biology Education. ACS Chem Biol 2018; 13:26-35. [PMID: 29192757 DOI: 10.1021/acschembio.7b00986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical biology derives intellectual vitality from its scientific interface: applying chemical strategies and perspectives to biological questions. There is a growing need for chemical biologists to synergistically integrate their research programs with their educational activities to become holistic teacher-scholars. This review examines how course-based undergraduate research experiences (CUREs) are an innovative method to achieve this integration. Because CUREs are course-based, the review first offers strategies for creating a student-centered learning environment, which can improve students' outcomes. Exemplars of CUREs in chemical biology are then presented and organized to illustrate the five defining characteristics of CUREs: significance, scientific practices, discovery, collaboration, and iteration. Finally, strategies to overcome common barriers in CUREs are considered as well as future innovations in chemical biology education.
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Affiliation(s)
- Aaron R. Van Dyke
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Daniel H. Gatazka
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Mariah M. Hanania
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
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10
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Buttner MJ, Schäfer M, Lawson DM, Maxwell A. Structural insights into simocyclinone as an antibiotic, effector ligand and substrate. FEMS Microbiol Rev 2018; 42:4604775. [PMID: 29126195 PMCID: PMC5812520 DOI: 10.1093/femsre/fux055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022] Open
Abstract
Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins.
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Affiliation(s)
- Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Schäfer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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11
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New Kid on the Block: LmbU Expands the Repertoire of Specialized Metabolic Regulators in Streptomyces. J Bacteriol 2017; 200:JB.00559-17. [PMID: 29084856 DOI: 10.1128/jb.00559-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces has an extensive natural product repertoire, including most of the naturally derived antibiotics. Understanding the control of natural product biosynthesis is central to antibiotic discovery and production optimization. Here, Hou et al. (J. Bacteriol. 200:00447-17, 2018, https://doi.org/10.1128/JB.00447-17) report the identification and characterization of a novel regulator-LmbU-that functions primarily as an activator of lincomycin production in Streptomyces lincolnensis Importantly, members of this new regulator family are associated with natural product biosynthetic clusters throughout the streptomycetes and their actinomycete relatives.
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12
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Mak S, Nodwell JR. Actinorhodin is a redox-active antibiotic with a complex mode of action against Gram-positive cells. Mol Microbiol 2017; 106:597-613. [PMID: 28906045 DOI: 10.1111/mmi.13837] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2017] [Indexed: 11/29/2022]
Abstract
Actinorhodin is a blue-pigmented, redox-active secondary metabolite that is produced by the bacterium Streptomyces coelicolor. Although actinorhodin has been used as a model compound for studying secondary metabolism, its biological activity is not well understood. Indeed, redox-active antibiotics in general have not been widely investigated at the mechanistic level. In this work, we have conducted a comprehensive chemical genetic investigation of actinorhodin's antibacterial effect on target organisms. We find that actinorhodin is a potent, bacteriostatic, pH-responsive antibiotic. Cells activate at least three stress responses in the presence of actinorhodin, including those responsible for managing oxidative damage, protein damage and selected forms of DNA damage. We find that mutations in the Staphylococcus aureus walRKHI operon can confer low-level resistance to actinorhodin, indicating possible targeting of the cell envelope. Our study indicates a complex mechanism of action, involving multiple molecular targets, that is distinct from other antibiotics.
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Affiliation(s)
- Stefanie Mak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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13
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14
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Bhukya H, Jana AK, Sengupta N, Anand R. Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence. J Struct Biol 2017; 198:134-146. [PMID: 28343010 DOI: 10.1016/j.jsb.2017.03.006] [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: 11/28/2016] [Revised: 03/13/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of γ-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3.95Å. Furthermore, to refine and compliment the results, atomistic molecular dynamics simulations were carried out using the X-ray structure as the template. The studies reveal that CprB binds to DNA as dimer of dimers with this mode of interaction results in minimal distortion in the DNA, enabling these proteins to recognize multiple sequences with varying affinity. Another crucial finding from our simulation results was that the positively charged N-terminal arm of CprB brings extra stability to the protein-DNA complex by interacting with the minor-groove of the DNA and anchoring itself to the phosphate backbone. Corroborating electrophoretic mobility shift assay and fluorescence anisotropy experiments showed that the mutant ΔN6-CprB exhibited about 7-8 fold reduced DNA binding. Comparison with other TetR-FTRs reveals that this strategy is also employed by over 25% of TetR-FTRs, where N-terminal anchoring mechanism is used to enhance selectivity for a particular DNA sequence.
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Affiliation(s)
- Hussain Bhukya
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asis K Jana
- India Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Neelanjana Sengupta
- Dept. of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, W. Bengal, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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15
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Niu G, Chater KF, Tian Y, Zhang J, Tan H. Specialised metabolites regulating antibiotic biosynthesis in Streptomyces spp. FEMS Microbiol Rev 2016; 40:554-73. [PMID: 27288284 DOI: 10.1093/femsre/fuw012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
Streptomyces bacteria are the major source of antibiotics and other secondary metabolites. Various environmental and physiological conditions affect the onset and level of production of each antibiotic by influencing concentrations of the ligands for conserved global regulatory proteins. In addition, as reviewed here, well-known autoregulators such as γ-butyrolactones, themselves products of secondary metabolism, accumulate late in growth to concentrations allowing their effective interaction with cognate binding proteins, in a necessary prelude to antibiotic biosynthesis. Most autoregulator binding proteins target the conserved global regulatory gene adpA, and/or regulatory genes for 'cluster-situated regulators' (CSRs) linked to antibiotic biosynthetic gene clusters. It now appears that some CSRs bind intermediates and end products of antibiotic biosynthesis, with regulatory effects interwoven with those of autoregulators. These ligands can exert cross-pathway effects within producers of more than one antibiotic, and when excreted into the extracellular environment may have population-wide effects on production, and mediate interactions with neighbouring microorganisms in natural communities, influencing speciation. Greater understanding of these autoregulatory and cross-regulatory activities may aid the discovery of new signalling molecules and their use in activating cryptic antibiotic biosynthetic pathways.
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Affiliation(s)
- Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Palanca C, Rubio V. Structure of AmtR, the global nitrogen regulator of Corynebacterium glutamicum, in free and DNA-bound forms. FEBS J 2016; 283:1039-59. [PMID: 26744254 DOI: 10.1111/febs.13643] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/23/2015] [Accepted: 01/05/2016] [Indexed: 11/29/2022]
Abstract
UNLABELLED Corynebacterium glutamicum is a bacterium used for industrial amino acid production, and understanding its metabolic pathway regulation is of high biotechnological interest. Here, we report crystal structures of AmtR, the global nitrogen regulator of C. glutamicum, in apo (2.25-Å and 2.65-Å resolution) and DNA-bound (3-Å resolution) forms. These structures reveal an all-α homodimeric TetR family regulator composed of a helix-turn-helix-hosting N-terminal DNA-binding domain and a C-terminal dimerization domain. AmtR has several unique structural features that appear to be invariant among AmtR proteins, which may be related to its regulation by the nitrogen-sensing trimeric protein GlnK rather than by small-molecule effectors. As compared with other TetR family members, AmtR has an extra C-terminal helix, a large extended external loop that resembles the flexible tranducer T-loop of GlnK in sequence, and a large open cavity towards the intersubunit region that changes shape upon DNA binding. The marked kinking of helix 4 decreases in the DNA-bound form. The binding of one AmtR dimer to its DNA operator involves not only the insertion of helices 3 and 3' in adjacent turns of the double-helix major groove, but also the anchoring of 19-residue, arginine-rich and proline-rich N-terminal extensions to two external minor grooves. Electrophoretic mobility shift assays with a deletion mutant reveal that the 19-residue extension is crucial for AmtR binding to DNA. N-extension anchoring explains the flanking by AT sequences of the recognized target DNA sequence core. The significance of these findings for the entire TetR family of regulators and for GlnK regulation of AmtR is discussed. DATABASE The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org [PDB ID codes 5DXZ (native AmtR), 5DY1 (SeMet-AmtR), and 5DY0 (AmtR·DNA)].
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Affiliation(s)
- Carles Palanca
- Instituto de Biomedicina de Valencia of the CSIC (IBV-CSIC), Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia of the CSIC (IBV-CSIC), Spain.,Group 739 of the Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER) del Instituto de Salud Carlos III, Spain
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17
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Wolański M, Łebkowski T, Kois-Ostrowska A, Zettler J, Apel AK, Jakimowicz D, Zakrzewska-Czerwińska J. Two transcription factors, CabA and CabR, are independently involved in multilevel regulation of the biosynthetic gene cluster encoding the novel aminocoumarin, cacibiocin. Appl Microbiol Biotechnol 2015; 100:3147-64. [PMID: 26637421 DOI: 10.1007/s00253-015-7196-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/19/2015] [Accepted: 11/22/2015] [Indexed: 11/30/2022]
Abstract
Aminocoumarins are potent antibiotics belonging to a relatively small group of secondary metabolites produced by actinomycetes. Genome mining of Catenulispora acidiphila has recently led to the discovery of a gene cluster responsible for biosynthesis of novel aminocoumarins, cacibiocins. However, regulation of the expression of this novel gene cluster has not yet been analyzed. In this study, we identify transcriptional regulators of the cacibiocin gene cluster. Using a heterologous expression system, we show that the CabA and CabR proteins encoded by cabA and cabR genes in the cacibiocin gene cluster control the expression of genes involved in the biosynthesis, modification, regulation, and potentially, efflux/resistance of cacibiocins. CabA positively regulates the expression of cabH (the first gene in the cabHIYJKL operon) and cabhal genes encoding key enzymes responsible for the biosynthesis and halogenation of the aminocoumarin moiety, respectively. We provide evidence that CabA is a direct inducer of cacibiocin production, whereas the second transcriptional factor, CabR, is involved in the negative regulation of its own gene and cabT-the latter of which encodes a putative cacibiocin transporter. We also demonstrate that CabR activity is negatively regulated in vitro by aminocoumarin compounds, suggesting the existence of analogous regulation in vivo. Finally, we propose a model of multilevel regulation of gene transcription in the cacibiocin gene cluster by CabA and CabR.
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Affiliation(s)
- Marcin Wolański
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland.
| | - Tomasz Łebkowski
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland
| | | | - Judith Zettler
- Pharmazeutische Biologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site, Tübingen, Germany
| | - Alexander K Apel
- Pharmazeutische Biologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site, Tübingen, Germany
| | - Dagmara Jakimowicz
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland.,Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Weigla 12, 53-114, Wrocław, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland.,Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Weigla 12, 53-114, Wrocław, Poland
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18
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Boutrin MC, Yu Y, Wang C, Aruni W, Dou Y, Shi L, Fletcher HM. A putative TetR regulator is involved in nitric oxide stress resistance in Porphyromonas gingivalis. Mol Oral Microbiol 2015; 31:340-53. [PMID: 26332057 DOI: 10.1111/omi.12128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 02/02/2023]
Abstract
To survive in the periodontal pocket, Porphyromonas gingivalis, the main causative agent of periodontal disease, must overcome oxidative and nitric oxide (NO) stress. Previously, we reported that, in the presence of NO comparable to stress conditions, the transcriptome of P. gingivalis was differentially expressed, and genes belonging to the PG1178-81 cluster were significantly upregulated. To further evaluate their role(s) in NO stress resistance, these genes were inactivated by allelic exchange mutagenesis. Isogenic mutants P. gingivalis FLL460 (ΔPG1181::ermF) and FLL461 (ΔPG1178-81::ermF) were black-pigmented, with gingipain and hemolytic activities comparable to that of the wild-type strain. Whereas the recovery of these isogenic mutants from NO stress was comparable to the wild-type, there was increased sensitivity to hydrogen peroxide-induced stress. RNA-Seq analysis under conditions of NO stress showed that approximately 5 and 8% of the genome was modulated in P. gingivalis FLL460 and FLL461, respectively. The PG1178-81 gene cluster was shown to be part of the same transcriptional unit and is inducible in response to NO stress. In the presence of NO, PG1181, a putative transcriptional regulator, was shown to bind to its own promoter region and that of several other NO responsive genes including PG0214 an extracytoplasmic function σ factor, PG0893 and PG1236. Taken together, the data suggest that PG1181 is a NO responsive transcriptional regulator that may play an important role in the NO stress resistance regulatory network in P. gingivalis.
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Affiliation(s)
- M-C Boutrin
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Y Yu
- School of Pharmacy, Fudan University, Shanghai, China
| | - C Wang
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - W Aruni
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Y Dou
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - L Shi
- School of Pharmacy, Fudan University, Shanghai, China
| | - H M Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.,Institute of Oral Biology, Kyung Hee University, Seoul, Korea
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Fernandez-López R, Ruiz R, de la Cruz F, Moncalián G. Transcription factor-based biosensors enlightened by the analyte. Front Microbiol 2015; 6:648. [PMID: 26191047 PMCID: PMC4486848 DOI: 10.3389/fmicb.2015.00648] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/15/2015] [Indexed: 01/17/2023] Open
Abstract
Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.
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Affiliation(s)
| | | | | | - Gabriel Moncalián
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria – Consejo Superior de Investigaciones CientíficasSantander, Spain
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20
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Production of specialized metabolites by Streptomyces coelicolor A3(2). ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:217-66. [PMID: 25131404 DOI: 10.1016/b978-0-12-800259-9.00006-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The actinomycetes are well-known bioactive natural product producers, comprising the Streptomycetes, the richest drug-prolific family in all kingdoms, producing therapeutic compounds for the areas of infection, cancer, circulation, and immunity. Completion and annotation of many actinomycete genomes has highlighted further how proficient these bacteria are in specialized metabolism, which have been largely underexploited in traditional screening programs. The genome sequence of the model strain Streptomyces coelicolor A3(2), and subsequent development of genomics-driven approaches to understand its large specialized metabolome, has been key in unlocking the high potential of specialized metabolites for natural product genomics-based drug discovery. This review discusses systematically the biochemistry and genetics of each of the specialized metabolites of S. coelicolor and describes metabolite transport processes for excretion and complex regulatory patterns controlling biosynthesis.
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21
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Wu H, Chen M, Mao Y, Li W, Liu J, Huang X, Zhou Y, Ye BC, Zhang L, Weaver DT, Zhang B. Dissecting and engineering of the TetR family regulator SACE_7301 for enhanced erythromycin production in Saccharopolyspora erythraea. Microb Cell Fact 2014; 13:158. [PMID: 25391994 PMCID: PMC4258057 DOI: 10.1186/s12934-014-0158-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saccharopolyspora erythraea was extensively utilized for the industrial-scale production of erythromycin A (Er-A), a macrolide antibiotic commonly used in human medicine. Yet, S. erythraea lacks regulatory genes in the erythromycin biosynthetic gene (ery) cluster, hampering efforts to enhance Er-A production via the engineering of regulatory genes. RESULTS By the chromosome gene inactivation technique based on homologous recombination with linearized DNA fragments, we have inactivated a number of candidate TetR family transcriptional regulators (TFRs) and identified one TFR (SACE_7301) positively controlling erythromycin biosynthesis in S. erythraea A226. qRT-PCR and EMSA analyses demonstrated that SACE_7301 activated the transcription of erythromycin biosynthetic gene eryAI and the resistance gene ermE by interacting with their promoter regions with low affinities, similar to BldD (SACE_2077) previously identified to regulate erythromycin biosynthesis and morphological differentiation. Therefore, we designed a strategy for overexpressing SACE_7301 with 1 to 3 extra copies under the control of PermE* in A226. Following up-regulated transcriptional expression of SACE_7301, eryAI and ermE, the SACE_7301-overexpressed strains all increased Er-A production over A226 proportional to the number of copies. Likewise, when SACE_7301 was overexpressed in an industrial S. erythraea WB strain, Er-A yields of the mutants WB/7301, WB/2×7301 and WB/3×7301 were respectively increased by 17%, 29% and 42% relative to that of WB. In a 5 L fermentor, Er-A accumulation increased to 4,230 mg/L with the highest-yield strain WB/3×7301, an approximately 27% production improvement over WB (3,322 mg/L). CONCLUSIONS We have identified and characterized a TFR, SACE_7301, in S. erythraea that positively regulated erythromycin biosynthesis, and overexpression of SACE_7301 in wild-type and industrial S. erythraea strains enhanced Er-A yields. This study markedly improves our understanding of the unusual regulatory mechanism of erythromycin biosynthesis, and provides a novel strategy towards Er-A overproduction by engineering transcriptional regulators of S. erythraea.
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Affiliation(s)
- Hang Wu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Meng Chen
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Yongrong Mao
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Weiwei Li
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Jingtao Liu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,Beijing Institute of Cell Biotechnology, Beijing, 100043, China.
| | - Xunduan Huang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Ying Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Lixin Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - David T Weaver
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
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22
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Bhukya H, Bhujbalrao R, Bitra A, Anand R. Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2). Nucleic Acids Res 2014; 42:10122-33. [PMID: 25092919 PMCID: PMC4150764 DOI: 10.1093/nar/gku587] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Antibiotic production and resistance pathways in Streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. To decipher the mode of DNA binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of CprB in complex with the consensus DNA element to a resolution of 3.25 Å. Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove. The crystal structure revealed that, CprB is bound to DNA as a dimer of dimers with the mode of binding being analogous to the broad spectrum multidrug transporter protein QacR from the antibiotic resistant strain Staphylococcus aureus. It was demonstrated that the CprB displays a cooperative mode of DNA binding, following a clamp and click model. Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator. Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).
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Affiliation(s)
- Hussain Bhukya
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Ruchika Bhujbalrao
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Aruna Bitra
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
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23
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Mak S, Xu Y, Nodwell JR. The expression of antibiotic resistance genes in antibiotic-producing bacteria. Mol Microbiol 2014; 93:391-402. [PMID: 24964724 DOI: 10.1111/mmi.12689] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/01/2022]
Abstract
Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. In many cases, the expression of resistance genes is tightly linked to that of antibiotic biosynthetic genes. In others, the resistance genes can be induced by their cognate antibiotics or by intermediate molecules from their biosynthetic pathways. The regulatory mechanisms that couple resistance to antibiotic biosynthesis are mechanistically diverse and potentially relevant to the origins of clinical antibiotic resistance.
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Affiliation(s)
- Stefanie Mak
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
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24
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García-Fernández E, Medrano FJ, Galán B, García JL. Deciphering the transcriptional regulation of cholesterol catabolic pathway in mycobacteria: identification of the inducer of KstR repressor. J Biol Chem 2014; 289:17576-88. [PMID: 24802756 PMCID: PMC4067193 DOI: 10.1074/jbc.m113.545715] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/02/2014] [Indexed: 11/06/2022] Open
Abstract
Cholesterol degradation plays a prominent role in Mycobacterium tuberculosis infection; therefore, to develop new tools to combat this disease, we need to decipher the components comprising and regulating the corresponding pathway. A TetR-like repressor (KstR) regulates the upper part of this complex catabolic pathway, but the induction mechanism remains unknown. Using a biophysical approach, we have discovered that the inducer molecule of KstR in M. smegmatis mc(2)155 is not cholesterol but 3-oxo-4-cholestenoic acid, one of the first metabolic intermediates. Binding this compound induces dramatic conformational changes in KstR that promote the KstR-DNA interaction to be released from the operator, retaining its dimeric state. Our findings suggest a regulatory model common to all cholesterol degrading bacteria in which the first steps of the pathway are critical to its mineralization and explain the high redundancy of the enzymes involved in these initial steps.
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Affiliation(s)
| | - Francisco Javier Medrano
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
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De Majumdar S, Yu J, Spencer J, Tikhonova IG, Schneiders T. Molecular basis of non-mutational derepression of ramA in Klebsiella pneumoniae. J Antimicrob Chemother 2014; 69:2681-9. [PMID: 25140579 DOI: 10.1093/jac/dku203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The ram locus, consisting of the romA-ramA genes, is repressed by the tetracycline-type regulator RamR, where regulation is abolished due to loss-of-function mutations within the protein or ligand interactions. The aim of this study was to determine whether the phenothiazines (chlorpromazine and thioridazine) directly interact with RamR to derepress ramA expression. METHODS Quantitative real-time PCR analyses were performed to determine expression levels of the romA-ramA genes after exposure to the phenothiazines. Electrophoretic mobility shift assays (EMSAs) and in vitro transcription experiments were performed to show direct binding to and repression by RamR. Direct binding of the RamR protein to the phenothiazines was measured by fluorescence spectroscopy experiments and molecular docking models were generated using the RamR crystal structure. RESULTS Exposure to either chlorpromazine or thioridazine resulted in the up-regulation of the romA-ramA genes. EMSAs and in vitro transcription experiments demonstrated that both agents reduce/abolish binding and enhance transcription of the target PI promoter upstream of the ramR-romA genes in Klebsiella pneumoniae compared with RamR alone. Fluorescence spectroscopy measurements demonstrated that RamR directly binds both chlorpromazine and thioridazine with micromolar affinity. Molecular docking analyses using the RamR crystal structure demonstrated that the phenothiazines interact with RamR protein through contacts described for other ligands, in addition to forming unique strong polar interactions at positions D152 and K63. CONCLUSIONS These data demonstrate that phenothiazines can modulate loci linked to the microbe-drug response where RamR is an intracellular target for the phenothiazines, thus resulting in a transient non-mutational derepression of ramA concentrations.
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Affiliation(s)
- Shyamasree De Majumdar
- Centre for Infection and Immunity, Health Sciences Building, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Jing Yu
- Centre for Infection and Immunity, Health Sciences Building, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS18 1TD, UK
| | - Irina G Tikhonova
- Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Thamarai Schneiders
- Centre for Infection and Immunity, Health Sciences Building, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
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Rossbach S, Kunze K, Albert S, Zehner S, Göttfert M. The Sinorhizobium meliloti EmrAB efflux system is regulated by flavonoids through a TetR-like regulator (EmrR). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:379-387. [PMID: 24224534 DOI: 10.1094/mpmi-09-13-0282-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The divergently oriented Sinorhizobium meliloti emrAB (SMc03168 and SMc03167) and emrR (SMc03169) genes are predicted to encode an efflux system of the major facilitator superfamily and a TetR-like transcriptional regulator, respectively. The transcription of the emrA gene was found to be inducible by flavonoids, including luteolin and apigenin, which are known inducers of the nodulation genes in S. meliloti. Interestingly, quercetin, which does not induce nodulation genes, was also a potent inducer of emrA, indicating that NodD is not directly involved in regulation of emrA. The likely regulator of emrAB is EmrR, which binds to palindrome-like sequences in the intergenic region. Several modifications of the palindromes, including an increase of the spacing between the two half sites, prevented binding of EmrR. Binding was also impaired by the presence of luteolin. Mutations in emrA had no obvious effect on symbiosis. This was in contrast to the emrR mutant, which exhibited a symbiotic deficiency with Medicago sativa. Conserved binding sites for TetR-like regulators within the intergenic regions between the emrAB and emrR genes were identified in many symbiotic and pathogenic members of the order Rhizobiales.
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27
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Yagüe P, Rodríguez-García A, López-García MT, Rioseras B, Martín JF, Sánchez J, Manteca A. Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures. PLoS One 2014; 9:e86296. [PMID: 24466012 PMCID: PMC3897704 DOI: 10.1371/journal.pone.0086296] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
Streptomyces species produce many clinically relevant secondary metabolites and exhibit a complex development that includes hyphal differentiation and sporulation in solid cultures. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that no differentiation took place. The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. Eighty-six percent of all transcripts showed similar abundances in liquid and solid cultures, such as those involved in the biosynthesis of actinorhodin (actVA, actII-4) and undecylprodigiosin (redF); activation of secondary metabolism (absR1, ndsA); genes regulating hydrophobic cover formation (aerial mycelium) (bldB, bldC, bldM, bldN, sapA, chpC, chpD, chpE, chpH, ramA, ramC, ramS); and even some genes regulating early stages of sporulation (wblA, whiG, whiH, whiJ). The two most important differences between transcriptomes from liquid and solid cultures were: first, genes related to secondary metabolite biosynthesis (CDA, CPK, coelichelin, desferrioxamine clusters) were highly up-regulated in liquid but not in solid cultures; and second, genes involved in the final stages of hydrophobic cover/spore maturation (chpF, rdlA, whiE, sfr) were up-regulated in solid but not in liquid cultures. New information was also provided for several non-characterized genes differentially expressed in liquid and solid cultures which might be regulating, at least in part, the metabolic and developmental differences observed between liquid and solid cultures.
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Affiliation(s)
- Paula Yagüe
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | | | - María Teresa López-García
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Beatriz Rioseras
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Juan Francisco Martín
- Instituto de Biotecnología de León, INBIOTEC, Parque Científico de León, León, Spain
| | - Jesús Sánchez
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- * E-mail:
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Deng W, Li C, Xie J. The underling mechanism of bacterial TetR/AcrR family transcriptional repressors. Cell Signal 2013; 25:1608-13. [PMID: 23602932 DOI: 10.1016/j.cellsig.2013.04.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 03/31/2013] [Accepted: 04/02/2013] [Indexed: 11/27/2022]
Abstract
Bacteria transcriptional regulators are classified by their functional and sequence similarities. Member of the TetR/AcrR family is two-domain proteins including an N-terminal HTH DNA-binding motif and a C-terminal ligand recognition domain. The C-terminal ligand recognition domain can recognize the very same compounds as their target transporters transferred. TetRs act as chemical sensors to monitor both the cellular environmental dynamics and their regulated genes underlying many events, such as antibiotics production, osmotic stress, efflux pumps, multidrug resistance, metabolic modulation, and pathogenesis. Compounds targeting Mycobacterium tuberculosis ethR represent promising novel antibiotic potentiater. TetR-mediated multidrug efflux pumps regulation might be good target candidate for the discovery of better new antibiotics against drug resistance.
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Affiliation(s)
- Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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Liu G, Chater KF, Chandra G, Niu G, Tan H. Molecular regulation of antibiotic biosynthesis in streptomyces. Microbiol Mol Biol Rev 2013; 77:112-43. [PMID: 23471619 PMCID: PMC3591988 DOI: 10.1128/mmbr.00054-12] [Citation(s) in RCA: 503] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Streptomycetes are the most abundant source of antibiotics. Typically, each species produces several antibiotics, with the profile being species specific. Streptomyces coelicolor, the model species, produces at least five different antibiotics. We review the regulation of antibiotic biosynthesis in S. coelicolor and other, nonmodel streptomycetes in the light of recent studies. The biosynthesis of each antibiotic is specified by a large gene cluster, usually including regulatory genes (cluster-situated regulators [CSRs]). These are the main point of connection with a plethora of generally conserved regulatory systems that monitor the organism's physiology, developmental state, population density, and environment to determine the onset and level of production of each antibiotic. Some CSRs may also be sensitive to the levels of different kinds of ligands, including products of the pathway itself, products of other antibiotic pathways in the same organism, and specialized regulatory small molecules such as gamma-butyrolactones. These interactions can result in self-reinforcing feed-forward circuitry and complex cross talk between pathways. The physiological signals and regulatory mechanisms may be of practical importance for the activation of the many cryptic secondary metabolic gene cluster pathways revealed by recent sequencing of numerous Streptomyces genomes.
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Affiliation(s)
- Gang Liu
- State Key Laboratory of Microbial Resources
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F. Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Anand S, Singh V, Singh AK, Mittal M, Datt M, Subramani B, Kumaran S. Equilibrium binding and kinetic characterization of putative tetracycline repressor family transcription regulator Fad35R from Mycobacterium tuberculosis. FEBS J 2012; 279:3214-28. [PMID: 22805491 DOI: 10.1111/j.1742-4658.2012.08707.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fatty acids play critical role in the survival and virulence of Mycobacterium tuberculosis (Mtb). Activation of fatty acids by acyl-CoA synthetases (Fad) into fatty acyl-CoA is the first and one of the crucial steps in fatty acid metabolism. Mtb possesses 36 fatty acyl-CoA synthetases, unlike Escherichia coli, which has single enzyme. However, the mechanisms by which the expression of these multiple Fad genes is regulated remain uncharacterized. We characterized the DNA- and ligand-binding properties of a putative tetracycline repressor family regulator, named Fad35R, located upstream of the Fad35 gene and ScoA-citE operon. We identified a palindromic regulatory motif upstream of Fad35 and characterized the binding of Fad35R to this motif. Equilibrium binding studies show that Fad35R binds to this motif with high affinity (K(d) ∼ 0.033 μm) and the specificity of binding was confirmed by an electromobility gel shift assay. Kinetic studies indicate that faster association (k(a,avg) ∼ 5.4 × 10(4) m(-1) · s(-1)) and slower dissociation rates (k(d,avg) ∼ 5.84 × 10(-4) s(-1)) confer higher affinity. The affinity for the promoter is maximum at 300 mm NaCl but decreases rapidly beyond this range. Ligand-binding studies indicate that Fad35R binds specifically to tetracycline and also binds to fatty acid derivatives. The promoter-binding affinity is decreased significantly in the presence of palmityl-CoA, suggesting that Fad35R can sense the levels of activated fatty acids and alter its DNA-binding activity. Our results suggest that Fad35R may be the functional homologue of FadR and controls the expression of genes in a metabolite-dependent manner.
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Affiliation(s)
- Sushma Anand
- Council of Scientific and Industrial Research, India, Institute of Microbial Technology, Chandigarh, India
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A two-step mechanism for the activation of actinorhodin export and resistance in Streptomyces coelicolor. mBio 2012; 3:e00191-12. [PMID: 23073761 PMCID: PMC3482498 DOI: 10.1128/mbio.00191-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many microorganisms produce secondary metabolites that have antibiotic activity. To avoid self-inhibition, the producing cells often encode cognate export and/or resistance mechanisms in the biosynthetic gene clusters for these molecules. Actinorhodin is a blue-pigmented antibiotic produced by Streptomyces coelicolor. The actAB operon, carried in the actinorhodin biosynthetic gene cluster, encodes two putative export pumps and is regulated by the transcriptional repressor protein ActR. In this work, we show that normal actinorhodin yields require actAB expression. Consistent with previous in vitro work, we show that both actinorhodin and its 3-ring biosynthetic intermediates [e.g., (S)-DNPA] can relieve repression of actAB by ActR in vivo. Importantly, an ActR mutant that interacts productively with (S)-DNPA but not with actinorhodin responds to the actinorhodin biosynthetic pathway with the induction of actAB and normal yields of actinorhodin. This suggests that the intermediates are sufficient to trigger the export genes in actinorhodin-producing cells. We further show that actinorhodin-producing cells can induce actAB expression in nonproducing cells; however, in this case actinorhodin is the most important signal. Finally, while the "intermediate-only" ActR mutant permits sufficient actAB expression for normal actinorhodin yields, this expression is short-lived. Sustained culture-wide expression requires a subsequent actinorhodin-mediated signaling step, and the defect in this response causes widespread cell death. These results are consistent with a two-step model for actinorhodin export and resistance where intermediates trigger initial expression for export from producing cells and actinorhodin then triggers sustained export gene expression that confers culture-wide resistance. IMPORTANCE Understanding the links between antibiotic resistance and biosynthesis is important for our efforts to manipulate secondary metabolism. For example, many secondary metabolites are produced at low levels; our work suggests that manipulating export might be one way to enhance yields of these molecules. It also suggests that understanding resistance will be relevant to the generation of novel secondary metabolites through the creation of synthetic secondary metabolic gene clusters. Finally, these cognate resistance mechanisms are related to mechanisms that arise in pathogenic bacteria, and understanding them is relevant to our ability to control microbial infections clinically.
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Yudistira H, McClarty L, Bloodworth RAM, Hammond SA, Butcher H, Mark BL, Cardona ST. Phenylalanine induces Burkholderia cenocepacia phenylacetic acid catabolism through degradation to phenylacetyl-CoA in synthetic cystic fibrosis sputum medium. Microb Pathog 2011; 51:186-93. [PMID: 21511027 DOI: 10.1016/j.micpath.2011.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 03/23/2011] [Accepted: 04/05/2011] [Indexed: 11/15/2022]
Abstract
Synthetic cystic fibrosis sputum medium (SCFM) is rich in amino acids and supports robust growth of Burkholderia cenocepacia, a member of the Burkholderia cepacia complex (Bcc). Previous work demonstrated that B. cenocepacia phenylacetic acid (PA) catabolic genes are up-regulated during growth in SCFM and are required for full virulence in a Caenorhabditis elegans host model. In this work, we investigated the role of phenylalanine, one of the aromatic amino acids present in SCFM, as an inducer of the PA catabolic pathway. Phenylalanine degradation intermediates were used as sole carbon sources for growth and gene reporter experiments. In addition to phenylalanine and PA, phenylethylamine, phenylpyruvate, and 2-phenylacetamide were usable as sole carbon sources by wild type B. cenocepacia K56-2, but not by a PA catabolism-defective mutant. EMSA analysis showed that the binding of PaaR, the negative regulator protein of B. cenocepacia PA catabolism, to PA regulatory DNA could only be relieved by phenylacetyl-Coenzyme A (PA-CoA), but not by any of the putative phenylalanine degradation intermediates. Taken together, our results show that in B. cenocepacia, phenylalanine is catabolized to PA and induces PA catabolism through PA activation to PA-CoA. Thus, PaaR shares the same inducer with PaaX, the regulator of PA catabolism in Escherichia coli, despite belonging to a different protein family.
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Affiliation(s)
- Harry Yudistira
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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Abstract
Actinomycete bacteria of the genus Streptomyces are major producers of bioactive compounds for the biotechnology industry. They are the source of most clinically used antibiotics, as well as of several widely used drugs against common diseases, including cancer . Genome sequencing has revealed that the potential of Streptomyces species for the production of valuable secondary metabolites is even larger than previously realized. Accessing this rich genomic resource to discover new compounds by activating "cryptic" pathways is an interesting challenge for synthetic biology. This approach is facilitated by the inherent natural modularity of secondary metabolite biosynthetic pathways, at the level of individual enzymes (such as modular polyketide synthases), but also of gene cassettes/operons and entire biosynthetic gene clusters. It also benefits from a long tradition of molecular biology in Streptomyces, which provides a number of specific tools, ranging from cloning vectors to inducible promoters and translational control elements. In this chapter, we first provide an overview of the synthetic biology challenges in Streptomyces and then present the existing toolbox of molecular methods that can be employed in this organism.
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Affiliation(s)
- Marnix H Medema
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Activation of the SoxR regulon in Streptomyces coelicolor by the extracellular form of the pigmented antibiotic actinorhodin. J Bacteriol 2010; 193:75-81. [PMID: 21037009 DOI: 10.1128/jb.00965-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The redox-sensitive transcription factor SoxR in enteric bacteria senses and regulates the cellular response to superoxide and nitric oxide. In other bacterial groups, however, it may respond to redox-active small molecules, as demonstrated for pyocyanin sensing in pseudomonads. The antibiotic-producing soil bacterium Streptomyces coelicolor contains a gene for an SoxR homologue (SCO1697) whose DNA recognition helix is identical to that of Escherichia coli SoxR. Using the E. coli SoxR binding sequence, we predicted five candidate genes of the SoxR regulon and demonstrated that SoxR binds to their promoter regions and activates their expression concurrently with the production of the blue antibiotic actinorhodin (a benzoisochromanequinone). These genes encode a probable NADPH-dependent flavin reductase (SCO2478), an NADPH-dependent quinone reductase (SCO4266), an ABC transporter (SCO7008), a monooxygenase (SCO1909), and a hypothetical protein (SCO1178). Addition of actinorhodin to exponentially growing cells activated the expression of SoxR target genes in an SoxR-dependent manner. The secreted γ-actinorhodin was over 10-fold more effective in activation than the intracellular form of actinorhodin, suggesting that SoxR is specified to respond more to exogenous signals than to intracellular metabolites. The ΔsoxR mutant was not compromised in resistance against oxidants but was slow in forming aerial mycelium on R2YE medium with reduced sporulation, and its production of actinorhodin and undecylprodigiosin was lowered by about 50% and 30%, respectively, compared to that of the wild type. These results support the proposal that SoxR senses redox-active molecules, such as actinorhodin in S. coelicolor, and induces a protective function against them. It also functions to ensure that cells undergo optimal differentiation and secondary metabolite production.
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35
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Repression of antibiotic production and sporulation in Streptomyces coelicolor by overexpression of a TetR family transcriptional regulator. Appl Environ Microbiol 2010; 76:7741-53. [PMID: 20935121 DOI: 10.1128/aem.00819-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The overexpression of a regulatory gene of the TetR family (SCO3201) originating either from Streptomyces lividans or from Streptomyces coelicolor was shown to strongly repress antibiotic production (calcium-dependent antibiotic [CDA], undecylprodigiosin [RED], and actinorhodin [ACT]) of S. coelicolor and of the ppk mutant strain of S. lividans. Curiously, the overexpression of this gene also had a strong inhibitory effect on the sporulation process of S. coelicolor but not on that of S. lividans. SCO3201 was shown to negatively regulate its own transcription, and its DNA binding motif was found to overlap its -35 promoter sequence. The interruption of this gene in S. lividans or S. coelicolor did not lead to any obvious phenotypes, indicating that when overexpressed SCO3201 likely controls the expression of target genes of other TetR regulators involved in the regulation of the metabolic and morphological differentiation process in S. coelicolor. The direct and functional interaction of SCO3201 with the promoter region of scbA, a gene under the positive control of the TetR-like regulator, ScbR, was indeed demonstrated by in vitro as well as in vivo approaches.
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Yu Z, Reichheld SE, Cuthbertson L, Nodwell JR, Davidson AR. Characterization of tetracycline modifying enzymes using a sensitive in vivo reporter system. BMC BIOCHEMISTRY 2010; 11:34. [PMID: 20831817 PMCID: PMC2949611 DOI: 10.1186/1471-2091-11-34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/11/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Increasing our understanding of antibiotic resistance mechanisms is critical. To enable progress in this area, methods to rapidly identify and characterize antibiotic resistance conferring enzymes are required. RESULTS We have constructed a sensitive reporter system in Escherichia coli that can be used to detect and characterize the activity of enzymes that act upon the antibiotic, tetracycline and its derivatives. In this system, expression of the lux operon is regulated by the tetracycline repressor, TetR, which is expressed from the same plasmid under the control of an arabinose-inducible promoter. Addition of very low concentrations of tetracycline derivatives, well below growth inhibitory concentrations, resulted in luminescence production as a result of expression of the lux genes carried by the reporter plasmid. Introduction of another plasmid into this system expressing TetX, a tetracycline-inactivating enzyme, caused a marked loss in luminescence due to enzyme-mediated reduction in the intracellular Tc concentration. Data generated for the TetX enzyme using the reporter system could be effectively fit with the known Km and kcat values, demonstrating the usefulness of this system for quantitative analyses. CONCLUSION Since members of the TetR family of repressors regulate enzymes and pumps acting upon almost every known antibiotic and a wide range of other small molecules, reporter systems with the same design as presented here, but employing heterologous TetR-related proteins, could be developed to measure enzymatic activities against a wide range of antibiotics and other compounds. Thus, the assay described here has far-reaching applicability and could be adapted for high-throughput applications.
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Affiliation(s)
- Zhou Yu
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
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Yu Z, Reichheld SE, Savchenko A, Parkinson J, Davidson AR. A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators. J Mol Biol 2010; 400:847-64. [PMID: 20595046 DOI: 10.1016/j.jmb.2010.05.062] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/21/2010] [Accepted: 05/25/2010] [Indexed: 11/17/2022]
Abstract
The tetracycline repressor family transcriptional regulators (TFRs) are homodimeric DNA-binding proteins that generally act as transcriptional repressors. Their DNA-binding activity is allosterically inactivated by the binding of small-molecule ligands. TFRs constitute the third most frequently occurring transcriptional regulator family found in bacteria with more than 10,000 representatives in the nonredundant protein database. In addition, more than 100 unique TFR structures have been solved by X-ray crystallography. In this study, we have used computational and experimental approaches to reveal the variations and conservation present within TFRs. Although TFR structures are very diverse, we were able to identify a conserved central triangle in their ligand-binding domains that forms the foundation of the structure and the framework for the ligand-binding cavity. While the sequences of DNA-binding domains of TFRs are highly conserved across the whole family, the sequences of their ligand-binding domains are so diverse that pairwise sequence similarity is often undetectable. Nevertheless, by analyzing subfamilies of TFRs, we were able to identify distinct regions of conservation in ligand-binding domains that may be important for allostery. To aid in large-scale analyses of TFR function, we have developed a simple and reliable computational approach to predict TFR operator sequences, a temperature melt-based assay to measure DNA binding, and a generic ligand-binding assay that will likely be applicable to most TFRs. Finally, our analysis of TFR structures highlights their flexibility and provides insight into a conserved allosteric mechanism for this family.
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Affiliation(s)
- Zhou Yu
- Department of Molecular Genetics, University of Toronto, 4285 Medical Sciences Building, 1 King's College Circle, Toronto, Ontario, Canada
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Isolation and Purification of a New Kalimantacin/Batumin-Related Polyketide Antibiotic and Elucidation of Its Biosynthesis Gene Cluster. ACTA ACUST UNITED AC 2010; 17:149-59. [DOI: 10.1016/j.chembiol.2010.01.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/06/2010] [Accepted: 01/14/2010] [Indexed: 11/24/2022]
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Analysis of two additional signaling molecules in Streptomyces coelicolor and the development of a butyrolactone-specific reporter system. ACTA ACUST UNITED AC 2010; 16:951-60. [PMID: 19778723 DOI: 10.1016/j.chembiol.2009.08.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/24/2009] [Accepted: 08/21/2009] [Indexed: 11/19/2022]
Abstract
gamma-Butyrolactone bacterial hormones regulate antibiotic production and morphological differentiation in Streptomyces species. One gamma-butyrolactone, SCB1, has been previously characterized in Streptomyces coelicolor. Here we report the characterization of two additional gamma-butyrolactones, named SCB2 (2-[1'-hydroxyoctyl]-3-hydroxymethylbutanolide) and SCB3 (2-[1'-hydroxy-6'-methyloctyl]-3-hydroxymethylbutanolide), possessing an antibiotic stimulatory activity. To elucidate the specificity determinants of these ligands for the receptor protein, ScbR, 30 chemically synthesized gamma-butyrolactone analogs were tested by utilizing the release of ScbR from DNA upon binding to a gamma-butyrolactone, which can be detected by kanamycin resistance. The butyrolactone detection method developed here revealed that ScbR shows preference toward a ligand possessing a 7-10 carbon C-2 side chain, a C-1'-beta-hydroxyl group, and a C-6'-methyl branch that coincides with SCB3. Moreover, this method was successfully used to screen for potential gamma-butyrolactone producers from commercial-antibiotic-producing Streptomyces.
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Le TBK, Fiedler HP, den Hengst CD, Ahn SK, Maxwell A, Buttner MJ. Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone in Streptomyces antibioticus. Mol Microbiol 2009; 72:1462-74. [PMID: 19460097 DOI: 10.1111/j.1365-2958.2009.06735.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because most antibiotics are potentially lethal to the producing organism, there must be mechanisms to ensure that the machinery responsible for export of the mature antibiotic is in place at the time of biosynthesis. Simocyclinone D8 is a potent DNA gyrase inhibitor produced by Streptomyces antibioticus Tü 6040. Within the simocyclinone biosynthetic cluster are two divergently transcribed genes, simR and simX, encoding proteins that resemble the TetR/TetA repressor-efflux pump pair that cause widespread resistance to clinically important tetracyclines. Engineered expression of simX from a strong, heterologous promoter conferred high level simocyclinone D8 resistance on Streptomyces lividans, showing that simX encodes a simocyclinone efflux pump. Transcription of simX is controlled by SimR, which directly represses the simX and simR promoters by binding to two operator sites in the simX-simR intergenic region. Simocyclinone D8 abolishes DNA binding by SimR, providing a mechanism that couples the biosynthesis of simocyclinone to its export. In addition, an intermediate in the biosynthetic pathway, simocyclinone C4, which is essentially inactive as a DNA gyrase inhibitor, also induces simX expression in vivo and relieves simX repression by SimR in vitro.
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Affiliation(s)
- Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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