SimReg1 is a master switch for biosynthesis and export of simocyclinone D8 and its precursors

Analysis of the simocyclinone biosynthesis (sim) gene cluster of Streptomyces antibioticus Tü6040 led to the identification of a putative pathway specific regulatory gene simReg1. In silico analysis places the SimReg1 protein in the OmpR-PhoB subfamily of response regulators. Gene replacement of simReg1 from the S. antibioticus chromosome completely abolishes simocyclinone production indicating that SimReg1 is a key regulator of simocyclinone biosynthesis. Results of the DNA-shift assays and reporter gene expression analysis are consistent with the idea that SimReg1 activates transcription of simocyclinone biosynthesis, transporter genes, regulatory gene simReg3 and his own transcription. The presence of extracts (simocyclinone) from S. antibioticus Tü6040 × pSSimR1-1 could dissociate SimReg1 from promoter regions. A preliminary model for regulation of simocyclinone biosynthesis and export is discussed.

[1]  J. Kormanec,et al.  Genetic manipulation of pathway regulation for overproduction of angucycline-like antibiotic auricin in Streptomyces aureofaciens CCM 3239 , 2011, Folia Microbiologica.

[2]  A. Pühler,et al.  A vector system with temperature-sensitive replication for gene disruption and mutational cloning in streptomycetes , 1989, Molecular and General Genetics MGG.

[3]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[4]  G. V. van Wezel,et al.  Chapter 5. Applying the genetics of secondary metabolism in model actinomycetes to the discovery of new antibiotics. , 2009, Methods in enzymology.

[5]  T. Le,et al.  A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase , 2009, Science.

[6]  J. Martín,et al.  PimM, a PAS domain positive regulator of pimaricin biosynthesis in Streptomyces natalensis. , 2007, Microbiology.

[7]  Jun Ishikawa,et al.  Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350 , 2008, Journal of bacteriology.

[8]  T. Le,et al.  Coupling of the biosynthesis and export of the DNA gyrase inhibitor simocyclinone in Streptomyces antibioticus , 2009, Molecular microbiology.

[9]  W. Witte,et al.  Antibiotic resistance. , 2013, International journal of medical microbiology : IJMM.

[10]  D. Hoffmeister,et al.  Production of landomycins in Streptomyces globisporus 1912 and S cyanogenus S136 is regulated by genes encoding putative transcriptional activators. , 2003, FEMS microbiology letters.

[11]  S. Walker,et al.  Coordination of export and glycosylation of landomycins in Streptomyces cyanogenus S136. , 2008, FEMS microbiology letters.

[12]  S. Kitani,et al.  Characterization of biosynthetic gene cluster for the production of virginiamycin M, a streptogramin type A antibiotic, in Streptomyces virginiae. , 2007, Gene.

[13]  Gilles P van Wezel,et al.  The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. , 2011, Natural product reports.

[14]  E. Takano,et al.  COMPLEX ENZYMES IN MICROBIAL NATURAL PRODUCT BIOSYNTHESIS, PART A: OVERVIEW ARTICLES AND PEPTIDES , 2009 .

[15]  S. Jensen,et al.  Use of the native flp gene to generate in-frame unmarked mutations in Streptomyces spp. , 2009, Gene.

[16]  M. Palumbo,et al.  Mapping Simocyclinone D8 Interaction with DNA Gyrase: Evidence for a New Binding Site on GyrB , 2009, Antimicrobial Agents and Chemotherapy.

[17]  T. Le,et al.  Crystallization and preliminary X-ray analysis of the TetR-like efflux pump regulator SimR. , 2011, Acta crystallographica. Section F, Structural biology and crystallization communications.

[18]  T. Kieser Practical streptomyces genetics , 2000 .

[19]  A. Khodursky,et al.  In Vivo and In Vitro Patterns of the Activity of Simocyclinone D8, an Angucyclinone Antibiotic from Streptomyces antibioticus , 2009, Antimicrobial Agents and Chemotherapy.

[20]  E. Takano,et al.  Chapter 6. Regulation of antibiotic production by bacterial hormones. , 2009, Methods in enzymology.

[21]  F. Flett,et al.  High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes. , 1997, FEMS microbiology letters.

[22]  A. Bechthold,et al.  IncP plasmids are most effective in mediating conjugation between Escherichia coli and streptomycetes , 2006, Russian Journal of Genetics.

[23]  L. Heide,et al.  Cloning and analysis of the simocyclinone biosynthetic gene cluster of Streptomyces antibioticus Tü 6040 , 2002, Archives of Microbiology.

[24]  Bruce Stillman,et al.  Cold Spring Harbor Laboratory , 1995, Current Biology.

[25]  T. Nakamura,et al.  DNA-binding activity of LndI protein and temporal expression of the gene that upregulates landomycin E production in Streptomyces globisporus 1912. , 2005, Microbiology.

[26]  P. Branny,et al.  Antibiotic resistance gene cassettes derived from the omega interposon for use in E. coli and Streptomyces. , 1997, Gene.

[27]  J. Martín,et al.  The two-component PhoR-PhoP system controls both primary metabolism and secondary metabolite biosynthesis in Streptomyces lividans , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Hopwood How do antibiotic‐producing bacteria ensure their self‐resistance before antibiotic biosynthesis incapacitates them? , 2007, Molecular microbiology.

[29]  C. Hutchinson,et al.  Mapping the DNA‐binding domain and target sequences of the Streptomyces peucetius daunorubicin biosynthesis regulatory protein, DnrI , 2002, Molecular microbiology.

[30]  R. Kratzke,et al.  Anti-proliferative effects of simocyclinone D8 (SD8), a novel catalytic inhibitor of topoisomerase II , 2008, Investigational new drugs.

[31]  K. Fan,et al.  Autoregulation of antibiotic biosynthesis by binding of the end product to an atypical response regulator , 2009, Proceedings of the National Academy of Sciences.

[32]  M. Bibb,et al.  Chapter 4. Analyzing the regulation of antibiotic production in streptomycetes. , 2009, Methods in enzymology.

[33]  V. Fedorenko,et al.  β-Glucuronidase as a Sensitive and Versatile Reporter in Actinomycetes , 2011, Applied and Environmental Microbiology.

[34]  K. O'Brien,et al.  Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. , 1992, Gene.

[35]  Frederick W. Dahlquist,et al.  Switched or Not?: the Structure of Unphosphorylated CheY Bound to the N Terminus of FliM , 2006, Journal of bacteriology.

[36]  A. Marina,et al.  Phosphorylation-independent activation of the atypical response regulator NblR. , 2008, Microbiology.

[37]  T. Le,et al.  Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression. , 2011, Journal of molecular biology.

[38]  A. Bechthold,et al.  Function of lanI in regulation of landomycin A biosynthesis in Streptomyces cyanogenus S136 and cross-complementation studies with Streptomyces antibiotic regulatory proteins encoding genes , 2008, Archives of Microbiology.

[39]  Yinhua Lu,et al.  Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165 , 2008, Applied Microbiology and Biotechnology.

[40]  D. Hopwood Genetic manipulation of Streptomyces : a laboratory manual , 1985 .

[41]  A. Zeeck,et al.  Simocyclinones: diversity of metabolites is dependent on fermentation conditions3 , 2001, Journal of Industrial Microbiology and Biotechnology.

[42]  A. Trefzer,et al.  Biosynthetic Gene Cluster of Simocyclinone, a Natural Multihybrid Antibiotic , 2002, Antimicrobial Agents and Chemotherapy.

[43]  M. Fernández-Moreno,et al.  Characterization of the Pathway-Specific Positive Transcriptional Regulator for Actinorhodin Biosynthesis inStreptomyces coelicolor A3(2) as a DNA-Binding Protein , 1999, Journal of bacteriology.

[44]  D. Hopwood Genetic manipulation in Streptomyces , 1983 .

[45]  U. Rix,et al.  Generation of new landomycins by combinatorial biosynthetic manipulation of the LndGT4 gene of the landomycin E cluster in S. globisporus. , 2004, Chemistry & biology.

[46]  Andreas Wietzorrek,et al.  Extracellular signalling, translational control, two repressors and an activator all contribute to the regulation of methylenomycin production in Streptomyces coelicolor , 2009, Molecular microbiology.

[47]  S. Horinouchi,et al.  Mining and Polishing of the Treasure Trove in the Bacterial Genus Streptomyces , 2007, Bioscience, biotechnology, and biochemistry.