Disclosing the Potential of the SARP-Type Regulator PapR2 for the Activation of Antibiotic Gene Clusters in Streptomycetes

Streptomyces antibiotic regulatory protein (SARP) family regulators are well-known activators of antibiotic biosynthesis in streptomycetes. The respective genes occur in various types of antibiotic gene clusters encoding, e.g., for polyketides, ribosomally and non-ribosomally synthesized peptides, or β-lactam antibiotics. We found that overexpression of the SARP-type regulator gene papR2 from Streptomyces pristinaespiralis in Streptomyces lividans leads to the activation of the silent undecylprodigiosin (Red) gene cluster. The activation happens upon the inducing function of PapR2, which takes over the regulatory role of RedD, the latter of which is the intrinsic SARP regulator of Red biosynthesis in S. lividans. Due to the broad abundance of SARP genes in different antibiotic gene clusters of various actinomycetes and the uniform activating principle of the encoded regulators, we suggest that this type of regulator is especially well suited to be used as an initiator of antibiotic biosynthesis in actinomycetes. Here, we report on a SARP-guided strategy to activate antibiotic gene clusters. As a proof of principle, we present the PapR2-driven activation of the amicetin/plicacetin gene cluster in the novel Indonesian strain isolate Streptomyces sp. SHP22-7.

[1]  J. Martín,et al.  The Balance Metabolism Safety Net: Integration of Stress Signals by Interacting Transcriptional Factors in Streptomyces and Related Actinobacteria , 2020, Frontiers in Microbiology.

[2]  A. Truman,et al.  Activation of Secondary Metabolite Gene Clusters in Streptomyces clavuligerus by the PimM Regulator of Streptomyces natalensis , 2019, Front. Microbiol..

[3]  Kai Blin,et al.  The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters , 2018, Nucleic Acids Res..

[4]  Complete Genome Sequence of Streptomyces sp. Strain SHP22-7, a New Species Isolated from Mangrove of Enggano Island, Indonesia , 2018, Microbiology Resource Announcements.

[5]  Kai Blin,et al.  Patscanui: an intuitive web interface for searching patterns in DNA and protein data , 2018, Nucleic Acids Res..

[6]  C. Méndez,et al.  New Insights into the Biosynthesis Pathway of Polyketide Alkaloid Argimycins P in Streptomyces argillaceus , 2018, Front. Microbiol..

[7]  Yijun Chen,et al.  Identification of truncated form of NosP as a transcription factor to regulate the biosynthesis of nosiheptide , 2018, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[8]  Richard H. Baltz,et al.  Gifted microbes for genome mining and natural product discovery , 2017, Journal of Industrial Microbiology & Biotechnology.

[9]  K. Shin‐ya,et al.  Production of a Novel Amide‐Containing Polyene by Activating a Cryptic Biosynthetic Gene Cluster in Streptomyces sp. MSC090213JE08 , 2016, Chembiochem : a European journal of chemical biology.

[10]  D. Newman,et al.  Natural Products as Sources of New Drugs from 1981 to 2014. , 2016, Journal of natural products.

[11]  Interspecies Complementation of the LuxR Family Pathway-Specific Regulator Involved in Macrolide Biosynthesis. , 2016, Journal of microbiology and biotechnology.

[12]  Yvonne Mast,et al.  A Complex Signaling Cascade Governs Pristinamycin Biosynthesis in Streptomyces pristinaespiralis , 2015, Applied and Environmental Microbiology.

[13]  S. Kitani,et al.  Differential contributions of two SARP family regulatory genes to indigoidine biosynthesis in Streptomyces lavendulae FRI-5 , 2014, Applied Microbiology and Biotechnology.

[14]  C. Barreiro,et al.  The gamma-butyrolactone receptors BulR1 and BulR2 of Streptomyces tsukubaensis: tacrolimus (FK506) and butyrolactone synthetases production control , 2014, Applied Microbiology and Biotechnology.

[15]  Hua Zhu,et al.  Triggers and cues that activate antibiotic production by actinomycetes , 2014, Journal of Industrial Microbiology & Biotechnology.

[16]  M. Díaz,et al.  Two-component systems in Streptomyces: key regulators of antibiotic complex pathways , 2013, Microbial Cell Factories.

[17]  J. Kormanec,et al.  A gene determining a new member of the SARP family contributes to transcription of genes for the synthesis of the angucycline polyketide auricin in Streptomyces aureofaciens CCM 3239. , 2013, FEMS microbiology letters.

[18]  Gang Liu,et al.  Molecular Regulation of Antibiotic Biosynthesis in Streptomyces , 2013, Microbiology and Molecular Reviews.

[19]  Yunchang Xie,et al.  Identification of the Biosynthetic Gene Cluster and Regulatory Cascade for the Synergistic Antibacterial Antibiotics Griseoviridin and Viridogrisein in Streptomyces griseoviridis , 2012, Chembiochem : a European journal of chemical biology.

[20]  K. Ochi,et al.  New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters , 2012, Applied Microbiology and Biotechnology.

[21]  David A. Hodgson,et al.  Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor , 2012, Nucleic acids research.

[22]  Siwen Niu,et al.  Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation , 2012, Applied and Environmental Microbiology.

[23]  Wei Gu,et al.  Improving genome assemblies by sequencing PCR products with PacBio. , 2012, BioTechniques.

[24]  Kai Blin,et al.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..

[25]  J. Kormanec,et al.  The role of two SARP family transcriptional regulators in regulation of the auricin gene cluster in Streptomyces aureofaciens CCM 3239. , 2011, Microbiology.

[26]  C. Prieto,et al.  Cross‐talk of global nutritional regulators in the control of primary and secondary metabolism in Streptomyces , 2011, Microbial biotechnology.

[27]  Richard A. Lewis,et al.  Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization , 2010, BMC Genomics.

[28]  Y. Igarashi,et al.  Mycolic Acid-Containing Bacteria Induce Natural-Product Biosynthesis in Streptomyces Species , 2010, Applied and Environmental Microbiology.

[29]  Shouji Yamamoto,et al.  Regulation of Lankamycin Biosynthesis in Streptomyces rochei by Two SARP Genes, srrY and srrZ , 2010, Bioscience, biotechnology, and biochemistry.

[30]  J. Aínsa.  Practical Streptomyces Genetics. T. Kieser, M. J. Bibb, M. J. Buttner, K. F. Chater, D. A. Hopwood , 2010 .

[31]  Yuanyuan Pan,et al.  SanG, a transcriptional activator, controls nikkomycin biosynthesis through binding to the sanN-sanO intergenic region in Streptomyces ansochromogenes. , 2010, Microbiology.

[32]  R. Garg,et al.  Regulation of valanimycin biosynthesis in Streptomyces viridifaciens: characterization of VlmI as a Streptomyces antibiotic regulatory protein (SARP). , 2010, Microbiology.

[33]  S. Kitani,et al.  Hierarchical control of virginiamycin production in Streptomyces virginiae by three pathway-specific regulators: VmsS, VmsT and VmsR. , 2009, Microbiology.

[34]  C. Méndez,et al.  Identification of transcriptional activators for thienamycin and cephamycin C biosynthetic genes within the thienamycin gene cluster from Streptomyces cattleya , 2008, Molecular microbiology.

[35]  B. Shen,et al.  Identification and Utility of FdmR1 as a Streptomyces Antibiotic Regulatory Protein Activator for Fredericamycin Production in Streptomyces griseus ATCC 49344 and Heterologous Hosts , 2008, Journal of bacteriology.

[36]  G. Challis,et al.  Elucidation of the Streptomyces coelicolor pathway to 2-undecylpyrrole, a key intermediate in undecylprodiginine and streptorubin B biosynthesis. , 2008, Chemistry & biology.

[37]  S. Horinouchi,et al.  AfsR recruits RNA polymerase to the afsS promoter: a model for transcriptional activation by SARPs. , 2007, Journal of molecular biology.

[38]  G. Challis,et al.  Elucidation of the Streptomyces coelicolor pathway to 4-methoxy-2,2'-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine biosynthesis. , 2006, Chemical communications.

[39]  Björn Sohlberg,et al.  Cross‐regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor , 2005, Molecular microbiology.

[40]  Eriko Takano,et al.  A bacterial hormone (the SCB1) directly controls the expression of a pathway‐specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor , 2005, Molecular microbiology.

[41]  Xiuhua Pang,et al.  Involvement of AlpV, a New Member of the Streptomyces Antibiotic Regulatory Protein Family, in Regulation of the Duplicated Type II Polyketide Synthase alp Gene Cluster in Streptomyces ambofaciens , 2005, Journal of bacteriology.

[42]  M. Bibb,et al.  Regulation of secondary metabolism in streptomycetes. , 2005, Current opinion in microbiology.

[43]  M. Osburne,et al.  Environmental DNA Fragment Conferring Early and Increased Sporulation and Antibiotic Production in Streptomyces Species , 2005, Applied and Environmental Microbiology.

[44]  J. Martín,et al.  Iron-regulatory proteins DmdR1 and DmdR2 of Streptomyces coelicolor form two different DNA-protein complexes with iron boxes. , 2004, The Biochemical journal.

[45]  M. Gasson,et al.  Cloning and engineering of the cinnamycin biosynthetic gene cluster from Streptomyces cinnamoneus cinnamoneus DSM 40005 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  J. Hoyt,et al.  Molecular characterization and analysis of the biosynthetic gene cluster for the azoxy antibiotic valanimycin , 2002, Molecular microbiology.

[47]  K. Ochi,et al.  Activation of Antibiotic Biosynthesis by Specified Mutations in the rpoB Gene (Encoding the RNA Polymerase β Subunit) of Streptomyces lividans , 2002, Journal of bacteriology.

[48]  J. Martín,et al.  CcaR Is an Autoregulatory Protein That Binds to the ccaR and cefD-cmcI Promoters of the Cephamycin C-Clavulanic Acid Cluster in Streptomyces clavuligerus , 2002, Journal of bacteriology.

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

[50]  N. J. Ryding,et al.  Regulation of the Streptomyces coelicolor Calcium-Dependent Antibiotic by absA, Encoding a Cluster-Linked Two-Component System , 2002, Journal of bacteriology.

[51]  N. Bate,et al.  Differential roles of two SARP‐encoding regulatory genes during tylosin biosynthesis , 2002, Molecular microbiology.

[52]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[53]  M. Bibb,et al.  Application of redD, the transcriptional activator gene of the undecylprodigiosin biosynthetic pathway, as a reporter for transcriptional activity in Streptomyces coelicolor A3(2) and Streptomyces lividans. , 2000, Journal of molecular microbiology and biotechnology.

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

[55]  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.

[56]  F. Lombó,et al.  The Mithramycin Gene Cluster of Streptomyces argillaceus Contains a Positive Regulatory Gene and Two Repeated DNA Sequences That Are Located at Both Ends of the Cluster , 1999, Journal of bacteriology.

[57]  S. Horinouchi,et al.  Involvement of two A‐factor receptor homologues in Streptomyces coelicolor A3(2) in the regulation of secondary metabolism and morphogenesis , 1998, Molecular microbiology.

[58]  M. Bibb,et al.  A novel family of proteins that regulates antibiotic production in streptomycetes appears to contain an OmpR‐like DNA‐binding fold , 1997, Molecular microbiology.

[59]  J. Martín,et al.  A regulatory gene (ccaR) required for cephamycin and clavulanic acid production in Streptomyces clavuligerus: amplification results in overproduction of both beta-lactam compounds , 1997, Journal of bacteriology.

[60]  J. White,et al.  bldA dependence of undecylprodigiosin production in Streptomyces coelicolor A3(2) involves a pathway-specific regulatory cascade , 1997, Journal of bacteriology.

[61]  E. Takano,et al.  Transcriptional regulation of the redD transcriptional activator gene accounts for growth‐phase‐dependent production of the antibiotic undecylprodigiosin in Streptomyces coelicolor A3(2) , 1992, Molecular microbiology.

[62]  S. Ōmura,et al.  Metabolism and Products of Actinomycetes - An Introduction , 1990 .

[63]  S. Horinouchi,et al.  Nucleotide sequence of afsB, a pleiotropic gene involved in secondary metabolism in Streptomyces coelicolor A3(2) and "Streptomyces lividans" , 1986, Journal of bacteriology.

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