Refactoring the silent spectinabilin gene cluster using a plug-and-play scaffold.

Natural products (secondary metabolites) are a rich source of compounds with important biological activities. Eliciting pathway expression is always challenging but extremely important in natural product discovery because an individual pathway is tightly controlled through a unique regulation mechanism and hence often remains silent under the routine culturing conditions. To overcome the drawbacks of the traditional approaches that lack general applicability, we developed a simple synthetic biology approach that decouples pathway expression from complex native regulations. Briefly, the entire silent biosynthetic pathway is refactored using a plug-and-play scaffold and a set of heterologous promoters that are functional in a heterologous host under the target culturing condition. Using this strategy, we successfully awakened the silent spectinabilin pathway from Streptomyces orinoci. This strategy bypasses the traditional laborious processes to elicit pathway expression and represents a new platform for discovering novel natural products.

[1]  M. Tanticharoen,et al.  Potent In Vitro Antimalarial Activity of Metacycloprodigiosin Isolated from Streptomycesspectabilis BCC 4785 , 2002, Antimicrobial Agents and Chemotherapy.

[2]  Kay Nieselt,et al.  The dynamic architecture of the metabolic switch in Streptomyces coelicolor , 2010, BMC Genomics.

[3]  Huimin Zhao,et al.  Direct cloning of large genomic sequences , 2012, Nature Biotechnology.

[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]  David J Newman,et al.  Natural products as sources of new drugs over the 30 years from 1981 to 2010. , 2012, Journal of natural products.

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

[7]  A. Brakhage,et al.  Activation of fungal silent gene clusters: a new avenue to drug discovery. , 2008, Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques.

[8]  R. D. Gietz,et al.  Yeast transformation by the LiAc/SS carrier DNA/PEG method. , 2014, Methods in molecular biology.

[9]  Elke Dittmann,et al.  Non‐Colinear Polyketide Biosynthesis in the Aureothin and Neoaureothin Pathways: An Evolutionary Perspective , 2007, Chembiochem : a European journal of chemical biology.

[10]  Satoshi Omura,et al.  Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism , 2010, Proceedings of the National Academy of Sciences.

[11]  B. Lugtenberg Faculty Opinions recommendation of Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. , 2001 .

[12]  I. Ahmad,et al.  Enhancement of xylitol production in Candida tropicalis by co-expression of two genes involved in pentose phosphate pathway , 2011, Bioprocess and Biosystems Engineering.

[13]  D J Newman,et al.  The influence of natural products upon drug discovery. , 2000, Natural product reports.

[14]  D. Hopwood,et al.  Streptomyces in nature and medicine : the antibiotic makers , 2007 .

[15]  H. Ikeda,et al.  Hyper-inducible expression system for streptomycetes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Gregory L Challis,et al.  Mining microbial genomes for new natural products and biosynthetic pathways. , 2008, Microbiology.

[17]  N. Kelleher,et al.  Heterologous production of fosfomycin and identification of the minimal biosynthetic gene cluster. , 2006, Chemistry & biology.

[18]  K. Rinehart,et al.  Spectinabilin, a new nitro-containing metabolite isolated from streptomyces spectabilis , 1976 .

[19]  B. Shen,et al.  Engineered production of iso-migrastatin in heterologous Streptomyces hosts. , 2009, Bioorganic & medicinal chemistry.

[20]  Rolf Müller,et al.  Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting , 2012, Nature Biotechnology.

[21]  H. Salis The ribosome binding site calculator. , 2011, Methods in enzymology.

[22]  H. Moriya,et al.  Establishing a New Methodology for Genome Mining and Biosynthesis of Polyketides and Peptides through Yeast Molecular Genetics , 2012, Chembiochem : a European journal of chemical biology.

[23]  R. Abed,et al.  Applications of cyanobacteria in biotechnology , 2009, Journal of applied microbiology.

[24]  Won-Kyung Hong,et al.  Enhanced production of ethanol from glycerol by engineered Hansenula polymorpha expressing pyruvate decarboxylase and aldehyde dehydrogenase genes from Zymomonas mobilis , 2010, Biotechnology Letters.

[25]  N. Kelleher,et al.  Cloning, expression, and biochemical characterization of Streptomyces rubellomurinus genes required for biosynthesis of antimalarial compound FR900098. , 2008, Chemistry & biology.

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

[27]  H. Gross Strategies to unravel the function of orphan biosynthesis pathways: recent examples and future prospects , 2007, Applied Microbiology and Biotechnology.

[28]  D. Newman,et al.  Natural products as sources of new drugs over the last 25 years. , 2007, Journal of natural products.

[29]  C. Hutchinson,et al.  Rapid engineering of polyketide overproduction by gene transfer to industrially optimized strains , 2003, Journal of Industrial Microbiology and Biotechnology.

[30]  Eung-Soo Kim,et al.  Transcriptome Analysis of an Antibiotic Downregulator Mutant and Synergistic Actinorhodin Stimulation via Disruption of a Precursor Flux Regulator in Streptomyces coelicolor , 2011, Applied and Environmental Microbiology.

[31]  C. Schmidt-Dannert,et al.  Discovery and characterization of terpenoid biosynthetic pathways of fungi. , 2012, Methods in enzymology.

[32]  M. Rondon,et al.  Identification of the Biosynthetic Gene Cluster and an Additional Gene for Resistance to the Antituberculosis Drug Capreomycin , 2007, Applied and Environmental Microbiology.

[33]  J. Jonák,et al.  Cloning and Characterization of the strOperon and Elongation Factor Tu Expression in Bacillus stearothermophilus , 2000, Journal of bacteriology.

[34]  Virginia W Cornish,et al.  Reiterative Recombination for the in vivo assembly of libraries of multigene pathways , 2011, Proceedings of the National Academy of Sciences.

[35]  Zengyi Shao,et al.  DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways , 2008, Nucleic acids research.

[36]  Brian F. Pfleger,et al.  Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes , 2006, Nature Biotechnology.

[37]  J. Engels,et al.  Promoter constructions for efficient secretion expression in Streptomyces lividans , 2004, Applied Microbiology and Biotechnology.

[38]  R. Biener,et al.  Comparative analysis of transcriptional activities of heterologous promoters in the rare actinomycete Actinoplanes friuliensis. , 2009, Journal of biotechnology.

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

[40]  Christine J. Martin,et al.  Increasing the efficiency of heterologous promoters in actinomycetes. , 2002, Journal of molecular microbiology and biotechnology.

[41]  U C Banerjee,et al.  Bioactive Compounds from Cyanobacteria and Microalgae: An Overview , 2005, Critical reviews in biotechnology.

[42]  R. Müller,et al.  Analysis of myxobacterial secondary metabolism goes molecular , 2006, Journal of Industrial Microbiology and Biotechnology.

[43]  G. Challis,et al.  Strategies for the Discovery of New Natural Products by Genome Mining , 2009, Chembiochem : a European journal of chemical biology.

[44]  Huimin Zhao,et al.  Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler. , 2011, Molecular bioSystems.

[45]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[46]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[47]  Corinna Lange,et al.  Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. , 2007, Nature chemical biology.

[48]  J. Vederas,et al.  [Drug discovery and natural products: end of era or an endless frontier?]. , 2011, Biomeditsinskaia khimiia.

[49]  A. Pineda-Lucena,et al.  Amino Acid Precursor Supply in the Biosynthesis of the RNA Polymerase Inhibitor Streptolydigin by Streptomyces lydicus , 2011, Journal of bacteriology.

[50]  Richard H. Baltz,et al.  Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters , 2010, Journal of Industrial Microbiology & Biotechnology.

[51]  Huimin Zhao,et al.  Iowa State University From the SelectedWorks of Zengyi Shao 2012 Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae , 2017 .

[52]  Huimin Zhao,et al.  Customized optimization of metabolic pathways by combinatorial transcriptional engineering , 2012, Nucleic acids research.

[53]  Yoshiyuki Sakaki,et al.  Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Huimin Zhao,et al.  Cloning and heterologous expression of the spectinabilin biosynthetic gene cluster from Streptomyces spectabilis. , 2010, Molecular bioSystems.

[55]  Yong Huang,et al.  Cloning, sequencing, analysis, and heterologous expression of the fredericamycin biosynthetic gene cluster from Streptomyces griseus. , 2005, Journal of the American Chemical Society.

[56]  Axel A Brakhage,et al.  Fungal secondary metabolites - strategies to activate silent gene clusters. , 2011, Fungal genetics and biology : FG & B.

[57]  H. Lee,et al.  Translation elongation factor 1-α gene from Pichia pastoris: molecular cloning, sequence, and use of its promoter , 2007, Applied Microbiology and Biotechnology.

[58]  J. Norimine,et al.  Characterization and gene expression of Babesia bovis elongation factor-1alpha. , 2006, International journal for parasitology.