Genome-wide analysis of regulatory networks controlling secondary metabolism in Streptomyces species

Antibiotic biosynthesis is controlled by complex regulatory networks involving many known and unknown interacting components. Two Streptomyces species were studied in this aspect in this study, S. clavuligerus , a natural producer of two important antibiotics, clavulanic acid and cephamycin C, and S. coelicolor, a model species for Streptomcyes molecular biology.; A two-component regulatory system was identified in Streptomyces clavuligerus based on its homology to a genetic locus encoding the global antibiotic regulator absA in S. coelicolor . Individual disruption of each of the components (cbsA1 and cbsA2) significantly enhanced biosynthesis of both cephamycin C and clavulanic acid. Further analysis of gene expression showed that mutants bearing genetic lesions in cbsA produced higher levels of transcripts for the pathway-specific regulatory genes, ccaR and claR.; The complete sequence of S. coelicolor genome provided us with the opportunity to make tools to monitor the transcriptome in a high-throughput manner. To facilitate the elucidation of the regulatory mechanism for antibiotic synthesis, whole-genome DNA microarrays for Streptomyces coelicolor were fabricated and hybridization conditions were optimized. Genomic DNA was used as common reference for all hybridizations to ease the comparison of transcript abundance between any two RNA samples. Because the log 2 ratio of cDNA over gDNA estimated the relative abundance of each transcript, a quantile normalization method was adapted from Affymetrix microarray analysis toolbox as the non-linear normalization method. S. coelicolor mutants of four regulatory genes as well as the WT were studied in detail with microarrays. Overall, many genes displayed dynamic transcript profiles along the processes of mycelial growth and antibiotic production. Cluster analysis of overall expression profiles revealed many groups of genes with well-correlated expression patterns. Cluster analysis of differential expression profiles between WT and mutants facilitated the identification of genes that were differentially expressed in mutants and provided insight of their functions by grouping the coordinately altered genes. The possible function of each targeted gene and their involvement in regulation of antibiotic synthesis are discussed.