DNA microarray analysis of global gene regulation by A-factor in Streptomyces griseus

Abstract

A-factor (2-isocapryloyl-3R-hydroxymethyl-γ-butyrolactone) is a microbial hormone that triggers morphological differentiation and secondary metabolism in Streptomyces griseus. The effects of A-factor on global gene expression were determined by DNA microarray analysis of transcriptomes obtained with the A-factor-deficient mutant ΔafsA. A-factor was added at a concentration of 25 ng ml−1 to mutant ΔafsA at the middle of the exponential growth phase, and RNA samples were prepared from the cells grown after A-factor addition for a further 5, 15 and 30 min, and 1, 2, 4, 8 and 12 h. The effects of A-factor on transcription of all protein-coding genes of S. griseus were evaluated by comparison of the transcriptomes with those obtained from cells grown in the absence of A-factor. Analysis of variance among the transcriptomes revealed that 477 genes, which were dispersed throughout the chromosome, were differentially expressed during the 12 h after addition of A-factor, when evaluated by specific criteria. Quality threshold clustering analysis with regard to putative polycistronic transcriptional units and levels of upregulation predicted that 152 genes belonging to 74 transcriptional units were probable A-factor-inducible genes. Competitive electrophoretic mobility shift assays using DNA fragments including putative promoter regions of these 74 transcriptional units suggested that AdpA bound 37 regions to activate 72 genes in total. Many of these A-factor-inducible genes encoded proteins of unknown function, suggesting that the A-factor regulatory cascade of S. griseus affects gene expression at a specific time point more profoundly than expected.

Biosynthetic genes for aminoglycoside antibiotics

“…In fact, its complex regulation system has been mostly established. 41 However, not so many biosynthetic enzymes have been characterized even now because, probably, the biosynthetic pathway for streptomycin is too unique to predict appropriate functions compared with other aminoglycoside biosynthetic genes. Among the streptomycin biosynthetic enzymes, Gln:scyllo-inosose aminotransferase StsC 15 and Arg:inosamine-phosphate amidinotransferase StrB1 16 are characterized biochemically.…”

Characterization of a Novel Sesquiterpene Cyclase Involved in (+)-Caryolan-1-ol Biosynthesis in Streptomyces griseus

“…Because gcoA was indicated to be a direct target of AdpA (19), a master regulator of secondary metabolism and morphological differentiation in S. griseus, we also analyzed by GC-MS the extracts of crude cell lysate of an adpA-deleted (⌬adpA) mutant (Fig. 3, iii).…”

“…The other two genes encode single-domain SC homologs (SGR2079 and SGR6065). Interestingly, our transcriptome analysis showed that the SGR2079 gene is transcribed in wild-type S. griseus in an AdpA-dependent manner (19), indicating that SGR2079 is involved in the production of one of the secondary metabolites under the control of A-factor. SGR2079 (335 amino acids) shows 29% amino acid sequence identity with the pentalenene synthase from Streptomyces sp.…”

The pleitropic regulator AdpAch is required for natamycin biosynthesis and morphological differentiation in Streptomyces chattanoogensis

“…In S. griseus, adpA is the sole target of the A-factor receptor (ArpA). By applying microarray and electrophoretic mobility shift assay (EMSA) analysis, AdpA has been shown to directly bind 37 promoter regions to activate 72 genes throughout the chromosome, including strR, the pathway-specific activator for streptomycin biosynthesis (Hara et al, 2009). While in S. coelicolor, adpA c transcription does not depend on the butyrolactone system, the DadpA c mutant is conditionally defective in morphological differentiation.…”