Global analysis of the cold-shock response in the model antibiotic producing actinomycete, Streptomyces coelicolor A3(2)

The cold shock (CS) response of the model actinomycete bacterium, Streptomyces coelicolor A3(2) has been characterized for the first time at the transcriptome and translatome level. Key players of the CS response reside in three operons encoding a CspA homologue, a DEAD box helicase and either a cystathionine-beta-synthase domain protein, or a protein of unknown function, or both ( SCO5921–SCO5918; SCO46984-SCO4686; SCO3731-SCO3733 ). Genes in the SCO5921-SCO5918 and SCO4684-SCO4686 operons are subjected to massive transcriptional induction, up to 2,000-fold, upon cold acclimation. Moreover, SCO5920 , SCO5919 and SCO5918 are the most highly upregulated at the transcriptional and translational level (potentiated). Cold adaptation resulted in transcriptional changes in 811 genes, with enrichment for four functional groups: helicases, transcription factors, phenylalanine metabolism and extracellular functions. Major CS-induced gene products are involved in assisting transcription and translation at low temperature including RNA helicases and RNA chaperone proteins (CS proteins). The considerable induction of these gene products is presumed to reflect their critical importance to removing excessive nucleic acid secondary structure in the high %G+C Streptomyces genome (>73% G+C).

Three novel CS-induced transcriptional regulators were identified: SCO1568, SCO4640 and SCO7014. Several putative cis-acting regulatory elements have been identified in the CspA-encoding cold-shock operons and other members of the CS regulon. Furthermore, two small non-coding RNAs are substantially induced by cold-shock, sRNA126 and sRNA208, and their expression correlates with that of the novel transcription factors.

Other upregulated genes were identified with functions in modification of cell membrane (e.g. delta fatty acid desaturase, des ( SCO3682 )) and cell wall structure (e.g. D-alanyl-D-alanine carboxypeptidase ( SCO7050 ) and SCO617 9)). Several membrane efflux transporter pumps conferring resistance to translation targeting antibiotics were induced, including pqrB which encodes a multidrug resistance efflux pump of the major facilitator superfamily and SCO4120, conferring ciprofloxacin and chloramphenicol resistance. The phenylacetate degradation (PAA) regulon is co-ordinately CS-induced. Exclusively translationally enhanced genes are enriched in the protein phosphorylation functional category. The highly conserved gene pair, SCO0818 and SCO0819 , encoding an ABC transporter ATP-binding protein and a transmembrane protein, is in this group.

The CS-induced transcriptional and translational cis-acting control regions identified in this study, within the massively induced SCO5921 and SCO4684 operons, could be exploited as novel synthetic biology tools for manipulating antibiotic biosynthetic gene clusters in this industrially important bacterial group.