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

Abstract

Cold-shock adaptation is essential for the survival of soil-dwelling sessile streptomycetes exposed to fluctuating environmental temperatures, yet the precise regulatory mechanisms underlying this response remain poorly understood. Here, we investigated the global transcriptional and translational responses of the model actinomycete, Streptomyces coelicolor A3(2), to cold-shock using integrated RNA-seq and polysome profiling. Cold-shock treatment in minimal liquid medium triggered significant transcriptional changes in 811 genes. Notably, three operons, encoding a CspA homologue, a DEAD-box helicase, and a cystathionine-{beta}-synthase (CBS) domain-containing protein and/or a protein of unknown function (SCO5921-SCO5918, SCO4684-SCO4686, and SCO3731-SCO3733) were identified as central players of the cold-shock response, exhibiting up to 2,000-fold transcriptional induction. Systems-level transcriptomic analysis further revealed the cold-shock induced activation of pathways associated with gluconeogenesis, coenzyme A metabolism, phenylacetate degradation, lipid raft remodelling, and extracellular functions, pointing to extensive metabolic reprogramming coordinated with membrane adaptation during cold acclimation. Polysome profiling unveiled strong translational potentiation of operonic genes downstream from the promoter proximal cspA homologue genes, a process potentially mediated by RNA secondary structures that overlap ribosome binding sites (RBSs). The pronounced induction of DEAD-box RNA helicases and CspA RNA chaperones is presumed to reflect their critical requirement for resolving excessive nucleic acid secondary structures inherent to the high G+C content genome of Streptomyces (>73% G+C), including the RBS-masking stem-loops within their own operons. Together, this study provides a comprehensive, system-level understanding of cold-shock adaptation in Streptomyces, highlighting a multi-layered regulatory architecture that couples metabolic reprogramming with RNA structure-dependent translational control to mitigate thermal stress. IMPORTANCEThis study characterizes the cold-shock response of the model actinomycete, S. coelicolor A3(2), for the first time at both the transcriptome and translatome levels. Combined with a machine-learning based iModulon framework, our findings provide critical insights on both metabolic adaptation and multi-layered regulatory mechanisms, including transcriptional networks and RNA structure-dependent translational control. Beyond advancing our fundamental understanding of cold acclimation in Streptomyces, we identified several putative cis-acting regulatory elements within the intergenic regions between the primary cold-shock genes (SCO4684 and SCO5921) and their downstream DEAD-box helicase-encoding genes. These regulatory elements, coupled with the exceptionally robust transcriptional and translational induction of the core cold-shock operons, significantly expands the synthetic biology toolkit for Streptomyces. Ultimately, these molecular components hold substantial potential for exploitation in optimizing and manipulating cryptic antibiotic biosynthetic gene clusters within this bacterial genus of considerable industrial importance.