Abstract
Streptomyces are efficient producers of various bioactive compounds, which are mostly synthesized by their secondary metabolite biosynthetic gene clusters (smBGCs). The smBGCs are tightly controlled by complex regulatory systems at transcriptional and translational levels to effectively utilize precursors that are supplied by primary metabolism. Thus, dynamic changes in gene expression in response to cellular status at both the transcriptional and translational levels should be elucidated to directly reflect protein levels, rapid downstream responses, and cellular energy costs. In this study, RNA-Seq and ribosome profiling were performed for five industrially important Streptomyces species at different growth phases, for the deep sequencing of total mRNA, and only those mRNA fragments that are protected by translating ribosomes, respectively. Herein, 12.0 to 763.8 million raw reads were sufficiently obtained with high quality of more than 80% for the Phred score Q30 and high reproducibility. These data provide a comprehensive understanding of the transcriptional and translational landscape across the Streptomyces species and contribute to facilitating the rational engineering of secondary metabolite production.
Highlights
Background & SummaryStreptomyces, which comprise the largest genus of Actinobacteria, are huge natural reservoir of secondary metabolites, including antibiotics, immunosuppressants, and other medicinal compounds[1,2,3,4,5,6]
Recent advancements in high-throughput sequencing have led to the development of the genome mining approach, which implicates that the genome of each Streptomyces species has more than 30 secondary metabolite biosynthetic gene clusters with potential to produce various unexplored secondary metabolites[2]
These secondary metabolites are synthesized by a series of enzymatic reactions, which depend on the supply of precursor molecules from primary metabolism, such as acetyl-coenzyme A and amino acids[7]
Summary
Streptomyces, which comprise the largest genus of Actinobacteria, are huge natural reservoir of secondary metabolites, including antibiotics, immunosuppressants, and other medicinal compounds[1,2,3,4,5,6]. Escherichia coli proteome analysis revealed that only approximately half of protein abundance is determined by transcriptional regulation, which indicates the existence of various post-transcriptional regulation[18] In this regard, deciphering translational dynamics is important to understanding post-transcriptional regulations that are closely related to cellular protein levels[19]. Several ribosome profiling studies in Streptomyces have been reported by our research group for S. coelicolor, S. clavuligerus, and S. lividans, which revealed translational buffering of secondary metabolism-related genes at a later growth phase and that translational abundance is more consistently maintained than transcript abundance[11,21,22]. Understanding the transcriptional and translational regulatory mechanisms and developing regulatory synthetic parts, such as promoters, ribosome-binding sequences, 5′ untranslated regions, and terminators[4] from the dataset allows rational genome engineering for efficient secondary metabolite production by Streptomyces[11]
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