Identification of Small RNAs in Streptomyces clavuligerus Using High-Resolution Transcriptomics and Expression...

Small non-coding RNAs play a pivotal role in regulating various metabolic processes in both prokaryotic and eukaryotic organisms. However, knowledge about small RNAs (sRNAs) in Streptomyces clavuligerus (S. clavuligerus) is scarce. This study aimed to use cutting-edge bioinformatics tools and a compendium of RNA-seq data to predict the potential coding of sRNAs that might be present in the genome of S. clavuligerus ATCC 27064. In the genome of S. clavuligerus, 606 intergenic regions (IGRs) are conserved, and 272 possess a highly thermodynamically stable and conserved secondary structure, indicating the presence of non-coding RNA in these regions. The transcriptome assembly of S. clavuligerus showed that the genome is completely functional, as all the annotated genes are expressed under the conditions analyzed. From this assembly, transcripts originating from IGRs were labeled as putative sRNAs, and their differential expression during the growth curve of S. clavuligerus for clavulanic acid (CA) production was established. The interactome of these differentially expressed (DE) RNAs displayed the sRNAs as global regulators, as they can have multiple mRNA targets. The functional annotation of the target genes of DE sRNAs demonstrated that they are directly involved in secondary metabolite production. Specifically, two sRNA have the genes of the biosynthetic gene cluster of CA as targets. Thus, these molecules add an additional layer to the regulatory cascade for CA biosynthesis, and we propose them as targets for metabolic engineering to increase CA production.