Investigating the transcriptome of Streptomyces venezuelae

Abstract

Bacterial transcriptomes are highly complex, comprising not only protein-coding RNAs and translation-related non-coding RNAs, but also non-coding RNAs that function as regulators of gene expression. The post-transcriptional modification of RNA sequences by RNA editing enzymes, which has recently been shown to affect diverse RNA substrates in several bacteria, can magnify this complexity further still. However, little is known about RNA editing and non-coding RNAs in Streptomyces venezuelae, a model organism for studying complex bacterial development and specialized metabolism. This thesis investigates RNA editing and non-coding regulatory RNAs in S. venezuelae using RNA sequencing data from wild type and mutant strains at various stages of development and under several laboratory-controlled conditions. We identified hundreds of adenosine-to-inosine editing events throughout the transcriptome and predicted the potential impact of the edits occurring in protein-coding RNAs. The potential role of the adenosine deaminase enzyme TadA in facilitating these RNA editing events is also considered. Additionally, we detected thousands of transcripts that are expressed from unannotated regions of the S. venezuelae genome, many of which we predict are non-coding RNAs. Furthermore, we highlight our efforts to characterize a highly expressed putative non-coding RNA that exhibits considerable sequence conservation in other streptomycetes. This work provides new insights into the transcriptomic complexity of S. venezuelae and expands our understanding of RNA-based regulation in bacteria.