Work over the past two decades has revealed that non-coding RNAs (ncRNAs) are prevalent in all kingdoms of life. Using RNA-seq we discovered hundreds of ncRNAs in the antibiotic-producing genus of bacteria, Streptomyces. These included trans-encoded small RNAS (sRNAs), cis-antisense RNAs, and a new type of antisense RNA we termed cutoRNAs (convergent untranslated overlapping RNAs) that arise when transcription termination does not occur in the intergenic region between two convergently arranged genes. Many of these ncRNAs feature prominently in the specialized metabolite biosynthetic clusters (e.g. antibiotics, anticancer agents, immunosuppressants). Hence, it is likely that understanding the functions of these RNAs will be important for new molecule discovery. We found that one highly expressed antisense RNA (ScbN) was expressed opposite the -butyrolactone synthase scbA in the model streptomycete Streptomyces coelicolor. However, ScbN had no detectible impact on the expression of scbA. Instead, the transcription terminator of scbN, which also forms a hairpin within the coding sequence of scbA, was found to reduce expression of scbA more than 10-fold. This led us to bioinformatically search for similar coding-sequence hairpins throughout all bacteria, leading to the discovery of many stable RNA structures with conserved locations throughout very divergent bacteria (e.g. Streptomyces, Escherichia coli, Bacillus subtilis). / Thesis / Doctor of Philosophy (PhD) / The flow of genetic information, from DNA to RNA to proteins, often portrays RNA as a mere intermediary molecule. An alternative, and perhaps more accurate, way to view RNA is that it is central to all cellular processes. Many RNAs are not translated into proteins and instead act as regulatory molecules, impacting the expression of other genes. In this work we found many examples of these regulatory RNAs in a group of bacteria known to produce many of the world’s antibiotics. Understanding the roles these regulatory RNAs play in impacting gene expression will be important for the discovery of new molecules, such as antibiotics. In addition to distinct regulatory RNAs mentioned above, we found that RNA structures within the coding sequences of mRNAs that are translated into proteins have dramatic regulatory consequences. We describe the characterization of one such RNA structure in a gene involved in bacterial communication, and develop a bioinformatic tool to hunt for other such structures conserved throughout bacteria.
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/22027 |
| Date | January 2017 |
| Creators | Moody, Matthew John |
| Contributors | Elliot, Marie A, Biology |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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