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. / Thesis / Master of Science (MSc) / All living things have DNA, which contains the instructions for maintaining life in the form of genes. These genes are copied into RNAs, and some of these RNA molecules are used to make proteins, which are the building blocks and machinery of cells. However, not all RNAs make proteins; some act as regulators, controlling which genes and proteins are active. Additionally, some proteins edit the instructions contained by RNA molecules after they are made, adding another layer of complexity to how cells regulate their activities. This thesis investigates these processes in Streptomyces venezuelae, a soil-dwelling bacterium known for its complex development and metabolism. We found hundreds of cases where RNA molecules are edited, potentially affecting their functions in the cell, and discovered thousands of non-protein-coding RNAs that may regulate genes or proteins. Our findings expand our understanding of how Streptomyces bacteria manage their complex genetic activities at the RNA level.
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/30311 |
| Date | January 2024 |
| Creators | McMurray, Brandon J. |
| Contributors | Elliot, Marie A., Biology |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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