Annotation and evolution of bacterial ncRNA genes

Abstract

Successful pathogenic bacteria must alter gene expression in response to changing and hostile environments. Non-coding RNAs (ncRNAs) contribute to adaptability and pathogenicity by forming complex regulatory networks, and include riboswitches, cis-regulatory elements and sRNAs. Despite their important biological function, the annotation and discovery of ncRNAs is hindered by a lack of sequence conservation or other distinguishing sequence features.

Studies of the evolutionary dynamics and origins of sRNA genes have been hindered by poor sequence conservation, which makes annotation via sequence homology challenging. The short length and relative simplicity of sRNA genes also make them interesting candidates for observing de novo gene formation from transcriptional noise, or exaptation from existing elements.

We have used a pipeline based on profile hidden Markov models to study the conservation patterns of sRNA genes from Salmonella Typhimurium. Our results show that sRNAs are both rapidly acquired and exhibit rapid sequence turnover. We found that horizontal gene transfer is the main driver of sRNA acquisition in Salmonella, and identified Salmonella-specific sRNAs that appear to be derived from phage control systems, and other mobile genetic elements, as well as Type I toxin-antitoxin systems. This method was then applied to study ncRNAs in Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker disease. We have generated transcriptomes of a pandemic strain of Psa in multiple growth conditions in vitro, and analysed gene expression changes and identified novel non-coding transcripts. We then studied the expression and conservation of these candidate ncRNAs, and identified several with predicted secondary structure motifs characteristic to known functional ncRNAs.

This thesis also includes a summary of two genome assembly projects of Gemmata and Legionella isolates, as part of larger collaborations. All diagrams in this thesis are my own work, unless otherwise stated