Investigating the evolution of mRNA : ncRNA avoidance in escherichia coli. (2018)
Type of ContentTheses / Dissertations
Thesis DisciplineCellular and Molecular Biology
Degree NameMaster of Science
PublisherUniversity of Canterbury
It is presumed that the levels of mRNA and protein should correlate relatively strongly however this correlation is often quite poor. Two main explanations have been invoked to explain this discrepancy, messenger RNA (mRNA) secondary structure and codon usage bias, however, these explanations only account for around 40% of the total variation in expression levels. More recently a new model has been proposed that explains more of the variation in mRNA and protein levels than either codon usage or mRNA secondary structure.
The mRNA: ncRNA avoidance model, presents evidence that non-specific interactions between non-coding RNAs (ncRNAs) and mRNAs significantly impact the discrepancy between mRNA and protein abundances. The model suggests that these crosstalk interactions between mRNAs and ncRNAs impact levels of mRNA translation, consequently genes that are highly-expressed demonstrate avoidance of such interactions.
Here I present a study that investigates how highly expressed mRNAs may have evolved to avoid unintentional interactions with the abundant ncRNAs in the cell. Synonymous variants of the araC gene of E. coli were designed for increased interaction with core ncRNAs. These alterations were predicted to lead to down regulation of the AraC protein and subsequently impact fitness. We hypothesised that evolution of avoidance could then be driven by creating a selective pressure for high expression of araC, such that the affinity of the designed araC mRNAs for ncRNAs would be lessened to increase translation levels. The findings here demonstrate that the alterations made to the araC variants, which are in line with the avoidance model, have an undetectable effect on fitness in E. coli. Furthering our understanding of how this phenomenon may have evolved has significant implications for the biology of RNA-RNA interaction.
RightsAll Rights Reserved
Showing items related by title, author, creator and subject.
Evolution of pyruvate kinase in the long-term evolution experiment of Escherichia coli: A structure/function study Zhu, Tong (University of Canterbury. Biological Sciences, 2008)This thesis examines Escherichia coli pyruvate kinase type 1 (PK1), a regulatory enzyme core to energy metabolism. Specifically, this thesis characterises a series of mutations in PK1 that were found when populations of ...
The effects of sub-lethal concentrations of biocides copper, pyrethrins and atrazine on antibiotic tolerance of Escherichia coli. Jun, Hyun (University of Canterbury, 2017)Biocides are used in different stages of crop production as herbicides, insecticides and fungicides. The toxicological mechanisms of these chemicals on their target organism is known, however, their sub-lethal effects on ...
Billington, Craig (University of Canterbury. Plant and Microbial Sciences, 1998)The dam (DNA adenine methylase) gene of Escherichia coli codes for an enzyme that converts adenine to N6-methyladenine at the sequence 5'GATC³’ shortly after DNA replication. dam mutants have pleiotropic phenotypes indicating ...