5 research outputs found
The identification of biologically important secondary structures in disease-causing RNA viruses
Masters of ScienceViral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The viral RNA molecules are responsible for two functions, firstly, their sequences contain the genetic code, which encodes the viral proteins, and secondly, they may form structural elements important in the regulation of the viral life-cycle. Using a host of computational and bioinformatics techniques we investigated how predicted secondary structure may influence the evolutionary dynamics of a group of single-stranded RNA viruses from the Picornaviridae family. We detected significant and marginally significant correlations between regions predicted to be structured and synonymous substitution constraints in these regions, suggesting that selection may be acting on those sites to maintain the integrity of certain structures. Additionally, coevolution analysis showed that nucleotides predicted to be base paired, tended to co-evolve with one another in a complimentary fashion in four out of the eleven species examined. Our analyses were then focused on individual structural elements within the genome-wide predicted structures. We ranked the predicted secondary structural elements according to their degree of evolutionary conservation, their associated synonymous substitution rates and the degree to which nucleotides predicted to be base paired coevolved with one another. Top ranking structures coincided with well characterized secondary structures that have been previously described in the literature. We also assessed the impact that genomic secondary structures had on the recombinational dynamics of picornavirus genomes, observing a strong tendency for recombination breakpoints to occur in non-coding regions. However, convincing evidence for the association between the distribution of predicted RNA structural elements and breakpoint clustering was not detected
Identification and ranking of pervasive secondary structures in positive sense single-stranded ribonucleic acid viral genomes
Philosophiae Doctor - PhDThe plasticity of single-stranded viral genomes permits the formation of secondary structures
through complementary base-pairing of their component nucleotides. Such structures have
been shown to regulate a number of biological processes during the viral life-cycle including,
replication, translation, transcription, post-transcriptional editing and genome packaging.
However, even randomly generated single-stranded nucleotide sequences have the capacity to
form stable secondary structures and therefore, amongst the numerous secondary structures
formed in large viral genomes only a few of these elements will likely be biologically
relevant. While it is possible to identify functional elements through series of laboratory
experiments, this is both excessively resource- and time-intensive, and therefore not always
feasible. A more efficient approach involves the use of computational comparative analyses
methods to study the signals of molecular evolution that are consistent with selection acting
to preserve particular structural elements. In this study, I systematically deploy a collection of
computationally-based molecular evolution detection methods to analyse the genomes of
viruses belonging to a number of ssRNA viral families (Alphaflexiviridae, Arteriviridae,
Caliciviridae, Closteroviridae, Coronavirinae, Flaviviridae, Luteoviridae, Picornaviridae,
Potyviridae, Togaviridae and Virgaviridae), for evidence of selectively stabilised secondary
structures. To identify potentially important structural elements the approach incorporates
structure prediction data with signals of natural selection, sequence co-evolution and genetic
recombination. In addition, auxiliary computational tools were used to; 1) quantitatively rank
the identified structures in order of their likely biological importance, 2) plot co-ordinates of
structures onto viral genome maps, and 3) visualise individual structures, overlaid with
estimates from the molecular evolution analyses. I show that in many of these viruses
purifying selection tends to be stronger at sites that are predicted to be base-paired within
secondary structures, in addition to strong associations between base-paired sites and those
that are complementarily co-evolving. Lastly, I show that in recombinant genomes breakpoint
locations are weakly associated with co-ordinates of secondary structures. Collectively, these
findings suggest that natural selection acting to maintain potentially functional secondary
structures has been a major theme during the evolution of these ssRNA viruses
Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses
Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures
through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base
pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are
(i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding
methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally
inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA
viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these
for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying
selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we
also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving
in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive
secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure
is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized
structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.Department of HE and Training approved lis