Browsing by Author "Collins, Lesley Joan"
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- ItemLost in the RNA world : non-coding RNA and the spliceosome in the eukaryotic ancestor : a thesis presented in partial fulfilment of the requirements for the degree of PhD in Bioinformatics at Massey University, Palmerston North, New Zealand(Massey University, 2004) Collins, Lesley JoanThe "RNA world" refers to a time before DNA and proteins, when RNA was both the genetic storage and catalytic agent of life; it also refers to today's world where non-coding RNA (ncRNA, RNA that does not code for proteins) is central to cellular metabolism. In eukaryotes, non-coding regions (introns) are spliced out of protein-coding mRNAs by the spliceosome, a massive complex comprised of five ncRNAs and about 200 proteins. This study examines the nature of the spliceosome and other non-coding RNAs, in the last common ancestor of eukaryotes, called here the eukaryotic ancestor. By looking at the differences between ncRNAs from diverse eukaryotic lineages, it may be possible to infer aspects of the eukaryotic ancestor's RNA systems. Comparing ncRNA and ncRNA-associated proteins involves the evaluation of the available software to search newly available basal eukaryotic genomes (such as Giardia lamblia and Plasmodium falciparum). ncRNAs are not often found using sequence-similarity based software, thus specialist ncRNA-search software packages were evaluated for their use in finding ncRNAs. One such program is RNAmotif, which was further developed during this study (with the help of its principle programmer), and which proved successful in recovering ncRNAs from basal eukaryotic genomes. In a similar manner, sequence-based search techniques may also fail to recover proteins from distantly related genomes. A new protein-finding technique called "Ancestral Sequence Reconstruction" (ASR) was developed in this thesis to aid in finding proteins that have diverged greatly between distantly-related eukaryotic species. A large amount of data was collected to investigate aspects of the eukaryotic ancestor, highlighting data management issues in this post-genomic era. Two databases were created P-MRPbase and SpliceSite to manage, sequence, annotation and results data from this project. Examination of the distribution of spliceosomal components and splicing mechanisms indicate that not only was a spliceosome present in the eukaryotic ancestor, it contained many of the components found in today's eukaryotes. Splicing in the eukaryotic ancestor may have used several mechanisms and have already formed links with other cellular processes such as transcription and capping. Far from being a simple organism, the last common ancestor of living eukaryotes shows signs of the molecular complexity seen today.
- ItemUse of RNA secondary structure for evolutionary relationships : investigating RNase P and RNase MRP : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, New Zealand(Massey University, 1998) Collins, Lesley JoanBioinformatics is applied here to examine whether RNA secondary structure data can reflect distant evolutionary relationships. This is important when there is little confidence in sequence data such as when looking at the evolution of RNase MRP (MRP). RNase P (P) and RNase MRP (MRP) are ribonucleoproteins (RNPs) that are involved in RNA processing and due to functional and secondary structure similarities, are thought to be evolutionary related. P activity is found in all cells, and fits the criteria for inclusion in the RNA world (Jeffares et al. 1998). MRP is found only in eukaryotes with essential functions in both the nucleus and mitochondria. The RNA components of P and MRP (pRNA and mrpRNA) cannot be aligned with any certainty, which leads to a lack of confidence in any phylogenetic trees constructed from them. If MRP evolved from P only in eukaryotes then it is an exception to the general process of the transfer of catalytic activity from RNA, to ribonucleoproteins, to proteins (Jeffares et al. 1998). An alternative possibility that MRP evolved with P in the RNA world (and has since been lost from all but the eukaryotes) is raised and examined. Quantitative comparisons of the pRNA and mrpRNA biological secondary structures have found that the third possibility of an organellar origin of MRP is unlikely Results show that biological secondary structure can be used in the evaluation of an evolutionary relatedness between MRP and P and may be extended to other catalytic RNA molecules. Although there are many protein families, this may be the first evidence of the existence of a family of RNA molecules, although it would be a very small family. Secondary structures derived with folding programs from pRNA and mrpRNA sequences are examined for use in the characterisation of catalytic RNA sequences. The high AT content in organellar genomes may hinder the identification of their catalytic RNA sequences. A search strategy is developed here to address this problem and is used to identify putative pRNA sequences in the chloroplast genomes of four green plants. A maize chloroplast pRNA-like sequence is examined in more detail and shows many characteristics seen in known pRNA sequences. Folding programs show some potential for the characterisation of possible catalytic RNA sequences with only a small bias in the results due to sequence length and AT content.