Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 06-003

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Titel:
RNase MRP and the RNA Processing Cascade in the Eukaryotic Ancestor

Author(s):
Michael D. Woodhams, Peter F. Stadler, David Penny, Lesley J. Collins

Submitted
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Abstract:
Background. Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. A simple example is the RNase MRP processing of ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simplified network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, named here as the Eukaryotic Ancestor.
Results. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches have uncovered previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of new and previously discovered RNase MRP RNAs along with analysis of the primary substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution.
Conclusions We conclude that RNase MRP can now be placed in the RNA-processing cascade present in the Eukaryotic Ancestor. This highlights the complexity of RNAprocessing in early eukaryotes.

Keywords: ncRNA genes, reading direction, support vector machine


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