RNase MRP and the RNA processing cascade in the eukaryotic ancestor

Michael D Woodhams,Lesley J Collins,David Penny,Peter F Stadler

doi:10.1186/1471-2148-7-s1-s13

Michael D Woodhams, Lesley J Collins + Show 2 more

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https://doi.org/10.1186/1471-2148-7-s1-s13

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Abstract

BackgroundWithin eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler 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, herein called the Eukaryotic Ancestor.ResultsWe 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, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution.ConclusionWe conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

Highlights

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and ribosomal RNA (rRNA)
A classic example is the cleavage of rRNA transcript by RNase MRP, a ribonucleoprotein complex consisting of a single RNA molecule and about 10 proteins [5,6,7]
Piccinelli [31] used a strategy based on hidden Markov Models (HMMs) of the P4 region of the MRP-RNA secondary structure to identify it in many eukaryotes

Summary

Introduction

Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. A classic example is the cleavage of rRNA transcript by RNase MRP, a ribonucleoprotein complex consisting of a single RNA molecule and about 10 proteins [5,6,7]. The processing of RNA by RNA can extend through several layers such as the snRNAs (small nuclear RNAs) in the spliceosome release snoRNAs (small nucleolar RNAs) from introns which in turn are involved in the modification of rRNA, tRNA or snoRNAs (see Figure 1). The network of these processes is called the eukaryotic RNA-processing cascade [8]. The question we ask here is: how ancient are these RNA-based processes?

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