RNase MRP and the RNA processing cascade in the eukaryotic ancestor

Abstract

Background: Within 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.

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, 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.

Conclusion: We 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.

Figure 1

The eukaryotic RNA-processing cascade. mRNA is cleaved by the spliceosome (comprised of snRNAs and proteins) to release the processed mRNA and introns. Some introns contain snoRNAs which in turn modify snRNAs, tRNAs and rRNAs. RNase P (P) cleaves pre-tRNA while RNase MRP (MRP) cleaves rRNA. The ribosomal complex (comprised of rRNAs) brings the tRNAs and mature mRNAs together for translation. The involvement of RNase P in pre-rRNA processing has been questioned recently in [59].

Figure 2

Hypothesis for the origin of MRP. This figure is based on [7], but modified to reflect present hypothesis of mitochondrial and eukaryotic evolution. The large black dots represent the point of duplication of the P-MRP ancestor. A: MRP was present in the last common ancestor of modern eukaryotes (the Eukaryotic Ancestor). Alternatively both MRP and P could have been present in the Last Universal Common Ancestor. B: MRP arose from a duplication of P after the Eukaryotic Ancestor, but before the ancestor of animals, fungi and plants. C: MRP arose from an early mitochondrial P within the Eukaryotic Ancestor.

Figure 3

Distribution of MRP in eukaryotes. Only some sub-branches are given for each of the main groups. To date MRP has not yet been characterized from Giardia (Diplomonads), Trypanosoma (Euglenozoa), Entamoeba (Amoebozoa) and Caenorhabditis (Animals – nematodes). The general structure of the eukaryotic tree is based on [33].

Figure 4

Promoter regions of Human MRP, P and U6.A. Organization of pre-rRNA based on [37]. In bacteria rRNA genes are co-transcribed as a polycistronic precursor (although exceptions are common). Most eukaryotes vary only in the length of their ITS regions, an extreme case being the microsporidian Encephalitozoon cuniculi which has completely lost its ITS2 having a fused 5.8S/28S subunit. RNase P and RNase MRP do not cleave the main transcripts but trim the ends of their respective substrates (the tRNA or 5.8S rRNA) after cleavage by other enzymes. In eukaryotes the 5S rRNA is transcribed separately by RNA polymerase III. B. The Diplomonad Giardia lamblia has the usual order of rRNA subunits with short ITS regions, however RNase MRP has not yet been characterized from this species. RNAstructure folding of G. lamblia ITS1 [56] showing a single stranded region between two stem loops that could possibly be an A3 site. Other foldings of this sequence and foldings of other sequences (DQ157272 and AF239841) produce just a single stem-loop.

Figure 5

MRP-RNA gene arrangement. Genes transcribed by RNA polymerase III (type III) usually contain a PSE (proximal sequence element) consisting of a TATA signal and PSE motif, and a DSE (distal sequence element) consisting of either a SP1, Oct or Staf binding site. Distances shown are approximate only. Key: T – TATA signal; PSE/USE – ; Oct – Octamer binding site; SP1 – SP1 binding site; Staf – Staf binding site. ? – Possible site. TT – Poly T termination signal. B-box – Downstream B-box motif.

Figure 6

Summary diagram of MRP-RNA secondary structure. Black features (P1, P2, P3a, P4, P5, P7) are universally present. Green features are nearly universal, red features are observed in a few organisms of limited phylogenetic range. Thick lines are paired regions while unpaired regions are shown as thin lines. Conserved sequence motifs are indicated for the P4 (5' and 3') P8 and CRIV regions.