Evolution of Fungal U3 snoRNAs: Structural Variation and Introns.

Sebastian Canzler,Peter Stadler,Jana Hertel

doi:10.3390/ncrna3010003

Abstract

The U3 small nucleolar RNA (snoRNA) is an essential player in the initial steps of ribosomal RNA biogenesis which is ubiquitously present in Eukarya. It is exceptional among the small nucleolar RNAs in its size, the presence of multiple conserved sequence boxes, a highly conserved secondary structure core, its biogenesis as an independent gene transcribed by polymerase III, and its involvement in pre-rRNA cleavage rather than chemical modification. Fungal U3 snoRNAs share many features with their sisters from other eukaryotic kingdoms but differ from them in particular in their 5’ regions, which in fungi has a distinctive consensus structure and often harbours introns. Here we report on a comprehensive homology search and detailed analysis of the evolution of sequence and secondary structure features covering the entire kingdom Fungi.

Highlights

The U3 small nucleolar RNA is a box C/D snoRNA with an exceptional structure.Like many other snoRNAs it is involved in pre-rRNA processing
U3 snoRNA genes were identified in all 147 genomes included in this study, supporting the indispensable nature of U3 in rRNA biogenesis
We found a total of 310 genes, i.e., the U3 snoRNAs, similar to small nuclear RNAs (snRNAs), tend to appear in multiple genomic copies

Summary

Introduction

Like many other snoRNAs it is involved in pre-rRNA processing. In contrast to typical box C/D snoRNAs [1,2] it does not guide 20 O-methylation. Instead it acts as a an RNA-chaperone mediating structural changes to ensure the correct pre-rRNA cleavage. Its sequence is overall only loosely conserved, it harbours eight highly conserved box motifs including the box C, C0 , D, and D0 motifs characteristic for box C/D snoRNAs. The molecule exhibits a strongly constrained secondary structure that shows lineage-specificity of the canonical 10 stems as well as frequent extensive expansions [3]. U3 snoRNAs share important features with small nuclear RNAs (snRNAs)

Methods

Results

Conclusion