Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function

• Published in: PloS one 2012-09, Vol.7 (9), p.e43786-e43786
• Main Authors: Kallberg, Yvonne, Segerstolpe, Åsa, Lackmann, Fredrik, Persson, Bengt, Wieslander, Lars
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Analysis; Animals; Binding; Bioinformatics; Biology; Biosynthesis; Branches; Conservation; Conserved Sequence; DNA Mutational Analysis; Eukaryotes; Evolution, Molecular; Evolutionary conservation; Gene expression; Genome, Fungal - genetics; Genomics; Humans; Laboratories; Life sciences; Microsporida - genetics; Microsporidia; Modular design; Molecular Biology; Molecular Sequence Data; molekylärbiologi; Nucleoli; Nucleotide sequence; Phylogeny; Protein folding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Reproducibility of Results; Ribonucleic acid; Ribosomes - metabolism; RNA; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; rRNA; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Sequence Alignment; Sequence Homology, Amino Acid; Yeast
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0043786

Ribosome biogenesis in eukaryotes requires coordinated folding and assembly of a pre-rRNA into sequential pre-rRNA-protein complexes in which chemical modifications and RNA cleavages occur. These processes require many small nucleolar RNAs (snoRNAs) and proteins. Rbm19/Mrd1 is one such protein that is built from multiple RNA-binding domains (RBDs). We find that Rbm19/Mrd1 with five RBDs is present in all branches of the eukaryotic phylogenetic tree, except in animals and Choanoflagellates, that instead have a version with six RBDs and Microsporidia which have a minimal Rbm19/Mrd1 protein with four RBDs. Rbm19/Mrd1 therefore evolved as a multi-RBD protein very early in eukaryotes. The linkers between the RBDs have conserved properties; they are disordered, except for linker 3, and position the RBDs at conserved relative distances from each other. All but one of the RBDs have conserved properties for RNA-binding and each RBD has a specific consensus sequence and a conserved position in the protein, suggesting a functionally important modular design. The patterns of evolutionary conservation provide information for experimental analyses of the function of Rbm19/Mrd1. In vivo mutational analysis confirmed that a highly conserved loop 5-β4-strand in RBD6 is essential for function.