ABSTRACT
Archaea use C/D box sno-like RNAs (sRNAs) to guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNAs are the most numerous archaeal small RNA class, most genomes have incomplete sRNA gene annotation because reliable, completely automated detection methods are unavailable. To study archaeal C/D box sRNA structure, function and evolution, we collected, predicted, and curated a comprehensive set of these sRNAs from six species within the crenarchaeal hyperthermophilic genus Pyrobaculum. We used high-throughput small RNA sequencing data, computational methods, and comparative genomics to curate 526 Pyrobaculum C/D box sRNAs and organized them into 110 families based on conservation of their guide sequences. Our comprehensive analysis provides a detailed narrative of C/D box sRNA evolutionary history, implications of target conservation on ribosome maturation, and sRNA impact on genome architecture. We find that in some cases the overlap of C/D box sRNAs with protein-encoding genes can abolish the ability of their guides to target rRNA and tRNAs. Numerous duplications and rearrangements of sRNA genes are illustrated, and some of these appear to employ a mechanism similar to the retrotransposition of C/D box sRNAs genes in eukaryotes. Finally, we used these annotations to train a new computational search model.
Footnotes
Email Addresses: Lauren Lui: lmlui{at}lbl.gov Andrew Uzilov: andrew.uzilov{at}gmail.com David Bernick: dbernick{at}soe.ucsc.edu Andrea Corredor: andrea.v.corredor{at}gmail.com Todd Lowe: lowe{at}soe.ucsc.edu Patrick P Dennis: dennispp{at}whitman.edu