Plasticity of archaeal C/D box sRNA biogenesis

• Published in: Molecular microbiology 2017-01, Vol.103 (1), p.151-164
• Main Authors: Tripp, Vanessa, Martin, Roman, Orell, Alvaro, Alkhnbashi, Omer S., Backofen, Rolf, Randau, Lennart
• Format: Article
• Language: English
• Subjects: Archaea - genetics; Archaea - metabolism; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Base Sequence - genetics; Biosynthesis; Genes, Archaeal - genetics; Microbiology; Molecular Sequence Data; Nucleic Acid Conformation; Nucleotide Motifs - genetics; Promoter Regions, Genetic - genetics; Ribonucleic acid; RNA; RNA, Ribosomal - genetics; RNA, Small Nuclear - genetics; RNA, Small Nuclear - metabolism; RNA, Small Nucleolar - genetics; RNA, Small Nucleolar - metabolism
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.13549

Summary Archaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2′‐O‐methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes. We found that the majority of these genes do not possess independent promoters but are rather located at positions that allow for co‐transcription with neighboring genes and their start or stop codons were frequently incorporated into the conserved boxC and D motifs. The biogenesis of plasmid‐encoded C/D box sRNA variants was analyzed in vivo in Sulfolobus acidocaldarius. It was found that C/D box sRNA maturation occurs independent of their genetic context and relies solely on the presence of intact RNA kink‐turn structures. The observed plasticity of C/D box sRNA biogenesis is suggested to enable their accelerated evolution and, consequently, allow for adjustments of the RNA modification landscape. C/D box sRNAs constitute one of the most abundant RNA families in Archaea and are used to guide methylation of target RNA molecules. We analyzed the biogenesis of this RNA family and observed its independence of the genetic context. This plasticity of C/D box sRNA biogenesis is suggested to enable their accelerated evolution and allow for adjustments of the RNA modification landscape. Graphical 59×44mm (300 × 300 DPI)