Plasticity of archaeal C/D box sRNA biogenesis

Abstract

SummaryArchaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2 0 -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 plasmidencoded 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.

Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across sixPyrobaculumspecies

“…There are also a few instances in our dataset where there are dual orphan guides, so it is possible that these sRNAs serve another purpose other than guiding methylation of tRNA or rRNA. (46). Preliminary data from our lab also supports the hypothesis that K-turns form in archaeal mRNAs and are bound by L7Ae (27).…”

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea

“…Members of this RNA family constitute a large faction of L7Ae interactors, and the presence of highly variable C/D box sRNA genes in closely related archaeal organisms suggests their fast evolution ( 14 ). Recently, we showed that C/D box sRNAs are often cotranscribed with adjacent genes whose promoters are “hijacked” for C/D box sRNA production ( 28 ). This scenario can explain differential C/D box sRNA expression patterns in the S. acidocaldarius sRNome.…”

Archaeal fibrillarin–Nop5 heterodimer 2′-O-methylates RNA independently of the C/D guide RNP particle

“…In both cases, we observed aFib-Nop5-dependent methylation of the 16S.5 ′ and 16S.C substrates (data not shown). Thus, the K-structures do not appear to be important for the stand-alone activity of aFib-Nop5, in contrast to their essential roles in bona fide archaeal C/D RNPs (Omer et al 2006;Tripp et al 2016). Further, we inspected the 3D structure of the bacterial ribosome small subunit (Wimberly et al 2000) and found that two target sites (C847 and G47) are located on one face of the RNA molecule separated by 70 Å from each other (Supplemental Fig.…”

“…The C/D guide RNAs are typically 50-70 nt long and contain conserved sequence motifs named C (RUGAUGA) and D (CUGA) boxes at their 5 ′ -and 3 ′ -ends, respectively, as well as internal C ′ and D ′ boxes. These motifs fold into Kink-turn (K-turn) (Klein et al 2001) and Kink-loop (Kloop) (Nolivos et al 2005) structures, respectively, which serve as a platform for the C/D RNP assembly (Tripp et al 2016). In a hierarchical manner, L7Ae has been shown to bind a K-structure in C/D guide RNA, followed by recruitment of a preassembled aFib-Nop5 heterocomplex (Bortolin et al 2003;Tran et al 2003;Gagnon et al 2012).…”