Abstract
Post-transcriptional modifications fulfill many important roles during ribosomal RNA maturation in all three domains of life. Ribose 2'-O-methylations constitute the most abundant chemical rRNA modification and are, for example, involved in RNA folding and stabilization. In archaea, these modification sites are determined by variable sets of C/D box sRNAs that guide the activity of the rRNA 2'-O-methyltransferase fibrillarin. Each C/D box sRNA contains two guide sequences that can act in coordination to bridge rRNA sequences. Here, we will review the landscape of archaeal C/D box sRNA genes and their target sites. One focus is placed on the apparent accelerated evolution of guide sequences and the varied pairing of the two individual guides, which results in different rRNA modification patterns and RNA chaperone activities.
Highlights
The chemical modification of RNA has long been known to play a role in a wide variety of cellular processes in all three domains of life
The most abundant RNA modification is the ribose-2'-O-methylation, which is commonly found on ribosomal RNAs and transfer RNAs and present on small nuclear RNAs in archaea and eukaryotes (Maden et al, 1995; Kiss-László et al, 1996; Tycowski et al, 1998; Omer et al, 2000; Vitali and Kiss, 2019)
Even though these tools and different strategies are available for C/D box sno-like RNA (sRNA) prediction, this class of RNA is still underrepresented in archaeal annotations (Gardner et al, 2010) and only a combination of RNA-seq analyses, comparative genomics and computational methods allow for complete C/D box sRNA identification (Lui et al, 2018)
Summary
The chemical modification of RNA has long been known to play a role in a wide variety of cellular processes in all three domains of life. While the usage of an artificial two-stranded RNA lacking the k-loop motif lead to the assembly of a monomeric complex consisting of one RNA and two copies of each protein, the usage of an in vitro transcribed natural C/D box sRNA sequence lead to the assembly of dimeric complex consisting of two RNAs and four copies of each protein (Figure 1B; Bleichert et al, 2009; Bleichert and Baserga, 2010; Xue et al, 2010; Lin et al, 2011; Bower-Phipps et al, 2012; Lapinaite et al, 2013) These results suggest that the nature of the RNA determines if mono- or diRNPs are assembled and influences these complexes’ functional roles. These and other findings on the structural diversity of C/D box sRNPs are extensively reviewed by Yu et al (2018)
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