Diversity, function, and processing of archaeal non-coding RNAs

Recent major progress in sequencing technology has yielded more than 80 complete archaeal genome sequences and thousands of partial archaea-derived genomic and transcriptome sequences from various environmental samples. As a result of this rapid increase in the amount of archaeal sequence data, an unexpected variety of non-coding RNAs (ncRNAs) has been detected in Archaea, including fragments of transfer RNA (tRNA), a new class of small nucleolar RNA (snoRNA), a clustered, regularly interspaced short palindromic repeat (CRISPR) RNA used as an antiviral defense, and enzymatically cleaved introns found in many types of precursor tRNA, ribosomal RNA (rRNA) and messenger RNA (mRNA). Furthermore, several RNA elements such as riboswitches and SECIS elements have been predicted to exist in the 5' and 3' untranslated regions of archaeal mRNA. In this review, we discuss the distribution, function, and processing machinery of these archaeal ncRNA/RNA elements and the diversity of archaeal species. We have revised the phylogeny of the domain Archaea by reconstructing the most recent phylogenetic tree based on 8488 archaeal 16S rRNA sequences collected from all possible databases. The most recent findings on archeal ncRNA are explained along with the phylogeny of archaeal species, providing a deeper understanding of the functional and evolutionary roles of all types of archaeal RNA.