Small regulatory RNAs in Archaea

Abstract

Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs and siRNAs typically bind to the 3′-untranslated region (3′-UTR) of their target mRNAs and influence translation efficiency and/or mRNA stability. In archaea, sRNAs have been identified in all species investigated using bioinformatic approaches, RNomics, and RNA-Seq. Their size can vary significantly between less than 50 to more than 500 nucleotides. Differential expression of sRNA genes has been studied using northern blot analysis, microarrays, and RNA-Seq. In addition, biological functions have been unraveled by genetic approaches, i.e., by characterization of designed mutants. As in bacteria, it was revealed that archaeal sRNAs are involved in many biological processes, including metabolic regulation, adaptation to extreme conditions, stress responses, and even in regulation of morphology and cellular behavior. Recently, the first target mRNAs were identified in archaea, including one sRNA that binds to the 5′-region of two mRNAs in Methanosarcina mazei Gö1 and a few sRNAs that bind to 3′-UTRs in Sulfolobus solfataricus, three Pyrobaculum species, and Haloferax volcanii, indicating that archaeal sRNAs appear to be able to target both the 5′-UTR or the 3′-UTRs of their respective target mRNAs. In addition, archaea contain tRNA-derived fragments (tRFs), and one tRF has been identified as a major ribosome-binding sRNA in H. volcanii, which downregulates translation in response to stress. Besides regulatory sRNAs, archaea contain further classes of sRNAs, e.g., CRISPR RNAs (crRNAs) and snoRNAs.

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

“…However, this simplicity has been challenged by the widespread use of high-resolution transcriptome mapping technologies [1,2]. Identification of overlapping genomic elements revealed modular operon organization that allows for conditional co-modulation of genes in bacteria and archaea [3,4].…”

Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus

“…However, archaeal sRNAs are poorly characterized42. 195 sRNAs were identified in this work (Supplementary Table S6), some are categorized in the most abundant transcripts in R15 (Supplementary Table S10).…”

Small RNAs in Bacteria and Archaea

“…In bacteria that encode the sRNA helper protein Hfq, pulldowns have enriched for putative regulatory sRNAs (e.g., Sittka et al, 2008;Zhang et al, 2003). By now, sRNAs have been identified in most major branches of the bacterial tree, and in several archaeal species (for an incomplete list, see: (Acebo, Martin-Galiano, Navarro, Zaballos, & Amblar, 2012;Albrecht, Sharma, Reinhardt, Vogel, & Rudel, 2010;Arnvig et al, 2011;Babski et al, 2014;DiChiara et al, 2010;Fouquier d'Herouel et al, 2011;Irnov, Sharma, Vogel, & Winkler, 2010;J€ ager et al, 2009;Liu et al, 2009;Mann et al, 2012;Marchfelder et al, 2012;Mitschke, Georg, et al, 2011;Sahr et al, 2012;Steglich et al, 2008;Xu, Chen, He, & Wang, 2014;Yoder-Himes et al, 2009)). Strikingly, the dRNA-seq method alone contributed to sRNA inventories and transcriptome maps in >25 bacterial/archaeal species an RNA whose action as "tRNA/mRNA" liberates ribosomes that are stuck on problematic mRNAs (Wassarman, Zhang, & Storz, 1999).…”