Abstract
Small RNAs have been studied in detail in domains Bacteria and Eukarya but, in the case of the domain Archaea, the knowledge is scarce and the physiological function of these small RNAs (sRNAs) is still uncertain. To extend the knowledge of sRNAs in the domain Archaea and their possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. The bioinformatic approach has allowed for the prediction of 295 putative sRNAs genes in the genome of H. mediterranei, 88 of which have been verified by means of RNA-Sequencing (RNA-Seq). The secondary structure of these sRNAs and their possible targets have been identified. Curiously, some of them present as possible target genes relating to nitrogen assimilation, such as glutamate dehydrogenase and the nitrogen regulatory PII protein. Analysis of RNA-Seq data has also revealed differences in the expression pattern of 16 sRNAs according to the nitrogen source. Consequently, RNomic and bioinformatic approaches used in this work have allowed for the identification of new sRNAs in H. mediterranei, some of which show different expression patterns depending on the nitrogen source. This suggests that these sRNAs could be involved in the regulation of nitrogen assimilation and can constitute an important gene regulatory network.
Highlights
Small RNAs play an essential role in the post-transcriptional regulation of many cellular processes in all domains of life, i.e., Eukarya, Bacteria, and Archaea
Since the candidate small RNAs (sRNAs) of H. volcanii aligned at many positions in the genome of H. mediterranei (E-value < 0.05, p-value < 0.05), the results obtained were prioritised by a function of identity, lower number of gaps, and lower number of mismatches
The candidate sRNAs of the remaining species aligned in fewer positions (E-value < 1) than H. volcanii in the genome of H. mediterranei, so it was not necessary to prioritise in the same way
Summary
Small RNAs (sRNAs) play an essential role in the post-transcriptional regulation of many cellular processes in all domains of life, i.e., Eukarya, Bacteria, and Archaea. There are different classes of these, the best studied being microRNA (miRNAs), small interference RNA (siRNAs), and piwi-interacting RNAs (piRNAs). These are approximately 20–30 nucleotides (nt) in length and are involved in development, cellular activities, and different physiology processes [1,2,3]. Different mechanisms of action of sRNAs have been described, most of which affect the translation of the target messenger RNA and/or its stability [4] They seem to be involved in the post-transcriptional regulation of metabolism, stress response, virulence processes, and so on. Cis-encoded sRNAs originate in the nonsense strand of an open reading frame
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