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Genes 2018, 9(2), 83; https://doi.org/10.3390/genes9020083

Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism

1
Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, Ap 99, E-03080 Alicante, Spain
2
Bioarray, S.L., 03202 Alicante, Spain
*
Authors to whom correspondence should be addressed.
Received: 30 December 2017 / Revised: 26 January 2018 / Accepted: 2 February 2018 / Published: 10 February 2018
(This article belongs to the Special Issue Genetics and Genomics of Extremophiles)
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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. View Full-Text
Keywords: haloarchaea; sRNA; nitrogen assimilation; RNA-Seq haloarchaea; sRNA; nitrogen assimilation; RNA-Seq
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Payá, G.; Bautista, V.; Camacho, M.; Castejón-Fernández, N.; Alcaraz, L.A.; Bonete, M.-J.; Esclapez, J. Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism. Genes 2018, 9, 83.

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