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

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Title: Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism
Authors: Payá, Gloria | Bautista, Vanesa | Camacho, Mónica | Castejón-Fernández, Natalia | Alcaraz, Luis A. | Bonete, María-José | Esclapez Espliego, Julia María
Research Group/s: Biotecnología de Extremófilos (BIOTECEXTREM)
Center, Department or Service: Universidad de Alicante. Departamento de Agroquímica y Bioquímica
Keywords: Haloarchaea | sRNA | Nitrogen assimilation | RNA-Seq
Knowledge Area: Bioquímica y Biología Molecular
Issue Date: 10-Feb-2018
Publisher: MDPI
Citation: Payá G, Bautista V, Camacho M, Castejón-Fernández N, Alcaraz LA, Bonete M-J, Esclapez J. Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism. Genes. 2018; 9(2):83. doi:10.3390/genes9020083
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.
Sponsor: This work was supported by grant BIO2013-42921-P from the Spanish Ministry of Economy and Competitiveness. Funds from “Programa Propio para el fomento de la I+D+i del Vicerrectorado de Investigación y Transferencia de Conocimiento” de la Universidad de Alicante are also acknowledged.
URI: http://hdl.handle.net/10045/73450
ISSN: 2073-4425
DOI: 10.3390/genes9020083
Language: eng
Type: info:eu-repo/semantics/article
Rights: © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Peer Review: si
Publisher version: http://dx.doi.org/10.3390/genes9020083
Appears in Collections:INV - BIOTECEXTREM - Artículos de Revistas

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