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The STUDIA UNIVERSITATIS BABEŞ-BOLYAI issue article summary
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Abstract: In Archaea domain, the knowledge about small RNAs (sRNAs) and the physiological function they carry out has been studied in less detail than in the rest of life domains. RNA-Seq has been performed in different nitrogen sources, 40 mM nitrate and 40 mM ammonium, to identify the sRNAs expressed in both conditions and understand the regulatory networks involved in the transcriptional regulation of nitrogen assimilation metabolism in H. mediterranei ATCC33500. In total, 460 sRNAs were identified manually by using the high-performance visualisation tool, Integrative Genomics Viewer (IGV). Significant differences were observed in the expression pattern of 102 sRNAs according to the nitrogen source after analysis of the RNA-Seq data differential expression. Moreover, the secondary structure of these sRNAs, their possible gene targets and the sequence conservation in other archaeas have been determined. In addition, the molecular function, cellular component and biological process of target genes were analysed based on nitrogen source. As result, sRNAs which show differences in their expression patterns, could be directly related to proteins involved in nitrogen assimilation pathways, such as glutamate dehydrogenase (sRNA311 and sRNA276), glutamine synthetase (sRNA274 and sRNA310), the nitrogen regulatory PII protein (sRNA228) and nitrate/nitrite transporter (sRNA451). Curiously, the sRNA87 could regulate the nitrous oxide reductase accessory protein NosL, which is involved in denitrification. Finally, 10 selected sRNAs were validated by RT-PCR. These results suggest that these sRNAs could be involved in the regulation of nitrogen assimilation and can be implicated in important gene regulatory mechanisms.
Keywords: gene regulation, haloarchaea, nitrogen metabolism, RNA-Seq, small RNAs (sRNAs).
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