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

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.

Putative small RNAs controlling detoxification of industrial cyanide-containing wastewaters by Pseudomonas pseudoalcaligenes CECT5344

“…In cells grown with a synthetic media with sodium cyanide 15 of these 20 sRNAs were also identified (Table 1), suggesting that the remained five sRNAs (sRNA150, sRNA184, sRNA511, sRNA559 and sRNA679) may have a regulatory role in detoxification of metals and metalloids that are also present in the jewelry wastewaters. Many of these sRNAs have the potential to form complex conformations similarly to those commonly associated with many other directly acting RNA transcripts, including known bacterial sRNAs [50,51]. From the 20 sRNAs analyzed, 16 sRNAs were amplified by RT-PCR (Fig 3), a percentage of success (80%) higher than those described in other studies [51,52,53].…”

“…Many of these sRNAs have the potential to form complex conformations similarly to those commonly associated with many other directly acting RNA transcripts, including known bacterial sRNAs [50,51]. From the 20 sRNAs analyzed, 16 sRNAs were amplified by RT-PCR (Fig 3), a percentage of success (80%) higher than those described in other studies [51,52,53]. Antisense RNAs, which are transcribed from the DNA strand opposite to the genes they regulate and display complementarity to their target RNA, are often located in the untranslated regions (UTRs) of the corresponding gene.…”

Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)

“…It is interesting to note the low abundance that we have found for the genus Haloferax in the Odiel evaporation pond. Although it grows optimally at 2.5 M NaCl (15% salinity) [ 37 ], Haloferax has been described to grow at salinities of 33.7% with growth rates higher than any other comparable extreme halophile [ 27 ]. Despite these characteristics, Haloferax is usually found at low percentage, around 1%, in solar saltern ponds with medium and high salinity (10–37%), as described for example in Santa Pola, Spain [ 30 ].…”

Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen

“…In vitro Sa-Lrp binds specifically to the promoters of genes involved in nitrogen metabolism, such as glutamine synthetase ( glnA -1, glnA -2, and glnA -3) and glutamate synthase ( gltB ) [20], suggesting that Sa-Lrp may regulate transcription of the GS/GOGAT pathway depending on N-signals. Transcriptional responses to N-conditions are best understood in the Euryarchaeota: the nitrogen-fixing methanogens [21,22] and the denitrifying halophile Haloferax mediterranei [8,23,24]. The methanogens use a master transcriptional repressor NrpR, secondary transcriptional activator NrpA, and small RNAs (sRNAs) to control the expression of glutamine synthetase ( glnA ) and nitrogenase ( nif ) genes in response to N-sources [22].…”

“…In addition, the transcript levels of the high affinity Amt-type ammonia transporter and PII (GlnK) regulators are up during N-starvation in H. mediterranei [27]. The regulatory network responsible for controlling the N-responses in non-methanogenic haloarchaea, however, is poorly understood; sRNAs are implicated in control of the Amt/PII and glutamate dehydrogenase ( gdhA1 ) genes [24], but a master NrpR or NrpA-type transcriptional regulator is not conserved.…”