Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification

Buddeweg, Anne; Daume, Michael; Randau, Lennart; Schmitz, Ruth A.

doi:10.1016/bs.mie.2018.08.003

Cited by 7 publications

(13 citation statements)

References 72 publications

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“…ncRNAs are present in the cells as single-stranded molecules in contrast to DNA, and therefore, they can easily adopt the G4 structures as a part of their 3D arrangement similarly to mRNAs [ 69 , 70 ]. It has been shown that ncRNAs play important roles in many cellular processes, including the regulation of gene transcription, post-transcriptional, and epigenetic regulations [ 71 , 72 ].…”

Section: Resultsmentioning

confidence: 99%

G-Quadruplexes in the Archaea Domain

et al. 2020

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The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.

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Section: Resultsmentioning

confidence: 99%

G-Quadruplexes in the Archaea Domain

et al. 2020

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“…Despite decades of research archaeal sRNA networks are still enigmatic. It is well established that archaeal sRNAs play crucial roles in gene regulatory networks related to metabolism and therefore are essential players in stress responses, but pin-pointing their interaction partners remained challenging (Buddeweg et al, 2018a). An inventory of small transcripts has been made for more than seven archaeal species, but only for four of them sRNA-target pairs have been identified (Buddeweg et al, 2018b; Gelsinger and DiRuggiero, 2018b; Orell et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Small RNAs have been well established as key-regulators of gene expression in both pro- and eukaryotic species (Storz et al, 2011; Wagner and Romby, 2015; Buddeweg et al, 2018a). But still, understanding of small RNAs (sRNAs) in the archaeal domain lags behind (Gomes-Filho et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…In contrast to asRNAs, for whom targets are readily deducible as they are by default able to extensively base pair with the transcript originating from the opposite strand, trans-acting sRNAs pose quite a challenge as to the identification of targeted mRNAs. More so, as they bind targets via imperfect base-pairing sRNAs may regulate multiple targets as demonstrated in bacteria (Papenfort and Vogel, 2009; Wagner and Romby, 2015) and by the few archaeal examples (reviewed in: (Buddeweg et al, 2018a; Gelsinger and DiRuggiero, 2018a; Gomes-Filho et al, 2018)).…”

Section: Introductionmentioning

confidence: 99%

“…But still, understanding of small RNAs (sRNAs) in the archaeal domain lags behind (Gomes-Filho et al, 2018). RNomics as well as more recent highthroughput approaches have been applied to several archaeal species to uncover the wealth of small transcripts found in this domain of life (reviewed in: (Marchfelder et al, 2012;Kliemt and Soppa, 2017;Buddeweg et al, 2018a;Gelsinger and DiRuggiero, 2018a)). With numbers in the hundred (Archaeoglobus fulgidus, Methanosarcina mazei, Sulfolobus solfataricus, Thermococcus kodakarensis, Pyrococcus abyssi, Haloferax mediterranei) or even thousand (Haloferax volcanii, Methanolobus psychrophilus), sRNAs are well established as widespread and abundant players within the transcriptome of various archaeal species (reviewed in: (Gelsinger and DiRuggiero, 2018a;Gomes-Filho et al, 2018;Payá et al, 2018)).…”

Section: Introductionmentioning

confidence: 99%

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A small RNA is linking CRISPR-Cas and zinc transport

Märkle

Maier

Maaß

et al. 2021

Preprint

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The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from H. volcanii for detailed characterization. The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. Three of the six up-regulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, ZnuC1) suggesting involvement of s479 in regulation of zinc transport. Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. Furthermore, electrophoretic mobility shift assays demonstrate a direct interaction of s479 with the target znuC1 mRNA. Proteome comparison of wild type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. Interestingly, s479 is not only encoded next to CRISPR-cas genes but the mature s479 contains a crRNA-like 5' handle and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. Together this might suggest that the CRISPR-Cas system is involved in s479 function.

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Small RNA-Sequencing Library Preparation for the Halophilic Archaeon Haloferax volcanii

Gelsinger¹,

DiRuggiero²

2022

Archaea

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Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification

Cited by 7 publications

References 72 publications

G-Quadruplexes in the Archaea Domain

G-Quadruplexes in the Archaea Domain

A small RNA is linking CRISPR-Cas and zinc transport

Small RNA-Sequencing Library Preparation for the Halophilic Archaeon Haloferax volcanii

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