A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius

Orell, Alvaro; Tripp, Vanessa; Aliaga-Tobar, Víctor; Albers, Sonja‐Verena; Maracaja-Coutinho, Vinícius; Randau, Lennart

doi:10.1093/nar/gky144

Cited by 28 publications

(28 citation statements)

References 55 publications

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“…One mechanism is the occlusion of a recognition site for a single-strand specific RNase by the sRNA. In archaea, stabilization of an RNA via duplex formation has recently been described for S. acidocaldarius (Orell et al, 2018). Seven genes in the genome of H. volcanii are annotated to encode RNases of different types, which might be involved in regulation.…”

Section: Discussionmentioning

confidence: 99%

A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions

2019

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The haloarchaeon Haloferax volcanii contains nearly 2800 small non-coding RNAs (sRNAs). One intergenic sRNA, sRNA132, was chosen for a detailed characterization. A deletion mutant had a growth defect and thus underscored the importance of sRNA132. A microarray analysis identified the transcript of an operon for a phosphate-specific ABC transporter as a putative target of sRNA132. Both the sRNA132 and the operon transcript accumulated under low phosphate concentrations, indicating a positive regulatory role of sRNA132. A kinetic analysis revealed that sRNA132 is essential shortly after the onset of phosphate starvation, while other regulatory processes take over after several hours. Comparison of the transcriptomes of wild-type and the sRNA132 gene deletion mutant 30 min after the onset of phosphate starvation revealed that sRNA132 controls a regulon of about 40 genes. Remarkably, the regulon included a second operon for a phosphate-specific ABC transporter, which also depended on sRNA132 for rapid induction in the absence of phosphate. Competitive growth experiments of the wild-type and ABC transporter operon deletion mutants underscored the importance of both transporters for growth at low phosphate concentrations. Northern blot analyses of four additional members of the sRNA132 regulon verified that all four transcripts depended on sRNA132 for rapid regulation after the onset of phosphate starvation. Importantly, this is the first example for the transient importance of a sRNA for any archaeal and bacterial species. In addition, this study unraveled the first sRNA regulon for haloarchaea.

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Section: Discussionmentioning

confidence: 99%

A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions

2019

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“…20 Double-stranded RNA structures are also created by antisense transcription and have been observed for regulatory RNAs and CRISPR RNAs of Sulfolobus acidocaldarius. 21,22 A regulatory RNA was found to be involved in biofilm formation and was shown to exist in complex with a reverse complementary RNA. Individual regulation of these two complementary RNA strands can be used to titrate regulatory RNAs.…”

Section: Tenax Lacks Helix H1 and Exhibits Altered Termini (Blue And mentioning

confidence: 99%

RNA stabilization in hyperthermophilic archaea

Gomes-Filho

Randau

2019

Annals of the New York Academy of Sciences

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Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA‐guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC‐rich regions are observed for many universal noncoding RNA families. Guide RNAs are often protected from degradation by their presence within ribonucleoprotein complexes. Modification and ligation of RNA termini can be employed to impair exonucleolytic degradation. Finally, antisense strand transcription promotes the formation of RNA duplexes and can be used to stabilize RNA regions. In our review, we provide examples of these RNA stabilization mechanisms that have been observed in hyperthermophilic archaeal model organisms.

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“…These products can be coding or non-coding RNAs, i.e. transcripts that do not encode a protein but are functional important players in the cellular regulation in organisms from all domains of life [1][2][3][4][5][6]. Microarrays and RNA sequencing (RNA-seq) are largescale technologies commonly used to measure transcript expression levels [7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

CORAZON: a web server for data normalization and unsupervised clustering based on expression profiles

et al. 2020

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Objective: Data normalization and clustering are mandatory steps in gene expression and downstream analyses, respectively. However, user-friendly implementations of these methodologies are available exclusively under expensive licensing agreements, or in stand-alone scripts developed, reflecting on a great obstacle for users with less computational skills. Results: We developed an online tool called CORAZON (Correlations Analyses Zipper Online), which implements three unsupervised learning methods to cluster gene expression datasets in a friendly environment. It allows the usage of eight gene expression normalization/transformation methodologies and the attribute's influence. The normalizations requiring the gene length only could be performed to RNA-seq, meanwhile the others can be used with microarray and/or NanoString data. Clustering methodologies performances were evaluated through five models with accuracies between 92 and 100%. We applied our tool to obtain functional insights of non-coding RNAs (ncR-NAs) based on Gene Ontology enrichment of clusters in a dataset generated by the ENCODE project. The clusters where the majority of transcripts are coding genes were enriched in Cellular, Metabolic, Transports, and Systems Development categories. Meanwhile, the ncRNAs were enriched in the Detection of Stimulus, Sensory Perception, Immunological System, and Digestion categories. CORAZON source-code is freely available at https ://gitla b.com/ integ rativ ebioi nform atics /coraz on and the web-server can be accessed at http://coraz on.integ rativ ebioi nform atics .me.

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A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius

Cited by 28 publications

References 55 publications

A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions

A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions

RNA stabilization in hyperthermophilic archaea

CORAZON: a web server for data normalization and unsupervised clustering based on expression profiles

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