Regulatory RNAs in <i>Haloferax volcanii</i>

Fischer, Susan M.; Benz, Juliane; Späth, B.; Jellen-Ritter, Angelika; Heyer, Ruth; Dörr, Marcella; Maier, Lisa‐Katharina; Menzel-Hobeck, Clemens; Lehr, Matthias; Jantzer, Katharina; Babski, Julia; Soppa, Jörg; Marchfelder, Anita

doi:10.1042/bst0390159

Cited by 21 publications

(22 citation statements)

References 46 publications

(62 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNomics, bioinformatic predictions coupled to experimental validation and high-throughput sequencing have led to the identification of more than 200 sRNAs in Hfx. volcanii ([30, 39, 113], unpublished results). About 30 deletion mutants of sRNA genes have been constructed, and currently, phenotyping is applied to unravel biological functions of sRNAs in Hfx.…”

Section: Genetics: Application Of Mutants To Characterize Importamentioning

confidence: 99%

Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology ofHaloferax volcanii

Soppa

2011

Archaea

Self Cite

View full text Add to dashboard Cite

The genome sequence of Haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, RNA modifications, small non-coding RNAs, and ubiquitin-like Small Archaeal Modifier Proteins. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. Notably, Hfx. volcanii is together with Halobacterium salinarum the only prokaryotic species for which a translatome analysis has been performed. The results revealed that the fraction of translationally-regulated genes in haloarchaea is as high as in eukaryotes. A highly efficient genetic system has been established that enables the application of libraries as well as the parallel generation of genomic deletion mutants. Facile mutant generation is complemented by the possibility to culture Hfx. volcanii in microtiter plates, allowing the phenotyping of mutant collections. Genetic approaches are currently used to study diverse biological questions–from replication to posttranslational modification—and selected results are discussed. Taken together, the wealth of functional genomic and genetic tools make Hfx. volcanii a bona fide archaeal model species, which has enabled the generation of important results in recent years and will most likely generate further breakthroughs in the future.

show abstract

Section: Genetics: Application Of Mutants To Characterize Importamentioning

confidence: 99%

Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology ofHaloferax volcanii

Soppa

2011

Archaea

Self Cite

View full text Add to dashboard Cite

show abstract

“…H. volcanii is studied as an archaeal model organism because it is easy to cultivate and easily genetically modified 24 - 26 . Recently, RNomics approaches revealed that H. volcanii contains 21 intergenic sRNAs and 18 antisense RNAs 27 - 29 . In this former study only RNAs in the size range of 130–460 nucleotides were analyzed from cells grown only under a single condition.…”

Section: Introductionmentioning

confidence: 99%

High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments inHaloferax volcanii

et al. 2012

Self Cite

View full text Add to dashboard Cite

To define the complete sRNA population of the halophilic archaeon Haloferax volcanii, we employed high throughput sequencing. cDNAs were generated from RNA ranging in size from 17 to 500 nucleotides isolated from cells grown at three different conditions to exponential and stationary phase, respectively. Altogether, 145 intergenic and 45 antisense sRNAs were identified. Comparison of the expression profile showed different numbers of reads at the six different conditions for the majority of sRNAs. A striking difference in the number of sRNA reads was observed between cells grown under standard vs. low salt conditions. Furthermore, the six highest numbers of reads were found for low salt conditions. In contrast, only slight differences between sRNA reads at different growth temperatures were detected. Attempts to delete four sRNA genes revealed that one sRNA gene is essential. The three viable sRNA gene deletion mutants possessed distinct phenotypes. According to microarray analyses, the removal of the sRNA gene resulted in a profound change of the transcriptome when compared with the wild type. High throughput sequencing also showed the presence of high concentrations of tRNA derived fragments in H. volcanii. These tRF molecules were shown to have different amounts of reads at the six conditions analyzed. Northern analysis was used to confirm the presence of the tRNA-derived fragments.

show abstract

“…Driven by the need for more specific and concrete experimental data about SmAP function in vivo, the past 3 y have seen progress on the cellular functions of these proteins, chiefly via proteomic and RNomic detection of interactions between SmAPs and other proteins or RNAs 121 . The basic strategy has been a “guilt by association” approach (e.g., the CLIP-Seq method), 122 wherein the relevant cellular pathways for a protein or RNA of unknown function are inferred based on the co-precipitated binding partners, a subset of which are presumed to have been functionally characterized.…”

Section: Sm Functional Roles In the Archaea: Scaffolds Or Chaperones mentioning

confidence: 99%

“…The basic strategy has been a “guilt by association” approach (e.g., the CLIP-Seq method), 122 wherein the relevant cellular pathways for a protein or RNA of unknown function are inferred based on the co-precipitated binding partners, a subset of which are presumed to have been functionally characterized. Much of this work has been pioneered by Marchfelder and coworkers in the euryarchaeote Haloferax volcanii 96 , 121 , 123 …”

Section: Sm Functional Roles In the Archaea: Scaffolds Or Chaperones mentioning

confidence: 99%

Archaeal and eukaryotic homologs of Hfq

et al. 2013

View full text Add to dashboard Cite

Hfq and other Sm proteins are central in RNA metabolism, forming an evolutionarily conserved family that plays key roles in RNA processing in organisms ranging from archaea to bacteria to human. Sm-based cellular pathways vary in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in each of these pathways being mediated by an RNA-associated molecular assembly built upon Sm proteins. Though the first structures of Sm assemblies were from archaeal systems, the functions of Sm-like archaeal proteins (SmAPs) remain murky. Our ignorance about SmAP biology, particularly vis-à-vis the eukaryotic and bacterial Sm homologs, can be partly reduced by leveraging the homology between these lineages to make phylogenetic inferences about Sm functions in archaea. Nevertheless, whether SmAPs are more eukaryotic (RNP scaffold) or bacterial (RNA chaperone) in character remains unclear. Thus, the archaeal domain of life is a missing link, and an opportunity, in Sm-based RNA biology.

show abstract

Regulatory RNAs in Haloferax volcanii

Cited by 21 publications

References 46 publications

Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology ofHaloferax volcanii

Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology ofHaloferax volcanii

High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments inHaloferax volcanii

Archaeal and eukaryotic homologs of Hfq

Contact Info

Product

Resources

About