Haloferax volcanii

Pohlschröder, Mechthild; Schulze, Stefan

doi:10.1016/j.tim.2018.10.004

Cited by 37 publications

(28 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Here, we describe the identification of RNA 3´ends of the halophilic model archaeon Haloferax volcanii and the subsequent determination of termination motifs. H. volcanii has been used for a plethora of biological studies [18,19], including the determination of nucleosome coverage [20] and a genome-wide identification of TSS [21]. H. volcanii requires high salt concentrations for optimal growth, and due to the high intracellular salt concentrations, RNA-protein interactions -including modes of transcription termination-may differ from those in mesophilic archaea.…”

Section: Introductionmentioning

confidence: 99%

Identification of RNA 3´ ends and termination sites in Haloferax volcanii

et al. 2020

View full text Add to dashboard Cite

Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3´termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea, Methanosarcina mazei and Sulfolobus acidocaldarius. In this study, only regions directly downstream of annotated genes were analysed, and thus, only part of the genome had been investigated. Here, we developed a novel algorithm (Internal Enrichment-Peak Calling) that allows an unbiased, genome-wide identification of RNA 3´termini independent of annotation. In an RNA fraction enriched for primary transcripts by terminator exonuclease (TEX) treatment we identified 1,543 RNA 3´termini. Approximately half of these were located in intergenic regions, and the remainder were found in coding regions. A strong sequence signature consistent with known termination events at intergenic loci indicates a clear enrichment for native TTS among them. Using these data we determined distinct putative termination motifs for intergenic (a T stretch) and coding regions (AGATC). In vivo reporter gene tests of selected TTS confirmed termination at these sites, which exemplify the different motifs. For several genes, more than one termination site was detected, resulting in transcripts with different lengths of the 3´untranslated region (3´UTR).

show abstract

Section: Introductionmentioning

confidence: 99%

Identification of RNA 3´ ends and termination sites in Haloferax volcanii

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Here, we describe the identification of RNA 3´ ends of the halophilic model archaeon Haloferax volcanii and the subsequent determination of termination motifs. H. volcanii has been used for a plethora of biological studies (18,19), including the determination of nucleosome coverage (20) and a genome-wide identification of TSS (21). H. volcanii requires high salt concentrations for optimal growth, and due to the high intracellular salt concentrations, RNA-protein interactions -including modes of transcription termination-may differ from those in mesophilic archaea.…”

Section: Introductionmentioning

confidence: 99%

Identification of RNA 3’ ends and termination sites in Haloferax volcanii

Berkemer

Maier

Amman

et al. 2019

Preprint

View full text Add to dashboard Cite

Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3´ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea. In this study, only part of the genome had been investigated. Here, we developed a novel algorithm that allows an unbiased, genomewide identification of RNA 3´ termini independent of annotation. In an RNA fraction enriched for primary transcripts by terminator exonuclease (TEX) treatment we identified 1,543 RNA 3´ termini. A strong sequence signature consistent with known termination events at intergenic loci indicates a clear enrichment for native TTS among them. Using these data we determined distinct putative termination motifs for intergenic (a T stretch) and coding regions (AGATC). In vivo reporter gene tests of selected TTS confirmed termination at these sites, which exemplify the different motifs. For several genes, more than one termination site was detected, resulting in transcripts with different lengths of the 3´ untranslated region .

show abstract

“…The development of a series of plasmid vectors and host strains for conditional overexpression of halophilic proteins in the haloarchaeon Hfx. volcanii during the last decade offers new approaches for large-scale production of haloarchaeal proteins and enzymes that are of interest in industry and biotechnology [20,82,83]. Nevertheless, new challenges have to be overcome to achieve the following: (i) coupling the production of the apoproteins with the synthesis of cofactors in the case of metalloproteins; (ii) exploring whether or not the culture media for these purposes must be enriched with metals to sustain the production of metallocofactors; and (iii) if metal supplementation is required, optimizing the compositions of culture media to avoid metal precipitation due to the high ionic strength of the cultures used for the growth of haloarchaea.…”

Section: Discussionmentioning

confidence: 99%

Heterologous and Homologous Expression of Proteins from Haloarchaea: Denitrification as Case of Study

Martínez‐Espinosa

2019

IJMS

View full text Add to dashboard Cite

Haloarchaea (halophilic microbes belonging to the Archaea domain) are microorganisms requiring mid or even high salt concentrations to be alive. The molecular machinery of these organisms is adapted to such conditions, which are stressful for most life forms. Among their molecular adaptations, halophilic proteins are characterized by their high content of acidic amino acids (Aspartate (Asp) and glumate (Glu)), being only stable in solutions containing high salt concentration (between 1 and 4 M total salt concentration). Recent knowledge about haloarchaeal peptides, proteins, and enzymes have revealed that many haloarchaeal species produce proteins of interest due to their potential applications in biotechnology-based industries. Although proteins of interest are usually overproduced in recombinant prokaryotic or eukaryotic expression systems, these procedures do not accurately work for halophilic proteins, mainly if such proteins contain metallocofactors in their structures. This work summarizes the main challenges of heterologous and homologous expression of enzymes from haloarchaea, paying special attention to the metalloenzymes involved in the pathway of denitrification (anaerobic reduction of nitrate to dinitrogen), a pathway with significant implications in wastewater treatment, climate change, and biosensor design.

show abstract

Haloferax volcanii

Cited by 37 publications

References 10 publications

Identification of RNA 3´ ends and termination sites in Haloferax volcanii

Identification of RNA 3´ ends and termination sites in Haloferax volcanii

Identification of RNA 3’ ends and termination sites in Haloferax volcanii

Heterologous and Homologous Expression of Proteins from Haloarchaea: Denitrification as Case of Study

Contact Info

Product

Resources

About