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Evolutionary and Functional Insights into the Ski2-like helicase Family in Archaea: A Comparison of Thermococcales ASH-Ski2 and Hel308 Activities

ABSTRACT: Evolutionary and Functional Insights into the Ski2-like helicase Family in Archaea: A Comparison of Thermococcales ASH-Ski2 and Hel308 Activities

PROVIDER: PRJNA956889 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24203809_1.fastq.gz	Fastqsanger.gz
	SRR24203809_2.fastq.gz	Fastqsanger.gz
	SRR24203810_1.fastq.gz	Fastqsanger.gz
	SRR24203810_2.fastq.gz	Fastqsanger.gz
	SRR24203811_1.fastq.gz	Fastqsanger.gz

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Evolutionary and Functional Insights into the Ski2-like helicase Family in Archaea: A Comparison of Thermococcales ASH-Ski2 and Hel308 Activities

Project description:RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5′-3′ aRNaseJ exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3′-5′ polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.

2024-03-04 | GSE229955 | GEO

Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities.

Project description:RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5'-3' aRNase J exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3'-5' polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ΔASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.

| S-EPMC10946056 | biostudies-literature

The Ski2-family helicase Obelus regulates Crumbs alternative splicing and cell polarity

Project description:We identified Obelus, a conserved Ski2-family DExD/H-box helicase in a screen for Drosophila mutants with defects in epithelial polarity and junctional organization. To identify the functional targets of Obelus we used RNA sequencing and compared the transcriptional and splicing profiles of staged wild-type embryos with obe1/obe2 and obe2/Df(3R)Exel6174 (obe2/Df) mutant embryos.

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Methylation comparison between ash tolerant and susceptible trees to ash dieback [methylation]

Project description:DNA was extracted from two ash tree samples, one tolerant and one susceptible to ash dieback. The DNA was sequenced using Nanopore technologies and the methylation was called against the new genome (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ) to identify differentially methylated regions between both samples. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics

2025-03-03 | GSE214552 | GEO

Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation

Project description:We performed RNA-seq and proteomics on naturally infested green ash (F. pennsylvanica) trees at low, medium and high levels of increasing emerald ash borer (A. planipennis) infestation. Our integrative analysis of the RNA-Seq and proteomics data identified 14 proteins and 4 transcripts that contribute most to the difference between highly infested and low infested trees.

2023-03-08 | GSE212332 | GEO

ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

Project description:ASH-1 orthologs are H3K36-specific methyltransferases that are conserved from fungi to humans but are poorly understood, in part because they are typically essential for viability. Here we examine the H3K36 methylation pathway of Neurospora crassa, which we find has just two H3K36 methyltransferases, ASH-1 and RNA polymerase II-associated SET-2. Our investigation of the interplay between SET-2 and ASH-1 uncovered a regulatory mechanism connecting ASH-1-catalyzed H3K36 methylation to repression of poorly transcribed genes. Our findings provide new insight into ASH-1 function, H3K27me2/3 establishment, and repression at facultative heterochromatin.

2018-08-14 | GSE118495 | GEO

ATRX histone binding and helicase activities have distinct roles in neuronal differentiation

Project description:ATRX histone binding and helicase activities have distinct roles in neuronal differentiation

| PRJNA798392 | ENA

Effects of ash-2, hsf-1, or ash-2 + hsf-1 RNAi on gene expression in Day 1 adult Q40::YFP C. elegans

Project description:To determine how gene expression changes in long-lived ash-2-deficient worms expressing the amyloidogenic Q40::YFP, and to assess how simultaneous depletion of hsf-1 effects these transcriptomic changes.

2023-10-16 | GSE227652 | GEO

Discriminating activities of DEAD-Box Helicase 41 from myeloid malignancy-associated germline variants by genetic rescue

Project description:Although DEAD-box helicase 41 (DDX41) is implicated in oncogenic and innate immune mechanisms, there are many unanswered questions about how the ever-increasing spectrum of genetic variants impacts DDX41 activity. Here, we describe a facile genetic rescue assay that discriminates activities of DDX41 from those of human myeloid malignancy-linked germline and somatic DDX41 mutants. Our analyses revealed that the variants were impaired in their intrinsic RNA-regulatory activities and to induce monocytic differentiation markers. It will be instructive to extend these analyses to more broadly conduct structure/function assessments for clinical genetic curation and leverage the quantitative assay to elucidate mechanisms and interventions that promote and/or oppose DDX41 function, thereby influencing DDX41-linked pathogenicity.

2022-12-04 | GSE208400 | GEO

SKI2 mediates degradation of RISC 5â-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis

Project description:A loss-of-function mutant in the SKI2 helicase in Arabidopsis was shown to accumulate 5'-cleavage fragments of several miRNA targets. Small RNAs in ski2 single and ski2/rdr6 double mutants (two biological replicates of each genotype) were next analysed by NGS. The data show that several miRNA targets produce RDR6-dependent siRNAs upon inactivation of SKI2. Files containing these NGS data are deposited here. Seeds were surface sterilized and germinated on MS medium for 2 weeks. The seedlings were grown on soil until flowering stage in a 16h light period. The inflorescences were harvested and used to prepare RNA. Small RNA libraries were prepared using the NEBnext Multiplex small RNA library prep kit for Illumina sequencing.

2015-10-20 | E-MTAB-3781 | biostudies-arrayexpress

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