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Thermococcus onnurineus

ABSTRACT: Genome-wide primary transcriptome landscape reveals the diversity of regulatory elements in archaeal genomes

PROVIDER: PRJNA339284 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4042633.fastq.gz	Fastqsanger.gz
	SRR4042634.fastq.gz	Fastqsanger.gz
	SRR4042635.fastq.gz	Fastqsanger.gz
	SRR4042636.fastq.gz	Fastqsanger.gz
	SRR4042637.fastq.gz	Fastqsanger.gz

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Thermococcus onnurineus

Project description:Thermococcus onnurineus overview

| PRJNA36273 | ENA

Extracellular Vesicles of the Hyperthermophilic Archaeon "Thermococcus onnurineus" NA1T.

Project description:Extracellular vesicles (EVs) produced by a sulfur-reducing, hyperthermophilic archaeon, "Thermococcus onnurineus" NA1(T), were purified and characterized. A maximum of four EV bands, showing buoyant densities between 1.1899 and 1.2828 g cm(-3), were observed after CsCl ultracentrifugation. The two major EV bands, B (buoyant density at 25°C [ρ(25)] = 1.2434 g cm(-3)) and C (ρ(25) = 1.2648 g cm(-3)), were separately purified and counted using a qNano particle analyzer. These EVs, showing different buoyant densities, were identically spherical in shape, and their sizes varied from 80 to 210 nm in diameter, with 120- and 190-nm sizes predominant. The average size of DNA packaged into EVs was about 14 kb. The DNA of the EVs in band C was sequenced and assembled. Mapping of the T. onnurineus NA1(T) EV (ToEV) DNA sequences onto the reference genome of the parent archaeon revealed that most genes of T. onnurineus NA1(T) were packaged into EVs, except for an ∼9.4-kb region from TON_0536 to TON_0544. The absence of this specific region of the genome in the EVs was confirmed from band B of the same culture and from bands B and C purified from a different batch culture. The presence of the 3'-terminal sequence and the absence of the 5'-terminal sequence of TON_0536 were repeatedly confirmed. On the basis of these results, we hypothesize that the unpackaged part of the T. onnurineus NA1(T) genome might be related to the process that delivers DNA into ToEVs and/or the mechanism generating the ToEVs themselves.

| S-EPMC4551206 | biostudies-literature

Thermococcus onnurineus NA1

Project description:Experimental evolution of a hyperthermophilic archaeon on carbon monoxide enhanced hydrogen productivity through novel mechanisms associated with genome, transcriptome and epigenome changes

| PRJNA296014 | ENA

Thermococcus onnurineus NA1

Project description:Hyperthermophilic bacterium

| PRJNA20773 | ENA

Thermococcus onnurineus NA1

Project description:Screening of a novel strong promoter by RNA sequencing and its application to H2 production in a hyperthermophilic archaeon

| PRJNA269922 | ENA

Thermococcus onnurineus NA1

Project description:Expression analysis of Thermococcus onnurineus NA1 KCTC10859 and an Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant in a T. onnurineus NA1 strain.

| PRJNA348351 | ENA

Genome-wide primary transcriptome landscape reveals the diversity of regulatory elements in archaeal genomes

Project description:We show the transcriptomic landscape of the H2-producing archaeon Thermococcus onnurineus NA1 in response to different growth conditions using primary and whole transcriptome sequencing. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA boxes, A-rich B recognition elements (BREs), and promoter proximal element (PPE) motifs in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). In addition, along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions during hydrogen production. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that orthologous genes are expressed from highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. This study suggests that closely related archaea maintain orthologous gene functions, but may diversify the elements that regulate them to adapt to their unique environmental habitats.

2017-06-12 | GSE85760 | GEO

Structural features of Cas2 from Thermococcus onnurineus in CRISPR-cas system type IV.

Project description:CRISPR-Cas is RNA-based prokaryotic immune systems that defend against exogenous genetic elements such as plasmids and viruses. Cas1 and Cas2 are highly conserved components that play an essential part in the adaptation stage of all CRISPR-Cas systems. Characterization of CRISPR-Cas genes in Thermococcus onnurineus reveals the association of the Cas2 gene with the putative type IV system that lacks Cas1 or its homologous genes. Here, we present a crystal structure of T. onnurineus Cas2 (Ton_Cas2) that exhibits a deep and wide cleft at an interface lined with positive residues (Arg16, Lys18, Lys19, Arg22, and Arg23). The obvious DNA recognizing loops in Cas2 from E. coli (Eco_Cas2) are absent in Ton_Cas2 and have significantly different shapes and electrostatic potential distributions around the putative nucleotide binding region. Furthermore, Ton_Cas2 lacks the hairpin motif at the C-terminus that is responsible for Cas1 binding in Eco_Cas2. These structural features could be a unique signature and indicate an altered functional mechanism in the adaptation stage of Cas2 in type IV CRISPR-Cas systems.

| S-EPMC5029534 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of Lon from Thermococcus onnurineus NA1.

Project description:Lon is an oligomeric ATP-dependent protease that degrades defective or denatured proteins as well as some folded proteins for the control of cellular protein quality and metabolism. Lon from Thermococcus onnurineus NA1 was purified and crystallized at 295 K. A 2.0 A resolution data set was collected using synchrotron radiation. The crystals belonged to space group P6(3), with unit-cell parameters a = 121.45, b = 121.45, c = 195.24 A. Assuming the presence of two monomers in the asymmetric unit, the solvent content was estimated to be about 60.7%.

| S-EPMC2805537 | biostudies-literature

Identification and characterization of inorganic pyrophosphatase and PAP phosphatase from Thermococcus onnurineus NA1.

Project description:Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in Thermococcus onnurineus NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in T. onnurineus NA1 and "Pyrococcus abyssi."

| S-EPMC2687159 | biostudies-literature

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