Methanocaldococcus jannaschii
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ABSTRACT:
PROVIDER: PRJNA95331 | ENA |
REPOSITORIES: ENA
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Project description:Growth and transcriptional profiles of the barophilic methanarchaeon Methanocaldococcus jannaschii were studied at temperatures up to 98C and pressures up to 500 atm. Application of 500 atm of hyperbaric pressure shifted the optimal growth temperature upwards, and heat shock from 88C to 98C at 500 atm resulted in termination of growth. Pressure shock of M. jannaschii from 7.8 to 500 atm over 15-min, the first pressure upshift reported for a barophile, did not accelerate growth. Transcriptional profiles indicated a similar pressure response under growth and heat shock at 500 atm and pressure shock to 500 atm suggesting that the commonly affected genes are important for high-pressure adaptation. Factorial microarray design allowed de-convolution of the interacting effect of elevated pressure and heat shock on expression profiles, thus suggesting genes that may contribute to the organism’s survival in the turbulent in situ conditions of deep-sea hydrothermal vents. Keywords: stress response, time course, high pressure, heat shock, pressure shock
2007-04-05 | GSE4620 | GEO
Project description:Effect of gas-substrate limitation on barophilic growth of Methanocaldocccus jannaschii at 500 atm.
| PRJNA94529 | ENA
Project description:Methanocaldococcus jannaschii TSS and transcriptome
| PRJNA342613 | ENA
Project description:Chromatin immunoprecipitation of Methanocaldococcus jannaschii transcription machinery
| PRJNA342581 | ENA
Project description:Barophilic growth of the hyperthermophilic methanarchaeon Methanocaldococcus jannaschii occurred when gas-substrate availability did not limit growth. In contrast, when growth was limited by gas transfer, no enhancement of growth was evident and a stress response was exhibited at both high and low pressure. A pressure-induced transcriptional response was evident, regardless of whether growth was enhanced by pressure. High-pressure adaptation of a barophilic organism can thus occur at the transcriptional level, even though the cells are stressed by low substrate availability and do not exhibit accelerated growth. Keywords: stress response, gas substrate limitation, bioreactor volume, high pressure
2006-08-01 | GSE4519 | GEO
Project description:GMP synthetases are enzymes that catalyze the conversion of XMP to GMP. The two-subunit type GMP synthetases are composed of a glutamine amidotransferase (GATase) subunit that catalyzes the conversion of Gln to Glu and ammonia, and the ATP pyrophosphatase (ATPPase) subunit that catalyzes the formation of AMP-XMP from ATP and XMP. The inactive GATase subunit is allosterically activated by the binding of substrates to the ATPPase subunit. Upon activation, the GATase subunit binds Gln and hydrolyzes it producing ammonia which is tunnelled to the ATPPase subunit. The two subunits form a tight complex to enable domain crosstalk. However, the Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is unique as the GATase (MjGATase) and ATPPase (MjATPPase) subunits interact transiently. Here, we employed enzyme kinetics, X-ray crystallography, cross-linking mass spectrometry (XL-MS) and integrative modelling to understand the mechanistic basis for the various steps in the catalytic cycle of MjGMPS.
2022-09-02 | PXD031519 | Pride
Project description:The purpose of this experiment was to compare the transcriptomes of M. jannaschii using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown under H2-replete, H2-limited and H2-syntrophy conditions. The RNA-seq reads were mapped to both M. jannaschii and T. paralvinellae genomes using BBSplit from BBMap package. BBSplit is an aligner tool that bins sequencing reads by mapping to them multiple references simultaneously and separates the reads that map to multiple references to a special "ambiguous" file for each of them. For further analyses we removed all ambiguously mapped reads to both genomes and worked with only the reads that unambiguously map to M. jannaschii genome. The mapped reads for M. jannaschii were then aligned to the M. jannaschii genome again and sorted using the STAR aligner version 2.5.1b . Aligned sequence reads were assigned to genomic features and quantified using featureCounts read summarization tool. Genes that were differentially expressed were identified using ‘DESeq2’ in the Bioconductor software framework in R. The differential gene expression analyses showed that the enzyme responsible for the reduction of methenyl group to a methylene group during carbon fixation switches from a H2-dependent enzyme to a coenzyme F420-dependent enzyme with decreasing H2 availability and into syntrophy. During syntrophy, the genes for energy generation on the membrane decreased in their expression levels.
2019-03-11 | GSE112986 | GEO
Project description:In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into ‘hypernucleosome’ particles of varying sizes with each dimer wrapping 30 bp of DNA. These are likely composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension that enables MJ1647 homo-tetramerisation. The accompanying paper solves the crystal structure of MJ1647, but this part of the study specifically uses MNase-seq methodology to explore the hypernucleosome protection landscape of the in vivo M. jannaschii nucleoid.
2022-10-22 | GSE216101 | GEO
Project description:The glutamine amidotransferase (GATase) from Methanocaldococcus jannaschii (Mj) harbours a stable post-translational modification, succinimide (SNN). As shown from earlier studies, the spontaneous deamidation of Asn109 leading to the formation of stable SNN in MjGATase, imparts hyper-thermostability to the protein. To examine which of the residues in the environment of Asn109 catalyses the conversion of Asn to SNN, several mutants of MjGATase were generated. The intact protein masses of these mutants along with the wild-type enzyme were obtained through mass spectrometric analysis. The wild-type enzyme shows a mass difference of 17 Da due to the formation of SNN whereas, the MjGATase mutants harboring unmodified Asn109 would retain the mass corresponding to that obtained from the sequence. The mass analysis of 12 MjGATase mutant proteins showed varied levels retaining intact Asn109 residue. Two double mutants showed almost entire population with the expected mass, thus, highlighting the involvement of the neighbouring residues in formation of SNN.
2026-06-08 | PXD075095 | Pride
Project description:A stable post-translational modification, succinimide (SNN), found in Methanocaldococcus jannaschii (Mj) glutamine amidotransferase (GATase) is shown to impart hyper-thermostability to the protein. To explore the role of neighbouring residues in enabling deamidation of Asn109 to SNN, intact protein mass analysis on 12 mutants of MjGATase was performed. Among these mutants, 8 showed varied proportions of mass corresponding to unmodified Asn109. SNN is known to undergo rapid hydrolysis to Asp/iso-Asp, hence, this population can also exist. As Asn intact and Asp/iso-Asp populations differ by only 1 Da, ambiguity exists in their assignment. Therefore, to determine the true levels of unmodified Asn109 population, in-gel trypsin digestion followed by MS/MS analysis of the tryptic peptides for 8 mutants and wild-type of MjGATase was conducted. The MS/MS analysis of two double mutants assured that they indeed retain Asn109 intact, forming a major population. This study points toward the presence of internal catalysts that enable the deamidation of Asn109 to SNN in MjGATase.
2026-06-08 | PXD075155 | Pride