Differential expression analysis of a hyperthermophilic archeaon Methanocaldococcus jannaschii upon hydrogen limitation and hydrogen syntrophy with Thermococcus paralvinellae
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PROVIDER: PRJNA449683 | ENA |
REPOSITORIES: ENA
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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:Purpose: Compare the transcriptomes of T. paralvinellae using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown on different carbon sources, under optimal and hydrogen stress conditions. Methods: T. paralvinellae was grown in triplicate at with either 0.5% maltose or 0.5% tryptone to investigate its catabolic pathways when grown on a sugar and peptides, respectively. It was also grown on 1% formate to determine the effect of formate on cell growth, metabolite production, and gene expression. It was also grown separately on maltose or tryptone media as before, except with hydrogen in the media to examine the effects of hydrogen inhibition. The cells remaining in the 2-liter bioreactor were concentrated by centrifugation. The resulting cell pellets were resuspended in TRIzol (Invitrogen) and total RNA was extracted using a Direct-zol RNA extraction kit (Zymo). RNA quantity was determined with Qubit fluorometry. RNA integrity was checked by a bioanalyzer and a Nanodrop spectrometer. Genewiz sequencing facilities performed rRNA removal, library construction, multiplexing and sequence the RNA with HiSeq2500, 2×100 Paired-End. We aligned the RNAseq reads to T. paralvinellae genome (STAR) and assigned aligned sequence reads to genomic features (featureCounts). We then quantified transcriptome and reported pairwise significant genes that are differentially expressed by DESeq available under Bioconductor (www.bioconductor.org) on Galaxy platform and in R. Results: Sequencing depths ranged from 29,974,378 to 45,240,342 sequences, with a mean of 38,990,002 and a median of 38,951,352 reads per sample. Of 2,138 genes annotated in the T. paralvinellae genome, 2084 transcripts were detected by RNA-Seq.Of the 2084 genes detected by transcriptomics, hydrogen stress caused only 48 genes to be differentially regulated (log2FC > 1, P < 0.05) with maltose and tryptone carbon sources. These included mostly genes associated with formate-dependent metabolism and transporters. The upregulated genes upon growth under H2 stress conditions indicate intrinsic formate production via formate hydrogen lyase and format secretion.
2017-12-19 | GSE101078 | GEO
Project description:Methanocaldococcus jannaschii TSS and transcriptome
| PRJNA342613 | ENA
Project description:Chromatin immunoprecipitation of Methanocaldococcus jannaschii transcription machinery
| PRJNA342581 | ENA
Project description:Effect of heat shock at 500 atm and pressure shock to 500 atm on Methanocaldococcus jannaschii
| PRJNA95331 | ENA
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: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:Effect of gas-substrate limitation on barophilic growth of Methanocaldocccus jannaschii at 500 atm.
| PRJNA94529 | ENA
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: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