Transcriptomic profiles of M. barkeri Fusaro DSMZ804 and Pyr+ strains
Ontology highlight
ABSTRACT:
ORGANISM(S): Methanosarcina barkeri str. Fusaro
PROVIDER: GSE70370 | GEO | 2015/07/01
SECONDARY ACCESSION(S): PRJNA288456
REPOSITORIES: GEO
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Project description:The goal of this work was to elucidate the mechanism by which pyruvate is utilized as a substrate in a mutant strain of Methanosarcina barkeri Fusaro. In this study, using RNAseq we gained insight into how the mutant strain modulate its transcriptional profile in order to use pyruvate as a substrate. In addition, we obtained information on how methanogens respond to pyruvate at the transcriptional level. The mRNA from of Methanosarcina barkeri Fusaro DSMZ804 and Pyr+ strains grown on a variety of substrates (methanol, acetate, methanol-acetate, methanol-pyruvate, methanol-pyruvate-acetate) were harvested sequenced and mapped to M. barkeri genome. Pairwise comparisons between two cell lines of the Pyr+ strain and the DSMZ 804 strain were performed in all substrates tested.
2015-07-01 | E-GEOD-70370 | biostudies-arrayexpress
Project description:Methylated sulfur compounds, including dimethylsulfide (DMS), methylmercaptopropionic acid (MMPA) and methylsulfide (MeSH), are well-documented to play roles in global sulfur cycle and climate homeostasis, yet the molecular mechanisms of how they are metabolized by methanogens remain largely uncharacterized. Here, using high-throughtput sequencing of RNA (RNA-seq), we gained insight into how methanogens respond to methylated sulfur compounds at the transcriptional level. The mRNA from wild-type of Methanosarcina acetivorans C2A grown on methylated sulfur compounds were harvested, sequenced and mapped to the genome. Then, we compared RNA-seq profiles to that grown on MeOH in search of unque genes.
2015-02-18 | E-GEOD-64349 | biostudies-arrayexpress
Project description:Methylated sulfur compounds, including dimethylsulfide (DMS), methylmercaptopropionic acid (MMPA) and methylsulfide (MeSH), are well-documented to play roles in global sulfur cycle and climate homeostasis, yet the molecular mechanisms of how they are metabolized by methanogens remain largely uncharacterized. Here, using high-throughtput sequencing of RNA (RNA-seq), we gained insight into how methanogens respond to methylated sulfur compounds at the transcriptional level.
2015-02-18 | GSE64349 | GEO
Project description:The potential of the earthworm Eisenia andrei to reduce soil methanogens, and thus methane emissions to the atmosphere, were assayed in a microcosm experiment. Soils were incubated for 2, 4 and 6 months. We measured microarray parameters (methanogenic diversity) at the start of incubation, as well as after 2, 4 and 6 months of incubation in microcosms with or without earthworms. Methanosarcina barkeri was the most abundant genus that was revealed by AnaeroChip in our experiment.
2011-11-11 | E-MEXP-2843 | biostudies-arrayexpress
Project description:The irreversible decarboxylation step, which commits 2-oxo acids to the Ehrlich pathway, was initially attributed to pyruvate decarboxylase. However, the yeast genome was shown to harbour no fewer than 5 genes that show sequence similarity with thiamine-diphosphate dependent decarboxylase genes. Three of these (PDC1, PDC5 and PDC6) encode pyruvate decarboxylases { while ARO10 and THI3 represent alternative candidates for Ehrlich-pathway decarboxylases. Transcriptome analysis and decarboxylase activity measurements on an S. cerevisiae aro10 strain, a double aro10 thi3 deletion strain and a quadruple pdc1,5,6,aro10 mutant strains grown in carbon–limited chemostat with phenylalanine as nitrogen source indicated that: i) PDC5 is strongly upregulated in an aro10 background (Fig. 2) and also encodes a broad-substrate α-keto acid decarboxylase. ii) PDC5 expression depends on the presence of THI3 (Fig. 2), and iii) in contrast to cell extracts from a strain expressing ARO10 only (pdc1,5,6, thi3), cell extract from a strain that only contains THI3 (pdc1,5,6,aro10) did not produce any α-keto acid decarboxylase activity . THI3 has recently been demonstrated to be involved in regulation of thiamine homeostasis in S. cerevisiae, which further suggests that its role in the Ehrlich pathway may be regulatory rather than catalytic. A systematic investigation of the catalytic properties of all five (putative) TPP-dependent decarboxylases (Aro10p, Thi3p, Pdc1p, Pdc5p, Pdc6p) is essential for a final resolution of the substrate specificity of these key enzymes in the Ehrlich pathway. Keywords: Strain comparison
2007-11-15 | GSE9590 | GEO
Project description:Transcriptional profile of wild type L. monocytogenes (EGDe) and a pycA mutant strain was compared on growth in BHI. The human pathogen L. monocytogenes is a facultatively intracellular bacterium that survives and replicates in the cytosol of many mammalian cells. The listerial metabolism, especially under intracellular conditions , is still poorly understood. Recent studies analyzed the carbon metabolism of L. monocytogenes by the 13C-isotopologue perturbation method in a defined minimal medium containing [U-13C6]glucose. It was shown that these bacteria produce oxaloacetate mainly by carboxylation of pyruvate due to an incomplete tricarboxylic acid cycle. Here we report that a pycA insertion mutant defective in pyruvate carboxylase (PYC) still grows, albeit at a reduced rate, in BHI medium, but is unable to multiply in a defined minimal medium with glucose or glycerol 36 as carbon source. Transcriptional profiling was performed on the pycA mutant and the wild type strain grown in BHI to get a closer insight into the effect of the pycA mutation in Listeria monocytogenes.
2010-02-10 | GSE19014 | GEO
Project description:The rivR gene encodes a putative transcriptional regulator, while the rivX gene encodes a putative small regulatory RNA. To determine the RivRX regulon during exponential phase growth in THY broth we compared parental strain MGAS2221 with isogenic rivRX mutant strain 2221ΔrivRX.
2012-12-01 | GSE36646 | GEO
Project description:Kumar2011 - Genome-scale metabolic network of Methanosarcina acetivorans (iVS941)
This model is described in the article:
Metabolic reconstruction of
the archaeon methanogen Methanosarcina Acetivorans.
Satish Kumar V, Ferry JG, Maranas
CD.
BMC Syst Biol 2011; 5: 28
Abstract:
BACKGROUND: Methanogens are ancient organisms that are key
players in the carbon cycle accounting for about one billion
tones of biological methane produced annually. Methanosarcina
acetivorans, with a genome size of ~5.7 mb, is the largest
sequenced archaeon methanogen and unique amongst the
methanogens in its biochemical characteristics. By following a
systematic workflow we reconstruct a genome-scale metabolic
model for M. acetivorans. This process relies on previously
developed computational tools developed in our group to correct
growth prediction inconsistencies with in vivo data sets and
rectify topological inconsistencies in the model. RESULTS: The
generated model iVS941 accounts for 941 genes, 705 reactions
and 708 metabolites. The model achieves 93.3% prediction
agreement with in vivo growth data across different substrates
and multiple gene deletions. The model also correctly
recapitulates metabolic pathway usage patterns of M.
acetivorans such as the indispensability of flux through
methanogenesis for growth on acetate and methanol and the
unique biochemical characteristics under growth on carbon
monoxide. CONCLUSIONS: Based on the size of the genome-scale
metabolic reconstruction and extent of validated predictions
this model represents the most comprehensive up-to-date effort
to catalogue methanogenic metabolism. The reconstructed model
is available in spreadsheet and SBML formats to enable
dissemination.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180035.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180035 | BioModels
Project description:The irreversible decarboxylation step, which commits 2-oxo acids to the Ehrlich pathway, was initially attributed to pyruvate decarboxylase. However, the yeast genome was shown to harbour no fewer than 5 genes that show sequence similarity with thiamine-diphosphate dependent decarboxylase genes. Three of these (PDC1, PDC5 and PDC6) encode pyruvate decarboxylases { while ARO10 and THI3 represent alternative candidates for Ehrlich-pathway decarboxylases. Transcriptome analysis and decarboxylase activity measurements on an S. cerevisiae aro10 strain, a double aro10 thi3 deletion strain and a quadruple pdc1,5,6,aro10 mutant strains grown in carbonââ¬âlimited chemostat with phenylalanine as nitrogen source indicated that:; i) PDC5 is strongly upregulated in an aro10 background (Fig. 2) and also encodes a broad-substrate ñ-keto acid decarboxylase. ii) PDC5 expression depends on the presence of THI3 (Fig. 2), and; iii) in contrast to cell extracts from a strain expressing ARO10 only (pdc1,5,6, thi3), cell extract from a strain that only contains THI3 (pdc1,5,6,aro10) did not produce any ñ-keto acid decarboxylase activity . THI3 has recently been demonstrated to be involved in regulation of thiamine homeostasis in S. cerevisiae, which further suggests that its role in the Ehrlich pathway may be regulatory rather than catalytic. A systematic investigation of the catalytic properties of all five (putative) TPP-dependent decarboxylases (Aro10p, Thi3p, Pdc1p, Pdc5p, Pdc6p) is essential for a final resolution of the substrate specificity of these key enzymes in the Ehrlich pathway. Experiment Overall Design: Comparison of glucose limited chemostat cultivations with phenylalanine as sole nitrogen sources of the following strains: Experiment Overall Design: - CENPK113-7D MATa MAL2-8c SUC2 Experiment Overall Design: - CENPK555-4A MATa MAL2-8c SUC2 ydr380w delta Experiment Overall Design: - CENPK5632-3B MATalpha MAL2-8c SUC2 ydr380w delta ydl080c delta Experiment Overall Design: - CENPK609-11A MATa MAL2-8c SUC2 pdc1, 5, 6 delta ydr380w delta
2008-06-16 | E-GEOD-9590 | biostudies-arrayexpress
Project description:Rgg-dependent transcriptional regulation in Streptococcus pyogenes strains MGAS5005 and CS101 was analyzed during post-exponential phase of growth Keywords: strain comparion, post-exponential growth, rgg mutant
2008-02-01 | GSE7341 | GEO