Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic profiles of M. barkeri Fusaro DSMZ804 and Pyr+ strains

ABSTRACT: 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.

ORGANISM(S): Methanosarcina barkeri str. Fusaro

SUBMITTER: William Metcalf

PROVIDER: E-GEOD-70370 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Transcriptomic profiles of M. barkeri Fusaro DSMZ804 and Pyr+ strains

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