Project description:Hydrogenases are a critical component of H2-dependent energy-conservation pathways in Methanosarcina barkeri. To allow phenotypic analysis of the hydrogenases, we constructed mutants lacking the frhADGB, freAEGB, vhtGACD, vhxGAC and echABCDEF operons, individually and in all possible combinations. In addition to measuring the effect of each deletion on growth, methane production, and hydrogenase activity, the effect on gene expression was measured by RNA sequencing to detect potential transcriptional regulation by the hydrogenases.
Project description:Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism
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.
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.
Project description:This study contains two experimental proteome, i.e., Methanosarcina barkeri MS was cultivated in 130 and 2100 mg/L ammonia nitrogen, respectively. To investigate how M. barkeri cells respond to high ammonia stress in protein molecular level, samples were collected for 4D-label free proteomic assay under each condition. These are raw data of the proteome.
Project description:Anaerobic methanogens are an important part of the global carbon cycle and energy supply. With industrialization, Fluoranthene (Flu) accumulated in soils, sediments, and sewage plants etc., giving an uncertain impact on methane production of methanogens. Here, the effect of Flu on Methanosarcina barkeri (M. barkeri) were investigated in this paper. The methane yield of strain with 0.01 and 0.1 mg/L Flu was 1.43 and 1.65 times higher than the control. The growth of M. barkeri was also maximized at Flu of 0.1 mg/L with 1.37-fold than control. The physiological features of M. barkeri were enhanced by 0.1 mg/L Flu, such as, cell viability (154%), total-EPS (1.82-fold), and SOD enzyme activity (1.28 times). Notably, TMT proteomics provided a novel insight to reveal that Flu activated the methanogenic metabolic pathway and ABC transporters of M. barkeri, particularly promoted it to synthesize MtrA/C/D/E/G/H (8.2 times total), FrhA/B/G, iron (III)/zinc/molybdenum/vitamin B12 ABC transporter proteins, and the groups of methyltransferase and coenzyme F420 hydrogenase. The upregulated expression of methanogenesis-related enzyme proteins resulted in increased generation and transfer of methane. Overall, this study shed light on the impact of organic pollutants on global carbon cycle of M. barkeri from the molecular biology perspective.
