Browsing by Author "Abdul Halim, Mohd Farid"
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Item Data for Formate dependent heterodisulfide reduction in a Methanomicrobiales archaeon(2020-12-01) Abdul Halim, Mohd Farid; Day, Leslie; Costa, Kyle; kcosta@umn.edu; Costa, Kyle; Costa LabHydrogenotrophic methanogens produce CH4 using H2 as electron donor to reduce CO2. In the absence of H2, many are able to use formate or alcohols as alternate electron donors. Methanogens from the order Methanomicrobiales are capable of growth with H2, but many lack genes encoding hydrogenases that are typically found in other hydrogenotrophic methanogens. In an effort to better understand electron flow in methanogens from the Methanomicrobiales, we undertook a genetic and biochemical study of heterodisulfide reductase (Hdr) in Methanoculleus thermophilus. Hdr catalyzes an essential reaction by coupling the first and last steps of methanogenesis through flavin-based electron bifurcation. Hdr from M. thermophilus co-purified with formate dehydrogenase (Fdh) and only displayed activity when formate was supplied as an electron donor. We found no evidence of an Hdr associated hydrogenase, and H2 could not function as an electron donor, even with Hdr purified from cells grown on H2. We found that cells catalyze a formate hydrogenlyase activity that is likely essential for generating the formate needed for the Hdr reaction. Together, these results highlight the importance of formate as an electron donor for methanogenesis and suggest the ability to use formate is closely integrated into the methanogenic pathway in organisms from the order Methanomicrobiales.Item DNA sequencing data of genomic DNA from Methanococcus maripaludis S2 suppressor strains that relies on Fdh2 when formate is the sole electron donor(2023-10-05) Abdul Halim, Mohd Farid; Costa, Kyle C.; Fonseca, Dallas R.; Niehaus, Thomas; kcosta@umn.edu; Costa, Kyle C.; University of Minnesota Costa LabThe data contains the Illumina Sequencing Reads of genome samples from Methanococcus maripaludis S2 suppressor mutant strains. These mutant strains has genomic deletion of both homologs of formate dehydrogenase (Fdh) and complemented with fdh2 homolog expressed from replicative vector. These strains only grew after prolonged incubations when suppressor mutations arise. These genome sequencing data revealed the gene mutations in these fdh2* suppressor strains.Item Mass spectrometry data of proteins identified in purified sample of Fdh2-Hdr complex(2023-10-05) Abdul Halim, Mohd Farid; Costa, Kyle C.; Fonseca, Dallas R.; Niehaus, Thomas; kcosta@umn.edu; Costa, Kyle C.; University of Minnesota Costa LabMass spectrometry data of proteins identified from purified Fdh2-Hdr complex from Methanococcus maripaludis. The purpose of this data is part of the manuscript submission to identify the protein component of Fdh2-Hdr complex when Methanoccus mariapludis relies on Fdh2 for growh on formate as the sole electron donor.Item Transcriptomics analysis (RNA-sequencing) of Methanococcus maripaludis wild-type strain and moeA deletion mutant.(2023-10-02) Abdul Halim, Mohd Farid; Costa, Kyle C.; Fonseca, Dallas; Niehaus, Thomas; kcosta@umn.edu; Costa, Kyle C.; University of Minnesota Costa LabTranscriptomic analysis of total RNA for Methanococcus maripaludis grown in McCas-formate medium. The data compared the RNA abundance between the wild-type strain and the mutant strain with the gene encoding molybdopterin molybdotransferase (moeA, MMP1619) deletion. Released for the submission of manuscript for publication.