model m-file  (COMSOL Inc)

Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet: Summary of sequenced genomes

Article Snippet: GEM modeling related files M. thermautotrophicus ΔH , This manuscript , Biomodels: MODEL2211290001.

Techniques: Plasmid Preparation, Sequencing

Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet: Fermentation data from the first experiment in chemostat bioreactors with M. thermautotrophicus ΔH (ΔH), M. thermautotrophicus Z-245 (ZZ), and M. marburgensis Marburg (MM) (A) Gas consumption (H 2 and CO 2 uptake), and CH 4 and biomass production data from quadruplicate ( N = 4, ΔH and MM) and triplicate ( N = 3, ZZ) bioreactors for the fermentation period of 7 days (mean ±1 standard deviation). For ZZ, we discarded one replicate due to a pump malfunction in this bioreactor and wash-out of the cells. Data for further analyses (transcriptomics, proteomics) were taken on day seven, as indicated by arrows. (B) Average gas consumption (H 2 and CO 2 uptake) and CH 4 and biomass production data during a steady-state period (days 4–7). For statistical analysis in pairwise comparisons with t -test, data points without suspected gross measurement error (red circles) were included, data points with suspected gross measurement error (gray circles) were excluded . (C) Average normalized product distribution (mean ±1 standard deviation), including statistical analysis by ANOVA (n = 11 (ΔH), n = 10 (ZZ), n = 16 (MM); ). ΔH, M. thermautotrophicus ΔH; ZZ, M. thermautotrophicus Z-245; MM, M. marburgensis Marburg: F , F value; F crit , F critical value.

Article Snippet: GEM modeling related files M. thermautotrophicus ΔH , This manuscript , Biomodels: MODEL2211290001.

Techniques: Standard Deviation

Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet: Wolfe Cycle adapted from Thauer with reactions involved in the energy metabolism Fluxes are from the proteomics reduced model (using intensity based absolute quantification (iBAQ) values), constrained with experimental data that was adjusted for gross measurement error. iBAQ values are given for proteins. Gene group is used as ID for the omics. For the PFL reaction, only M. thermautotrophicus ΔH has the gene; thus, the gene ID is used (ISG35_01600). For the FDH_F420, only M. thermautotrophicus Z-245 has the formate dehydrogenase cassette; thus, the gene IDs are used (ISG36_07610 and ISG36_07615). Red text refers to metabolites that are exchanged across the membrane. Microbes : ΔH, M. thermautotrophicus ΔH; MM, M. marburgensis Marburg; ZZ, M. thermautotrophicus Z-245. Compounds : CH 4 , methane; CO, carbon monoxide; CoA, Coenzyme A; CoB, coenzyme B; CoM, coenzyme M; CoM-S-S-CoB, CoM-CoB heterodisulfide; CO 2 , carbon dioxide; F, formyl; Fd ox/rd , ferredoxin oxidized/reduced; H 2 , hydrogen; H + , proton; H 4 MPT, tetrahydromethanopterin; M, methyl; Me, methenyl; MFR, methanofuran; My, methylene; Na + , sodium ion. Reactions/Enzymes: ATPM, ATP maintenance (pseudo reaction); CODHr2, CO dehydrogenase/acetyl-CoA synthase; Eha/Ehb, energy converting hydrogenases; EX_biomass_e, biomass exchange (pseudo reaction); EX_ch4_e, CH 4 exchange (pseudo reaction); EX_co2_e, CO 2 exchange (pseudo reaction); EX_h2_e, H 2 exchange (pseudo reaction); FDHf420, F 420 -dependent formate dehydrogenase; FDH_F420, F 420 -dependent formate dehydrogenase cassette; FRH, F 420 -reducing hydrogenase; FTRM, FMFR/H 4 MPT formyltransferase; FWD, FMFR dehydrogenase (tungsten- and molybdenum-dependent isozymes); HMD, MeH 4 MPT hydrogenase; MCH, MeH 4 MPT cyclohydrolase; MCR, MCoM reductase (I and II); MER, MyH 4 MPT reductase; MTD, MyH 4 MPT dehydrogenase; MTR, MH 4 MPT/CoM methyltransferase; MVHHDR, F 420 -non-reducing hydrogenase with the heterodisulfide reductase; NAATP, ATP synthase; Nat3_1, Na + /H + antiporter; PFL, pyruvate formate-lyase; POR2, pyruvate synthase. Other: ◊, activating protein; •, not detected; X, no gene. For an extended figure see Figure S4 .

Article Snippet: GEM modeling related files M. thermautotrophicus ΔH , This manuscript , Biomodels: MODEL2211290001.

Techniques: Quantitative Proteomics, Membrane

Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet: Fermentation data from the second experiment in chemostat bioreactors with M. thermautotrophicus ΔH pMVS1111A:P hmtB - fdh Z-245 (ΔH) and M. thermautotrophicus Z-245 (ZZ) (A) Gas consumption (H 2 and CO 2 uptake) or sodium formate consumption, and CH 4 and biomass production data from quadruplicate bioreactors for the fermentation period of 11 (ΔH H ) and 17 (ΔH F and ZZ F ) days (mean ±1 standard deviation). Formate uptake rates were only determined once steady state was reached and all formate provided was consumed. (B) Average sodium formate consumption and H 2 , CO 2, CH 4 , and biomass production data during the steady-state period (days 13–17) for ΔH F ( N = 3) and ZZ F ( N = 4). For statistical analysis in pairwise comparisons with t -test, data points without suspected gross measurement error (red circles) were included, and data points with suspected gross measurement error (gray circles) were excluded . (C) Average normalized product distribution (mean ±1 standard deviation), including a statistical analysis by ANOVA for ΔH F ( N = 3) and ZZ F ( N = 4) . CH 4 , methane; CO 2 , carbon dioxide; H 2 , molecular hydrogen; ΔH, M. thermautotrophicus ΔH pMVS1111A:P hmtB - fdh Z-245 ; ZZ, M. thermautotrophicus Z-245; F, sodium formate as substrate; H, H 2 and CO 2 as substrates; F , F value; F crit , F critical value.

Article Snippet: GEM modeling related files M. thermautotrophicus ΔH , This manuscript , Biomodels: MODEL2211290001.

Techniques: Standard Deviation

Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet:

Article Snippet: GEM modeling related files M. thermautotrophicus ΔH , This manuscript , Biomodels: MODEL2211290001.

Techniques: Virus, Recombinant, Staining, Sequencing, RNA Sequencing, Software, Combined Bisulfite Restriction Analysis Assay, Mass Spectrometry

Journal: iScience

Article Title: An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

doi: 10.1016/j.isci.2023.108016

Figure Lengend Snippet:

Article Snippet: GEM modeling related files M. thermautotrophicus Z-245 , This manuscript , Biomodels: MODEL2211290002.

Techniques: Virus, Recombinant, Staining, Sequencing, RNA Sequencing, Software, Combined Bisulfite Restriction Analysis Assay, Mass Spectrometry