Absolute Proteome Quantification in the Gas-Fermenting Acetogen Clostridium autoethanogenum

Abstract

Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C 1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation.

Characterisation of acetogen formatotrophic potential usingE. limosum

“…• Our proteomic analysis can not determine absolute quantifications due to differences in mass spectrometer protein constituent signal response. However using a spiked protein analysis, (Valgepea et al 2022) found a linear relationship between the log 10 of mass spectrometer intensity and log 10 anchor protein concentrations using a similar instrument setup to here. Since we can not be certain of the injected sample protein mass, we instead scaled protein concentrations by the pta enzyme, which Valgepea et al (2022) showed was largely consistent across different gas fermentation conditions.…”

Molecular understanding ofEubacterium limosumchemostat methanol metabolism

“…(2022), 24 found a linear relationship between the log 10 anchor protein concentrations and log 10 of mass spectrometer intensity. Due to slight variability of the injected sample protein mass, we scaled protein concentrations using the pta enzyme, which was shown by Valgepea et al (2022) to be largely constant across multiple gas fermentation conditions. There have been few E. limosum proteins assayed, and so to provide an estimate of kinetic parameters, k cat and K m , we undertook BLAST analysis of key proteins against known protein assays. This was used to verify deep learning models predicting kinetic parameters for the WLP central carbon metabolism using protein amino acid sequences as input.…”

“…By making several further assumptions, we can get likely order of magnitude estimates for J as follows. Whilst our proteomic analysis is not able to determine absolute quantifications due to differences in MS protein constituent signal responses, E can still be estimated, as during a spiked protein analysis with similar setup, Valgepea et al . (2022), 24 found a linear relationship between the log 10 anchor protein concentrations and log 10 of mass spectrometer intensity.…”

“… Whilst our proteomic analysis is not able to determine absolute quantifications due to differences in MS protein constituent signal responses, E can still be estimated, as during a spiked protein analysis with similar setup, Valgepea et al . (2022), 24 found a linear relationship between the log 10 anchor protein concentrations and log 10 of mass spectrometer intensity. Due to slight variability of the injected sample protein mass, we scaled protein concentrations using the pta enzyme, which was shown by Valgepea et al (2022) to be largely constant across multiple gas fermentation conditions. There have been few E. limosum proteins assayed, and so to provide an estimate of kinetic parameters, k cat and K m , we undertook BLAST analysis of key proteins against known protein assays.…”

“…Whilst our proteomic analysis is not able to determine absolute quantifications due to differences in MS protein constituent signal responses, E can still be estimated, as during a spiked protein analysis with similar setup, Valgepea et al . (2022), 24 found a linear relationship between the log 10 anchor protein concentrations and log 10 of mass spectrometer intensity. Due to slight variability of the injected sample protein mass, we scaled protein concentrations using the pta enzyme, which was shown by Valgepea et al (2022) to be largely constant across multiple gas fermentation conditions.…”