In Vivo Enzyme Catalytic Rates in Formate-Growing Methanococcus maripaludis

Area of Science:

• Biochemistry
• Microbiology
• Metabolic Engineering

Background:

• Enzyme turnover numbers (kcat) quantify intrinsic catalytic capacity but are scarce for anaerobic Archaea.
• In vivo catalytic rates of C1 metabolism enzymes in methanogens remain largely unquantified.
• Methanogens like Methanococcus maripaludis are key players in C1 compound utilization.

Purpose of the Study:

• To determine the in vivo catalytic rates of 99 enzymes in Methanococcus maripaludis during growth on formate.
• To compare experimentally determined in vivo rates with computationally predicted enzyme turnover numbers.
• To provide quantitative insights into methanogenic C1 metabolism for metabolic engineering.

Main Methods:

• Utilized proteomics data and genome-scale metabolic modeling.
• Constrained simulations with experimental data across multiple growth rates.
• Compared in vivo rates (kapp) with sequence-derived maximum turnover numbers (kcat) predicted by machine learning.

Main Results:

• Quantified in vivo catalytic rates for 99 M. maripaludis enzymes.
• Found no correlation between sequence-derived turnover numbers and maximum in vivo catalytic rates.
• Established quantitative data for enzymes involved in C1 metabolism.

Conclusions:

• Predicted enzyme capacities do not accurately reflect in vivo performance in M. maripaludis.
• Quantitative insights can guide metabolic engineering strategies for methanogens.
• Engineered methanogens hold potential for biotechnological production from C1 compounds.