Investigating the native functions of [NiFe]-CODH through genomic context analysis

Area of Science:

• Biochemistry
• Genomics
• Enzymology

Background:

• Nickel-iron carbon monoxide dehydrogenases ([NiFe]-CODHs) catalyze CO oxidation to CO2.
• Understanding functional diversity in [NiFe]-CODHs is crucial for biocatalytic CO2 reduction.
• The molecular basis for varying catalytic rates and O2 tolerance in CODH variants is poorly understood.

Purpose of the Study:

• Investigate the biochemical roles of different CODH clades (A-F) using comparative genomics.
• Determine the functional specialization and interdependencies of CODH clades based on gene clustering and operon architecture.
• Identify CODH clades suitable as primary biocatalyst targets for CO2 reduction.

Main Methods:

• Comparative genomics and synteny analysis of 1376 CODH and 1545 hybrid cluster protein sequences.
• Analysis of gene clustering patterns and operon architecture across different CODH clades.
• Correlation of gene associations with known or inferred biochemical functions.

Main Results:

• Approximately 30% of genomes encode multiple CODH isoforms, indicating functional redundancy or specialization.
• Distinct gene clustering patterns correlate with biochemical functions: Clades A, E, F link to catalytic activity and maturation; Clade B to transporters; Clade C to electron transfer; Clade D to regulation.
• Clades A, E, and F show distributional exclusivity and contain essential maturation machinery, correlating with catalytic activity.
• Clades C and D frequently co-occur with active CODHs, suggesting auxiliary or regulatory roles.

Conclusions:

• Clades A, E, and F are identified as primary targets for developing [NiFe]-CODH biocatalysts.
• Clades C and D play significant roles in CODH regulation and electron transfer processes.
• Genomics provides a framework for predicting CODH phenotypes and guiding enzyme engineering for CO2 reduction.