Classification and phylogeny of hydrogenases

Area of Science:

• Biochemistry and Molecular Biology
• Microbial Metabolism and Evolution

Background:

• Hydrogenases (H2ases) are vital enzymes catalyzing molecular hydrogen oxidation, central to microbial energy metabolism.
• H2ases are classified into [Fe]-H2ases, [NiFe]-H2ases, and metal-free H2ases, with [Fe]- and [NiFe]-H2ases being the most studied.
• Existing data suggest distinct phylogenetic origins and structural characteristics for [Fe]- and [NiFe]-H2ases.

Purpose of the Study:

• To analyze the phylogenetic relationships and structural modularity of [Fe]- and [NiFe]-H2ases.
• To investigate the distribution of H2ase classes across different domains of life (Archaea, Bacteria, Eucarya).
• To propose a rationalized nomenclature for H2ase-encoding genes based on comparative sequence analysis.

Main Methods:

• Comparative analysis of protein sequences and structures of characterized H2ases.
• Phylogenetic tree construction using sequence alignments of catalytic subunits.
• Bioinformatic analysis of microbial genome sequences to assess H2ase distribution and identify accessory domains.

Main Results:

• Strong evidence supports the phylogenetic distinctiveness of [Fe]- and [NiFe]-H2ases.
• [Fe]-H2ases are found in Bacteria and Eucarya, while [NiFe]-H2ases are primarily in Archaea and Bacteria.
• H2ase structure exhibits modularity, with accessory domains often shared with other redox complexes like Complex I.
• Maturation pathways for [NiFe]-H2ases appear distinct from those of [Fe]-H2ases, further supporting their divergence.

Conclusions:

• The study clarifies the evolutionary history and classification of hydrogenases.
• The modular nature of H2ases and the distinctness of their maturation processes highlight significant evolutionary divergence.
• A simplified and rationalized nomenclature for H2ase genes is proposed based on the findings.