Classification and phylogeny of hydrogenases

Abstract

Hydrogenases (H 2ases) catalyze the reversible oxidation of molecular hydrogen and play a central role in microbial energy metabolism. Most of these enzymes are found in Archaea and Bacteria, but a few are present in Eucarya as well. They can be distributed into three classes: the [Fe]-H 2ases, the [NiFe]-H 2ases, and the metal-free H 2ases. The vast majority of known H 2ases belong to the first two classes, and over 100 of these enzymes have been characterized genetically and/or biochemically. Compelling evidence from sequences and structures indicates that the [NiFe]- and [Fe]-H 2ases are phylogenetically distinct classes of proteins. The catalytic core of the [NiFe]-H 2ases is a heterodimeric protein, although additional subunits are present in many of these enzymes. Functional classes of [NiFe]-H 2ases have been defined, and they are consistent with categories defined by sequence similarity of the catalytic subunits. The catalytic core of the [Fe]-H 2ases is a ca. 350-residue domain that accommodates the active site (H-cluster). A few monomeric [Fe]-H 2ases are barely larger than the H-cluster domain. Many others are monomeric as well, but possess additional domains that contain redox centers, mostly iron–sulfur. Some [Fe]-H 2ases are oligomeric. The modular structure of H 2ases is strikingly illustrated in recently unveiled sequences and structures. It is also remarkable that most of the accessory domains and subunits of H 2ases have counterparts in other redox complexes, in particular NADH-ubiquinone oxidoreductase (Complex I) of respiratory chains. Microbial genome sequences are bringing forth a significant body of additional H 2ase sequence data and contribute to the understanding of H 2ase distribution and evolution. Altogether, the available data suggest that [Fe]-H 2ases are restricted to Bacteria and Eucarya, while [NiFe]-H 2ases, with one possible exception, seem to be present only in Archaea and Bacteria. H 2ase processing and maturation involve the products of several genes which have been identified and are currently being characterized in the case of the [NiFe]-H 2ases. In contrast, near to nothing is known regarding the maturation of the [Fe]-H 2ases. Inspection of the currently available genome sequences suggests that the [NiFe]-H 2ase maturation proteins have no similar counterparts in the genomes of organisms possessing [Fe]-H 2ases only. This observation, if confirmed, would be consistent with the phylogenetic distinctiveness of the two classes of H 2ases. Sequence alignments of catalytic subunits of H 2ases have been implemented to construct phylogenetic trees that were found to be consistent, in the main, with trees derived from other data. On the basis of the comparisons performed and discussed here, proposals are made to simplify and rationalize the nomenclature of H 2ase-encoding genes.