Classification and phylogeny of hydrogenases

Hydrogenases (H(2)ases) catalyze the reversible oxidation of molecular hydr ogen 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(2)ases, th e [NiFe]-H(2)ases, and the metal-free H(2)ases. The vast majority of known H(2)ases belong to the first two classes, and over 100 of these enzymes hav e been characterized genetically and/or biochemically. Compelling evidence from sequences and structures indicates that the [NiFe]- and [Fe]-H(2)ases are phylogenetically distinct classes of proteins. The catalytic core of th e [NiFe]-H(2)ases is a heterodimeric protein, although additional subunits are present in many of these enzymes. Functional classes of [NiFe]-H(2)ases have been defined, and they are consistent with categories defined by sequ ence similarity of the catalytic subunits. The catalytic core of the [Fe]-H (2)ases is a ca. 350-residue domain that accommodates the active site (H-cl uster). A few monomeric [Fe]-H(2)ases are barely larger than the H-cluster domain. Many others are monomeric as well. but possess additional domains t hat contain redox centers, mostly iron-sulfur. Some [Fe]-H(2)ases are oligo meric. The modular structure of H(2)ases is strikingly illustrated in recen tly unveiled sequences and structures. It is also remarkable that most of t he accessory domains and subunits of H(2)ases have counterparts in other re dox complexes, in particular NADH-ubiquinone oxidoreductase (Complex I) of respiratory chains. Microbial genome sequences are bringing forth a signifi cant body of additional H(2)ase sequence data and contribute to the underst anding of H(2)ase distribution and evolution. Altogether, the available dat a suggest that [Fe]-H(2)ases are restricted to Bacteria and Eucarya, while [NiFe]-H(2)ases, with one possible exception, seem to be present only in Ar chaea and Bacteria. H(2)ase processing and maturation involve the products of several genes which have been identified and are currently being charact erized in the case of the [NiFe]-H(2)ases. In contrast, near to nothing is known regarding the maturation of the [Fe]-H(2)ases. Inspection of the curr ently available genome sequences suggests that the [NiFe]-H(2)ase maturatio n proteins have no similar counterparts in the genomes of organisms possess ing [Fe]-H(2)ases only. This observation, if confirmed, would be consistent with the phylogenetic distinctiveness of the two classes of H(2)ases. Sequ ence alignments of catalytic subunits of H(2)ases 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 perfor med and discussed here, proposals are made to simplify and rationalize the nomenclature of H(2)ase-encoding genes. (C) 2001 Federation of European Mic robiological Societies. Published by Elsevier Science BN. All rights reserv ed.