H2-metabolizing prokaryotes

Abstract

The reversible splitting of H2 into protons and electrons is a key process in the metabolism of many prokaryotes and has been studied extensively in a wide range of bacteria and archaea. Environmental H2 is an energy source for aerobic H2 oxidizers, methanogens, acetogens, and sulfate reducers and is a source of reducing power for anoxygenic phototrophs. H2 is released as a terminal metabolic product of both facultative and obligate fermenters. It is a byproduct of N2 fixation and phosphite oxidation. The H2-consuming and H2-evolving processes of microorganisms impact the global atmospheric H2 balance. N2 fixation in seas and lakes is a significant source of atmospheric H2. Soils are a major H2 sink. Entirely H2-based microbial ecosystems are widespread on the planet. The most important of them consists of the granitic layers of the planet's crust, which on aggregate harbor a huge fraction of the total biomass on Earth. More spectacular are the submarine hydrothermal vents spewing H2-rich fluids. Current scenarios of pre- and protobiotic evolution envisage such sites as the cradle of terrestrial life. Based on their metal content, hydrogenases, the enzymes which catalyze the splitting of H2, can be divided into three groups of independent phylogenetic origin: [NiFe], [FeFe], and [Fe] hydrogenases. Three-dimensional structures available for representatives of all three groups reveal some remarkable features of these enzymes. The actual catalyst is a NiFe or Fe metallocomplex encased in a protein. Tunnels in the protein allow H2 to access or egress from the active site. A series of FeS clusters form an electrical circuit connecting the active site with binding sites (for cytochromes, pyridine nucleotides, and other redox partners) at the surface of the enzyme. The assembly and insertion of the active-site metallocomplex into the hydrogenase apoenzyme is an intricate, multistep process requiring several specialized accessory proteins. The genetic determinants for the hydrogenase catalytic components and for the accessory proteins are solitary or clustered. The mechanisms governing the expression of hydrogenase genes vary depending on physiological context. In obligate fermenters, for instance, expression of hydrogenase genes is typically constitutive. In facultative H2 oxidizers, on the other hand, hydrogenase gene expression is controlled by H2-sensing regulatory proteins. The diversity of metabolic processes involving H2 as an intermediate and the ubiquitous occurrence of hydrogenases in microbes testify to the importance of H2 metabolism in primeval cellular life forms.