title: Iron hydrogenases and the evolution of anaerobic eukaryotes.
abstract: Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic protozoa scattered throughout the eukaryotic tree. Hydrogenases also play a central role in the hydrogen and syntrophic hypotheses for eukaryogenesis. Here, we show that sequences related to iron-only hydrogenases ([Fe] hydrogenases) are more widely distributed among eukaryotes than reports of hydrogen production have suggested. Genes encoding small proteins which contain conserved structural features unique to [Fe] hydrogenases were identified on all well-surveyed aerobic eukaryote genomes. Longer sequences encoding [Fe] hydrogenases also occur in the anaerobic eukaryotes Entamoeba histolytica and Spironucleus barkhanus, both of which lack hydrogenosomes. We also identified a new [Fe] hydrogenase sequence from Trichomonas vaginalis, bringing the total of [Fe] hydrogenases reported for this organism to three, all of which may function within its hydrogenosomes. Phylogenetic analysis and hypothesis testing using likelihood ratio tests and parametric bootstrapping suggest that the [Fe] hydrogenases in anaerobic eukaryotes are not monophyletic. Iron-only hydrogenases from Entamoeba, Spironucleus, and Trichomonas are plausibly monophyletic, consistent with the hypothesis that a gene for [Fe] hydrogenase was already present on the genome of the common, perhaps also anaerobic, ancestor of these phylogenetically distinct eukaryotes. Trees where the [Fe] hydrogenase from the hydrogenosomal ciliate Nyctotherus was constrained to be monophyletic with the other eukaryote sequences were rejected using a likelihood ratio test of monophyly. In most analyses, the Nyctotherus sequence formed a sister group with a [Fe] hydrogenase on the genome of the eubacterium Desulfovibrio vulgaris. Thus, it is possible that Nyctotherus obtained its hydrogenosomal [Fe] hydrogenase from a different source from Trichomonas for its hydrogenosomes. We find no support for the hypothesis that components of the Nyctotherus [Fe] hydrogenase fusion protein derive from the mitochondrial respiratory chain.
authors.affiliation: Department of Zoology, Natural History Museum, London, England.
authors.forename: D S
authors.initials: DS
authors.lastname: Horner
authors.forename: P G
authors.initials: PG
authors.lastname: Foster
authors.forename: T M
authors.initials: TM
authors.lastname: Embley
mesh_terms: D000595:Amino Acid Sequence; D000693:Anaerobiosis; D000818:Animals; D003600:Cytosol / Q000201:enzymology; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D016828:Diplomonadida / Q000201:enzymology / Q000235:genetics; D004748:Entamoeba histolytica / Q000201:enzymology / Q000235:genetics; D056890:Eukaryota / Q000201:enzymology / Q000235:genetics*; D005057:Eukaryotic Cells / Q000201:enzymology; D019143:Evolution, Molecular; D006864:Hydrogenase / Q000235:genetics*; D007506:Iron-Sulfur Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014246:Trichomonas vaginalis / Q000201:enzymology / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D016054:DNA, Protozoan; D007506:Iron-Sulfur Proteins; C118830:iron hydrogenase; D006864:Hydrogenase