The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis

Abstract

It is generally accepted that hydrogenosomes (hydrogen-producing organelles) evolved from a mitochondrial ancestor. However, until recently, only indirect evidence for this hypothesis was available. Here, we present the almost complete genome of the hydrogen-producing mitochondrion of the anaerobic ciliate Nyctotherus ovalis and show that, except for the notable absence of genes encoding electron transport chain components of Complexes III, IV, and V, it has a gene content similar to the mitochondrial genomes of aerobic ciliates. Analysis of the genome of the hydrogen-producing mitochondrion, in combination with that of more than 9,000 genomic DNA and cDNA sequences, allows a preliminary reconstruction of the organellar metabolism. The sequence data indicate that N. ovalis possesses hydrogen-producing mitochondria that have a truncated, two step (Complex I and II) electron transport chain that uses fumarate as electron acceptor. In addition, components of an extensive protein network for the metabolism of amino acids, defense against oxidative stress, mitochondrial protein synthesis, mitochondrial protein import and processing, and transport of metabolites across the mitochondrial membrane were identified. Genes for MPV17 and ACN9, two hypothetical proteins linked to mitochondrial disease in humans, were also found. The inferred metabolism is remarkably similar to the organellar metabolism of the phylogenetically distant anaerobic Stramenopile Blastocystis. Notably, the Blastocystis organelle and that of the related flagellate Proteromonas lacertae also lack genes encoding components of Complexes III, IV, and V. Thus, our data show that the hydrogenosomes of N. ovalis are highly specialized hydrogen-producing mitochondria.

FIG. 1.

Organellar gene maps of Nyctotherus ovalis and Euplotes minuta. Red: Complex I genes, blue: rRNA genes, green: ribosomal proteins, yellow: Complex III and IV genes, gray: unidentified open reading frames, pink: repeat region, dark gray: atp9 gene, and white: intergenic spacers. Capital letters indicate the various tRNA genes. Arrows: direction of transcription.

FIG. 2.

ML phylogeny of the Nyctotherus ovalis hydrogen-producing mitochondrion, based on a concatenated alignment of seven mitochondrial Complex I encoded proteins (Nad1, Nad2, Nad3, Nad4, Nad4L, Nad5, and Nad6). Only bootstrap values of 50% and higher are indicated.

FIG. 3.

Tentative reconstruction of the metabolism of the hydrogen-producing mitochondria of Nyctotherus ovalis. The metabolism is based on proteins that are orthologous to mitochondrial proteins (Methods) and proteins derived from HGT that are likely to have an organellar location based on their metabolic function. It includes the results of metabolic experiments described in Boxma et al. (2005). In red: metabolism linked to NADH (green) oxidation and electron transfer as well as solute carriers. In yellow are the proteins that seem to have been acquired by HGT. In blue: glycine metabolism. In orange: intermediate metabolism. Dotted arrows stand for metabolic steps we assume to be present based on biological experiments, broken arrows for the inferred metabolism for which we did not find the gene yet. AAC: ADP/ATP carrier; ACS: acetyl-CoA synthetase, AMP-forming (EC: 6.2.1.1); ALT: alanine amino transferase; ASCT: acetate:succinate CoA transferase; Cyt c1: cytochrome c1; CβS: cystathione β synthase; EfTu: elongation factor Tu; ETF: electron transfer flavoprotein; Fe-hyd: FeFe hydrogenase; FRD/SDH: fumarate reductase/succinate dehydrogenase; GDH: glutamate dehydrogenase; GLO1: glyoxalase I; MCF Pet 8: mitochondrial carrier family; MDH: malate dehydrogenase; ME: malic enzyme; Met tRNA ft: methionyl-tRNA formyltransferase; MMM: methyl malonyl CoA mutase; MOC: malate:oxoglutarate carrier; NADH-DH: NADH :quinone oxidoreductase; PCC: propionyl CoA carboxylase; PDH: pyruvate dehydrogenase; RQ: rhodoquinone; SCS: succinyl-CoA synthetase; SHMT: serine hydroxymethyl transferase; *includes several enzymes involved in branched-chain amino acid metabolism.