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Hydrogenosomes and their highly reduced relatives, mitosomes, generally lack an organelle genome5,6,7,8, hampering clarification of their origin. Two models for the origin of hydrogenosomes are currently debated. The first posits that the ancestral mitochondrial endosymbiont gave rise to aerobically functioning mitochondria, which subsequently evolved into hydrogenosomes by the acquisition of genes encoding enzymes essential for an anaerobic metabolism9,10,11,12,13. The second hypothesis presumes that hydrogenosomes and mitochondria originated from one and the same ancestral—facultatively anaerobic—(endo)symbiont, followed by specialization to aerobic and anaerobic niches during eukaryotic evolution13,14.

To address this issue we investigated DNA in hydrogenosomes of N. ovalis, which was previously identified by immunocytochemical methods15. Intact N. ovalis hydrogenosomes isolated by cell fractionation contained DNA between 20 and 40 kilobases (kb) long. Long-range polymerase chain reaction (PCR) with this DNA with the use of specific primers for the hydrogenosomal small-subunit (SSU) ribosomal RNA15 and nad7 (obtained earlier by PCR with degenerated primers) yielded a 12-kb fragment of the organellar genome. It encodes four genes of a mitochondrial complex I (nad2, nad4L, nad5 and nad7), two genes encoding mitochondrial ribosomal proteins RPL 2 and RPL 14, and a tyrtRNA gene (Fig. 1). Nad2 and nad4L, which are generally poorly conserved among ciliates, could be identified by using multiple sequence alignments and an analysis of their membrane-spanning domains as described previously16. Phylogenetic analysis revealed clustering of these genes with their homologues from the mitochondrial genomes of aerobic ciliates (Fig. 2, and Supplementary Information). All genes exhibit a characteristic mitochondrial codon-usage and lack amino-terminal extensions that could function as a mitochondrial targeting signal (Table 1). Complementary DNAs isolated for nad5 and nad7 show that they are transcribed. Translation with a nuclear genetic code from N. ovalis, rather than the ciliate mitochondrial code, leads to numerous stop codons (not shown). Five additional open reading frames (ORFs 236, 262, 71, 161 and 199) do not show significant sequence similarity to ORFs from the mitochondrial genomes accessible in the EMBL database. Two ORFs overlap with neighbouring ORFs as in other mitochondrial genomes17.

Figure 1: A 14,027-bp fragment (mtg 1) of the hydrogenosomal genome of N. ovalis var.
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Blaberus Amsterdam. Black boxes, RNA coding genes; shaded boxes, genes with significant similarity to mitochondrial genes; white boxes, unknown ORFs (named according to the number of codons); arrows, cDNAs identified so far. The numbers indicate the nucleotide positions on the 14-kb clone (mtg 1). The longest ORF (4,179–9,728) contains a stretch with significant similarity to nad5. A potential start codon for a putative nad5 transcript is marked with an asterisk.

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Figure 2: Phylogenetic analysis of hydrogenosomal genes.
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Both the organellar 12S (SSU) rRNA gene (b) and the nuclear hsp60 (c) reveal a ciliate ancestry for the hydrogenosome of N. ovalis. The same is true for the components of a ‘mitochondrial’ complex I, the nad7 (49 kDa; organellar, a) and 51 kDa (nuclear, d) genes. The phylogenies were derived using MrBayes and neighbour joining: the topologies correspond to the maximum-likelihood (MrBayes) approach, and the values at the nodes indicate the posterior probability for the partition and its bootstrap value, respectively. Only values higher than 50% are indicated. See Supplementary Information. EB, Eubacteria.

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Table 1 Nyctotherus ovalis genes encoding mitochondrial proteins and RNAs
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Macronuclear gene-sized chromosomes encoding the 24-kDa, 51-kDa and 75-kDa subunits of mitochondrial complex I and the Fp and Ip subunits of mitochondrial complex II were cloned with a PCR-based approach. These have a nuclear codon usage, are transcribed (Table 1), encode a putative N-terminal mitochondrial targeting signal and branch with their mitochondrial homologues from aerobic ciliates in phylogenetic analyses (Fig. 2, Table 1 and Supplementary Information). They are similar to the two complex I-like Ndh51 and Ndh24 proteins discovered in Trichomonas vaginalis18,19, because a phylogenetic analysis including the mitochondrial homologues from N. ovalis and certain aerobic ciliates reveals that all these proteins belong to a cluster of mitochondrial complex I homologues (see Supplementary Information). Thus, in N. ovalis, 7 of the 14 genes encoding core proteins of mitochondrial complex I, and two of the four proteins of mitochondrial complex II, have been identified so far. They are well conserved, are transcribed, and cluster with the mitochondrial homologues of their aerobic (ciliate) relatives, indicating that the hydrogenosomes of N. ovalis have retained parts of a functional mitochondrial electron-transport chain.

Hydrogenosomes of N. ovalis have typical mitochondrial cristae and contain cardiolipin11. They are closely associated with endosymbiotic methanogens, which are biomarkers for hydrogen formation by the N. ovalis hydrogenosomes20 (Fig. 3a). The organelles stain with Mitotracker Green FM and fluoresce with rhodamine 123, indicating the presence of a membrane potential (Fig. 3). Carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) (5 µM) prevented staining with rhodamine 123, indicating the possible presence of a proton gradient. Moreover, staining of the hydrogenosomes with rhodamine 123 was also prevented after incubation of the ciliates with rotenone, piericidin, fenazaquin and 1-methyl-4-phenylpyridinium (MPP+) (classical inhibitors of mitochondrial complex I (ref. 21)), but not with cyanide (1 mM) or antimycin A (inhibitors of mitochondrial complex III and IV; Fig. 3). Similarly, treatment with cyanide and salicylhydroxamic acid (SHAM), inhibitors of mitochondrial complex IV of the respiratory chain and the plant-like alternative oxidase known from certain mitochondria3, respectively, neither killed N. ovalis nor interfered with its oxygen consumption under aerobic conditions (not shown). These observations not only indicate the absence of a functional complex III and IV and the absence of a terminal (plant-like) alternative oxidase, but also reveal the presence of a functional mitochondrial complex I as the source of the organellar proton gradient3. The oxygen consumption of N. ovalis observed under aerobic conditions is most probably a detoxification mechanism, and longer exposure to atmospheric oxygen kills the ciliates effectively.

Figure 3: Hydrogenosomes of N. ovalis exhibit complex I activity.
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a, b, Electron micrographs of a hydrogenosome of N. ovalis (a) and a mitochondrion of Euplotes sp. (b). White arrowheads mark cristae; m, endosymbiotic methanogenic archaeon15,20. c, Fluorescence picture of N. ovalis hydrogenosomes (bright dots), which were released from the cell by gentle squashing after being stained in vivo with ethidium bromide. d, Rhodamine 123 (R123) also stains the hydrogenosomes, the only organelles matching the expected size (compare a, and Supplementary Information). e, Mitotracker green FM stains the same organelles. The inserts in d and e (outside the ciliate) show the organelles seen in the box inside the ciliate. f, h, i, Incubation of living cells with inhibitors of mitochondrial complex I (MPP+ (f), piericidin (h) and rotenone (i))21 completely prevents staining of the organelles by R123. g, Incubation with cyanide (1 mM) or antimycin A (not shown) does not interfere with staining by R123. For additional information see the text and Supplementary Information. Scale bars, 1 µm (a, also applies to b); 10 µm (c–i).

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Metabolic experiments using tracer amounts of uniformly labelled (U-) 14C-glucose revealed that N. ovalis catabolizes glucose predominantly into acetate, lactate, succinate and smaller amounts of ethanol, in addition to CO2 (Table 2). The presence of oxygen did not cause significant changes in the pattern of excreted end products (not shown). Notably, incubations in the presence of [6-14C]glucose did not result in the formation of labelled CO2. Because 14C-labelled CO2 is released from [6-14C]glucose by successive decarboxylations through multiple rounds in the Krebs cycle, the absence of labelled CO2 after application of [6-14C]glucose indicates the absence of a complete Krebs cycle. The observed excretion of 14C-labelled CO2 after incubation with [U-14C]glucose could be the result of either pyruvate dehydrogenase (PDH) activity, as in typical aerobic mitochondria, or pyruvate:ferredoxin oxidoreductase (PFO) activity, as in the hydrogenosomes of T. vaginalis. A third possibility for pyruvate catabolism, pyruvate formate lyase activity22,23, can be excluded because no detectable amounts of formate were produced from [U-14C]glucose (Table 2). We failed to identify genes for PFO but succeeded in isolating three of the four PDH genes, namely the E1α, E1β and E2 subunits, which are expressed as cDNA, indicating that N. ovalis uses a mitochondrial PDH for oxidative decarboxylation. Significant amounts of 14C-labelled succinate from both [U-14C]glucose and [6-14C]glucose (Table 2) indicate that endogenously produced fumarate is used as a terminal electron acceptor, as in some anaerobic mitochondria3. Fumarate reduction in N. ovalis (to account for the production of succinate) is most probably catalysed by a membrane-bound complex II (see above; Table 1, and Supplementary Information), which is coupled to complex I through electron transport mediated by quinones3. Mass spectrometry coupled to liquid chromatography of lipid extracts from N. ovalis revealed the presence of small amounts of quinones (rhodoquinone 9 and menaquinone 8) at a concentration of about 1 pmol per mg protein (Supplementary Information). This amount is at least two orders of magnitude lower than in other eukaryotes known to possess anaerobic mitochondria producing succinate24. The low concentration of quinones in N. ovalis cells might reflect the intermediate state of their hydrogenosomes, occupying a position between mitochondria (which contain a membrane-bound electron transport chain) and previously characterized hydrogenosomes (which do not)1,3,4,5,13,18.

Table 2 Glucose metabolism of Nyctotherus ovalis
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Although an FoF1-ATP synthase has not yet been identified, the hydrogenosome of N. ovalis has retained certain basal energy-generating functions of an aerobically functioning mitochondrion3. To explore the presence of additional ‘mitochondrial’ traits in N. ovalis, we performed a reciprocal Smith–Waterman sequence comparison between about 2,000 six-frame-translated clones from our genomic DNA library of N. ovalis and the yeast25 and human26 mitochondrial proteins. We identified 53 additional nuclear genes encoding potential mitochondrial proteins in addition to components of the mitochondrial import machinery (Table 1, and Supplementary Information).

In contrast, the hydrogenase of N. ovalis does not exhibit any mitochondrial traits. This hydrogenase is rather unusual in comparison with other eukaryotic hydrogenases because it seems to be a fusion of a [Fe] hydrogenase with two accessory subunits of different evolutionary origin4,15. These subunits should allow NADH reoxidation in combination with the [Fe] hydrogenase, because they exhibit a significant sequence similarity to the hox F and hox U subunits of β-proteobacterial [Ni–Fe] hydrogenases, in contrast to similar, recently described hydrogenosomal proteins (24 and 51 kDa) of putative mitochondrial origin from T. vaginalis18,19. The ‘mitochondrial’ 24-kDa and 51-kDa genes of N. ovalis are clearly different from the above-mentioned hydrogenase modules and are likely to function in mitochondrial complex I (Fig. 3, Table 1, and Supplementary Information). Moreover, the catalytic centre of the hydrogenase (the H-cluster) clusters neither with any of the hydrogenases of Trichomonas, Piromyces and Neocallimastix studied so far, nor with any of the hydrogenase-related Nar proteins, which seem to be shared by all eukaryotes. Rather, the N. ovalis hydrogenase is more closely related to [Fe] hydrogenases from δ-proteobacteria4,15,27. These observations suggest that the hydrogenase of N. ovalis has been acquired by lateral gene transfer.

It should be realized that the hydrogenosome of N. ovalis is so far unique and not representative of all hydrogenosomes, which seem to have evolved repeatedly and independently—albeit from the same ancestral mitochondrial-type organelle. All our data identify the hydrogenosome of N. ovalis as a ciliate-type mitochondrion that produces hydrogen. The presence of respiratory-chain activity of mitochondrial complex I and II, in combination with hydrogen formation, characterizes the N. ovalis hydrogenosome as a true missing link in the evolution of mitochondria and hydrogenosomes.

Methods

Strains

Nyctotherus ovalis ciliates were isolated from the hindgut of the cockroach Blaberus sp. (strain Amsterdam), taking advantage of their unique (anodic) galvanotactic swimming behaviour28. After the ciliate's arrival at the anode, cells were picked up with a micropipette, inspected individually under a dissecting microscope at ×40 magnification, collected in an Eppendorf tube and washed three times with anaerobic electromigration buffer. Ciliates belonging to the Euplotes crassus/vannus/minuta complex were cultured in artificial sea water, feeding on bacteria growing on an immersed small piece of meat (approx. 1 g of beef steak). In addition, the ciliates were fed with Escherichia coli, which were added at weekly intervals. Ciliates were harvested by centrifugation.

Microscopy

Electron microscopy of N. ovalis and Euplotes sp. was performed as described previously11,15.

Fluorescence microscopy was performed with a Noran OZ video-rate confocal microscope as described previously29. Inhibitors were used in concentrations of 1 mM. They were dissolved in N. ovalis culture medium28. The rotenone solution contained 10% dimethyl sulphoxide, the fenazaquin solution 1% dimethyl sulphoxide.

Metabolite and quinone determinations

Micro-aerobic incubations with N. ovalis were performed in rotating (20 r.p.m.) sealed incubation flasks containing 5 ml incubation medium (containing 10,000–15,000 cells). All incubations were performed for 48 h and contained either 10 µCi [U-14C]glucose or 10 µCi [6-14C]glucose (2.07 GBq mmol-1), both from Amersham. Incubations were terminated by the addition of 300 µl 6 M HCl to lower the pH from 7.2 to 2.0. N. ovalis cells were separated from the medium by centrifugation (5 min at 500g and 4 °C); excreted end products were analysed by anion-exchange chromatography on a Dowex 1X8 column. Quinones were separated by liquid chromatography and detected with a Sciex API 300 triple quadrupole mass spectrometer (see Supplementary Information).

Isolation of organellar DNA

N. ovalis cells were washed once with isolation buffer (0.35 M sucrose, 10 mM Tris-HCl pH 7, 2 mM EDTA) and disrupted in a Dounce homogenizer. Nuclei were centrifuged at 3,000g for 5 min, and organelles were pelleted from the supernatant at 10,000g for 30 min. Genomic DNA was isolated by using standard procedures or after lysis of the cells in 8 M guanidinium chloride.

Genomic DNA library

Gene-sized chromosomes were randomly amplified by PCR with telomere-specific primers, size-fractionated in agarose gels, and cloned in pGEM-T-easy (Promega). Clones with sizes between 0.5 and 5 kb were end-sequenced and analysed manually by TBLASTX (http://www.ncbi.nlm.nih.gov/BLAST). Searches were conducted with BLASTN and FASTA.

c-DNA library

RNA was isolated with the RNeasy Plant minikit (Qiagen). cDNA was prepared with the Smart Race cDNA amplification kit (Clontech). Expressed sequence tags were amplified by PCR with the universal adapter primer provided with the kit and the various, specific internal primers.

Complete macronuclear gene-sized chromosomes

Telomere-specific primers in combination with internal gene sequences allow a straightforward recovery of the complete gene30. The specific (internal) primers were based on the DNA sequences of internal fragments of the various genes, which were recovered previously by PCR with degenerated primers for conserved parts of the various genes.

Phylogenetic analysis

Protein sequences were aligned with ClustalW and Muscle; unequivocally aligned positions were selected with Gblocks or manually. Phylogenies were inferred with maximum likelihood by using a discrete gamma-distribution model with four rate categories plus invariant positions and the Poisson amino acid similarity matrix, and neighbour joining as implemented in ClustalW, correcting for multiple substitutions with the Gonnet amino acids identity matrix, and bootstrapping with 100 samples.

ORFs with a lower size limit of 100 nucleotides were identified with ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). tRNAs were identified with tRNAscan-SE (http://www.genetics.wustl.edu/eddy/tRNAscan-SE). Potential mitochondrial import signals were detected with MITOP (http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter). Sequence searches were performed with BLASTX (http://www.ncbi.nlm.nih.gov/BLAST), BLASTN and FASTA. For references on phylogenetic analysis see Supplementary Information.