Evolution of hydrogenosomes in anaerobic ciliates

Abstract

Within ciliates (protozoa of the phylum Ciliophora), anaerobic species are widespread and typically possess organelles which produce H2 and ATP, called hydrogenosomes. Hydrogenosomes are mitochondrial homologues and are a product of evolutionary convergence, having been found in wide-ranging and diverse anaerobic eukaryotes. Ciliates seem to have evolved hydrogenosomes on multiple occasions from the mitochondria of their aerobic ancestors. The hydrogenosomes of the ciliate Nyctotherus ovalis were studied in detail previously but little is known about the hydrogenosomes from other ciliate species. In the present study seven species of ciliate, Cyclidium porcatum, Metopus contortus, Metopus es, Metopus striatus, Nyctotherus ovalis, Plagiopyla frontata and Trimyema sp. were cultured and their hydrogenosomes were investigated using genomic and transcriptomic sequencing from whole genome amplifications from single and small numbers of isolated cells. The data were then used to reconstruct putative hydrogenosome metabolic pathways. Components of these pathways are typically encoded by the ciliate nuclear genomes but Nyctotherus ovalis, Metopus contortus, Metopus es, Metopus striatus and Cyclidium porcatum have also retained mitochondrial (now hydrogenosomal) genomes which were sequenced for the first time. The most complete of these genomes were from Nyctotherus ovalis and Metopus contortus. These have both retained genes for proton-pumping subunits of the electron transport chain Complex I and ribosomal subunits needed for their synthesis. The ciliates Plagiopyla frontata and Trimyema sp. appear to have completely lost the organelle genome during the conversion of mitochondria into hydrogenosomes. The ciliate hydrogenosomes for which the most data was obtained appear to have retained some of the enzymes needed to produce energy by substrate-level phosphorylation but some species have also retained a partial electron transport chain and Cyclidium porcatum has retained nuclear encoded subunits of the mitochondrial F1F0 ATP synthase complex. Nuclear genes encoding enzymes that play a key role in H2 production, FeFe-hydrogenase, pyruvate: ferredoxin oxidoreductase and pyruvate: NADPH+ oxidoreductase, were also sequenced from the sampled ciliates and their evolutionary origins were investigated using phylogenies. These suggest that ciliate FeFe-hydrogenases are monophyletic and iii have a separate bacterial origin from FeFe-hydrogenases in other eukaryotes. No evidence was found to support an alpha-proteobacteria or mitochondrial ancestry of these enzymes as predicted by the Hydrogen Hypothesis (Martin and Müller, 1998). Each of the ciliates investigated contained methanogenic Archaea endosymbionts, which can consume the H2 produced by the hydrogenosomes. Some of these endosymbionts were identified to the species-level. The associations they have formed with their hosts appear to be stable over short time-scales but not over longer evolutionary periods, as closely related ciliates like Nyctotherus ovalis and Metopus contortus do not have closely related endosymbionts, providing no evidence for long-term co-speciation.