From the foregoing section it should be clear that there is vast diversity in the structure, function and evolutionary history of mitochondrion-derived organelles in anaerobic protists. Although much has yet to be learned about these disparate organellar systems, several evolutionary scenarios regarding their evolutionary history seem possible. The two most likely scenarios are shown in Fig. 10.5 and are discussed next.
First, it is possible that enzymes of aerobic and anaerobic energy metabolism found in mitochondrion-related organelles of present-day eukaryotes originated with the a-proteobacterial symbiont that gave rise to mitochondria (Fig. 10.5, top), which could have been a facultative aerobe (e.g. Martin and Müller 1998 and Rotte et al. 2000 provide a biochemical rationale for this view). After the initial symbiotic integration of the mitochondrial ancestor, many endosymbiont genes were transferred to the nucleus, some of which were
Fig. 10.5. Evolution of mitochondria and anaerobic organelles. Two possible scenarios for the evolution of diverse mitochondrial-derived organelles. (a) The aerobic and anaerobic metabolic pathways were present in the mitochondrial ancestor, followed by differential loss of functions in different extant eukaryote lineages. (b) The mitochondrial ancestor contained enzymes for aerobic metabolism, and the origin of anaerobes occurred via the acquisition of enzymes of anaerobic metabolism by lateral gene transfer (LGT). The order of gains and losses is unknown and the order depicted in the diagram is arbitrary
Fig. 10.5. Evolution of mitochondria and anaerobic organelles. Two possible scenarios for the evolution of diverse mitochondrial-derived organelles. (a) The aerobic and anaerobic metabolic pathways were present in the mitochondrial ancestor, followed by differential loss of functions in different extant eukaryote lineages. (b) The mitochondrial ancestor contained enzymes for aerobic metabolism, and the origin of anaerobes occurred via the acquisition of enzymes of anaerobic metabolism by lateral gene transfer (LGT). The order of gains and losses is unknown and the order depicted in the diagram is arbitrary retargeted to the endosymbiont-derived compartment. Subsequently, during the diversification of eukaryotes, predominantly aerobic lineages lost the capacity to perform anaerobic energy metabolism (i.e. they lost enzymes like PFO and hydrogenase), retaining only aerobic respiratory functions and other processes such as FeS cluster biogenesis. Other lineages became specifically adapted to anaerobic niches, and lost aerobic respiratory functions and their mitochondrial genome, but retained the endosymbiont as an ATP-producing hydrogenosome (also retaining the ISC system for FeS cluster biogenesis). Further reductions of hydrogenosomes, or direct evolutionary reduction from the common mitochondrial ancestor, could have led to the origin of mitosomes in disparate anaerobic or parasitic lineages (Fig. 10.5, top).
An alternative scenario would have the common ancestral mitochondrial endosymbiont contribute only the capacity for ATP generation via aerobic respiration as well as the other common mitochondrial processes. In this view, mitochondria in aerobic eukaryotic lineages reflect the ancestral functions that the endosymbiont was originally selected for. Subsequently, some lineages of eukaryotes acquired the capacity to perform anaerobic metabolism, perhaps by acquiring enzymes such as PFO and hydrogenase via LGT. Some anaerobes utilized these enzymes in the cytosol, and, as they become exclusively anaerobic, their mitochondria degenerated to mitosomes, carrying out only essential functions such as FeS cluster biogenesis. In other anaerobes, these proteins acquired mitochondrial-targeting signals yielding hydrogenosomes that, in most cases, lost the capacity for aerobic respiration and their genome. This scenario and other minor variants of this view are shown in Fig. 10.5, bottom.
Both of these hypotheses are consistent with the observed diversity of organelle types. For instance, the existence of transitional hydrogeno-some/mitochondrial organelles such as those of Nyctotherus would be expected under either scenario. One way to test between them is to consider the phylogenies of the proteins involved in aerobic and anaerobic energy metabolism. A a-proteobacterial origin can be inferred for quite a few proteins involved in mitochondrial aerobic energy metabolism, although not for all of them (Esser et al. 2004; J. Leigh and A.J. Roger, unpublished results). The phylogenies of PFO and hydrogenase are somewhat more confusing (Fig. 10.4). The eukaryote PFO/PNO sequences seem to form a weakly supported monophyletic group, but the branching order within this group and the affinities of the clade as a whole within the eubacteria are poorly resolved (Fig. 10.4a). The situation for Fe-hydrogenase is even worse, as eukaryotes are not monophyletic but branch in a similar part of the phylogeny. Furthermore, their relationships to each other and to bacteria are completely unresolved. The only well-resolved relationship of note is the emergence of one of the Entamoeba homologs from within the diplomonad group, suggesting its recent origin by LGT. It is possible that much better taxonomic sampling of eukaryote and prokaryote homologs may help resolve these phylogenies. On a more sceptical note, it seems equally possible that deep relationships within these trees have been erased by saturation of sequence changes, and will forever remain a mystery.
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