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Eukaryotic Origins: How and When Was the Mitochondrion Acquired?

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Eukaryotic Origins: How and When Was the Mitochondrion Acquired? Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Eukaryotic Origins: How and When Was the Mitochondrion Acquired? Anthony M. Poole1,2,3 and Simonetta Gribaldo4 1School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand 2Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand 3Allan Wilson Centre for Molecular Ecology and Evolution, University of Canterbury, Christchurch 8140, New Zealand 4Institut Pasteur, Unite´ Biologie Mole´culaire du Gene chez les Extreˆmophiles, De´partement de Microbiologie, Paris 75724, France Correspondence: [email protected]; [email protected] Comparative genomics has revealed that the last eukaryotic common ancestor possessed the hallmark cellular architecture of modern eukaryotes. However, the remarkable success of such analyses has created a dilemma. If key eukaryotic features are ancestral to this group, then establishing the relative timing of their origins becomes difficult. In discussions of eukaryote origins, special significance has been placed on the timing of mitochondrial ac- quisition. In one view, mitochondrial acquisition was the trigger for eukaryogenesis. Others argue that development of phagocytosis was a prerequisite to acquisition. Results from comparative genomics and molecular phylogeny are often invoked to support one or the other scenario. We show here that the associations between specific cell biological models of eukaryogenesis and evolutionary genomic data are not as strong as many suppose. Disen- tangling these eliminates many of the arguments that polarize current debate. dvances across the biological sciences have this methodology, yet at the same time, it reveals Ain recent years shed considerable light on its Achilles’ heel; what emerges is a LECA that the evolution of the eukaryote cell. Reconstruc- is so completely eukaryotic in nature as to ren- tion of the most recent ancestor of all modern der it wholly unremarkable. Consequently, the eukaryotes (also called last eukaryotic common path from the initial ancestor of the eukaryotic ancestor or LECA) visible through the lens of lineage (also called first eukaryotic common comparative genomics has led to a consensus ancestor, or FECA) to the LECA is effectively view that, before the diversification of eukary- an event horizon (Je´kely 2005); although gene otes into the extant phyla we see today, the ma- duplications can be traced across this horizon jor features of the eukaryote cell had already (Makarova et al. 2005), the defining features of evolved (Koonin 2010; Poole 2010; Koumandou the eukaryote cell all evolved before the diversi- et al. 2013). This is testimony to the power of fication of modern eukaryotes. The real chal- Editors: Patrick J. Keeling and Eugene V. Koonin Additional Perspectives on The Origin and Evolution of Eukaryotes available at www.cshperspectives.org Copyright # 2014 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a015990 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a015990 1 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press A.M. Poole and S. Gribaldo lenge is, thus, to establish how and in what order reveal three recurring points of debate: the tim- these features arose in the lineage leading to the ing (i.e., whether mitochondrial acquisition was LECA. an early or a late step in eukaryogenesis), the Among hallmark eukaryote features, the nature of the host (a protoeukaryote or an ar- timing of mitochondrial acquisition has re- chaeon), and the mechanism of acquisition ceived particular attention. There is unanimous (syntrophy, bacteriovory, or phagotrophy). Tra- agreement on three aspects of mitochondrial ditionally, these different features of models for origins. First, it is beyond doubt that all known eukaryote origins have been strongly coassoci- present-day eukaryotes descend from an an- ated (e.g., an early acquisition by an archaeal cestor that already possessed a mitochondrion host via syntrophy [reviewed in Lopez-Garcia (Mu¨ller et al. 2012). The Archezoa hypothe- and Moreira 1999] or a late acquisition of mito- sis, which proposed that a few amitochondriate chondria by a protoeukaryote host via phago- lineages represent the earliest divergences be- trophy [Cavalier-Smith 2002]). In this article, fore mitochondrial acquisition (Cavalier-Smith we argue that coassociation has led to a lightning 1987), has been unequivocally falsified (Embley rod effect (Sober 1999) inwhich refuting a “bad” andMartin2006;vanderGiezen2009).Whereas idealeadstoerroneous“refutation”ofassociated eukaryotes that are genuinely ancestrally ami- good ideas. tochondriate could plausibly persist, this ap- Phylogeny and comparative genomics anal- pears on current data to be unlikely. Second, yses have resulted in enormous progress on there is full agreement that one of the partners eukaryote origins. It is now clear that all eukary- in this association was a bacterial cell (Gray otes evolved from a mitochondrion-bearing an- 2012). Finally, there is no doubt that the host cestor (Mu¨ller et al. 2012), that the main fea- cell is more closely related to modern archaea tures of modern eukaryote cell architecture were than it is to any lineage of bacteria, although its present in that ancestor (Koumandou et al. precise nature is a matter of ongoing debate 2013), and that there has been extensive trans- (Embley and Martin 2006; Poole and Penny fer of genes of mitochondrial origin into the 2007b; Gribaldo et al. 2010; Koonin 2010; Guy eukaryote nuclear genome (Esser et al. 2004). and Ettema 2011; Forterre 2013; Martijn and However, such results do not obviously fit only Ettema 2013). one scenario. We therefore examine whether Endosymbiosis is a process that has had a phylogenomic analyses are sufficiently specific profound impact on all extant eukaryotes, and as to be compatible with only one scenario, and is one of the clearest examples of an evolution- whether timing, host type, and mechanism of ary transition (Maynard Smith and Szathma´ry acquisition are obligatorily coassociated. We 1995). Mitochondrial acquisition is so funda- find that existing tests are not sufficiently spe- mental that it is ubiquitously reflected in mod- cific to distinguish between scenarios, and key ern eukaryote cell biology; modern mitochon- features of traditional models are not obligato- dria, mitosomes, and hydrogenosomes all trace rily coassociated. Further progress is possible, back to this ancestral endosymbiont (Muller but rests on being clear on what these analyses et al. 2012). Given the huge energetic gains as- can and cannot tell us. Indeed, several recent sociated with oxidative phosphorylation (Lane models are starting to pull apart these histori- 2011), it seems reasonable to expect that ac- cal coassociations and we argue that this trend quisition of mitochondria was so advantageous serves to highlight points of consensus, which that mitochondrion-bearing lineages ultimately are far greater than may be expected given the, swept to fixation, explaining why no “living at times, vigorous nature of debate. We believe fossils”ofintermediatestagespersist.Thismakes this will lead to a more nuanced view of eukary- it particularly difficult to establish when the ote origins because specific assertions on tim- mitochondrion was acquired along the path ing, nature of the host, and mechanism of ac- leading to the LECA. Given this uncertainty, quisition can, and should, be independently the numerous scenarios for eukaryote origins assessed. 2 Cite this article as Cold Spring Harb Perspect Biol 2014;6:a015990 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Eukaryogenesis and Mitochondrial Origins THE INFERENCE OF A MITOCHONDRION IN eukaryogenesis (i.e., closer to the FECA than THE LECA DOES NOT NECESSARILY IMPLY the LECA) (Fig. 1). Although many have since THAT MITOCHONDRIAL ACQUISITION fallen from favor, syntrophic models based on COINCIDES WITH EUKARYOTE ORIGINS metabolic interactions between at least one bac- terium and an archaeon (Martin and Mu¨ller If the unequivocal presence of a mitochondrion 1998; Moreira and Lopez-Garcia 1998; Lopez- in the LECA has been a fantastic accomplish- Garcia and Moreira 1999) remain popular. ment of the application of phylogenetic meth- Recent phylogenetic analyses (Rivera and Lake ods to eukaryotes, the rejection of the Archezoa 2004; Cox et al. 2008; Guy and Ettema 2011; hypothesis has caused significant upheaval, with Williams et al. 2012) showing eukaryotes emerg- not wholly justified consequences. Eschewing ing fromwithin Archaeaarecommonlyassumed the view that a fully formed eukaryote cell was as consistent with these models, and the view the host to the mitochondrial ancestor, nu- that eukaryogenesis was driven by mitochon- merous alternative models emerged or were re- drial acquisition has become associated with invigorated (Martin et al. 2001) that place mi- this phylogenetic topology (i.e., mitochondri- tochondrial acquisition as a very early event in on-first models) (Fig. 1), and have somehow led FECA LECA Intermediate (host: A/E?) Amoebozoa Opisthokonta Excavata Eukaryogenesis Archaeplastida SAR Mito-first Mito-last Archezoa (Host: A) (Host: E) (Host: E) Figure 1. Timing of mitochondrial acquisition in eukaryogenesis. The relative timing of the acquisition
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