Eur. J. Biochem. 270, 1599–1618 (2003) Ó FEBS 2003 doi:10.1046/j.1432-1033.2003.03499.x REVIEW ARTICLE Mitochondrial connection to the origin of the eukaryotic cell Victor V. Emelyanov Gamaleya Institute of Epidemiology and Microbiology, Moscow, Russia Phylogenetic evidence is presented that primitively amito- organelle may have occurred in a safe milieu via numer- chondriate eukaryotes containing the nucleus, cytoskele- ous, often dramatic, changes involving both partners, ton, and endomembrane system may have never existed. which resulted in successful coupling of the host glycolysis Instead, the primary host for the mitochondrial progeni- and the symbiont respiration. Establishment of a potent tor may have been a chimeric prokaryote, created by energy-generating organelle made it possible, through fusion between an archaebacterium and a eubacterium, in rapid dramatic changes, to develop genuine eukaryotic which eubacterial energy metabolism (glycolysis and elements. Such sequential, or converging, global events fermentation) was retained. A Rickettsia-like intracellular could fill the gap between prokaryotes and eukaryotes symbiont, suggested to be the last common ancestor of the known as major evolutionary discontinuity. family Rickettsiaceae and mitochondria, may have pene- Keywords: endosymbiotic origin; energy metabolism; mito- trated such a host (pro-eukaryote), surrounded by a single chondrial ancestor; respiration; rickettsiae; fusion hypo- membrane, due to tightly membrane-associated phospho- thesis; eukaryogenesis; phylogenetic analysis; paralogous lipase activity, as do present-day rickettsiae. The relatively protein family. rapid evolutionary conversion of the invader into an From a genomics perspective, it is clear that both archae- fusion between an archaebacterium and a eubacterium, with bacteria (domain Archaea) and eubacteria (domain Bac- their genomes having mixed in some way [1,3,6,21–24]. The teria) contributed substantially to eukaryotic genomes [1–7]. so-called Archezoa concept (Fig. 1A) implies that the host It is also evident that eukaryotes (domain Eukarya) for the mitochondrial symbiont has been yet a eukaryote, acquired eubacterial genes from a single mitochondrial i.e. possessed at least some features distinguishing eukary- ancestor during endosymbiosis [8–14], which probably otes from prokaryotes [1,17,25–30]. The gene ratchet occurred early in eukaryotic evolution [10,11,15–17]. This hypothesis, recently proposed by Doolittle [28], suggests does not, however, necessarily mean that the mitochondrial that such an archezoon might have acquired eubacterial ancestor was the only source of bacterial genes, although the genes via endocytosis upon feeding on eubacteria. In effect, number of transferred genes could be large enough given the these firmly established facts and relevant ideas address two fundamental difference in gene content between bacteria important, yet simple, questions about mitochondrial and organelles [10,11]. According to the archaeal hypothesis origin. (a) Were the genes of eubacterial provenance first (Fig. 1A, left panel), a primitively amitochondriate eukary- derived from the mitochondrial ancestor or already present ote originated from an archaebacterium, and eubacterial in the host genome before the advent of the organelle? (b) genes were acquired from a mitochondrial symbiont [1, Did eukaryotic features such as the nucleus, endomembrane 18–20]. The alternative fusion, or chimera, theory (Fig. 1A, system, and cytoskeleton evolve before or after mitochond- right panel) posits that an amitochondriate cell emerged as a rial symbiosis? There is little doubt that mitochondria monophyletically arose from within the a subdivision of proteobacteria, with Correspondence to V. V. Emelyanov, Department of General their closest extant relatives being obligate intracellular Microbiology, Gamaleya Institute of Epidemiology and symbionts of the order Rickettsiales [9–11,13,22,31–44]. Microbiology, Gamaleya Street 18, 123098 Moscow, Russia. This relationship was established by phylogenetic analyses Fax: + 7095 1936183, Tel.: + 7095 7574644, of both small [34,37,39] and large [34] subunit rRNA, as well E-mail: [email protected] as Coband Cox1 subunitsof the respiratory chain using all Abbreviations: ER, endoplasmic reticulum; LGT, lateral gene transfer; a-proteobacterial sequences from finished and unfinished LBA, long-branch attraction; GAPDH, glyceraldehyde-3-phosphate genomes known to date (V. V. Emelyanov, unpublished dehydrogenase; TPI, triose phosphate isomerase; PFO, pyruvate– results). The four corresponding genes always reside in the ferredoxin oxidoreductase; Bya, billion years ago; ValRS, valyl-tRNA organellar genomes and are therefore appropriate tracers for synthetase; MSH, MutS-like; IscS, iron–sulfur cluster assembly the origin of the organelle itself [10,45]. Thus, a sister-group protein; AlaRS, alanyl-tRNA synthetase. relationship of eukaryotes and rickettsiae to the exclusion of Dedication: This paper is dedicated to Matti Saraste, Managing Editor free-living micro-organisms of the a subdivision revealed in of FEBS Letters, who died on 21 May 2001. phylogenetic analysis of a particular gene (protein), regard- (Received 30 October 2002, revised 20 December 2002, less of whether or not it serves an organelle, would confirm accepted 4 February 2003) the acquisition of such a gene by Eukarya from a 1600 V. V. Emelyanov (Eur. J. Biochem. 270) Ó FEBS 2003 Fig. 1. The main competing theories of euk- aryotic origin. Schematic diagrams describing the Archezoa (A) and anti-Archezoa (B) hypotheses, and their archaeal (a) and fusion (f) versions as envisioned from genomic and biochemical perspectives. Abbreviations: AR, archaeon; BA, bacterium; CH, chimeric pro- karyote; AZ, archezoon; EK, eukaryote; MAN, mitochondrial ancestor; FLA, free- living a-proteobacterium; RLE, rickettsia-like endosymbiont; N, nucleus with multiple chromosomes; E, endomembrane system; C, cytoskeleton; M, mitochondria. mitochondrial progenitor. This canonical pattern for the orthologs), reliable alignment of the sequences needed endosymbiotic origin may provide a reference framework in for phylogenetic analysis are hardly possible. This is best attempts to distinguish between the above hypotheses. exemplified by the cytoskeletal proteins actin and tubulin, It should be realized that the archaeal hypothesis is much the distant homologs of which have been suggested to be easier to reject than to confirm. Indeed, the latter may be prokaryotic FtsA and FtsZ, respectively [55,56]. Curi- accepted only if most eubacterial-like eukaryal genes turned ously, actin was recently argued to derive from MreB out to be a-proteobacterial in origin, with the origin of the [57]. On the other hand, when one considers a eukaryotic remainder being readily ascribed to lateral gene transfer protein highly homologous to bacterial counterparts and (LGT). Of importance to this issue, several cases of a show that it arose from the same lineage as the putative LGT from various eubacterial taxa to some protists mitochondrion, the possibility remains that it first have recently been reported [46–54] in good agreement with appeared in Eukarya even before the endosymbiotic the above gene transfer ratchet. It is, however, an open event, but was subsequently displaced by an endosym- question whether such acquisitions occurred early in euka- biont homolog. Furthermore, such a single ubiquitous ryotic evolution, e.g. before mitochondrial origin. protein would not be characteristic of a eukaryote. Whereas the sources of eubacterial genes may in principle One way to circumvent this problem was prompted by be established in this way on the basis of multiple Gupta [23]. As convincingly argued in this work, the phylogenetic reconstructions, how and when the characteri- emergence of endoplasmic reticulum (ER) forms of con- stically eukaryotic structures (and hence the eukaryote itself) served heat shock proteins via duplication of ancestral genes appeared is difficult to assess. At first glance, there can be no in a eukaryotic lineage may be indicative of the origin of ER appropriate molecular tracers for the origin of the nucleus, per se [23]. Here I put forward an approach based on logical endomembrane, and cytoskeleton. Nonetheless, phylo- interpretation of phylogenetic data involving such eukary- genetic methods can still be applied to proteins, the otic paralogs (multigene families). If phylogenetic analysis appearance of which might have accompanied the origin reveals branching off of the sequences from free-living of the respective eukaryotic compartments [21,23]. a-proteobacteria before a monophyletic cluster represented Unfortunately if one considers a specifically eukaryotic by rickettsial and paralogous eukaryotic sequences, i.e. a protein (which implies poor homology with bacterial canonical pattern, this would mean that paralogous Ó FEBS 2003 Mitochondria and eukaryogenesis (Eur. J. Biochem. 270) 1601 duplication (multiplication) of protein, which must have have the same function and localize to the same or similar accompanied the origin of the corresponding eukaryotic subcellular compartment. Paralogous genes emerged via structure, occurred subsequent to mitochondrial origin. duplication (multiplication) of a single gene followed by Otherwise it would be improbable that this protein was specialization of the resulting copies either recruited to multiplied to meet the requirements of the emerging different compartments/structures or adapted to serve