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Mitocogs: Clusters of Orthologous Genes from Mitochondria and Implications for the Evolution of Eukaryotes Sivakumar Kannan, Igor B Rogozin and Eugene V Koonin*

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Mitocogs: Clusters of Orthologous Genes from Mitochondria and Implications for the Evolution of Eukaryotes Sivakumar Kannan, Igor B Rogozin and Eugene V Koonin* Kannan et al. BMC Evolutionary Biology 2014, 14:237 http://www.biomedcentral.com/1471-2148/14/237 RESEARCH ARTICLE Open Access MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes Sivakumar Kannan, Igor B Rogozin and Eugene V Koonin* Abstract Background: Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire. Results: Clusters of orthologous mitochondrial protein-coding genes (MitoCOGs) were constructed from all available mitochondrial genomes and complemented with nuclear orthologs of mitochondrial genes. With minimal exceptions, the mitochondrial gene complements of eukaryotes are subsets of the superset of 66 genes found in jakobids. Reconstruction of the evolution of mitochondrial genomes indicates that the mitochondrial gene set of the last common ancestor of the extant eukaryotes was slightly larger than that of jakobids. This superset of mitochondrial genes likely represents an intermediate stage following the loss and transfer to the nucleus of most of the endosymbiont genes early in eukaryote evolution. Subsequent evolution in different lineages involved largely parallel transfer of ancestral endosymbiont genes to the nuclear genome. The intron density in nuclear orthologs of mitochondrial genes typically is nearly the same as in the rest of the genes in the respective genomes. However, in land plants, the intron density in nuclear orthologs of mitochondrial genes is almost 1.5-fold lower than the genomic mean, suggestive of ongoing transfer of functional genes from mitochondria to the nucleus. Conclusions: The MitoCOGs are expected to become an important resource for the study of mitochondrial evolution. The nearly complete superset of mitochondrial genes in jakobids likely represents an intermediate stage in the evolution of eukaryotes after the initial, extensive loss and transfer of the endosymbiont genes. In addition, the bacterial multi-subunit RNA polymerase that is encoded in the jakobid mitochondrial genomes was replaced by a single-subunit phage-type RNA polymerase in the rest of the eukaryotes. These results are best compatible with the rooting of the eukaryotic tree between jakobids and the rest of the eukaryotes. The land plants are the only eukaryotic branch in which the gene transfer from the mitochondrial to the nuclear genome appears to be an active, ongoing process. Keywords: Mitochondria, Genome evolution, Gene loss, Gene transfer, Introns, Clusters of orthologous genes * Correspondence: [email protected] National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA © 2014 Kannan et al.; licensee BioMed Central ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Kannan et al. BMC Evolutionary Biology 2014, 14:237 Page 2 of 16 http://www.biomedcentral.com/1471-2148/14/237 Background derived mitochondria-like organelles have lost the ability The mitochondrion is a membrane-bounded organelle to generate ATP by oxidative phosphorylation with oxy- that performs multiple, pivotal roles in the eukaryotic gen as the terminal acceptor although hydrogenosomes cell. The primary function of the mitochondria is the can generate ATP by substrate phosphorylation [26]. synthesis of ATP through the oxidative electron trans- The only known function of mitosomes is their involve- port chain but mitochondria are also involved in other ment in iron-sulfur cluster assembly [27]. biological functions such as intracellular signaling in- Given the bacterial ancestry of mitochondria, one cluding induction of programmed cell death [1-3]. Al- might expect the mitochondrial proteome to be of bac- though for many years several groups of protists have terial origin. However, the mitochondrial proteome is a been considered primary amitochondriate forms, the complex mosaic of proteins of diverse origins [28,29]. current consensus is that all extant eukaryotes possess Many proteins that function in the mitochondria indeed either typical mitochondria or organelles that appear to appear to originate from bacteria although mostly not be derived mitochondria such as mitosomes or hydroge- from known alpha-proteobacteria [30,31]. In addition, nosomes [4-6]. Mitochondria (but not mitosomes or several key proteins involved in replication and tran- most hydrogenosomes) possess their own genome, albeit scription of the mitochondrial genome are of bacterio- a drastically reduced one, and a translation machinery phage origin [32,33] whereas a large number of proteins that translates the mRNAs transcribed from the mito- do not have identifiable orthologs outside the eukaryotic chondrial genes to synthesize a small but essential subset lineage [34-36]. The non-alpha-proteobacterial origins of mitochondrial proteins [7,8]. of a large fraction of mitochondrial proteins might have It is considered firmly established that the mitochondria to do with the fluidity of bacterial genomes because of in all eukaryotes are monophyletic and that the ancestor which the gene complement of the mitochondrial ances- of all extant mitochondria originated from a unique endo- tor could have been substantially different from those symbiotic event that occurred over a billion years ago of any of the extant alpha-proteobacteria [31]. Recently, [9,10]. Phylogenetic analyses unequivocally indicate that the “pre-endosymbiont” hypothesis has been proposed the endosymbiont that gave rise to the mitochondria was under which the mitochondrial proteins of non-alpha- an alpha-proteobacterium, most likely affiliated with rick- proteobacterial origin were already present and functional ettsia and/or the SAR11 group [9,11-14]. A recent gen- in an endogenously formed organelle in the eukaryotic omic survey focused on the evolution of bioenergetic host cell and were adopted by the proto-mitochondria fol- pathways has suggested that the closest extant relatives of lowing endosymbiosis [37]. the mitochondria are methylotrophic alpha-proteobacteria After endosymbiosis, most of the genes of the endo- such as Rhodobacterales [15]. The mitochondrial endo- symbiont were lost or transferred from the endosymbi- symbiosis undoubtedly was a pivotal event in eukaryogen- ont to the nuclear genome. Even the most gene-rich, esis and later in the origin of multicellular life forms. Two bacteria-like mitochondrial genomes of certain jakobids, classes of hypotheses have been proposed with regard to such as Andalucia and Reclinomonas, encompass a max- the host of the endosymbiont and the subsequent evolu- imum of 106 genes of which 72 are protein-coding tionary scenario [6]. The “archezoan” hypotheses postulate [38,39] compared to at least several hundred genes in that the host was a proto-eukaryote with already devel- the smallest alpha-proteobacterial genomes, even those oped eukaryotic features, such as the advanced endomem- of endosymbionts [40]. brane system, including the nucleus, the cytoskeleton and It has been estimated that at least 1,500 proteins con- the phagocytic capacity that enabled the engulfment of the tribute to the maintenance and functioning of mammalian alpha-proteobacterial endosymbiont [16-19]. The alterna- mitochondria [41]. The mitochondrial genome encodes tive, symbiogenetic hypotheses posit that the host was a only a miniscule fraction of these proteins (as few as 3 in prokaryote, most likely an archaeon, and the endosymbi- the apicomplexan Plasmodium falciparum and as many as otic event triggered the emergence of the hallmark 72 in the jakobid Andalucia goyodi) whereas the nuclear eukaryotic features of cellular organization including the genome encodes the rest of the proteins that are synthe- nucleus [6,20-24]. Regardless of the exact nature of the sized in the cytosol and imported into the mitochondria. host or the endosymbiont, it is clear that this unique event Given this dominance of nuclear-encoded proteins, it is has dramatically and permanently altered the course of not immediately clear why mitochondria retain their gen- eukaryotic evolution. ome. Several explanatory hypotheses have been proposed. After endosymbiosis, mitochondria followed the path (1) Proteins that are encoded in the mitochondrial genome of reductive evolution both in terms of the organelle are extremely hydrophobic which would hamper their structure and functions, and the genome. In several line- import into mitochondria. This reasoning might account ages, the mitochondria have severely degenerated to be- for some but not for all proteins that are encoded in the come hydrogenosomes or mitosomes [5,25,26]. These mitochondrial genome [42]. (2) Some mitochondria, for Kannan et al. BMC Evolutionary Biology 2014, 14:237 Page 3 of 16 http://www.biomedcentral.com/1471-2148/14/237 example those of metazoa, employ a non-standard genetic
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