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by: Ezequiel Orn


Ezequiel Orn
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K. Sathasivan

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K. Sathasivan
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This 17 page Class Notes was uploaded by Ezequiel Orn on Sunday September 6, 2015. The Class Notes belongs to BIO 311C at University of Texas at Austin taught by K. Sathasivan in Fall. Since its upload, it has received 9 views. For similar materials see /class/181723/bio-311c-university-of-texas-at-austin in Biology at University of Texas at Austin.




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Date Created: 09/06/15
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Mitochondria and the Rise ofEukaryows Authors Mark v der G1ezen Source B1osc1mce 618 5947601 2 11 Pubhshed By Amencan Insutute ofB1olog1cal Sc1ence 5 URL hip www b1oone orgdo1full1015ZSb1o 2011 618 5 umquot mu um w mun u quot1m m R1 0quot h w ofoque39s Terms of Use avalable atwww Moons orggggmgms of use in noquot 1 A Commemal xtsemci1hbmnesand msemh mm m an cnmmangrml ufnuxmmng amass 1o cmch research Mitochondria and the Rise of Eukaryotes MARK VAN DER GIEZEN There can be little doubt that mitochondria do not need much ofan introduction It is widely known that they are the powerhouses of the cell and that theyproduce all oftheATP adenosine triphosphate needed to sustain life In addition all eukaryotes organisms with a cell nucleus contain these important organellesior so it was thought Here lies an interestingparadox Although it was generally believed thatall eukaryotes did have mitochondria it was also generally believed that the serial endosymbiosis theory was correct the endosymbiosis theory required the existence of eukaryotes without mitochondria This assumption was formalized with the nowedisproven Archaoa hypothesis which stated that several groups of primitive eukaryotes were ofpremitochondrial descent Thisparadoxically defined group ofamitochondriate eukaryotes has resulted in a spate ofpublications that have significantly changed the perception of the role ofmitochondria in overall cellular metabolism and that have important ramifications for our understanding of the origin ofeukaryotic life Keywords anaerobic mitochondria anoxia evolution cell biology eukaryotes Early history Mitochondria gure 1 were rst described by the Swiss anatomist and physiologist Von Ko39lliker in 1856 when he was studying muscle tissue These sacrosomes were later termed mitochondria by Benda in 1898 who observed the organelles during spermatogenesis Mitochondrion is a combination of the Greek words mitos thread and choni dros granule At the turn of the previous century bioloi gists were intrigued by the various cellular structures that they encountered and they posited several ideas regarding the origin of these organelles One of those ideas was that cermin organelles were bacterial symbionts that had taken up residence inside eukaryotic cells For example in 1905 Mereschowsky suggested that the cell nucleus and chloroi plasts were of bacterial origin and Portier suggested the same for mitochondria in 1918 reviewed in Martin 2007 However serious opposition from the scienti c commur nity led to a nearly 507year silence about the possibility of a bacterial origin of mitochondria Scienti c interest in mitochondria continued nonetheless especially after it became possible to purify the organelles opening the door to functional studies The impormnt role of mitochondria in early scienti c research might be apparent from the famous names associated with these organelles Arguably it might be the organelle that has resulted in the most Nobel Prizes Warburg who won the Nobel Prize in 1931 realized that cellular respiration was associated with insoluble subcellur lar structures that we now know were mitochondria Krebs who won the Nobel Prize in 1953 localized the enzymes from the citric acid cycle to mitochondria The ability to purify inmct functional mitochondria greatly aided further work by Palade who won the Nobel Prize in 1974 Per haps the most amazing discovery was that ATP adenosine triphosphate production in mitochondria has nothing to do with substrateilevel phosphorylation Mitchell s ground breaking work to explain oxidative phosphorylation with his chemiosmotic hypothesis led to a Nobel Prize in 1978 Determining the composition and structures of the com plexes involved in oxidative phosphorylation in particular that of ATP synthase resulted in a Nobel Prize for Walker and Boyer in 1997 Interest in the evolutionary origin of mitochondria was reignited after the discovery that these organelles conmined their own genomes Nass and Nass 1963 This nding followed logically from earlier work that indicated that mitochondrial inheritance does not follow Mendelian rules Mitchell and Mitchell 1952 and that mitochondria synthee size their own proteins McLean et al 1958 This renewed interest in mitochondrial evolution resulted in the seminal reformulation of the endosymbiont theory by Lynn Margulis Sagan 1967 The serial endosymbiosis theory suggested that a bacterial endosymbiont esmblished itself inside a protoe eukaryote and became the mitochondrion Although the concept was considered heretical some 40 years earlier the scienti c community was now ready to consider this novel idea Schwartz and Dayhoff s 1978 phylogenetic analysis indeed suggested that mitochondrialeencoded cytochromes were of an alphaeproteobacterial nature Comparison of eukaryotic mitochondrial 16S ribosomal RNA with that of alpha and bemeproteobacteria clearly indicated the alpha proteobacterial nature of mitochondrial RNA as well Yang et al 1985 Even nucleariencoded chaperonins destined BioScience 61 5947601r ISSN 00063568 electronic ISSN 152573244r 2011 by American Institute of Biological Sciences All rights reserved Request permission to photocopy or reproduce article content at the University of California Press s Rights and Permissions Web site at wwwucpressj0urnalscom reprintinfnaspr doi10r1525bior2011r61r8r5 594 BioScience 39 August 20 Vol 6 No 8 wwwbiosciencemagorg Lysnsnme MlGrDhDdy a p parwsamel En nplasmlc muculum wan rlhusumes Figure l A tyyiml euka ryu tic cell A schematic represenmtinn nfa classic which became the mitochondrion the eyol e of mitoc dilar t g ryotes This narrative can still efoundinma e t c However a finding reported by clark and Roger i 1 Mitochondua 3 S i 9 Golgi ap aralus eukaryntir mgandles Sumr2181an Williams University nfExeter for the mitochondria were shown to provide evidence o a proteobacterial origin Gupta et al 1939 Th 7 Ch 1 merit in the contain genes with mitochondrial ancestry in th i 0 es extensively reyiewe i ya der Gieze 2009 This could perhaps be explained by saying that the Arc ewa di once ntain mit chondria but subs quentl t them an ldentlr ed mitoch ndrial proteins would be the st remaining chondriate and could therefore not e taken as eukaryotes that were related to the protoeukaryote that took ch elated to an organism similar to R PYDWZzeku Kurland and Andersson 2000 The conlusion During 1990s explain the origin of eukaryotes and their mitochondria The archaebacterial ha mitochondrial endosy io t was o bacterial ongmGrayet al 1999Earlierwi h oth sis had indicated 1 h t e CavalierrSmlth 1933 postulated miti eami o o alp arproteo chewa hyp 2 Ole id tame a mall1X and mlcmspondlav These amitochondriates would therefore have been ideal u that ultimately became the mltochondnon Molecular phylogenies had indeed n the d e s a n aryotes evolved from archaebacteria nd quent th e protoeukaryote took up an alphaeproteobacterium www bioscizmzmug 07g Archezoa hypothesis was that the laboratories that identi ed o Illed these a 6116 Tova 612119991003 etal were allsurroun e ytwomemr branes suggesting that they might be previously undetected mquot In Win Mitochondrial remnants T ere are two classes of organelles that are surrounded by ranes plastids and mitochondri e o g an these organelles which n itutes strong case that these r nelles a mitochondria related rous nam a e en given to e dwide into two grou oset at production also called metabolic type H afterMartin and that do i i ii are not type I are called minimize Hydrogenosomes The discovery of hydrogenosomes predates the Archezoa hypo hesis since ese le ere rst de ribed by t 7 h Cerkasoyoya and colleag es 197 Early studies were focused on clarifying the carbon AuguszzollVol 51 No 8 t BioScimac 595 uxes through this organelle and such work provided a clear comparative framework for further studies in the eld Simii lar to mitochondria hydrogenosomes convert pyruvate into carbon dioxide and ATP but they use different enzymes to do so Muller 1993 The evolutionary origin of hydrogenosomes was not clear and was hotly debated at the time for a historii cal overview see Muller 2007 The rst hydrogenosomes were discovered in sexually transmitted trichomonads and more recently have been found in many different eukaryotes van der Giezen 2009 It was however the smrt of molecular work that revealed the evolutionary links of these organelles The gene encoding the trichomonad hydrogenosomal ferredoxin was the rst to be sequenced and surprisingly seemed to conmin a short mitochondrial presequence that was missing from the mature protein Johnson et al 1990 Further stud ies revealed more of these presequences on hydrogenosomal proteins and not only on those from trichomonads but also on hydrogenosomal proteins from ciliates and fungi The presequences resembled mitochondrial targeting signals that are normally needed to correctly mrget and import proteins into the mitochondrial matrix Studies using heterologous hosts demonstrated the suf ciency and essentiality of these hydrogenosomal presequences to mrget hydrogenosomal and reporter proteins to mitochondria Bradley et al 1997 van der Giezen et al 1998 Thus hydrogenosomes and mitochondria were found to share the same protein import machinery The discovery of mitochondrial chaperones with clear mitochon7 drial phylogenies and mitochondrialelike mrgeting signals more or less sealed the deal with respect to the mitochondrial origin of hydrogenosomes M itosomes The second class of mitochondrial organellesithe mitosomesiwas discovered only at the end of the previous century Tovar et al 1999 Antibodies raised against the previously discovered mitochondrial Hsp60 Clark and Roger 1995 showed a discrete localization suggesting the presence of an organelle in E histolytim When the pumtive organellar mrgeting signal was removed from the E histolytica Hsp60 the protein accumulated in the cytosol a phenotypical trait that could be reversed by the addition of a genuine mitochonr drial mrgeting signal from another protein from a completely different organism Tovar et al 1999 Later using antibodies raised against mitochondrial chaperones researchers discovi ered mitosomes in the apicomplexan Cryptosporidium purvum Riordan et al 1999 and the microsporidian Trachipleistm phom hominis Williams et al 2002 In the case of the excavate Gimdia intestinalis antibodies raised against proteins involved in ironisulfur cluster synthesis were used Tovar et al 2003 because it had become clear that mitochondria play essential roles in the production of such clusters as cofactors for many enzymes Lill et al 1999 Genes encoding enzymes involved in ironisulfur cluster assembly had indeed been identi ed in Trichomomzs vaginulis and G in testinalis Tachezy et al 2001 and their phylogenetic history suggested a mitochondrial orir gin for their proteins The discovery of the involvement of the S96 BioScience 39 August 20 Vol 6 No 8 proteins in ironisulfur cluster assembly and their localization to tiny organelles surrounded by two membranes in Gimi dim convincingly demonstrated the mitochondrial nature of these organelles Tovar et al 2003 Similar studies on other mitosomeiconmining organisms con rmed these ndings All such organisms have proteins involved in ironisulfur cluster assembly that are localized to their mitosomes LaGier et al 2003 Ali et al 2004 van der Giezen et al 2004 Goldberg et al 2008 Maralikova et al 2010 Interestingly two amoei bae E histolytim and Mustigamoeba balamuthi seem to have replaced their mitochondrial ironisulfur clusteriassembly proteins with a simpler system Ali et al 2004 van der Giezen et al 2004 Gill et al 2007 In neither of these organisms do the proteins conmin targeting signals which suggests that they might not be mrgeted to the organelles although in the case of Entamoelm the discussion is ongoing Mieichi et al 2009 Maralikova et al 2010 Many mitosomal proteins conmin as do hydrogenosomal proteins presequences that resemble mitochondrial mrgeting signals suggesting the presence of similar protein import mechanisms and these have indeed been identi ed reviewed in Lithgow and Schneider 2010 Mitochondrial genomes The assumption that bacteria at the time of the mitochondrial endosymbiotic event were as complex as current bacteria can be justi ed on the basis of biogeochemical evidence Nisbet and Sleep 2001 We can therefore assume that their genomes were probably as large as those of modern bacteria Remnants of these bacterial genomes are still visible in moderniday mitochondria Human mitochondria for example conmin a small circular genome nearly 17 kilobases kb in size that encodes various mitochondrial proteins However bacterial genomes range from 160 kb to 13 megabases Koonin 2009 some DNA was lost during the transition from endosymbiont to mitochondrion Such DNA has either been lost entirely or has been transferred to the host nucleus through a process known as endosymbiotic gene transfer Timmis et al 2004 Phylogenetic analysis of genes still encoded on mitochondrial genomes has been one of the strongest pieces of evidence in support of the alphaiproteobacterial origin of mitoi chondria Gray et al 1999 However the rst hydrogenoi somes and mitosomes discovered had lost their organellar genomes completely Although this nding was perfectly aligned with ideas of why mitochondria remin genomes Allen 2003 it implied that the evolutionary relationship of hydrogenosomes and mitosomes could only indirectly be determined The recent discovery of hydrogenosomes with genomes has changed this and analyses of the organellar genomes of the cockroach intestinal ciliate Nyctotherus ovalis de Graaf et al 2011 and the human intestinal pathogen Blastocystis Pe reziBrocal and Clark 2008 clearly show the mitochondrial nature of these organelles The organellar genome from another intestinal anaerobe Protemmoms lace erme Pe reziBrocal et al 2010 which is predicted to conmin hydrogenosomes also supports this notion although the nature of this organelle has not been completely determined wwwbiosciencemagorg Better sampling When the distribution of mitosomes and hydrogenosomes is plotted on a eukaryotic phylogenetic tree it becomes clear that they are omnipresent in eukaryotes and that this distribur tion has important implications gure 2 A theor favored eages Embley et al 1995 suggests that hydrogenosomes are some sort of evolutionary stable state that occurs as a resu t of similar evolutionary pressures van der Giezen 2009 When studies in which yeast was used have provided a wealth of information about mitochondrial function however yeast 39 39 chithat o longer independent evolutionary history are identical either in t t O n H card most of the classical mitochondrial features such as oxidative phosr of hydrogenosomal hydrogenas sal eukaryotic Narl proteins Balk et One of the problems here lies in the generally poor sampling of model organisms Most founding mitochondrial biochemir cal work has been done on animal mitochondria In addition Archaeplastida an planls Green algae Red algae Chromalveolata Ciliates Dmo agellates Apicomplexa Slramenopiles Rhizaria Forammllerans Racllolarians U ml chondria can be seen in the classic book by the great electron have revealed that there 1 recent reviews have discussed the extended metabolic reperr toire discovered in the various mitochondrial forms Mentel and Martin 2008 van der Giezen 2009 Ginger et al 2010 In um mitochondrial biochemistry present across all six eukaryotic supergroups van der Giezen 2009 Ginger et al 2010 But mitochondria were aerobic The general perception is that mitochondria are rich in oxygen as a result of extensive oxidative phosphorylation Amoebozo Enlamoeba Slime molds Opisthokonta Animals Fungi Excavata ELIglenids richomonas Giardla 4 2 Figuiezr39 39 I I Untilrzrzntly 39 quot39t 139 quot 139 I kingdoms H0wmzr 11 394 the zukmyatzs Simpson and Regen 2004 The dashed mat indicates umzrtaintyabaut branching order at the base i Thepmsenrz of mi DSun e u afdatu but hydmgenesomes and mitasomes are expected WWW biascxem emag mg AugustZOll Val 61Na 8 BioScience 597 activities However the extensively folded inner memo brane is more likely to act as an oxygen scrubber and the mitochondrial matrix arguably has the lowest oxygen tension of the cell Oxygen itself is not very reactive but the free radicals that are generated by the electron transport chain will react with oxygen to produce relatively longrlived mately results in the aging of the cell It has been suggested that the role of mitochondria is to protect the cell the host of the endosymbiont from the dangers of molecular oxygen Kurland and Andersson 2000 H 2000 some 24 billion to 2 billion years ago as is evidenced by the disappearance of massrindependent fractionation of sulfur Dietrich et al 2006 However this rst oxygenation 39 n of every n an unexpected ocean chemistry Oxidatively weathr ered sulfate ended up in the oceans where it reacted with molecular hydrogen resulting in hydrogen sul de Anbar and Knoll 2002 These reducing sul dic oceans are called Can eld means Dietrich et al 2006 and would have been a shelter for anaerobic life for several billion years Martin et al 2003 If the planet s oceans had been anaerobic for several billion years Dietrich et al 2006 and had reached which would explain the widespread anaerobic biochemistry in every eukaryotic branch It now seems that even some true multicellular animals can live under continuous anoxic conditions Last year Danovaro and colleagues 2010 reported the rst metazoan gure 3 from a completely anoxic habitat Mentel and Martin 2010 Currently the tendency is to dismiss ancestral eukaryotic anaerobic biochemistry by suggesting that all of Er o g o E Q 2 2 o 2 r o o a q o a a o 2 r o o EF E o lt o scienti cally questionable when a more simple explan exists All eukaryotes may have been capable of anaerobic biochemistry from the star A different scenario Various theories have been proposed to explain the origin of eukaryotes The fundamental differences amon these theor ries were recently reviewed by O Malley 2010 In the present 598 BioSCience AugustZDll Val 61 Na 8 Figum 3 Dagmarrhanging animals Itis gznmully believed that multicellular organisms unmatcompletz their Ii 2 12d hydrogenosomes 611520431119 itromztms to Photograph Anmm39o Pusczddu Antona Iton article I will discuss how all the ndings from the last 10 to 15 years tinto our current understanding of eukaryotic evor lution The serial endosymbiosis theory relied on the existence such a primarily amitochondriate lineage could be explained by a mass extinction event but there is no evidence for this Similarly the force that forged the endosymbiosis has been suggested to be ATP or oxygen removal As has been argued elsewhere eg Martin and Muller 1998 Lane 2010 no known organism leaks ATP to the environment therefore it seems highly unlikely that the free transfer of ATP from endosymbiont to host was the curre removal as was discussed above seems unlikely because as recently as a half billion years ago many parts of the planet were still anaerobic whereas we know that eukaryotes arose WWW biascxencemag mg nearly two billion years ago In addition having an oxygen magnet inside an oxygenisensitive organism seems from an engineering point of view absurd to say the least There are serious issues relating to the origin and nature of both the host and the endosymbiont Let s rst have a look at the host Ever since Woese and colleagues 1990 described the existence of a third domain of life the Archaea not Archezoa have been put forward as the closest relatives of the eukaryotes Many singleegene trees have resolved this threeidomainiofilife tree with eukaryotes sister to the Archaea Harris et al 2003 However methods aimed at identifying the root of the universal tree of life have not been able to reveal this threeidomain relationship eg Baldauf et al 1996 These studies suggest that the host lineage of eukaryotes arose from within the Archaeaimore particularly from within the Crenarchaeota or eocytes Lake et al 1984 All recent largeiscale analyses show strong sup port for this withinitheeArchaea hypothesis Pisani et al 2007 Cox et al 2008 Kelly et al 2011 With regard to the endosymbiont earlier singleigene phylogenies suggested that an ancestral relative of the obligate intracellular parasite R prowazekii was related to the mitochondrial endosymbiont Again more recent largeiscale analyses do not demonstrate such a relationship and facultative anaerobes such as Rhodolmcter an alpha proteobacterium do seem to be more closely related to the mitochondrial endosymbiont Esser et al 2004 Atteia et al 2009 Rhodolmcter species are freeiliving and facultai tive anaerobic photosynthesizers and are less derived than Rickettsiu which are obligate parasites Therefore Rhoda buster might be more similar to the bacterial symbiont at the time of the endosymbiosis The anaerobic biochemistry of Rhodolmcter species would account for the discovered anaerobic biochemistry of hydrogenosomes and mitoi somes Combining the ideas described above would sug7 gest that a facultative anaerobe similar to the presentiday Rhodobacter became the endosymbiont inside an archaeai bacterium which resulted in a eukaryote with powerful mitochondria Interestingly just before the discovery of the rst mitosome Tovar et al 1999 a novel theory had been postulated to explain the origin of both eukaryotes and mitochondria The novelty was that this theory is not based on similarities among certain cell biological features but on the biochemical capabilities of the host and endosymbiont This distinction is important because biochemical capabilities are the consequence of the pres ence or absence of enzymes that are encoded on genomes and that can be reconstructed using genomics studies This hydrogen hypothesis states that a hydrogeniproducing eubacterium eg Rhodobucter capable of both aerobic and anaerobic biochemistry was mken up by a hydrogen dependent archaeabacterium Martin and Muller 1998 This theory therefore explains the widespread presence of enzymes required for anaerobic biochemistry among the eukaryotes these would have been present from the smrt In addition the hypothesis explains the presence of the two wwwbiosciencemagprg distinct gene classes in the eukaryotes Rivera et al 1998 and ts comformbly with more recent largeiscale analyses that suggest that eukaryotes arose from within the Archaea Pisani et al 2007 Cox et al 2008 Kelly et al 2011 Critii cism leveled against such a syntrophic model hinged on the idea that bacterial fusions have never been observed This turned out to be incorrect We know of two such casesia cyanobacterium with an internal bacterium Wujek 1979 and the double mealybug symbionts Von Dohlen et al 2001 Most important the event that led to mitochondria was the same that led to the eukaryotes Because of this single event one need not invoke the presence of primitive amitochondriate eukaryotes which have indeed never been found An interesting thermodynamic explanation of why eukaryotes could never have evolved without mitochone dria has recently appeared Lane and Martin 2010 It goes without saying that the hypothesis that mitochondria and eukaryotes share their origins in a common event is con troversial and other theories have been put forward as well see eg de Duve 2007 The significance The resurrection and elaboration of the idea that mitochondria are of bacterial origin Sagan 1967 has stood the test of time However the theory stating that a strictly aerobic bacterium related to moderniday Rickettsiu took up residence inside a primitive eukaryote has not Studies into the supposedly primitive amitochondriate lineages have clearly indicated that these lineages all have mitochondria of some sort In addition with the wealth of genomic informa tion now available and the recent appearance of bioinfori matics pipelines able to analyze such large data sets it has become apparent that perhaps alphaeproteobacteria other than Rickettsia might be more similar to the bacterium that became the mitochondrion Why would this be important Can all these obscure organelles in even more obscure protismn lineages not be assigned to the margins of scienti c research Cerminly not the largeiscale genomics and cell biological studies result ing from the Archezoa hypothesis have revealed something unsuspected thus far The evolutionary relationships among major eukaryotic groups are completely different from what was previously thought Simpson and Roger 2004 Cure rently it seems that the diversity of eukaryotic life is best described as six major supergroups gure 2 This knowL edge is important when one tries to understand overall cell biological and biochemical features which would be dif cult to grasp if one were studying only model organisms For example yeast is one such model organism from the Fungi and a multitude of animal model organisms exist eg mouse fruit y Cuenorhabditis elegans However we now know that these are relatively closely related opisthokonts and that comparative studies will not be good proxies for organisms outside the opisthokonts When it comes to major human parasites such as the malariaicausing chromalveolate Plasmodium falcipmum or the sexually transmitted excavate AugustZOIJ Vol 6 No8 39 BioScience S99 T vaginalis information gleaned from yeast or mice is of little use We cannot extrapolate cell biological and biochemical processes over such expansive evolutionary dismnces Betterisourced model organisms across all six eukaryotic supergroups will enable elucidation of core eukaryotic features and lineageispeci c accessories The core features will be important for understanding the basics of eukaryotic life whereas the accessories will allow for the development of speci c drug targets for diseaseicausing organisms for example Current nextigeneration sequencing and bioinformatics efforts exist for many underrepresented eukaryotic groups and the protist community is perhaps at the forefront of these elds In addition the presence of many eukaryotic genomes for each eukaryotic supere group might allow for more holistic approaches to reveal hitherto hidden features of the eukaryotic domain as did pangenomics for bacterial vaccine development Medini et al 2005 Acknowledgments Because of space restrictions not all relevant publications in this exciting eld could be acknowledged and I do apologize in advance to those whose work could not be cited Nick Lane and Bryony Williams are thanked for useful comments and suggestions Finally I am grateful for the support from the Wellcome Trust and the University of Exeter to conduct research into unusual mitochondria References cited Ali V Shigem Y Tokumoto U Takahashi Y Nozaki T 2004 An intestinal 39 39 39 anmn ha 14139 mlan nn e e anonr nitr 7 gen 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origin of eukaryotes Proceedings of the National Academy o Sciences 105 2035amp20361 Danovaro R Dell Anno A Pusceddu A Gambi C Heiner I Mobjerg Krisr sen R 2010 The rst metazoa living in permanently anoxic condir tions BMC Biology 8 30 C 2007 The origin of eukaryotes A reappraisal Nature Reviews Genetics 8 3957403 De Graaf RM et al2011 The organellar genome andmetabolic potential of the hydrogenrproducing mitochondrion of Nyaotherus ovalis Molecur lar Biology and Evolution doi101093molbeVmsr059 Dietrich LE Tice MM Newman DK 2006 The corevolution of life and Earth Current Biology 16 R39ErR400 Embley TM Finlay BI Dyal PL Hirt RP Wilkinson M Williams AG 1995 Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates Proceedings of the Royal Society B 262 8 7 3 Esser C et al 2004 A genome phylogeny for mitochondria among alphar proteobacteria and a predominantly eubacterial ancestry of yeastnucler ar genes Molecular Biology and Evolution 21 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