The Energetics of Genome Complexity2

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  21 OCTOBER 2010 | VOL 4 6 7 | NATURE| 1 ©2010 Macmillan Publishers Limited. All rights reserved HYPOTHESIS doi:10.1038/nature0!8 The energetics of genome complexity Nick Lane 1  & William Martin 2 All complex life is composed of ekar!otic ncleated# cells$ T%e ekar!otic cell arose fromprokar!otes st once in for 'illion !ears( andot%er)ise prokar!otes s%o) no tendenc! toe*ol*e +reater complexit!$ W%! not, Prokar!otic+enome si-e is constrained '! 'ioener+etics$ T%eendos!m'iosis t%at +a*e rise to mitoc%ondriarestrctred t%e distri'tion of .NA in relation to'ioener+etic mem'ranes( permittin+ aremarka'le /00(0001fold expansion in t%enm'er of +enes expressed$ T%is *ast leap in+enomic capacit! )as strictl! dependent onmitoc%ondrial po)er( and prere2isite toekar!ote complexit!3 t%e ke! inno*ation enrote to mlticelllar life$ espite 'ondless'ioc%emicalin+enit!(prokar!otes %a*enot e*ol*ed morp%olo+icalcomplexit! 'e!ond t%erdimentar! le*el seen inc!ano'acteria orplanctom!cetes in for 'illion!ears of e*oltion$ Incontrast( complexmlticelllar or+anisms %a*ee*ol*ed independentl! in atleast six di4erent ekar!otic+rops 5 $ Ekar!otic cells are+enerall! lar+er and more%i+%l! strctred t%anprokar!otic cells( )it% mc%'i++er +enomes andproteomes( 't t%e criticaldi4erence ena'lin+ t%atcomplexit! %as remainedelsi*e$ 6irtall! e*er!7ekar!otic8 trait is also fondin prokar!otes( incldin+ . ncles1like strctres / (recom'ination 9 ( linearc%romosomes : ( internalmem'ranes ; ( mltiplereplicons < ( +iant si-e = (extreme pol!ploid! > ( d!namicc!toskeleton ? ( predation 50 (parasitism 55 ( introns andexons 5/ ( intercelllarsi+nallin+ 59   2orm sensin+#(endoc!tosis1like processes 5: and e*en endos!m'ionts 5;(5< $@acteria made a start p*irtall! e*er! a*ene of ekar!otic complexit!( 'tt%en stopped s%ort$ W%!,Poplation +eneticapproac%es addressin+ t%ee*oltionar! di*ide 'et)eenprokar!otes and ekar!otesfocs on poplation si-e3 if t%e rst ekar!otes )ere fe)in nm'ers( t%e! coldtolerate man! ne) mtationsand a lar+er +enome si-e   de#artment o$ %enetics& 'volution and 'nvironment& (niversit) *ollege London& %o+er ,treet& London -1' & (. 2 nstitut $r otani  4einrich54eine5(niversit6t& 7sseldor$& (niversit6tsstrasse 1&!022 7sseldor$& %erman).  RESEARCH HYPOTHESIS 93 2 | NATURE | VOL 4 6 7 | 21 OCTOBER 2010 ©2010 Macmillan Publishers Limited. All rights reserved   t%ro+% )eakened prif!in+selection 5= $ @t )%! doprokar!otes )it% smallpoplation si-es not tend to'ecome ekar!otic, If t%econstraint )as circlarc%romosomes 5> ( )%! didn8t'acteria )it% strai+%tc%romosomes and mltiplereplicons 'ecome complex, If p%a+oc!tosis o4ered t%edecisi*e ad*anta+e 5?(/0 ( )%!didn8t ekar!otes e*ol*erepeatedl! from prokar!otesfor t%e same reasons, T%e ans)er %in+es pont%e ni2eness of ekar!oteori+ins$ All ekar!otes s%are acommon ancestor( )%ic%arose from prokar!otes stonce in for 'illion !ears$Benomic c%imaerism pointsto t%e ori+in of ekar!otes inan endos!m'iosis 'et)eenprokar!otes /51/: $ Allekar!otes eit%er possessmitoc%ondria( or once did andlater lost t%em /;(/< ( placin+ t%eori+in of mitoc%ondria and t%eekar!otic cell as plasi'l!t%e same e*ent /= $ Was t%eac2isition of mitoc%ondriat%e critical step to)ardsekar!ote +enomecomplexit!, If so( )%at salientad*anta+e did t%e! confer,It is not aero'ic respirationCman! mitoc%ondria areanaero'ic /> ( and man! free1li*in+ prokar!otes aero'ic /? $W%ereas mitoc%ondriaena'led aero'ic respiration inlar+e ekar!otes( and ox!+enis all 't essential formlticelllar life( ox!+en itself cannot explain )%! t%ere areno aero'ic mlticelllarprokar!otes more complext%an c!ano'acteria$Mitoc%ondria did not protectt%eir %ost cell a+ainst an7ox!+en cata1 strop%e8 90 $ T%ere is no e*idence for sc%a catastrop%e in t%e+eolo+ical record( or inmicro'ial p%!lo+en!Danaero'es are not a 'ranc% of micro'ial di*ersit!( eit%erekar!otic or prokar!otic$Hi+%er ox!+en le*els did notscor t%e oceans of anaero'es( 't prodcedslp%idic oceans( )%ic%persisted for more t%an a'illion !ears 95 $ Ox!+en is notreacti*e in t%e a'sence of sin+le1electron donors %enceits accmlation in t%e air#D't sin+le1electron donors are'i2itos in mitoc%ondria(makin+ t%em an!t%in+ ot%ert%an protecti*e$ Mitoc%ondriado not e*en increaserespirator! rate3 +ram for+ram( man! prokar!otesrespire faster t%anekar!otes 9/(99 $ Mitoc%ondriado compartmentali-erespiration )it%in t%e cell 9: D't prokar!otes cancompartmentali-e t%emsel*estoo( and some respire o*erlocall! in*a+inatedmem'ranes ; $ Wit% fasterrespiration and internalcompartments( 'acteria)old e*en seem to %a*e anener+etic ad*anta+e o*ermitoc%ondrion1'earin+ cells$W%! did t%e! not reali-e t%atad*anta+e( )%! did onl!mitoc%ondrion1'earin+ cellse*ol*e tre complexit!, T%e ans)er( )e posit(resides ltimatel! inmitoc%ondrial +enes$ @!ena'lin+ oxidati*ep%osp%or!lation across a )idearea of internal mem'ranes(mitoc%ondrial +enes ena'leda ro+%l!/00(0001fold rise in+enome si-e compared )it%'acteria$ W%ereas t%eener+etic cost of possessin++enes is tri*ial( t%e cost of expressin+ t%em as protein isnot and consmes most of t%ecell8s ener+! 'd+et$Mitoc%ondria increased t%enm'er of proteins t%at a cellcan e*ol*e( in%erit andexpress '! for to six ordersof ma+nitde( 't t%isre2ires mitoc%ondrial .NA$Ho) so, A fe) calclationsare in order$ Ener+! per +eneexpressed  21 OCTOBER 2010 | VOL 4 6 7 | NATURE| 3 ©2010 Macmillan Publishers Limited. All rights reserved  T%e massi*e di4erence inmean +enome si-e 'et)eenprokar!otes and ekar!otes ismost re*ealin+l! 2antied interms of ener+! a*aila'le per+ene$ @! 7ener+! per +ene8()e mean t%e cost of expressin+ t%e +ene$ T%e costof .NA replication itself acconts for st / of t%eener+! 'd+et of micro'ialcells drin+ +ro)t% /? $ Incontrast( protein s!nt%esisacconts for a remarka'leF=; of a cell8s total ener+!'d+et /? $ If t%e 'acterial+enome is increased tenfoldin si-e( t%e cost of replicatin+t%e +enome itself )old stillonl! accont for a'ot /0 of t%e cell8s existin+ ener+!'d+et alt%o+% 500 timesmore .NA )old tre'le t%ecell8s ener+! 'd+et( and5(000 times more .NA )oldraise t%e ener+! 'd+et /01fold( so cop!in+ t%e .NA of aekar!ote1si-ed +enome)old 'e a serios cost for'acteria#$ @t t%e mostimmediate and pressin+constraint of increasin++enome si-e e*en tenfold ist%at ten times as man!proteins )old need to 'eexpressed 9; $ If Escherichia coli %ad ::(000 proteins instead of :(:00( it )old need toallocate a portion of its =;protein ener+! dedication tot%e s!nt%esis of t%ese ne)proteins$ E. coli  normall!de*otes on a*era+e 0$05= of its total ener+! 'd+et toeac% protein$ If it cold %al*et%is expenditre( onl! ? G50  :  of t%e ener+! 'd+etcold 'e dedicated to eac% of t%e :0(000 ne) proteins( amere 5/0t% t%at for eac% pre1existin+ protein( %ardl! a*ia'le proposition$ And )eret%eener+! 'd+et for existin+proteins %al*ed( )%ic% +eness%old compensate *iaredced expression, A cellt%at %al*ed its ri'osomenm'er( car'on meta'olismor respirator! c%ain )old%ardl! prosper$ Plainl!( toraise +ene nm'er tenfold( E.coli  mst also increase itsener+! 'd+et '! close totenfoldD and t%erein lies t%epro'lem$ T%is ener+etic 'arriercannot 'e circm*ented '!s!nt%esi-in+ re+lator!proteins at lo) cop! nm'er(as ri'osomal nm'ers attest$An a*era+e 'acterim sc%as E. coli  %as p to 59(000ri'osomes 9< ( )%ereas a%man li*er cell %as 59million on t%e ro+%endoplasmic reticlmalone 9= C5(000 to 50(0001foldmore$ T%is lar+e di4erenceentails ener+etic costs t%atare orders of ma+nitde%i+%er in ekar!otic cells$Ekar!otes are enormosl!expanded in cell *olme(t%eir c!tosol is packed )it% amassi*e *ariet! of %i+%l!expressed strctral proteins Ji+$ 5#$ If a 'acterial cellcold add t%osands of ne)re+lator! proteins prodcedat *er! fe) copies per cell(t%e additional ener+etic costmi+%t 'e a4orda'le and anad*ance in complexit!ima+ina'le$ @t a re+lator!protein arsenal of ekar!oticdimensions is nkno)n inprokar!otes( for )it%ot  RESEARCH HYPOTHESIS 93 4 | NATURE | VOL 4 6 7 | 21 OCTOBER 2010 ©2010 Macmillan Publishers Limited. All rights reserved Figure 1 | Cell comle!i #$cell %imlici # &'( e'erg#%ul# )or *o +,& ( Transmission electron micro+rap% of a ekar!ote( a complex cell( t%e protist Euglena gracilis    scale 'ar( ; mm#$ * ( c ( Jlorescence micro+rap%s of .API1 stained +iant prokar!otes Epulopiscium fshelsoni    * #and Thiomargarita namibiensis    c # scale 'ars in * and c ( ;0 mm#$ Alt%o+% t%e prokar!otes are ;1/0 times lar+er t%an t%e ekar!ote see scale 'ars#( t%e! lack tre complexit!$ T%eir ncleoids acti*e c%romosomes3 Korescent )%ite dots in * ( )%ite arro)s in c # are ti+%tl! co1locali-ed )it% t%e plasma mem'rane( t%e site of c%emiosmotic ATP s!nt%esis in prokar!otes /?(;5 $ T%e dark area a'o*e t%e ncleoids in c is a lar+e *acole$ ( ( e (  Transmission electron micro+rap%s of mitoc%ondria( site of c%emiosmotic ATP s!nt%esis in ekar!otes /?(;5 $ All mitoc%ondria retain core +enomes of t%eir o)n( )%ic% are necessar! for t%e control of mem'rane potential across a circmscri'ed area of mem'rane( ena'lin+ a 50 : 150 ; 1fold increase in t%e total area of internali-ed 'ioener+etic mem'rane$ ( ( A sin+le folded mitoc%ondrion in t%e dinoKa+ellate Oxyrrhis marina    osmim1xed#$ e (
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