Evolutionary Systems Biology PDF
Preview Evolutionary Systems Biology
Advances in Experimental Medicine and Biology Volume751 EditorialBoard: IRUNR.COHEN,TheWeizmannInstituteofScience ABELLAJTHA,N.S.KlineInstituteforPsychiatricResearch JOHND.LAMBRIS,UniversityofPennsylvania RODOLFOPAOLETTI,UniversityofMilan Forfurthervolumes: www.springer.com/series/5584 Orkun S. Soyer Editor Evolutionary Systems Biology 123 Editor OrkunS.Soyer UniversityofExeter Exeter,Devon,UK ISSN0065-2598 ISBN978-1-4614-3566-2 ISBN978-1-4614-3567-9(eBook) DOI10.1007/978-1-4614-3567-9 SpringerNewYorkHeidelbergDordrechtLondon LibraryofCongressControlNumber:2012940413 ©SpringerScience+BusinessMedia,LLC2012 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerptsinconnection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. 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Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface EvolutionarySystemsBiologyisanemergingfieldandascientificsynthesisinthe making.Thereiscurrentlynosingledefinitionthatcapturesallthefacetsofthisfast- developingfield (as discussed below, there may neverbe one).There is, however, one binding aim at the core of this synthesis to understand better the genotype– phenotypemappingatthecellularlevelanditsevolution. Theabstractnotionsofgenotypeandphenotypewerefirstproposedbygeneticist WilhelmJohannsentodescribebroadlythelow-levelmechanismsandtheirhigher level manifestations in biological systems. These abstract notions became highly usefultostudytheevolutionaryprocessatdifferentbiologicallevels.Forexample, in the context of macromoleculessuch as RNA, primary sequence and secondary structurecan be taken as the genotypeand phenotype,while in a cellular context, one can define all the genes and their interactions in a given cell as the genotype and physiological behavior of the cell as the phenotype. Construction of such biologically meaningful genotype–phenotypedefinitions immediately leads to the natural formulation of several challenging questions: which phenotype a given genotype leads to and vice versa? What are the key features of the genotype– phenotype mapping, is it, for example, a one-to-one mapping or one-to-many? Which evolutionaryprocesses have shaped the genotype–phenotypemapping and how?Howdoesevolutionsteerinthegenotype–phenotypemap? Theanswerstothesequestionsholdthekeytomanymorespecificquestionsin the context of particular biological systems both at the cellular and higher levels. For example, a full understanding of the genotype–phenotype map in metabolic networkswouldallowustopredictwhichenvironmentsacellcansurvivein,which newenvironmentsitcanadaptto,andwhichperturbationswouldalteritsmetabolic state(i.e.,howrobustitistoperturbations).Similarly,understandinghowevolution, underspecificenvironmentalconditions,shapesthegenotype–phenotypemapmight allowustoinfergeneticstructuresandphysiologicalcapabilitiesinmicrobeswith differentlifestyles.Thus,adetailedunderstandingofthegenotype–phenotypemap andhowevolutionsteersinitandshapesitatthesametimeisdirectlylinkedtoour abilitytounderstandandmanipulatebiologicalsystems. v vi Preface Evolutionary Systems Biology, with its focus on better understanding the genotype–phenotype map, is thus bound to be an overarching field linking to several existing fields including systems biology, population and quantitative ge- netics,systemsmedicine,andsyntheticbiology.ResearchinEvolutionarySystems Biology either uses techniques, concepts, and data generated in these fields, or makessignificantcontributionstothembyprovidingconceptualandsystem-specific insights.ThisisthereasonEvolutionarySystemsBiologyhasmanyfacets,employs diverse research techniques, integrates different data sets, and eludes, so far, a compact self-description. The last feature might remain so, even when the field matures,asitmightwellbethatacompleteunderstandingofgenotype–phenotype mapsrequiresanumbrellafieldsuchasEvolutionarySystemsBiology. Theopeningchapterofthisbookaimstodefinethemanyfacetsofthisumbrella fromphilosophicalandhistoricalperspectives.Theinsightfultreatmentthereinalso identifies the centrality of the genotype–phenotypemap in Evolutionary Systems Biology.A significant part of the currentresearch in the field, coveredin the first partof thebook,isaimedat understandingthe shapeof these maps.Chapters2–7 presentseveraldifferentapproachesforachievingthisgoalandtheirfindingsinthe context of different genotype–phenotype maps. While a full description of these maps might be difficult to achieve, especially due to high dimensionality of the genotypic spaces considered, it might be possible to identify unique genotypic features that underlie specific phenotypes. Deciphering such potential features (which one might call “design principles”) is discussed in Chaps.8 and 9. As withanybiologicalproperty,such featuresandtheoverallshapeofthe genotype– phenotypemapsaretheresultofevolutionitself.Thus,asignificantresearcheffortis devotedtounderstandinghowcombinationsofevolutionaryprocesses(adaptiveor neutral),environmentalconditions(fluctuatingenvironments,speciesinteractions), and biophysical constraints/realities (e.g., noise, multilevel nature of biological systems)shapethegenotypesandgenotype–phenotypemaps.Thesecondpartofthe book,comprisingChaps.10–16,givesa detailedsummaryofthefindingsofthese effortstodate.Asillustratedinthesetwoparts,EvolutionarySystemsBiologyasa fieldalreadypossessesastrongintegrativenature,makinguseofdiverseapproaches including mechanistic models, experimental measurements at pathway and cell- scale, comparative analysis of genomic data, in silico evolution, experimental evolution,reverseengineering,andsystemdynamicsanalyses.Chapters17and18 indicatethatcombiningsomeoftheseapproacheswithquantitativeandpopulation geneticsmightpresentahighlysignificantanduniquefacetofEvolutionarySystems Biology. It is expected that this combination would allow novel findings that would not be possible by employing population genetics and systems biology in isolation. The combination of understanding the key features of genotype– phenotypemaps, and the evolutionaryforcesresulting in these, is already making significantcontributionstoourunderstandingofbiologicalsystemsandourability tomanipulatethem.Thesecontributionsareexemplifiedinthecontextofsynthetic biologyinChap.19andintheinsightfuldiscussionofrobustnessinChap.20. Thiscollectionofchaptersrepresentsthefirstsystematicattempttodemonstrate all the different facets of the emerging field of Evolutionary Systems Biology. Preface vii Itbringstogetherthemanyaspectsofthefieldanddemonstratesitscurrentbreadth and wealth. It is possible that some readers might find that certain areas are not represented as much as they should have been or that are all together omitted. I hope that such potential shortcomings are minimal and can be forgiven by the considerationthattheprimarypurposeofthisbookistoexciteandinformthereader abouttheemergingfieldofEvolutionarySystemsBiologyandfacilitateitsfurther development.Letushopethatmanysuchvolumeswillfollowthisoneasthefield matures. Evolutionary Systems Biology increasingly takes shape as a key research direction in our quest towards deciphering broad biological principles. For any researcher who shares this aim, this book will provide a highly interesting and, hopefully,thought-provokingread. Providingthe reader with an understandingof the motivationbehindEvolutionarySystems Biology,its key findingsto date, and thewiderangeofapproachesanddatasetsitdrawson,thisbookwouldalsoserve asabasisforagraduatelevelcourseorundergraduatereadingclub. Iwouldliketogivemysincerethankstoallcontributingauthorsfortheirtimely andhardworkinputtingthisvolumetogetherandtoSpringerandtheeditorialteam ledbyMelanieWilichinskyTuckerfortheircommitmentinmakingitareality. Exeter,Devon OrkunS.Soyer Contents 1 Evolutionary Systems Biology: Historical and Philosophical Perspectives on an Emerging Synthesis..................................................................... 1 MaureenA.O’Malley 2 MetabolicNetworksandTheirEvolution ............................... 29 AndreasWagner 3 OrganizationPrinciplesinGeneticInteractionNetworks............. 53 ChristopherJacobsandDanielSegre` 4 EvolutionofRegulatoryNetworks:NematodeVulva InductionasanExampleofDevelopmentalSystemsDrift ............ 79 RalfJ.Sommer 5 Life’sAttractors ............................................................ 93 JohannesJaegerandAntonCrombach 6 EvolutionaryCharacteristicsofBacterial Two-ComponentSystems.................................................. 121 XiaSheng,MaximeHuvet,JohnW.Pinney, andMichaelP.H.Stumpf 7 ComparativeInteractionNetworks:BridgingGenotype toPhenotype................................................................. 139 PedroBeltrao,ColmRyan,andNevanJ.Krogan 8 Evolution In Silico: From Network Structure toBifurcationTheory...................................................... 157 PaulFranc¸ois 9 OntheSearchforDesignPrinciplesinBiologicalSystems............ 183 JuanF.Poyatos ix x Contents 10 TowardaTheoryofMultilevelEvolution:Long-Term Information Integration Shapes the Mutational LandscapeandEnhancesEvolvability................................... 195 PaulienHogeweg 11 Evolutionary Principles Underlying Structure andResponseDynamicsofCellularNetworks.......................... 225 ArnoSteinacherandOrkunS.Soyer 12 Phenotypic Plasticityand Robustness: Evolutionary StabilityTheory, Gene ExpressionDynamicsModel, andLaboratoryExperiments ............................................. 249 KunihikoKaneko 13 GeneticRedundanciesandTheirEvolutionaryMaintenance......... 279 JianzhiZhang 14 EvolutionofResourceandEnergyManagement inBiologicallyRealisticGeneRegulatoryNetworkModels ........... 301 DovJ.StekelandDafydJ.Jenkins 15 ReverseEcology:FromSystemstoEnvironmentsandBack.......... 329 RoieLevyandElhananBorenstein 16 Bacteria–VirusCoevolution............................................... 347 AngusBucklingandMichaelBrockhurst 17 The Genotype–PhenotypeMaps of Systems Biology andQuantitativeGenetics:DistinctandComplementary............. 371 ChristianR.LandryandScottA.Rifkin 18 HowEvolutionarySystemsBiologyWillHelpUnderstand AdaptiveLandscapesandDistributionsofMutationalEffects........ 399 LaurenceLoewe 19 BuildingSyntheticSystemstoLearnNature’sDesignPrinciples..... 411 EricA.Davidson,OliverP.F.Windram,andTravisS.Bayer 20 TheRobustnessContinuum............................................... 431 SashaF.LevyandMarkL.Siegal Index............................................................................... 453
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