系统生物学Geochip

GeoChip:AHighThroughputGenomicsTechnologyforLinkingMicrobialCommunityStructuretoFunctionsCommunityGenomeArraysWholeGenomeMicroarraysFunctionalGeneArraysGeneExpressionPatternsProteinarrayMicrobialCommunityDiversity&MechanismsGenomicTechnologyMicrobialfunctionalGenomicsMicrobialEcology&ExtremophilesOligonucleotideArraysProducingMagneticNanoparticlesUraniumReductionCommunity&EcosystemGenomicsSomeGrandChallengesin21stCenturyBiologyLinkinggenomicstoecologyLinkinggenomicstoecologicalprocessesandfunctionsResponsestoCO2,globalwarmingandwaterprecipitationLinkingbiodiversitytoecosystemfunctionsInformationalscalingFromcellstoindividuals,populations,communities,ecosystemsandbiosphere.Spatial,temporalChallengesinMicrobialEcology•Extremelyhighdiversity:5000species/gsoil•Uncultured:99%ofthemicrobialspeciesareuncultured•Small:Difficulttosee•Limiteduseofmorphology:Itcouldnotprovideenoughinformationandresolutiontodifferentiatedifferentmicroorganisms•Molecularbiology:Greatlyadvanceourunderstandingofmicrobialdiversity•Limitationsofconventionalmolecularbiologytools:Slow,complicated,labor-intensive,insensitive,unquantitative,and/orsmall-scale.•Genomicstechnologies:RevolutioninmicrobialecologyMicroarrays:Glassslidesorothersolidsurfacecontainingthousandsofgenesarrayedbyautomatedequipment.FGAscontainprobesfromthegenesinvolvedinvariousgeochemical,ecologicalandenvironmentalprocesses.C,N,S,PcylcingsOrganiccontaminantdegradationMetalresistanceandreductionTypicalformat:50meroligonucleotidearraysUsefulforstudyingmicrobialcommunitiesFunctionalgenediversityandactivityLimitedphylogeneticdiversity.GeoChiporFunctionalGeneArrays(FGAs)Detectingfunctions:GeochemicalprocessesHigherresolution:Species-strainlevelresolutionQuantitative:noPCRisinvolvedMainadvantagesofGeoChipcomparedtootherapproachesSpecificity,sensitivity,quantitationWuetal.2001;AEM:67:5780-5790Rheeetal.2004,AEM70:4303-4317Tiquiaetal.2004.BioTechniques36,664-675Wuetal.2004;EST,38:6775-6782Heetal,2007;TheISMEJ,1:67-77HeandZhou,2008,AEM,inpressProbedesigncriteriaHeetal.2005.AEM.71:3753-3760Liebichetal.AEM,72:1688-1691Newprobedesigningsoftware:CommOligoLietal.2005.Nucl.AcidsRes.33:6114-6123Wholecommunitygenomeamplification(WCGA)Wuetal.2006.AEM:72:4931-4941.WholecommunityRNAamplification(WCRA)Gaoetal,2007,AEM:73:563-571.Review:Gentryetal.2006,MicrobialEcology,52:159-175.ZhouandThompson,2002,CurrOpionBiotech:13:204-207Zhou,2003;CurrOpion.Microbiol,6:288-294ApplicationsHeetal,2007;TheISMEJ,1:67-77,Leighetal,2007,TheISMEJ,1:163-179Yergeauetal,2007,TheISMEJ,1:134-148.Wueta.,2008,AEM,inpressZhouetal.2008.PNAS,105:7768-7773Issuesrelatedtospecificity,sensitivityandquantitationProbesDesignedforaSecondGenerationFGA(GeoChip2.0)•Nitrogencycling:5089•Carboncycling:9198•Sulfatereduction:1006•Phosphorusutilization:438•Organiccontaminantdegradation:5359•Metalresistanceandoxidation:2303•300probesfromcommunitysequencesTotal:23,408genes•23,000probesdesigned•WillbeveryusefulforcommunityandecologicalstudiesGeoChipformicrobialcommunityanalysisHe,Z,TJGentry,CWSchadt,LWu,JLiebich,SCChong,ZHuang,WWu,BGu,PJardine,CCriddle,andJ.Zhou.2007.GeoChip:acomprehensivemicroarrayforinvestigatingbiogeochemical,ecologicalandenvironmentalprocesses.TheISMEJ.1:67-77.Highlightedby:•ApressreleasebyNaturePressOffice•ReportedbymanyNewspapers•NationalEcologyObservatoryNetworks(NEON),Roadmap•NationalAcademyofSciences,MetagenomicsreportNewfeaturesforGeoChip3.0GeoChip3.0ismorecomprehensiveandmorerepresentative.Itcovers47,000genesequencesof290genefamilies.AutomaticallyretrievedsequencesbykeywordsisverifiedbyHUMMERandthenunrelatedsequencesareremoved.Asoftwarepackageforsequenceretrieval,probeandarraydesign,probeverification,arrayconstruction,arraydataanalysis,andinformationstorage.Automaticupdategreatlyfacilitatesthemanagementofsuchacomplicatedfunctionalgenearray.NewanalysispipelinewithmanystatisticalandmathematicaltoolsSummaryofGeoChip3.0probeandsequenceinformationbycategoryGenecategory#Genes#probes#uniqueprobes#groupprobes#coveredCDSCarbondeg312727116715604737Carbonfix58981827161806Energyprocession241337736449Mathane325417183434MetalResistance434917609430810458Nitrogen133561210514566892OrganicRemediation19088152244657116948gyrB111646295352251Phosphorus35991834161212Sulphur313289523761773TotalSummary2942467686191605746960CarbondegradationGene/categoryUniqueprobeGroupprobeTotalprobeTotalcoveredCDSCarbondegradationacetylglucosaminidase3275107214amyA61170231467amyX05512apu4268ara216586174ara_fungi23103350cda1161725cellobiase364177145endochitinase199168367606endoglucanase642488109exochitinase15163163exoglucanase5496383glucoamylase233558111glx1742133isopullulanase0112lip2542939mannanase2092945mnp1721922nplT4162039pectinase2722933phenol_oxidase12681207272pulA2188109231xylA187290188xylanase6067127221Subtotal87897218503192CarbonfixationandmethanemetabolismGene/categoryUniqueprobeGroupprobeTotalprobeTotalcoveredCDSCarbonfixationaclB20133353CODH136376138FTHFS68126194323pcc8249257585rubisco139146285