Current trends in high throughput proteomics in cyanobacteri1Word文件下载.docx
- 文档编号:4545682
- 上传时间:2023-05-03
- 格式:DOCX
- 页数:16
- 大小:343.44KB
Current trends in high throughput proteomics in cyanobacteri1Word文件下载.docx
《Current trends in high throughput proteomics in cyanobacteri1Word文件下载.docx》由会员分享,可在线阅读,更多相关《Current trends in high throughput proteomics in cyanobacteri1Word文件下载.docx(16页珍藏版)》请在冰点文库上搜索。
Abstract
Advancementsingenomesequencingandhighthroughputproteomicsofcyanobacterialstrainsledto13publishedreports,fromasmallnumberoflaboratories.ThesesuccessfulstudiesfocusedonSynechocystis,NostocandAnabaenastrains,prochlorococcus,andhalotolerantEuhalothece.Theimplicationsofemergingquantitativeaspectsdevelopedandappliedintheselarge-scalestudiesareassessedinthewakeofadvancedcyanobacterialresearch.Furthermore,contributionsfromtraditionalandearlyhighthroughputanalysisofcyanobacterialproteomicsarecomparedandsummarised.Finally,opinionsareprovidedtolinkboththetrendsandthefuturechallenges.Thisreviewaimstopushthesynergybetweenproteomicsandcyanobacterialresearchtoimproveboththetechnicalandbiologicalsignificance.
Abbreviations:
HTT,highthroughputtechniques,MS,massspectrometryortandemmassspectrometry,MS/MS,fragmentpeptidescan,LC,liquidchromatography,2DGE,two-dimensionalgelelectrophoresis,1DGE,one-dimensionalgelelectrophoresis,MALDI,matrixassistedlaserdesorptionionisation,MALDI-TOF/TOF,MALDIinterface-tandemtime-of-flightanalyser,Qq-TOF,electrosprayquadrupoletime-of-flightanalyser,Q-IT,electrosprayquadrupoleiontrapanalyser,LC-MALDI,liquidchromatographyMALDIspottinginterface,m/z,massoverchargeratio,ICAT,isotopecodedaffinitytags,iTRAQ,isobarictagsforrelativeandabsolutequantification
Keywords:
Shotgunproteomics,Highthroughputproteomics,Cyanobacteriaproteomics,Cyanobacteria,Post-genomicstudy
1.
Introduction
Theimportanceofsystemsbiology,andtheconcurrentneedfortightanditerativeintegrationwiththequantitativeaspectsofbiologyhasreceivedwidespreadattention[1],[2],[3],[4].Thereisagrowingawarenessthatisolatedobservationsarenolongersufficienttoproperlydescribechangesinabiologicalsystem.Togetherwiththeadvancementsintraditionalbiology,molecularbiology,computationalandsystem-wideengineeringandmodelling,aspectsofsystemsbiologyhavealsofunctionedtocomotivatetheiterativedevelopmentofhighthroughputtechniques(HTT)tore-addressbiologicalquestionsataglobalscale.Ineffect,thecontinualdesiretoachievelargerscaleanalysesandtheaspirationsofsystems-widelevelunderstanding,havehelpedcreatesynergybetweentheseundertakings.Evidenttothis,thesuccessoftheHumanGenomeSequencingProjecthasproventobeoneofthemostimportantlandmarksofthisendeavour[5].
RecentyearshavewitnesseddifferentHTTstrategiesbeingexplored.Theseadvancementsweremadetotargetvariouskey–omicaspectsalongthecentraldogmaofbiology,namelythegenome,transcriptome,proteomeandmetabolome.TechniquessuchasDNAmicroarraysweredevisedtoprofilethetranscriptome,openingupanevengreaterhorizonforsystems-levelunderstanding[6].Similarly,implicationsfortheglobalstudyofproteinswerequicklyrealisedbythecreationoftheproteomicssubject.WiththerecentadvancementsinHTTbasedmassspectrometryortandemmassspectrometry(MS),thesubjecthasalsoseenasubstantialresearchpush[7],[8].Withtherecentbreakthroughsinbiotechnology,thegreaterselectionofmorehighthroughputproteomictechniqueshasalsoeffectivelydissolvedtheboundariessetbytheclassicalelectrophoresisworkflows;
yieldingevengreaterinsightsconcerningtheintegration,functionandregulationoftheproteome[9].
Theever-increasingnumbersofsuccessfulcyanobacterialgenomesequencingprojects(34genomessequenced:
KazusaCyanobase,accessed24thJanuary2009)havespearheadedthemodernisationofcyanobacterialresearch.Theseoxygenicphotoauthotrophicbacteriaareamongtheoldestandmostpopulousorganismsonourplanet[10],[11].Owingtotheirpotentialforindustrialapplicationsinareasincludingbio-fuels,agriculture,drug-discoveryandbiopharmaceuticalprecursors,cyanobacteriahavebecomeanimportantresearcharea[12],[13].
Whileearliercyanobacterialproteinresearchendeavourswerehypothesis-drivenandstudiedspecificenzymesandtheirisolatedfunctions,theincreasingavailabilityofhighthroughputtoolsthatprovidecyanobacteriabiologistswiththeabilitytoperformquasi-globalprofilingofproteinsiscertainlywelcomed[14].Cyanobacterialresearchershaverecentlybeenabletoharnessanumberofthestate-of-the-arthighthroughputqualitativeandquantitativeproteomictechniques.AtotalofthirteenhighthroughputbasedstudiesshowninTable1,extendingbackto2005whenthefirststudywasreported,arecomparedandassessed.
Thisreviewaimstosummariseanumberofrecenttrendsobservedinhighthroughputcyanobacterialproteomics,extendinganearlierreportin2003byBurjaetal.whichnecessarilyfocusedontraditionaltechniques[15].Togetherwithoveralladvancementsinthefieldofproteomics,acriticalviewintothechallengesandopportunitiespresentinthissubjectisprovided.
2.
Earlygelproteomicsappliedtocyanobacteria
Earliereffortsincyanobacterialproteomicsreliedalmostexclusivelyontheuseofsingleormultidimensionalgelelectrophoresis[16].Themethodologiescloselyfollowedtheoriginal1975studyfeaturingtheuseoftwo-dimensionalgelelectrophoresis(2DGE)[17].Theonlymajordeparturewasthetestingofnewproteinextractionprotocols[16].However,thedevelopmentoftheseextractiontechniquesisperhapsthemostimportantcontributionoftheearlyexperimentstothefoundationoftoday’shighthroughputproteomicsworkflows[14].Indeed,extractionmethodsforcyanobacteriadifferlargelyfromthoseemployedforotherbacteria,andresemblemorecloselythoseusedinplantscience(inparticular,intheiruseofchaotrophs,i.e.,ureaandthioureaanddetergentssuchasCHAPSandTriton).
Theareasofinterestofgelproteomicsincludethecombinationoftargetedandextensiveprofilingofproteomechangesasaresultofenvironmentalperturbations.Earlystudieshavealreadyemployedstrategiesthatenabletargetedanalysisviaeithercellularenrichments,2DGEwithnarrowisoelectricfocusingranges,ortheuseofantibodiestoanchorspecificproteins[18],[19],[20].Cyanobacterialproteomicsusing2DGE(2DGEingeneral)lackstheessentialthroughputrequiredforeffectivelarge-scaleanalysis,eventhoughprotocolsingel-basedproteomicshavebeenhighlydeveloped,andcontinuetoimprove.Moststudiespriorto2000reliedoneitherearlymassspectrometry-basedmatrixassistedlaserdesorptionionisation(MALDI)peptide-mass-fingerprintingorchemical-basedN-terminalsequencing[21],[22].Eventually,anumberofgel-basedstudiesutilisedthestrengthsoftandemmassspectrometryanalysistosequencetheprotein.Thepreliminary2DGEstudyofNostocpunctiformeATCC29133proteomepublishedin2004isonesuchexample[23].
Thereweregrowingintereststhentounderstandtheproteomeexpressionduringvariousimportantenvironmentalperturbations,andtheunderstandingofmembraneproteinsandtheirlocalisationwithinthecellwallsofcyanobacteria.Cyanobacterialproteomicspublicationsinthelate1990scontinuinginto2002havefocusedonsubjectsrangingfromtheaforementionedareas,totheanalysisofsaltstressonSynechocystissp.tothestudyofUVstimulations,andstudyingcellulardifferentiationsinNostocsp.PCC7120[13],[24].Forexample,earlierreportsbyNorlingetal.demonstratedtheextensiveoptimisationrequiredtoprofileandstudythylakoidandmembrane-boundproteinsandtheirsuccessfulcharacterisation[20],[25],[26].OthernotablepublishedstudiesincludetheearlyworkonNostocsp.PCC7120andN.punctiformeATCC29133,whoseproteomeswerepreliminarilyprofiled[23],[27].Therearereviewsthatdiscussoverlapsintheapplicationsofcyanobacterialgelproteomics,whicharebeyondthescopeofthisreport[15],[24].
3.
Highthroughputproteomics
Withtheemergenceofhigh-resolutionliquidchromatography(LC)andmoreadvancedtandemmassspectrometers(MS),proteomicsisbecomingincreasinglylessreliantongelstoprovidegoodproteomecoverage.Thefieldof‘gel-free’proteomicshasthustakentheroleofspearheadinghighthroughputanalysisofproteins[9].Itmostnotablyledtotheintroductionof“shotgunproteomics”,atermcoinedafteritsseeminglyrandomnatureoftheanalysis.Usingshotgunproteomics,proteomesaredirectlydigestedandanalysedinsituusingacombinationofrigorousliquidchromatographicseparationandanalysisusinghighspeedtandemmassspectrometry[28],[29],[30].Therationaleofshotgunproteomicswasfirstintroducedin2001byYatesetal.,whoappliedacombinatorialtechniqueoftwo-dimensionalLCandanelectrosprayion-trapMStoprofiletheSaccharomycescerevisiaeproteome[31].Thetechnicalimpactofthepublicationwasrevolutionary,asthemethodopenedupopportunitiestoperformfastandreliableidentificationofproteins.Thethroughputratewasalsolarge,ordersofmagnitudesfasterthangelproteomics(identificationofover1400proteinscanbeobtainedwithrelativeeasecomparedto2DGE).FollowingYatesetal.’sapplication,agreatdealofsoftwarehadtobedevelopedinordertohandletheselarge-scaleshotgundatasets[32],[33].Althoughthevariouspiecesofsoftwaregenerallyserveasimilarpurpose,theirapproachandintendedusagesdiffer.Identificationofthepeptideidentityreliesonthematchingofpeptidefragmentpeptidescan(MS/MS)fragmentstotheirtheoreticalones;
e.g.,asperformedbyMASCOTandSEQUEST[34],[35].GiventhedependencyofcontemporaryMSsearchsoftwareonthesequ
- 配套讲稿:
如PPT文件的首页显示word图标,表示该PPT已包含配套word讲稿。双击word图标可打开word文档。
- 特殊限制:
部分文档作品中含有的国旗、国徽等图片,仅作为作品整体效果示例展示,禁止商用。设计者仅对作品中独创性部分享有著作权。
- 关 键 词:
- Current trends in high throughput proteomics cyanobacteri1
链接地址:https://www.bingdoc.com/p-4545682.html