Escherichia coli K12 a cooperatively developed annotation snapshot.docx

Escherichia coli K12 a cooperatively developed annotation snapshot.docx

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EscherichiacoliK12acooperativelydevelopedannotationsnapshot

EscherichiacoliK-12acooperativelydevelopedannotationsnapshot—2005

MonicaRiley,*TakashiAbe,1MarthaB.Arnaud,2MaryK.B.Berlyn,3FrederickR.Blattner,4RoyR.Chaudhuri,5JeremyD.Glasner,4TakashiHoriuchi,6IngridM.Keseler,7TakehideKosuge,1HirotadaMori,8,9NicoleT.Perna,4GuyPlunkett,III,4KennethE.Rudd,10MargretheH.Serres,GavinH.Thomas,11NicholasR.Thomson,12DavidWishart,13andBarryL.Wanner14

JosephineBayPaulCenter,MarineBiologicalLaboratory,WoodsHole,MA02543,USA

1CenterforInformationBiologyandDNADataBankofJapan,NationalInstituteofGenetics,ResearchOrganizationofInformationandSystems,Yata1111,Mishima,Shizuoka411-8540,Japan

2DepartmentofGenetics,CandidaGenomeDatabaseStanfordUniversitySchoolofMedicine,Stanford,CA94305-5120,USA

3DepartmentofMolecular,CellularandDevelopmentalBiology,YaleUniversity,NewHaven,CT06520-8103,USA

4GenomeCenterofWisconsin,425HenryMall,UniversityofWisconsin,Madison,WI53706,USA

5DivisionofImmunityandInfection,UniversityofBirmingham,Edgbaston,BirminghamB152TT,UK

6NationalInstituteforBasicBiology,Nishigonaka38,Myodaiji,Okazaki444-8585Aichi,Japan

7SRIInternational,333RavenswoodAvenue,MenloPark,CA94025-3493,USA

8GraduateSchoolofBiologicalSciences,NaraInstituteofScienceandTechnology,Ikoma,Nara630-0101,Japan

9TheInstituteofAdvancedBiosciences,KeioUniversity,Tsuruoka,Yamagata997-0017,Japan

10DepartmentofBiochemistryandMolecularBiology,TheUniversityofMiamiMillerSchoolofMedicine,Miami,FL33140,USA

11DepartmentofBiology,UniversityofYork,POBox373,YorkYO105YW,UK

12TheWellcomeTrustSangerInstitute,GenomeCampus,Hinxton,CambridgeCB101SA,UK

13DepartmentofComputingScienceandBiologicalSciences,2-21AthabascaHallUniversityofAlberta,Edmonton,Alberta,CanadaT6G2E8

14DepartmentofBiologicalSciences,PurdueUniversity,915W.StateStreet,WestLafayette,IN47907-2054,USA

*Towhomcorrespondenceshouldbeaddressed.Tel:

+15082697388;Fax:

+15084574727;Email:

mriley@mbl.edu

CorrespondencemayalsobeaddressedtoBarryL.Wanner.Tel:

+17654948034;Fax:

+17654940876;Email:

blwanner@purdue.edu

ReceivedNovember5,2005;RevisedDecember5,2005;AcceptedDecember5,2005.

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Top 

Abstract 

INTRODUCTION 

RESULTSANDDISCUSSION 

RESULTS 

SUPPLEMENTARYDATA 

SupplementaryMaterial 

REFERENCES 

Abstract

Thegoalofthisgroupprojecthasbeentocoordinateandbringup-to-dateinformationonallgenesofEscherichiacoliK-12.Annotationofthegenomeofanorganismentailsidentificationofgenes,theboundariesofgenesintermsofprecisestartandendsites,anddescriptionofthegeneproducts.Knownandpredictedfunctionswereassignedtoeachgeneproductonthebasisofexperimentalevidenceorsequenceanalysis.Sincebothkindsofevidenceareconstantlyexpanding,noannotationiscompleteatanymomentintime.ThisisasnapshotanalysisbasedonthemostrecentgenomesequencesoftwoE.coliK-12bacteria.Anaccurateandup-to-datedescriptionofE.coliK-12genesisofparticularimportancetothescientificcommunitybecauseexperimentallydeterminedpropertiesofitsgeneproductsprovidefundamentalinformationforannotationofinnumerablegenesofotherorganisms.AvailabilityofthecompletegenomesequenceoftwoK-12strainsallowscomparisonoftheirgenotypesandmutantstatusofalleles.

Top 

Abstract 

INTRODUCTION 

RESULTSANDDISCUSSION 

RESULTS 

SUPPLEMENTARYDATA 

SupplementaryMaterial 

REFERENCES 

INTRODUCTION

EscherichiacolistrainK-12isarguablythesingleorganismaboutwhichthemostisknown.Originallyisolatedin1922,itwascatapultedtoprominencebythediscoveryofstrainK-12'sabilitytocarryoutgeneticrecombinationbyconjugation

（1）and,soonafter,bygeneralizedtransduction

（2）.ThestrainK-12hasbeenwidelydistributedtolaboratoriesacrosstheworld.Overtheensuingyearsitbecametheprimarymodelorganismforbasicbiology,moleculargeneticsandphysiologyofbacteria,andwasthefoundingworkhorseofthebiotechnologyindustry.

AnnotationofE.colihasnotonlyservedtheE.colicommunity,buthasformedabasisforextrapolationofgenefunctionstovirtuallyeveryotherprokaryotic,aswellaseukaryotic,genomethroughanalogybasedonproteinsequencesimilarities.Assuch,theaccuracyandcompletenessoftheE.coliinformationisofgreatimportancetothecommunityofbiologistsworkinginalldisciplinesandwithallorganisms.WereportheretheworkofagroupofscientistsdedicatedtofullreviewandupdateoftheannotationofE.coliK-12.

TheentiregenomesequenceofK-12strainMG1655wasfirstcompletedandannotatedbyagroupassembledbyF.R.Blattner（3）.ThegenomeofasecondK-12strain,W3110,wascompletedrecentlyunderthedirectionofTakashiHoriuchiattheNationalInstituteforBasicBiologyinJapan（4）.AtthesametimethesequenceofthegenomeofMG1655wascorrectedandupdated.MG1655waschosenforitscloserelationshipwiththeoriginalE.colistrainK-12（calledEMG2）,whereasW3110waschosenbecauseithasbeenwidelyusedasa‘wild-type’strainbymanyinvestigationsworldwidefromthe1950s.BothhadbeencuredoftheλprophageandlacktheF+fertilityfactorofancestralE.coliK-12EMG2.MG1655andW3110are1-and2-stepdescendentsofE.coliK-12W1485（F+,λ−）,respectively,whichisinturnadirectdescendentofEMG2（4,5）.

Bycomparingandre-sequencingregionsofdiscrepanciesbetweenMG1655andW3110,highlyaccurategenomeshavenowbeencreatedforbothstrains（4）.CorrectionstotheoriginalMG1655genome（3）areat243sites（totaling358nt）,acorrectionrate8yearslaterof~7in105.WorkdonebytheparticipantsofanE.coliannotationworkshopheldinNovember2003reconciledsequencedifferencesthatledtodepositofacorrectedMG1655genomesequenceentry（GenBank™U00096.2,releasedinJune2004）.SubsequentworkdoneinaMarch2005workshopintroducedadditionalchanges.Theparticipantsoftheseworkshopshaveco-authoredthismanuscript.

AlthoughbothMG1655andW3110areisolatesoftheE.coliK-12strain,theirgenomesarenotidentical.ThedifferentlengthsoftheMG1655（4639675nt）andW3110（4646332nt）genomesreflectalargernumberofinsertionsequence（IS）elementsandabsenceofadefectivephageintheW3110genome.Otherdifferencesarefoundintheoccurrenceofmutations,reflectingchangesthatpresumablyoccurredduringmaintenanceoftheculturesinseparatelaboratories.

Genomeannotation,ofnecessity,isanongoingprocess.Intheinterimfrom1997,manyscientists,notorganizedasagroup,butunitedintellectuallybytheirinterestindevelopingaunifiedvisionoftheorganism,havecontinuedtoupgrade,updateandcollatenewinformationaboutE.coliasithasemerged.Thishasresultedinanumberofpublicdatabaseswithinformationongenes,genomicsandproteinsofE.coliK-12,noneidentical,eachwithadifferentemphasis.Othermoregeneraldatabasescontaininformationrelevanttomanyorganisms,helpfulininterpretationofgenesequences.

ThegoalofthecurrentprojectwastoconsolidatetheworkofscientistswhohavebeenworkingindependentlybydevelopingourbestconsensusonthestatusandpropertiesofeachofthegenesofE.coliK-12atthepresentmoment.Thegoalwasdecidedlynottocreateanewdatabase,butinstead,topresenttothepublicacomprehensive,updatedannotationofE.coliK-12whichwouldbepresentedbothinspreadsheetandsimpleflat-fileformats.Thelattercaneasilybeparsedbycomputersandreadersalikeandthereforecanbeincorporatedintoextantdatabasesbytheirproviders.TheseareavailableasSupplementaryTable1.xls,SupplementaryTable1.txtand,toaidininterpretingthedata,SupplementaryTable1ExplanatoryNotes.LessextensiveinformationfromthenewMG1655andW3110annotationshavebeenincludedinnewGenBank™andDNADataBankofJapan（DDBJ）entries,accessionnumberU00096.3andDDBJAP009048,respectively.

Werefertothisoutcomeasa‘snapshot’toemphasizethatinformationaboutE.coligenesandtheirproductsareamovingtarget,andovertakenrapidlywithmorerecentinformation.Theauthorshavemadenoplanstodevelopthissnapshotfurther.HighlydesirablewouldbetheestablishmentofanaccessiblecommunityresourceofdataonE.coliK-12withcommunityparticipation,ongoingmaintenanceandcontinuousupdatingofallinformation.AtthismomentinterestedmembersoftheE.colicommunityareapplyingtoNIHforsupporttoestablisha‘K-12informationresource’.

Top 

Abstract 

INTRODUCTION 

RESULTSANDDISCUSSION 

RESULTS 

SUPPLEMENTARYDATA 

SupplementaryMaterial 

REFERENCES 

RESULTSANDDISCUSSION

Theworkshops

Theneedtoconsolidatetheeffortsofscientistswhohadbeenworkingindependentlywasasubjectofdiscussionataninformal‘E.coliconsortium’meetingorganizedbyBarryWanneran