RNA Turnover in Bacteria, Archaea and Organelles PDF
Preview RNA Turnover in Bacteria, Archaea and Organelles
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON MELVIN I. SIMON AND Division of Biology California Institute of Technology Pasadena, California, USA Founding Editors SIDNEY P. COLOWICK NATHAN O. KAPLAN AND AcademicPressisanimprintofElsevier 525BStreet,Suite1900,SanDiego,California92101-4495,USA 84Theobald’sRoad,LondonWC1X8RR,UK Copyright#2008,ElsevierInc.AllRightsReserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronic ormechanical,includingphotocopy,recording,oranyinformationstorageandretrievalsystem, withoutpermissioninwritingfromthePublisher. Theappearanceofthecodeatthebottomofthefirstpageofachapterinthisbookindicatesthe Publisher’sconsentthatcopiesofthechaptermaybemadeforpersonalorinternaluseofspecific clients.Thisconsentisgivenonthecondition,however,thatthecopierpaythestatedpercopyfee throughtheCopyrightClearanceCenter,Inc.(www.copyright.com),forcopyingbeyondthat permittedbySections107or108oftheU.S.CopyrightLaw.Thisconsentdoesnotextendtoother kindsofcopying,suchascopyingforgeneraldistribution,foradvertisingorpromotionalpurposes, forcreatingnewcollectiveworks,orforresale.Copyfeesforpre-2008chaptersareasshownonthe titlepages.Ifnofeecodeappearsonthetitlepage,thecopyfeeisthesameasforcurrentchapters. 0076-6879/2008$35.00 PermissionsmaybesoughtdirectlyfromElsevier’sScience&TechnologyRightsDepartmentin Oxford,UK:phone:(+44)1865843830,fax:(+44)1865853333,E-mail:permissions@elsevier. com.Youmayalsocompleteyourrequeston-lineviatheElsevierhomepage(http://elsevier.com), by selecting ‘‘Support & Contact’’ then ‘‘Copyright and Permission’’ and then “Obtaining Permissions.” ForinformationonallElsevierAcademicPresspublications visitourWebsiteatelsevierdirect.com ISBN-13: 978-0-12-374377-0 PRINTEDINTHEUNITEDSTATESOFAMERICA 08 09 10 11 9 8 7 6 5 4 3 2 1 C ONTRIBUTORS HirojiAiba Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa,Nagoya,Japan SorayaA¨ıt-Bara Laboratoire de Microbiologie et Ge´ne´tique Mole´culaire, UMR 5100, Centre National de la Recherche Scientifique et Universite´ Paul Sabatier, Toulouse, France Mo´nicaAmblar Unidad de Investigacio´n Biome´dica, Instituto de Salud Carlos III (Campus de Majadahonda),Madrid,Spain Cec´ıliaMariaArraiano Instituto de Tecnologia Qu´ımica e Biolo´gica, Universidade Nova de Lisboa, Oeiras,Portugal AnaBarbas Instituto de Tecnologia Qu´ımica e Biolo´gica, Universidade Nova de Lisboa, Oeiras,Portugal DavidH.Bechhofer Mount Sinai School of Medicine of New York University, Department of PharmacologyandSystemsTherapeutics,NewYork,USA JoelG.Belasco KimmelCenterforBiologyandMedicineattheSkirballInstituteandDepartment ofMicrobiology,NewYorkUniversitySchoolofMedicine,NewYork,USA LionelBe´nard CNRSUPR9073(affiliatedwithUniversite´deParis7;DenisDiderot),Institutde BiologiePhysico-Chimique,Paris,France JonathanA.Bernstein DepartmentofPediatrics,StanfordUniversity,Stanford,CA94305,USA SandrineBoisset INSERMU851,CentreNationaldeRe´fe´rencedesStaphylocoques,Universite´de LyonI,Lyon,France xv xvi Contributors DouglasJ.Briant DepartmentofBiochemistryandMolecularBiology,UniversityofBritishColum- bia,Vancouver,BritishColumbia,Canada AgamemnonJ.Carpousis Laboratoire de Microbiologie et Ge´ne´tique Mole´culaire (LMGM), Centre National de la Recherche Scientifique (CNRS) and Universite´ Paul Sabatier, Toulouse,France HelenaCelesnik KimmelCenterforBiologyandMedicineattheSkirballInstituteandDepartment ofMicrobiology,NewYorkUniversitySchoolofMedicine,NewYork,USA Cle´mentChevalier ArchitectureetRe´activite´del’ARN,CNRS,Universite´deStrasbourg,Institutde BiologieMole´culaireetCellulaire,Strasbourg,France MikkelChristensen-Dalsgaard Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle,Newcastle,UnitedKingdom Ciara´nCondon CNRSUPR9073(affiliatedwithUniversite´deParis7;DenisDiderot),Institutde BiologiePhysico-Chimique,Paris,France ElenaConti Max-PlanckInstituteofBiochemistry,Martinsried,Germany GlenA.Coburn DepartmentofBiochemistryandMolecularBiology,UniversityofBritishColum- bia,Vancouver,BritishColumbia,Canada AtilioDeana KimmelCenterforBiologyandMedicineattheSkirballInstituteandDepartment ofMicrobiology,NewYorkUniversitySchoolofMedicine,NewYork,USA HiliGiladi DepartmentofGenetics,UniversityofGeorgia,Athens,Georgia,USA GianniDeho` Dipartimento di Scienze biomolecolari e Biotecnologie, Universita` degli Studi di Milano,Milan,Italy GintarasDeikus Mount Sinai School of Medicine of New York University, Department of PharmacologyandSystemsTherapeutics,NewYork,USA MurrayP.Deutscher DepartmentofBiochemistryandMolecularBiology,UniversityofMiamiSchool ofMedicine,Miami,Florida,USA Contributors xvii Andre´ Dietrich Institut de Biologie Mole´culaire des Plantes, Centre National de la Recherche Scientifique,Unite´ PropredeRecherche2357,Universite´ deStrasbourg,France MarcDreyfus E´cole Normale Supe´rieure, Laboratoire de Ge´ne´tique Mole´culaire, Paris, France, andCentreNationaldelaRechercheScientifique(CNRS),Paris,France DanielKarzaiDulebohn Department of Biochemistry and Cell Biologyand Center for Infectious Diseases ofStonyBrookUniversity,StonyBrook,NewYork,USA ElenaEvguenieva-Hackenberg Institutfu¨rMikrobiologieundMolekularbiologie,UniversityofGiessen,Giessen, Germany PierreFechter Architecture et Re´activite´ de l’ARN, Universite´ de Strasbourg, CNRS, IBMC, Strasbourg,France DominiqueGagliardi Institut de Biologie Mole´culaire des Plantes, Centre National de la Recherche Scientifique,Unite´ PropredeRecherche2357,Universite´ deStrasbourg,France ThomasGeissmann Architecture et Re´activite´ de l’ARN, Universite´ de Strasbourg, CNRS, IBMC, Strasbourg,France ZhiyunGe Department of Biochemistry and Cell Biologyand Center for Infectious Diseases ofStonyBrookUniversity,StonyBrook,NewYork,USA KennGerdes Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle,Newcastle,UnitedKingdom PawelGolik DepartmentofGeneticsandBiotechnology,WarsawUniversity,Warsaw,Poland, andInstituteofBiochemistryandBiophysicsPAS,Warsaw,Poland ElianeHajnsdorf CNRS UPR9073; Institut de Biologie Physico-Chimique; Universite´ Paris Diderot,Paris7,Paris,France JanetS.Hankins Department of Biochemistry and Molecular Biology, University of British Columbia,Vancouver,BritishColumbia,Canada xviii Contributors NarumiHino-Shigi Department of Chemistry and Biotechnology, Graduate School of Engineering, UniversityofTokyo,Tokyo,Japan SarahHolec Institut de Biologie Mole´culaire des Plantes, Centre National de la Recherche Scientifique,Unite´ PropredeRecherche2357,Universite´ deStrasbourg,France EricHuntzinger MaxPlanckInstituteforDevelopmentalBiology,Tu¨bingen,Germany RobertJedrzejczak Synchrotron Radiation Research Section, MCL, National Cancer Institute, ArgonneNationalPuchtaLaboratory,Argonne,Illinois,USA StefanieS.Jourdan AstburyCentreforStructuralMolecularBiology,UniversityofLeeds,Leeds,LS2 9JT,UnitedKingdom A.WaliKarzai Department of Biochemistry and Cell Biologyand Center for Infectious Diseases ofStonyBrookUniversity,StonyBrook,NewYork,USA VanessaKhemici Laboratoire de Microbiologie et Ge´ne´tique Mole´culaire (LMGM), Centre National de la Recherche Scientifique (CNRS) and Universite´ Paul Sabatier, Toulouse,France LouiseKime AstburyCentreforStructuralMolecularBiology,UniversityofLeeds,Leeds,LS2 9JT,UnitedKingdom GabrieleKlug Institutfu¨rMikrobiologieundMolekularbiologie,UniversityofGiessen,Giessen, Germany SidneyR.Kushner DepartmentofGenetics,UniversityofGeorgia,Athens,Georgia,USA HeikeLange Institut de Biologie Mole´culaire des Plantes, Centre National de la Recherche Scientifique,Unite´ PropredeRecherche2357,Universite´ deStrasbourg,France Pei-HsunLin InstituteofMolecularBiology,AcademiaSinica,Taipei115,Taiwan SueLin-Chao InstituteofMolecularBiology,AcademiaSinica,Taipei115,Taiwan Contributors xix ZhongweiLi Department of Biomedical Science, Florida Atlantic University, Boca Raton, Florida,USA EsbenLorentzen Birkbeck College London, Institute of Structural Molecular Biology, London, UnitedKingdom GeorgeA.Mackie DepartmentofBiochemistryandMolecularBiology,UniversityofBritishColum- bia,Vancouver,BritishColumbia,Canada KimikaMaki Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa,Nagoya,Japan MichalMalecki DepartmentofGeneticsandBiotechnology,WarsawUniversity,Warsaw,Poland ValerieF.Maples DepartmentofGenetics,UniversityofGeorgia,Athens,Georgia,USA NathalieMathy CNRS,InstitutdeBiologiePhysico-Chimique,Paris,France PierluigiMauri Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (Milan),Italy KennethJ.McDowall AstburyCentreforStructuralMolecularBiology,UniversityofLeeds,Leeds,LS2 9JT,UnitedKingdom WenzhaoMeng DepartmentsofChemistry,TempleUniversity,Philadelphia,Pennsylvania,USA XinMiao Department of Biochemistry and Molecular Biology, University of British Columbia,Vancouver,BritishColumbia,Canada BijoyK.Mohanty DepartmentofGenetics,UniversityofGeorgia,Athens,Georgia,USA TeppeiMorita Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa,Nagoya,Japan AsutekaNagao Department of Chemistry and Biotechnology, Graduate School of Engineering, UniversityofTokyo,Tokyo,Japan xx Contributors LilianNathania DepartmentsofChemistry,TempleUniversity,Philadelphia,Pennsylvania,USA RhondaH.Nicholson DepartmentsofBiology,TempleUniversity,Philadelphia,Pennsylvania,USA AllenW.Nicholson Departments of Biology and Chemistry, Temple University, Philadelphia, Pennsylvania,USA IrinaA.Oussenko Mount Sinai School of Medicine of New York University, Department of PharmacologyandSystemsTherapeutics,NewYork,USA MartinOvergaard Department of Biochemistry and Molecular Biology, University of Southern Denmark,Odense,Denmark OlivierPellegrini CNRSUPR9073(affiliatedwithUniversite´deParis7;DenisDiderot),Institutde BiologiePhysico-Chimique,Paris,France AlexandreV.Pertzev DepartmentsofChemistry,TempleUniversity,Philadelphia,Pennsylvania,USA LeonoraPoljak Laboratoire de Microbiologie et Ge´ne´tique Mole´culaire (LMGM), Centre National de la Recherche Scientifique (CNRS) and Universite´ Paul Sabatier, Toulouse,France VictoriaPortnoy DepartmentofBiologyTechnion,IsraelInstituteofTechnology,Haifa,Israel FlorenceProux E´cole Normale Supe´rieure, Laboratoire de Ge´ne´tique Mole´culaire, Paris, France, andCentreNationaldelaRechercheScientifigure(CNRS),Paris,France AnniePrud’homme-Genereux Department of Biochemistry and Molecular Biology, University of British Columbia,Vancouver,BritishColumbia,Canada OlgaPuchta DepartmentofGeneticsandBiotechnology,WarsawUniversity,Warsaw,Poland, andInstituteofBiochemistryandBiophysicsPAS,Warsaw,Poland YuliaRedko CNRSUPR9073(affiliatedwithUniversite´deParis7;DenisDiderot),Institutde BiologiePhysico-Chimique,Paris,France Contributors xxi PhilippeRe´gnier CNRS UPR9073; Institut de Biologie Physico-Chimique; Universite´ Paris Diderot,Paris7,Paris,France JamieRichards Department of Biochemistry and Cell Biologyand Center for Infectious Diseases ofStonyBrookUniversity,StonyBrook,NewYork,USA PascaleRomby Architecture et Re´activite´ de l’ARN, Universite´ de Strasbourg, CNRS, IBMC, Strasbourg,France GadiSchuster DepartmentofBiologyTechnion,IsraelInstituteofTechnology,Haifa,Israel DharamSingh InstituteofMolecularBiology,AcademiaSinica,Taipei115,Taiwan ShimynSlomovic DepartmentofBiologyTechnion,IsraelInstituteofTechnology,Haifa,Israel PiotrP.Stepien DepartmentofGeneticsandBiotechnology,WarsawUniversity,Warsaw,Poland, andInstituteofBiochemistryandBiophysicsPAS,Warsaw,Poland LeighM.Stickney DepartmentofBiochemistryandMolecularBiology,UniversityofBritishColum- bia,Vancouver,BritishColumbia,Canada ThomasSundermeier Department of Biochemistry and Cell Biologyand Center for Infectious Diseases ofStonyBrookUniversity,StonyBrook,NewYork,USA TsutomuSuzuki Department of Chemistry and Biotechnology, Graduate School of Engineering, UniversityofTokyo,Tokyo,Japan Franc¸oisVandenesch INSERMU851,CentreNationaldeRe´fe´rencedesStaphylocoques,Universite´de LyonI,Lyon,France SteffenWagner Institutfu¨rMikrobiologieundMolekularbiologie,UniversityofGiessen,Giessen, Germany KristofferSkovboWinther Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle,Newcastle,UnitedKingdom
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