Table Of ContentAdvances in Experimental Medicine and Biology 883
Nevan J. Krogan
Mohan Babu Editors
Prokaryotic
Systems
Biology
Advances in Experimental Medicine and Biology
Volume 883
EditorialBoard:
IRUNR.COHEN,TheWeizmannInstituteofScience,Rehovot,Israel
ABELLAJTHA,N.S.KlineInstituteforPsychiatricResearch,Orangeburg,NY,USA
JOHND.LAMBRIS,UniversityofPennsylvania,Philadelphia,PA,USA
RODOLFOPAOLETTI,UniversityofMilan,Milan,Italy
Moreinformationaboutthisseriesathttp://www.springer.com/series/5584
Nevan J. Krogan • Mohan Babu
Editors
Prokaryotic Systems Biology
123
Editors
NevanJ.Krogan MohanBabu
CellularandMolecularPharmacology DepartmentofBiochemistry
UniversityofCalifornia,SanFrancisco UniversityofRegina
SanFrancisco,California,USA Regina,Saskatchewan,Canada
ISSN0065-2598 ISSN2214-8019 (electronic)
AdvancesinExperimentalMedicineandBiology
ISBN978-3-319-23602-5 ISBN978-3-319-23603-2 (eBook)
DOI10.1007/978-3-319-23603-2
LibraryofCongressControlNumber:2015955839
SpringerChamHeidelbergNewYorkDordrechtLondon
©SpringerInternationalPublishingSwitzerland2015
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof
thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,
broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation
storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology
nowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication
doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant
protectivelawsandregulationsandthereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbook
arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor
theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany
errorsoromissionsthatmayhavebeenmade.
Printedonacid-freepaper
SpringerInternational PublishingAGSwitzerlandispartofSpringerScience+Business Media(www.
springer.com)
Contents
1 MetagenomicsasaToolforEnzymeDiscovery:Hydrolytic
EnzymesfromMarine-RelatedMetagenomes .......................... 1
Ana Popovic,AnatolyTchigvintsev,Hai Tran, Tatyana
N.Chernikova,OlgaV.Golyshina,MichailM.Yakimov,
PeterN.Golyshin,andAlexanderF.Yakunin
2 InvestigatingBacterialProteinSynthesisUsingSystems
BiologyApproaches ........................................................ 21
AllaGagarinovaandAndrewEmili
3 BiologyandAssemblyoftheBacterialEnvelope ....................... 41
KarineDufresneandCatherineParadis-Bleau
4 ComparativeGenomicsandEvolutionaryModularity
ofProkaryotes............................................................... 77
CedoljubBundalovic-TormaandJohnParkinson
5 Predicting Functional Interactions Among Genes
inProkaryotesbyGenomicContext...................................... 97
G.Moreno-HagelsiebandG.Santoyo
6 FunctionalImplicationsofDomainOrganizationWithin
ProkaryoticRhomboidProteases......................................... 107
RashmiPanigrahiandM.JoanneLemieux
7 Mapping Transcription Regulatory Networks
withChIP-seqandRNA-seq .............................................. 119
JosephT.Wade
8 Quantitative and Systems-Based Approaches
for Deciphering Bacterial Membrane Interactome
andGeneFunction ......................................................... 135
Viktor Deineko, Ashwani Kumar, James Vlasblom,
andMohanBabu
v
vi Contents
9 TowardNetworkBiologyinE.coliCell.................................. 155
Hirotada Mori, Rikiya Takeuchi, Yuta Otsuka,
StevenBowden,KatsushiYokoyama,AiMuto,IgorLibourel,
andBarryL.Wanner
10 GeneticInteractionScoringProcedureforBacterialSpecies ......... 169
OmarWagihandLeopoldParts
11 Mapping the Protein-ProteinInteractome Networks
UsingYeastTwo-HybridScreens ......................................... 187
SeesandraVenkatappaRajagopala
12 Biogenesis of Escherichia coli DMSO Reductase:
A Network of Participants for Protein Folding
andComplexEnzymeMaturation........................................ 215
CatherineS.ChanandRaymondJ.Turner
13 MicrobialProteomeProfiling and Systems Biology:
ApplicationstoMycobacteriumtuberculosis............................. 235
OlgaT.SchubertandRuediAebersold
14 StructuralAspectsofBacterialOuterMembrane
ProteinAssembly ........................................................... 255
CharlesCalmettes,AndrewJudd,andTrevorF.Moraes
15 SubstrateInteractionNetworksoftheEscherichia coli
Chaperones:TriggerFactor,DnaKandGroEL ........................ 271
VaibhavBhandariandWalidA.Houry
16 Genetic, Biochemical, and Structural Analyses
ofBacterialSurfacePolysaccharides..................................... 295
Colin A. Cooper, Iain L. Mainprize, and NicholasN.
Nickerson
Index............................................................................... 317
Contributors
RuediAebersold InstituteofMolecularSystemsBiology,Zurich,Switzerland
FacultyofScience,UniversityofZurich,Zurich,Switzerland
Mohan Babu Department of Biochemistry, University of Regina, Regina, SK,
Canada
Vaibhav Bhandari Departmentof Biochemistry,University of Toronto,Toronto,
ON,Canada
StevenBowden GraduateSchoolofBiologicalSciences,NaraInstituteofScience
andTechnology,Takayama,Ikoma,Nara,Japan
Cedoljub Bundalovic-Torma Department of Molecular Structure and Function,
HospitalforSickChildren,Toronto,ON,Canada
CharlesCalmettes Departmentof Biochemistry,Universityof Toronto,Toronto,
ON,Canada
Catherine S. Chan Department of Biological Sciences, University of Calgary,
Calgary,AB,Canada
Tatyana N. Chernikova School of Biological Sciences, Bangor University,
Gwynedd,UK
Colin A. Cooper Department of Molecular and Cellular Biology, University of
Guelph,Guelph,ON,Canada
Viktor Deineko Departmentof Biochemistry, University of Regina, Regina, SK,
Canada
Karine Dufresne Department of Microbiology, Infectiology and Immunology,
UniversitédeMontréal,Montreal,QC,Canada
AndrewEmili DepartmentofMolecularGenetics,UniversityofToronto,Toronto,
ON,Canada
vii
viii Contributors
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto,
Toronto,ON,Canada
Peter N. Golyshin School of Biological Sciences, Bangor University, Gwynedd,
UK
Alla Gagarinova Department of Molecular Genetics, University of Toronto,
Toronto,ON,Canada
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto,
Toronto,ON,Canada
OlgaV. Golyshina Schoolof BiologicalSciences, Bangor University,Gwynedd,
UK
WalidA.Houry DepartmentofBiochemistry,UniversityofToronto,Toronto,ON,
Canada
Andrew Judd Departmentof Biochemistry,Universityof Toronto,Toronto,ON,
Canada
AshwaniKumar DepartmentofBiochemistry,UniversityofRegina,Regina,SK,
Canada
M. Joanne Lemieux Department of Biochemistry, University of Alberta,
Edmonton,AB,Canada
IgorLibourel TheBiotechnologyInstitute,UniversityofMinnesota,St.Paul,MN,
USA
Iain L. Mainprize Departmentof Molecular and Cellular Biology,Universityof
Guelph,Guelph,ON,Canada
Trevor F. Moraes Department of Biochemistry, University of Toronto, Toronto,
ON,Canada
G.Moreno-Hagelsieb DepartmentofBiology,WilfridLaurierUniversity,Water-
loo,ON,Canada
HirotadaMori GraduateSchoolofBiologicalSciences,NaraInstituteofScience
andTechnology,Takayama,Ikoma,Nara,Japan
Ai Muto Graduate School of Biological Sciences, Nara Institute of Science and
Technology,Takayama,Ikoma,Nara,Japan
NicholasN.Nickerson DepartmentofMolecularandCellularBiology,University
ofGuelph,Guelph,ON,Canada
NicholasN.Nickerson DepartmentofInfectiousDiseases,GenentechInc.,South
SanFrancisco,CA,USA
Yuta Otsuka Graduate School of Biological Sciences, Nara Institute of Science
andTechnology,Takayama,Ikoma,Nara,Japan
Contributors ix
RashmiPanigrahi DepartmentofBiochemistry,UniversityofAlberta,Edmonton,
AB,Canada
Catherine Paradis-Bleau Department of Microbiology, Infectiology and
Immunology,UniversitédeMontréal,Montreal,QC,Canada
John Parkinson Department of Molecular Structure and Function, Hospital for
SickChildren,Toronto,ON,Canada
Leopold Parts EMBL-EBI (South Building), Wellcome Trust Genome Campus,
SaffronWalden,UnitedKingdom
Ana Popovic Department of Chemical Engineering and Applied Chemistry,
UniversityofToronto,Toronto,ON,Canada
Seesandra Venkatappa Rajagopala J. Craig Venter Institute, Rockville, MD,
USA
G.Santoya InstituodeInvestigacionesQuímicoBiológicas,UniversidadMichoa-
canadeSanNicolásdeHidalgo,Morelia,Michoacán,Mexico
OlgaT.Schubert InstituteofMolecularSystemsBiology,Zurich,Switzerland
SystemsBiologyGraduateSchool,Zurich,Switzerland
Rikiya Takeuchi Graduate School of Biological Sciences, Nara Institute of
ScienceandTechnology,Takayama,Ikoma,Nara,Japan
Anatoly Tchigvintsev Department of Chemical Engineering and Applied
Chemistry,UniversityofToronto,Toronto,ON,Canada
HaiTran SchoolofBiologicalSciences,BangorUniversity,Gwynedd,UK
Raymond J. Turner Department of Biological Sciences, University of Calgary,
Calgary,AB,Canada
JamesVlasblom DepartmentofBiochemistry,UniversityofRegina,Regina,SK,
Canada
Joseph T. Wade New York State Department of Health, Wadsworth Center,
Albany,NY,USA
DepartmentofBiomedicalSciences,UniversityatAlbany,Albany,NY,USA
Omar Wagih EMBL-EBI (South Building), Wellcome Trust Genome Campus,
SaffronWalden,UnitedKingdom
Barry L. Wanner Department of Biological Sciences, Purdue University, West
Lafayette,IN,USA
MichailM.Yakimov InstituteforCoastalMarineEnvironment,Messina,Italy
AlexanderF.Yakunin DepartmentofChemicalEngineeringandAppliedChem-
istry,UniversityofToronto,Toronto,ON,Canada
Katsushi Yokoyama Graduate School of Biological Sciences, Nara Institute of
ScienceandTechnology,Takayama,Ikoma,Nara,Japan
