Metabolic Network Reconstruction and Modeling: Methods and Protocols

412 Pages·2018·10.944 MB·English

by  Marco Fondi

Methods in
Molecular Biology 1716
Marco Fondi Editor
Metabolic
Network
Reconstruction
and Modeling
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Metabolic Network
Reconstruction and Modeling
Methods and Protocols
Edited by
Marco Fondi
Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
Editor
MarcoFondi
DepartmentofBiology
UniversityofFlorence
SestoFiorentino,Florence,Italy
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7527-3 ISBN978-1-4939-7528-0 (eBook)
https://doi.org/10.1007/978-1-4939-7528-0
LibraryofCongressControlNumber:2017959614
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Preface
Thanks to the large diffusion of bacterial genome analysis, determining the genome
sequenceof(almostany)organismshasbecomearoutinetask.Oneofthemostimportant
drawbacks associated with the booming of genomics resides in the possibility to quickly
deriveacomprehensivemetabolicreconstructionofacellandtousecomputationalsimula-
tionstopredictitsmetaboliclandscape.
Metabolic modeling confers to microbiologists the opportunity to further expand the
knowledge offered by genome sequence alone. Indeed, despite the analysis of genome
sequence per se that can provide interesting and fundamental hints on microbial life (e.g.,
genome structure, presence/absence patterns, and phylogenetic features), many questions
mayremainunresolved.Thismaylimitthestudyofmicrobialgenomicstotheassemblyand
the interpretation of gene lists. To provide a system-level picture of cellular life and gain
someinsightson,forexample,theeffectofgenedeletionsand/ornutritionalfluctuations,
more sophisticated analytic tools have to be exploited. Constraint-based metabolic model-
ing (CBMM) represents one of these methodologies, combining good predictive abilities
witharelativelysimpleconceptualandpracticalframework.Thislatterpointprobablybest
explainsthesuccessandtherecentspreadingofthisapproachas,ultimately,CBMMallows
both the generation of testable hypotheses and the reduction of the amount of wet-lab
experimentstobeperformed,savingtime,efforts,andcosts.
This book is intended to provide the most recent methodologies about the study of
cellular metabolism using in silico approaches. The volume is ideally divided into three
distinct parts. In the first part tools and methodologies for metabolic reconstructions and
basicCBMMarepresented(Chapters1–10).Thesecondpartofthebook(Chapters11,12,
and13)containsprotocolsforthegenerationofexperimentaldatathatcanguidemetabolic
reconstructionandmodeling,namelytranscriptomics,proteomics,andmutantsgeneration.
The final part of the book (Chapters 14–18) covers more advanced methodologies for
quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis,
host-pathogen metabolic interactions, and multiobjective optimization. In each of these
parts the most up-to-date protocols and procedures for metabolic reconstruction and
CBMM will be provided. The aim of the present book is then to serve as a “field guide”
bothforqualifiedinvestigatorsoncellularmetabolism(includingcomputationalbiologists,
microbiologists,physiologists,biochemists)whowanttoupdatetheir technicalknowledge
andforless-experiencedresearcherswhowanttostartworkingwithCBMM.
SestoFiorentino,Florence,Italy MarcoFondi
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 ReconstructingHigh-QualityLarge-ScaleMetabolicModelswithmerlin...... 1
OscarDias,MiguelRocha,Euge´nioCamposFerreira,andIsabelRocha
2 AnalyzingandDesigningCellFactorieswithOptFlux....................... 37
PauloVilac¸a,PauloMaia,HugoGiesteira,IsabelRocha,
andMiguelRocha
3 TheMONGOOSERationalArithmeticToolbox ........................... 77
ChristopherLeandLeonidChindelevitch
4 TheFASTCOREFamily:For theFastReconstructionofCompact
Context-SpecificMetabolicNetworksModels.............................. 101
MariaPiresPachecoandThomasSauter
5 ReconstructionandAnalysisofCentralMetabolisminMicrobes.............. 111
JanakaN.Edirisinghe,Jose´P.Faria,NomiL.Harris,
BenjaminH.Allen,andChristopherS.Henry
6 UsingPSAMMfor theCurationandAnalysisofGenome-Scale
MetabolicModels....................................................... 131
KeithDufault-Thompson,JonLundSteffensen,andYingZhang
7 IntegrationofComparativeGenomicswithGenome-ScaleMetabolic
ModelingtoInvestigateStrain-SpecificPhenotypicalDifferences ............. 151
JonathanMonkandEmanueleBosi
8 Template-AssistedMetabolicReconstructionandAssembly
ofHybridBacterialModels............................................... 177
TizianoVignolini,AlessioMengoni,andMarcoFondi
9 IntegratedHost-PathogenMetabolicReconstructions....................... 197
AnuRaghunathanandNeemaJamshidi
10 MetabolicModelReconstructionandAnalysisofanArtificial
MicrobialEcosystem .................................................... 219
ChaoYe,NanXu,XiulaiChen,andLimingLiu
11 RNASequencingandAnalysisinMicroorganismsforMetabolicNetwork
Reconstruction......................................................... 239
EvaPinatelandCleliaPeano
12 DifferentialProteomicsBasedon2D-DifferenceIn-GelElectrophoresis
andTandemMassSpectrometryfor theElucidationofBiological
ProcessesinAntibiotic-ProducerBacterialStrains........................... 267
GiuseppeGalloandAndreaScaloni
13 TechniquesforLarge-ScaleBacterialGenomeManipulationand
CharacterizationoftheMutantswithRespecttoInSilicoMetabolic
Reconstructions ........................................................ 291
GeorgeC.diCenzoandTurloughM.Finan
vii
viii Contents
14 ComputationalPredictionofSyntheticLethalsinGenome-Scale
MetabolicModelsUsingFast-SL ......................................... 315
KarthikRaman,AdityaPratapa,OmkarMohite,
andShankarBalachandran
15 CouplingFluxes,Enzymes,andRegulationinGenome-ScaleMetabolic
Models ................................................................ 337
PaulA.Jensen
16 DynamicFluxBalanceAnalysisUsingDFBAlab ............................ 353
JoseAlbertoGomezandPaulI.Barton
17 DesigningOptimizedProductionHostsbyMetabolicModeling ............. 371
ChristianJungreuthmayer,MatthiasP.Gerstl,DavidA.Pen˜aNavarro,
MichaelHanscho,DavidE.Ruckerbauer,andJu€rgenZanghellini
18 OptimizationofMulti-OmicGenome-ScaleModels:Methodologies,
Hands-onTutorial,andPerspectives ...................................... 389
SupreetaVijayakumar,MaxConway,PietroLi(cid:2)o,andClaudioAngione
Index ...................................................................... 409
Contributors
BENJAMINH.ALLEN (cid:1) BiosciencesDivision,OakRidgeNationalLaboratory,OakRidge,
TN,USA
CLAUDIOANGIONE (cid:1) DepartmentofComputerScienceandInformationSystems,Teesside
University,Middlesbrough,TeesValley,UK
SHANKARBALACHANDRAN (cid:1) DepartmentofComputerScienceandEngineering,Indian
InstituteofTechnologyMadras,Chennai,India;IntelResearchLabs,Bangalore,India
PAULI.BARTON (cid:1) ProcessSystemsEngineeringLaboratory,Cambridge,MA,USA
EMANUELEBOSI (cid:1) DepartmentofBiology,UniversityofFlorence,SestoFiorentino,Italy
XIULAICHEN (cid:1) StateKeyLaboratoryofFoodScienceandTechnology,JiangnanUniversity,
Wuxi,Jiangsu,China
LEONID CHINDELEVITCH (cid:1) SchoolofComputingSciences,SimonFraserUniversity,Burnaby,
BC,Canada
MAXCONWAY (cid:1) ComputerLaboratory,UniversityofCambridge,Cambridge,UK
OSCARDIAS (cid:1) CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal
GEORGEC.DICENZO (cid:1) DepartmentofBiology,McMasterUniversity,Hamilton,ON,
Canada
KEITHDUFAULT-THOMPSON (cid:1) DepartmentofCellandMolecularBiology,Collegeofthe
EnvironmentandLifeSciences,UniversityofRhodeIsland,Kingston,RI,USA
JANAKA N.EDIRISINGHE (cid:1) ComputationInstitute,UniversityofChicago,Chicago,IL,USA;
MathematicsandComputerScienceDivision,ArgonneNationalLaboratory,Argonne,IL,
USA
JOSE´ P.FARIA (cid:1) ComputationInstitute,UniversityofChicago,Chicago,IL,USA;
MathematicsandComputerScienceDivision,ArgonneNationalLaboratory,Argonne,IL,
USA
EUGE´NIOCAMPOSFERREIRA (cid:1) CentreofBiologicalEngineering,UniversityofMinho,Braga,
Portugal
TURLOUGH M.FINAN (cid:1) DepartmentofBiology,McMasterUniversity,Hamilton,ON,
Canada
MARCOFONDI (cid:1) DepartmentofBiology,UniversityofFlorence,SestoFiorentino,Florence,
Italy
GIUSEPPE GALLO (cid:1) LaboratoryofMolecularMicrobiologyandBiotechnology,STEBICEF
Department,UniversityofPalermo,Palermo,Italy
MATTHIASP.GERSTL (cid:1) AustrianCentreofIndustrialBiotechnology,Vienna,Austria;
DepartmentofBiotechnology,UniversityofNaturalResourcesandLifeSciences,Vienna,
Austria
HUGOGIESTEIRA (cid:1) SilicoLifeLda,Braga,Portugal
JOSEALBERTOGOMEZ (cid:1) ProcessSystemsEngineeringLaboratory,Cambridge,MA,USA
MICHAELHANSCHO (cid:1) AustrianCentreofIndustrialBiotechnology,Vienna,Austria;
DepartmentofBiotechnology,UniversityofNaturalResourcesandLifeSciences,Vienna,
Austria
NOMIL.HARRIS (cid:1) EnvironmentalGenomicsandSystemsBiologyDivision,E.O.Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA
ix
x Contributors
CHRISTOPHERS.HENRY (cid:1) ComputationInstitute,UniversityofChicago,Chicago,IL,USA;
MathematicsandComputerScienceDivision,ArgonneNationalLaboratory,Argonne,IL,
USA
NEEMAJAMSHIDI (cid:1) InstituteofEngineeringinMedicine,UniversityofCalifornia-SanDiego,
LaJolla,CA,USA;DepartmentofRadiologicalSciences,UniversityofCalifornia,Los
Angeles,CA,USA
PAULA.JENSEN (cid:1) DepartmentofBioengineeringandCarlR.WoeseInstituteforGenomic
Biology,UniversityofIllinoisatUrbana-Champaign,Urbana,IL,USA
CHRISTIAN JUNGREUTHMAYER (cid:1) TGM-TechnologischesGewerbemuseum,HTBLuVAWien
XX,Vienna,Austria;AustrianCentreofIndustrialBiotechnology,Vienna,Austria
CHRISTOPHERLE (cid:1) SchoolofComputingSciences,SimonFraserUniversity,Burnaby,BC,
Canada
PIETROLIO´ (cid:1) ComputerLaboratory,UniversityofCambridge,Cambridge,UK
LIMING LIU (cid:1) StateKeyLaboratoryofFoodScienceandTechnology,JiangnanUniversity,
Wuxi,Jiangsu,China
PAULOMAIA (cid:1) SilicoLifeLda,Braga,Portugal
ALESSIOMENGONI (cid:1) DepartmentofBiology,UniversityofFlorence,SestoFiorentino,Florence,
Italy
OMKARMOHITE (cid:1) DepartmentofBiotechnology,BhupatandJyotiMehtaSchoolofBiosciences,
IndianInstituteofTechnologyMadras,Chennai,India
JONATHANMONK (cid:1) DepartmentofBioengineering,UniversityofCalifornia,LaJolla,CA,
USA
DAVIDA.PEN˜ANAVARRO (cid:1) AustrianCentreofIndustrialBiotechnology,Vienna,Austria;
DepartmentofBiotechnology,UniversityofNaturalResourcesandLifeSciences,Vienna,
Austria
MARIAPIRESPACHECO (cid:1) LifeSciencesResearchUnit,UniversityofLuxembourg,Belvaux,
Luxembourg
CLELIAPEANO (cid:1) InstituteofGeneticandBiomedicalResearch,UoSMilan,National
ResearchCouncil,HumanitasClinicalandResearchCenter,Milan,Italy
EVAPINATEL (cid:1) InstituteforBiomedicalTechnologies(ITB),NationalResearchCouncil
(CNR),Segrate,Milan,Italy
ADITYAPRATAPA (cid:1) DepartmentofBiotechnology,BhupatandJyotiMehtaSchoolofBiosciences,
IndianInstituteofTechnologyMadras,Chennai,India;DepartmentofComputerScience,
VirginiaTech,Blacksburg,VA,USA
ANURAGHUNATHAN (cid:1) ChemicalEngineeringDivision,NationalChemicalLaboratory,
Pune,India
KARTHIKRAMAN (cid:1) DepartmentofBiotechnology,BhupatandJyotiMehtaSchoolofBiosciences,
IndianInstituteofTechnologyMadras,Chennai,India;RobertBoschCentreforData
ScienceandArtificialIntelligence(RBC-DSAI),IndianInstituteofTechnologyMadras,
Chennai,India;InitiativeforBiologicalSystemsEngineering(IBSE),IndianInstituteof
TechnologyMadras,Chennai,India
ISABEL ROCHA (cid:1) CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal;
SilicoLifeLda,Braga,Portugal
MIGUELROCHA (cid:1) CentreofBiologicalEngineering,UniversityofMinho,Braga,Portugal;
SilicoLifeLda,Braga,Portugal
DAVIDE.RUCKERBAUER (cid:1) AustrianCentreofIndustrialBiotechnology,Vienna,Austria;
DepartmentofBiotechnology,UniversityofNaturalResourcesandLifeSciences,Vienna,
Austria
Contributors xi
THOMASSAUTER (cid:1) LifeSciencesResearchUnit,UniversityofLuxembourg,Belvaux,
Luxembourg
ANDREA SCALONI (cid:1) ProteomicandMassSpectrometryLaboratory,ISPAAM,National
ResearchCouncil,Naples,Italy
JONLUNDSTEFFENSEN (cid:1) DepartmentofCellandMolecularBiology,Collegeofthe
EnvironmentandLifeSciences,UniversityofRhodeIsland,Kingston,RI,USA
TIZIANOVIGNOLINI (cid:1) LENS,EuropeanLaboratoryforNon-linearSpectroscopy,Universityof
Florence,SestoFiorentino,Florence,Italy
SUPREETAVIJAYAKUMAR (cid:1) DepartmentofComputerScienceandInformationSystems,Teesside
University,Middlesbrough,TeesValley,UK
PAULOVILAC¸A (cid:1) SilicoLifeLda,Braga,Portugal
NANXU (cid:1) StateKeyLaboratoryofFoodScienceandTechnology,JiangnanUniversity,Wuxi,
Jiangsu,China
CHAOYE (cid:1) StateKeyLaboratoryofFoodScienceandTechnology,JiangnanUniversity,Wuxi,
Jiangsu,China
Ju€RGENZANGHELLINI (cid:1) AustrianCentreofIndustrialBiotechnology,Vienna,Austria;
DepartmentofBiotechnology,UniversityofNaturalResourcesandLifeSciences,Vienna,
Austria
YING ZHANG (cid:1) DepartmentofCellandMolecularBiology,CollegeoftheEnvironmentand
LifeSciences,UniversityofRhodeIsland,Kingston,RI,USA