Horizontal Gene Transfer: Methods and Protocols

411 Pages·2020·10.665 MB·English

by  Fernando de la Cruz

Methods in
Molecular Biology 2075
Fernando de la Cruz Editor
Horizontal
Gene Transfer
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
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Horizontal Gene Transfer
Methods and Protocols
Edited by
Fernando de la Cruz
Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander,
Cantabria, Spain
Editor
FernandodelaCruz
InstitutodeBiomedicinayBiotecnolog´ıadeCantabria
UniversidaddeCantabria-CSIC
Santander,Cantabria,Spain
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9876-0 ISBN978-1-4939-9877-7 (eBook)
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Preface
There is a fundamental difference between prokaryotes and eukaryotes in their evolution
mechanisms and, consequently, in their genetic organization. Eukaryotes evolve within
species, limited by sexual reproduction, while prokaryotes largely evolve by horizontal
gene transfer (HGT), limited by the boundaries of gene exchange between species. In
prokaryotes, HGT is pervasive, occurs contemporarily, and is an all-important mechanism
of genetic originality. It can even be stated that bacterial genome structure and evolution
cannotbeunderstoodunlesswecontemplatethedirecteffectsofHGT.Conversely,HGTin
eukaryotes is an evolutionary mechanism that operates at a different timescale. Most
eukaryoticspeciesareconfinedwithinthelimitsoftheirownspeciesbysexualreproduction.
Consequently,andwithduerespecttoaffectedactors,activeinterspecificHGTispresently
residual in eukaryotic organisms (not its cumulative effects, which are of extraordinary
interest).
Not surprisingly, therefore, the technologies used to study HGT in prokaryotes and
eukaryotesarevastlydifferentandtheiraudiencesquiteseparate.Thisbookconcentrateson
technologiesusedtostudyHGTinprokaryotes.TheelementsinvolvedinprokaryoticHGT
are called mobile genetic elements (MGEs). There is a need for individualizing and func-
tionallydescribingactiveMGEsifweattempttounderstandtheirstructure,epidemiology,
andevolution.Inorder toachieveit,updatedmethodsfor theirdetectionandisolationare
shownin PartI ofthisbook.Themain molecularprocesses involvedinHGTareconjuga-
tion,transformation,andtransduction.PartIIdealswithmethodsinvolvedintheanalysisof
these molecular processes. Again, quantitative description of these processes is required to
attemptacomparative,functionaldescriptionofthedifferentprocesses.Thereisamyriadof
MGEs,andeachonemusthavedifferentialspecificationsthatjustifytheirexistenceinever-
evolving microbial ecosystems. Because of HGT, and the ups and downs of particular
MGEs, bacterial populations adapt and evolve. Part III puts together a series of methods
to analyze the adaptation and evolution of MGEs, with special attention to bioinformatics
tools, as well as methods derived from the activity of MGEs that found utilities elsewhere.
MethodsforthemetagenomicanalysisofMGEswillhopefullybethesubjectofalaterbook.
Santander,Spain FernandodelaCruz
v
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I METHODS FOR THE DETECTION AND ISOLATION
OF MOBILE GENETIC ELEMENTS
1 PlasmidDNAIsolationandVisualization:IsolationandCharacterization
ofPlasmidsfromClinicalSamples......................................... 3
KaitlinA.Tagg,CarolaVenturini,MuhammadKamruzzaman,
AndrewN.Ginn,andSallyR.Partridge
2 IsolationandVisualizationofPlasmidsfromGram-Positive
BacteriaofInterestinPublicHealth....................................... 21
AnaR.Freitas,CarlaNovais,Luı´saPeixe,andTeresaM.Coque
3 Detection,Isolation,andCharacterizationofPlasmidsintheEnvironment .... 39
KhaldBlau,SvenJechalke,andKorneliaSmalla
4 BacteriophageIsolationandCharacterization:Phages
ofEscherichiacoli ....................................................... 61
JuanJofreandMaiteMuniesa
5 DetectionandCharacterizationofTransposonsinBacteria................... 81
CatherineGuynet,PhanThaiNguyenLe,MichaelChandler,
andBaoTon-Hoang
PART II METHODS TO QUANTIFYAND CHARACTERIZE HORIZONTAL
GENE TRANSFER
6 MeasuringPlasmidConjugationUsingAntibioticSelection.................. 93
JorgeRodriguez-GrandeandRaulFernandez-Lopez
7 MeasuringPlasmidConjugationUsingFluorescentReporters................ 99
CarolinaPalencia-Gandara,RaulRuiz,andRaulFernandez-Lopez
8 MethodstoQuantifyDNATransferinEnterococcus......................... 111
CarlaNovais,AnaR.Freitas,RicardoLe(cid:1)on-Sampedro,Luı´saPeixe,
andTeresaM.Coque
9 QuantifyingandCharacterizingDistributiveConjugalTransfer
inMycobacteriumsmegmatis.............................................. 123
RyanR.Clark,ToddA.Gray,andKeithM.Derbyshire
10 SpectrophotometricAssaystoQuantifytheActivityofT4SSATPases ......... 135
ElenaCabez(cid:1)onandIgnacioArechaga
vii
viii Contents
11 IdentificationofRelaxase-DNACovalentComplexesandDNAStrand
TransferReactionProductsbyPolyacrylamideGelElectrophoresis ........... 145
Marı´aLucasandGabrielMoncalia´n
12 FirstBiochemicalStepsonBacterialTranspositionPathways ................. 157
CatherineGuynet,EmilienNicolas,BaoTon-Hoang,Jean-YvesBouet,
andBernardHallet
13 NaturalTransformationinEscherichiacoli ................................. 179
YokoKomiyamaandSumioMaeda
14 IntegronIdentificationinBacterialGenomesandCassette
RecombinationAssays................................................... 189
ClaireVit,Ce´lineLoot,Jose´AntonioEscudero,AleksandraNivina,
andDidierMazel
15 MethodstoIdentifyandAnalyzeVesicle-ProtectedDNATransfer............ 209
AlbaBlesaandJose´Berenguer
16 MeasuringPlasmidStabilityinGram-NegativeBacteria...................... 223
Damia´nLobato-Ma´rquez
17 Methodsfor theAnalysisandCharacterizationofDefense
MechanismsAgainstHorizontalGeneTransfer:CRISPRSystems ............ 235
AliciaCalvo-Villaman˜a´n,AudeBernheim,andDavidBikard
PART III OMICS, BIOINFORMATICS, MATHEMATICAL MODELING,
AND TECHNOLOGICAL APPLICATIONS OF HGT
18 TheMobilome:MetagenomicAnalysisofCircularPlasmids,
Viruses,andOtherExtrachromosomalElements ........................... 253
PatrickDenisBrowne,WitoldKot,TueSparholtJørgensen,
andLarsHestbjergHansen
19 IdentifyingConjugativePlasmidsandIntegrativeConjugative
ElementswithCONJscan................................................ 265
JeanCury,SophieS.Abby,OliviaDoppelt-Azeroual,BertrandNe´ron,
andEduardoP.C.Rocha
20 PlasmidFinderandInSilicopMLST:IdentificationandTyping
ofPlasmidRepliconsinWhole-GenomeSequencing(WGS) ................. 285
AlessandraCarattoliandHenrikHasman
21 MOBscan:AutomatedAnnotationofMOBRelaxases....................... 295
M.PilarGarcilla´n-Barcia,SantiagoRedondo-Salvo,LuisVielva,
andFernandodelaCruz
22 PlasmidTypingandClassification......................................... 309
LauraVillaandAlessandraCarattoli
23 PlasmidReconstructionfromNext-GenData:ADetailedProtocol
for theUseofPLACNETwfor theReconstructionofPlasmids
fromWGSDatasets..................................................... 323
Marı´adeToro,ValF.Lanza,LuisVielva,SantiagoRedondo-Salvo,
andFernandodelaCruz
Contents ix
24 StatisticalAnalysisofAccessoryGenome................................... 341
MiguelD.Ferna´ndez-de-Bobadilla,TeresaM.Coque,
andValF.Lanza
25 InferringHorizontalGeneTransfer withDarkHorse,Phylomizer,
andETEToolkits....................................................... 355
LuisDelaye,CarlosVargas,AmparoLatorre,andAndre´sMoya
26 MethodstoStudyFitnessandCompensatoryAdaptation
inPlasmid-CarryingBacteria............................................. 371
JavierDelaFuente,JeronimoRodriguez-Beltran,andAlvaro SanMillan
27 ABroadHostRangePlasmid-BasedRoadmapforssDNA-Based
RecombineeringinGram-NegativeBacteria................................ 383
Toma´sAparicio,Vı´ctordeLorenzo,andEstebanMartı´nez-Garcı´a
28 ConjugativeAssemblyGenomeEngineering(CAGE)....................... 399
MarcGu¨ell
Index ...................................................................... 411
Contributors
SOPHIES.ABBY (cid:1) Universite´GrenobleAlpes,CNRS,GrenobleINP,TIMC-IMAG,Grenoble,
France
TOMA´SAPARICIO (cid:1) SystemsandSyntheticBiologyProgram,CentroNacionaldeBiotecnologı´a
(CNB-CSIC),Madrid,Spain
IGNACIO ARECHAGA (cid:1) DepartamentodeBiologı´aMolecular,InstitutodeBiomedicinay
Biotecnologı´adeCantabria(IBBTEC),UniversidaddeCantabria-CSIC,Santander,
Spain
JOSE´ BERENGUER (cid:1) CentrodeBiologı´aMolecularSeveroOchoa,UniversidadAut(cid:1)onomade
Madrid-ConsejoSuperiordeInvestigacionesCientı´ficas,Madrid,Spain
AUDEBERNHEIM (cid:1) SyntheticBiologyGroup,MicrobiologyDepartment,InstitutPasteur,
Paris,France;E´coleDoctoraleFIRE—ProgrammeBettencourt,CentredeRecherches
Interdisciplinaires,Paris,France;MicrobialEvolutionaryGenomics,Departmentof
GenomesandGenetics,InstitutPasteur,Paris,France;AgroParisTech,Paris,France
DAVIDBIKARD (cid:1) SyntheticBiologyGroup,MicrobiologyDepartment,InstitutPasteur,Paris,
France
KHALDBLAU (cid:1) InstituteforEpidemiologyandPathogenDiagnostics,JuliusKu¨hn-Institut
(JKI),FederalResearchCentreforCultivatedPlants,Braunschweig,Germany
ALBABLESA (cid:1) CentrodeBiologı´aMolecularSeveroOchoa,UniversidadAut(cid:1)onomade
Madrid-ConsejoSuperiordeInvestigacionesCientı´ficas,Madrid,Spain;Departmentof
Biotechnology,FacultyofExperimentalSciences,UniversidadFranciscodeVitoria,
Madrid,Spain
JEAN-YVESBOUET (cid:1) LaboratoiredeMicrobiologieetGe´ne´tiqueMole´culaires,Centrede
BiologieInte´grative(CBI),CentreNationaldelaRechercheScientifique(CNRS),
Universite´deToulouse,UPS,Toulouse,France
PATRICKDENIS BROWNE (cid:1) DepartmentofEnvironmentalScience,AarhusUniversity,
Roskilde,Denmark;DepartmentofPlantandEnvironmentalSciences,
UniversityofCopenhagen,Frederiksberg,Denmark
ELENACABEZO´N (cid:1) DepartamentodeBiologı´aMolecular,InstitutodeBiomedicinay
Biotecnologı´adeCantabria(IBBTEC),UniversidaddeCantabria-CSIC,Santander,
Spain
ALICIA CALVO-VILLAMAN˜A´N (cid:1) SyntheticBiologyGroup,MicrobiologyDepartment,Institut
Pasteur,Paris,France;E´coleDoctoraleFIRE—ProgrammeBettencourt,Centrede
RecherchesInterdisciplinaires,Paris,France
ALESSANDRACARATTOLI (cid:1) DepartmentofMolecularMedicine,SapienzaUniversityofRome,
Rome,Italy
MICHAELCHANDLER (cid:1) LaboratoiredeMicrobiologieetGe´ne´tiqueMole´culaires,Centrede
BiologieInte´grative(CBI),CentreNationaldelaRechercheScientifique(CNRS),
Universite´deToulouse,UPS,Toulouse,France;DepartmentofBiochemistry,Molecularand
CellularBiology,GeorgetownUniversityMedicalCenter,Washington,DC,USA
RYANR.CLARK (cid:1) NewYorkStateDepartmentofHealth,WadsworthCenter,Albany,NY,
USA
xi