Table Of ContentTomás G. Villa · Miguel Viñas Editors
Horizontal
Gene
Transfer
Breaking Borders Between Living
Kingdoms
Horizontal Gene Transfer
(cid:129)
Tomás G. Villa Miguel Viñas
Editors
Horizontal Gene Transfer
Breaking Borders Between Living Kingdoms
Editors
TomásG.Villa MiguelViñas
FacultyofPharmacy, FacultyofMedicine
DepartmentofMicrobiology UniversityofBarcelona
UniversityofSantiagodeCompostela Barcelona,Spain
SantiagodeCompostela,Spain
ISBN978-3-030-21861-4 ISBN978-3-030-21862-1 (eBook)
https://doi.org/10.1007/978-3-030-21862-1
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Contents
PartI HorizontalGeneTransferAmongBacteriaandBacteriophages
HorizontalGeneTransferinBacteria,anOverviewofthe
MechanismsInvolved. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
T.G.Villa,L.Feijoo-Siota,A.Sánchez-Pérez,JL.R.Rama,andC.Sieiro
AlternativeWaystoExchangeDNA:UnconventionalConjugation
AmongBacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
AlbaBlesaandJoséBerenguer
HorizontalGeneTransferBetweenBacteriophagesandBacteria:
AntibioticResistancesandToxinProduction. . . . . . . . . . . . . . . . . . . . . 97
T.G.Villa,L.Feijoo-Siota,JL.R.Rama,A.Sánchez-Pérez,andM.Viñas
GenomicIslandsandtheEvolutionofMultidrug-ResistantBacteria. . . . 143
MarioJuhas
HorizontalGeneTransferandGenomeEvolutioninthePhylum
Actinobacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
CooperJ.Park,JoshuaT.Smith,andCherylP.Andam
Photobacteriumdamselae:HowHorizontalGeneTransferShaped
TwoDifferentPathogenicLifestylesinaMarineBacterium. . . . . . . . . . 175
CarlosR.Osorio
PartII HorizontalGeneTransferBetweenBacteriaandAnimals,
Plants,AmoebaandFungi
HorizontalGeneTransferinMetazoa:ExamplesandMethods. . . . . . . 203
YukiYoshida,ReubenW.Nowell,KazuharuArakawa,andMarkBlaxter
HorizontalGeneTransferBetweenWolbachiaandAnimals. . . . . . . . . . 227
TrinidaddeMiguel,OudeZhu,andTomásG.Villa
v
vi Contents
HorizontalGeneTransferinObligateParasites. . . . . . . . . . . . . . . . . . . 235
J.M.Ageitos,M.Viñas,andT.G.Villa
AssociationBetweenHorizontalGeneTransferandAdaptation
ofGastricHumanPathogenHelicobacterpyloritotheHost. . . . . . . . . . 257
SurekhaChallaandNageswaraRaoReddyNeelapu
TheRhizobiaceaeBacteriaTransferringGenestoHigherPlants. . . . . . 269
Martha-HelenaRamírez-Bahena,AlvaroPeix,andEncarnaVelázquez
RoleofHorizontalGeneTransferinEvolutionofthePlantGenome. . . . 291
NageswaraRaoReddyNeelapu,MalayRanjanMishra,TitashDutta,
andSurekhaChalla
FungalHorizontalGeneTransfer:AHistoryBeyondthePhylogenetic
Kingdoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
CarlosBarreiro,SantiagoGutiérrez,andElíasR.Olivera
TransferofSecondaryMetaboliteGeneClusters:Assemblyand
Reorganizationoftheβ-LactamGeneClusterfromBacteriato
FungiandArthropods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
J.F.MartínandP.Liras
HorizontalGeneTransferAmongNeisseriaSpeciesandHumans. . . . . 361
S.Sánchez,T.deMiguel,T.G.Villa,A.R.Gorringe,andI.M.Feavers
ImplicationsofLateralorHorizontalGeneTransferfromBacteria
totheHumanGastrointestinalSystemforCancerDevelopmentand
Treatment. . . . .. . . .. . . .. . . .. . . . .. . . .. . . .. . . .. . . . .. . . .. . . .. 377
A.G.Abril,P.G.Lanzi,andV.Notario
RoleofHorizontalGeneTransferinCancerProgression. . . . . . . . . . . . 399
A.G.AbrilandV.Notario
Part I
Horizontal Gene Transfer Among Bacteria
and Bacteriophages
Horizontal Gene Transfer in Bacteria,
an Overview of the Mechanisms Involved
T.G.Villa,L.Feijoo-Siota,A.Sánchez-Pérez,JL.R.Rama,andC.Sieiro
Abstract Bacterialtransformation,transduction,and“conjugation”canbeconsid-
eredthefirsthorizontaltransfermechanismsinlivingorganisms;thesemechanisms
haveoccurredsincetheoriginofbacteriaandarestillcurrent.Althoughmechanis-
tically quite different, the three processes aim to achieve the main objective of all
cells, the ability to survive and adapt to new environments. Transformation, trans-
duction,and“conjugation”implementDNArecombination,creatinggeneticdiver-
sityand,hence,allowingbacteriatoacquirenewcapabilitiesandevolve,resultingin
additional, improved, environmental adaptations that enhance bacterial survival.
This chapter summarizes old paradigms and novel findings in these three genetic
processesandincludesthelatestresearchontherecentlydescribedvesicle-mediated
bacterialcommunicationmechanism.
Keywords Horizontalgenetransfer·Bacterialtransformation·Transduction·
Conjugation·Bacterialvesicles
1 Introduction
Horizontal gene transfer (HGT) was not even suspected to occur in the bacterial
world a century ago, although there were already a variety of data indicating its
existence.Itwasthenalreadyestablished,forexample,thatbacteriacanchangetheir
pathogenicityprofile,altertheirabilitytoutilizedifferentnutrients,ormodifytheir
physiology to form biofilms in response to different factors (these biofilms were
notedtooccasionallybreakdown,bysomeunknownmechanism).Inthemajorityof
T.G.Villa(*)·L.Feijoo-Siota·JL.R.Rama
FacultyofPharmacy,DepartmentofMicrobiology,UniversityofSantiagodeCompostela,
SantiagodeCompostela,ACoruña,Spain
A.Sánchez-Pérez
FacultyofVeterinaryScience,UniversityofSydney,Sydney,NSW,Australia
C.Sieiro
FacultyofSciences,DepartmentofMicrobiology,UniversityofVigo,Vigo,Pontevedra,Spain
©SpringerNatureSwitzerlandAG2019 3
T.G.Villa,M.Viñas(eds.),HorizontalGeneTransfer,
https://doi.org/10.1007/978-3-030-21862-1_1
4 T.G.Villaetal.
cases, biofilm breakage is accompanied by the release of cytoplasmic contents,
includinggenomicDNA(Maetal.2009),whichcancontributenotonlytobacterial
antibioticresistance(Tetzetal.2009;SadykovandBayles2012)butalsopromote
horizontalgenetransfer(MolinandTolker-Nielsen2003).
WhenAvery,MacLeod,andMcCartyunraveled,in1944,thechemicalnatureof
theGriffith’s“transformationprinciple,”theynotonlydiscoveredthegeneticbasis
of inheritance but also shed light into the many then unknown aspects of bacterial
genetics. In fact, the main conclusion of their publication was: “The evidence
presented supports the belief that a nucleic acid of the desoxyribose type is the
fundamentalunitofthetransformingprincipleofPneumococcusTypeIII.”
ThestoryofthebacterialtransformationprocessstartedinEnglandwithFrederick
Griffith(1879–1941)who,after8yearsoflongandpatientwork,published(1928)one
ofthemostpivotalpapersinmicrobiology.Hisarticle,thatisknownworldwideasthe
Griffith’s experiment, reported that he successfully transformed an attenuated,
nonencapsulated (denominated R, for rough colonies) bacteria into a fully encapsu-
lated, virulent (known as S, for smooth colonies) strain. He, nonetheless, could not
identify the chemical nature of the transforming principle. Griffith’s results were
confirmedthesameyearbyDawson(1928),who2yearslater(Dawson1930)further
expandedhisresearchonthetransformationofS.pneumococci.Theseearlypublica-
tionsonthestreptococcaltransformationprocesswerefollowedbynumerousothers,
many originating from Dawson’s group at the Rockefeller Institute for Medical
ResearchintheUSA,whicharecurrentlyoverlookedbymicrobiologists(forinstance,
the publications in 1923 by Heidelberger and Avery and in 1923 by Avery and
Heidelberger, as well as the 1925 article by Avery et al.). Genetic transformation is
notidenticalinalltypesofbacteria,infactthereareprofounddifferencesbetweenthis
processinGram-positiveandGram-negativeorganisms,seebelow.
Research carried out in the second half of the twentieth century demonstrated a
high complexity in bacterial genomes. In this manner, a typical bacterium can
contain, in addition to its own chromosome, several replicons that are capable of
interacting with one another and even form stable co-integrates. They include not
only plasmids but also bacteriophages that can integrate into the bacterial chromo-
someeitheratspecificpoints,suchasbacteriophageλ,oratdifferentpositions(i.e.,
P2). In addition, some replicons can integrate virtually anywhere in the bacterial
chromosome and can, hence, originate a variety of different mutations, some of
whicharelethaltothebacterialhost(i.e.,Mubacteriophage).
For many years, bacterial transformation constituted the only horizontal gene
transfer process fully demonstrated and documented in nature. But in the 1940s, a
secondprocesswasdescribedbyLederbergandTatum(1946),whodenominatedit
“bacterialconjugation”,asitwasreminiscent ofthe“true”eukaryoticconjugation;
althoughitrequiresphysicalcontactbetweenbothpartners,itinvolvesthetransferof
a single chain of double-stranded DNA. It was initially thought that all bacterial
conjugationfollowedthemodelofE.coli(Wollmanetal.1956),but,infact,there
aremanytypesofbacterialconjugation,andsomeofthemareexceedinglydifferent
fromtheprocessundergonebyEnterobacteriaceae.
Transduction,thethirdclassicalwayofHGTinbacteria,ismediatedbybacterial
viruses, known as bacteriophages or phages. Although bacteriophages were
HorizontalGeneTransferinBacteria,anOverviewoftheMechanismsInvolved 5
discoveredatthebeginningofthetwentiethcenturybyTwort(1915)andD’Herelle
(1917), their ability to transfer genetic material was not recognized until 1952.
Norton Zinder and Joshua Lederberg (1952) demonstrated that these subcellular
structurescantransfergeneticpropertiesbetweendifferentbacterialstrains,andeven
between unrelated bacterial species. Zinder and Lederberg concluded: “The mech-
anismofgeneticexchangefoundintheseexperimentsdiffersfromsexualrecombi-
nation in E. coli in many respects so as to warrant a new descriptive term,
transduction.”Inaddition,thesenewultramicroscopicviruses,asTwortreferredto
them, were soon used in the therapy of certain bacterial diseases, such as in the
treatment of bacterial dysentery. It must be noted that all three mechanisms, trans-
formation, transduction, and conjugation, are limited by restriction-modification
(R-M) systems. This means that, for naked DNA or a phage DNA to be protected
fromdegradationbytherecipientstrainrestrictases,itmustbederivedfromahost
possessingthesameR-Msystemastherecipientbacteria,henceprotectingtheDNA
bymethylation.This,inturn,determineshowquicklygeneticmarkersaretransmit-
ted by HGT. Transmission is fast for DNA protected from degradation, while
unprotected DNA is disseminated at a much slower rate. In accordance, the
restriction-modification (R-M) system can potentially hinder bacterial HGT, as
indicated by Johnston et al. in 2013. In fact, while the three HGT mechanisms
increase genetic diversity, the R-M system is set to minimize bacterial genetic
diversity, by degrading foreign DNA to protect bacteria from either bacteriophage
infection or from naked DNA that could have a detrimental effect on the recipient
strain.
2 Transformation
This chapter will only address “natural” bacterial transformation, defined as an
exceptional ability of certain bacteria to accept naked DNA (either dsDNA or
ssDNA; Miao and Guild 1970). This precludes the inclusion of bacteria, such as
Escherichiacoli,lackingthatnaturalprocess,althoughtheyareofgreatimportance
tomicrobiologistsandbiotechnologists.
A review of the literature on genetics and microbiology in the early twentieth
centuryrevealsthatthescientistsofthetimewereconstantlyfocusingtheirattention
onthefactthatbacteriainpureculturecouldundergodramatictransformations,not
onlyintheirmetabolicabilitiesbutevenintheirmorphologicalappearance,bothat
thecellularandcolonylevel.Asanexample,hereisanextractfromtheDuvaland
Couret(1912,TulaneUniversity,NewOrleans,Louisiana,USA)publicationonthe
experimental production of leprosy in the monkey Macacus rhesus: “The experi-
mentalworkservesnotonlytoemphasizethisfact,butisproofthatatransformation
fromtheslenderbeadedrodsofthetissuestosolidlystainingdiplococcoidformsof
culture does occur for Bacillus leprae; and, conversely, that the coccoid forms of
culturemayagainassumetheslenderbeadedappearancebypassagethroughwarm-
bloodedanimals.”Advancesinbacterialtransformationstartedtogathermomentum
aftertheFrederickGriffithpublicationin1928,althoughthechemicalnatureofthe
