Genomics of Actinobacteria: Tracing the Evolutionary History of an

54 Pages·2007·1.52 MB·English

MICROBIOLOGYANDMOLECULARBIOLOGYREVIEWS,Sept.2007,p.495–548 Vol.71,No.3
1092-2172/07/$08.00(cid:1)0 doi:10.1128/MMBR.00005-07
Copyright©2007,AmericanSocietyforMicrobiology.AllRightsReserved.
Genomics of Actinobacteria: Tracing the Evolutionary History of
an Ancient Phylum†
Marco Ventura,1* Carlos Canchaya,2 Andreas Tauch,3 Govind Chandra,4
Gerald F. Fitzgerald,2 Keith F. Chater,4 and Douwe van Sinderen2*
DepartmentofGenetics,BiologyofMicroorganisms,Anthropology,Evolution,UniversityofParma,Parma,Italy1;
Alimentary Pharmabiotic Centre and Department of Microbiology, National University of
Ireland, Cork, Ireland2; Institute for Genome Research and Systems Biology Center for
Biotechnology,BielefeldUniversity,Universitaetsstrasse25,D-33615Bielefeld,
Germany3;andDepartmentofMolecularMicrobiology,JohnInnesCentre,
NorwichResearchPark,Colney,Norwich,UnitedKingdom4
D
o
w
INTRODUCTION.......................................................................................................................................................497
n
GeneralFeaturesofActinobacteria.......................................................................................................................497 lo
EvolutionandDynamicsofBacterialGenomes.................................................................................................497 a
Geneduplications...............................................................................................................................................497 d
e
HGT......................................................................................................................................................................497 d
Genedecay...........................................................................................................................................................498 f
r
Genomerearrangements....................................................................................................................................498 o
m
TaxonomyofActinobacteria....................................................................................................................................498

ActinobacterialGenomeSequencingProjects.....................................................................................................498 h
t
GENOMICSOFBIFIDOBACTERIUM....................................................................................................................499 tp
GeneralFeatures.....................................................................................................................................................499 :/
/
ComparativeBifidobacterialGenomeAnalysis..................................................................................................501 m
DNARegionsAcquiredbyHGTinBifidobacterialGenomes..........................................................................501 m
Prophage-LikeElementsinBifidobacteria..........................................................................................................501 b
r
ExtrachromosomalDNAElements.......................................................................................................................502 .a
BifidobacteriaandCarbohydrateMetabolism....................................................................................................502 s
m
BifidobacteriaandPrebioticProperties..............................................................................................................503
.
InteractionofBifidobacteriawiththeGIT.........................................................................................................504 o
r
GENOMICSOFTROPHERYMA..............................................................................................................................504 g
/
GeneralFeatures.....................................................................................................................................................504 o
TropherymaComparativeGenomeAnalysis........................................................................................................504 n

DNARegionAcquiredbyHGTinT.whippleiGenomes...................................................................................504 A
TropherymaGenomeandBiologicalLifestyle.....................................................................................................505 p
r
InteractionofTropherymawiththeEnvironment..............................................................................................505 il
GENOMICSOFPROPIONIBACTERIUM...............................................................................................................506 1
1
GeneralFeatures.....................................................................................................................................................506 ,

ExtrachromosomalDNAElementsinPropionibacterium..................................................................................506 2
0
DNARegionAcquiredbyHGT.............................................................................................................................506 1
Prophage-LikeElementsinPropionibacterium....................................................................................................506 9

P.acnesGenomeandBiologicalLifestyle...........................................................................................................506 b
y
InteractionofP.acneswithItsEnvironment.....................................................................................................508
g
GENOMICSOFMYCOBACTERIUM......................................................................................................................508 u
e
GeneralFeatures.....................................................................................................................................................508
s
GenomicsofM.tuberculosis...................................................................................................................................508 t
M.tuberculosisgenomearchitecture.................................................................................................................509
M.tuberculosisgenomeandbiologicallifestyle...............................................................................................509
ComparativegenomicswithintheM.tuberculosiscomplex...........................................................................509
*Corresponding author. Mailing address for Marco Ventura: De-
partmentofGenetics,BiologyofMicroorganisms,Anthropologyand
Evolution,UniversityofParma,parcoAreadelleScienze11a,43100
Parma, Italy. Phone: [phone]. Fax: [phone]. E-mail:
[email protected]. Mailing address for Douwe van Sinderen:
Alimentary Pharmabiotic Centre and Department of Microbiology,
Bioscience Institute, National University of Ireland, Western Road,
Cork, Ireland. Phone: [phone]. Fax: [phone]. E-mail:
[email protected].
†Supplementalmaterialforthisarticlemaybefoundathttp://mmbr
.asm.org/.
495
496 VENTURA ET AL. MICROBIOL.MOL.BIOL.REV.
Prophage-likeelementsinM.tuberculosis.......................................................................................................510
GenomicsofM.bovis..............................................................................................................................................511
M.bovisgenomearchitecture............................................................................................................................511
M.bovisgenomeandbiologicallifestyle..........................................................................................................511
ComparativeGenomicsofM.bovisandM.tuberculosis....................................................................................511
GenomicsofM.leprae............................................................................................................................................511
GenomicsofM.aviumsubsp.paratuberculosis....................................................................................................513
ExtrachromosomalDNAElementsinMycobacterium........................................................................................513
GENOMICSOFNOCARDIA....................................................................................................................................514
GeneralFeatures.....................................................................................................................................................514
NocardiaComparativeGenomeAnalysis.............................................................................................................514
ExtrachromosomalDNAElementsinNocardia..................................................................................................514
N.farcinicaGenomeandBiologicalLifestyle......................................................................................................514
GENOMICSOFCORYNEBACTERIUM..................................................................................................................514
GeneralFeatures.....................................................................................................................................................514
CorynebacteriumGenomeArchitecture.................................................................................................................515 D
o
CorynebacteriumComparativeGenomeAnalysis................................................................................................516 w
DNARegionsinC.glutamicumAcquiredbyHGT.............................................................................................517 n
Prophage-LikeElementsintheC.glutamicumGenome....................................................................................518 lo
DNAAcquiredbyHGTintheC.efficiensGenome............................................................................................518 a
d
Prophage-LikeElementintheGenomeofC.diphtheriae.................................................................................519 e
DNARegionsintheC.diphtheriaeGenomeAcquiredbyHGT.......................................................................519 d

DNARegionsintheC.jeikeiumGenomeAcquiredbyHGT............................................................................519 fr
o
ExtrachromosomalDNAElements.......................................................................................................................520 m
CorynebacterialGenomesandBiologicalLifestyle............................................................................................521
h
AdherencetopharyngealepithelialcellsbyC.diphtheriae...........................................................................521 t
t
AdaptationtoaminoacidproductionbyC.glutamicumandC.efficiens....................................................521 p
:
AdaptationtoelevatedtemperaturesbyC.efficiens.......................................................................................521 //
m
AdaptationtothelipophiliclifestylebyC.jeikeium.......................................................................................521
m
GENOMICSOFLEIFSONIA....................................................................................................................................522
b
GeneralFeatures.....................................................................................................................................................522 r
.
ExtrachromosomalDNAElementsinLeifsonia.................................................................................................522 a
s
DNARegionsAcquiredbyHGTinLeifsonia......................................................................................................522 m
Prophage-LikeElementsinLeifsonia...................................................................................................................522 .
o
L.xylisubsp.xyliGenomeandBiologicalLifestyle...........................................................................................522 r
g
GENOMICSOFTHEMYCELIALACTINOBACTERIA:STREPTOMYCES,FRANKIA,AND /

THERMOBIFIDA.................................................................................................................................................523 o
n
GeneralFeatures.....................................................................................................................................................523
A
ArchitectureofMycelialActinobacterialGenomes............................................................................................523
p
ComparativeGenomicsofMycelialActinobacterialGenomes.........................................................................524 r
Multiplyrepresentedmetabolicgenes.............................................................................................................525 il
1
GenesunexpectedlymissingfrommycelialActinobacteria............................................................................525 1
,
Conservonsandtransposons.............................................................................................................................525
2
DNARegionsinMycelialActinobacterialGenomesAcquiredbyHGT.........................................................525 0
1
StreptomycesExtrachromosomalElements..........................................................................................................526
9
Prophage-LikeElementsinStreptomyces.............................................................................................................526
b
MycelialActinobacterialGenomesandBiologicalLifestyle.............................................................................526 y

Ecology..................................................................................................................................................................526 g
u
Secondarymetabolism........................................................................................................................................527 e
P450cytochromes(CYPs)..................................................................................................................................527 s
t
Development........................................................................................................................................................527
SpecializeduseoftherareUUAleucinecodon..............................................................................................529
COMPARATIVEGENOMICSOFACTINOBACTERIA........................................................................................530
SyntenyofActinobacterialGenomes....................................................................................................................530
ActinobacterialCoreGenomeSequences:Phylogenomics................................................................................531
IMPACTOFACTINOBACTERIALGENOMICSONTAXONOMY.................................................................531
NewApproachestoInvestigateTaxonomicRelationshipsinActinobacteriaBasedonWhole-Genome
Sequences.............................................................................................................................................................534
ActinobacterialTaxonomyBasedonMultilocusApproach..............................................................................536
CONCLUSIONS.........................................................................................................................................................537
ACKNOWLEDGMENTS...........................................................................................................................................538
REFERENCES............................................................................................................................................................538
VOL.71,2007 GENOMICS OF ACTINOBACTERIA 497
INTRODUCTION tracetheevolutionarydevelopmentofbacteriabasedontheir
currentgenomestructure(8,183,243,398).
GeneralFeaturesofActinobacteria
Gene duplications. It was previously thought that bacterial
genomeshaveevolvedfromamuchsmallerancestralgenome
In terms of number and variety of identified species, the
throughnumerousgeneduplicationeventsandtheconsequent
phylumActinobacteriarepresentsoneofthelargesttaxonomic
generation of paralogs (244). However, an analysis based on
unitsamongthe18majorlineagescurrentlyrecognizedwithin
thecurrentlyavailablebacterialgenomedatadoesnotsupport
the domain Bacteria (406), including 5 subclasses and 14 sub-
this theory and shows that gene duplications contribute only
orders (404). It comprises gram-positive bacteria with a high
G(cid:1)C content in their DNA, ranging from 51% in some modestly to genome evolution (79). Despite this, it has been
noted that genes involved in a specific adaptation have been
corynebacteriatomorethan70%inStreptomycesandFrankia.
preserved after duplications, suggesting that gene duplication
An exception to this is the genome of the obligate pathogen
Tropherymawhipplei,withlessthan50%G(cid:1)C. doeshaveanevolutionaryrole(79).Thisisnicelyillustratedby
the mycobacterial paranome, which largely corresponds to a
Actinobacteria exhibit a wide variety of morphologies, from
functionalclassofgenesinvolvedinfattyacidmetabolism,in
coccoid (Micrococcus) or rod-coccoid (e.g., Arthrobacter ) to D
fragmenting hyphal forms (e.g., Nocardia spp.) or permanent agreement with the complex nature of the mycobacterial cell o
wallandprobablyreflectingadaptiveevolutionofthiscellular w
and highly differentiated branched mycelium (e.g., Streptomy- n
cesspp.)(15).Theyalsoexhibitdiversephysiologicalandmet- structure(79,432). lo
HGT. The introduction of novel or alien genes by HGT a
abolic properties, such as the production of extracellular en-
d
zymes and the formation of a wide variety of secondary allows for rapid niche-specific adaptation, which in turn may e
lead to bacterial diversification and speciation (80). Bacterial d
metabolites (389). Notably, many such secondary metabolites
arepotentantibiotics(255),atraitthathasturnedStreptomyces genomeevolutionisbasedonthecombinedoutcomeofgenes fro
species into the primary antibiotic-producing organisms ex- acquiredthroughcelldivision,i.e.,verticallyinherited,andby m
ploitedbythepharmaceuticalindustry(29).Furthermore,var- HGT(482).Takingthisconcepttoitsextreme,onecanclaim h
iousdifferentlifestylesareencounteredamongActinobacteria, thattwobacterialtaxaaremorerelatedtoeachotherthanto ttp
andthephylumincludespathogens(e.g.,Mycobacteriumspp., athirdonenotbecausetheyshareamorerecentancestorbut :/
/
because they exchange genes more frequently (151). HGT is m
Nocardia spp., Tropheryma spp., Corynebacterium spp., and
heldresponsibleforenhancingthecompetitivenessofbacteria m
Propionibacterium spp.), soil inhabitants (Streptomyces spp.),
in their natural environments. For example, in some patho- b
plant commensals (Leifsonia spp.), nitrogen-fixing symbionts r
(Frankia), and gastrointestinal tract (GIT) inhabitants (Bi- genic bacteria, segments of DNA containing many virulence .a
s
fidobacterium spp.). Unusual developmental features are dis- genesandgeneclusters,calledpathogenicityislands,appearto m
played by many actinobacterial genera, such as formation of have been acquired by HGT (321). Actinobacterial examples .o
sporulatingaerialmyceliuminStreptomycesspeciesortheper- of transmission of virulence genes through HGT are rare rg
(376).Ofthese,thefollowingthreecasesappeartorepresent /
sistentnonreplicatingstateexhibitedbycertainmycobacteria.
o
Actinobacteria are widely distributed in both terrestrial and obviousHGTevents:(i)phagesofCorynebacteriumdiphtheriae n
aquatic(includingmarine)ecosystems,especiallyinsoil,where carry the major diphtheria toxin gene, (ii) a linear plasmid A
carries the genes for the macrolide toxin responsible for the p
theyplayacrucialroleintherecyclingofrefractorybiomate- r
rials by decomposition and humus formation (152, 403). Fur- ulceration that gives Mycobacterium ulcerans its name (411), il
1
thermore,manybifidobacteriaareusedasactiveingredientsin and (iii) a large segment of the chromosome of Streptomyces 1
a variety of so-called functional foods due to their perceived turgidiscabiesconcernedwithcausingpotatoscabcanbetrans- , 2
health-promoting or probiotic properties, such as protection ferred by conjugation (280). In addition, it has been argued 0
1
against pathogens mediated through the process of competi- that the Mycobacterium tuberculosis Rv0986-8 virulence 9
tiveexclusion,bilesalthydrolaseactivity,immunemodulation, operon, which plays an important role in parasitism of host b
phagocytic cells by increasing the ecological fitness of the in- y
andtheabilitytoadheretomucusortheintestinalepithelium
g
(273,329,407). fectingmycobacterium(339),wasacquiredhorizontallybythe u
ancestor of M. tuberculosis, Mycobacterium prototuberculosis. e
The actinobacterial genomes sequenced so far belong to s
OthergeneticstudiesoftheancestralM.prototuberculosisspe- t
organismsrelevanttohumanandveterinarymedicine,biotech-
cies have indicated that various HGT events occurred before
nology,andecology,andtheobservedgenomicheterogeneity
theevolutionarybottleneckthatledtotheemergenceoftheM.
isassumedtobeareflectionoftheirbiodiversity.Thisreview
tuberculosis complex (167), probably from the Indian subcon-
willgiveanaccountoftherecentexplosionofactinobacterial
tinent(124).
genomicsdataandwillplacethisinabiologicalandevolution-
Bioinformatic methods to identify HGT events are based
arycontext.
principally on the analysis of divergence in the G(cid:1)C content
(GC deviation), dinucleotide differences, four-letter genomic
EvolutionandDynamicsofBacterialGenomes signatures,and/orcodonusage,thoughgeneticistswouldoften
be satisfied with HGT as the explanation for genes found in
The principal genetic events that determine genome shape onlyoneorganism.Ifthelatteriscorrect,itwouldmeanthat
and structure are believed to be gene duplication, horizontal HGT frequency is rather low (below 10% of the total gene
genetransfer(HGT),geneloss,andchromosomalrearrange- complement) (243, 398). Interestingly, a recent analysis
ments. Despite efforts to quantify the relative contribution of showedthatmanyoftheproteinsthatappearedtobespecific
eachoftheseprocesses,noreliablemodelcanyetexplainand for actinobacteria are also encoded by the genome of an al-
498 VENTURA ET AL. MICROBIOL.MOL.BIOL.REV.
phaproteobacterium, Magnetospirillum magnetotacticum, but eliminated rapidly, and thus only rarely persist in bacterial
not by any other sequenced alphaproteobacterial genome, genomes(320).Otherbacteriashowalowerlevelofgeneloss:
leading to the proposal that M. magnetotacticum acquired intheobligateintracellularpathogenRickettsiaprowazekiionly
thesegenesbyHGTfromactinobacterialspecies(137). 76% of the potential coding capacity is used, while just 12
TwootherinterestingcasesofHGTbetweenChlamydiaand pseudogeneswereidentified(9);andarecentgenomeanalysis
a subset of Actinobacteria (e.g., Streptomyces, Tropheryma, Bi- oftwoStreptococcusthermophilusstrains(33)foundthat10%of
fidobacterium, Leifsonia, Arthrobacter, and Brevibacterium) thegeneswerepseudogenes,perhapsreflectingadaptationofS.
have recently been described (158). In the enzyme serine hy- thermophilustoitsspecializedenvironment,milk(33).
droxymethyltransferase(GlyAprotein),twoconservedinserts Whenallbacterialgenomesarecomparedwitheachother,
of3and31aminoacids(aa)arepresentinvariouschlamydiae asetofonly50to100genes,whicharecalledthecoregenome
aswellastheabove-mentionedsubsetofActinobacteria.Sim- sequences, appear to be maintained universally (for a review,
ilarly,thesebacteriacontainaconserved16-amino-acidinsert seereference147).
in the peptidoglycan biosynthesis enzyme UDP-N-acetylglu- Genome rearrangements. Apart from the events described
cosamineenolpyruvyltransferases(MurA).Thefunctionaland intheprevioussectionsthataffectgenecontent,theorganiza-
D
physiological significance of these apparent HGT events be- tion of a genome is subject to change through chromosome o
tweenchlamydiaeandActinobacteriaispresentlyunclear. rearrangements. Synteny, a term used here to indicate the w
n
Gene decay. Bacterial genome size is determined by the conservation of gene order between genomes, can be applied lo
outcomeofseveralopposingforces.Deletionbiasandgenetic asaphylogenetictooltoinvestigaterelationshipsbetweenspe- a
d
driftcausegenomestocontract,whileselectionongenefunc- cies, since the degree of genome rearrangements increases e
tionpromotesgenomestopreserveDNA.Genomeincrements linearly in relation to the time of divergence of bacterial taxa d

depend on both gene duplications and acquisition of alien (236,484). fr
o
DNA,coupledtoadaptivebenefits(293).DNAlossmayrange Chromosomalrearrangementsarelargelydependentonthe m
fromlargedeletionsthatspanmultiplelocitodeletionsofone activity of repeated and mobile elements such as insertion h
orafewnucleotides(7).Theinfluenceofthesedifferentroutes sequences (ISs), transposons, prophage sequences, and plas- tt
p
is variable among bacterial lineages (293). Inactivating and mids(233).Bacterialgenomescontainingahigherrepeatden- :
/
/
deleteriousmutationsingeneswithlittlecontributiontofitness sity have higher rates of rearrangements, leading to an accel- m
canbetransmittedtoprogenyandaccumulateinpopulations, erated loss of gene order (371). Homologous recombination m
eventually leading to gene loss; whereas such mutations in events between such repeat sequences catalyze both gene re- b
r
genes that are critical will prevent the production of progeny arrangement and gene loss in the genome, thus leading to .a
s
and so will be eliminated from populations, resulting in the diversification of taxa. Such recombination events may have m
preservationofthefunctionalgene(320). promoted speciation in the T. whipplei taxon (357). Further- .
o
Geneinactivationandlossareparticularlyapparentinsev- more, chromosome evolution is influenced by large chromo- r
g
eral bacterial groups with a host-associated lifestyle, in which somalrearrangements,e.g.,largeinversions,roughlysymmet- /

o
thehostsuppliesmanyofthemetabolicintermediates,thereby ricallycenteredaroundthereplicationorigin,whichleadtothe n
obviating the need to maintain many biosynthetic genes. In occurrence of X-shaped patterns in the alignments of whole A
endosymbiotic bacteria, such as Buchnera and Rickettsia, loss genomes(117). p
r
ofindividuallocioroperonsistheonlysourceofdivergencein il
1
the gene inventories between species (289, 419). A clear ex- 1
ample of genome degradation is provided by Mycobacterium TaxonomyofActinobacteria ,
2
leprae, which has discarded more than 1,000 genes compared 0
Actinobacteriaincludemanyorganismsthatexhibit,orhave 1
with M. tuberculosis (84). Moreover, the presence of an even atendencytowards,mycelialgrowth.16SrRNAgenesequenc- 9
larger set of nonfunctional genes, i.e., pseudogenes, in M. b
ing has led to the recognition of 39 families and 130 genera,
leprae indicates that this genome contraction is still in progress. y
whichalsoincludehigh-G(cid:1)Cgram-positivebacteriawithsim- g
Althoughthecriteriaforidentifyingpseudogenesdifferamong plermorphology,suchasbifidobacteriaandmicrococci(Fig.1) u
studies,theoverallrationaleisidentical:thepredictedprotein e
(119). The deepest branch separates bifidobacteria from all s
must be altered to a degree that abolishes its function. The t
other known families. The divergence of actinobacteria from
thresholdsappliedforpseudogeneidentificationarebasedon
otherbacteriaissoancientthatitisnotpossibletoidentifythe
theknownsizeandorganizationoffunctionaldomainswithin
phylogenetically closest bacterial group to Actinobacteria with
proteins, the observed length variation within individual gene
confidence(119).
families, and available information on experimentally dis-
Actinobacteriahaveauniquemolecularsynapomorphy,i.e.,
ruptedproteins(320).Generally,pseudogenesincludecasesin
a shared derived character: a homologous insertion of about
which a stop codon or deletion has resulted in an encoded
100 nucleotides between helices 54 and 55 of the 23S rRNA
protein that is less than 80% of the length of its functional
gene(375).
counterpart in the contrasted genome and cases in which a
frameshift or insertion has altered more than 20% of the
amino acid sequence (263). Most of the pseudogenes so far
ActinobacterialGenomeSequencingProjects
annotated in bacterial genomes are among the open reading
frames (ORFs) whose functions are unknown. The lack of Thefirstactinobacterialgenometobesequencedwasthatof
pseudogenes shared among multiple strains of the same spe- theparadigmstrainofthehumantuberculosisagent,M.tuber-
cies suggests that pseudogenes are generated continually, are culosis H37Rv (83). In the last few years, genomes of 20 dif-
VOL.71,2007 GENOMICS OF ACTINOBACTERIA 499
D
o
w
n
lo
a
d
e
d

f
r
o
m

h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
FIG. 1. PhylogenetictreeofActinobacteriabasedon1,500nucleotidesof16SrRNA.Scalebar,5nucleotides.Familiescontainingmembers .o
subjectedtocompletegenomesequencingatthetimeofthiswritingaredepictedinbold.Ordersareindicated. r
g
/

o
n
ferent Actinobacteria (in some cases multiple strains of the GENOMICSOFBIFIDOBACTERIUM A
same species) have been sequenced to completion (Table 1), p
GeneralFeatures r
whilesequencingofgenomesfromrepresentativesof43other il
high-G(cid:1)C bacteria are still in progress (Table 1) (http://www The Bifidobacteriaceae family comprises four genera, Bi- 11
.ncbi.nlm.nih.gov/genomes/lproks.cgi). fidobacterium,Gardnerella,Scardovia,andParascardovia(404), , 2
Although most of the sequenced genomes in Table 1 are 0
of which only the first contains more than one species. Bi- 1
circular, like most bacterial genomes, Streptomyces genomes fidobacteria form a deep-branching lineage within the Acti- 9
arelinear.Usingpulsed-fieldgelelectrophoresis,thegenomes b
nobacteria (136, 137). The Bifidobacterium genus contains six
of some other, still-unsequenced mycelial Actinobacteria taxa, y
phylogeneticclusters,namedB.boum,B.asteroides,B.adoles- g
suchasActinomyces,Amycolatopsis,Actinoplanes,Streptoverti- u
centis,B.longum,B.pullorum,andB.pseudolongum(448).
cillium, and Micromonospora, were also shown to be linear, e
Bifidobacteria are nonmotile, nonsporulating, non-gas-pro- s
withsizesrangingfrom7.7Mb(e.g.,Micromonosporachalcea) t
ducing, anaerobic, and saccharoclastic bacteria. They have
to9.7Mb(Streptoverticilliumabikoense),whilesometimesalso
beenisolatedfromfivedifferent,thoughsomewhatconnected,
harboring large linear plasmids (362). Linear plasmids, typi-
ecologicalniches:theintestine,theoralcavity,food,theinsect
cally possessing short inverted repeats at their termini and
protein-bound 5(cid:2) ends, are often present in Actinobacteria gut,andsewage.ThosethatinhabittheGIT(e.g.,B.breve,B.
(216). longumbiotypelongum,andB.longumbiotypeinfantis)have
Belowweexaminerelevantgenomicinformationfromsome been the subject of growing interest due to their probiotic
ofthebest-knownactinobacterialtaxa(Bifidobacterium,Myco- properties. Bifidobacteria ferment a large variety of oligosac-
bacterium, Streptomyces, Corynebacterium, Thermobifida, Leif- charidesintheGIT,someofwhich,inparticularthosethatare
sonia,Frankia,Nocardia,Propionibacterium,andTropheryma), not digested by their host, are commercially exploited to en-
partially in the light of what is known for Escherichia coli or hancebifidobacterialnumbers(aswellasotherprobioticbac-
Bacillussubtilis,asparadigmsofgram-negativeproteobacteria teria) in situ, a practice that is referred to as the prebiotic
andgram-positivelow-G(cid:1)C-contentbacteria,respectively.We concept(146).
discusshowgenomicinformationcanbeusedtogaininsights Of the currently recognized 29 Bifidobacterium species,
intothephysiology,genetics,andevolutionofActinobacteria. three strains that belong to the B. longum and B. adolescentis
500 VENTURA ET AL. MICROBIOL.MOL.BIOL.REV.
TABLE 1. Publisheddataforactinobacterialgenomes
Genome No.of %G(cid:1)C No.ofrRNA No.of No.of
Microorganism Reference
size(bp) ORFs content operons tRNAs pseudogenesa
Bifidobacteriumlongum 2,266,000 1,730 60 4 66 ND 384
biotypelongumNCC2705
Corynebacteriumdiphtheriae 2,488,635 2,320 53.5 5 54 48 60
NCTC13129
Corynebacteriumefficiens 3,147,090 2,950 63.4 5 56 ND 316
YS-314
Corynebacteriumglutamicum 3,309,401 2,993 53.8 5 60 ND 195
ATCC13032
Corynebacteriumjeikeium 2,462,499 2,104 61.4 3 50 68 427
K411
FrankiaalniACN14a 7,497,934 6,786 72 2 62 12 319
Frankiasp.strainCc13 5,433,628 4,618 70 2 61 50 NCBIsource
NC_007777 D
Leifsoniaxylisubsp.xyli 2,584,158 2,351 67.7 1 49 307 300 o
CTCB07 w
Mycobacteriumaviumsubsp. 4,829,781 4,350 69.3 1 47 0 268 n
paratuberculosisK-10 lo
a
Mycobacteriumbovis 4,345,492 3,953 65.63 1 49 23 139 d
AF2122/97 e
MycobacteriumlepraeTN 3,268,203 1,605 57.79 1 49 1116 84 d

Mycobacteriumtuberculosis 4,411,532 3,994 65.61 1 49 6 83 fr
o
H37Rv
m
Mycobacteriumtuberculosis 4,403,836 4,250 65.60 1 49 ND 126

CDC1551 h
t
Mycobacteriumsp.strain 5,705,448 5,391 68 2 59 21 NCBIsource t
p
MCS NC_008146 :
/
Nocardiafarcinica 6,021,225 5,674 70.8 3 61 0 198 /m
IFM10152 m
Propionibacteriumacnes 2,560,265 2,297 60 3 51 17 46
b
KPA171202 r
.
StreptomycescoelicolorA3 8,667,507 7,769 72 6 80 56 26 a
Streptomycesavermitilis 9,025,608 7,577 70 6 82 0 194 s
m
MA-4680
.
ThermobifidafuscaYX 3,642,249 3,110 67 4 63 7 281 o
r
Tropherymawhipplei 925,938 783 46 1 54 1 27 g
TW08/27 /
o
TropherymawhippleiTwist 927,303 808 46 1 54 0 357 n

aND,notdetermined. A
p
r
il
1
phylogeneticgroupshavebeensequencedtocompletion(Ta- in the nucleotide composition of the leading DNA strand 1
,
ble2),whilethesequencesofothers,e.g.,B.dentiumBd1,are (129); and a typical presumptive origin-of-replication region 2
atvariousstagesofcompletion:detailedsequenceinformation (350),includingageneconstellationneartheorigin(compris- 0
1
for some of these genomes is expected to become publicly ingrpmH,dnaA,dnaN,andrecF),aparticularGCnucleotide 9
availableinthenearfuture.Furthermore,genomesequencing skew ([G-C]/[G(cid:1)C]), and the presence of multiple DnaA b
y
ofB.breveM-16V,B.breveYacult,B.animalissubsp.lactis,B. boxes and AT-rich sequences immediately upstream of the
g
longumbiotypelongum,andB.longumbiotypeinfantis(276)is dnaAgene(77). u
e
under way. These genomes range in size from 1.9 to 2.9 Mb The number of rRNA operons in bifidobacteria varies be- s
andgenerallydisplayarchitecturalfeaturesofatypicalbacte- tweenoneandfive(58),perhapsreflectingdifferentecological t
rialchromosome.Someofthesearetheco-orientationofgene strategies(230).ThenumberoftRNAgenesinthebifidobac-
transcriptionandDNAreplication(288);aG-rich,C-poorbias terialgenomessequencedsofarisrelativelystable,i.e.,54and
TABLE 2. Generalfeaturesofbifidobacterialgenomes
Genomesize No.of %G(cid:1)C No.ofrRNA
Microorganism Statusa Reference
(bp) ORFs content operonsb
B.longumbiotypelongumNCC2705 C 2,266,000 1,730 60 4 384
B.longumbiotypelongumDJO10A UF 2,375,800 1,811 59 4 NCBIsourceNZ_AABM00000000
B.adolescentisATCC15703 C 2,084,445 1,564 59 5 NCBIsourceNC_008618
B.breveUCC2003 C 2,422,668 1,868 59 2 254
B.dentiumBd1 UF (cid:3)2,600,000 (cid:3)2,270 59.2 NA NCBIsource(projectID17583)
aC,finished;UF,unfinished.
bNA,notavailable.
VOL.71,2007 GENOMICS OF ACTINOBACTERIA 501
D
o
w
n
lo
FIG. 2. Comparativegenomemapsoftheprophage-likeelementsdetectedinBifidobacteriumgenomes.Genessharingsimilarityarelinked. a
d
Probablefunctionsofencodedproteinsidentifiedbybioinformaticanalysisareindicated.Themodularstructureiscolorcoded:red,lysogeny;
e
green,DNApackagingandhead;blue,tail;mauve,tailfiber;violet,lysismodule;yellow,transcriptionalregulator;orange,DNAreplication;gray, d
unknowngenes;black,genessimilartootherfunctionallyunknownbacteriophagegenes.Verticalbluelines,tRNAgenes. f
r
o
m

56 in B. breve UCC2003 and B. longum biotype longum inB.longumbiotypelongumNCC2705havebeenacquiredvia h
t
NCC2705, respectively. These are representative of all 20 HGT, as part of the adaptation of this organism to a specific tp
:
aminoacids,withredundanttRNAsforallaminoacidsexcept ecological niche. For example, a region encoding rhamnosyl /
/
m
cysteine,histidine,isoleucine,phenylalanine,andtryptophan. transferases seems to have been acquired from streptococci
m
(384), while two other regions that contain genes encoding
b
ComparativeBifidobacterialGenomeAnalysis restriction-modification systems also appear to have been ac- r.
a
quired through HGT. Overall, about 5% of the B. longum
s
Dot plot comparisons (at the nucleotide level) of the fully biotypelongumNCC2705genomecontentseemstohavebeen m
sequenced bifidobacterial genomes revealed a high degree of recentlyacquiredbythismechanism(384). .o
conservationandsyntenyacrosstheentiregenomes.,i.e.,those rg
of B. longum biotype longum NCC2705, B. longum biotype /
o
longum DJO10A, B. breve UCC2003, and B. adolescentis Prophage-LikeElementsinBifidobacteria n

ACC15703. Preliminary analysis against the draft genome se- A
quencesofB.dentiumBd1confirmedandextendedthisresult. Untilrecentlybifidobacteriawerenotconsideredtobesuit- p
r
However,therearealsoseveralbreakpointregionsthatseem able targets for phage infection. However, prophage-like ele- il
1
to represent inversions or DNA insertion/deletion points (S. ments, designated Bbr-1, Bl-1, and Blj-1, are present in the 1
LeahyandD.VanSinderen,unpublisheddata). genomes of B. breve UCC2003, B. longum biotype longum , 2
Recently,aB.longumbiotypelongumNCC2705-basedspot- NCC2705, and B. longum biotype longum DJO10A (455). 0
1
tedDNAmicroarraywasemployedtocomparethegenomesof These prophage-like elements display homology to genes of 9
10 bifidobacterial strains, including other B. longum biotype double-strandedDNAphagesthatinfectabroadphylogenetic b
longumstrainsaswellasthecloselyrelatedB.longumbiotype range of bacteria. Surprisingly, using the proteomic tree y
g
infantisandB.longumbiotypesuistaxa(232).Resultsrevealed method to investigate the evolution of these phages (373), it u
sevenlargegenomeregionsofvariability,themajorityofwhich became clear that the Bbr-1, Bl-1, and Blj-1 prophage-like es
encompassDNAwithadeviatingG(cid:1)Ccontent.Theseregions elementsexhibitaclosephylogeneticrelationshipwithphages t
correspond to a prophage remnant; a cluster of genes for infectinglow-G(cid:1)Cbacteria(e.g.,lactococcalandstaphylococ-
enzymesinvolvedinsugarmetabolism,suchasan(cid:4)-mannosi- cal phages) (455), perhaps because these bacteria and their
dase;andacapsularpolysaccharidebiosynthesisgenecluster, phageshavesharedthesameecologicalniche(i.e.,theanimal
whichcouldplayaroleinhost-bacteriuminteractions(seeFig. GIT)duringtheirevolution,therebyallowingDNAexchange.
S1inthesupplementalmaterial).Thoughveryuseful,microar- ThismaythereforepointtoDNAtransfereventsbetweenlow-
ray-basedcomparativegenomeanalysessufferfromsomelim- and high-G(cid:1)C bacteria. Perhaps such phages originally in-
itations.Itisnotpossibletoidentifyregionspresentinthetest fectedtheancestorofhigh-G(cid:1)Cgram-positivebacteria,inline
strainsbutabsentfromthestrainthatwasusedtoconstructthe with the concept that high-G(cid:1)C gram-positive bacteria origi-
array,anditwillgenerallynotallowsyntenystudies. natedfromlow-G(cid:1)Cancestors(455).TheunfinishedB.den-
tium Bd1 genome contains at least two prophage-like ele-
ments, one of which resembled that of the NCC2705 Bl-1
DNARegionsAcquiredbyHGTinBifidobacterialGenomes
prophage(Fig.2).Notably,allthreepublishedbifidobacterial
It has been suggested that selected genes involved in sugar prophage-like elements are integrated in a tRNAMet gene,
metabolismaswellasintheproductionofexopolysaccharides whichisthefirstcaseofthistRNAgeneasatargetforphage
502 VENTURA ET AL. MICROBIOL.MOL.BIOL.REV.
integration in any gram-positive or gram-negative bacterium necessaryfordegradingmostoftheseglycans(CAZydatabase;
(56). Analysis of the distribution of this integration site re- see below), which are supplied instead by the distal GIT mi-
vealedthattheattBsitesarewellconservedinmanybifidobac- crobiome (16). The human GIT microbiome is enriched in
terial species and in a phylogenetically unrelated bacterium, genesinvolvedinmetabolismofsugars,includingglucose,ga-
Thermosynechococcus elongatus BP-1 (306), but surprisingly lactose, fructose, arabinose, mannose, and xylose, as well as
notinothersequencedActinobacteria. other sugars that escape digestion by the host’s enzymes, in-
The 36.9-kb Blj-1 prophage is induced by mitomycin C or cludingmanyprebioticcompounds,suchasfructooligosaccha-
hydrogenperoxideandisthefirstreportedinducibleandmo- rides, galactooligosaccharides, glucooligosaccharides, xylooli-
lecularly characterized Bifidobacterium prophage, presenting gosaccharides, lactulose, and raffinose (for reviews, see
possibilitiesforfurtherstudiesonthebiologyofbifidophages. references 148, 161). Gill et al. (148) describe more than 81
Interestingly, the Blj-1 element possesses a putative reverse different glycoside hydrolase families distributed in a mixture
transcriptase-encodinggene,ahomologofwhichwasshownto ofanaerobicbacteria,i.e.,theGITmicrobiome,whichincludes
representadiversity-generatingretroelement(275,455). Bifidobacteriales, Clostridiales, Bacteroidales, Enterobacteriales,
The Bbr-1 and Bl-1 prophage-like elements appear to be Fusobacterales, Thermoanaerobacteriales, and Methanobacteria
D
defective prophages, although they may constitute functional (148, 447. Many of these enzymes are not represented in the o
satellitephages,whosemobilitydependsonhelperphagesina human glycobiome. Moreover, GIT mucus provides an abun- w
n
manner similar to that described for the cryptic mycophages dantreservoirofglycansformicrobiota,whichservetoreduce lo
Rv1andRv2(175,455). the effects of marked changes in the availability of dietary a
d
polysaccharides(16). e
Thetypeofsugaravailableislikelytoinfluencethespecies d
ExtrachromosomalDNAElements
composition and abundance of the microbiota along the GIT fr
o
Plasmidsarenotubiquitousinbifidobacteria(332,392),and (447). In this context, bacteria such as Lactobacillus are par- m
whenpresenttheyaresmall,i.e.,rangingfrom1.5kbto15kb. ticularly prevalent in the upper GIT, where they mainly fer- h
CompletelysequencedplasmidsfromdifferentB.longumbio- mentrelativelysimplemono-,di-,andtrisaccharides(447).In tt
p
type longum strains include pMB1 (378); pKJ36 and pKJ50 contrast,bacteriaactiveinthelowerpartsofthecolon,suchas :
/
/
(332,333);pBLO1(384);pNAC1,pNAC2,andpNAC3(95); bifidobacteria,probablyowetheirspecificecologicalsuccessto m
pDOJH10SandpDOJH10L(260);pTB6(421);pB44(GenBank their capacity to metabolize complex carbohydrates. It there- m
accessionnumberNC004443);andpNAL8(162).Inaddition,six forecomesasnosurprisethatgenesforcomplexsugarmetab- b
r
plasmidsfromotherbifidobacterialspecieshavebeensequenced: olismaboundinthegenomesofB.breveandB.longumbiotype .a
s
pVS809 from Bifidobacterium globosum (285), pCIBb1 from B. longum.Accordingtothesequence-basedclassificationofcar- m
breve (327), pNBb1 from B. breve (GenBank accession number bohydrate-active enzymes (CAZy), over 8% of the annotated .
o
E17316), pAP1 from B. asteroides (GenBank accession number genes of these bifidobacterial genomes may encode enzymes r
g
Y11549),pBC1fromBifidobacteriumcatenulatum(5),andp4M involvedinthemetabolismofcarbohydrates,includingvarious /

o
from Bifidobacterium pseudocatenulatum (GenBank accession glycosylhydrolasesforutilizationofdiverse,butinmostcases n
numberNC003527).Theseplasmidsdonotencodeanyobvious notidentified,plant-deriveddietaryfiberorcomplexcarbohy- A
phenotypictrait,exceptfortheplasmidisolatedfromB.bifidum dratestructures.Relativelyfewoftheseglycosylhydrolasesare p
r
NCFB1454(492),whichwasproposedtoencodeabacteriocin, predicted to be secreted, including those that are thought to il
1
bifidocinB. hydrolyze arabinogalactans and arabinoxylans (384). Instead, 1
Mostoftheplasmidscontaincharacteristicgeneticfeatures mostofthebifidobacterialglycosylhydrolasesarepredictedto ,
2
for plasmid replication via a rolling-circle replication system, be intracellular, and the genes that encode them are almost 0
1
i.e.,repB,traA,andmobgenes.Incontrast,pDOJH10SfromB. without exception associated with genes predicted to encode 9
longumbiotypelongumDJO10AandpBC1fromB.catenula- systems for the uptake of structurally diverse carbohydrate b
tumcontainsequenceshomologoustoreplicationfunctionsof substrates(seebelow).Moreover,carbohydrate-modifyingen- y

g
theta-typereplicatingplasmids(5,260). zymesmayalsoshapetheoverallmetabolicstateofthecolon u
Repproteinsfromdifferentbifidobacterialplasmidsdonot to sustain a microbiota that indirectly provides the host with e
s
cluster together phylogenetically (110) but resemble replica- about 10 to 15% of its calories from the degradation of com- t
tion proteins from different hosts, including gram-negative plexcarbohydratesthroughshort-chainfattyacids(447).
bacteriasuchasE.coli(5,260)(Fig.3).Horizontaltransferis Bifidobacteriacanalsoutilizesialicacid-containingcomplex
alsoindicatedforpDOJH10S,whichmayhavebeenacquired carbohydrates in mucin, glycosphingolipids, and human milk
from another Actinobacteria member, possibly Rhodococcus (187, 465). Thus, the mammalian host supplies substrates for
rhodochrous(260). intestinalcommensalssuchasbifidobacteriaandlactobacilli,in
a remarkable symbiotic (or altruistic) relationship (94, 308).
Starchandamylopectinareotherexamplesofpolysaccharides
BifidobacteriaandCarbohydrateMetabolism
which may escape digestion in the upper human GIT and
Mammalian(includinghuman)biologyispartiallyshapedby whichareplant-derivedhigh-molecular-weightcarbohydrates.
the vast community of commensal bacteria that colonize the Theabilitytodegradethesesugarsappearstoberestrictedto
GIT.Plant-basedfoodsthatarecommonlyconsumedbymam- certain species or to certain strains of a particular species,
malsarerichincomplexpolysaccharidesthatcontain,among includingB.breveandB.adolescentis(379).
others,glucose,fructose,xylan,pectin,andarabinosemoieties. Nearly10%ofthetotalbifidobacterialgenecontentisded-
Mammalian genomes do not appear to encode the enzymes icated to sugar internalization, via ABC transporters, per-
VOL.71,2007 GENOMICS OF ACTINOBACTERIA 503
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froFmIGg.ra3m.-Ppohsyiltoivgeenaentdicgrrealmat-inoengshatipivseobfaRcteepriap.rTotheeinpshfyrloomgeancettiincotbreaectweraisalcapllcausmlatidedsabnydthseevseerqaulepnrcoetodtiysptaenpcleasmmeitdhsoodfudsiifnfegrtehnetnpelaigsmhbiodrf-ajominiliinegs ril 1
algorithm. 1
,

2
0
1
9

b
meases,andprotonsymportersratherthanphosphoenolpyru- BifidobacteriaandPrebioticProperties
y
vate-phosphotransferase systems (PEP-PTSs) (384), though a g
PEP-PTShasbeenexperimentallydemonstratedinB.breveto Prebiotics, such as fructo- and galactooligosaccharides, are u
e
beactivefortheinternalizationofglucose(108).ThePTSacts indigestiblefoodingredientsthatbeneficiallyaffectthehostby s
t
through the concomitant internalization and phosphorylation selectivelystimulatinggrowthofcommensalbacteria(36,370).
ofcarbohydrates,inwhichthetransferofphosphatefromPEP Bifidobacterialgenomeshavearicharsenalofgenesforsuch
totheincomingsugarismediatedviaaphosphorylationchain prebiotic metabolism (116, 176, 218, 259). For example, B.
involving enzyme I (EI), histidine-containing protein (HPr), breve UCC2003 has a fos operon encompassing a putative
andEII.TheB.longumbiotypelongumNCC2705genomehas permease-encoding gene, a gene specifying an unknown pro-
asingleEII-encodinglocus,andthatofB.breveUCC2003has tein, and a (cid:5)-fructofuranosidase gene, which has been shown
four(287).Thelattersystemwasshowntotransportfructose, tobeinvolvedinfructooligosaccharidedegradation(380).Pre-
but it appears to transport glucose as well (287). This differ- bioticoligosaccharidesarealsoprovidedinhumanmilk(467).
ence in the number of PEP-PTSs may indicate that B. breve Theseincludegalactooligosaccharides(325)rangingindegree
more frequently encounters less complex sugars in its pre- of polymerization from 3 to over 32 galactose moieties (247).
ferred niche, the GITs of infants, than B. longum biotype Certain bifidobacteria can also hydrolyze high-molecular-
longumencountersintheGITsofadults,whereitisprevalent. weightprebioticcarbonsources,suchastrans-galactooligosac-
Thus, the different diets of infants and adults may affect the charides, the latter through an extracellular enzyme encoded
compositionsoftheirGITmicrobiomes. bygalA(176).
504 VENTURA ET AL. MICROBIOL.MOL.BIOL.REV.
InteractionofBifidobacteriawiththeGIT ergy metabolism, dependence on external amino acids, and a
lowerG(cid:1)Ccontent(i.e.,46%)thanfree-livingrelatives(302).
Themolecularbasisofinteractionswiththehostepithelium Alargeamountofcodingcapacityisdevotedtothebiosyn-
has been investigated in detail for several pathogens such as thesisofsurface-associatedfeaturesthatmaysustaintheintri-
Listeria monocytogenes and Salmonella spp. (256, 291), but cate interaction with eukaryotic cells. These surface features
little is known about this for commensal bacteria such as bi- include a prominent family of predicted surface proteins
fidobacteria. Bifidobacterial genome analyses did not reveal termed WiSP (Wnt-induced secreted protein), ranging in size
clear candidate genes for GIT-bifidobacterial interaction. from103to2,308aaresidues.OnlyafewWiSPfamilymem-
However,bifidobacteriaarepredictedtoencodecellenvelope- bers contain a predicted transmembrane motif near the C
associatedstructureswhichmayplayaroleinhostassociation. terminusthatcananchorsuchproteinstothebacterialmem-
Allsequencedbifidobacteriaappeartoencodeanextracellular brane.AlignmentofalltheWiSPmembersrevealedthepres-
polysaccharide(EPS)orcapsularpolysaccharide,andsuchan enceofasingle(cid:5)-strandmotif(27).
extracellular structure may be important in bacterial adher- The two T. whipplei genomes contain many noncoding re-
encetohostcells,whileitcouldalsocontributetoresistanceto petitive DNA regions, which may promote recombination
D
stomachacidsandbilesalts(338). events that allow the bacteria to expose different sets of pro- o
ThevariousdifferentEPSclusterspresentinthecommensal teins at their surface, possibly in response to host defense w
microorganism Bacteroides tetaiotamicron help to avoid im- actionsand/orspecificenvironmentalconditions(27,357).All nlo
mune recognition by the host (240). The B. longum biotype thesegenomecharacteristicsarediscussedindetailbelow.Itis a
longumNCC2705genomehastworegionsrelatedtopolysac- noteworthythatthegenomesofT.whippleiTwistandTW08/27 de
charide biosynthesis that, like the cps/eps cluster of B. breve contain 808 and 784 coding sequences (CDSs), respectively, d

UCC2003, are flanked by IS elements and show a strong di- with only a small number of pseudogenes. This apparent low fr
vergence in G(cid:1)C content relative to the remainder of the degree of gene decay, which contrasts with the conspicuous om
genome.Theseappeartobeagenetichallmarkofcps/epsloci gene decay of M. leprae (see below), may be related to the h
examinedthusfar(127)andmayfacilitateinter-andintraspe- complete absence of mobile genetic elements within the ge- tt
p
ciestransferofsuchgeneclusters. nomes,oritmaymeanthatmostredundantDNAhasalready :
/
Genespredictedtoencodeglycoprotein-bindingfimbria-like beenremoved. /m
structures, which have been identified in the genome se- m
quences of both B. longum biotype longum NCC2705 and B. b
TropherymaComparativeGenomeAnalysis r
longumbiotypelongumDJO10A,maymediateanotherinter- .
a
actionwiththehost(232,384).Inaddition,B.longumbiotype ThetwoavailableT.whippleigenomicsequencesare(cid:6)99% sm
longumNCC2705encodesaserpin-likeproteaseinhibitorthat identicalbutdifferbyalargechromosomalinversion(Fig.4). .
o
hasbeendemonstratedtocontributetohostinteractioninthe Theextremitiesofthisinversionincludetwoidenticalnucleo- r
g
GIT (199). The NCC2705 serpin is an efficient inhibitor of tide sequences corresponding to the WND domain of the /

human neutrophil and pancreatic elastases, whose release by WiSPs.Consequently,theinversioneventcauseddifferencesin on
activated neutrophils at the sites of intestinal inflammation the WiSPs in the two strains: TW08/27 has eight copies of A
representsaninterestingmechanismofinnateimmunity(199). WND domain sequences that are identical across an 800-bp p
r
nucleotidespan,whereastherestoftheseWiSPgenesdonot il
1
displayanyDNAsimilarity.ThissuggeststhatWNDmotifsact 1
GENOMICSOFTROPHERYMA both as coding regions and as DNA repeats to promote ge- ,
2
GeneralFeatures nomerecombination(357). 0
1
ThecomparisonofT.whippleigenomesequenceswiththose 9
TheonlysequencedmemberofthegenusTropherymaisT. of other reduced bacterial genomes (less than 1 Mb), such as b
whipplei, the causative agent of Whipple’s disease, which is Mycoplasmaspecies,Ureaplasma,andBuchnerarevealedare- y

g
characterized by intestinal malabsorption leading to cachexia duced complement repertoire of genes for most functional u
and death. T. whipplei isolates are typically found in human categories(357).However,mycoplasmasaregeneticallybetter e
s
intracellularniches,suchasinsideintestinalmacrophagesand equipped for carbohydrate metabolism and transport, and t
circulating monocytes (355, 356). However, extracellular and Buchnera displays a larger gene content devolved to energy
metabolically active T. whipplei cells have been found in the production and conversion. This variability shows that small
intestinallumen(130).AnenvironmentalreservoirofT.whip- bacterial genomes did not necessarily follow the same reduc-
plei is also suspected, as PCR experiments revealed its pres- tiveevolutionarypathway.
enceinsewagewater(283).
Phylogenetic analyses based on the 16S rRNA, 5S rRNA,
DNARegionAcquiredbyHGTinT.whippleiGenomes
23S rRNA, groEL, and rpoB genes placed T. whipplei within
the phylum Actinobacteria (282, 479). T. whipplei was difficult HGT events appear to be less frequent for intracellular
to propagate until relatively recently, when cultivation meth- bacteria with small genomes than for free-living bacteria (27,
ods using human fibroblasts were established (354). Two T. 40,321,357).InT.whippleiTwist,onlyninegenes,about1%
whipplei strains, TW08/27 and Twist, have been fully se- oftheentiregenome,appeartohavebeenacquiredbyHGT.
quenced(27,357).Bothstrainshaveasmallgenome(lessthan These encompass aminoacyl-tRNA synthetase-encoding genes,
1 Mb) (Table 1) bearing the traits of strictly host-adapted genesinvolvedinnucleotidemetabolism(purBandpyrB),and
microorganisms,whichincludepronounceddeficienciesinen- genesspecifyinghypotheticalproteins(357).