Genomics of Actinobacteria

54 Pages·2007·1.51 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
INTRODUCTION.......................................................................................................................................................497
GeneralFeaturesofActinobacteria.......................................................................................................................497
EvolutionandDynamicsofBacterialGenomes.................................................................................................497
D
Geneduplications...............................................................................................................................................497 o
w
HGT......................................................................................................................................................................497 n
lo
Genedecay...........................................................................................................................................................498 a
d
Genomerearrangements....................................................................................................................................498 e
d
TaxonomyofActinobacteria....................................................................................................................................498 fro
ActinobacterialGenomeSequencingProjects.....................................................................................................498 m
GENOMICSOFBIFIDOBACTERIUM....................................................................................................................499 m
m
GeneralFeatures.....................................................................................................................................................499 b
ComparativeBifidobacterialGenomeAnalysis..................................................................................................501 r.a
s
DNARegionsAcquiredbyHGTinBifidobacterialGenomes..........................................................................501 m
Prophage-LikeElementsinBifidobacteria..........................................................................................................501 .o
rg
ExtrachromosomalDNAElements.......................................................................................................................502 a
BifidobacteriaandCarbohydrateMetabolism....................................................................................................502 t P
BifidobacteriaandPrebioticProperties..............................................................................................................503 en
n
InteractionofBifidobacteriawiththeGIT.........................................................................................................504 S
GENOMICSOFTROPHERYMA..............................................................................................................................504 ta
GeneralFeatures.....................................................................................................................................................504 te U
TropherymaComparativeGenomeAnalysis........................................................................................................504 n
iv
DNARegionAcquiredbyHGTinT.whippleiGenomes...................................................................................504 o
n
TropherymaGenomeandBiologicalLifestyle.....................................................................................................505 J
InteractionofTropherymawiththeEnvironment..............................................................................................505 an
u
GENOMICSOFPROPIONIBACTERIUM...............................................................................................................506 a
GeneralFeatures.....................................................................................................................................................506 ry 3
ExtrachromosomalDNAElementsinPropionibacterium..................................................................................506 1
DNARegionAcquiredbyHGT.............................................................................................................................506 , 20
0
Prophage-LikeElementsinPropionibacterium....................................................................................................506 8

P.acnesGenomeandBiologicalLifestyle...........................................................................................................506
InteractionofP.acneswithItsEnvironment.....................................................................................................508
GENOMICSOFMYCOBACTERIUM......................................................................................................................508
GeneralFeatures.....................................................................................................................................................508
GenomicsofM.tuberculosis...................................................................................................................................508
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
CorynebacteriumComparativeGenomeAnalysis................................................................................................516
DNARegionsinC.glutamicumAcquiredbyHGT.............................................................................................517
Prophage-LikeElementsintheC.glutamicumGenome....................................................................................518
DNAAcquiredbyHGTintheC.efficiensGenome............................................................................................518 D
o
Prophage-LikeElementintheGenomeofC.diphtheriae.................................................................................519 w
n
DNARegionsintheC.diphtheriaeGenomeAcquiredbyHGT.......................................................................519 lo
DNARegionsintheC.jeikeiumGenomeAcquiredbyHGT............................................................................519 ad
e
ExtrachromosomalDNAElements.......................................................................................................................520 d
CorynebacterialGenomesandBiologicalLifestyle............................................................................................521 fro
m
AdherencetopharyngealepithelialcellsbyC.diphtheriae...........................................................................521
m
AdaptationtoaminoacidproductionbyC.glutamicumandC.efficiens....................................................521 m
AdaptationtoelevatedtemperaturesbyC.efficiens.......................................................................................521 b
AdaptationtothelipophiliclifestylebyC.jeikeium.......................................................................................521 r.as
m
GENOMICSOFLEIFSONIA....................................................................................................................................522
.o
GeneralFeatures.....................................................................................................................................................522 rg
ExtrachromosomalDNAElementsinLeifsonia.................................................................................................522 a
DNARegionsAcquiredbyHGTinLeifsonia......................................................................................................522 t P
e
Prophage-LikeElementsinLeifsonia...................................................................................................................522 nn
L.xylisubsp.xyliGenomeandBiologicalLifestyle...........................................................................................522 S
ta
GENOMICSOFTHEMYCELIALACTINOBACTERIA:STREPTOMYCES,FRANKIA,AND te
THERMOBIFIDA.................................................................................................................................................523 U
n
GeneralFeatures.....................................................................................................................................................523 iv
ArchitectureofMycelialActinobacterialGenomes............................................................................................523 on
ComparativeGenomicsofMycelialActinobacterialGenomes.........................................................................524 J
a
Multiplyrepresentedmetabolicgenes.............................................................................................................525 nu
a
GenesunexpectedlymissingfrommycelialActinobacteria............................................................................525 ry
Conservonsandtransposons.............................................................................................................................525 3
1
DNARegionsinMycelialActinobacterialGenomesAcquiredbyHGT.........................................................525 , 2
StreptomycesExtrachromosomalElements..........................................................................................................526 00
8
Prophage-LikeElementsinStreptomyces.............................................................................................................526
MycelialActinobacterialGenomesandBiologicalLifestyle.............................................................................526
Ecology..................................................................................................................................................................526
Secondarymetabolism........................................................................................................................................527
P450cytochromes(CYPs)..................................................................................................................................527
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
agreement with the complex nature of the mycobacterial cell
fragmenting hyphal forms (e.g., Nocardia spp.) or permanent
wallandprobablyreflectingadaptiveevolutionofthiscellular
and highly differentiated branched mycelium (e.g., Streptomy-
structure(79,432).
cesspp.)(15).Theyalsoexhibitdiversephysiologicalandmet-
HGT. The introduction of novel or alien genes by HGT
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 ow
metabolites (389). Notably, many such secondary metabolites lead to bacterial diversification and speciation (80). Bacterial nlo
arepotentantibiotics(255),atraitthathasturnedStreptomyces genomeevolutionisbasedonthecombinedoutcomeofgenes ade
acquiredthroughcelldivision,i.e.,verticallyinherited,andby d
species into the primary antibiotic-producing organisms ex- HGT(482).Takingthisconcepttoitsextreme,onecanclaim fro
ploitedbythepharmaceuticalindustry(29).Furthermore,var- m
iousdifferentlifestylesareencounteredamongActinobacteria, thattwobacterialtaxaaremorerelatedtoeachotherthanto m
athirdonenotbecausetheyshareamorerecentancestorbut m
andthephylumincludespathogens(e.g.,Mycobacteriumspp., b
Nocardia spp., Tropheryma spp., Corynebacterium spp., and because they exchange genes more frequently (151). HGT is r.a
s
Propionibacterium spp.), soil inhabitants (Streptomyces spp.), heldresponsibleforenhancingthecompetitivenessofbacteria m
in their natural environments. For example, in some patho- .o
plant commensals (Leifsonia spp.), nitrogen-fixing symbionts rg
(Frankia), and gastrointestinal tract (GIT) inhabitants (Bi- ggeenniecsabnacdtegreinae, cselugsmteerns,tscaolfleDdNpaAthocognentaicinitiyngislmanadnsy,avpirpuelaernctoe at P
fidobacterium spp.). Unusual developmental features are dis- e
played by many actinobacterial genera, such as formation of have been acquired by HGT (321). Actinobacterial examples nn
of transmission of virulence genes through HGT are rare S
sporulatingaerialmyceliuminStreptomycesspeciesortheper- ta
sAisctteinnotbnaocnterreiapliacraetinwgidsetalytedeisxthriibbiuteteddbiyncebrottahintemryrecostbraiacltearniad. (o3b7v6io).uOsHftGhTeseev,ethnets:fo(il)lopwhianggesthorfeCeocraysneesbaapctpeeriaurmtodirpehptrheesreianet te Un
aquatic(includingmarine)ecosystems,especiallyinsoil,where carry the major diphtheria toxin gene, (ii) a linear plasmid iv o
theyplayacrucialroleintherecyclingofrefractorybiomate- carries the genes for the macrolide toxin responsible for the n J
rials by decomposition and humus formation (152, 403). Fur- ulceration that gives Mycobacterium ulcerans its name (411), anu
and (iii) a large segment of the chromosome of Streptomyces a
thermore,manybifidobacteriaareusedasactiveingredientsin ry
a variety of so-called functional foods due to their perceived turgidiscabiesconcernedwithcausingpotatoscabcanbetrans- 3
1
health-promoting or probiotic properties, such as protection ferred by conjugation (280). In addition, it has been argued , 2
against pathogens mediated through the process of competi- that the Mycobacterium tuberculosis Rv0986-8 virulence 00
8
operon, which plays an important role in parasitism of host
tiveexclusion,bilesalthydrolaseactivity,immunemodulation,
phagocytic cells by increasing the ecological fitness of the in-
andtheabilitytoadheretomucusortheintestinalepithelium
fectingmycobacterium(339),wasacquiredhorizontallybythe
(273,329,407).
ancestor of M. tuberculosis, Mycobacterium prototuberculosis.
The actinobacterial genomes sequenced so far belong to
OthergeneticstudiesoftheancestralM.prototuberculosisspe-
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-
physiological significance of these apparent HGT events be- tion of a genome is subject to change through chromosome
tweenchlamydiaeandActinobacteriaispresentlyunclear. rearrangements. Synteny, a term used here to indicate the
Gene decay. Bacterial genome size is determined by the conservation of gene order between genomes, can be applied
outcomeofseveralopposingforces.Deletionbiasandgenetic asaphylogenetictooltoinvestigaterelationshipsbetweenspe-
D
driftcausegenomestocontract,whileselectionongenefunc- cies, since the degree of genome rearrangements increases ow
tionpromotesgenomestopreserveDNA.Genomeincrements linearly in relation to the time of divergence of bacterial taxa nlo
depend on both gene duplications and acquisition of alien (236,484). ad
e
DNA,coupledtoadaptivebenefits(293).DNAlossmayrange Chromosomalrearrangementsarelargelydependentonthe d
fromlargedeletionsthatspanmultiplelocitodeletionsofone activity of repeated and mobile elements such as insertion fro
m
orafewnucleotides(7).Theinfluenceofthesedifferentroutes sequences (ISs), transposons, prophage sequences, and plas- m
is variable among bacterial lineages (293). Inactivating and mids(233).Bacterialgenomescontainingahigherrepeatden- m
b
deleteriousmutationsingeneswithlittlecontributiontofitness sity have higher rates of rearrangements, leading to an accel- r.a
s
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- .org
genes that are critical will prevent the production of progeny arrangement and gene loss in the genome, thus leading to a
and so will be eliminated from populations, resulting in the diversification of taxa. Such recombination events may have t P
e
preservationofthefunctionalgene(320). promoted speciation in the T. whipplei taxon (357). Further- nn
Geneinactivationandlossareparticularlyapparentinsev- more, chromosome evolution is influenced by large chromo- S
ta
eral bacterial groups with a host-associated lifestyle, in which somalrearrangements,e.g.,largeinversions,roughlysymmet- te
thehostsuppliesmanyofthemetabolicintermediates,thereby ricallycenteredaroundthereplicationorigin,whichleadtothe Un
obviating the need to maintain many biosynthetic genes. In occurrence of X-shaped patterns in the alignments of whole iv o
endosymbiotic bacteria, such as Buchnera and Rickettsia, loss genomes(117). n J
ofindividuallocioroperonsistheonlysourceofdivergencein an
u
the gene inventories between species (289, 419). A clear ex- a
ample of genome degradation is provided by Mycobacterium TaxonomyofActinobacteria ry 3
1
leprae, which has discarded more than 1,000 genes compared Actinobacteriaincludemanyorganismsthatexhibit,orhave , 2
with M. tuberculosis (84). Moreover, the presence of an even 00
atendencytowards,mycelialgrowth.16SrRNAgenesequenc- 8
larger set of nonfunctional genes, i.e., pseudogenes, in M.
ing has led to the recognition of 39 families and 130 genera,
leprae indicates that this genome contraction is still in progress.
whichalsoincludehigh-G(cid:1)Cgram-positivebacteriawithsim-
Althoughthecriteriaforidentifyingpseudogenesdifferamong
plermorphology,suchasbifidobacteriaandmicrococci(Fig.1)
studies,theoverallrationaleisidentical:thepredictedprotein
(119). The deepest branch separates bifidobacteria from all
must be altered to a degree that abolishes its function. The
other known families. The divergence of actinobacteria from
thresholdsappliedforpseudogeneidentificationarebasedon
otherbacteriaissoancientthatitisnotpossibletoidentifythe
theknownsizeandorganizationoffunctionaldomainswithin
phylogenetically closest bacterial group toActinobacteria 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
fro
m
m
m
b
r.a
s
m
.o
rg
a
t P
e
n
FIG. 1. PhylogenetictreeofActinobacteriabasedon1,500nucleotidesof16SrRNA.Scalebar,5nucleotides.Familiescontainingmembers n
subjectedtocompletegenomesequencingatthetimeofthiswritingaredepictedinbold.Ordersareindicated. Sta
te
U
n
ferent Actinobacteria (in some cases multiple strains of the GENOMICSOFBIFIDOBACTERIUM iv o
swahmileessepqeucieensc)inhgavoefbgeeennomseeqsuferonmcedretporecsoemntpalteitvieosno(fT4a3boleth1e)r, GeneralFeatures n Jan
high-G(cid:1)C bacteria are still in progress (Table 1) (http://www ua
The Bifidobacteriaceae family comprises four genera, Bi- ry
.ncbi.nlm.nih.gov/genomes/lproks.cgi). fidobacterium,Gardnerella,Scardovia,andParascardovia(404), 31
Although most of the sequenced genomes in Table 1 are of which only the first contains more than one species. Bi- , 2
circular, like most bacterial genomes, Streptomyces genomes fidobacteria form a deep-branching lineage within the Acti- 008
arelinear.Usingpulsed-fieldgelelectrophoresis,thegenomes
nobacteria (136, 137). The Bifidobacterium genus contains six
of some other, still-unsequenced mycelial Actinobacteria taxa,
phylogeneticclusters,namedB.boum,B.asteroides,B.adoles-
suchasActinomyces,Amycolatopsis,Actinoplanes,Streptoverti-
centis,B.longum,B.pullorum,andB.pseudolongum(448).
cillium, and Micromonospora, were also shown to be linear,
Bifidobacteria are nonmotile, nonsporulating, non-gas-pro-
withsizesrangingfrom7.7Mb(e.g.,Micromonosporachalcea)
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
Leifsoniaxylisubsp.xyli 2,584,158 2,351 67.7 1 49 307 300
CTCB07
Mycobacteriumaviumsubsp. 4,829,781 4,350 69.3 1 47 0 268
paratuberculosisK-10
Mycobacteriumbovis 4,345,492 3,953 65.63 1 49 23 139 D
o
AF2122/97 w
n
MycobacteriumlepraeTN 3,268,203 1,605 57.79 1 49 1116 84 lo
Mycobacteriumtuberculosis 4,411,532 3,994 65.61 1 49 6 83 ad
H37Rv ed
Mycobacteriumtuberculosis 4,403,836 4,250 65.60 1 49 ND 126 fro
CDC1551 m
Mycobacteriumsp.strain 5,705,448 5,391 68 2 59 21 NCBIsource m
MCS NC_008146 m
b
Nocardiafarcinica 6,021,225 5,674 70.8 3 61 0 198 r.a
IFM10152 s
m
Propionibacteriumacnes 2,560,265 2,297 60 3 51 17 46 .o
KPA171202 rg
StreptomycescoelicolorA3 8,667,507 7,769 72 6 80 56 26 a
Streptomycesavermitilis 9,025,608 7,577 70 6 82 0 194 t P
e
MA-4680 n
n
ThermobifidafuscaYX 3,642,249 3,110 67 4 63 7 281 S
Tropherymawhipplei 925,938 783 46 1 54 1 27 ta
TW08/27 te
U
TropherymawhippleiTwist 927,303 808 46 1 54 0 357 n
iv
aND,notdetermined. o
n
J
a
n
u
phylogeneticgroupshavebeensequencedtocompletion(Ta- in the nucleotide composition of the leading DNA strand ary
ble2),whilethesequencesofothers,e.g.,B.dentiumBd1,are (129); and a typical presumptive origin-of-replication region 3
1
atvariousstagesofcompletion:detailedsequenceinformation (350),includingageneconstellationneartheorigin(compris- , 2
0
for some of these genomes is expected to become publicly ingrpmH,dnaA,dnaN,andrecF),aparticularGCnucleotide 0
8
availableinthenearfuture.Furthermore,genomesequencing skew ([G-C]/[G(cid:1)C]), and the presence of multiple DnaA
ofB.breveM-16V,B.breveYacult,B.animalissubsp.lactis,B. boxes and AT-rich sequences immediately upstream of the
longumbiotypelongum,andB.longumbiotypeinfantis(276)is dnaAgene(77).
under way. These genomes range in size from 1.9 to 2.9 Mb The number of rRNA operons in bifidobacteria varies be-
andgenerallydisplayarchitecturalfeaturesofatypicalbacte- tweenoneandfive(58),perhapsreflectingdifferentecological
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
FIG. 2. Comparativegenomemapsoftheprophage-likeelementsdetectedinBifidobacteriumgenomes.Genessharingsimilarityarelinked. D
Probablefunctionsofencodedproteinsidentifiedbybioinformaticanalysisareindicated.Themodularstructureiscolorcoded:red,lysogeny; o
w
green,DNApackagingandhead;blue,tail;mauve,tailfiber;violet,lysismodule;yellow,transcriptionalregulator;orange,DNAreplication;gray, n
unknowngenes;black,genessimilartootherfunctionallyunknownbacteriophagegenes.Verticalbluelines,tRNAgenes. loa
d
e
d
fro
56 in B. breve UCC2003 and B. longum biotype longum inB.longumbiotypelongumNCC2705havebeenacquiredvia m
NCC2705, respectively. These are representative of all 20 HGT, as part of the adaptation of this organism to a specific m
m
aminoacids,withredundanttRNAsforallaminoacidsexcept ecological niche. For example, a region encoding rhamnosyl b
cysteine,histidine,isoleucine,phenylalanine,andtryptophan. transferases seems to have been acquired from streptococci r.a
s
m
(384), while two other regions that contain genes encoding
.o
ComparativeBifidobacterialGenomeAnalysis restriction-modification systems also appear to have been ac- rg
Dot plot comparisons (at the nucleotide level) of the fully qbiuoitryepdetlhornoguugmhNHCGCT2.70O5vgeernalol,maebcoountte5n%tseoefmtshetoBh.avloenbgeuemn at Pe
n
sequenced bifidobacterial genomes revealed a high degree of recentlyacquiredbythismechanism(384). n S
conservationandsyntenyacrosstheentiregenomes.,i.e.,those ta
of B. longum biotype longum NCC2705, B. longum biotype te
U
longum DJO10A, B. breve UCC2003, and B. adolescentis Prophage-LikeElementsinBifidobacteria n
iv
ACC15703. Preliminary analysis against the draft genome se- o
quencesofB.dentiumBd1confirmedandextendedthisresult. Untilrecentlybifidobacteriawerenotconsideredtobesuit- n J
However,therearealsoseveralbreakpointregionsthatseem able targets for phage infection. However, prophage-like ele- an
u
to represent inversions or DNA insertion/deletion points (S. ments, designated Bbr-1, Bl-1, and Blj-1, are present in the ary
LeahyandD.VanSinderen,unpublisheddata). genomes of B. breve UCC2003, B. longum biotype longum 3
1
Recently,aB.longumbiotypelongumNCC2705-basedspot- NCC2705, and B. longum biotype longum DJO10A (455). , 2
tedDNAmicroarraywasemployedtocomparethegenomesof These prophage-like elements display homology to genes of 00
8
10 bifidobacterial strains, including other B. longum biotype double-strandedDNAphagesthatinfectabroadphylogenetic
longumstrainsaswellasthecloselyrelatedB.longumbiotype range of bacteria. Surprisingly, using the proteomic tree
infantisandB.longumbiotypesuistaxa(232).Resultsrevealed method to investigate the evolution of these phages (373), it
sevenlargegenomeregionsofvariability,themajorityofwhich became clear that the Bbr-1, Bl-1, and Blj-1 prophage-like
encompassDNAwithadeviatingG(cid:1)Ccontent.Theseregions elementsexhibitaclosephylogeneticrelationshipwithphages
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
defective prophages, although they may constitute functional (148, 447. Many of these enzymes are not represented in the
satellitephages,whosemobilitydependsonhelperphagesina human glycobiome. Moreover, GIT mucus provides an abun-
manner similar to that described for the cryptic mycophages dantreservoirofglycansformicrobiota,whichservetoreduce
Rv1andRv2(175,455). the effects of marked changes in the availability of dietary
D
polysaccharides(16). ow
ExtrachromosomalDNAElements Thetypeofsugaravailableislikelytoinfluencethespecies nlo
composition and abundance of the microbiota along the GIT ad
e
Plasmidsarenotubiquitousinbifidobacteria(332,392),and (447). In this context, bacteria such as Lactobacillus are par- d
whenpresenttheyaresmall,i.e.,rangingfrom1.5kbto15kb. ticularly prevalent in the upper GIT, where they mainly fer- fro
m
CompletelysequencedplasmidsfromdifferentB.longumbio- mentrelativelysimplemono-,di-,andtrisaccharides(447).In m
type longum strains include pMB1 (378); pKJ36 and pKJ50 contrast,bacteriaactiveinthelowerpartsofthecolon,suchas m
b
(332,333);pBLO1(384);pNAC1,pNAC2,andpNAC3(95); bifidobacteria,probablyowetheirspecificecologicalsuccessto r.a
s
pDOJH10SandpDOJH10L(260);pTB6(421);pB44(GenBank their capacity to metabolize complex carbohydrates. It there- m
accessionnumberNC004443);andpNAL8(162).Inaddition,six forecomesasnosurprisethatgenesforcomplexsugarmetab- .org
plasmidsfromotherbifidobacterialspecieshavebeensequenced: olismaboundinthegenomesofB.breveandB.longumbiotype a
pVS809 from Bifidobacterium globosum (285), pCIBb1 from B. longum.Accordingtothesequence-basedclassificationofcar- t P
e
breve (327), pNBb1 from B. breve (GenBank accession number bohydrate-active enzymes (CAZy), over 8% of the annotated nn
E17316), pAP1 from B. asteroides (GenBank accession number genes of these bifidobacterial genomes may encode enzymes S
ta
Y11549),pBC1fromBifidobacteriumcatenulatum(5),andp4M involvedinthemetabolismofcarbohydrates,includingvarious te
from Bifidobacterium pseudocatenulatum (GenBank accession glycosylhydrolasesforutilizationofdiverse,butinmostcases Un
numberNC003527).Theseplasmidsdonotencodeanyobvious notidentified,plant-deriveddietaryfiberorcomplexcarbohy- iv o
phenotypictrait,exceptfortheplasmidisolatedfromB.bifidum dratestructures.Relativelyfewoftheseglycosylhydrolasesare n J
NCFB1454(492),whichwasproposedtoencodeabacteriocin, predicted to be secreted, including those that are thought to an
u
bifidocinB. hydrolyze arabinogalactans and arabinoxylans (384). Instead, a
ry
Mostoftheplasmidscontaincharacteristicgeneticfeatures mostofthebifidobacterialglycosylhydrolasesarepredictedto 3
1
for plasmid replication via a rolling-circle replication system, be intracellular, and the genes that encode them are almost , 2
i.e.,repB,traA,andmobgenes.Incontrast,pDOJH10SfromB. without exception associated with genes predicted to encode 00
8
longumbiotypelongumDJO10AandpBC1fromB.catenula- systems for the uptake of structurally diverse carbohydrate
tumcontainsequenceshomologoustoreplicationfunctionsof substrates(seebelow).Moreover,carbohydrate-modifyingen-
theta-typereplicatingplasmids(5,260). zymesmayalsoshapetheoverallmetabolicstateofthecolon
Repproteinsfromdifferentbifidobacterialplasmidsdonot to sustain a microbiota that indirectly provides the host with
cluster together phylogenetically (110) but resemble replica- about 10 to 15% of its calories from the degradation of com-
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
D
o
w
n
lo
a
d
e
d
fro
m
m
m
b
r.a
s
m
.o
rg
a
t P
e
n
n
S
ta
te
U
n
iv
o
n
J
FIG. 3. PhylogeneticrelationshipsofRepproteinsfromactinobacterialplasmidsandseveralprototypeplasmidsofdifferentplasmidfamilies a
n
fromgram-positiveandgram-negativebacteria.Thephylogenetictreewascalculatedbythesequencedistancemethodusingtheneighbor-joining u
a
algorithm. ry
3
1
, 2
0
0
8

meases,andprotonsymportersratherthanphosphoenolpyru- BifidobacteriaandPrebioticProperties
vate-phosphotransferase systems (PEP-PTSs) (384), though a
PEP-PTShasbeenexperimentallydemonstratedinB.breveto Prebiotics, such as fructo- and galactooligosaccharides, are
beactivefortheinternalizationofglucose(108).ThePTSacts indigestiblefoodingredientsthatbeneficiallyaffectthehostby
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
stomachacidsandbilesalts(338). events that allow the bacteria to expose different sets of pro-
ThevariousdifferentEPSclusterspresentinthecommensal teins at their surface, possibly in response to host defense
microorganism Bacteroides tetaiotamicron help to avoid im- actionsand/orspecificenvironmentalconditions(27,357).All
mune recognition by the host (240). The B. longum biotype thesegenomecharacteristicsarediscussedindetailbelow.Itis
D
longumNCC2705genomehastworegionsrelatedtopolysac- noteworthythatthegenomesofT.whippleiTwistandTW08/27 ow
charide biosynthesis that, like the cps/eps cluster of B. breve contain 808 and 784 coding sequences (CDSs), respectively, nlo
UCC2003, are flanked by IS elements and show a strong di- with only a small number of pseudogenes. This apparent low ad
vergence in G(cid:1)C content relative to the remainder of the degree of gene decay, which contrasts with the conspicuous ed
genome.Theseappeartobeagenetichallmarkofcps/epsloci gene decay of M. leprae (see below), may be related to the fro
m
examinedthusfar(127)andmayfacilitateinter-andintraspe- complete absence of mobile genetic elements within the ge- m
ciestransferofsuchgeneclusters. nomes,oritmaymeanthatmostredundantDNAhasalready m
b
Genespredictedtoencodeglycoprotein-bindingfimbria-like beenremoved. r.a
structures, which have been identified in the genome se- s
m
quences of both B. longum biotype longum NCC2705 and B. .o
longumbiotypelongumDJO10A,maymediateanotherinter- TropherymaComparativeGenomeAnalysis arg
actionwiththehost(232,384).Inaddition,B.longumbiotype ThetwoavailableT.whippleigenomicsequencesare(cid:6)99% t P
e
longumNCC2705encodesaserpin-likeproteaseinhibitorthat identicalbutdifferbyalargechromosomalinversion(Fig.4). nn
hasbeendemonstratedtocontributetohostinteractioninthe Theextremitiesofthisinversionincludetwoidenticalnucleo- S
GIT (199). The NCC2705 serpin is an efficient inhibitor of tide sequences corresponding to the WND domain of the tate
human neutrophil and pancreatic elastases, whose release by WiSPs.Consequently,theinversioneventcauseddifferencesin Un
activated neutrophils at the sites of intestinal inflammation the WiSPs in the two strains: TW08/27 has eight copies of iv o
representsaninterestingmechanismofinnateimmunity(199). WND domain sequences that are identical across an 800-bp n J
nucleotidespan,whereastherestoftheseWiSPgenesdonot an
u
displayanyDNAsimilarity.ThissuggeststhatWNDmotifsact a
GENOMICSOFTROPHERYMA ry
both as coding regions and as DNA repeats to promote ge- 3
1
GeneralFeatures nomerecombination(357). , 2
ThecomparisonofT.whippleigenomesequenceswiththose 00
8
TheonlysequencedmemberofthegenusTropherymaisT. of other reduced bacterial genomes (less than 1 Mb), such as
whipplei, the causative agent of Whipple’s disease, which is Mycoplasmaspecies,Ureaplasma,andBuchnerarevealedare-
characterized by intestinal malabsorption leading to cachexia duced complement repertoire of genes for most functional
and death. T. whipplei isolates are typically found in human categories(357).However,mycoplasmasaregeneticallybetter
intracellularniches,suchasinsideintestinalmacrophagesand equipped for carbohydrate metabolism and transport, and
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).