REVIEWS
Pathogenomics of Xanthomonas:
understanding bacterium–plant
interactions
Robert P. Ryan*, Frank-Jörg Vorhölter‡, Neha Potnis§, Jeffrey B. Jones§,
Marie-Anne Van Sluys||, Adam J. Bogdanove¶ and J. Maxwell Dow*
Abstract | Xanthomonas is a large genus of Gram-negative bacteria that cause disease in
hundreds of plant hosts, including many economically important crops. Pathogenic species
and pathovars within species show a high degree of host plant specificity and many exhibit
tissue specificity, invading either the vascular system or the mesophyll tissue of the host. In
this Review, we discuss the insights that functional and comparative genomic studies are
providing into the adaptation of this group of bacteria to exploit the extraordinary diversity
of plant hosts and different host tissues.
Pathovars
Pathogenic variants within a
species that are defined by
a characteristic host range
and/or tissue specificity.
*BIOMERIT Research Centre,
Department of Microbiology,
BioSciences Institute,
University College Cork,
Ireland.
‡
Department of Proteome and
Metabolome Research,
Faculty of Biology, Bielefeld
University, P.O. Box 100131,
Bielefeld D‑33501, Germany.
§
Department of Plant
Pathology, University of
Florida, Gainesville Florida
3261, USA.
||
Departamento de Botânica,
Instituto de Biociências,
Universidade de São Paulo,
CEP 05508–900,
Sao Paulo, Brazil.
¶
Department of Plant
Pathology, Iowa State
University, Ames,
Iowa 50011, USA.
Correspondence to J.M.D. e‑mail: [email protected]
doi:10.1038/nrmicro2558
Published online 11 April 2011
Xanthomonas (from the Greek xanthos, meaning ‘yellow’,
and monas, meaning ‘entity’) is a large genus of Gramnegative, yellow-pigmented bacteria that are associated
with plants. The genus, which resides at the base of the
Gammaproteobacteria1, comprises 27 species (FIG. 1) that
collectively cause serious diseases in ~400 plant hosts,
including a wide variety of economically important
crops, such as rice, citrus, banana, cabbage, tomato, pepper and bean. Individual species can comprise multiple
pathovars2. Pathogenic species and pathovars show a high
degree of host plant specificity and many also exhibit
tissue specificity, invading either the xylem elements
of the vascular system or the intercellular spaces of the
meso­phyll parenchyma tissue of the host (FIG. 2). For
example, Xanthomonas campestris includes host-specific
pathovars that infect different brassicaceous, solanaceous
and other plant species, whereas Xanthomonas oryzae
infects rice and some of its wild relatives. Both species comprise pathovars that either invade through the
vascular system (for example, X. oryzae pv. oryzae and
X. campestris pv. campestris) or colonize the intercellular
spaces of the parenchyma tissue (for example, X. oryzae
pv. oryzicola and X. campestris pv. armoraciae).
Diseases caused by Xanthomonas spp. often start
with contaminated seeds, although the pathogens can
be spread to healthy plants by agricultural practices such
as pruning and misting of seedbeds, by rainwater, by the
formation of aerosols that can carry bacteria from adjacent infected fields, by contaminated soil and possibly
by insects. These bacteria initially grow epiphytically
(on leaf surfaces) and then enter into the host through
or wounds to spread systemically through
the vascular system, or through stomata to colonize the
mesophyll parenchyma. Entry through hydathodes is
promoted by cycles of changing humidity. The bacteria
colonize guttation droplets that form at the hydathodes
by exudation under conditions of high humidity. Upon
a decrease in humidity, this guttation fluid, together
with the bacteria, is withdrawn into the plant. Many
Xanthomonas spp. can survive in the soil in association
with dead plant material to form a source of inocula for
future crops, which can also become infected through
wounds in the roots3.
Functional and comparative genomic studies are clarifying how this group of bacteria has adapted to exploit an
extraordinary diversity of plant hosts and host tissues. An
improved understanding of the pathogenic adaptations
of Xanthomonas spp. will promote the development of
much needed improvements in bacterial plant disease
control and prevention. In the following sections we
discuss how functional and comparative genomics are
shedding light on Xanthomonas spp. pathogenicity, adaptation and evolution. In particular, we focus on recent
studies describing the identification of novel factors that
contribute to virulence, the conservation and function of
known pathogenicity factors within the genus, and the
steps that are being taken towards the identification of
determinants of host and/or tissue specificity.
hydathodes
Xanthomonas spp. genome features
To date, the complete genome sequences of 11
Xanthomonas strains have been determined, and draft
344 | MAY 2011 | VOLUME 9
www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
:CPVJQOQPCURGTHQTCPU0%22$
:CPVJQOQPCUGWXGUKECVQTKC0%22$
:CPVJQOQPCUCNHCNHCG0%22$
:CPVJQOQPCUOGNQPKU0%22$
:CPVJQOQPCUCZQPQRQFKU0%22$
:CPVJQOQPCUHWUECPU0%22$
:CPVJQOQPCUEKVTK./)
:CPVJQOQPCUDTQOK0%22$
:CPVJQOQPCUXCUKEQNC0%22$
:CPVJQOQPCUQT[\CG0%22$
:CPVJQOQPCUHTCICTKCG0%22$
:CPVJQOQPCUCTDQTKEQNC0%22$
:CPVJQOQPCUECORGUVTKU0%22$
:CPVJQOQPCURQRWNK0%22$
:CPVJQOQPCUJQTVQTWO0%22$
:CPVJQOQPCUJQTVQTWO0%22$
:CPVJQOQPCUICTFPGTK0%22$
:CPVJQOQPCUE[PCTCG0%22$
:CPVJQOQPCURKUK0%22$
:CPVJQOQPCUXGUKECVQTKC0%22$
:CPVJQOQPCUEWEWTDKVCG0%22$
:CPVJQOQPCUECUUCXCG0%22$
:CPVJQOQPCUEQFKCGK0%22$
Parenchyma
Plant tissue in the leaf
mesophyll that has a diverse
range of functions, including
photosynthesis, storage,
secretion and short-distance
transport.
Xanthomonads
Members of the family
Xanthomonadaceae, which
is a family of Gram-negative
bacteria that includes species
from the genera Xanthomonas
and Xylella (which cause plant
diseases) and species from the
genus Stenotrophomonas (one
of which, Stenotrophomonas
maltophilia, is an opportunistic
human pathogen).
Type II secretion system
A two-step secretion system
that secretes proteins which
are first translocated across the
inner membrane by the general
secretion pathway.
Type III secretion system
A multisubunit protein
apparatus that is used to
secrete or inject effector
proteins which contribute to
interactions with eukaryotic
cells.
:CPVJQOQPCUJ[CEKPVJK0%22$
:CPVJQOQPCUUCEEJCTK0%22$
:CPVJQOQPCUCNDKNKPGCPU0%22$
:[NGNNCHCUVKFKQUCCE
5VGPQVTQRJQOQPCUUR./)6
Hydathodes
Secretory organs in leaves,
usually of angiosperms, that
are located at the leaf margin
and that secrete guttation fluid,
which may contain a variety of
organic and inorganic solutes.
:CPVJQOQPCUVJGKEQNC0%22$
:CPVJQOQPCUVTCPUNWEGPU0%22$
Figure 1 | Phylogenetic analysis of bacteria within the genus Xanthomonas and the related genera Xylella
0CVWTG4GXKGYU^/KETQDKQNQI[
and Stenotrophomonas. This neighbour-joining tree is based on the DNA gyrase subunit B (gyrB)
gene sequence of
Xanthomonas spp., Xylella fastidiosa and a Stenotrophomonas sp. Bootstrap values (for 1,000 replicates) are given at the
nodes, and branches with <50% bootstrap support were collapsed to better reveal the phylogenetic structure. The scale
bar represents 0.1 changes per nucleotide position. In addition to gyrB, analysis of 16S–23S ribosomal RNA intergenic
spacer sequences and a combination of molecular markers, such as repetitive element sequence-based PCR (rep-PCR),
amplified fragment length polymorphism (AFLP) and other fingerprints, have been used to establish the taxonomic status
of the genus. A species can contain pathovars, which are pathogenic variants that infect diverse plant hosts and/or exhibit
different patterns of plant colonization. Up to 80 pathovars have been recognized so far.
genomes of a further seven strains are available, in total
comprising seven species and nine pathovars (TABLE 1).
Sequencing projects that are currently in progress will add
to this count 4. Importantly, complete and draft genome
sequences are also now available for other xanthomonads,
namely Xylella fastidiosa and Stenotrophomonas spp.
such as Stenotrophomonas maltophilia4.
Gene content and genome plasticity. A typical
Xanthomonas sp. genome sequence is predicted to
encode more than 4,000 proteins, a common set of
which are responsible for energy acquisition and most
cellular functions. Two pathogenesis-associated gene
clusters are found in all Xanthomonas spp. genomes:
xps, which encodes a type II secretion system (T2SS),
and the cluster regulation of pathogenicity factors (rpf),
which regulates the synthesis of pathogenicity factors.
In addition, two other pathogenesis-associated gene
clusters are found in all Xanthomonas spp. genomes
(with the exception of Xanthomonas albilineans): the
hypersensitive response and pathogenicity (hrp) genes,
which encode a type III secretion system (T3SS), and the
gum genes, which encode synthases for the extracellular
polysaccharide xanthan. Intriguingly, Xanthomonas spp.
genomes consist of approximately the same number of
genes from alphaproteobacterial, betaproteobacterial
and gammaproteobacterial origin, and the remaining
genes are from phylogenetically distant groups such as
the Archaea, the Eukarya and viruses. The presence of
some of these genes in Xanthomonas spp. might be the
result of horizontal transfer events5,6.
Large-scale comparative analysis is revealing extra­
ordinary genome plasticity within the genus Xanthomonas.
Almost all of these bacteria have a single circular chromo­
some that ranges in size from 4.8 Mb to 5.3 Mb, with a
GC content of more than 60% and with a similar gene
NATURE REVIEWS | MICROBIOLOGY
VOLUME 9 | MAY 2011 | 345
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
/QPQEQV[NGFQPQWUJQUVU
8CUEWNCTRCVJQIGPU
:CPVJQOQPCUCNDKNKPGCPU
.GCHUECNFQHUWICTECPG
:CPVJQOQPCUQT[\CGRX
QT[\CG
4KEGDCEVGTKCNDNKIJV
:CPVJQOQPCUXCUKEQNCRX
OWUCEGCTWO
$CPCPC:CPVJQOQPCUYKNV
&KEQV[NGFQPQWUJQUVU
8CUEWNCTRCVJQIGPU
:CPVJQOQPCUECORGUVTKU
RXECORGUVTKU
$NCEMTQVQHETWEKHGTU
:CPVJQOQPCUOCPKJQVKU
%CUUCXCDCEVGTKCNDNKIJV
8CUEWNCTDWPFNG
/GUQRJ[NNKERCVJQIGPU
:CPVJQOQPCU
ECORGUVTKURX
CTOQTCEKCG
.GCHURQVQHETWEKHGTU
:CPVJQOQPCUEKVTK
RXEKVTK
%KVTWUECPMGT
:CPVJQOQPCU
GWXGUKECVQTKC
$CEVGTKCNURQVQHRGRRGT
CPFVQOCVQ
/GUQRJ[NNKERCVJQIGPU
:CPVJQOQPCUQT[\CGRX
QT[\KEQNC
4KEGDCEVGTKCNNGCHUVTGCM
:CPVJQOQPCUVTCPUNWEGPU
$CEVGTKCNNGCHUVTGCM
KPEGTGCNU
/GUQRJ[NNEGNN
Figure 2 | Xanthomonas species and pathovars show host and tissue specificity. Different
bacteria from the genus
0CVWTG4GXKGYU^/KETQDKQNQI[
Xanthomonas attack monocotyledonous and dicotyledonous plants to cause a range of diseases. These pathogens show a
high level of host plant specificity and many exhibit tissue specificity, invading either the xylem elements of the vascular
system (vascular pathogens) or the intercellular spaces of the mesophyll tissue (mesophyllic pathogens) of the host. Some
bacteria such as the cassava pathogen Xanthomonas manihotis produce unusually diverse symptoms and are capable of
colonizing both mesophyllic and vascular tissue.
Type III effectors
Bacterial proteins that are
delivered into a host cell
through a type III secretion
system, which is required for
pathogenesis. Contributions of
individual effectors to disease
vary, and some trigger host
defence.
Type IV secretion systems
Secretion systems typically
comprising a macromolecular
complex that spans the
bacterial inner and outer
membranes and can also span
the membrane of eukaryotic
host cells. These secretion
systems contribute to various
biological functions, including
the exchange of genetic
material with other bacteria
and the translocation of
oncogenic DNA and effector
proteins into eukaryotic host
cells.
content in all species, but whole-genome alignments
have revealed a large number of inversions, translocations and insertions or deletions. Further, at least one
member of the genus, X. albilineans, with a genome of
3.7 Mb, seems to represent a lineage that is undergoing genome reduction7, which is thought to be related
to its nearly exclusive existence within the xylem of its
host, sugarcane. Similarly, X. fastidiosa, with a genome
of ~2.7 Mb, is found only in association with host plant
xylem or with the insect vector that transmits it. Other
vascular pathogens such as X. campestris pv. campestris
and X. oryzae pv. oryzae do not show similar genome
reduction, and this may reflect their lifestyle, which is
not limited to growth in the xylem but can involve the
colonization of seed surfaces and growth on dead plant
parts in the soil8.
Additional genetic variation within Xanthomonas spp.
comes from the presence of plasmids in some strains,
which range in size from less than 2 kb to 183 kb (TABLE 1).
Some of these plasmids were first detected by genome
sequencing. Many carry genes that encode factors or
functions that are putatively associated with virulence,
such as type III effectors, secreted extra­cellular enzymes
and type IV secretion systems (T4SSs), as well as proteins of unknown function. Interestingly, the pXCV183
plasmid of Xanthomonas euvesicatoria encodes a putative Dot/Icm T4SS that is most similar to that involved
in the virulence of the human pathogen Legionella
pneumophila9.
Insertion sequences and genome diversity. Genome
diversity among Xanthomonas spp. is also driven by a
large set of insertion sequence (IS) elements, which are
transposable DNA entities that can move between bacterial species and that are usually carried on plasmids
with a broad host range. The genus Xanthomonas has
been colonized by ten IS transposase lineages that are
unevenly distributed among the genomes sequenced
to date. IS3 and IS5 families are present in all chromosomes, whereas IS256, IS3 and IS4 are plasmid borne
in Xanthomonas citri pv. citri, as well as Xanthomonas
axonopodis pv. vesicatoria, but have amplified to high
copy numbers in the chromosome of the four sequenced
X. oryzae genomes. A global analysis of the distribution
of the IS elements along the chromosome also provides
evidence of their association with genomic breaks, gene
islands and gene clusters that are specific to particular
species10,11, indicating that they are a driving force in
genome diversification in the genus. The extent of IS
element amplification differs across clades in the genus,
although the evolutionary forces that account for these
differences have not yet been defined.
Advances in functional genomics
The determination of the genome sequence of several
species and pathovars from the genus Xanthomonas has
facilitated functional analyses that aim to understand
the molecular basis of virulence, host specificity and the
mode of pathogenesis (BOX 1). For example, knowledge
of complete genome sequences has greatly accelerated
the identification of genes that are involved in these
processes through random mutagenesis using transposable elements12–14. These methods, however, can
leave many genes untested because transposon insertion is not always random, as has been shown for the
insertion of the transposon Tn5-gusA in the genome of
X. campestris pv. campestris 4. Guided by the complete
genome sequence, however, many of the genes that
were not disrupted by Tn5-gusA could be inactivated by
site-directed insertion of the suicide vector pK18mob,
346 | MAY 2011 | VOLUME 9
www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
Table 1 | General features of the sequenced genomes from Xanthomonas spp.
Species
Pathovar
Strain
Strain or
Host
pathovar
abbreviation
Disease
Genome Plasmids
size (Mb)
Sequencing
status
Xanthomonas
albilineans
ND
GPE PC73
Xal
Sugarcane
Leaf scald
3.77
None
Complete
Xanthomonas
axonopodis
phaseoli
ND
Xap
Beans
Bacterial blight NA
None
Draft
JCVI*
manihotis
ND
Xam
Cassava
Bacterial blight NA
None
Draft
JCVI*
Xanthomonas
campestris
campestris
ATCC 33913
Xcc
Crucifers
Black rot
5.08
None
Complete
72
8004
Xcc
Crucifers
Black rot
5.15
None
Complete
13
B100
Xcc
Crucifers
Black rot
5.10
None
Complete
73
756C
Xca
Crucifers
Leaf spot
4.94
None
Complete
NCBI§
Xvm
Banana
Enset wilt
4.88
None
Draft
74
Draft
74
armoraciae
‡
musacearum NCPPB4381
Refs
7
vasculorum
NCPPB702
Xvv
Sugarcane
Gumming
disease
5.40
None
Xanthomonas citri
citri¶
306
Xac
Citrus
Citrus canker
5.27
pXAC64 and Complete
pXCC33
72
Xanthomonas
euvesicatoria#
ND
85‑10
Xcv
Tomato and Leaf spot
pepper
5.42
pXCV38,
Complete
pXVC2,
pXCV19 and
pXCV183
75
Xanthomonas fuscans ND
subsp. aurantifolii
ICPB 11122
Xaub
Citrus
Citrus canker
4.70
None
Draft
48
ICPB 10535
Xauc
Citrus
Citrus canker
5.00
None
Draft
48
Xanthomonas oryzae oryzae
KACC10331
Xoo
Rice
Bacterial blight 4.94
None
Complete
76
PXO99A
oryzicola
||
Xoo
Rice
Bacterial blight 5.20
None
Complete
61
MAFF 311018 Xoo
Rice
Bacterial blight 4.94
None
Complete
77
AX01947
Xoo
Rice
Bacterial blight 5.10
None
Draft
JCVI*
BLS256
Xoc
Rice
Bacterial streak 4.80
None
Complete
NCBI§
NA, data not available; ND, not defined. *Sequence available at the J. Craig Venter Institute (JCVI) website. ‡Originally classified as X. campestris pv. armoraciae,
now called X. campestris pv. raphani78. §Sequence available at the National Center for Biotechnology Information (NCBI) website. ||Also known as Xanthomonas
vasicola. ¶Originally classified as Xanthomonas axonopodis pv. citri, now called Xanthomonas citri pv. citri. #Originally classified as Xanthomonas campestris pv.
vesicatoria, now grouped into a new species called Xanthomonas euvesicatoria.
Two-component regulators
Part of a mechanism that
allows bacteria to sense and
respond to changes in many
different environmental cues.
These systems typically consist
of a membrane-bound histidine
kinase that senses a specific
environmental stimulus, and
the corresponding response
regulator that mediates the
cellular response.
TonB-dependent
transporters
A family of proteins in the
outer membrane of
Gram-negative bacteria that
sense environmental signals or
substrates and thus trigger
changes in gene transcription
or uptake of the substrate
across the outer membrane.
These functions are dependent
on the energy-transducing
protein TonB.
suggesting that they were not essential. The combination of mutants derived by Tn5‑gusA and pK18mob is
currently being used to create a comprehensive mutant
library of X. campestris pv. campestris 4. Signature-tagged
mutagenesis has also been developed for X. campestris
pv. campestris, for which a mutant library has been constructed that is based on a set of 412 transposons, each
barcoded with two tags (BOX 1). This library is being
used in competition assays to identify genes that are
relevant in carbohydrate use and pathogenesis4.
As an approach for the identification of virulence
factors, several laboratories have used genome sequence
information to identify and functionally analyse subsets of genes that encode proteins that are similar to
known virulence factors or that have a related function.
Examples include the examination of the role of type III
effectors, two-component regulators , TonB-dependent
transporters (TBDTs) and proteins that are important
for intracellular signalling pathways involving the
second messenger cyclic di-GMP (BOX 1).
TonB-dependent transporters. A systematic analysis of
the role of the 72 TBDTs in X. campestris pv. campestris
has provided insight into how the pathogen scavenges for
plant carbohydrates during infection15. Although TBDTs
are mainly known to transport iron–siderophore complexes and vitamin B12 into the bacterial periplasm, one
TBDT (SuxA) of X. campestris pv. campestris transports
sucrose with a very high affinity. This TBDT, together
with an inner-membrane transporter, a sucrose hydrolase and a regulatory protein, is encoded on a carbohydrate utilization (CUT) locus. A genome context survey
showed that several of the genes encoding TBDTs belong
to other CUT loci. One of these loci has been implicated
in the synthesis and catabolism of N‑acetylglucosamine
(GlcNAc)16. This CUT system is believed to involve the
external generation of GlcNAc-containing carbohydrates
and their uptake through the outer and inner membranes followed by intracellular catabolism of GlcNAc.
Mutational analysis indicates the importance of this
pathway in the generation and catabolism of GlcNAc
in planta, which is an unexpected finding for a phytopathogenic bacterium, as homopolymers of GlcNAc
are unknown in plants. Although other polymers of
plant origin are potential sources of GlcNAc-containing
oligosaccharides, the possibility that this CUT locus is
involved in recycling bacterial peptidoglycan cannot be
excluded.
NATURE REVIEWS | MICROBIOLOGY
VOLUME 9 | MAY 2011 | 347
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
Box 1 | Functional genomic analyses of the virulence of Xanthomonas spp.
Mapping insertion sites within transposon-based mutant libraries
•Construction of Tn5-gusA library in Xanthomonas campestris pv. campestris13.
•Identification of candidate virulence factors in Xanthomonas oryzae pv. oryzicola79.
•Identification of pathogenesis and adaptation genes in Xanthomonas citri subsp. citri12.
•Construction of Tn5 library in Xanthomonas oryzae pv. oryzae79.
•Construction of a signature-tagged mutagenesis library in X. campestris pv. campestris4.
•Expansion of Tn5-gusA library in X. campestris pv. campestris by site-directed mutagenesis with pK18mob (REF. 4).
Directed mutagenesis of subsets of genes encoding specific functions
•Genes encoding TonB-dependent transporters of X. campestris pv. campestris15.
•Type III effector genes with a plant-inducible promoter (PIP) box in X. campestris pv. campestris80.
•Genes encoding non-transcription activator-like (non-TAL) effectors in X. oryzae pv. oryzae28.
•Genes encoding two-component response regulators in X. campestris pv. campestris81.
•Genes encoding GGDEF, EAL and HD‑GYP* domain proteins involved in cyclic di-GMP synthesis and degradation20.
•Genes encoding proteins that contain a PilZ domain involved in regulation by cyclic di-GMP (REF. 82).
Construction and use of microarrays or macroarrays
•Expression profiling of virulence genes in Xanthomonas axonopodis pv. citri using a macroarray83.
•Construction of a DNA microarray of X. axonopodis pv. citri48.
•Comparative regulation of virulence gene expression in X. oryzae pv. oryzae and X. oryzae pv. oryzicolae using
microarrays29.
•In planta gene expression of X. oryzae pv. oryzae using microarray32.
•Comparative genome hybridization to reveal genetic diversity in X. campestris pv. campestris using microarray33.
•Virulence-related signalling mediated by the diffusible signal factor (DSF) cell-to-cell signal in X. campestris pv.
campestris using a microarray30,31.
Elucidation of metabolic pathways
•Reconstruction of metabolic pathways involved in xanthan biosynthesis in X. campestris pv. campestris73.
Proteomic analysis of virulence-related processes
•Comparative proteomics of pathogenic and non-pathogenic strains of X. campestris pv. campestris84.
•Analysis of proteins associated with outer-membrane vesicles in X. campestris pv. campestris34.
•Identification of a biofilm-dispersing enzyme produced by X. campestris pv. campestris35.
•Comparative proteomics of X. campestris pv. campestris in resistant and susceptible hosts85.
*The names GGDEF, EAL and HD‑GYP derive from the conserved amino acid motifs present in these protein domains.
Cyclic di-GMP
A bacterial second messenger
that is involved in the
regulation of a wide variety of
cellular processes.
Cyclic di-GMP signalling systems and virulence. Cyclic
di-GMP is a second messenger with a role in the regulation of a range of cellular functions in diverse bacteria17–19. Cellular levels of cyclic di-GMP are controlled
through synthesis that is catalysed by proteins containing
a GGDEF domain and degradation by proteins harbouring either EAL or HD‑GYP domains (the names of these
three domains derive from their conserved amino acid
motifs). These domains are mostly found in combination with other signalling domains, suggesting that their
activities in cyclic di-GMP turnover can be modulated
by environmental cues.
The genome of X. campestris pv. campestris encodes
three proteins with an HD‑GYP domain and 34 proteins with GGDEF and/or EAL domains20. In a systematic analysis, the contribution of these proteins to
virulence in Chinese radish was examined. Among
the 13 proteins with important roles in virulence, the
regulator RpfG (which harbours an HD‑GYP domain)
is involved in signal transduction following perception
of a cell-to-cell signal, which is known as a diffusible
signal factor (DSF). The findings indicate the existence
of a regulatory network that may allow X. campestris
pv. campestris to integrate information from cell-tocell signalling with other environmental inputs, such
as reduced oxygen concentrations or the presence of
specific amino acids (such as glutamine), to modulate
the synthesis of virulence factors. Glutamine is the
most abundant amino acid in the guttation fluid of
Arabidopsis thaliana21, which is a host for X. campestris
pv. campestris. Both reduced oxygen concentrations
and the presence of glutamine are therefore environmental conditions that are likely to be encountered
by the pathogen during disease. Other cyclic di-GMP
signalling systems are dedicated to various tasks;
for instance, influencing motility, which contributes
to virulence but has no effect on the synthesis of
virulence factors.
Although the three genes encoding HD‑GYP
domain proteins are conserved in all Xanthomonas
spp. genomes, genes encoding GGDEF and/or
EAL domain proteins are not conserved in all the
genomes. Of the 37 cyclic di-GMP signalling proteins that are encoded by X. campestris pv. campestris,
348 | MAY 2011 | VOLUME 9
www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
Box 2 | Type III effectors
Two broad classes of type III effectors have been recognized in Xanthomonas spp.:
transcription activator-like (TAL) effectors and non-TAL effectors. TAL effectors
activate host gene expression and are characterized by common structural features,
including nuclear localization signals, an acidic activation domain that is typical of
transcription factors, and a central region that confers target specificity and contains
several repeats of about 34 amino acids each49. Non-TAL effectors are a structurally and
functional diverse group of proteins (TABLE 3).
In some plants, bacterial effectors are recognized by the host cell and trigger a
resistance response called the hypersensitive response (HR). Because of this action,
these effectors were originally named avirulence (avr) gene products, although they
may promote disease in susceptible hosts (see, for example, REF.62). The recognition of
Avr proteins is mediated by products of plant resistance (R) genes and restricts host
range.
Differences in the complement of effectors between different Xanthomonas strains of
the same pathovar may determine host specificity at the cultivar level. Effector
recognition may also underpin the host range restriction of pathovars within a species40
and of the species themselves50,51,63 to particular plants. Although this has not yet been
demonstrated, the complement of effectors could potentially influence tissue
specificity. For example, tissue-specific expression of R genes that mediate the
response to a particular effector could restrict a pathogen to either vascular or
mesophyllic colonization.
Furthermore, the absence of effectors that subvert tissue-specific defence responses
or are otherwise required for growth in certain tissues might also contribute to tissue
specificity.
36 are retained by X. campestris pv. armoraciae, 34
by X. citri pv. citri, 31 by X. oryzae pv. oryzicola and
25 by X. oryzae pv. oryzae (which also has an additional gene). Intriguingly, ten genes that encode
cyclic di‑GMP signalling proteins with important
roles in the virulence of X. campestris pv. campestris
on Chinese radish are retained in the X. oryzae pv.
oryzae genome, suggesting that they may represent a
core set of virulence factors.
Non-host resistance
A host–pathogen interaction in
which all members of a plant
species exhibit resistance to all
strains of a pathogen.
Two-component signal transduction systems.
Xanthomonas spp. genomes encode a large range of twocomponent signal transduction systems, which link the
sensing of different environmental cues to alterations
in gene expression and other cellular processes. These
systems comprise a sensory histidine kinase as well as
a response regulator with a CheY-like receiver domain
that is attached to different classes of output domain.
Insertional inactivation of genes encoding 51 of the 54
response regulators in X. campestris pv. campestris, followed by testing in plants, identified two novel response
regulators (XCC1958 and XCC3107) that influence virulence in addition to RpfG (which has previously been
described as an element in the DSF signalling system)22.
The output domain of XCC3107 (also known as virulence and growth regulator (VgrR)) is predicted to bind
DNA, whereas XCC1958 (also known as regulation of
adaptation and virulence (RavR)) contains a receiver
domain together with GGDEF and EAL domains
(which are implicated in cyclic di-GMP signalling).
Further work has suggested that XCC1958 and the sensor kinase RavS are involved in regulating the expression of virulence genes in response to reduced oxygen
concentrations, a situation that may be encountered
within plants23.
Type III effectors. Xanthomonas spp. use the Hrp T3SS
to inject effector proteins into the cytoplasm of the plant
cell24–27, where these proteins promote disease by diverse
mechanisms (BOX 2). A number of type III effectors have
been identified individually using translocation screens
or mutational analyses (see the following section),
but with the availability of whole genome sequences,
genome-wide, reverse genetics approaches have become
possible. For example, until recently, knowledge of the
function of effectors in X. oryzae pv. oryzae was limited
to those belonging to the transcription activator-like
(TAL) family. A comprehensive study of the non-TAL
effectors that are encoded in the genome of X. oryzae
pv. oryzae str. PXO99A has implicated XopZ, a protein of
unknown function, in virulence28. This strain contains
two identical copies of the xopZ gene, and only strains
with mutations of both genes show reduced virulence.
Interestingly, related genes are found in most of the
sequenced Xanthomonas spp. genomes (BOX 1).
Construction of gene chips or microarrays. Genome
sequence information has also guided the design of
probes that are used in the construction of gene chips
or microarrays for transcriptome and comparative
genome hybridization studies (BOX 1). These arrays
have been used to examine differences in transcriptional regulation of hrp genes between pathovars of
X. oryzae29, to identify genes regulated by a cell-to-cell
DSF in X. campestris pv. campestris 30,31 and to identify
genes that are expressed in X. oryzae pv. oryzae during
infection of rice plants32. In this study of rice plants,
gene expression in an African isolate of X. oryzae pv.
oryzae was examined at different time points during
infection. In addition to identifying several IS elements
and genes involved in secretion and transport, adhesion and plant cell wall degradation, this work identified various new potential virulence factors that are
associated with African, but not Asian, strains of this
pathovar. These include 24 genes with no similarity
to other proteins, one IS element and a gene encoding a haemolysin that is also found in X. campestris
pv. campestris. Microarray-based comparative genome
hybridization analysis of 18 virulent strains of X. campestris pv. campestris led to the identification of avrXccC
(also known as xopAH) and avrXccE1 as determinants
of the host specificity of X. campestris pv. campestris
str. 8004 on mustard and Chinese cabbage, respectively,
and avrBs1 as a determinant of non-host resistance on
pepper 33.
Proteomic analysis of virulence factors. Genome
sequence information also facilitates proteomic
approaches to identifying genes that are important in virulence. Analysis of the composition and cargo of outermembrane vesicles that are released from X. campestris
pv. campestris during growth has identified a number
of proteins that act as triggers of basal plant resistance
responses, such as the oxidative burst 34. A proteomic
approach has also allowed the identification of an extracellular enzyme as endo‑1,4-β-mannosidase–cellulase
(ManA), an endo-mannanase that is responsible for
NATURE REVIEWS | MICROBIOLOGY
VOLUME 9 | MAY 2011 | 349
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
biofilm dispersal in the same pathovar (BOX 1). A strain
with a mutation in manA showed reduced disease symptoms in Chinese radish, suggesting a role for biofilm
dispersal in virulence35.
Comparative genomics and host adaptation
Comparative genomic analysis between Xanthomonas
spp. has revealed the conservation of certain genes and
gene clusters that are associated with virulence, as well as
differences in genetic content that may be related to host
and/or tissue specificity. It is evident that differentiation
in host and tissue specificity does not involve major
modifications or wholesale exchange of pathogenicity
gene clusters. Instead, it is likely to be associated with
subtle changes in a small number of genes within these
clusters and/or differences outside the clusters, potentially among genes encoding secreted substrates or regulatory targets11. Although several candidates have been
identified, no determinant of host or tissue specificity
has yet been defined.
Type II secretion systems. Plant cell wall-degrading
enzymes, such as cellulase, polygalacturonase, xylanase
and protease, are secreted by T2SSs. All Xanthomonas spp.
and the phylogenetically related X. fastidiosa and
Stenotrophomonas spp. possess a T2SS called Xps, which
has been shown to contribute to virulence in X. campestris
pv. campestris, X. oryzae pv. oryzae, X. oryzae pv. oryzicola and X. euvesicatoria14,36–38. A second T2SS known
as the Xcs system is found in certain species, including X. campestris pv. campestris, X. citri pv. citri and
X. euvesicatoria, but it does not seem to have a function
in virulence38.
Interestingly, homologues of T2SS substrates from
other Xanthomonas spp. are not secreted by the T2SS
of X. euvesicatoria. This indicates that the substrate
specificity of T2SSs can differ among Xanthomonas
spp. 38. Comparative analysis of the XpsD protein,
which forms the secretion channel in the Xps system, revealed amino acid differences at three positions (residues 494, 696 and 698) that correlate with
vascular or mesophyll tissue specificity among the
strains analysed 11. However, subsequent analysis of
the mesophyllic pathogens Xanthomonas gardneri and
X. euvesicatoria indicated that this correlation does
not hold for position 494 (N.P. and J.B.J., unpublished
observations).
All Xanthomonas spp. genomes have numerous genes
that encode putative enzymes for the degradation of the
plant cell wall. Some genes, such as cbhA, which encodes
a cellobiosidase, are found only in the xylem-invading
Xanthomonas spp. and in X. fastidiosa, whereas others are conserved in all species. Differences between
Xanthomonas spp. in the complement of the genes that
encode enzymes for the degradation of the plant cell
wall might reflect differences in cell wall composition
among the respective hosts or tissues, and could also
be related to differences in the symptoms produced by
infection. It remains to be tested whether the differences
in XpsD relate to the substrate specificity of the various
Xps systems.
Type III secretion systems. Most Xanthomonas spp.
possess an Hrp T3SS to inject effectors into the host
cells (BOX 2). Remarkably, X. albilineans does not possess the typical Hrp T3SS but does possess a T3SS that is
similar to the Salmonella pathogenicity island 1 (SPI‑1)
system that is found in Erwinia spp.7. The function of
this system and the identity of its associated effectors in
X. albilineans are unknown, although its occurrence
in bacterial pathogens and symbionts of insects has led to
the suggestion that X. albilineans (which is not known
to be transmitted by insects) may have an insect-associated
lifestyle. However, X. fastidiosa, which is transmitted by
insects, does not seem to possess any T3SS.
Genome sequence mining has provided insights
into the diverse range of type III effectors possessed by
Xanthomonas spp., with clues to their possible contribution towards host specificity 27. So far, a total of 52 effector families have been identified, along with three harpin
proteins — these are helper or accessory proteins that
assist in effector translocation39.
Most sequenced Xanthomonas spp. genomes contain a core set of nine genes that encode type III effectors (xopR, avrBs2, xopK, xopL, xopN, xopP, xopQ, xopX
and xopZ) (TABLE 2). The exceptions are X. campestris
pv. armoraciae, which has only six known effectors, and
X. albilineans, for which no effectors have been identified.
Moreover, four additional genes (pthA, xopF1, xopE2 and
avrXacE3) that encode type III effectors are conserved in
X. axonopodis 40. The mutation of genes encoding core
effectors usually leads to reduced virulence and fitness
of the pathogen28,41–46, but in some cases this has been
observed to depend on the strain being tested47.
A few type III effector-encoding genes are associated
with only certain species, or with different species that
attack common hosts. For example, xopAL1, xopAC,
xopAD, avrXccC and xopAL2 are unique to X. campestris
strains that infect cruciferous plants. The genes xopE3
and xopA1 are localized to a genomic island and are
specific to the citrus pathogens X. citri pv. citri str. 306
and Xanthomonas fuscans subsp. aurantifolii strains B
and C48. Finally, xopE4 is found only in X. fuscans subsp.
aurantifolii strains B and C48. The contribution of these
genes to the ability to cause disease in specific hosts
remains to be tested.
Strikingly, genes that encode TAL effectors are
unevenly distributed among Xanthomonas spp. and
pathovars. They are numerous in some pathogens —
for example, X. oryzae pvs. oryzae and oryzicola — but
present as single-copy genes or absent altogether from
many others. TAL effectors, which are characterized by
a highly recombinogenic repeat region that has a direct
role in their function (BOX2), are potential determinants
of host and tissue specificity 49.
Some effectors have roles as avirulence factors in the
restriction of host range (BOX 2). They typically determine
specificity at the level of pathogen race (races within a
pathovar are differentiated by their ability to cause disease on different varieties of the same host) and host
cultivar by triggering defence responses in certain host
varieties that possess a specific resistance gene. However,
in some cases effectors can determine specificity at the
350 | MAY 2011 | VOLUME 9
www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
Table 2 | Distribution and function of genes encoding type III effectors throughout the sequenced Xanthomonas spp. genomes*
Effectors
Functional domain or motif
Distribution
Refs
XopR
Unknown
All Xanthomonas spp. except Xal
28,86
AvrBs2
Sequence related to agrocinopine synthase and glycerol
phosphodiesterase
All Xanthomonas spp. except Xca and Xal
44,63,87,88
XopK
Unknown
All Xanthomonas spp. except Xca and Xal
28,86
XopL
Leucine-rich repeats
All Xanthomonas spp. except Xca and Xal
28,80
XopN
α-helical Armadillo and HEAT repeats, and irregular α-helical
repeats, suggesting multiple protein–protein interactions
All Xanthomonas spp. except Xca and Xal
45,89
XopP
Unknown
All Xanthomonas spp. except Xal
45,89
XopQ
Inosine-uridine nucleoside N‑ribohydrolase
All Xanthomonas spp. except Xca and Xal
80
XopX
Methionine-rich protein
All Xanthomonas spp. except Xca and Xal
46
XopZ
Unknown
All Xanthomonas spp. except Xca and Xal
28
AvrBsT (also known as
XopJ2)
C55-family cysteine protease and Ser/Thr acetyltransferase
Some Xcv strains (plasmid borne)
38,90
XopC
Phosphoribosyl transferase domain and haloacid
dehalogenase-like hydrolase
Only in Xcv (xopC); only in Xoo strains
(xopC2-inactivated version in Xac and Xcv)
28,47
XopF1
Unknown
Xcv, Xca, Xoo, Xoc, Xvv and Xvm
47
XopF2
Unknown
Xcv, Xvm and Xvv
47
XopJ
C55-family cysteine protease and Ser/Thr acetyltransferase
Xcv
47
XopO
Unknown
Xcv and Xoc
47
XopAE
Leucine-rich repeats
Xag, Xac, Xoo, Xoc, Xvm and Xvv (hpaG/
hpaF pseudogene in Xcv)
91
AvrXccC (also known
as XopAH)
Unknown
Only in Xcc
79
XopE2
Putative transglutaminase
Xcv, Xac and Xcc
80
XopAM
Unknown
Xcc, Xvm and Xvv
80
PthA–AvrBs3 family
Transcriptional activator
Xac, Xoo, Xcv and Xg
XopD
C48-family small ubiquitin-like modifier (SUMO) cysteine
protease, with an EAR motif (putatively involved in
transcriptional repression), and a DNA-binding and nuclear
localization domain
Xcv, Xcc str. B100, chimeric version in Xcc
str. ATCC 33913 and Xcc str. 8004
Core effectors
‡
Variable effectors
§
||
62,92–94
95–98
Xac, Xanthomonas citri pv. citri; Xag, Xanthomonas axonopodis pv. glycines; Xal, Xanthomonas albilineans str. GPE PC73; Xca, Xanthomonas campestris pv.
armoraciae; Xcc, Xanthomonas campestris pv. campestris; Xcv, Xanthomonas euvesicatoria str. 85‑10; Xg, Xanthomonas gardneri; Xoc, Xanthomonas oryzae pv.
oryzicola; Xoo, Xanthomonas oryzae pv. oryzae; Xvm, Xanthomonas campestris pv. musacearum; Xvv, Xanthomonas campestris pv. vasculorum. *This list only includes
effectors with a demonstrated role in pathogenicity or induction of resistance. ‡Core effectors are found in almost all Xanthomonas spp., with the exception of Xal
(which has none) and Xca (which has only XopR and XopP). §Variable effectors are found in only a limited number of strains. ||This family also includes the PthXo1
effector, which has recently been described to manipulate plant sugar efflux transporters effecting ‘nutrient gain’ (REF. 99).
level of plant species. For example, the gene avrGf1 is
responsible for the exclusion of grapefruit from the
range of host species infected by X. citri pv. citri str. Aw
(REF. 50). Interestingly, the gene xopAG, which belongs
to the same family as avrGf1, also limits the host range
of X. fuscans pv. aurantifolii str. C to exclude grapefruit.
X. fuscans pv. aurantifolii str. B, which causes disease
in grapefruit, has an almost identical xopAG gene, but
it is inactivated by an inserted transposon48. The gene
avrXv3 restricts the host range of Xanthomonas perforans
to tomato and triggers a defence response on pepper 51.
Adhesins. As do many bacteria, Xanthomonas spp. synthesize both fimbrial and non-fimbrial adhesins, which
are involved in bacterial attachment to surfaces and
contribute to virulence52–54. The non-fimbrial adhesins
include filamentous haemagglutinin-like proteins, such
as FhaB, as well as homologues of the autotransporter
adhesin YapH from Yersinia spp. and other proteins
(XadA and XadB) that are related to YadA from Yersinia
spp. Fimbrial adhesins include type IV pili and related
proteins, such as the type IV pilus secretin PilQ52–54. It has
been shown for X. oryzae pv. oryzae that some adhesins
are preferentially involved in different stages of infection
— namely, attachment to leaf surfaces, entry, colonization and later survival inside plant tissue52. For example,
XadA and XadB affect leaf attachment and entry into the
host but are not important for colonization thereafter,
whereas PilQ seems to have no role in leaf attachment
or entry but is required for multiplication and spread
NATURE REVIEWS | MICROBIOLOGY
VOLUME 9 | MAY 2011 | 351
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
within the leaf. By contrast, FhaB seems to be involved in
colonization of both the leaf surface and the apoplast
in X. citri pv. citri 53. Comparative genome analysis indicates that fhaB is absent in some strains of X. citri pv. citri
and X. oryzae pv. oryzae, whereas in X. euvesicatoria there
are two related ORFs, fhaB1 and fhaB2. Two copies of
xadA and yapH are found in X. campestris pv. campestris
str. 306 and in X. euvesicatoria str. 85‑10; two copies of
yapH are also present in X. oryzae pv. oryzae str. KACC,
and there are two pilQ orthologues in X. euvesicatoria
str. 85‑10. The various combinations of adhesins in each
species might relate to the different specificities of these
pathogens towards host tissues, as has been speculated
for Ralstonia solanacearum55, although a clear relationship
is not evident.
Lipopolysaccharides and xanthan. Lipopolysaccharide
(LPS) and the extracellular polysaccharide xanthan
(which is characteristic of the genus Xanthomonas)
contribute to the ability of Xanthomonas spp. to cause
disease13,35,56–58. An LPS biosynthesis gene cluster, defined
by a 14–26 kb region that is flanked by etfA and metB,
is highly variable in terms of size and gene composition across sequenced xanthomonads. This variability
is seen not only at the levels of species and pathovar but
also between strains, suggesting recent horizontal gene
transfers59. However, variations in the LPS biosynthesis
cluster are not correlated with differences in host or tissue specificity 11. The gum cluster comprises 12 genes,
gumB to gumM, that encode proteins that are involved
in the synthesis and secretion of xanthan13,56,58. However,
the gum cluster is absent from X. albilineans 7, whereas
X. fastidiosa lacks some of the gum genes but is capable
of synthesizing a related polysaccharide that lacks the
terminal mannose residues and is not pyruvylated.
Toxins. The production of toxins in Xanthomonas spp. is
currently thought to be restricted to X. albilineans, which
produces albicidin, a virulence factor 7 that is synthesized
by a hybrid modular non-ribosomal peptide synthetase–
polyketide synthase (NRPS–PKS). Furthermore, other
NRPS enzymes that are related to the Pseudomonas
syringae syringomycin synthetase (SyrE), which is
responsible for the synthesis of the phytotoxin syringo­
mycin, are encoded by the genomes of X. axonopodis
pv. citri 60 and X. oryzae pv. oryzicola (A.B., unpublished
observations), but whether they synthesize toxins is not
known. Moreover, several Xanthomonas spp. possess
genes that encode NRPS enzymes which are similar to
enterobactin synthase component F (EntF), which is
involved in the synthesis of the siderophore enterobactin
in Escherichia coli, but a role in virulence has not been
reported.
Evolutionary trends and adaptation to plant hosts
Comparative analysis of Xanthomonas spp. has revealed
that their genomes are highly plastic and experiencing
rapid evolution. As noted, X. albilineans has undergone
considerable genome reduction, which may be associated with its xylem-limited lifestyle. In addition to
genome size, evolutionary trends have also been inferred
from detailed comparisons between pathogenicity gene
clusters, the complement of particular sets of genes, the
content of IS elements and the structure of the clustered regularly interspersed short palindromic repeats
(CRISPR) elements7.
Pathogenesis-associated gene clusters. Phylogenetic trees
derived from amino acid alignments of the products of
the gum, xps, xcs, hrp and rpf gene clusters generally
reflect strain phylogeny based on 16S ribosomal RNA or
DNA gyrase subunit B (gyrB) gene sequences, although
slight variations have been observed11. The gum cluster
is conserved, except for gumN and sequences downstream; however, the functions of the products of these
genes remain obscure. The xcs and xps T2SS clusters
are conserved, except in the rice pathogens X. oryzae
pv. oryzae and X. oryzae pv. oryzicola, in which xcs is
missing. Although the hrp gene cluster is conserved,
sequences flanking the core genes for the T3SS vary
with respect to the content of putative effector-encoding
genes and IS elements. Variation at the rpf cluster is
more pronounced, although the rpf genes with established functions in cell-to-cell signalling are conserved.
The differences observed in these gene clusters among
Xanthomonas spp. and the close relatives X. fastidiosa
and S. maltophilia suggest that the xps and rpf clusters
were probably present in an ancestral Xanthomonas sp.
genome, whereas the hrp, gum and xcs clusters seem to
be recent acquisitions in the Xanthomonas lineage. The
xcs cluster seems to have subsequently been lost from
the X. oryzae lineage.
Rapid evolution in X. oryzae. Several lines of evidence
are indicative of rapid evolution in the X. oryzae lineage.
The pathovars of X. oryzae contain the greatest number
and diversity of IS elements of all the sequenced xantho­
monads. These pathovars are also unusual in their abundance of TAL effector genes61, which are probable hot
spots for recombination and adaptation. By contrast,
these pathovars have a reduced complement of cyclic
di-GMP signalling proteins compared with that of other
Xanthomonas spp.20.
Further evidence of marked diversification within the
X. oryzae lineage has been obtained by analysis of
the CRISPR regions of strains of X. oryzae pv. oryzae.
These regions are identified by a set of CRISPRassociated (cas) genes, which are followed by a leader
sequence and then a variable number of alternating
spacers and repeats. The repeats are identical, whereas
the spacers represent foreign DNA that was laterally
transferred from a bacteriophage or a plasmid. These
spacers may have a role in protection against phage
infection. Considerable variation in the number
of spacers is seen between the three sequenced strains
of X. oryzae pv. oryzae. Furthermore, most of the spacers are unique to each strain, attesting to the rapid
evolution of these regions. The marked overall diversity within just one Xanthomonas species is striking. It
is interesting that the host of X. oryzae is one of our
most ancient domesticated crops subjected to sustained
selective breeding.
352 | MAY 2011 | VOLUME 9
www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
Box 3 | Bioinformatic applications for ‘omics’ analyses of xanthomonads
New approaches to DNA sequencing, also known as second-generation sequencing
methods, have not only resulted in a huge leap in the amount of genomic data but have
also promised to revolutionize our understanding of the complexity, plasticity and
regulation of Xanthomonas transcriptomes through the analysis of RNA. The new
sequence technologies will also empower proteomic analyses, allowing the identification
of individual proteins from complex samples, and metabolomic studies that rely on
genome data as initial blueprints for the reconstruction of metabolic pathways.
Integration and mining of these large and diverse data sets will increasingly rely on
powerful bioinformatic applications. In addition to the well-established GenDB
software for the annotation of bacterial genomes64, there are now applications for
comparative genomics (EDGAR65), transcriptomics (EMMA66), proteomics (QuPE67) and
metabolomics (MeltDB68). The comparison of data from different genomes — from
whole-genome alignments to the grouping of orthologous genes — is greatly
facilitated by EDGAR, which is a tool that was implemented for research on
Xanthomonas spp. but which is also useful for the analysis of other bacterial pathogens
of plants or animals. Recently, applications for enhanced data visualization (ProMeTra69)
and the automated generation of metabolic networks in computer-readable format
(CARMEN70) have been added to facilitate systems biology. All the software mentioned
above is freely available and is installed and maintained locally at the Center for
Biotechnology (CeBiTec) of Bielefeld University, Germany. A common software
interface, termed BRIDGE71, enables the transparent exchange of data between
individual applications. All applications support data import and export in formats that
are generally accepted in the respective scientific disciplines.
Concluding statements
Despite considerable progress in understanding the
mechanisms of pathogenesis of Xanthomonas spp., there
are still several outstanding questions that should guide
future research. First, the ecology of these microorganisms is poorly understood. Very little is known about the
functions that contribute to epiphytic growth, preference
for portal of entry and modulation of the action of stomata. Moreover, the modes of dissemination remain to
be fully described. Second, the determinants of host and
tissue specificity have not been identified. The power
1.
2.
3.
4.
5.
6.
Jun, S.‑R., Sims, G. E., Wu, G. A. & Kim, S.‑H.
Whole-proteome phylogeny of prokaryotes by feature
frequency profiles: an alignment-free method with
optimal feature resolution. Proc. Natl Acad. Sci. USA
107, 133–138 (2010).
An interesting whole-proteome phylogeny study of
prokaryotes that shows the Xanthomonadaceae
family profiles clustered with the
Betaproteobacteria.
Parkinson, N. et al. Phylogenetic analysis of
Xanthomonas species by comparison of partial
gyrase B gene sequences. Int. J. Syst. Evol. Microbiol.
57, 2881–2887 (2007).
Highlights the complexity of the Xanthomonas spp.
and details useful genetic tools for species
discrimination.
Dar, G. H., Anand, R. C. & Sharma, P. K. Genetically
engineered microorganisms to rescue plants from frost
injury. Adv. Biochem. Eng. Biotechnol. 50, 1–19
(1993).
Ryan, R. P. et al. Passing GO (gene ontology) in plant
pathogen biology: a report from the Xanthomonas
Genomics Conference. Cell. Microbiol. 11,
1689–1696 (2009).
Comas, I., Moya, A., Azad, R. K., Lawrence, J. G. &
Gonzalez-Candelas, F. The evolutionary origin of
Xanthomonadales genomes and the nature of the
horizontal gene transfer process. Mol. Biol. Evol. 23,
2049–2057 (2006).
Lima, W. C., Paquola, A. C. M., Varani, A. M., Van
Sluys, M. A. & Menck, C. F. M. Laterally transferred
genomic islands in Xanthomonadales related to
pathogenicity and primary metabolism. FEMS
Microbiol. Lett. 281, 87–97 (2008).
7.
8.
9.
10.
11.
12.
13.
14.
of comparative genomics for defining the adaptations
that cause host and tissue specificity, as well as the core
genes that are essential for pathogenesis, is proportional to the number of genome sequences available.
Therefore, sequencing the genomes of a wider diversity of strains, pathovars and species from the genus
Xanthomonas would be extremely useful. In particular,
high-resolution comparative analysis of genomes of
many pathogenic and epiphytic strains should be a priority and is now an attainable objective thanks to the
availability of high-throughput sequencing methods and
advanced bioinformatics (BOX 3).
Effector proteins confer specificity at the levels of
pathogen race and host cultivar, and these proteins
might also function as determinants of host species and
tissue specificity. For that reason, the characterization
of these proteins, the identification of their molecular
targets in the plant and the consequences of targeting
effectors as a potential approach to modulate host susceptibility or resistance merit continued attention. The
identification of new plant resistance (R) genes and
the engineering of the promoters of known R genes to
recognize multiple TAL effectors from disparate pathogens are possible approaches towards the development
of broad-range and durable disease resistance in crops.
Interference with central pathogenicity mechanisms,
such as effector secretion or cell-to-cell signalling, may
also afford a route to effective disease control. Finally,
an in-depth knowledge of multiple genome sequences
from Xanthomonas spp. will allow the development of
highly discriminative tools for disease diagnosis with
potential applications in epidemiology. In summary, an
ongoing effort in comparative genomics of Xanthomonas
spp. will be key to the future development of strategies
for the sustainable management of crop diseases that are
attributable to this diverse group.
Pieretti, I. et al. The complete genome sequence of
Xanthomonas albilineans provides new insights into
the reductive genome evolution of the xylem-limited
Xanthomonadaceae. BMC Genomics 10, 1471–1475
(2009).
Darrasse, A. et al. Transmission of plant-pathogenic
bacteria by nonhost seeds without induction of
an associated defense reaction at emergence.
Appl. Environ. Microbiol. 76, 6787–6796 (2010).
Cazalet, C. et al. Analysis of the Legionella
longbeachae genome and transcriptome uncovers
unique strategies to cause legionnaires’ disease. PLoS
Genet. 6, e1000851 (2010).
Lima, W. C., Van Sluys, M. A. & Menck, C. F. M. Nongamma‑proteobacteria gene islands contribute to the
Xanthomonas genome. OMICS 9, 160–172 (2005).
Lu, H. et al. Acquisition and evolution of plant
pathogenesis-associated gene clusters and candidate
determinants of tissue-specificity in Xanthomonas.
PLoS ONE 3, e3828 (2008).
Laia, M. L. et al. New genes of Xanthomonas citri
subsp. citri involved in pathogenesis and adaptation
revealed by a transposon-based mutant library. BMC
Microbiol. 9, 12 (2009).
Qian, W. et al. Comparative and functional genomic
analyses of the pathogenicity of phytopathogen
Xanthomonas campestris pv. campestris. Genome
Res. 15, 757–767 (2005).
An excellent study demonstrating the power of
comparative and functional genomics to provide
valuable information about Xanthomonas spp.
pathogenicity.
Wang, L. F., Rong, W. & He, C. Z. Two Xanthomonas
extracellular polygalacturonases, PghAxc and PghBxc,
NATURE REVIEWS | MICROBIOLOGY
15.
16.
17.
18.
19.
20.
21.
22.
are regulated by type III secretion regulators HrpX and
HrpG and are required for virulence. Mol. Plant
Microbe Interact. 21, 555–563 (2008).
Blanvillain, S. et al. Plant carbohydrate scavenging
through TonB-dependent receptors: a feature shared
by phytopathogenic and aquatic bacteria. PLoS ONE
2, e224 (2007).
A systematic mutagenesis study of Xanthomonas
spp. TonB-dependent receptors identifying a new
type of CUT locus that is required for pathogenicity.
Boulanger, A. et al. Identification and regulation of the
N‑acetylglucosamine utilization pathway of the plant
pathogenic bacterium Xanthomonas campestris pv.
campestris. J. Bacteriol. 192, 1487–1497 (2010).
Hengge, R. Principles of c‑di‑GMP signalling in
bacteria. Nature Rev. Microbiol. 7, 263–273 (2009).
Romling, U. & Simm, R. Bacterial sensing and
signaling. Prevailing concepts of c‑di‑GMP signaling.
Contrib. Microbiol. 5, 161–181 (2009).
Schirmer, T. & Jenal, U. Structural and mechanistic
determinants of c‑di‑GMP signalling. Nature Rev.
Microbiol. 7, 724–735 (2009).
Ryan, R. P. et al. Cyclic di-GMP signalling in the
virulence and environmental adaptation of
Xanthomonas campestris. Mol. Microbiol. 63,
429–442 (2007).
Pilot, G. et al. Overexpression of glutamine dumper 1
leads to hypersecretion of glutamine from hydathodes of
Arabidopsis leaves. Plant Cell 16, 1827–1840 (2004).
Qian, W., Han, Z. J., Tao, J. & He, C. Z. Genome-scale
mutagenesis and phenotypic characterization of twocomponent signal transduction systems in
Xanthomonas campestris pv. campestris ATCC 33913.
Mol. Plant Microbe Interact. 21, 1128–1138 (2008).
VOLUME 9 | MAY 2011 | 353
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
23. He, Y. W., Boon, C., Zhou, L. & Zhang, L. H.
Co-regulation of Xanthomonas campestris virulence
by quorum sensing and a novel two-component
regulatory system RavS/RavR. Mol. Microbiol. 71,
1464–1476 (2009).
24. Grant, S. R., Fisher, E. J., Chang, J. H., Mole, B. M. &
Dangl, J. L. Subterfuge and manipulation: type III
effector proteins of phytopathogenic bacteria. Ann.
Rev. Microbiol. 60, 425–449 (2006).
25. Nomura, K., Melotto, M. & He, S. Y. Suppression of
host defense in compatible plant–Pseudomonas
syringae interactions. Curr. Opin. Plant Biol. 8,
361–368 (2005).
26. Rohmer, L., Guttman, D. S. & Dangl, J. L. Diverse
evolutionary mechanisms shape the type III effector
virulence factor repertoire in the plant pathogen
Pseudomonas syringae. Genetics 167, 1341–1360
(2004).
27. White, F. F., Potnis, N., Jones, J. B. & Koebnik, R. The
type III effectors of Xanthomonas. Mol. Plant Pathol.
10, 749–766 (2009).
A thorough review of type III effectors that are
associated with Xanthomonas strains.
28. Song, C. F. & Yang, B. Mutagenesis of 18 type III
effectors reveals virulence function of XopZ(PXO99) in
Xanthomonas oryzae pv. oryzae. Mol. Plant Microbe
Interact. 23, 893–902 (2010).
29. Seo, Y. S. et al. A two-genome microarray for the rice
pathogens Xanthomonas oryzae pv. oryzae and
X. oryzae pv. oryzicola and its use in the discovery of a
difference in their regulation of hrp genes. BMC
Microbiol. 8, 99 (2008).
30. He, Y. W. et al. Xanthomonas campestris cell–cell
communication involves a putative nucleotide receptor
protein Clp and a hierarchical signalling network. Mol.
Microbiol. 64, 281–292 (2007).
31. He, Y. W. et al. Genome scale analysis of diffusible
signal factor regulon in Xanthomonas campestris pv.
campestris: identification of novel cell–cell
communication-dependent genes and functions. Mol.
Microbiol. 59, 610–622 (2006).
An insightful study using the first oligomicroarray
developed for Xanthomonas spp. to assess
the effect of the DSF on gene expression in
X. campestris.
32. Soto-Suarez, M. et al. In planta gene expression
analysis of Xanthomonas oryzae pathovar oryzae,
African strain MAI1. BMC Microbiol. 10, 170 (2010).
33. He, Y. Q. et al. Comparative and functional genomics
reveals genetic diversity and determinants of host
specificity among reference strains and a large
collection of Chinese isolates of the phytopathogen
Xanthomonas campestris pv. campestris. Genome
Biol. 8, R218 (2007).
34. Sidhu, V. K., Vorholter, F. J., Niehaus, K. & Watt, S. A.
Analysis of outer membrane vesicle associated
proteins isolated from the plant pathogenic bacterium
Xanthomonas campestris pv. campestris. BMC
Microbiol. 8, 87 (2008).
35. Dow, J. M. et al. Biofilm dispersal in Xanthomonas
campestris is controlled by cell–cell signaling and is
required for full virulence to plants. Proc. Natl Acad.
Sci. USA 100, 10995–11000 (2003).
36. Dow, J. M., Scofield, G., Trafford, K., Turner, P. C. &
Daniels, M. J. A gene cluster in Xanthomonas
campestris pv. campestris required for pathogenicity
controls the excretion of polygalacturonate lyase the
the other enzymes. Physiol. Mol. Plant Pathol. 31,
261–271 (1987).
37. Jha, G., Rajeshwari, R. & Sonti, R. V. Bacterial type
two secretion system secreted proteins: double-edged
swords for plant pathogens. Mol. Plant Microbe
Interact. 18, 891–898 (2005).
38. Szczesny, R. et al. Functional characterization of the
Xcs and Xps type II secretion systems from the plant
pathogenic bacterium Xanthomonas campestris pv
vesicatoria. New Phytol. 187, 983–1002 (2010).
39. Zheng Q. F., Guo, M. & Alfano, J. R. Pseudomonas
syringae HrpJ is a type III secreted protein that is
required for plant pathogenesis, injection of effectors,
and secretion of the HrpZ1 harpin. J. Bacteriol. 188,
6060–6069 (2006).
40. Hajri, A. et al. A “repertoire for repertoire” hypothesis:
repertoires of type three effectors are candidate
determinants of host specificity Xanthomonas. PLoS
ONE 4, e6632 (2009).
41. Al-Saadi, A. et al. All five host-range variants of
Xanthomonas citri carry one pthA homolog with 17.5
repeats on citrus, but that determines none determine
host-range pathogenicity variation. Mol. Plant
Microbe Interact. 20, 934–943 (2007).
42. Duan, Y. P., Castaneda, A., Zhao, G., Erdos, G. &
Gabriel, D. W. Expression of a single, host-specific,
bacterial pathogenicity gene in plant cells elicits
division, enlargement, and cell death. Mol. Plant
Microbe Interact. 12, 556–560 (1999).
43. Gassmann, W. et al. Molecular evolution of virulence
in natural field strains of Xanthomonas campestris pv.
vesicatoria. J. Bacteriol. 182, 7053–7059 (2000).
44. Kearney, B. & Staskawicz, B. J. Widespread
distribution and fitness contribution of Xanthomonas
campestris avirulence AVRBS2. Nature 346,
385–386 (1990).
45. Kim, J. G. et al. Xanthomonas T3S effector XopN
suppresses PAMP-triggered immunity and interacts
with a tomato atypical receptor-like kinase and TFT1.
Plant Cell 21, 1305–1323 (2009).
46. Metz, M. et al. The conserved Xanthomonas
campestris pv. vesicatoria effector protein XopX is a
virulence factor and suppresses host defense in
Nicotiana benthamiana. Plant J. 41, 801–814
(2005).
47. Roden, J. A. et al. A genetic screen to isolate type III
effectors translocated into pepper cells during
Xanthomonas infection. Proc. Natl Acad. Sci. USA
101, 16624–16629 (2004).
A description of an elegant functional screen for
large-scale identification of type III effectors.
48. Moreira, L. M. et al. Novel insights into the genomic
basis of citrus canker based on the genome sequences
of two strains of Xanthomonas fuscans subsp.
aurantifolii. BMC Genomics 11, 238 (2010).
49. Bogdanove, A. J., Schornack, S. & Lahaye, T. TAL
effectors: finding plant genes for disease and defense.
Curr. Opin. Plant Biol. 13, 394–401 (2010).
This review examines the most important
research into TAL effectors that have a role in
plant disease.
50. Rybak, M., Minsavage, G. V., Stall, R. E. & Jones, J. B.
Identification of Xanthomonas citri ssp. citri host
specificity genes in a heterologous expression host.
Mol. Plant Pathol. 10, 249–262 (2009).
51. Astua-Monge, G. et al. Resistance of tomato and
pepper to T3 strains of Xanthomonas campestris pv.
vesicatoria is specified by a plant-inducible. Mol. Plant
Microbe Interact. 13, 911–921 (2000).
52. Das, A., Rangaraj, N. & Sonti, R. V. Multiple adhesinlike functions of Xanthomonas oryzae pv. oryzae are
involved in promoting leaf attachment, entry, and
virulence on rice. Mol. Plant Microbe Interact. 22,
73–85 (2009).
53. Gottig, N., Garavaglia, B. S., Garofalo, C. G., Orellano,
E. G. & Ottado, J. A filamentous hemagglutinin-like
protein of Xanthomonas axonopodis pv. citri, the
phytopathogen responsible for citrus canker, is
involved in bacterial virulence. PLoS ONE 4, e4358
(2009).
54. Ray, S. K., Rajeshwari, R., Sharma, Y. & Sonti, R. V.
A high‑molecular‑weight outer membrane protein of
Xanthomonas oryzae pv. oryzae exhibits similarity to
non-fimbrial adhesins of animal pathogenic bacteria
and is required for optimum virulence. Mol. Microbiol.
46, 637–647 (2002).
55. Guidot, A. et al. Genomic structure and phylogeny of
the plant pathogen Ralstonia solanacearum inferred
from gene distribution analysis. J. Bacteriol. 189,
377–387 (2007).
56. Chou, F. L. et al. The Xanthomonas campestris gumD
gene required for synthesis of xanthan gum is involved
in normal pigmentation and virulence in causing black
rot. Biochem. Biophys. Res. Com. 233, 265–269
(1997).
57. Kingsley, M. T., Gabriel, D. W., Marlow, G. C. &
Roberts, P. D. The opsX locus of Xanthomonas
campestris affects host range and biosynthesis of
lipoplysaccharide and excellular polysaccharide.
J. Bacteriol. 175, 5839–5850 (1993).
58. Rajeshwari, R. & Sonti, R. V. Stationary-phase
variation due to transposition of novel insertion
elements in Xanthomonas oryzae pv. oryzae.
J. Bacteriol. 182, 4797–4802 (2000).
59. Patil, P. B., Bogdanove, A. J. & Sonti, R. V. The role of
horizontal transfer in the evolution of a highly variable
lipopolysaccharide biosynthesis locus in
xanthomonads that infect rice, citrus and crucifers.
BMC Evol. Biol. 7, 243 (2007).
60. Van Sluys, M. A. et al. Comparative genomic analysis
of plant-associated bacteria. Ann. Rev. Phytopathol.
40, 169–189 (2002).
61. Salzberg, S. L. et al. Genome sequence and rapid
evolution of the rice pathogen Xanthomonas oryzae
pv. oryzae PXO99A. BMC Genomics 9, 204 (2008).
354 | MAY 2011 | VOLUME 9
62. Schornack, S., Minsavage, G. V., Stall, R. E., Jones,
J. B. & Lahaye, T. Characterization of AvrHah1, a novel
AvrBs3‑like effector from Xanthomonas gardneri with
virulence and avirulence activity. New Phytol. 179,
546–556 (2008).
63. Minsavage, G. V. et al. Gene for gene relationships
specifying disease resistance in Xanthomonas
campestris pv. vesicatoria pepper interactions. Mol.
Plant Microbe Interact. 3, 41–47 (1990).
64. Meyer, F. et al. GenDB — an open source genome
annotation system for prokaryote genomes. Nucleic
Acids Res. 31, 2187–2195 (2003).
65. Blom, J. et al. EDGAR: A software framework for the
comparative analysis of prokaryotic genomes. BMC
Bioinformatics 10, 154 (2009).
66. Dondrup, M. et al. EMMA 2‑A MAGE-compliant
system for the collaborative analysis and integration
of microarray data. BMC Bioinformatics 10, 50 (2009).
67. Albaum, S. P. et al. Qupe‑a rich internet application to
take a step forward in the analysis of mass
spectrometry-based quantitative proteomics
experiments. Bioinformatics 25, 3128–3134 (2009).
68. Neuweger, H. et al. MeltDB: a software platform for the
analysis and integration of metabolomics experiment
data. Bioinformatics 24, 2726–2732 (2008).
69. Neuweger, H. et al. Visualizing post genomics datasets on customized pathway maps by ProMeTra‑
aeration‑dependent gene expression and metabolism
of Corynebacterium glutamicum as an example. BMC
Syst. Biol. 3, 82 (2009).
70. Schneider, J. et al. CARMEN - Comparative analysis
and in silico reconstruction of organism-specific
metabolic networks. Genet. Mol. Res. 9, 1660–1672
(2010).
71. Goesmann, A. et al. Building a BRIDGE for the
integration of heterogeneous data from functional
genomics into a platform for systems biology.
J. Biotechnol. 106, 157–167 (2003).
72. da Silva, A. C. R. et al. Comparison of the genomes of
two Xanthomonas pathogens with differing host
specificities. Nature 417, 459–463 (2002).
The first published genome sequences of two
pathogenic Xanthomonas spp. that cause disease
in very distinct hosts.
73. Vorhoelter, F. J. et al. The genome of Xanthomonas
campestris pv. campestris B 100 and its use for the
reconstruction of metabolic pathways involved in
xanthan biosynthesis. J. Biotechnol. 134, 33–45
(2008).
74. Studholme, D. J. et al. Genome-wide sequencing data
reveals virulence factors implicated in banana
Xanthomonas wilt. FEMS Microbiol. Lett. 310,
182–192 (2010).
75. Thieme, F. et al. Insights into genome plasticity and
pathogenicity of the plant pathogenic bacterium
Xanthomonas campestris pv. vesicatoria revealed by
the complete genome sequence. J. Bacteriol. 187,
7254–7266 (2005).
76. Lee, B. M. et al. The genome sequence of
Xanthomonas oryzae pathovar oryzae KACC10331,
the bacterial blight pathogen of rice. Nucleic Acids
Res. 33, 577–586 (2005).
77. Ochiai, H., Inoue, Y., Hasebe, A. & Kaku, H.
Construction and characterization of a Xanthomonas
oryzae pv. oryzae bacterial artificial chromosome
library. FEMS Microbiol. Lett. 200, 59–65 (2001).
78. Fargier, E. & Manceau, C. Pathogenicity assays restrict
the species Xanthomonas campestris into three
pathovars and reveal nine races within X. campestris
pv. campestris. Plant Pathol. 56, 805–818 (2007).
79. Wang, L., Makino, S., Subedee, A. & Bogdanove, A. J.
Novel candidate virulence factors in rice pathogen
Xanthomonas oryzae pv. oryzicola as revealed by
mutational amalysis. Appl. Environ. Microbiol. 73,
8023–8027 (2007).
80. Jiang, W. et al. Identification of six type III effector
genes with the PIP box in Xanthomonas campestris
pv. campestris and five of them contribute individually
to full pathogenicity. Mol. Plant Microbe Interact. 22,
1401–1411 (2009).
81. Qian, W., Han, Z. J. & He, C. Z. Two-component signal
transduction systems of Xanthomonas spp.: a lesson
from genomics. Mol. Plant Microbe Interact. 21,
151–161 (2008).
82. McCarthy, Y. et al. The role of PilZ domain proteins in
the virulence of Xanthomonas campestris pv.
campestris. Mol. Plant Pathol. 9, 819–824 (2008).
83. Astua-Monge, G. et al. Expression profiling of
virulence and pathogenicity genes of Xanthomonas
axonopodis pv. citri. J. Bacteriol. 187, 1201–1205
(2005).
www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
REVIEWS
84. Chung, W. J. et al. Qualitative and comparative
proteomic analysis of Xanthomonas campestris pv.
campestris 17. Proteomics 7, 2047–2058 (2007).
85. Villeth, G. R. et al. Comparative proteome analysis of
Xanthomonas campestris pv. campestris in the
interaction with the susceptible and the resistant
cultivars of Brassica oleracea. FEMS Microbiol. Lett.
298, 260–266 (2009).
86. Furutani, A. et al. Identification of novel type III
secretion effectors in Xanthomonas oryzae pv. oryzae.
Mol. Plant Microbe Interact. 22, 96–106 (2009).
87. Swords, K. M. M., Dahlbeck, D., Kearney, B., Roy, M.
& Staskawicz, B. J. Spontaneous and induced mutations
in a single open reading frame alter both virulence and
avirulence in Xanthomonas campestris pv. vesicatoria
avrBs2. J. Bacteriol.178, 4661–4669 (1996).
88. Wichmann, G. & Bergelson, J. Effector genes of
Xanthamonas axonopodis pv. vesicatoria promote
transmission and enhance other fitness traits in the
field. Genetics 166, 693–706 (2004).
89. Jiang, B. L. et al. The type III secretion effector
XopXccN of Xanthomonas campestris pv. campestris
is required for full virulence. Res. Microbiol. 159,
216–220 (2008).
90. Kim, N. H., Choi, H. W. & Hwang, B. K. Xanthomonas
campestris pv. vesicatoria effector AvrBsT induces cell
death in pepper, but suppresses defense responses in
tomato. Mol. Plant Microbe Interact. 23, 1069–1082
(2010).
91. Kim, J. G. et al. Characterization of the Xanthomonas
axonopodis pv. glycines Hrp pathogenicity island.
J. Bacteriol. 185, 3155–3166 (2003).
92. Yang B. & White, F. F. Diverse members of the AvrBs3/
PthA family of type III effectors are major virulence
determinants in bacterial blight disease of rice. Mol.
Plant Microbe Interact. 17, 1192–1200 (2004).
93. Sugio, A., Yang, B., Zhu, T. & White, F. F. Two type III
effector genes of Xanthomonas oryzae pv. oryzae
control the induction of the host genes OsTFIIAγ1 and
OsTFX1 during bacterial blight of rice. Proc. Natl
Acad. Sci. USA 104, 10720–10725 (2007).
94. Yang, B., Sugio, A. & White, F. F. Avoidance of host
recognition by alterations in the repetitive and
C‑terminal regions of AvrXa7, a type III effector of
Xanthomonas oryzae pv. oryzae. Mol. Plant Microbe
Interact. 18, 142–149 (2005).
95. Chosed, R. et al. Structural analysis of Xanthomonas
XopD provides insights into substrate specificity of
ubiquitin-like protein proteases. J. Biol. Chem. 282,
6773–6782 (2007).
96. Hotson, A., Chosed, R., Shu, H. J., Orth, K. &
Mudgett, M. B. Xanthomonas type III effector XopD
targets SUMO-conjugated proteins in planta. Mol.
Microbiol. 50, 377–389 (2003).
97. Kim, J. G. et al. XopD SUMO protease affects host
transcription, promotes pathogen growth, and
delays symptom development in Xanthomonasinfected tomato leaves. Plant Cell 20, 1915–1929
(2008).
This is the first description of the effector protein
XopD, a cysteine protease with DNA-binding
activity.
98. Noel, L., Thieme, F., Nennstiel, D. & Bonas, U. Two
novel type III-secreted proteins of Xanthomonas
NATURE REVIEWS | MICROBIOLOGY
campestris pv. vesicatoria are encoded within the hrp
pathogenicity island. J. Bacteriol.184, 1340–1348
(2002).
99. Chen, L.‑Q. et al. Sugar transporters for intercellular
exchange and nutrition of pathogens. Nature 468,
527–532 (2010).
This is the first report demonstrating that TAL
effectors are also involved in sugar efflux
transporter modulation and not just suppression
of plant defence responses.
Acknowledgements
The work of the authors has been supported in part by grants
awarded by the Science Foundation of Ireland (SFI 07/IN.1/
B955 to J.M.D. and SFI 09/SIRG/B1654 to R.P.R.) and a
European Society of Clinical Microbiology and Infectious
Diseases (ESCMID) research grant (to R.R.P). The authors
thank Y. McCarthy for helpful comments on the manuscript.
Competing interests statement
The authors declare no competing financial interests.
FURTHER INFORMATION
J. Maxwell Dow’s homepage:
http://publish.ucc.ie/researchprofiles/D010/mdow
J. Craig Venter Institute: http://www.jcvi.org/
National Center for Biotechnology Information:
http://www.ncbi.nlm.nih.gov/
ALL LINKS ARE ACTIVE IN THE ONLINE PDF
VOLUME 9 | MAY 2011 | 355
© 2011 Macmillan Publishers Limited. All rights reserved