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Mechanisms and Evolution
of Virulence in Oomycetes
Rays H.Y. Jiang1 and Brett M. Tyler2
1
The Broad Institute of the Massachusetts Institute of Technology and Harvard,
Cambridge, Massachusetts 02142; email: [email protected]
2
Center for Genome Research and Biocomputing and Department of Botany and Plant
Pathology, Oregon State University, Corvallis, Oregon, 97331;
email: [email protected]
Annu. Rev. Phytopathol. 2012. 50:295–318
Keywords
The Annual Review of Phytopathology is online at
phyto.annualreviews.org
genome evolution, effectors, transposable elements, host-pathogen
interactions, host specificity
This article’s doi:
10.1146/annurev-phyto-081211-172912
c 2012 by Annual Reviews.
Copyright All rights reserved
0066-4286/12/0908-0295$20.00
Abstract
Many destructive diseases of plants and animals are caused by
oomycetes, a group of eukaryotic pathogens important to agricultural,
ornamental, and natural ecosystems. Understanding the mechanisms
underlying oomycete virulence and the genomic processes by which
those mechanisms rapidly evolve is essential to developing effective
long-term control measures for oomycete diseases. Several common
mechanisms underlying oomycete virulence, including protein toxins
and cell-entering effectors, have emerged from comparing oomycetes
with different genome characteristics, parasitic lifestyles, and host
ranges. Oomycete genomes display a strongly bipartite organization
in which conserved housekeeping genes are concentrated in syntenic
gene-rich blocks, whereas virulence genes are dispersed into highly dynamic, repeat-rich regions. There is also evidence that key virulence
genes have been acquired by horizontal transfer from other eukaryotic
and prokaryotic species.
295
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PLANT OOMYCETE PATHOGENS
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Plant oomycete pathogens cause a vast array
of destructive diseases of plants important
to agriculture, forestry, ornamental and
recreational plantings, and natural ecosystems
(both terrestrial and aquatic) (1, 27, 53). The
most destructive pathogens occur within the
class Peronosporomycetidae, in the orders
Peronosporales (Phytophthora species and
downy mildews), Pythiales (Pythium species),
and Albuginales (Albugo and other white rusts)
(Figure 1). Plant pathogenic species in this
class likely have a common evolutionary origin.
Some plant pathogens occur in the class Saprolegniomycetidae (32), which otherwise consists
mainly of animal pathogens and saprophytes,
Phytophthora
ramorum
and among basal oomycetes such as Eurychasma
(90) (Figure 1). Plant pathogenicity has likely
evolved independently in these lineages within
the oomycetes.
Oomycetes have evolved a wide diversity
of infectious lifestyles. Necrotrophs such as
Pythium typically attack plant tissues with compromised immunity, such as seedlings, fruit,
and stressed plants, and typically have very
broad host ranges (1). Hemibiotrophs, such as
most Phytophthora species, biotrophically initiate infection, with little damage to host tissues,
then switch to necrotrophic growth once colonization has been established (1). However, the
period of biotrophy may range from as short
as a few hours in the cases of Phytophthora sojae
Phytophthora
capsici
Phytophthora sojae
Plasmopara
Phytophthora infestans
Phytophthora phaseoli
Hyaloperonospora
arabidopsidis
Pythium ultimum
Albugo candida
Pythium insidiosum
Albugo laibachii
Leptomitus
Brevilegnia
Aphanomyces
Eurychasma
Achlya
Aquatic
environment
Plant pathogen
Animal pathogen
Algal pathogen
Saprolegnia
parasitica
Evolution of pathogenicity
Evolution of obligate biotrophy
Figure 1
Distribution of plant and animal pathogenicity across the oomycetes. Inferred independent instances of the
evolution of pathogenicity and obligate biotrophy are indicated. The pathogens with whole-genome
sequences are in red. Color gradients generally indicate pathogenic specialization to plants ( green) or animals
(orange).
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(112) and Phytophthora parasitica to several days
in the cases of Phytophthora infestans (30) and
its close relatives. Obligate biotrophy, in which
the pathogen is fully dependent on the host, has
arisen at least twice within the oomycetes, once
within the downy mildews and once within the
white rusts (101, 121).
Although oomycetes and fungi have evolved
plant pathogenicity independently within
distinct kingdoms of life (Stramenopila and
Mycota, respectively), these organisms display
many morphological and physiological traits in
common. Common traits, such as osmotrophic
nutrition, filamentous hyphae, and airborne
and waterborne spores, are also found among
saprotrophic species in each kingdom and
speculatively may have laid the foundation
for the evolution of pathogenicity in each
kingdom. Traits common to pathogens in each
kingdom, such as haustoria and other forms of
specialized infection hyphae, effector proteins
that enter host cells, and expanded families
of hydrolytic enzymes, are likely indicative of
traits essential for a phytopathogenic lifestyle.
Much of our current understanding of
the mechanisms and evolution of virulence
in oomycetes has built on expressed sequence
tag (EST) and genome sequencing completed
over the past 10 years (52). Genome sequences
include those of P. sojae (95 Mb) (116), sudden
oak death pathogen Phytophthora ramorum
(65 Mb) (116), the late blight pathogen P. infestans (240 Mb) (39) and four close relatives (79),
the necrotroph Pythium ultimum (42.8 Mb)
(55), and four biotrophs: Hyaloperonospora
arabidopsidis (100 Mb) (6), Albugo laibachii
(37 Mb) (50), Albugo candida (53 Mb) (57), and
Pseudoperonospora cubensis (105). The expressed
sequences of oomycete pathogens of mammals
and marine organisms have also become available, including the human pathogen Pythium
insidiosum (51), the fish pathogen Saprolegnia
parasitica (110), and the marine algae pathogen
Eurychasma dicksonii (37).
Here, we review current understanding of
the molecular and genetic mechanisms of virulence in oomycete plant pathogens and how
they have evolved, including the roles of
transposons, genome partitioning, and horizontal gene transfer (HGT) in accelerating the
emergence and diversification of these notoriously adaptable pathogens.
MECHANISMS OF VIRULENCE
The principal theme to emerge from the genomic studies is that virulence in oomycetes
depends extensively, possibly entirely, on large,
rapidly diversifying protein families (39, 115,
116). These families include extracellular toxins, hydrolytic enzymes and inhibitors, and effector proteins that can enter the cytoplasm
of plant cells (113). This contrasts with fungal pathogens in which secondary metabolite
toxins play a strong role, and families of virulence proteins are less extensively expanded and
diversified (115).
Plants protect themselves from infection by
oomycetes and other pathogens through diverse sets of constitutive and induced defenses
that include physical and chemical barriers,
antimicrobial enzymes and peptides, antimicrobial chemicals [phytoanticipins, phytoalexins,
and reactive oxygen species (ROS)], and in
the case of biotrophic and hemibiotrophic
pathogens, programmed cell death (PCD) (45).
Successful pathogens, including oomycetes,
must avoid, suppress, or tolerate these defenses, as well as gain nutrition from the host
(108). Inducible plant defenses consist of two
overlapping modules identified by the microbial molecules that induce them (45, 102).
Commonly occurring microbial molecules that
trigger defenses in a wide diversity of plants
are referred to as microbe- (or pathogen-)
associated molecular patterns (MAMPs or
PAMPs) and the responses triggered by them
as MAMP- (or PAMP-) triggered immunity
(MTI or PTI). Cell surface receptor-like kinases (RLKs) commonly mediate the detection
of MAMPs and the induction of PTI (45, 67).
Plants also produce intracellular receptors that
can directly or indirectly detect the presence
of intracellular pathogen effectors, resulting in
effector-triggered immunity (ETI) (45). ETI is
generally a more rapid and vigorous response
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Oomycete
PI
3
1
P
IE
P
PRR
Pr
IE
IE
2
IE
6
IE
IE
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IE
1
5
IE
Pr
PI
Pr
4
Pr
IE
NB-LRR
IE
7
IE
7
IE
IE
Cell
death
IE
PTI
Other
responses
10
IE
RONS
IE
IE
10
Nucleus
Plant cell
IE
Other
responses
9
9
IE
ETI
8
8
Pr
P
PAMP
IE
Intracellular
effector
PI
Protease inhibitor
PRR
NB-LRR
Protease
Pattern recognition
receptor
Nucleotide-binding leucine-richrepeat resistance protein
Figure 2
Suppression of plant immunity by oomycete effectors. Oomycete pathogens
secrete intracellular effectors (IEs) that enter the host cytoplasm. Plants may
secrete proteases (Pr) that can degrade intracellular or extracellular effectors
in the apoplast, but pathogens may secrete protease inhibitors (PIs) that
block those proteases, or else produce effectors that block secretion .
Recognition of pathogen-associated molecular patterns (PAMPs) by patternrecognition receptors (PRRs) produces signaling events that activate
PAMP-triggered immune responses (PTI). Recognition of intracellular
effectors by nucleotide-binding site leucine-rich repeat receptors (NBS-LRRs)
leads to effector-triggered immune responses (ETI). Signaling events for
both PTI and ETI may be inhibited by intracellular effectors . Both PTI and
ETI can produce programmed cell death , and effectors may inhibit the
triggering of cell death or the cell death machinery itself. PTI and ETI both
involve transcriptional changes , and nuclear-targeted effectors may directly
interfere with signaling within the nucleus or transcriptional events. PTI and
ETI involve numerous other responses , including the production of reactive
oxygen and nitrogen species (RONS), and effectors may also interfere with
those responses.
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than PTI and more often includes PCD. The
majority of plant intracellular receptors are
nucleotide-binding site leucine-rich repeat
(NBS-LRR) proteins (45). NBS-LRR proteins
that can detect effectors and trigger effective
resistance are called resistance (R) proteins,
and the effectors they detect have historically
been called avirulence (Avr) proteins (45).
Most plant-associated symbionts, including
pathogens, have evolved protein or chemical
effectors that suppress or reprogram PTI and
ETI (109) (Figure 2). These effectors may
act outside the plant cell, in the apoplast, or
at the plant plasma membrane, or they may
enter into the cytoplasm of the plant cell to
reprogram its physiology (109). Effectors may
be secreted directly into the apoplast from the
pathogen hyphae, or in the case of biotrophic
and hemibiotrophic oomycetes, may be secreted from specialized intracellular hyphae,
including haustoria (64). These specialized
hyphae penetrate the plant cell wall but remain
encased in the host plasma membrane (64).
The haustorial cell wall, extrahaustorial space,
and extrahaustorial membrane may become
significantly differentiated to facilitate delivery
of effectors and acquisition of nutrients (64).
Extracellular Toxins
Several large families of proteins that trigger
cell death in host plants have been found
in oomycete genomes, including the NLPs
(necrosis and ethylene inducing peptide-like
proteins) (76), the PcF family (69, 70), and the
Scr family (59). NLPs trigger cell death in a
wide range of dicotyledonous hosts, producing
a response with many similarities to PTI (33,
78). NLP families are dramatically expanded
in Phytophthora species (40 to 80 copies) (39,
116), although not in the genomes of Py.
ultimum (necrotrophic) (55) or H. arabidopsidis
(obligately biotrophic) (6, 15). Many of the
expansion events in Phytophthora species
have occurred subsequent to speciation (39,
116), supporting a key role for NLPs in the
interaction with the plant host. An increase
in gene expression coincident with the switch
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to necrotrophy has led to the hypothesis
that NLPs are responsible for this switch
in infection strategy (75). NLPs may have
roles other than triggering cell death, as
the small number of NLPs encoded in the
H. arabidopsidis genome do not trigger cell
death (6). Two white rust genomes (A. laibachii
and A. candida) lacked NLP genes altogether
(50, 57). NLP genes are also widely distributed
in fungal pathogens and in a few bacterial plant
pathogens, and it has been hypothesized that
horizontal transfer of NLP genes from fungi
to oomycetes was a key event in the emergence
of oomycetes as plant pathogens (84).
The related PcF (Phytophthora cactorum factor) and Scr (secreted cysteine-rich) toxin families are specific to oomycetes and show much
greater heterogeneity among species (39, 59,
69, 116). The numbers of PcF/Scr family genes
in Phytophthora and Pythium genomes are highly
heterogeneous (39, 55, 69, 116). The PcF subfamily is expanded in P. sojae (16 genes), and
the Scr family is expanded in P. infestans (11
genes), whereas P. ramorum and Py. ultimum
contain only one and three genes, respectively
(39, 55, 116). The absence of the genes from the
genomes of obligate biotrophs H. arabidopsidis
(6), A. laibachii (50), and A. candida (57) is consistent with the proteins triggering cell death
during infection.
Hydrolytic Enzymes
Plant tissues, especially the intercellular
apoplastic spaces, are rich in complex carbohydrates. Accordingly, oomycete genomes,
like those of other plant pathogens, are rich in
genes encoding a wide array of carbohydratedegrading enzymes, including pectin esterases,
pectate lyases, glucanases, and cellulases (39,
116). In addition, a rich abundance of lipases
and proteases is also secreted. Approximately
30 to 60 proteins in each class were predicted
to be secreted by each Phytophthora species
(39, 116). Interestingly, although classified
as a necrotroph, Py. ultimum contains fewer
glycoside hydrolase genes and a more limited
ability to degrade complex carbohydrates,
such as cellulose and xylans, than Phytophthora
species; it was speculated that the difference
reflects that Pythium species may quickly infect
immature tissue; degrade readily accessible
carbohydrates, such as pectins, starch, and
sucrose; and then focus on reproduction (55).
H. arabidopsidis, A. laibachii, and A. candida all
have greatly reduced numbers of genes encoding hydrolytic enzymes; because carbohydrate
fragments produced by these enzymes are
potent triggers of PTI, their depletion in these
obligate biotrophs suggests adaptation for
stealth (6, 50, 57). Similar genomic adaptation
for stealth has been observed in fungal obligate
biotrophs and mutualists (25, 61, 62, 96).
Enzyme Inhibitors
Because oomycetes secrete a large battery of
virulence proteins, a natural defense for plants
is the production of proteases to degrade the
virulence proteins. Accordingly, oomycetes are
predicted to secrete proteinase inhibitors targeted against the plant proteins. The sequenced
Phytophthora and Pythium genomes contain 18
to 38 genes encoding secreted inhibitors of serine and cysteine proteases (39, 55, 116). In
P. infestans, two serine protease inhibitors, EPI1
and EPI10, can bind to and inhibit a tomato
protease P69B that was responsible for 27%
of the pathogen-induced protease activity in
the apoplast (103, 104). Furthermore, two P.
infestans cysteine protease inhibitors, EPIC1
and EPIC2b, can bind to and inhibit the cysteine proteases C14, Pip1, and Rcr3 (95, 106).
Mutations in the tomato Rcr3 gene or silencing of C14 resulted in increased susceptibility
to P. infestans (95). Cysteine protease inhibitors
also play a demonstrated role in infection by
biotrophic fungi such as Cladosporium fulvum
(95).
Cell-Entering RxLR Effectors
One of the best-studied classes of virulence
proteins to emerge from the genome sequencing of oomycete pathogens is RxLR effectors,
named for a conserved N-terminal amino acid
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sequence motif (arginine, any amino acid,
leucine, arginine) (47, 114). The sequenced
Phytophthora genomes contain approximately
350 to 550 genes that encode these rapidly
evolving small secreted proteins (39, 44, 116).
Many, but not all, of the proteins carry a more
variable second motif, dEER [aspartate (less
well conserved), glutamate, glutamate, arginine] at varying distances C-terminal to the
RxLR motif (44). Approximately half of the
encoded RxLR effectors carry additional conserved motifs in the C terminus, called W, Y,
and L motifs, often in repeating blocks of consecutive W, Y, and L motifs (44).
RxLR effectors include the products of
nearly all 18 oomycete avirulence genes that
have been cloned to date. Those genes include PsAvr1a (77), PsAvr1b (92), PsAvr1k (23,
46), PsAvr3a/5 (21, 77), PsAvr3b (20), PsAvr3c
(19), and PsAvr4/6 (22) from P. sojae; PiAvr1
(119), PiAvr2 (34), PiAvr3a (3), PiAvr3b (56),
PiAvrBlb1 (73, 120), PiAvrBlb2 (68), and
PiAvrVnt1 (119) from P. infestans; and HaATR1
(82), HaATR13 (2), and HaATR39 (35) from
H. arabidopsidis. HaATR5 from H. arabidopsidis
(4) resembles other RxLR effectors but lacks
a canonical RxLR motif. Where known, the R
genes matching RxLR avirulence effectors encode intracellular NBS-LRR proteins (5, 12,
29, 31, 35, 40, 56, 60, 71, 72, 86, 94, 117, 118).
Hence, these effectors must have a mechanism
to enter into host cells. The RxLR and dEER
motifs are required for entry of RxLR effectors
into host plant cells, and the N-terminal domain carrying the motifs, plus approximately
10 amino acid residues on each side of the motifs, appear to be sufficient for cell entry (24,
38, 46, 47, 125). The mechanism of entry mediated by the RxLR-dEER domain is still an
area of active research. Current data suggest
that RxLR effectors (and some fungal RxLRlike effectors) secreted into the apoplast can enter host plant cells in the absence of pathogenencoded machinery, such as the bacterial type
III secretion system or the Plasmodium Pexel
translocon (46, 47, 74, 80). Further data suggest that RxLR effectors bind to cell-surface
phosphatidylinositol-3-phosphate (PI3P) be-
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fore entering host cells by receptor-mediated
endocytosis (46, 74, 97), although the literature is not yet fully consistent on this point (26,
128). In a fascinating parallel, PI3P binding by
RxLR-like Pexel motifs is involved in the delivery of effectors in erythrocytes by the malaria
parasite Plasmodium (7, 8). Fungal effectors also
appear to enter via a pathogen-independent
mechanism that may involve RxLR-like motifs
and binding to PI3P (46, 74, 80). On the other
hand, an RxLR-like effector from the oomycete
fish pathogen Saprolegnia parasitica appears to
enter via a pathogen-independent mechanism
but utilizes binding to tyrosine sulfate rather
than PI3P (124). Further careful work is needed
to clarify the situation.
Recent structural studies of six oomycete
RxLR effectors [PcAvr3a4 (13), PcAvr3a11
(128), PiRD2 (13), PsAvh5 (97), HaATR1 (18),
and HaATR13 (54)] have provided additional
insights into the structure and evolution of
these proteins. Crystal structures were generated for PcAvr3a4, PiRD2, and HaATR1,
whereas nuclear magnetic resonance (NMR)
data were collected for PcAvr3a11, PsAvh5, and
HaATR13. PcAvr3a4, PcAvr3a11, and PsAvh5
are members of a closely related subfamily of
RxLR effectors (the 1b3a subfamily; 97) that
also includes PsAvr1b and PiAvr3a, whereas
PiRD2, HaATR1, and HaATR13 are distinct. Nevertheless, the C-terminal domains
of PcAvr3a4, PcAvr3a11, PsAvh5, PiRD2, and
HaATR1 exhibited a common novel fold comprising three helices that span the conserved
C-terminal W and Y motifs, called the WY
fold (97, 126). In this fold, the highly conserved
tryptophan and tyrosine residues that give the
W and Y motifs their name contact each other
to form the hydrophobic core of the fold (97,
126). In PcAvr3a4, PcAvr3a11, and PsAvh5,
a fourth helix corresponding to a positively
charged K motif is present, forming a fourhelix bundle (13, 97, 128). In PiRD2, a dimer is
formed between two three-helix WY domains
(13). HaATR1 contains two WY domains arranged in a helical spiral (18). HaATR13 has a
distinct structure consisting of three helices and
a C-terminal disordered loop (54). Win et al.
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(126) speculated that the WY fold formed a flexible scaffold that supported rapid changes in the
primary sequence and structural architecture of
RxLR effectors driven by the host-pathogen coevolutionary conflict.
In all six structural studies, the RxLR domains were found or inferred to be disordered,
raising questions about how they could bind
PI3P and how they promote cell entry. Yaeno
et al. (128) showed that a positively charged
C-terminal patch corresponding to the K motif contributed strongly to PI3P binding by
PcAvr3a11, PsAvr1b, and PiAvr3a but could
not detect binding of the RxLR domains to
PI3P using lipid blots. Sun et al. (97) used NMR
and surface plasmon resonance to demonstrate
that residues in both the C-terminal domain
and in the RXLR motif of PsAvh5 contacted
PI3P and were required both for efficient PI3P
binding and for efficient host-cell entry. Further detailed structural and functional studies
of the interaction of RxLR effectors with PI3P
and other elements of the plasma membrane,
including effectors that lack positively charged
C-terminal motifs, are required to understand
in more detail how RxLR effectors utilize PI3P,
RxLR, and dEER motifs to achieve cell entry.
The functions of RxLR effectors in manipulating host physiology are beginning to
emerge. The common theme in each case is the
suppression of PAMP- and effector-triggered
immune responses, especially suppression of
cell death associated with these responses
(108, 109). PiAvr3a could suppress cell death
triggered by the PAMP INF1 (11). This
process appears to involve binding of PiAvr3a
to a positive regulator of defense-related cell
death, CMPG1 (10). PsAvr1b appears to have
the ability to suppress cell death generally,
even in yeast and even when triggered by the
mouse proapoptotic protein BAX, suggesting
that it may target conserved elements of the
eukaryotic cell death pathway (23). PiSNE1
is another effector with a powerful ability
to suppress plant cell death, even cell death
triggered by NLP toxins (49). HaATR1 and
HaATR13 could suppress PAMP-triggered
responses in Arabidopsis, including deposition
of callose and accumulation of ROS (93).
PsAvr3b, which is a nudix hydrolase that can
destroy NADP and ADP-ribose, also is a powerful suppressor of ROS accumulation (20).
PiAvrBlb2 appears to suppress plant defenses
via a different mechanism; it accumulates on
the inner face of the host plasma membrane and
the plasma membrane–derived extrahaustorial
membrane, where it inhibits secretion of host
defense proteins, such as the cysteine protease
C14 (14). PiAvrBlb1 (also called ipiO1) may
interfere with defense by disrupting RGDmotif-mediated adhesions between the plant
cell wall and the plasma membrane (36, 91).
High-throughput screens of the functions
of the RxLR effectors encoded in oomycete
genomes are beginning to fill in the broader
picture of how these innumerable effectors
contribute jointly to infection. Oh et al. (68)
conducted a survey of 16 effectors encoded
in the P. infestans genome, finding that two
suppressed cell death triggered by the PAMP
INF1, two triggered R gene–mediated cell
death, and one triggered R gene–independent
cell death. Wang et al. (122) conducted a much
larger survey of 169 predicted P. sojae effectors,
finding that 63% (107/169) suppressed cell
death, and 11 triggered R gene–independent
cell death. Of 49 that were screened in more detail, 40 suppressed effector-triggered cell death,
and 20 suppressed PAMP (INF1)-triggered cell
death. Thus, P. sojae effectors appear to be heavily targeted to suppression of cell death. Several
surveys of the functions of H. arabidopsidis effectors have been conducted, including a yeast
two-hybrid screen for protein-protein interactions (66), a screen of the intracellular locations
of the effectors (17), and a screen of the ability
to suppress immunity against bacteria (28). The
yeast two-hybrid screen, involving 131 proteins
corresponding to alleles of 99 genes, revealed
many effectors interacting with large numbers
of host proteins (66). For example, HaATR1
interacted with 19 targets, and HaATR13
interacted with 24 targets. The majority of the
targets were proteins that interacted with receptors involved in PTI or ETI, suggesting that
H. arabidopsidis effectors are heavily targeted to
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suppression of the plant immune system (66).
This conclusion is supported by the observation
that of 64 H. arabidopsidis RxLR effectors tested,
approximately 70% promote the growth of
bacteria in Arabidopsis (28). The majority (66%)
of 49 H. arabidopsidis effectors were targeted
partially or entirely to the host nucleus, suggesting that interference with nuclear signaling
and/or transcription is a common mechanism
for suppressing host immunity (17). A minority
of H. arabidopsidis effectors were targeted to
the plasma membrane or tonoplast (17).
An unexpected finding from transcriptomic
analysis of RxLR effectors is that a relatively
small percentage (approximately 10% to 15%)
of the effector genes are moderately to highly
transcribed during infection (16, 39, 122). Furthermore, resequencing surveys revealed that
only approximately 10% to 15% of predicted
P. sojae RxLR effectors show evidence of significant positive selection (122). These results
suggest that these pathogens rely heavily on a
small number of elite effectors. Gene-silencing
experiments have begun to confirm that a
number of these elite effectors are individually
essential for full virulence. These include
PiAvr3a (10), PsAvh172 (122), PsAvh238
(122), and PsAvr3b (20). The transcriptome
analysis of P. sojae effectors also identified two
overall patterns of expression: immediate-early
effectors were strongly expressed prior to infection and moderately induced upon infection
(two- to tenfold), whereas early effectors were
very weakly expressed prior to infection, but
strongly induced (10- to 120-fold) during the
first 12 h of infection (122). The ability to suppress ETI was concentrated among immediateearly effectors, whereas the ability to suppress
PTI was concentrated among early effectors,
suggesting that P. sojae utilizes a preemptive
strategy to suppress ETI prior to the expression
of effectors for the suppression of PTI (122).
Given the ability of RxLR effectors to travel
through the apoplast and enter host cells in the
absence of the pathogen (46, 92), this observation suggests that immediate-early effectors
may travel ahead of the pathogen to preemptively suppress ETI, whereas early effectors
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might be delivered from haustoria, where they
would suppress both PTI and ETI (Figure 3).
Cell-Entering Crinkler Effectors
Oomycete pathogens produce a second major
class of small secreted effector proteins called
crinklers, named for their ability to produce
crinkling and necrosis when overexpressed in
transient expression assays (107). Like RxLR
effectors, crinklers are rapidly evolving, highly
diverse, and modular (39). They consist of
a well-conserved N-terminal domain required
for host-cell entry (the crinkler domain) (89)
connected to a very diverse collection of Cterminal domains (39). Crinkler effectors are
among the most highly expressed pathogen
genes both prior to and during infection (39,
81, 111). The highly diverse C-terminal domains of these effectors suggest that they may
have a wide diversity of functions, possibly created by opportunistic fusions of an N-terminal
domain consisting of secretion and host-cell
entry signals to a C-terminal domain derived
from an intracellular protein. Several crinklers
examined to date appear targeted to the host
nucleus (58, 89), and one crinkler has the ability to suppress cell death (58). Several crinklers
are essential for virulence (58). An intriguing
aspect of crinkler evolution is that these proteins are much more widely distributed among
oomycete pathogens than RxLR effectors (32).
They have been found in the orders Saprolegniales (32), Pythiales (55), and Albuginales (50,
57) as well as Peronosporales (127), whereas
RxLR effectors have been found only in the
latter two orders. Thus, they may be very ancient to pathogenic oomycetes (89) and/or have
been disseminated by HGT. Even more intriguingly, there are hints that crinkler-like effectors may be present in the chytrid fungus
Batrachochytrium dendrobatidis, possibly as a result of HGT (98).
Other Classes of
Cell-Entering Effectors
Given the opportunistic nature of pathogen
evolution and adaptation, it is plausible that
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essio
ETI suppr
11
P
10
9
n
ssio
pre
up
TI s
n
Apoplast
0
3
6
IE
Hours post infection
P
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Oomycete
IE
IE
E
IE
P
PAMP
IE
Immediate-early
effector
E
Early effector
ETI
IE
ETI
Plant cell
Haustorium
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Transcript (log2)
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P
IE
E
P
PTI
E
Figure 3
Programmed expression of RxLR effectors in Phytophthora sojae. (Upper left) Aggregate transcript levels of
RxLR effector genes (log2 microarray signal) during the first 6 h post-infection (adapted from 122). Genes
expressed prior to contact with the pathogen (immediate-early genes) encode effectors that mostly suppress
effector-triggered immunity (ETI), whereas genes that are predominantly expressed following infection
(early genes) encode effectors that suppress both PAMP-triggered immunity (PTI) and ETI. (Lower right)
Speculative model in which immediate-early effectors diffuse through the apoplast ahead of the pathogen,
directly entering host cells to preemptively suppress ETI, whereas early effectors enter from pathogen
haustoria. Lightning symbols indicate signaling events.
new mechanisms of host-cell entry have arisen
through chance binding of a secreted pathogen
protein to a host-cell surface molecule.
Computational and experimental analyses of
candidate effector proteins in Albugo laibachii
have uncovered a novel motif, CHXC (cysteine, histidine, anything, cysteine) associated
with host-cell entry (50). Novel motifs reminiscent of, but distinct from, RxLR motifs were
found among candidate Pythium effectors also
present in Phytophthora species, although the
functionality of these has not been determined
yet (55).
GENOME CHARACTERISTICS
The whole-genome sequences of major
pathogens have revealed common features of
oomycete genomes as well as unique aspects of
pathogen evolution. Several patterns related
to pathogenesis, such as genome reduction
associated with biotrophy and repeat-driven
virulence change, have emerged from genome
analysis and comparisons.
Core Proteome and
Lineage-Specific Genes
The currently sequenced oomycete species display divergent lifestyles. A large fraction of
their genes are unique to each pathogen lineage
(6, 39, 55, 116). Nonetheless, a common proteome can be identified by ortholog analysis
across phylogenetically divergent species (116).
The Phytophthora species P. infestans, P. sojae,
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and P. ramorum share a core set of 8,492 ortholog clusters (39). The species of Albugo and
Phytophthora belong to different phylogenetic
groups in oomycetes, and they share from 4,826
(A. laibachii versus H. arabidopsidis) to 5,722
(A. laibachii versus P. infestans) orthologous
genes (50). Taken together, a set of conserved 5,000 to 6,000 orthologs represents the
core cellular processes of oomycetes, including DNA replication, transcription, and protein
translation.
In the core proteome, genes involved in
cellular processes related to pathogenesis are
underrepresented. In contrast, gene families
expanded in specific lineages are enriched in
functions associated with pathogenesis. These
lineage-specific genes are probably responsible
for different pathogenic traits among oomycete
species, such as adaption to different environments and modulation of host physiology.
Families showing lineage-specific expansions
are very fluid, and distinct subfamilies are
expanded (or lost) in individual lineages.
For example, the members of the RxLR and
crinkler effector families appear largely specific
to particular Phytophthora or Hyaloperonospora
species (6, 39, 116). In Albugo, the novel class
of CHXC effectors exhibits lineage-specific
expansion in the two sequenced Albugo species
(50, 57). Similarly, for the biotrophic oomycete
Pseudoperonospora cubensis that causes downy
mildew of cucurbits, a family of PcQNE
effectors has been identified from a partially
sequenced genome (105). Massive duplication
of this family in a lineage-specific fashion
suggests its important role in pathogenesis.
Py. ultimum possesses several distinct families
of lineage-specific genes associated with root
parasitism and opportunistic pathogenesis (55).
The signature of lineage-specific expansion
is also characteristic of pathogenesis-related
genes in species other than oomycete plant
pathogens. Different species of the malaria
parasite Plasmodium have distinct massively
expanded families that play important roles,
such as host modification and antigenic variation, in pathogenesis (99, 100, 123). The
fish oomycete pathogen Saprolegnia parasit-
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ica has many lineage-specific expanded protease and lectin families that are likely associated with animal parasitism (110; R.H.Y. Jiang,
unpublished data).
From Compact Genome to Massive
Repeat Expansion
Some oomycetes have a compact genome
(<50 Mb) (55, 57), whereas others, such as P. infestans and its nearest relatives, have the largest
and most complex genomes (>200 Mb) sequenced so far in the kingdom of Stramenopiles
(39, 79). All sequenced oomycete genomes encode similar numbers of genes, ranging from
14,000 to 19,000; it is the large difference in
the repeat content that accounts for the genome
size differences. More than 75% of A. laibachii
is nonrepeated, whereas approximately 75% of
P. infestans is made up of repeats (Figure 4a)
(39, 50). Many of the repetitive regions of these
large genomes are highly dynamic and prone
to evolutionary changes, apparently due to fast
bursts of mobile element activities. Below, we
discuss the expansion of genomes by repeated
elements and the resulting genome dynamics.
Genome Reduction in
Obligate Pathogens
Obligate parasitism has evolved at least three
times independently in oomycetes: in basal
marine algae parasites, such as Eurychasma; in
the land plant white rust pathogens, such as
Albugo; and in the land plant downy mildew
pathogens, such as Peronospora, Bremia, Pseudoperonospora, and Hyaloperonospora (101).
Genome sequences have become available
from the two branches of land plant obligate
plant pathogens, Albugo (50, 57) and Hyaloperonospora (6); these sequences provided insights
into the evolutionary processes leading to
highly specialized parasitism (Figure 4b). One
common trend is that the intimate association
with host cells has resulted in relaxed selection
and loss of several biosynthetic pathways (63).
The same trend has been observed in obligate
fungal plant pathogens (63) and in intracellular
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a
b
200
100
Expansion of
effectors
Phytophthora
infestans
240 Mb
300
Albugo
laibachii
37 Mb
Loss of
Reduction of
Degeneration cellular
hydrolytic
apparatus
enzymes and of biosynthetic
capabilities
toxins
Phytophthora
Pythium
Albugo
Aphanomyces
Saprolegnia
c
Eurychasma
Specialization
of haustoria
Evolutionary
processes of
obligate pathogens
0
Plasmodium
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Genome sizes (Mb)
DNA transposon
LTR retrotransposon
Other repeat
Nonrepetitive
Hyaloperonospora
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Obligate parasitism
Genome reduction
Expansion of effectors
Repeat expansion
Host cell targeting
Loss of plastid
Secondary
endosymbiosis
Evolutionary trends
shaping the
oomycete genome
Figure 4
Genome evolution of oomycetes. (a) Genome composition of small and large oomycete genomes. DNA
transposons include PiggyBac, Helitron, Crypton, Mutator, hAT, and Mariner. Long terminal repeat (LTR)
retrotransposons include LTR-Gypsy and LTR-Copia. (b) Evolutionary processes of obligate pathogens.
The degeneration processes are indicated with down-pointing arrows. The expansion processes are indicated
with up-pointing arrows. (c) Major evolutionary events shaping oomycete genomes. Whole-genome
sequences are available for Plasmodium, Albugo, Pythium, Phytophthora, and Hyaloperonospora. Color gradients
indicate progressive pathogenic specialization.
parasites of animals and humans, such as various Apicomplexa species, including the malaria
parasite Plasmodium (123). For example, close
association with the host provides obligate
pathogens with a ready source of organic
nitrogen. Degeneration of inorganic nitrogen
(nitrate) assimilation pathways has been found
in biotrophic fungi [powdery mildew (96)
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and rust fungi (25)], in the malaria parasite
Plasmodium (50, 100), and in the oomycete plant
parasites Albugo and Hyaloperonospora (6, 50).
Another evolutionarily convergent feature
of biotrophs is the reduction in the number
and diversity of hydrolytic enzymes able to
attack host components, particularly cell wall–
hydrolyzing enzymes, presumably reflecting an
infection strategy of minimizing host damage
to avoid eliciting host immune responses (6).
Similar reduction has been observed in
biotrophic plant pathogenic fungi (25, 48, 63,
88, 96) and mutualistic fungi (61, 62). The
ability to produce zoospores for waterborne
dissemination has been lost in many lineages of
downy mildew pathogen, in favor of airborne
conidial dispersal. In H. arabidopsidis, many
genes associated with zoospore formation
and motility have been lost as compared with
soilborne Phytophthora and Pythium species (6).
For example, none of 90 flagella-associated
genes in Phytophthora could be detected in
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H. arabidopsidis, representing a further dramatic
example of genome minimization.
EVOLUTIONARY ORIGINS
OF OOMYCETE GENOMES
Pathogenicity has evolved multiple times independently in all major domains of eukaryotes. Oomycetes evolved within the eukaryotic kingdom of Stramenopila, which includes
some of the most important photosynthetic
marine algae, such as diatoms and brown algae. Three major evolutionary trends shaping
oomycete genomes are the loss of photosynthetic plastids (116), novel protein domain combinations, and HGT from bacteria and fungi
(Figure 5).
Pathogenesis-Related Horizontal
Gene Transfer
HGT enables the transfer of genetic material
between otherwise reproductively isolated
Genes for
phytopathogenesis
from fungi
Major flows of
horizontal gene transfer
to oomycetes
Fungi
Opisthokonta
Animals
Plants
Green algae
Archaeplastida
Red algae
Saprolegnia
Phytophthora
Secondary
endosymbiosis
from red algae
Genes acquired
from bacteria
Apicomplexa
Ciliates
Chromalveolata
Figure 5
Gene acquisitions from horizontal gene transfer in oomycetes. The three major flows of genes are annotated
in ovals. Only three eukaryotic domains are drawn schematically on the tree. The direction of gene transfer
is indicated by arrows. Multiple acquisitions have occurred from different fungal species and bacterial species
(84, 85, 116).
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lineages. The evolution of pathogenicity of
oomycetes appears to have been greatly facilitated by extensive cross-kingdom HGT events
between fungi and oomycetes and between
bacteria and oomycetes (65, 84, 85). A wholegenome analysis revealed an estimated 7.6% of
the secretome of P. ramorum has been acquired
from fungi by HGT (84). A gene-by-gene
phylogenetic analysis suggested a pattern of 33
transfers from fungi to oomycetes. Comparative genomics showed that the HGT events
probably are associated with the radiation of
plant pathogenic oomycetes because these
genes were not detected in the animal parasitic
oomycete Saprolegnia or the free-living sister
taxon of Hyphochytrium (84). One of the most
striking examples of likely acquisition of key
pathogenicity genes from fungi involves the
NLP toxins. As detailed above, these toxins can
be found in bacteria, fungi, and oomycetes and
can trigger immune responses in diverse dicotyledonous plants. The wide distribution of
these genes in fungi but narrower distribution
within plant pathogenic oomycetes in the class
Peronosporomycetidae (Phytophthora, Pythium,
and downy mildews) suggests a major role for
these genes in the emergence of oomycetes
as plant pathogens (84). Another possible
example of HGT from bacteria to oomycetes
is the transglutaminases from Phytophthora and
downy mildews that act as PAMPs, activating
defense responses in plants; homologs of this
protein are found in a marine Vibrio bacterium
(83).
In Eurychasma dicksonii, a widespread
pathogen of marine brown algae, an EST survey (37) revealed unique pathogenicity factors in Eurychasma, such as alginate lyases, that
can break down alginates, a key component
of the brown algal cell wall and an abundant
biopolymer in coastal waters (37). Interestingly,
the Eurychasma alginate lyase genes have similarity with those of marine invertebrates and
fungi, hinting at possible HGT (37). Phylogenetic analysis revealed that the oomycete
enzyme shows homology with enzymes from
Pseudomonas syringae, Chlorella virus, and algal
gastropods (37). Furthermore, alginate lyases
are not present in any of the other sequenced
oomycetes.
GENOMICS OF HOST
SPECIFICITY
Genomic Signatures of Host Range
Oomycete pathogens display an enormous
spectrum of host ranges, from extremely broad
host-range Pythium species that have hundreds
or thousands of hosts to downy mildews that
are often specialized to a single host. The
molecular basis of host range is not yet evident from genome sequencing studies, as not
enough examples of each pathogen have been
examined. Win et al. (127) observed that recently duplicated families of RxLR effectors
were less diversified in the broad host-range
pathogen P. ramorum than in the narrow hostrange pathogen P. sojae. This suggests that diversifying selection may be weaker in broad
host-range pathogens, possibly because loss of
a host species due to the emergence of a new
R gene may exert weaker selective pressure on
the pathogen population to adapt. Emergence
of a new R gene in the host of a narrow hostrange pathogen would, however, exert extreme
pressure on the pathogen population to adapt
through diversification of its effector repertoire.
Host Jumps and Specialization
Major mechanisms responsible for the emergence of new pathogens include host-range
expansion and host jumps. Genome analysis of
four closely related Phytophthora species that
appear to have undergone recent host jumps
has shed light on one example of genome
adaptation. The four species infect hosts from
different plant families as follows: P. infestans
causes late blight disease on Solanum species,
including potato and tomato (Solanaceae);
P. ipomoeae infects morning glory, Ipomoea
longipedunculata (Convolvulaceae); P. mirabilis
infects four o’clock, Mirabilis jalapa (Nyctaginaceae); and P. phaseoli is pathogenic on lima
beans, Phaseolus lunatus (Leguminosae). These
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four Phytophthora species belong to a very
closely related clade of pathogen species (clade
1c; 9) that display 99.9% sequence identity
among their ribosomal DNA internal transcribed spacer regions. Genomic regions rich
in repeats show higher rates of structural polymorphisms among these species (79). Furthermore, these dynamic regions frequently harbor
genes with signatures of positive selection,
which is a hallmark of pathogen host adaptation. Consistent with these dynamic genes
being involved in infection, these repeat-rich
regions are enriched in genes induced in planta.
Genes involved in epigenetic processes, such
as histone methyltransferases, are also enriched
in these dynamic regions (79). Histone modification is considered to be a key epigenetic regulatory mechanism in most eukaryotes, such as
P. infestans. Thus, epigenetic regulation could
mediate rapid expression changes needed for
the host adaptation. Taken together, these observations support the idea that genome compartments with accelerated gene evolution are
playing important roles in host jumps in this
pathogen lineage.
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GENOME PARTITIONING AND
MECHANISMS OF PLASTICITY
Successful pathogens often possess plastic and
dynamic genomes. The genomes of oomycetes
are partitioned into conserved syntenic regions
and highly repetitive species-specific regions
(6, 39, 55, 116). The conserved regions mostly
harbor housekeeping genes, and the highly
variable regions contain genes underlying
pathogenicity and host range. The fungal
pathogen Leptosphaeria maculans displays
similar genome partitioning (87).
The genome architecture of oomycetes is
remarkably uneven. In the larger Phytophthora
genomes, especially P. infestans and its sister
species, the genome architecture is separated
into large gene-dense partitions and even
larger repeat-rich partitions (39, 79, 116). The
structural partitioning of oomycete genomes
has led to several functional consequences
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for these pathogens, such as different rates of
gene evolution, uneven paces of gene family
expansion, differential gene expression, and
pathogen speciation (Figure 6c). As discussed
in the previous section, adaptation to new host
plants most likely involves mutation and copy
number changes in hundreds of effector genes,
which mostly populate repeat-rich partitions
(79). Thus, the highly dynamic partitions foster
emergence of new pathogens.
Syntenic Ortholog-Rich Partitions
In oomycetes, there is a high degree of
synteny (conserved gene order) among the
core ortholog genes of Phytophthora species
that also extends to downy mildews such as
H. arabidopsidis (6, 39, 116). The conservation is
eroded to a certain degree in comparison with
the Py. ultimum genome (55) and even more so
in comparisons with the more divergent Albugo
species (50, 57). Conserved runs of more than
100 genes spanning genomic regions of several
megabases can be observed among Phytophthora
species. Many of these runs are also conserved
in H. arabidopsidis (6). Conserved synteny over
broad regions of the Py. ultimum and Phytophthora genomes can be identified by the ortholog
content; however, the local gene order has been
greatly rearranged (55). As a result, only short
runs of up to 10 orthologs were found to be
collinear between Py. ultimum and Phytophthora
species. As the evolutionary distance further
increases between species, such as between
Phytophthora and Albugo, only small conserved
genomic regions can be identified (50, 57).
Dynamic Repeat-Rich Partitions
Separating the blocks of conserved synteny
among oomycete genomes are highly dynamic
lineage-specific regions that are enriched in
transposable elements (6, 39, 55, 116). These
dynamic regions are the sites for two major evolutionary processes; one is rapid changes in the
repertoires of pathogenesis-related genes, and
the other is the loss of biochemical functions or
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Phytophthora
sojae
Phytophthora
sojae
Phytophthora
sojae
Phytophthora infestans
Phytophthora
ramorum
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b
Phytophthora infestans
crinkler gene cluster
Gene cluster of nitrate reductase
and nitrate transporter
Phytophthora infestans Sc1.25
Phytophthora sojae Sc_87
Hyaloperonospora Sc_20
Gene loss
c
Genome territory partitioning in Phytophthora infestans
Repeat rich / gene sparse
Lack of synteny
Effectors and epigeneticsrelated genes
Induction at early
infection
Elevated SNPs and
CNVs associated
with host jump
Repeat sparse
Gene rich
Conserved synteny
Oomycete ortholog
Suppressed
at early
infection
Conserved between
species
Figure 6
Genome organization of oomycetes. (a) Conserved synteny and expansion of the crinkler gene family in
Phytophthora species. The tandemly repeated crinkler genes are represented by red triangles. The crinkler
gene cluster disrupts the collinearity between Phytophthora infestans scaffold 1.6 and other Phytophthora
species. Panel a is adapted from Reference 39. (b) Nitrate and nitrite reductase genes are conserved between
Phytophthora genomes but have been deleted from the Hyaloperonospora arabidopsidis genome. Panel b is
adapted from Reference 6. (c) Genome territory partitioning of P. infestans. The distinct genome
environments show different properties in synteny, gene content, expression, and evolutionary rates.
Abbreviations: SNP, single nucleotide polymorphism; CNV, copy number variation.
cellular apparatus due to pathogen specialization. Not surprisingly, therefore, effector genes
tend to localize to repeat-rich regions, where
they display rapid expansion and diversification.
Host-imposed immune pressure drives the
rapid evolution of pathogen effector genes
(2, 82, 92, 127). These effector genes are frequently rearranged, duplicated, or expanded,
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and they are enriched in dynamic genomic regions (41–43, 77). For example, most of the
hundreds of RxLR effector genes are located in
regions without conserved synteny (44). Even
for the remaining 10% of RxLR genes residing
in syntenic genomic regions, frequent gene rearrangements have occurred (44). The crinkler
and NLP gene families have also undergone lineage specific expansions in Phytophthora species
(39, 116). For example, P. infestans has almost
200 CRN genes. Dozens of CRN genes are often
clustered and are located in the nonsyntenic regions (Figure 6a). In P. infestans, helitron transposons may have facilitated rapid tandem gene
duplications of the CRN families (39).
Genome degeneration associated with obligate biotrophy has also led to rearrangements
and deletions. For example, in the obligate
biotroph H. arabidopsidis, which has lost the
ability to produce motile zoospores, the gene
encoding the flagellar inner arm dynein 1 heavy
chain α is missing. The genomic context of this
gene is conserved even between oomycetes as
distant as Py. ultimum and A. laibachii. In contrast, the syntenic region in the H. arabidopsidis
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genome has become populated by diverse mobile elements (50).
CONCLUSIONS
As a group of successful pathogens that have
parasitized diverse host taxa, oomycetes have
evolved many virulence traits to adapt to novel
hosts, colonize new tissue types, and cope
with host immune responses. In this review,
we have summarized recent discoveries from
oomycete comparative genomics regarding virulence mechanisms employed by oomycetes
and the genomic mechanisms that underlie
the adaptability of oomycete virulence. Understanding these mechanisms of virulence
and adaptability is instrumental for designing
management strategies for oomycete diseases.
The high level of genome plasticity and everexpanding reservoirs of effectors will require us
to locate the most essential targets for genetic
resistance or chemical controls. The unique
metabolic features of oomycetes and common
effector translocation pathways may offer key
treatment targets.
SUMMARY POINTS
1. Pathogenicity has independently evolved multiple times within oomycetes. Most terrestrial plant pathogens within the Peronosporomycetidae likely share a single acquisition
of pathogenicity.
2. The pathogenesis mechanisms in oomycetes depend extensively on large protein families.
These rapidly diversifying families include extracellular toxins, hydrolytic enzymes and
inhibitors, and effector proteins that can enter the cytoplasm of plant cells.
3. Oomycete cell-entering effectors target numerous host cellular processes, commonly
resulting in suppression of PAMP-triggered immunity, effector-triggered immunity, and
programmed cell death.
4. Genome evolution of oomycetes has been characterized by genome reduction in obligate
pathogens and repeat-driven genome expansion in some species with large genomes.
5. Oomycete genomes have a mosaic origin, with genes acquired from secondary endosymbionts, from fungi, and from bacteria.
6. Genome partitioning of oomycetes into conserved ortholog-rich regions and dynamic
repeat-rich regions has facilitated effector protein family expansion, diversification, and
adaptation to new hosts.
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FUTURE ISSUES
1. The potentially powerful role of epigenetics in generating diversity and adaptation at the
transcriptional level is poorly studied.
2. The same family of toxins or effectors may well adopt different roles in pathogenesis
in different pathogen species or against different plant host species. More resolution in
their function is needed.
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3. The mechanism(s) by which RxLR, crinkler, and other cell-entering effectors reach
the cytoplasm is still poorly understood. The role of PI3P in particular remains highly
controversial. Effector entry mechanisms are a promising target for novel disease control
strategies.
4. The role of HGT events in oomycete evolution and adaptation might be underestimated; with more genome resources and computational tools, the source and functions
of acquired genetic elements could be further studied.
5. By combining evolutionary and molecular analyses of pathogenicity mechanisms, it may
be possible to identify new targets for disease control that resist pathogen adaptation.
DISCLOSURE STATEMENT
R. Jiang is not aware of any affiliations, memberships, funding, or financial holdings that might
be perceived as affecting the objectivity of this review. B. Tyler discloses a patent application
(“Methods and Compositions to Protect Plants and Animals against Pathogen Infection by Blocking Entry of Virulence Proteins” Serial No. 61/128,080), a paid consultancy with Monsanto, Inc.
(2011), and the following grants awarded over the past three years:
- NSF BREAD: “Engineering novel resistance against fungal and oomycete pathogens in
developing country crop plants.” PI: B. Tyler; 3 co-PIs
- NSF: “How do oomycete and fungal effectors enter host plant cells?” PI: B. Tyler; 3 co-PIs
- NSF:”Comparative functional genomics of oomycete effector proteins.” PI: J. McDowell;
co-PI: B. Tyler
- USDA AFRI: “Integrated management of oomycete diseases of soybean and other crop
plants.” PI: B. Tyler. 18 co-PIs.
- USDA AFRI: “Management of the switchgrass rust disease by deploying host resistant genes
and monitoring the dynamics of pathogen populations.” PI: B. Zhao. co-PIs: B. Tyler, et al.
- USDA AFRI: “Insect effectors in molecular plant-insect interactions.” PI: J. Stuart co-PIs:
B. Tyler, et al.
- USDA AFRI: “Probing oomycete-host interactions using an effector ORFeome and effector
protein microarrays.” PI: D. Kumar; co-PIs: B. Tyler, et al.
- USDA AFRI: “Comparative genomics of host range in Phytophthora parasitica.” PI: B. Tyler;
2 co-PIs
- USDA AFRI: “Genome sequence of the oomycete aquaculture pathogen Saprolegnia parasitica.” PI: B. Tyler; 3 co-PIs
- USDA AFRI/NSF: “Phytophthora sojae: A high quality reference sequence for the
oomycetes.” PI: B. Tyler; 6 co-PIs
- USDA AFRI: “Function of Phythopthora sojae effector Avr1b in infection.” PI: B. Tyler; 1
co-PI
www.annualreviews.org • Virulence in Oomycetes
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ACKNOWLEDGMENTS
We thank Jeannette Copley for manuscript assistance. This work was supported by federal
funds from NIAID grant number HHSN27220090018C and USDA grant 2008–35600-04646 to
R.H.Y.J. and by grants 2004–35600-15055, 2007-35600-18530, 2007–35319-18100, and 2011–
68004-30104 to B.M.T. from the Agriculture and Food Research Initiative of the USDA National
Institute of Food and Agriculture and by grants EF-0412213, MCB-0731969, IOS-0744875, and
IOS-0924861 from the U.S. National Science Foundation.
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Contents
Annual Review of
Phytopathology
Volume 50, 2012
An Ideal Job
Kurt J. Leonard p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1
Arthur Kelman: Tribute and Remembrance
Luis Sequeira p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p15
Stagonospora nodorum: From Pathology to Genomics
and Host Resistance
Richard P. Oliver, Timothy L. Friesen, Justin D. Faris, and Peter S. Solomon p p p p p p p p p p23
Apple Replant Disease: Role of Microbial Ecology
in Cause and Control
Mark Mazzola and Luisa M. Manici p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p45
Pathogenomics of the Ralstonia solanacearum Species Complex
Stéphane Genin and Timothy P. Denny p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p67
The Genomics of Obligate (and Nonobligate) Biotrophs
Pietro D. Spanu p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p91
Genome-Enabled Perspectives on the Composition, Evolution, and
Expression of Virulence Determinants in Bacterial Plant Pathogens
Magdalen Lindeberg p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 111
Suppressive Composts: Microbial Ecology Links Between Abiotic
Environments and Healthy Plants
Yitzhak Hadar and Kalliope K. Papadopoulou p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 133
Plant Defense Compounds: Systems Approaches to Metabolic Analysis
Daniel J. Kliebenstein p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 155
Role of Nematode Peptides and Other Small Molecules
in Plant Parasitism
Melissa G. Mitchum, Xiaohong Wang, Jianying Wang, and Eric L. Davis p p p p p p p p p p p p 175
New Grower-Friendly Methods for Plant Pathogen Monitoring
Solke H. De Boer and Marı́a M. López p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 197
Somatic Hybridization in the Uredinales
Robert F. Park and Colin R. Wellings p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 219
v
PY50-FrontMatter
ARI
9 July 2012
19:8
Interrelationships of Food Safety and Plant Pathology: The Life Cycle
of Human Pathogens on Plants
Jeri D. Barak and Brenda K. Schroeder p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 241
Plant Immunity to Necrotrophs
Tesfaye Mengiste p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 267
Mechanisms and Evolution of Virulence in Oomycetes
Rays H.Y. Jiang and Brett M. Tyler p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 295
Variation and Selection of Quantitative Traits in Plant Pathogens
Christian Lannou p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 319
Annu. Rev. Phytopathol. 2012.50:295-318. Downloaded from www.annualreviews.org
by WIB6215 - Karlsruhe Institute of Technology - KIT on 04/14/13. For personal use only.
Gall Midges (Hessian Flies) as Plant Pathogens
Jeff J. Stuart, Ming-Shun Chen, Richard Shukle, and Marion O. Harris p p p p p p p p p p p p p p 339
Phytophthora Beyond Agriculture
Everett M. Hansen, Paul W. Reeser, and Wendy Sutton p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 359
Landscape Epidemiology of Emerging Infectious Diseases
in Natural and Human-Altered Ecosystems
Ross K. Meentemeyer, Sarah E. Haas, and Tomáš Václavı́k p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 379
Diversity and Natural Functions of Antibiotics Produced by Beneficial
and Plant Pathogenic Bacteria
Jos M. Raaijmakers and Mark Mazzola p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 403
The Role of Secretion Systems and Small Molecules in Soft-Rot
Enterobacteriaceae Pathogenicity
Amy Charkowski, Carlos Blanco, Guy Condemine, Dominique Expert, Thierry Franza,
Christopher Hayes, Nicole Hugouvieux-Cotte-Pattat, Emilia López Solanilla,
David Low, Lucy Moleleki, Minna Pirhonen, Andrew Pitman, Nicole Perna,
Sylvie Reverchon, Pablo Rodrı́guez Palenzuela, Michael San Francisco, Ian Toth,
Shinji Tsuyumu, Jacquie van der Waals, Jan van der Wolf,
Frédérique Van Gijsegem, Ching-Hong Yang, and Iris Yedidia p p p p p p p p p p p p p p p p p p p p p p 425
Receptor Kinase Signaling Pathways in Plant-Microbe Interactions
Meritxell Antolı́n-Llovera, Martina K. Ried, Andreas Binder,
and Martin Parniske p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 451
Fire Blight: Applied Genomic Insights of the
Pathogen and Host
Mickael Malnoy, Stefan Martens, John L. Norelli, Marie-Anne Barny,
George W. Sundin, Theo H.M. Smits, and Brion Duffy p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 475
Errata
An online log of corrections to Annual Review of Phytopathology articles may be found at
http://phyto.annualreviews.org/
vi
Contents