"Frontmatter". In: Plant Genomics and Proteomics

parasitica.
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∑ PBS2—A mutant in this gene has reduced RPS5- and RPM1-mediated
resistance. It is potentially involved in transduction of R gene-
mediated disease resistance.
∑ PAD4—Encodes a lipaselike gene that is also important for salicylic
acid signaling. PAD4 is also required for runaway cell death in the
lsd1 mutant. Importantly, this novel function of PAD4 is operative
when runaway cell death in lsd1 is initiated through an R gene that
does not require PAD4 for disease resistance (Rusterucci et al., 2001).
∑ EDS1—This is a component of R gene-mediated disease resistance in
Arabidopsis thaliana with homology to eukaryotic lipases. EDS1 is
essential for disease resistance conferred by the structural subset of
resistance (R) proteins, the TIR-NBS-LRR proteins, but is not required
by the CC-NBS-LRR proteins (Peart et al., 2002). EDS1 is also required
for runaway cell death in the lsd1 mutant. Importantly, this novel
function of EDS1 is operative when runaway cell death in lsd1 is 
initiated through an R gene that does not require EDS1 for disease
resistance as is also the case for PAD4 (Rusterucci et al., 2001).
It is clear that each of these genes can have effects in various other resistance
pathways and not just in interactions with the R genes. 
In addition to the direct pathways from the R gene to resistance, there
are also the salicylic acid-mediated responses and jasmonic acid/ethylene-
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RESISTANCE
3 classes fo R genes based on their response cascades
R genes
RPM1
RPS5
NDR1
PBS2
Additional genes
necessary for
resistance
response
R genes
RPP2, 4 10
RPS4
EDS1
PAD4
R genes
RPP7, 8 13
Unknown
FIGURE 7.2.
Possible positions of some of the Arabidopsis genes in signal transduc-
tion networks that control the effect of resistance genes. The box containing the word
“resistance” represents the final expression of resistance. Three R-gene-dependent
pathways are shown, one that requires NDR1 and PBS2, a second that requires EDS1
and PAD4, and a third for which the required genes have not been reported.
(Reprinted from Curr. Opin. Plant Biol. 4, Glazebrook, Genes controlling the expres-
sion of defense responses in Arabidopsis—2001 status, 301–308, Copyright 2001, with
permission from Elsevier.)

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mediated responses (Glazebrook, 2001). The salicylic acid-dependent sig-
naling response is important for SAR that is activated throughout a plant in
response to particular types of infection. Some of the same genes, for
example, the PAD4 gene, that are involved in resistance mediated by the
gene-for-gene pathway are also involved in the salicylic acid signaling
pathway. The SAR response and the signaling response to jasmonic acid/
ethylene appear to be much more complex than the direct pathway between
the R gene and the expression of resistance. As more mutants involved in
these pathways are identified (and multiple mutant analyses performed) the
interrelationships and dependence of each of the points in the pathways with
respect to each other are likely to become clearer. 
Genome-wide expression profiling that includes mutants affecting
disease resistance responses will result in the identification of the genes
important in the regulation and expression of disease responses. Disease
resistance pathways have many common elements that overlap with the
responses induced by other stresses. Therefore, there exists a network of
genes that are activated in response to a wide range of stimuli but do not
have any essential role in the development of resistance per se. The devel-
opment of these expression profiles for a wide range of stimuli will there-
fore help in identifying those genes that are integral and essential for the
expression of specific resistances. 
As has been indicated in other chapters, the fact that a gene is observed
to have differential expression under various conditions does not necessar-
ily lead to an understanding of its role in the phenomenon under investiga-
tion. Rather, the level of product associated with that transcript and the
proteins with which that product is intimately associated in the cell to
mediate the responses are essential, but currently missing, pieces of infor-
mation. The LRR domains of the R proteins are thought to act as the deter-
minants of specificity and ligand binding. For example, in the yeast
two-hybrid system an interaction between the LRR-like domain of the 
rice resistance protein Pita and the Avr-Pita protein was demonstrated 
(Nimchuck et al., 2001). However in the complex signaling pathways, espe-
cially those involved in SAR and the jasmonic acid/ethylene signaling
responses, the extent and number of proteins that form complexes with the
resistance proteins has yet to be determined. The characterization of the
extent of these interactions should go a long way toward providing an
understanding of the basic mechanisms by which the R genes act, and how
pathogens can bypass the defenses, and so direct attention to possible posi-
tions in these pathways for interventions that can lead to new methods of
disease resistance for crop plants. 
The unraveling of the importance and contributions all of the players
will use the whole suite of current genomics methodology. Thus:
∑ Expression profiling will identify those genes that are modulated in
response to disease challenge in both the host and the pathogen.
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∑ Proteomics techniques, especially those using transgenics, will allow
the isolation of the in vivo protein complexes and the identity of the
involved components.
∑ Insertional mutagenesis, and other mutagenesis studies, will identify
the involvement of each of these genes. 
Considering the apparent redundancy of the pathways through which
the resistance is developed, the unraveling of these pathways by mutant
analyses is likely to involve various combinations of multiple mutants in a
single line. These experimental determinations will be necessary to fully
understand the roles of each of the players in mediating the wide range of
resistance responses.
To possibly use resistance genes across wide species barriers, the resis-
tance phenomena will need to be studied across both a wide range of plant
species and a wide range of pathogen types. Such studies will necessitate
the characterization of the interacting proteins and the regions of the pro-
teins involved in such interactions. The introduction of resistance genes into
heterologous systems has only conferred resistance when the transfers have
been among species that are closely related. Therefore, understanding the
reasons for this may elucidate any specific evolutionary constraints that have
been imposed across the plant kingdom. Natural selection has been acting
on the R gene loci over much longer periods than those during which plant
breeders have been recruiting the various forms of these genes for crop
improvement (Jones, 2001). The effect on fitness of changing the R gene
profile, particularly with respect to “stacking” R genes to provide more
durable resistances, also must be considered. Because R genes are thought
to be always expressed and to function as alert first responders, the stack-
ing of many resistance genes into a single genotype may not provide the
desired durable resistance, while still leading to a reduction in yield in the
absence of the pathogen. 
R
ESPONSE TO
S
YMBIOSIS
The interaction of plant roots with the soil environment is a much less well-
developed area of research and knowledge compared with the study of
above-ground interactions. The roots mine the soil for nutrients, and the
nutrient uptake is affected by symbiotic interactions with arbuscular myc-
orrhizal fungi, which supply plants with phosphate and other nutrients. In
legumes the development of the nitrogen-fixing nodules is a highly specific
interaction between the appropriate bacteria and the response of the legume
host plant. This interaction allows for the invasion of the plant root, with the
cooperation of the plant, in the form of the development of an infection
thread and the formation of the nodule, so that the bacteria are provided
with the appropriate environment in which they can fix nitrogen. So how is
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this invasion controlled and how does the plant host differentiate it from the
reaction with pathogenic bacteria? Similarly, how are the fungal hypha
accommodated during colonization by mycorrhizal fungi without causing a
plant defense reaction?
Because Arabidopsis is a poor host for mycorrhiza and does not undergo
nodulation by Rhizobium, it is not a particularly suitable model system for
the study of symbiosis. As was the case for disease resistance, the symbiotic
relationship must be considered from two points of view, namely, those of
the host plant and the symbiont. 
The lack of a genomic sequence for any of the legumes has certainly
slowed the pace at which the genes that are responsible for symbiosis have
been isolated. Despite this, numerous plant mutants that affect the legume-