"Frontmatter". In: Plant Genomics and Proteomics

A
BIOTIC
I
NTERACTIONS
The individual plant species of today are the results of evolution in response
to a multitude of biotic and abiotic environmental variations. The ways that
plants have coped with the number of biotic stresses have been considered
above. However, plants also encounter a myriad of abiotic stressful envi-
ronmental conditions including heat, drought, salt and various metals such
as aluminum, as well as variations in light. Thus plants under stress inte-
grate a diverse range of environmental and metabolic signals through a
network of signal transduction pathways that function to regulate changes
in gene expression. 
If the plant is growing under optimal conditions, cellular homeostasis is
achieved through the coordination of a wide variety of biochemical path-
ways. If the plant is growing under suboptimal conditions, generally termed
stress, then the integration of the various pathways that normally achieve
cellular homeostasis can be disrupted, because these pathways may them-
selves be differentially affected by the stressful conditions. This disruption
is frequently accompanied by the formation of reactive oxygen species
(ROS). Because many stress responses are mediated through a response to
ROS, plants make use of common pathways that allow them to acclimate to
a range of different stresses, irrespective of the initiating event. Therefore, 
to provide adequate protection against such a hazardous environment a
common signaling system has evolved, known as cross-tolerance (Bowler
and Fluhr, 2000). 
Any investigation of these stress responses in plants must also be asso-
ciated with an understanding of the physiology of the organism. In addition,
it is insufficient to characterize the responses simply at the transcriptionally
level because it is clear that many of the important physiological modifica-
tions occur through the activation of protein kinases, and therefore the pro-
teome also must be characterized. 
Many of the stress responses in plants have been investigated individu-
ally. However, under normal conditions the plants may experience a combi-
nation of stresses that may result in changes somewhat different from those
observed in response to any single stress. Therefore, the understanding of
plant responses to more complex combinations of perturbations is important
especially with reference to the applicability of the conclusions to crop
improvement. Such combinations of stresses frequently occur in parts of the
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world where sophisticated genomics technology is only just beginning 
to make an impact, and where food security issues are of paramount 
importance. 
The understanding of abiotic stress tolerance, and the breeding for stress
tolerance, have proved difficult because of the large number of genes appar-
ently involved. The lack of traditionally bred plant lines that are multiply
stress tolerant and high yielding, itself another complex trait, is a conse-
quence of these difficulties. The application of genomics techniques to the
problem has resulted in a large amount of data, especially concerning 
transcriptional regulation (Bohnert et al., 2001).
D
ROUGHT
S
TRESS
Around the world water availability is probably the dominant environmen-
tal factor that limits plant productivity, so the search for drought tolerance
is of vital importance. Drought-tolerant plants are, by definition, able to
maintain the water content of their tissues or able to survive a reduction in
tissue water content or recover when the drought stress is relieved. Plant
survival under drought conditions can be achieved by two very different
mechanisms. The strategy can be based on drought avoidance, whereby the
plant architecture avoids experiencing the stress by, for example, develop-
ing a deep root system. Alternatively, the tolerance can be achieved through
mechanisms by which the plant mitigates the effects of the drought stress
and is able to recover when water again becomes available. Drought stress
usually results in the suppression of respiration and photosynthesis. Stom-
atal closure and osmotic adjustment are among the responses by which the
plant can limit water loss. 
The identification of the genes with primary roles in any of the stress tol-
erances requires a series of correlations to be established and then direct ver-
ification through forward or reverse genetic manipulations to confirm the
function of each of the identified genes. Some of the useful correlations
include:
∑ That between the presence of a gene and a specific phenotype
∑ That which establishes a role for the gene in the evolution of a par-
ticular phenotype
∑ That which establishes the importance of a particular mechanism, for
example, protection during drying and repair on rehydration 
The availability of microarrays allows the global expression patterns in
response to many stresses to be determined. At the next level, the use of pro-
teomics allows the pattern of protein variation to be characterized. A com-
bination of the two approaches is necessary to generate a complete picture
of the response of plants to this particular stress. It must also be recognized
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that the degree of variation existing among the various levels of stress tol-
erance, and tolerance mechanisms, requires the experiments to be performed
on a wide range of biological material. Thus the proteomic analysis of rice
leaves during drought stress and recovery (Slaekedeh et al., 2002) detected
more than a 1000 protein spots. However, of these proteins, 42 showed sig-
nificant changes in abundance under stress, but 27 of them exhibited a dif-
ferent response pattern in the two cultivars used. Sixteen of these forty-two
proteins were identified through MS (15) or by cloning of the respective
cDNA (1). Eleven of the proteins were from major cellular pathways known
to be responsive to drought stress including protein synthesis, photosyn-
thesis, carbon metabolism, and oxidative stress tolerance. Novel observa-
tions included the upregulation of an S-like RNase homolog that was lacking
the two active site histidines necessary for RNase activity.
The 16 drought-responsive rice proteins are not closely related to the 16
drought-responsive maize proteins previously identified (Riccardi et al.,
1998). Whether this is due to the fact that many drought-responsive proteins
are still unidentified, or that the tissues sampled were somewhat different,
awaits clarification. All of these characterizations are in the early stages, and
much more data are likely to be reported in the near future that may, but not
necessarily, lead to a clearer understanding of the various mechanisms
involved in drought tolerance and the roles of the genes responsible for those
mechanisms. 
Because plants do not necessarily experience these stresses in isolation
from one another, it is important to characterize the responses to multiple
simultaneous stresses. When this was done in tobacco, the combined effect
of drought and heat shock resulted in a pattern of response, at the level of
gene expression, that was somewhat different from that observed when
either of these stresses was applied singly (Rizhsky et al., 2002). Physiolog-
ical measurements on tobacco plants simultaneously subjected to the com-
bination of these two stresses resulted in closure of stomata, suppression of
photosynthesis, an increase in respiration, and increased leaf temperature.
The genes that were expressed, as shown by transcription levels, under the
combination of stresses could be split into three categories:
∑ Genes that had been induced during either heat shock or drought
stress alone and were now suppressed under the combination of
stresses
∑ Genes that followed the expected expression pattern based on their
activity under either of the stresses singly
∑ Genes that were specifically induced only when the combination of
stresses was applied 
These results with a combination of stresses that may be more typical of
the conditions that plants encounter in the field were different from those
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when either of the stresses was applied individually. They were also differ-
ent from previously observed responses of plants to other single abiotic
stresses. Therefore, the integration of plant responses to suboptimal growth
conditions resulting from a combination of perturbations may not be simply
predicted from their responses to each of those stresses applied individually.
One of the goals of understanding plant responses to abiotic stresses is
to develop strategies for modifying plants in order to improve productivity
under such conditions. However, such strategies must be based on the
appropriate body of information. In other words, the information must be
obtained from plants grown in an environment that is equivalent in all, or
most, respects to the conditions that the modified plant will encounter. In
addition, the wide range of multiple stresses with which plants have to cope
are unlikely to be alleviated by the addition of a single gene or signal trans-
duction pathway. If such a simple fix was available, it is likely that it would
have emerged through the process of natural selection in some plant species.