Genomic Analysis of MAP Kinase Cascades In: Arabidopsis Defense Responses
Genomic Analysis of MAP Kinase Cascades In: Arabidopsis Defense Responses
Genomic Analysis of MAP Kinase Cascades In: Arabidopsis Defense Responses
Review
1. MAP
Introduction
kinase genomics Cvetkovska et al.
Plant diseases have been known from the very beginnings of organized agriculture
and have frequently been associated with hunger and suffering. One of the most
famous examples in history is the Irish potato famine of the 1840s, caused by late
blight of potato, whose agent, the fungus Phytophthora infestans, is the so-called
“plant destroyer” (Holub, 2001). Since then, new ways to protect crops from
disease and to increase their productivity have evolved, for example, through the
use of pesticides and higher yielding plant varieties. Today, with the emergence of
new genetic and biomolecular techniques, it becomes possible to understand more
fully, and potentially to enhance, the plant’s defense mechanism and thus produce
crops that are more resistant to disease.
Arabidopsis thaliana was first used as a model plant for the study of plant-
pathogen interactions about 20 years ago. Since then there has been exceptional
progress in discovering the molecular and genetic basis for disease resistance in
this plant (Buell, 1998). Arabidopsis was chosen as a model for several reasons. It
*
Author for correspondence. e-mail: Tim_Xing@Carleton.ca;
tel: (613) 520-2600 ext 8981; fax: (613) 520-3539.
332 Cvetkovska et al.
exhibits all of the major defense responses found in other flowering plants, it has
a relatively small genome that has been completely sequenced (The Arabidopsis
genome initiative, 2000), it has a short generation time, and small size for easy
screening tests. But perhaps the most valuable factor is that numerous mutants
have been isolated, which made possible the identification of genes responsible
for different phenotypes (Buell, 1998; Glazebrook et al., 1997; The Arabidopsis
genome initiative, 2000).
Within the Arabidopsis genome there are approximately 1000 protein kinase
genes and 200 phosphatase genes (Xing et al., 2002). The large pool of kinases
and phosphatases indicates the importance of phosphorylation and dephos-
phorylation mechanisms in the growth and development of Arabidopsis. Indeed,
phosphorylation is one of the main methods of post-translational modification that
regulate protein stability, biological activity and cellular location. This process
also has an effect on protein-protein interactions such as formation of protein
complexes and protein docking. Phosphorylation affects serine, threonine, tyrosine
and histidine residues in both eukaryotes and prokaryotes, and has been consid-
ered a universal regulator of cellular activities in all living systems (Huber et al.,
1994). This paper gives an overview of mitogen-activated protein kinase (MAPK)
pathways in plant defense responses in Arabidopsis.
All of the MAP kinases are classified based on two methods. The first is a
phylogenetic analysis based on the Arabidopsis genome and EST sequencing project
(MAPK project). The classification is comprised of six subfamilies, possibly
representing at least six functional groups (Zhang and Klessig, 2001). This
assumption has not yet been tested, and the classification remains to be further
affirmed by molecular and biochemical studies. It is important to notice that the
phylogenetic relationships may not represent functional relationships. The second
method is based on functional analysis involving specific features and sequence
signature motifs (Jonak et al., 2002). Table 1 summarizes the specialized signa-
ture motifs and the kinase classes they determine.
All MAPKs have a Thr-Glu-Tyr (TEY) activation motif, except MPK17/
18/19, in which Asp (TDY) replaces the Glu residue, and a specific domain
required for MAPKK docking (Zhang and Klessig, 2001). A specific feature of
the TDY group of MAPKs, which the TEY group lacks, is their long carboxy
terminal extension. Shared features of all MAPKKs include a putative MAPK
docking domain at the N-terminus. MAPKKKs constitute the largest group of
MAPK cascade kinases in Arabidopsis and are divided in two groups, one
containing MEKK-like and ZR1-interacting kinases (ZIKs) which had been shown
to function as true MAPKKKs, and the other composed of Raf-like protein kinases,
to which no specific function has been assigned yet (Ichimura, 2002).
A specific nomenclature that unifies all Arabidopsis MAPKs has been pro-
posed (Ichimura et al., 2002). For example, in this scheme, the gene for a MAPK
is named MPK and the gene for a MAPKK is called MKK. Although the prefix
At (for Arabidopsis thaliana) is not included in the official name of the gene, it is
a useful species marker for comparative or homologue studies on MAPKs of
different plant species. One drawback of this system is that it is not definitive yet
because the structure and function of many members of the family are still not
fully characterized. In addition, so far it has proven impossible to provide a
nomenclature system that will unify the MAPKs of all plant species.
Table 1. A list of Arabidopsis MAPK signalling components based on Jonak, et al. (2002).
lysine residue, which has been shown to be involved in ATP binding. There is
also a bipartite nuclear localization signal domain, which is a common motif
found in most proteins and mediates the transport of nuclear proteins into the
nucleus (Voet et al., 1998).
It is known that MAPKKKs can be regulated by other protein kinases or by
binding to specific effectors. The receptor-mediated activation can occur through
physical interaction and/or phosphorylation by the receptor itself (Jonak et al.,
2002). In this particular cascade, that would be the putative flagellin receptor
kinase (FLS2 LRR), and this receptor kinase could potentially activate the
MAPKKK by phosphorylating the Ser/Thr residues found in this domain. How-
ever, no conclusive research has been done and most of the speculations remain
unconfirmed.
A study on the interaction of this MAPKKK with other proteins revealed
that AtMEKK1 has the ability to phosphorylate other kinases (Ichimura et al.,
1998). When AtMEKK1 was expressed in Arabidopsis leaves, the defence
responses of the plant were activated against both fungal (B. cinerea) and bacte-
rial pathogens (P. syringae) (Asai et al., 2002). This was taken as a strong indica-
tion that this particular MAPKKK is in fact a part of a signal transduction cascade
involved in pathogen resistance in Arabidopsis. It is known however that AtMEKK1
can interact and activate four different MAPKKs and thus transmit signals in four
different cascades involved in touch, cold and water stress, in addition to the
pathogen resistance cascade discussed here (Mizoguchi et al., 1996; Ichimura et
al., 1998a). These data, in addition to the fact that the MAPKKK is the largest
group of kinases in the MAPK cascade suggests that these members of the
cascade function as divergent factors within the MAPK cascade module (Jonak et
al., 2002).
N-terminus. This domain has the general structure: K/R-K/R-K/R-X (1-6)-L-X-L/V/I, and
its function is to assist in the binding of the MAPK to the MAPKK (Jonak et al.,
2002). The precise function and mode of action of this domain is still not clear,
except in Medicago, where this domain in SIMKK (stress-induced MAPKK) is
required, but not sufficient, for MAPK activation. The Ser/Thr active site is cru-
cial for the activity of the kinase. This site comprises an activation loop, which
has the general structure S/TXXXXXS/T. MAPKK is activated by MAPKKK
through phosphorylation at the Ser/Thr and Ser/Thr residues (Hirt, 1997; Xing et
al., 2001). In transgenic studies, AtMKK4 and AtMKK5 were both shown to con-
fer resistance to fungal and bacterial pathogens when activated by flagellin, even
though their function could be redundant (Asai et al., 2002). It is also interesting
that the same MAPKKs are involved in HR defense mechanism against pathogens
(Ren et al., 2002). Thus, in addition to confirming the position of AtMKK4/5 in
the cascade, this study also showed that this cascade could be activated by other
elicitors.
A single MAPKK can interact with and activate more than one MAPK, and
thus acts as another divergent factor in the module. This has been shown in studies
of Arabidopsis as well as alfalfa, tobacco and tomato (Jonak et al., 2002; Zhang et
al., 2000; Xing et al., 2001). Knowing that both MAPKKKs and MAPKKs have a
divergent function, and considering the total number of different kinases in the
plant, it is easy to grasp the complexity of the cascade.
al. (2000) showed that AtMPK6 is activated by cold, humidity, touch and wounding.
The kinase was also found to be induced by three different elicitors from bacteria
(flagellin) and fungi (xylanase and chitin) (Nuhse et al., 2000). Further study on
the flagellin-induced pathway confirmed the role of AtMPK6 in the pathogen
resistance cascade and also marked the position of AtMPK6 with respect to the
other steps in the pathway, i.e., it is activated by AtMEKK1 and AtMKK4 (Asai
et al., 2002).
Since a single MAPK is activated by several different elicitors through
different MAPKKs and MAPKKKs, these kinases probably represent the converging
point of the cascade. After their activation, they further phosphorylate different
downstream targets so that different responses on the cellular level can be activated
accordingly.
ERF 56 GCCGCC (GCC box) Fujimoto et al., 2000, Gutterson and Reuber, 2004
Myb 125 Type I: (T/C)AAC(T/G) Type II: G(G/T)T(A/T)G(G/T)T Jin and Martin, 1999
TGA 10 TGACGTCA (TGA box) Eulgem 2005, Rushton and Somssich, 1998
Whirly 3 GTCAAAA(A/T) (PB element) Desveaux et al., 2005
WRKY 74 C/T- T-G-A-C-T/C Ulker and Somissch, 2004, Eulgem et al., 2000
Cvetkovska et al.
MAP kinase genomics 339
acid marker gene that controls the synthesis of salicylic acid in the infected tissue
and induces systemic acquired resistance in the plant, and PR-2, which encodes a
β-1,3-glucanase (an antifungal compound) (Rushton et al., 1996). Some RLKs,
α-amylases, ethylene-induced DNA binding proteins, reverse transcriptases, protein
kinases and different disease resistance gene products were also regulated by
WRKYs (Du and Chen, 2000).
4. Proteomic approaches
Many kinases involved in plant signalling can be regulated at transcriptional,
translational and post-translational levels, and the relative contribution of each to
the overall response varies. Therefore a proteomic approach is valuable in under-
standing regulatory networks because it deals with identifying new proteins in
relation to their function, and ultimately aims to unravel how their expression and
modification is controlled.
Peck et al. used 32P to pulse-label suspension-cultured cells of Arabidopsis
in conjunction with 2-dimentional electrophoresis (2DE) and mass spectrometry
(MS) to identify proteins that are rapidly phosphorylated in response to bacterial
and fungal elicitors (Peck et al., 2001). One of these proteins, AtPhos43, was
identified by nano-electrospray ionization (ESI) tandem MS and was found to be
phosphorylated within minutes after treatment with flagellin. By measuring 32P
incorporation into AtPhos43 in defence response mutants, they found that
phosphorylation of AtPhos43 after flagellin treatment was dependent on FLS2, a
receptor-like kinase involved in flagellin reception. It has also been found that this
protein was phosphorylated in response to both fungal and bacterial elicitors, and
related proteins are phosphorylated in other monocot and dicot species (Peck,
2003; Peck et al., 2001). However, it is very interesting that in the examination of
proteins that were phosphorylated in Arabidopsis upon treatment with flagellin
only a few of the phosphoproteins were found to be regulated at the transcriptional
level (Peck, 2003). This observation is consistent with other studies that have
shown that the level of gene expression does not necessarily correlate with the
protein levels in a cell (Gygi et al., 1999) or that the genes required for a response
are not necessarily the same genes that are differentially regulated as a result of
the response (Birrel et al., 2002; Giaever et al., 2002). For these reasons, it is
believed that analysis of protein levels and protein modification profiles gives the
best indication of the final players in a cellular response.
Proteomic approaches have been applied to monitor downstream compo-
nents of specific MAPK pathways. tMEK2 is a known MAPK kinase in tomato
and was previously shown to regulate the expression of β-1,3-glucanase and
endochitinase genes in response to certain pathogen attacks (Xing et al., 2001).
When 2DE was used to compare soluble proteins from wild-type and transgenic
tomato plants carrying tMEK2MUT, in which the tMEK2 is constitutively active
(Xing et al., 2003), it was found that some of the proteins were phosphorylated in
the tMEK2MUT transgenic tomato plant but not in wild-type plants. Eleven such
proteins were identified by liquid chromatography (LC)-ESI MS and MALDI-
TOF, including superoxide dismutase, glutathione peroxidase, GrpE, and calreticulin
(C. Rampitsch and N. Bykova, unpublished).
340 Cvetkovska et al.
Based on the number of MAPKKKs, MAPKKs and MAPKs, there can theoreti-
cally be numerous combinations (23 × 10 × 60 = 13800) of pathways. Recent
comparative genomics analysis has indicated such complexity in MAPK pathways
in two other species (rice and poplar) with completed genome sequences (Hamel
et al., unpublished results). How can plants manage such a vast number of possi-
bilities? It has been discovered that in mammalian systems different kinases are
assembled into distinct modules by scaffold proteins. Scaffold proteins are impor-
tant for preventing cross-talk between different cascades, and allow a given kinase
to function in more than one module without affecting the specificity of the
response (Morrison and Davis, 2003; Yoshioka, 2004). As recently shown for
Medicago OMTK1, some MAPKKKs also seem able to act as scaffold proteins,
assembling specific MAPK pathway components into particular modules
(Nakagami et al., 2004). Scaffold proteins have not been identified in Arabidopsis
MAP kinase pathways, but considering the fact that MAP kinases are conserved
among eukaryotes it is plausible that Arabidopsis and other plants have the same
mode of pathway assembly.
As shown in the analysis of the specific MAPK cascade components
involved in pathogen induced signalling, one MAPK can be activated by multiple
signals, and can itself phosphorylate more than one kinase. Taking the work by
Asai et al. (2002) as an example, AtMEKK1 was shown to react with four different
MAPKKs. One of them was AtMKK4, which also had the ability to
phosphorylate more MAPKs. In turn, AtMPK6, the last kinase in the cascade,
induced transcriptional factors that induced the activation of several genes. This
shows only a small part of the entire MAPK signalling cascade. It can be con-
cluded that there is no one distinct pathway that can be distinguished for one
specific signal in plants. Instead, the MAP kinases act as a network of signalling
components, and the final response of the plant depends on more conditions than
just the type of pathogen that infects it.
Genetic knockout approaches are very effective in deciphering signalling
pathways. However, as stress response cascades are obviously crucial for the well
being of the plant, manipulating them might be detrimental for the health of the
plant. This is probably one of the main reasons why not many Arabidopsis
mutants are known for the genes encoding kinases in MAPK modules. Moreover,
since the MAPKs are regulated post-translationally by phosphorylation, the loss
of a functional gene product might not reveal the exact function of a MAPK cascade
(Zhang and Klessig, 2001). A combination of genetic, biochemical, genomic and
proteomic studies will reveal a much more complex picture of MAPK pathways
in plant defense responses.
6. Acknowledgements
This work was supported by a research grant to T.X. from Natural Sciences and
Engineering Research Council of Canada, and by research grants to C.R and N.B.
from Agriculture and Agri-Food Canada Genomics Initiative.
MAP kinase genomics 341
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