Trends in Plant Science
Reassessing the MAP3K and MAP4K relationships
Section snippets
Relationship trees
The dataset summarized in Figure 2 shows the major ste and Raf families and subfamilies (see also Table 1). Most of the 347 sequences analysed cluster together into large clades [i.e. MEKK, MAP2K, MAP4K, CDC, ZIK, Raf sensu stricto, Raf-related and mixed lineage kinases (mlks)]. Most of the other PSTKs are classified into the large plant receptor-like kinase (rlk) superfamily, which contains more than 600 members in Arabidopsis [3]. Previous analyses 2, 4, 5 indicated that functional MAP3Ks
‘Raf’ superfamily
The tree separated a large monophyletic clade, the ‘Raf’ superfamily that is significantly supported by the bootstrap value. This clade includes 18 MLKs, 14 Rafs sensu stricto, 20 plant Rafs and 45 plant Raf-related kinases. Each of the Raf sensu stricto, plant Raf, MLK and plant Raf-related families are supported by highly significant or significant bootstrap values. As shown in Figure 2, all plant Raf-related kinases (representing 45 predicted kinases) are divergent from the animal Raf sensu
STE family
The STE family is supported by a significant bootstrap value, suggesting that the family is monophyletic (Figure 2). It consists of the STE11/ste20 and STE7 clades previously defined [20]. Several STE proteins are protein kinases that putatively act sequentially upstream of the MAPKs: the MAP2K/MEKs, the MAP3K/MEKKs and the MAP4Ks. Other kinases within the STE family include the plant MEKK-related kinases, the CDC kinases and the plant ZIK sequences. Each of the ZIK, plant MEKK-related, MAP2K,
Conserved features of primary structure
The pattern of amino acid residues found for many subdomains is conserved among family members. Careful analysis revealed that protein kinase subdomain relationships reflect similar substrate specificity and mode of regulation [36]. The catalytic loop region (subdomain VIb) includes the invariant aspartate (catalytic base) and the activation loop region (subdomain VIII) includes the highly conserved glutamate. Both regions participate in peptide–substrate recognition 37, 38. In many kinases, a
Relationships and outcomes
Plant MAPK pathway components belong to a broad range of subfamilies, groups and subgroups of evolutionarily related proteins. These plant clades are separated from non-plant members in all the relationship trees we built for MPK, MKK, MEKK, CDC, MAP4K and Raf. In the same way, we observed that plant CDKs separated from animal and yeast lineages. In most cases, the closest available non-plant sequences are from the Dictyostelium genome. (This was confirmed for MPK, MKK, MEKK, CDC and MAP4Ks of
Glossary
Glossary
- AGC:
- clade consisting of the cyclic-nucleotide-dependent subfamily (PKA and PKG), the PKC subfamily and the ribosomal S6 kinase subfamily.
- CaMK:
- family consisting of calcium/calmodulin-interacting protein kinase and SNF1 protein kinase.
- CDC:
- subfamily of STE kinases.
- CMGC:
- family containing the CDK, MAPK, GSK-3 and CK2 families.
- DUF26:
- protein family containing DUF (domain of unknown function).
- ERK:
- extracellular regulated kinase (a MAPK).
- GCK:
- germinal centre kinase.
- MAPK:
- mitogen-activated protein kinase;
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