We obtained 33 class I human and worm PDZ domains from a recent large-scale study on the specificity map of PDZ domains [ 13].
Consolidating both previous and present studies, at least three alleles contributing to leaf rust resistance [ Rph9, Rph12 (Rph9.z) and Rph9.am (Rph9.am)], each with distinct race specificity, map to chromosome 5HL at potentially the same locus.
Our results indicate that monoclonal antibodies with a limited spectrum of neutralizing activity can be easily isolated, while those with a broad pattern of cross-clade reactivity are rare, in line with the study of Walker et al [40] and consistent with inferences from serum neutralization specificity mapping analyses [21].
Indeed, several studies have attempted to capture the binding mechanism of PDZs in a selectivity model, using approaches based on Domain Interaction Footprints (DIF) [27], specificity maps [14], dissociation constants [28], trigram and bigram frequencies [29], support vector machines (SVMs) [30], and Bayesian models [17].
Fig. 5A shows the structure of human MAGI1 PDZ2, bound to a viral peptide, with the residues that define peptide-binding specificity mapped onto the structure (in yellow).
Motif analysis showed robust enrichment of the hybrid motif at these sites, reproducing the exquisite specificity mapped in the hMSC ATF4 cistrome.
We applied the approach to PDZ, SH3 and kinase domains, and evaluated the results using both residue proximity in co-crystal structures and verified binding specificity maps from mutagenesis studies.
Sdp1 is a stress inducible dual-specificity MAP kinase phosphatase that negatively regulates the MAP kinase cell integrity pathway [33, 34, 35].
Dual-specificity MAP kinase phosphatases (MKPs) are capable of dephosphorylating phosphotyrosine as well as phosphothreonine residues of MAP kinases and thus influence important cellular processes such as proliferation, differentiation, apoptosis and survival [ 115].
As shown in Table 2, we found regulation of BCK1, coding for the MAPKKK of the pathway; SLT2, the terminal kinase; MLP1, encoding a putative Ser/Thr kinase with similarity to Slt2p; and SDP1, whose product is a dual-specificity MAP kinase phosphatase acting on and regulating the phosphorylated/active form of Slt2p [ 23].
The results not only confirmed previously known Drosophila TF binding specificities mapped using different approaches (mainly yeast one hybrid), but also added roughly 110 new TF binding motifs.
