Functional assignment of MAPK phosphatase domains

Abstract

Mitogen-activated protein kinase (MAPK) pathways are well conserved in most organisms, from yeast to humans. The principal components of these pathways are MAP kinases whose activity is regulated by phosphorylation, implicating various MAPK protein effectors-in particular, protein phosphatases that inactivate MAPKs by dephosphorylation. The molecular basis of binding specificity of such regulatory phosphatases to MAPKs is poorly understood. To try to pinpoint potential functional regions within the sequences and to help identify new family members, we have applied a multimotif pattern-recognition approach to characterize two MAPK phosphatase subfamilies (tyrosine-specific and dual specificity) that are crucial in the regulation of MAPKs. We built "fingerprints" for these two subfamilies that are unique to, and highly discriminatory for, each group of proteins. The fingerprints were used in a genome-wide screen, identifying more than 80 MAPK phosphatase domains, several of which were in partial sequences or unclassified proteins. We confirmed experimentally that one predicted MAPK phosphatase orthologue in Xenopus binds to ERK1/2, suggesting a role in MAPK signaling and thus supporting our functional predictions. Further analysis, mapping the fingerprints on the three-dimensional structure of MAPK phosphatases, revealed that some of the fingerprint motifs reside in the N-terminal noncatalytic regions coinciding with reported MAPK binding sites, while others lie within the catalytic phosphatase domain. These results also suggest the presence of putative allosteric sites in the catalytic region for modulation of protein-protein interactions, and provide a framework for future experimental validation.

Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics

“…MSG5 encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is required for restricting signaling by the cell integrity pathway in yeast [33]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [34]. The functions of ARL1 and ERG24 and their potential roles in chitosan resistance are described in more detail in the Discussion.…”

Phylogenetic and genetic linkage between novel atypical dual-specificity phosphatases from non-metazoan organisms

“…Using bioinformatics, modeling analysis, and biochemical tools, we have defined a novel family of DSPs with members belonging to species of plants, fungi, kinetoplastids, and slime molds (PFA-DSPs) (Romá-Mateo et al 2007). PFA-DSPs share the presence of four common amino acid motifs (PF1-PF4 fingerprint motifs; average side, 16 residues), which segregates this family from other DSP families (Attwood and Findlay 1993;Nordle et al 2007) (http://www.bioinf.manchester.ac.uk/ dbbrowser/PRINTS/index.php). The catalytic domains of PFA-DSPs do not have significant homology at the amino acid level with DSP catalytic domains from animals (with the exception of the signature catalytic motif), but the three-dimensional folding of the PFA-DSP AtPFA-DSP1/ At1g05000 resembles that of mammalian DSPs (Aceti et al 2008).…”

A Novel Phosphatase Family, Structurally Related to Dual-specificity Phosphatases, that Displays Unique Amino Acid Sequence and Substrate Specificity

“…Accession numbers for sequences in (a) and (b) are given in Supplementary Tables 2 and 4. and, similarly, a fingerprint created for MKPs matched no atypical DUSP proteins. 34 As a consequence of their evolutionary divergence, members of the atypical DSP-II subfamily display heterogeneous amino acid sequences and protein size, thus making impossible the identification of common fingerprint motifs. However, DUSP15 and DUSP22, as well as DUSP11/PIR1, RNGTT/MCE1, and DUSP23, can be clustered as highly related proteins within this heterogeneous group (Fig.…”