The Evolutionary History of MAP Kinases in Eukaryotes

The Evolutionary History of MAP Kinases in Eukaryotes

Mitogen-activated protein kinases (MAPKs) are pivotal enzymes in eukaryotic signal transduction pathways, influencing a myriad of cellular activities. These kinases are ubiquitous across eukaryotes, underscoring their evolutionary antiquity. The MAPK family is bifurcated into classical and atypical kinases, with the former subdivided into several groups. Terrestrial plants possess four classical MAPK groups (MAPK-A to MAPK-D) that are integral to their stress response mechanisms. In opisthokonts, which encompass fungi and animals, classical MAPKs diverge into two principal branches: the ERK/Fus3-like kinases and the p38/Hog1-like kinases. These branches have further evolved in metazoans into subfamilies such as ERK1/2, ERK5, p38, and JNK. The evolutionary trajectory of MAPKs is intricate, with certain kinases exhibiting ambiguous origins due to either extensive divergence or their status as early derivatives of the MAPK lineage.

Diversification of MAPKs in Vertebrates and Their Functional Specialization

In vertebrates, the MAPK family has undergone significant expansion, partly due to two rounds of whole-genome duplication. This has resulted in multiple paralogs within each kinase group. For instance, ERK1 and ERK2 are homologous to the Drosophila kinase rolled, while JNK1, JNK2, and JNK3 are orthologous to the Drosophila gene basket. The p38 kinases in vertebrates also exhibit paralogous relationships, with p38 alpha and beta as one pair, and p38 gamma and delta as another. The exact timing of these duplications is ambiguous, as multiple p38 homologs are present across various metazoans. The ERK5 kinase, vital for vascular development in vertebrates, represents a specialized lineage that has disappeared in protostomes but is retained in cnidarians, sponges, and some unicellular relatives of multicellular animals.

Early Split and Diversity of Classical and Atypical MAP Kinases

The classical and atypical MAP kinases diverged early in the history of eukaryotes. This is evidenced by the significant divergence among existing genes and the presence of atypical MAPKs in basal eukaryotes. For example, the genome of Giardia lamblia, an early-diverging eukaryote, encodes two MAPK genes: one with similarities to mammalian MAPKs and another akin to mammalian ERK7. In the multicellular amoeba Dictyostelium discoideum, the ddERK1 protein is a classical MAPK, whereas ddERK2 resembles mammalian ERK7 and ERK3/4 proteins. Atypical MAPKs are also present in higher plants, though their functions are less well-characterized due to a paucity of research.

Substrate Recognition and Specificity in MAP Kinase Signaling

MAP kinases, belonging to the CMGC kinase group, are distinguished by a consensus sequence for substrate recognition, typically a serine or threonine preceding a proline. To maintain signaling precision, MAPKs have developed additional substrate-recognition strategies beyond the prototypical SP/TP motifs. Unlike cyclin-dependent kinases (CDKs), which depend on the cyclin subunit for substrate identification, MAPKs utilize auxiliary regions on their kinase domains for this purpose. Notably, the hydrophobic docking groove and the negatively charged CD-region are crucial for recognizing D-motifs, which consist of positively charged amino acids followed by hydrophobic residues in an alternating pattern. These motifs are crucial for the interaction and activation between MAP2Ks and MAPKs and are also found in MAP kinase phosphatases, regulators, and scaffolding proteins.

Cooperation of Binding Sites and Negative Feedback in MAPK Pathways

Beyond D-motifs, MAP kinases possess additional substrate-binding sites, such as the DEF site, which recognizes peptides with an FxFP consensus sequence. This site is particularly important for substrates that must selectively bind to active MAP kinases. These motifs can work in concert, as exemplified by the Elk family of transcription factors, which contain both D-motif and FxFP motifs. The FxFP motif in the KSR1 scaffold protein also renders it a substrate for ERK1/2, establishing a negative feedback loop that modulates the intensity of ERK1/2 signaling. This complex network of substrate recognition and binding ensures the specificity and regulated activity of MAP kinase signaling pathways.