A phylogenetic study of the members of the MAPK and MEK families across Viridiplantae

Abstract

Protein phosphorylation is regulated by the activity of enzymes generically known as kinases. One of those kinases is Mitogen-Activated Protein Kinases (MAPK), which operate through a phosphorylation cascade conformed by members from three related protein kinase families namely MAPK kinase kinase (MEKK), MAPK kinase (MEK), and MAPK; these three acts hierarchically. Establishing the evolution of these proteins in the plant kingdom is an interesting but complicated task because the current MAPK, MAPKK, and MAPKKK subfamilies arose from duplications and subsequent sub-functionalization during the early stage of the emergence of Viridiplantae. Here, anin silicogenomic analysis was performed on 18 different plant species, which resulted in the identification of 96 genes not previously annotated as components of the MAPK (70) and MEK (26) families. Interestingly, a deeper analysis of the sequences encoded by such genes revealed the existence of putative domains not previously described as signatures of MAPK and MEK kinases. Additionally, our analysis also suggests the presence of conserved activation motifs besides the canonical TEY and TDY domains, which characterize the MAPK family.

ICE‐SCREAM comes in different flavors: Angiosperms encode two types of ICE proteins predicted to differ in their regulation by OST1 and MPK3/6

“…MPKs in general have a highly conserved sequence in which many domains have been identified that can be used to distinguish between different groups of MPKs in green plants (González‐Coronel et al, 2021; Jonak et al, 2002 ) . Group A MPKs (to which MPK3/6 orthologs belong) were reported to be present in many plant species including the fern S. cucullata but not the lycophyte S. moelendorfii or the bryophytes P. patens and M. polymorpha ( González‐Coronel et al, 2021). Our analyses confirmed these findings; top BLAST hits with AtMPK3/6 sequence in the more primitive plants were more like group B MPKs.…”

“…We highlight separately one domain which is characteristic for Group A&B MPKs. This domain is thought to participate in the selection of the MPK substrate because it is predicted to be on the outside of the folded protein (domain 12 in González-Coronel et al, 2021). Additional recognized sequences with a proposed function are the docking motif and the activation domain.…”

Subfamily C7 Raf-like kinases MRK1, RAF26, and RAF39 regulate immune homeostasis and stomatal opening inArabidopsis thaliana

“…This activates the GTPase Ras, which then binds to and activates Raf, which serves as a MAPK kinase kinase (MKKK), phosphorylating and activating a MAPK kinase MEK, which then phosphorylates and activates a MAPK (originally named extracellular signal regulated kinase; ERK) (Terrell & Morrison, 2019). Reflecting the expansion of the protein kinase family in the plant kingdom, there are 20 MAPKs, 10 MKKs, and 80 MKKKs in Arabidopsis (González-Coronel et al , 2021) – many more than in mammals. Despite their number, very little is known about MKKKs.…”

“…Sequence homology defines three distinct subclasses known as MKKK, ZIK, and Raf-like kinases. There are 48 Raf-like kinases in Arabidopsis, divided into eleven subfamilies: B1-B4 and C1-C7 (Jonak et al , 2002; González-Coronel et al , 2021). Phylogenetic analyses indicate that plant Raf-like kinases do not cluster with metazoan MKKK or Raf kinases (Tang & Innes, 2002; Champion et al , 2004) and are considered a plant (Pl)-specific family of tyrosine kinase-like (TKL) proteins (TKL-Pl-4) (Lehti-Shiu & Shiu, 2012).…”

“…Phylogenetic analyses indicate that plant Raf-like kinases do not cluster with metazoan MKKK or Raf kinases (Tang & Innes, 2002; Champion et al , 2004) and are considered a plant (Pl)-specific family of tyrosine kinase-like (TKL) proteins (TKL-Pl-4) (Lehti-Shiu & Shiu, 2012). Despite this divergence, TKL-Pl-4 kinases share sequence features with metazoan Rafs and MLKs and therefore may function biochemically as MKKKs in MAPK cascades (Champion et al , 2004; Lehti-Shiu & Shiu, 2012; González-Coronel et al , 2021), however this has not been comprehensively studied.…”