Large-scale analysis of the N-terminal regulatory elements of the kinase domain in plant receptor-like kinase family

The N-terminal regulatory element of the kinase domain (NRE), which includes juxtamembrane segment (JM) of Receptor-like kinases (RLKs) and the N-terminal extension segment of the kinase domain in RLCKs, is the key component that regulates the activities of RLKs and RLCKs. However, their feature and functions remain largely unexplored. Herein, we perform a systematic analysis of 510,233 NRE sequences in RLKs and RLCKs from 528 plants by integrating information theory and genome-wide analysis to unravel their common characteristics and diversity. Recombinant RLKs are used to explore the structural-functional relationship of the newly-discovered motifs in vitro. Most NRE segments are around 40-80 amino acids, featuring a serine-rich region and a 14-amino-acid motif ‘FSYEELEKATBNFS’ which harbors a characteristic α-helix connecting to the core kinase domain. This α-helix suppresses FERONIA’s kinase activity. Motif discovery algorithm has identified 29 motifs with known phosphorylation sites highly conserved in RLK and RLCK classes, especially the motif ‘VGPWKpTGLpSGQLQKAFVTGVP’ in LRR-VI-2 class. The NRE phosphorylation of an LRR-VI-2 member MDIS1 modulates the auto-phosphorylation of its co-receptor MIK1, indicating NRE’s potential role as a “kinase switch” in RLK activation. Consequently, the characterization of phosphorylatable NRE motifs improves the accuracy in predicting phosphorylatable serines. Altogether, our study provides an enriched and comprehensive dataset to investigate NRE segments from individual RLKs and helps understand the underlying mechanism of action of the RLK signal transduction and kinase activation processes in plant adaptation.