Plant LRR-RLKs structure

In plants, the leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are composed of an extracellular LRR domain (ECD) responsible for ligand binding, a single membrane-spanning helix (TM), and a cytoplasmic kinase domain (KD). The extracellular LRR motifs share canonical plant specific LRR consensus sequences (CS): LxxLxLxxNxL(s/t)GxLPxxLGxLxx (x represents any amino acid), where the LxxLxLxxNxL(s/t)GxLP segments are the plant-specific LRR highly conserved segment (HCS).

The Phyto-LRR prediction program

Since the program is based on the position specific scoring matrix (PSSM) algorithm and its training dataset are 4000 LRR motifs HCSs from LRR-RLKs of 17 land plant species (Tab. 1), this plant LRR prediction program could identify plant LRRs effectively, especially for LRR motifs in plant LRR-RLKs. The program also has an offline version in the form of a python package, which has been published on PyPI: https://pypi.org/project/predict-phytolrr/.

The database of the plant LRR repeats

In this database, a total of 55457 LRR motifs were identified from 3987 LRR-RLK genes in 17 represented land plants (Tab. 1) using the "Phyto-LRR-predict" program, which is freely accessible at the Predict LRRs page. The sequence second structure and the soluble accessibility were obtained from the SSpro and ACCpro20 programs in the SCRATCH suite (Magnan CN & Baldi P., 2014). Moreover, since the ectodomains are heavily asparagine-linked (N-) glycosylated, the database also integrated with the predicted canonical N-glycosylation sites (Asn-x-Ser/Thr (x ≠ Pro)).

Table 1: Number of LRR-RLK genes in 17 represented land plants

Species Five Digit Code Number of LRR-RLKs
Amborella trichopoda AMBTR 108
Arabidopsis lyrata ARALY 207
Arabidopsis thaliana ARATH 213
Brachypodium distachyon BRADI 222
Brassica rapa BRARA 273
Glycine max GLYMA 424
Marchantia polymorpha MARPL 102
Medicago truncatula MEDTR 316
Oryza sativa ssp. Indica ORYSI 287
Oryza sativa ssp. Japonica ORYSJ 281
Phoenix dactylifera PHODC 149
Physcomitrella patens PHYPA 162
Populus trichocarpa POPTR 373
Selaginella moellendorffii SELML 138
Solanum lycopersicum SOLLC 213
Solanum tuberosum SOLTU 291
Zea mays MAIZE 228
Total 3987