Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.).

Yudi Zang,Guiqin Qu,Yanping Song,Zongyan Sun,Di Chen,Qiaoli Zhang,Yuetong Yi

doi:10.3390/genes11101186

Abstract

The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum L.). In this study, 11 SlWAK and 18 SlWAKL genes were identified in an uneven distribution in 9 of 12 chromosomes. GUB-WAK-bind (wall-associated receptor kinase galacturonan-binding) and epidermal growth factor (EGF) domains appear more often in SlWAK proteins. However, more SlWAKLs (wall-associated kinase like) have a WAK-assoc (wall-associated receptor kinase C-terminal) domain. Based on their phylogenetic relationships, 29 SlWAK-RLKs (wall associated kinase-receptor like kinases) were clustered into three distinct categories analogous to those in Arabidopsis thaliana. High similarities were found in conserved motifs of the genes within each group. Cis-elements in the promoter region of these 29 genes were found mainly in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), anaerobic, light, wound, and MYB transcription factors. Public tomato genome RNA-seq data indicates that multiple SlWAK-RLKs showed different expression patterns under developmental and ripening stages of fruits, such as SlWAK4, SlWAKL11, SlWAKL9, SlWAKL15, SlWAKL14, and SlWAKL1, their RPKM (Reads Per Kilo bases per Million reads) value constantly increases during the fruit expansion period, and decreases as the fruit matures. In tomato leaves, our RNA-seq data showed that nine SlWAK-RLKs transcripts (SlWAK3, SlWAK4, SlWAK10, SlWAKL1, SlWAKL2, SlWAKL3, SlWAKL5, SlWAKL14, and SlWAKL18) were significantly induced (p < 0.001), and three transcripts (SlWAK2, SlWAK5, and SlWAKL15) were significantly inhibited (p < 0.001) under mechanical wounding. The qRT-PCR (Quantitative reverse transcription polymerase chain reaction) of SlWAKL1 and SlWAKL6 verify these results.

Highlights

Plants are constantly challenged by various biotic and abiotic stresses, causing severe dehydration of plant cell and irreversible damage, which causes substantial losses in the yield and quality of a crop [1].To survive and multiply in the changing environment, plants have formed a sophisticated and intricateGenes 2020, 11, 1186; doi:10.3390/genes11101186 www.mdpi.com/journal/genesGenes 2020, 11, 1186 signal transmission network to regulate their own growth and development
This study aimed to provide a comprehensive view of the wall-associated kinase (WAK)-receptor-like protein kinases (RLKs) genes in tomato and to identify members involved in the development and ripening of tomato as well as the wounding response
18 SlWAKL (Supplementary Table S4) proteins with typical Kinase domain were obtained based on the BLASTp search against the tomato genome database

Summary

Introduction

Plants are constantly challenged by various biotic and abiotic stresses, causing severe dehydration of plant cell and irreversible damage, which causes substantial losses in the yield and quality of a crop [1].To survive and multiply in the changing environment, plants have formed a sophisticated and intricateGenes 2020, 11, 1186; doi:10.3390/genes11101186 www.mdpi.com/journal/genesGenes 2020, 11, 1186 signal transmission network to regulate their own growth and development. Transmembrane sensing signaling proteins are the main regulators in this signaling pathway They can sense extracellular signals and pass them into intracellular signal-responsive molecules to make plants respond . There is a class of proteins on the cell surface that sense and transmit signals in animals, called receptor tyrosine kinases (RTKs). The molecular structure and function of transmembrane signaling proteins in plants are similar to those of animal RTKs, the extracellular signaling molecules or ligands that bind to them have not been identified, so they are called receptor-like protein kinases (RLKs). As receptors for signaling molecules, they can sense external environmental stimuli, participate in intracellular signal transmission processes and play important roles in plant growth, development, and communication between plants and environment [4]

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