In silico characterization and expression analysis of selected Arabidopsis receptor-like kinase genes responsive to different MAMP inducers

Abstract

Candidate Arabidopsis thaliana S-domain receptor-like kinase (SD-RLK) (At1g11330, At1g61430, and At1g61610) and leucine-rich repeat receptor-like kinase (LRR-RLK) (At1g51850, At2g19190, and At5g45840) genes were characterized utilizing PlantPAN, AGRIS, and AthaMap databases. Following determination of the main conserved domains, both classes of RLKs were found to be structurally similar with extracellular, transmembrane, and intracellular domains including a serine/threonine kinase domain, which might suggest a functional role in intracellular signal transduction. This established that the RLK genes had a superficially similar structure but distinct ligand binding domains. The expressions of these genes in response to a treatment with microbe-associated molecular pattern molecules (MAMPs), namely lipopolysaccharides, flg22 peptide from flagellin, peptidoglycan, chitosan, and ergosterol were compared. The candidate RLKs, potentially involved in surveillance, were found to be responsive to the elicitation treatments. Furthermore, differential regulation that was observed at the transcriptional level as well as the intensity of responses could possibly be correlated to the promoter architecture. With the use of in silico analyses, the architectures of 1 000 bp promoter regions upstream from the transcription start sites were determined. The analyses also revealed putative defense-related cis-regulatory elements that included W-boxes, MYB factor, AP2/ERF-, GT1- and ATHB-5 binding sites. The frequency at which these cis-elements occurred in each promoter differed, and the number or clusters within the core-regulatory region of individual promoters might be indicative of the responsiveness of each gene to the MAMP elicitation.