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Molecular characterisation and structural assessment of an RXLR effector from Phytophthora palmivora, the coconut bud rot pathogen

Phytophthora species are phytopathogenic oomycetes that damage a wide variety of crops. Phytophthora delivers effectors, which are secretory proteins, into the host cells. Effectors promote infection by reprogramming the host cellular machinery and are key determinants of oomycete virulence. The major class of Phytophthora effector proteins contains the RXLR motif. In this study, we have carried out the molecular and structural characterisation of an RXLR effector (RXLR6744) from a virulent P. palmivora isolated from bud rot disease-affected coconut palm. The open reading frame (ORF) of the RXLR6744, amplified using RT-PCR, had a length of 411 bp. The gene was found to encode a predicted protein of 136 amino acids and had a molecular weight of 15.52 kDa. Phylogenetic analysis of the amino acid sequence revealed that it was closely related to RXLR proteins from P. palmivora (causing black pod disease in cocoa) and related species P. megakarya. Topology analysis revealed that the protein was composed of six α-helices. The structural prediction was undertaken by computer-aided homology modelling. From the Ramachandran plot analysis, it could be observed that the majority (96.3%) of amino acids were present in the preferred region, 3.7 per cent of amino acid residues were present in the allowed region, and no residues were observed in the disallowed region. The structure showed an average quality of 94.4 per cent, indicating it to be a high-quality structure. This study provides the detailed characterisation of an RXLR effector from P. palmivora. It will aid the elucidation of its role in pathogenesis and facilitate further refined investigations of the structure/function relationships of oomycete effectors.