Amplification, Cloning and In silico Prediction of Full Length Elicitin Gene from Phytophthora capsici, the Causal Agent of Foot Rot Disease of Black Pepper

Abstract

Elicitins are a family of small proteins secreted by Phytophthora, which induce leaf necrosis in infected plants. Here, we report the cloning of Elicitin gene from P. capsici, an Oomycete plant pathogen which causes significant damage to a broad range of host plants. Elicitin sequence was amplified using primers designed from the known Elicitin genes of other Phytophthora organisms based on their conserved motifs. The PCR amplified product size of 256 bp length and the BLAST analysis of the sequenced product showed perfect match with alpha-elicitin sequences of P. capsici. Subsequently, attempt was made to characterize the complete gene of elicitin from genome sequence information of P. capsici, by querying the amplified product against the genome. Local BLAST search against full genome identified entire coding sequence. Further sequence analysis identified promoter sequence, transcription start site, a leader signal sequence and a core elicitin domain, with a conserved 6 Cysteine residues. In addition, the three dimensional structure of capsicein was modelled, and the binding affinity of sterol and capsicein was studied using molecular docking. The developed model predicted strong binding affinity for Tyr 47.