Bioinformatic analysis and molecular characterization of ethylene-responsive transcription factor RAP2-12 from olive

Abstract

Ethylene-responsive transcription factorRAP2-12is associatedwith ethylene-response, activation of hypoxic gene and hypoxiatolerance of plants. Under normal aerobic conditions it localizesto the plasma membrane but under hypoxia conditions it accu-mulates in the nucleus. It expresses in leaves, seedlings, seeds andflowers. By far, there is no report describingRAP2-12gene inolive (OeRAP2-12). In this study, we aimed to gather informa-tion about ethylene-responsive transcription factor OeRAP2-12.Nucleotide BLAST (to find the similarity of genes in differentorganisms), protein BLAST (BLASTp and BLASTx to find thesimilarity of proteins in different organisms), BioEdit (to buildthe predicted protein, to prepare a hydropathy graph, to preparegraphs of amino acid composition and nucleotide composition),Phylogenetic analysis (to make phylogenetic trees from thenucleotide sequence and from the predicted amino acidsequence), ExPASY software (to find isoelectric point and molec-ular mass of the predicted protein), SWISS-MODEL (to buildpredicted three-dimensional protein), STRING (to find protein-protein interactions and protein similarities) and Primer3 (todesign primers) program were utilized to conduct the analyses.BLAST analyses revealedOeRAP2-12had a diverse sequenceamong other plants. Amino acid composition analysis revealedOeRAP2-12 has 392 amino acids. Its calculated molecular massis 43.1 kDa and calculated theoretical isoelectric point (pI) is4.69. OeRAP2-12 protein is rich in serine and asparagines andtherefore presents a hydrophilic character. Primers to amplify thefull lengthOeRAP2-12were designed using Primer3 software.Phylogenetic analyses based on nucleotide and amino acidsequences revealed genetic trees that grouped plants based on OeRAP2-12.OeRAP2-12sequences from different olive cultivarsare being obtained to determine its polymorphism among olivecultivars. Analyses and studies about gene’s functions are stillcontinuing.