Identification and in silico characterization of hemocyanin gamma-type subunit protein in Vibrio harveyi infected freshwater prawn, Macrobrachium rosenbergii

Abstract

Aim: Identification of full-length ORF of hemocyanin subunit-1 (Mr_HC_1) from the hepatopancreas transcriptome of freshwater prawn, Macrobrachium rosenbergii infected with Vibrio harveyi and characterization of its sequence and structure by in silico tools and softwares. Methodology: Illumina HiSeq and de novo assembled unigenes were scanned against PANM-DB to screen Mr_HC_1. FGENESH gene prediction and SMART programs were used to predict the ORF region. Subsequently, Clustal X2 and MEGA in-silico tools were used to understand the sequence relatedness and evolutionary status of Mr_HC_1. Structural prediction was performed by SWISS-MODEL and Ramachandran plot modeling programs. Results: The full-length ORF was 1983 bp in length encoding a polypeptide of 661 amino acid residues. Mr_HC_1 showed a putative signal peptide of 21 amino acid residues at the N-terminus and three hemocyanin domains. Homology analysis of Mr_HC_1 amino acid sequence confirms maximum identity to M. nipponense hemocyanin subunit-1 (Mn_HC_1). Phylogenetic analysis showed that Mr_HC_1 is more closely related to the hemocyanin.-type subunit of freshwater shrimps. Homology modeling of Mr_ HC_1 showed homo-hexameric protein containing 12 copper ions. With a QMEAN score of-3.33 and model-template sequence identity of 59.15%, the predicted model of Mr_HC_1 is convincing. Interpretation: This study characterizes the hemocyanin gamma-type subunit protein of freshwater prawn, M. rosenbergii for future studies on host defense mechanisms.