Identification and in silico characterization of hemocyanin γ-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 γ-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 γ-type subunit protein of freshwater prawn, M rosenbergii for future studies on host defense mechanisms.