Journal of Environmental Biology

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

B.B. Patnaik^1,2*, S. Baliarsingh¹, S. Sahoo³, J.M. Chung⁴, Y.S. Lee⁴, I. Nayak⁵ and J. Mohanty³ 

¹School of Biotech Sciences, Trident Academy of Creative Technology, Bhubaneswar-751 024, India

²P.G. Department of Bio-Science and Bio-technology, Fakir Mohan University, Balasore- 756 089, India

³ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar- 751 002, India

⁴School of Life Sciences and Biotechnology, College of Natural Sciences, Soonchunhyang University,  Chungnam-31538, South Korea

⁵Department of Zoology, Annamalai University, Annamalai Nagar- 608 002, India

*Corresponding Author Email : drbharatbhusan4@gmail.com

Received: 20.07.2020                                            Revised: 15.10.2020                                                                  Accepted: 30.11.2020

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.       

Key words: Hemocyanin subunit-1, In silico studies, Macrobrachium rosenbergii, Structural prediction, Transcriptome

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