Comparison of amino acid sequence profiles and 3-D structure prediction of Coat Protein of Sweet potato feathery mottle virus (SPFMV) reveal strain variation

Authors

  • Jayanta Tarafdar
  • Swati Chakraborty
  • Manoj Kumar
  • Nayan Adhikary
  • Sarbani Das
  • Subham Dutta

Abstract

Sweet potato feathery mottle virus (SPFMV) under Potyviridae family is the most widespread disease in sweet potato (Ipomoea batatas L.) across the world and causes differential symptoms of feathery mottle and degeneration of leaves and deformed storage root. The present study highlights the enhanced molecular resolution and 3-D prediction of amino acid of coat protein of seven SPFMV strains. Viral coat protein (CP) derived from an isolate (Gene bank Accession No.HM035545 and poly protein ID D6R1L4_9POTV) BCKV, India showed close relationship with RC (Russet Crack) strain and diverged from the strains 4C, EA, S, O and K1 of SPFMV. Protein Feature View of PDB entries mapped with watermelon mosaic virus (WMV) Polyprotein (PF00767) to a UniProtKB sequence S480335 predicted structural similarities for the SPFMV strains in PDB ID 5ODV for WMV. Analysis of Nuclear Localization Signal (NLSs) and its prediction of CP sequences unveiled the key amino acids in the corresponding amino acid sequences of SPFMV strains required for systemic infection, viral particle formation and insect transmission and showed typically rich in arginine and lysine residues. SPFMV,BCKV isolate revealed a significant correlation between clustering of the viruses and geographical origin and sequence variation in coat protein gene of SPFMV from different subcontinents of the world is an interesting natural mutational phenomenon compared to the conserved coat protein domain of several plant viruses instead. Thelogenetic studies of polyprotein of SPFMV, BCKV isolate showed evolutionary compatibility with other viral taxa and a motif Asp-Ala-Gly (DAG) with the nucleotide sequence GATGCGGGA (nt 31-39) was found at the N-terminal region of coat protein (CP) gene of BCKV are same to other isolates and highly conserved domain which is required for aphid transmissibility. About 20 amino acids downstream from the DAG motif, there is a potential trypsin cleavage cited that is conserved in all potyviruses. Keywords : Sweet potato, Coat protein, SPFMV, Amino acid profile, 3-D Structure
Vol. 49 No. 2 (2023): Journal of Root Crops

Downloads

Published

2024-08-28

How to Cite

Jayanta Tarafdar, Swati Chakraborty, Manoj Kumar, Nayan Adhikary, Sarbani Das, & Subham Dutta. (2024). Comparison of amino acid sequence profiles and 3-D structure prediction of Coat Protein of Sweet potato feathery mottle virus (SPFMV) reveal strain variation. JOURNAL OF ROOT CROPS, 49(2), 10–23. Retrieved from https://journal.isrc.in/index.php/jrc/article/view/656

Issue

Vol. 49 No. 2 (2023): Journal of Root Crops

Section

Research Articles

License

Dear Author(s)

We need your written permission before we can publish your accepted article in the Journal of Root Crops.   Please read this form carefully, complete it and palace your signature below. A scanned copy of this form may be mailed to us within two days of receipt of this letter. Our email ID is: isrc_ctcri@yahoo.com  or    editor_jrc@yahoo.com  or sreekumarctcri@gmail.com 

 

Details:

In consideration of the publication in the Journal of Root Crops of our contribution entitled

(Name of the paper): .................................................................................................................

.................................................................................................................................................... by us (all Authors’ names) ..........................................................................................................

....................................................................................................................................................

 
   

 

 

A.  To be filled in if copyright belongs to you

                      I/we hereby assign to Indian Society for Root Crops, Thiruvananthapuram, India, the full copyright in all forms and media in the said contribution, including open/ restricted access to online version. They own the rights to freely grant or distribute the paper to any third party or public

    Please tick this box if you are the sole author of the paper

    Please tick this box if you are authorised to execute this copyright transfer on behalf of all the authors of the above article

 

Name (block letters): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .......

Institution/Company:..................................................................................................................

....................................................................................................................................................

Signature:.....................................................................; Date: ....................................................

 
   

 

 

B. To be filled in if copyright does not belong to you

1. Name and address of copyright holder:................................................................................

........................................................................................................................................................................................................................................................................................................

 

2. The copyright holder hereby grants Indian Society for Root Crops, Thiruvananthapuram, India the full copyright in all forms and media in the said contribution, including open/ restricted access to online version. They own the rights to freely grant or distribute the paper to any third party or public.

 

 (Signature of copyright holder or authorised agent)