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Isolation, Characterization, and Structure Analysis of a Non-TIR-NBS-LRR Encoding Candidate Gene from MYMIV-Resistant Vigna mungo

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Abstract

Yellow mosaic disease of Vigna mungo caused by Mungbean yellow mosaic India virus (MYMIV) is still a major threat in the crop production. A candidate disease resistance (R) gene, CYR1 that co-segregates with MYMIV-resistant populations of V. mungo has been isolated. CYR1 coded in silico translated protein sequence comprised of 1,176 amino acids with coiled coil structure at the N-terminus, central nucleotide binding site (NBS) and C-terminal leucine-rich repeats (LRR) that belongs to non-TIR-NBS-LRR subfamily of plant R genes. CYR1 transcript was unambiguously expressed during incompatible plant virus interactions. A putative promoter-like sequence present upstream of this candidate gene perhaps regulates its expression. Enhanced transcript level upon MYMIV infection suggests involvement of this candidate gene in conferring resistance against the virus. In silico constructed 3D models of NBS and LRR regions of this candidate protein and MYMIV-coat protein (CP) revealed that CYR1-LRR forms an active pocket and successively interacts with MYMIV-CP during docking, like that of receptor–ligand interaction; indicating a critical role of CYR1 as signalling molecule to protect V. mungo plants from MYMIV. This suggests involvement of CYR1 in recognizing MYMIV-effector molecule thus contributing to incompatible interaction. This study is the first stride to understand molecular mechanism of MYMIV resistance.

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Acknowledgments

We are thankful to the Director, Bose Institute for providing us the lab facilities and for a senior research fellowship to S.M. We also thank the Department of Biotechnology, India, for the financial assistance (Sanction no. BT/01/COE/06/03) and for granting a RAship to S.P.

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  1. Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VIIM, Kolkata, 700054, India

    Soumitra Maiti, Sujay Paul & Amita Pal

  2. Center for Genomic Sciences, National Autonomous University of Mexico, Morelos, Mexico

    Sujay Paul

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Correspondence to Amita Pal.

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12033_2011_9488_MOESM1_ESM.tif

Supplementary Fig. 1: RLM-RACE products. 5′RP represents the nested 5′ RACE product (a) and 3′RP represents the 3′ RACE product (b), M = molecular weight marker (100 bp + 1.5 kb). (TIFF 5069 kb)

12033_2011_9488_MOESM2_ESM.tif

Supplementary Fig. 2: NCBI-Conserved domain search result of CYR1. Domain search result shows presence of the NB-ARC domain and leucine rich repeats (TIFF 3102 kb)

12033_2011_9488_MOESM3_ESM.tif

Supplementary Fig. 3: Secondary structure of CYR1 protein of Vigna mungo predicted through GorIV server. Predicted secondary structure of CYR1 revealed alpha helix, extended strand and random coil regions represented by blue, red and pink colour bars, respectively. (TIFF 753 kb)

Supplementary Fig. 4: PROSA energy plot calculated for the CYR1-NBS homology model. (TIFF 1856 kb)

12033_2011_9488_MOESM5_ESM.tif

Supplementary Fig. 5: PROSA Z-score value. PROSA Z-score value calculated for the CYR1-NBS homology model is -3.7, as shown by arrow. (TIFF 1640 kb)

12033_2011_9488_MOESM6_ESM.tif

Supplementary Fig. 6: The receptor–ligand interaction between CYR1-LRR and MYMIV-CP predicted by GRAMM-X and represented in surface structure using PyMol. (TIFF 8069 kb)

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Maiti, S., Paul, S. & Pal, A. Isolation, Characterization, and Structure Analysis of a Non-TIR-NBS-LRR Encoding Candidate Gene from MYMIV-Resistant Vigna mungo . Mol Biotechnol 52, 217–233 (2012). https://doi.org/10.1007/s12033-011-9488-1

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