Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement

Abstract

Biotic stress is a major cause of heavy loss in grape productivity. In order to develop biotic stress-resistant grape varieties, the key defense genes along with its pathway have to be deciphered. In angiosperm plants, lipase-like protein phytoalexin deficient 4 (PAD4) is well known to be essential for systemic resistance against biotic stress. PAD4 functions together with its interacting partner protein enhanced disease susceptibility 1 (EDS1) to promote salicylic acid (SA)-dependent and SA-independent defense pathway. Existence and structure of key protein of systemic resistance EDS1 and PAD4 are not known in grapes. Before SA pathway studies are taken in grape, molecular evidence of EDS1: PAD4 complex is to be established. To establish this, EDS1 protein sequence was retrieved from NCBI and homologous PAD4 protein was generated using Arabidopsis thaliana as template and conserved domains were confirmed. In this study, computational methods were used to model EDS1 and PAD4 and simulated the interactions of EDS1 and PAD4. Since no structural details of the proteins were available, homology modeling was employed to construct three-dimensional structures. Further, molecular dynamic simulations were performed to study the dynamic behavior of the EDS1 and PAD4. The modeled proteins were validated and subjected to molecular docking analysis. Molecular evidence of stable complex of EDS1:PAD4 in grape supporting SA defense pathway in response to biotic stress is reported in this study. If SA defense pathway genes are explored, then markers of genes involved can play pivotal role in grape variety development especially against biotic stress leading to higher productivity.

Keywords:

• biotic stress
• EDS1
• grape
• GROMACS
• molecular dynamics simulation
• PAD4
• salicylic acid pathway
• systemic resistance

Acknowledgement

Authors are thankful to authorities of ICAR for creation of national facility: Advanced Supercomputing Hub for Omics Knowledge in Agriculture (ASHOKA) at our centre.

Additional information

Funding

This work was supported by World Bank through National Agricultural Innovation Project (Establishment of National Agriculture Bioinformatics Grid in ICAR) under the grant [30(68)/2009/Bio-Informatics/NAIP/O&M dated 31st March, 2010] of Indian Council of Agricultural Research (ICAR), New Delhi, Ministry of Agriculture, Government of India.