The document summarizes research on the coat protein of the Tomato yellow leaf curl viral (TYLCV) disease, which causes significant damage to tomato crops in India. Key findings include: 1) Sequence analysis found mutations in the coat protein that provide insights into the evolutionary divergence of Indian virus isolates and their ability to systematically infect plants. 2) Structural modeling predicted the coat protein binds double-stranded DNA through interactions facilitated by surface loops and neutral patches on the protein. 3) Docking simulations showed the coat protein binds plant DNA through electrostatic and van der Waals interactions, helping the virus infect tomato and other plants.

1. Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein S. Prasanth Kumar 1 , Yogesh T. Jasrai* 1 , Himanshu A. Pandya 1 and Rakesh M. Rawal 2 1 Bioinformatics Laboratory, Department of Botany, USSC, Gujarat University, Ahmedabad- 380 009. 2 Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer & Research Institute (GCRI), Ahmedabad- 380 016. S. PRASANTH KUMAR Bioinformatics Laboratory, Department of Botany, Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA Category: ORIGINAL RESEARCH PRESENTATION

2. Tomato Leaf Curl Disease (TLCD) Tomato ( Solanum lycopersicum ) Solanaceous plant Symptoms: Yellowing of leaf lamina with upward leaf curl, Leaf distortion, Shrinking of the leaf surface and Stunted plant growth Vector: Whitefly ( Bemisia tabaci, Bemisia argentifolii) Causal agent: Tomato yellow leaf curl virus (TYLCV) Family: Geminiviridae Genera: Begomovirus Isolates: Known tropical and sub- tropical including Indian subcontinent Other hosts: Eggplant, Potato, Tobacco and Pepper Whitefly (Vector) † Tomato plant showing symptoms † Coat protein of Geminivirus* Courtesy: † U.S. Dept. of Agriculture, * Protein Databank (PDB)

3. TYLCV Indian Isolates & Disease Management SUPPRESS WHITEFLY TRANSMISSION Imidacloprid-based systemic insecticides (e.g., Admire® Pro, Provado®) PROBLEMS Significantly affects the fruiting Contaminates soil nutrients TYLCV-RESISTANT TOMATO VARIETIES (BHN Seed, Golden Valley Seed, Hazera Seed, Sakata Seed, Seminis Seed, Zeraim Gedera) PROBLEM Under stress, resistant intolerable to symptoms Disease can spread to nearby growing Solanaceous plants AVOID GROWING SOLANACEOUS PLANTS NEARBY PROBLEM Economical ? New Delhi Lucknow Varanasi Mirzapur Vadodara Bangalore TYLCV Indian Isolates

4. Objectives of the Study Examine the evolutionary background of Coat Protein from Indian strains. Study the molecular properties of coat protein facilitating its biochemical function, virulence. Learn the electronic features of coat protein essential for interaction with a spectrum of bio-molecules (ssDNA, dsDNA and virulence protein). Characterize the hotspot specific amino acid mutations in making Indian isolates, a newly emerging factor for TYLCD.

5. Methodology at a Glance TYLCV Coat protein Sequence Level Analysis NLS Signal Phylogenetic Analysis DNA binding properties Structure Level Analysis DNA binding properties Coat protein modeling Plant DNA Modeling Docking Simulation Electrostatic Interaction & Molecular Assemblage

6. Sequence Level Analysis GenBank CAA88227.1 | AAD51286.1 | AAK19178.1 | AAL26553.1 | AAL78666.1 | AAO25668.1 | AAM21566.1 | AAB08929.1 | AAA92817.1 | CAA76209.1 Sequence positions Disorder probability MSKRPADMLIFTPASKVRRR LNFDSPSVSRAAAPIVRVTKAKAWANRPM N-terminal of Coat protein (Karyophilic) DISORDERED PROFILE Disopred Nuclear Localization Signal Importin α -dependent NLS Score: 10.5 Exclude NLS for further analysis

7. Phylogenetic Analysis (Truncated for Clarity) Multiple Sequence Alignment (MSA) of Coat Protein from Indian strains Coat proteins are also conserved in their regions

8. Structure modeling of Coat Protein No close homolog having PDB data No close structural neighbor

9. Structure Validation Only 1 Outlier Ramachandran Plot (99.5 % favored model)

10. Coat Protein Active Site Prediction Active Site Prediction Server Active Site Residues: KDMHTVNSPLAIRYFCGEQ Cavity point x= 48.934 y= 58.666 z= -4.295 Volume of the Cavity = 14411 Å 3

11. Coat protein DNA binding properties Sequence-based DNA binding properties prediction

12. Coat protein DNA binding properties Structure-based DNA binding properties prediction + 63 representative DNA binding proteins Pscore = 0.31 Parea = 2102.26 A protein with Pscore > 0.12 & Parea > 250 is considered as dsDNA binding protein

13. DNA Structure Modeling Sequence : Plant DNA Conformation : Eukaryotic (B-DNA) DNA Modeling rule : Watson-Crick accounted Base-pair : 99 Base-pair parameters : Default Bending : Normal Temperature : physiological pH (7.4) Ion concentration : Mg 2+ , Na + present Cross view Lateral view

14. DNA Structure Modeling Plant DNA TYLCV Coat protein Binding energy: -264139 Kcal/mol HADDOCK score : 12.0 Kcal/mol RMSD from the overall lowest energy structure : 4.3 Å Van der Waals energy: 66.9 Kcal/mol Electrostatic energy: -827.4 Kcal/mol Desolvation energy: 125.7 Kcal/mol Buried Surface Area: 2099.6 Å 3

15. Molecular Interface Plant DNA TYLCV Coat protein Major grove of DNA Loop conformation of protein

16. Electrostatic potential at Interface Units are in Plant DNA TYLCV Coat protein Neutral patches as interface

17. Electrostatic potential of Coat protein

18. Protein family –Worldwide Isolates pfam00844: Gemini_coat Geminivirus coat protein/ nuclear export factor BR1 family

19. Evolutionary Divergence P/Q Q/H E/D Mutation Conserved residue Amino acids crucial for Systemic Infection, Particle Formation, and Insect Transmission* *Noris et al., 1998. J. Virol. 72(12): 10050–10057

20. Molecular Assemblage Molecular Assemblage built using coordinates of coat protein Coat protein Coat protein Ribbon Model Surface Model

21. Major Outcomes TYLCV Indian isolates are conserved among themselves and diverged with respect to geographical locations . Amino acid mutations in the hotspot of protein (essential for systemic infection, particle formation and insect transmission) provides signs of evolutionary divergence. Coat protein’s N-terminal is karyophilic in nature as demonstrated by NLS Signal and the member of a nuclear export family BR1 (result of Pfam annotation). This karyophilic nature is further confirmed by Disordeness peak. Coat protein beside virulence in nature, also known to interact NON-SPECIFICALLY with other viral proteins and double stranded DNA (both viral and plasmid DNA in vitro* ). *Liu et al., 1997. J. Gen. Virol 78, 1265–1270 .

22. Major Outcomes Phylogenetic analysis of coat protein revealed that Vadodara isolate is a close neighbor of Varanasi and Kello strains . We further emphasize the role of coat protein virulence in the emergence of evolutionary compatibility, distinguished new Indian species in disease prevention and the need of studies to safeguard plant biodiversity and breeding for resistant varieties. Coat protein’s neutral patches contributes in making interaction with DNA . We explored the positive patches to interact with negatively charged DNA, but it was ruled out primarily due to the geometrical constraints rather a charge-charge interaction. Sequence- and Structure- based approaches validated the DNA binding properties and are scattered throughout the protein. Loop geometrical components of coat protein plays a vital role in interacting with DNA and helical content was found to contribute for molecular assemblage

23. Major Citations Noris et al., 1998. Amino Acids in the Capsid Protein of Tomato Yellow Leaf Curl Virus That Are Crucial for Systemic Infection, Particle Formation, and Insect Transmission. J. Virol. 72(12): 10050–10057. Liu et al., 1997. Maize streak virus coat protein binds single- and double stranded DNA in vitro. J. Gen. Virol. 78, 1265–1270. Henryk Czosnek. Tomato Yellow Leaf Curl Virus Disease Management, Molecular Biology, Breeding for Resistance. Springer Verslag , ISBN 978-1-4020-4768-8 (Chap. 3 to 5). Zhang et al., 2001. Structure of the Maize Streak Virus Geminate Particle. Virol. 279, 471-477. Chakraborty et al., 2003. Tomato leaf curl Gujarat virus, a New Begomovirus Species Causing a Severe Leaf Curl Disease of Tomato in Varanasi, India. Virol. 93(12): 1485-1495. Image Courtesy : U.S. Dept. of Agriculture- Tomato disease photographs Protein Databank (PDB)-Structure coordinates

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