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Uncovering the Interaction Interface Between Harpin (Hpa1) and Rice Aquaporin (OsPIP1;3) Through Protein–Protein Docking: An In Silico Approach

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Abstract

Hpa1 (a type of harpin) is involved in T3SS (Type III Secretion System) assembly in the infection mechanism by Xanthomonas Oryzae pv. oryzae (Xoo). Hpa1 interacts with the plasma membrane components of plants thereby assisting effector proteins toward the cytoplasm, wherein effectors execute their pathological functions. Independently, harpins also induce hypersensitive response and systemic acquired resistance in plants. However, lack of knowledge regarding the plant–harpin interaction mechanism constrains the pathway of its agricultural application. Although an in vitro study proved that Hpa1 protein can interact with OsPIP1;3, a rice aquaporin, the structural basis of the interaction is yet to be discovered. The presented work is the first of its kind where an in silico approach is used for the PPI (protein–protein interaction) of harpin protein. The study discovered participation of Hpa1 N-terminal amino acids at the interface. Besides, MD simulation studies were performed to assess the stability. RMSD values were 0.35 ± 0.049, 0.73 ± 0.11, and 0.50 ± 0.065 nm for OsPIP1;3, Hpa1, and Hpa1-OsPIP1;3 complex, respectively. Additionally, Residue-wise fluctuations have also been studied post-MDS. Taken together, these findings not only give a solid foundation for a deeper knowledge of various interacting target molecules with Harpin protein orthologs but also bring a new avenue for the structural–functional relationship study of harpin proteins.

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Abbreviations

HR:

Hypersensitive response

SAR:

Systemic acquired resistance

T3SS:

Type III translocation system

Xoo :

Xanthomonas oryzae pv. Oryzae

BB:

Bacterial blight

LRR-RLK:

Leucine-rich repeat receptor-like serine/threonine kinases

GRAVY:

Grand average of hydropathicity

I-TASSER:

Iterative Threading Assembly Refinement

C-score:

Confidence score

CASTp:

Computed Atlas of Surface Topography of protein

HADDOCK program:

High Ambiguity Driven protein–protein DOCKing

AIRs:

Ambiguous interaction restraints

RMSD:

Root mean square deviation

TM score:

Template modeling score

SUB-Y2H:

Split-ubiquitin yeast two-hybrid

BiFC:

Bimolecular fluorescence complementation

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Authors and Affiliations

  1. Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India

    Jaimini Patoliya, Khushali Thaker & Rushikesh Joshi

  2. Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India

    Khushbu Rabadiya

  3. Gujarat Biotechnology University, Gandhinagar, Gujarat, 382355, India

    Dhaval Patel

  4. Department of Life Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India

    Nayan K. Jain

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Patoliya, J., Thaker, K., Rabadiya, K. et al. Uncovering the Interaction Interface Between Harpin (Hpa1) and Rice Aquaporin (OsPIP1;3) Through Protein–Protein Docking: An In Silico Approach. Mol Biotechnol 66, 756–768 (2024). https://doi.org/10.1007/s12033-023-00690-6

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