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Integrative homology modeling and structural analyses of Cicer arietinum phenylalanine ammonia lyase (ca PAL) with co-expressed protein trans cinnamate 4 monooxygenase (C4H1) give clues to their interaction during stress response in chickpeas

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Abstract

The sessile nature of plant makes its immune response more interesting as well as complex. The lack of mobile defender cells increases its further dependency on cellular signaling events and protein-protein interaction. Chickpea (Cicer arietinum) is an important legume crop and its production is seriously curtailed by wilt disease caused by Fusarium oxysporum f. sp. ciceris (Foc). Several attempts have been made to solve the complex metabolic signaling in this host-pathogen interplay. Reactive oxygen species and salicylic acid signaling were known to play a pivotal role in defense signaling against Foc in chickpeas. Phenylalanine ammonia lyase (PAL) is an important protein that senses the redox homoeostasis of the cell to produce salicylic acid in response to pathogenic attacks. In chickpea, although many works have been done on ROS signaling but detailed structural analysis of PAL is missing. Structural information on PAL is necessitated to gain more insight into this plant pathogen interplay. The present study focuses towards determination of physico-chemical properties, secondary organization, and tertiary structure prediction of PAL protein. The structure is validated through Ramachandran plot, Z score analysis, and energy minimization to gain the optimal structure. Finally, the interaction of PAL with other proteins was analyzed by STRING interaction map generator. Cluster analysis revealed that trans cinnamate 4 monooxygenase (C4H) is the best interactor of PAL. Further, the docking study also confirmed its interaction with PAL. This finding may be helpful for further in-depth study of these two protein entities to develop sustainable resistance in chickpeas upon Foc infection.

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Abbreviations

C4H1:

trans cinnamate 4 monooxygenase

PAL:

Phenylalanine ammonia lyase

SA:

Salicylic acid

Foc1:

Fusarium oxysporum f.sp. ciceris race 1

ROS:

Reactive oxygen species

PR1:

Pathogenesis related protein 1

GRAVY:

Grand average hydropathy

RMSD:

Root mean square deviation

PMDB:

Protein model data base

MeJA:

Methyl jasmonate

ICS1:

Isochorismate synthase 1/ chalcone synthase

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Acknowledgements

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. The author is sincerely thankful to the institutions and organizations for developing and providing access to the bioinformatics facilities to conduct the study.

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  1. Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India

    Anirban Bhar

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Bhar, A. Integrative homology modeling and structural analyses of Cicer arietinum phenylalanine ammonia lyase (ca PAL) with co-expressed protein trans cinnamate 4 monooxygenase (C4H1) give clues to their interaction during stress response in chickpeas. Vegetos (2024). https://doi.org/10.1007/s42535-024-00811-9

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