In silico characterization, molecular docking, and dynamic simulation of a novel fungal cell-death suppressing effector, MoRlpA as potential cathepsin B-like cysteine protease inhibitor during rice blast infection

Abstract

The blast fungus Magnaporthe oryzae is one of the most notorious pathogens affecting rice production worldwide. The cereal killer employs a special class of small secreted proteins called effectors to manipulate and perturb the host metabolism. In turn, the host plants trigger effector-triggered immunity (ETI) via localized cell death and hypersensitive response (HR). We have identified and characterized a novel secreted effector MoRlpA from M. oryzae by extensive in silico methods. The localization studies suggested that it is exclusively secreted in the host apoplasts. Interestingly, MoRlpA interacts with a protease, cathepsin B from rice with highest affinity. The 3D structural models of both the proteins were generated. Cathepsin B-like cysteine proteases are usually involved in programmed cell death (PCD) and autophagy in plants which lead to generation of HR upon infection. Our results suggest that MoRlpA interacts with rice cathepsin B-like cysteine protease and demolish the host counter-attack by suppressing cell death and HR during an active blast infection. This was further validated by molecular docking and molecular dynamic simulation analyses. The important residues involved in the rice-blast pathogen interactions were deciphered. Overall, this research highlights stable interactions between MoRlpA-OsCathB during rice blast pathogenesis and providing an insight into how this novel RlpA protease inhibitor-cum-effector modulates the host’s apoplast to invade the host tissues and establish a successful infection. Thus, this research will help to develop potential fungicide to block the binding region of MoRlpA target so that the cryptic pathogen would be recognized by the host.

HIGHLIGHTS

• For the first time, a novel secreted effector protein, MoRlpA has been identified and characterised from M. oryzae in silico

• MoRlpA contains a rare lipoprotein A-like DPBB domain which is often an enzymatic domain in other systems

• MoRlpA as an apoplastic effector interacts with the rice protease OsCathB to suppress the cell death and hypersensitive response during rice blast infection

• The three-dimensional structures of both the MoRlpA and OsCathB proteins were predicted

• MoRlpA-OsCathB interactions were analysed by molecular docking and molecular dynamic simulation studies

Communicated by Ramaswamy H. Sarma

Keywords:

• Rare lipoprotein A
• molecular docking
• MD simulations
• effector-protease interaction
• hypersensitive response
• cell-death suppression

Disclosure statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Author contributions

Conceptualization of the research by NS; protocol designed by DS, investigation and data analysis performed by DS and SM; DS, SM, and NS designed the manuscript; DS, SM, KG, and NS wrote the paper and NS critically reviewed the manuscript. The manuscript was approved by all authors.

Additional information

Funding

This work was supported by the Science and Engineering Research Board (SERB), Department of Science & Technology (DST), Government of India [Grant No. SRG/2019/001681] provided to NS. Used infrastructure supported by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, New Delhi under the DBT-BUILDER programme [BT/INF/22/SP45088/2022] provided to DLS, PU, Kolkata is gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.