Variation in the LRR region of Pi54 protein alters its interaction with the AvrPi54 protein revealed by in silico analysis

Abstract

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae is a destructive disease of rice and responsible for causing extensive damage to the crop. Pi54, a dominant blast resistance gene cloned from rice line Tetep, imparts a broad spectrum resistance against various M. oryzae isolates. Many of its alleles have been explored from wild Oryza species and landraces whose sequences are available in the public domain. Its cognate effector gene AvrPi54 has also been cloned from M. oryzae. Complying with the Flor’s gene-for-gene system, Pi54 protein interacts with AvrPi54 protein following fungal invasion leading to the resistance responses in rice cell that prevents the disease development. In the present study Pi54 alleles from 72 rice lines were used to understand the interaction of Pi54 (R) proteins with AvrPi54 (Avr) protein. The physiochemical properties of these proteins varied due to the nucleotide level polymorphism. The ab initio tertiary structures of these R- and Avr- proteins were generated and subjected to the in silico interaction. In this interaction, the residues in the LRR region of R- proteins were shown to interact with the Avr protein. These R proteins were found to have variable strengths of binding due to the differential spatial arrangements of their amino acid residues. Additionally, molecular dynamic simulations were performed for the protein pairs that showed stronger interaction than Pi54tetep (original Pi54 from Tetep) protein. We found these proteins were forming h-bond during simulation which indicated an effective binding. The root mean square deviation values and potential energy values were stable during simulation which validated the docking results. From the interaction studies and the molecular dynamics simulations, we concluded that the AvrPi54 protein interacts directly with the resistant Pi54 proteins through the LRR region of Pi54 proteins. Some of the Pi54 proteins from the landraces namely Casebatta, Tadukan, Varun dhan, Govind, Acharmita, HPR-2083, Budda, Jatto, MTU-4870, Dobeja-1, CN-1789, Indira sona, Kulanji pille and Motebangarkaddi cultivars show stronger binding with the AvrPi54 protein, thus these alleles can be effectively used for the rice blast resistance breeding program in future.

A genome-wide survey of interaction between rice and Magnaporthe oryzae via microarray analysis

“…There are also three NBS-LRR proteins involved in pathogen identification. The NBS-LRR domain is a typical domain of resistance genes and plays an important role in the defense against microbial invasion [ 3 ]. In addition, serine/threonine protein kinase plays an important role in disease resistance in rice.…”

“…These genes are located in the clusters of all chromosomes except Chr3. These resistance gene coding proteins have specific domains, and most of the resistance genes encode N end curly coiled-coil spiral domain, nucleotide binding sites and the C end with leucine-rich repeats (CC-NBS-LRR) [ 3 , 4 ].…”

In silico modelling and characterization of eight blast resistance proteins in resistant and susceptible rice cultivars

“…This paper sheds light on the modeling of eight hypothetical resistance proteins showing homology to the template models which are mainly involved in defense mechanisms. Similar protein modeling carried out and reported on the orthologue of Pi54 designated as Pi54of from Oryza officinalis was studied and modeled [ 8 , 47 ].…”

Design, Synthesis, Crystal Structure, and Fungicidal Activity of Two Fenclorim Derivatives

“…Colorless single crystals of compounds 6 and 7 were obtained by slowly evaporating a methanol solution containing pure compounds 6 and 7 at room temperature. Single crystal X-ray diffraction data of compounds 6 and 7 were obtained using a SuperNova, Dual, Cu at zero, AtlasS2 diffractometer (Agilent, CA, USA) equipped with MoKα radiation (λ = 1.54184 Å) at 100.00(10) K. The crystal dimensions of compounds 6 and 7 were 0.11 × 0.11 × 0.08 mm 3 and 0.14 × 0.13 × 0.12 mm 3 , respectively.…”

“…Plant diseases caused by fungi can significantly affect the growth and development of crops such as potato, soybean, and rice, and reduce the yield (20% perennial yield losses and 10% postharvest losses) of crop plants globally [1][2][3][4]. Meanwhile, fungal plant diseases also cause fresh fruit yield loss due to the shortening of storage times and secretion of fungal toxins that can damage human health [5,6].…”