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

Abstract

Background Nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes are the largest class of plant resistance genes which play an important role in the plant defense response. These genes are better conserved than others and function as a recognition-based immune system in plants through their encoded proteins. Results Here, we report the effect of Magnaporthe oryzae, the rice blast pathogen inoculation in resistant BR2655 and susceptible HR12 rice cultivars. Transcriptomic profiling was carried out to analyze differential gene expression in these two cultivars. A total of eight NBS-LRR uncharacterized resistance proteins (RP1, RP2, RP3, RP4, RP5, RP6, RP7, and RP8) were selected in these two cultivars for in silico modeling. Modeller 9.22 and SWISS-MODEL servers were used for the homology modeling of eight RPs. ProFunc server was utilized for the prediction of secondary structure and function. The CDvist Web server and Interpro scan server detected the motif and domains in eight RPs. Ramachandran plot of eight RPs confirmed that the modeled structures occupied favorable positions. Conclusions From the present study, computational analysis of these eight RPs may afford insights into their role, function, and valuable resource for studying the intricate details of the plant defense mechanism. Furthermore, the identification of resistance proteins is useful for the development of molecular markers linked to resistance genes.

In-Silico Diversity Analysis of Disease Resistant NBS-LRR Protein Variants in Oryza Sativa

“…This is consistent with literature which reports acidic I of six out of eight variants. In case of NBS-LRR3 and LRR8, our findings were not consistent with previous one because these two isoforms showed basic values (Chandrakanth et al, 2020). The molecular weights were found to be 213.008 kDa, 369.87806 kDa, 223.861 kDa, 364.19279 kDa, 253.28646 kDa, 267.58843 kDa, 308.94675kDa and 252.92825 kDa.…”

“…The values for aliphatic index were found in the range of 27.23 to 32.05 which are totally inconsistent with the values range 88.09 to 103.58 reported in previous work (Chandrakanth et al, 2020). Aliphatic index is the measure of the proportion of protein comprising of aliphatic amino acids and is directly related with thermal stability of protein (Karshikoff et al, 2015).…”

“…In present study we have selected eight, Avr effector interacting, variants of NBS-LRR resistant protein which have been reported to be associated with resistance development against Magnaporthe oryzae in two varieties of rice cultivars i.e. BR2655 and HR12 (Chandrakanth et al, 2020). Objectives of present project were the characterization of these variants at the level of 2D and 3D configuration and physicochemical properties which might be helpful in isolating these resistance imparting genes from different rice plants and engineering them into same plant thus producing rice crops with potential pathogens resistance.…”

Comparative In-silico Analysis of Structural and Functional Attributes of Microbial Lipases

“…Following the 3D structural modelling study, secondary structure and functional analysis was performed by Profunc which predicted the probable functions based on the 3D structure of the target protein (45). The secondary structure predicted by Profunc displayed the presence of α-helix, β-strands, and random coils as used in the protein modelling and characterization of eight blast resistance proteins in resistant and susceptible rice cultivars by Chandrakanth et al in order to study the intricate details of the plant defense mechanism (46). Validation of a 3D structure is a very important part of structure prediction.…”

Plant-Derived Antimicrobial Peptides Are Effective in Combating the Pathogenicity of SARS-CoV-2, a Novel Therapeutic Approach

“…Plants themselves are exposed to a variety of pathogenic microbes. In response to this, plants have developed their defenses [3], [4]. Antimicrobial peptides (AMR) were first isolated from tobacco mosaic virus-infected tobacco leaves, and there onwards, several AMPs have been isolated [5], [6].…”