title: Prediction of Phenotypic Effects of Variants Observed in LOC_Os04g36720 of FRO1 Gene in Rice (Oryza sativa L.).
abstract: In rice, ferric-chelate reductase-1 (FRO1) (LOC_Os04g36720) gene was present on chromosome number 4 and its beginning and ending coordinates where coding sequence lies are 22182599 and 22186943, respectively. It plays a vital role in metal homeostasis and iron transportation in plants. Based on the alignment results, location of single-nucleotide variants is located in open reading frame and their effects of variants were predicted using SIFT sequence tool. The non-synonymous variants at position 342 and 436 lies in helical and coil parts of the protein, respectively, as predicted by Psi-pred server. PSI-Blast which resulted in significant hits and the most similar protein sequence (Accession ID: NP_001052896) with available sequence features displayed 100 % identity with query cover of 99 %. Results suggest the non-synonymous variant at position 436 (Accession ID: TBGI204002) lies in FAD-binding domain and nsSNV at position 342 (Accession ID: TBGI203998) lies in periphery of NADP. The SNPs were also analyzed for the deleterious effect by PANTHER subPSEC scores and I-mutant score, and it was postulated that SNPs would be hampering on biological as well as molecular function of FRO 1 gene of rice. A cutoff of -3 corresponds to a 50 % probability that a score is deleterious. From this, the probability that a given variant will cause a deleterious effect on protein function is estimated by Pdeleterious, such that a subPSEC score of -4 corresponds to a Pdeleteriousof 0.79. Hence, to study the phenotypic consequences of variant TBGI204002, we performed comparative molecular docking studies of native modeled protein and protein with induced mutation as receptors and FAD as ligand to be utilized for binding. The docking process was performed by AutoDock 4.2 software with Lamarckian Genetic algorithm as computational algorithm. Results suggest binding energies are higher in case of mutation-induced protein which suggests presence of variant TBGI204002 enhances binding of FAD ligand at FAD-binding domain site. In case of TBGI203998, similar comparative docking procedure was performed with FAD as binding ligand, which suggests presence of variant does not impact FAD binding at the domain site. We revealed impact of SNPs on the protein structure and its function using sequence-based tools.
authors.affiliation: Aditya Biotech Lab and Research Pvt. Ltd., Raipur, Chhattisgarh, India. dbt.rakesh@gmail.com.
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Meena
authors.affiliation: Aditya Biotech Lab and Research Pvt. Ltd., Raipur, Chhattisgarh, India.
authors.forename: Sayane
authors.initials: S
authors.lastname: Shome
authors.affiliation: Aditya Biotech Lab and Research Pvt. Ltd., Raipur, Chhattisgarh, India.
authors.forename: Sanket
authors.initials: S
authors.lastname: Thakur
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D062105:Molecular Docking Simulation; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software
chemical_list: D010940:Plant Proteins
keywords: FRO1 gene; Non-synonymous variants; PANTHER subPSEC scores and I-mutant score; Rice; Synonymous