Expression profiling and in silico homology modeling of Inositol penta kis phosphate 2-kinase, a potential candidate gene for low phytate trait in soybean.

Autor: Basak N; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.; Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India., Krishnan V; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India., Pandey V; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.; Quality and Basic Sciences Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India., Punjabi M; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India., Hada A; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India., Marathe A; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.; Biotechnology Lab, ICAR-National Institute of Biotic Stress Management, Raipur, Chattisgarh 493225 India., Jolly M; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India., Palaka BK; Centre for Bioinformatics, Pondicherry University, Puducherry, 605 014 India., Ampasala DR; Centre for Bioinformatics, Pondicherry University, Puducherry, 605 014 India., Sachdev A; Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India.
Jazyk: angličtina
Zdroj: 3 Biotech [3 Biotech] 2020 Jun; Vol. 10 (6), pp. 268. Date of Electronic Publication: 2020 May 27.
DOI: 10.1007/s13205-020-02260-y
Abstrakt: Low phytate soybeans are desirable both from a nutritional and economic standpoint. Inositol 1, 3, 4, 5, 6-penta kis phosphate 2-kinase (IPK1), optimizes the metabolic flux of phytate generation in soybean and thus shows much promise as a likely candidate for pathway regulation. In the present study, the differential spatial and temporal expression profiling of GmIpk1 and its two homologs Glyma06g03310 and Glyma04g03310 were carried out in Glycine max L. var Pusa 9712 revealing the early stages of seed development to be the potential target for gene manipulation. NCBI databank was screened using BLASTp to retrieve 32 plant IPK1 sequences showing high homology to Gm IPK1 and its homologs. Bio-computational tools were employed to predict the protein's properties, conserved domains, and secondary structures. Using state-of-the-art in silico physicochemical approach, the three-dimensional (3D) Gm IPK1 protein model (PMD ID-PM0079931), was developed based on Arabidopsis thaliana (PDB ID: 4AQK). Superimposition of 4AQK and best model of Gm IPK1 revealed that the Gm IPK1 aligned well and shows a sequence identity score of 54.32% with 4AQK and a low RMSD of 0.163 nm and almost similar structural features. The modeled structure was further refined considering the stereochemical geometry, energy and packing environment between the model and the template along with validation of its intrinsic dynamics. Molecular dynamics simulation studies of Gm IPK1 were carried out to obtain structural insights and to understand the interactive behavior of this enzyme with ligands ADP and IP 6 . The results of this study provide some fundamental knowledge on the distinct mechanistic step performed by the key residues to elucidate the structure-function relationship of Gm IPK1, as an initiative towards engineering "low phytate soybean".
Competing Interests: Conflict of interestThe authors declare that they have no conflicts of interest related to this work.
(© King Abdulaziz City for Science and Technology 2020.)
Databáze: MEDLINE
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