Insilico structural modeling of normal and mutated subunits of ADP-glucose pyrophosphorylase from Triticum aestivum to study protein-protein interactions
DOI:
https://doi.org/10.14719/pst.2701Keywords:
AGPase, homology modeling, Secondary Structure, small and large subunits, docking, T.aestivumAbstract
ADP-glucose pyrophosphorylase is a heterotetrameric enzyme with pairs of large subunits (LS) and small subunits (SS) involved in starch biosynthesis. The increase in grain yield and plant biomass is brought about by the deregulation of endosperm. Thus, AGPase has attracted widespread interest in improving starch content in crop improvement. The data herein conclusively shows that mutation insertion involved in conformational changes is responsible for the decrease in a pocket in the mutated subunit. This type of conformational change might be beneficial for better protein-protein interaction. The present study is aimed to model and compare the structure of normal and mutatedlarge subunits of wheat AGPase to studytheir structural differences. Mutations by insertion are involved in conformational changes that are responsible for the decrease in the pocket in the mutated subunit. Such conformational changes are often beneficial to study PPI (protein-protein interactions). Further investigations were carried out using docking studies to gain insight into interaction. Based on these studies, it may be suggested that such type of mutationsare usually beneficial for starch production in wheat which is considered one of the significant Indian food crops.
Downloads
References
Calderini DF, Castillo FM, Arenas MA, Molero G, Reynolds MP, Craze M et al. Overcoming the trade-off between grain weight and number in wheat by the ectopic expression of expansin in developing seeds leads to increased yield potential. New Phytol. 2021; 230(2):629-40. doi: 10.1111/nph.17048.
Kumar R, Mukherjee S, Ayele BT. Molecular aspects of sucrose transport and its metabolism to starch during seed development in wheat: A comprehensive review. Biotechnol Adv. 2018;36:pp. 954-67. 10.1016/j.biotechadv.2018.02.015.
Altemimi AB. Extraction and optimization of potato starch and its application as a stabilizer in yogurt manufacturing. Foods. 2018;7:14. doi: 10.3390/foods7020014.
Precha-atsawanan S, Puncha-arnon S, Wandee Y. Physicochemical properties of partially debranched waxy rice starch. Food Hydrocol. 2018;79:71-80. 10.1016/j.foodhyd.2017.12.014.
Singh N, Jiwani G, Rocha LS, Mazaheri R. Bioagents and volatile organic compounds: An emerging control measures for rice bacterial diseases. Bacterial Diseases of Rice and Their Management. 2023 May 5;255-74. https://doi.org/10.1201/9781003331629.
Singh N, Pandey R, Chandraker SK, Pandey S, Malik S, Patel D. Use of wild edible plants can meet the needs of future generation. In:Agro-biodiversity and Agri-ecosystem Management. Singapore: Springer Nature Singapore. 2022 Jul 16;pp. 341-66. https://doi.org/10.1007/978-981-19-0928-3_18.
Apriyanto A, Compart J, Fettke J. A review of starch, a unique biopolymer - Structure, metabolism and in planta modifications. Plant Sci. 2022;318:111223. doi: 10.1016/j.plantsci..111223
Srivastava RP, Kumar S, Singh L, Madhukar M, Singh N, Saxena G et al. Major phenolic compounds, antioxidant, antimicrobial and cytotoxic activities of Selinumcarvifolia (L.) collected from different altitudes in India. Frontiers in Nutrition. 2023;10. 10.3389/fnut.2023.1180225.
Dixit P, Singh N, Singh L, Srivastava RP, Pandey S, Singh S et al. Screening for the biochemical profile and biological activity in Cephalotaxusand Taxus collected from North-Eastern Himalayas. ACS Agricultural Science and Technology. 2023 Jul 18;3(8):694-700. https://doi.org/10.1021/acsagscitech.3c00126
MacNeill GJ, Mehrpouyan S, Minow MAA, Patterson JA, Tetlow IJ, Emes MJ. Starch as a source, starch as a sink: The bifunctional role of starch in carbon allocation. J Exp Bot. 2017; 68:4433-53. doi: 10.1093/jxb/erx291
Cho YG, Kang KK. Functional analysis of starch metabolism in plants. Plants. 2020;9:p. 1152. 10.3390/plants9091152
Huang L, Tan H, Zhang C, Li Q, Liu Q. Starch biosynthesis in cereal endosperms: an updated review over the last decade. Plant Commun. 2021;2: Article 100237. 10.1016/J.XPLC.2021.100237
Sahu N, Singh N, Arya KR, Reddy SS, Rai AK, Shukla V et al. Assessment of the dual role of Lyonia ovalifolia (Wall.) Drude in inhibiting AGEs and enhancing GLUT4 translocation through LC-ESI-QTOF-MS/MS determination and in silico studies. Frontiers in Pharmacology. 2023 Mar 27;14:1073327. https://doi.org/10.3389/fphar.2023.1073327/
Ferrero DML, Diez MD, Kuhn ML, Falaschetti CA, Piattoni CV, Iglesias AA et al.On the roles of wheat endosperm ADP-glucose pyrophosphorylase subunits. Front Plant Sci. 2018;9:1498. https://doi.org/10.3389/fpls.2018.01498
Hwang SK, Singh S, Maharana J, Kalita S, Tuncel A, Rath T et al. Mechanism underlying heat stability of the rice endosperm cytosolic ADP-glucose pyrophosphorylase. Front Plant Sci. 2019; 10:70. https://doi.org/10.3389/fpls.2019.00070
Sun H, Li J, Song H, Yang D, Deng X, Liu J et al. Comprehensive analysis of AGPase genes uncovers their potential roles in starch biosynthesis in lotus seed. BMC Plant Biol. 2020; 20:1-15. 10.1186/S12870-020-02666-Z.
Gadewar M, Prashanth GK, Babu MR, Dileep MS, Prashanth PA, Rao S et al. Unlocking nature's potential: Green synthesis of ZnO nanoparticles and their multifaceted applications- A concise overview. Journal of Saudi Chemical Society. 2023 Nov 25; 101774. https://doi.org/10.1016/j.jscs.2023.101774.
Kim KH, Kim JY. Understanding wheat starch metabolism in properties, environmental stress condition and molecular approaches for value-added utilization. Plants (Basel). 2021;25:10(11):2282. doi: 10.3390/plants10112282. PMID: 34834645; PMCID: PMC8624758.
Begcy K, Sandhu J, Walia H. Transient heat stress during early seed development primes germination and seedling establishment in rice. Front Plant Sci. 2018;9:1768. doi: 10.3389/fpls.2018.01768.
Goel S, Singh M, Grewal S, Razzaq A, Wani SH. Wheat proteins: a valuable resources to improve nutritional value of bread. Frontiers in Sustainable Food Systems. 2021 Nov 17;5:769681. https://doi.org/10.3389/fsufs.2021.769681
Molero G, Joynson R, Pinera-Chavez FJ, Gardiner LJ, Rivera-Amado C, Hall A, Reynolds MP. Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential. Plant Biotechnol J. 2019;17:1276-88. https://doi.org/10.1111/pbi.13052
Rivera-Amado C, Trujillo-Negrellos E, Molero G, Reynolds MP, Sylvester-Bradley R, Foulkes MJ. Optimizing dry-matter partitioning for increased spike growth, grain number and harvest index in spring wheat. Field Crops Res. 2019;240:154-67. https://doi.org/10.1016/j.fcr.2019.04.016.
Quintero A, Molero G, Reynolds MP, Calderini DF. Trade-off between grain weight and grain number in wheat depends on G×E interaction: A case study of an elite CIMMYT panel (CIMCOG). European J Agro. 2018;92:17-29.DOI: 10.1016/j.eja.2017.09.007
Rajak BK, Rani P, Singh N, Singh DV. Sequence and structural similarities of ACCase protein of Phalaris minor and wheat: An insight to explain herbicide selectivity. Frontiers in Plant Science. 2023a Jan 4;13:1056474. https://doi.org/10.3389/fpls.2022.1056474
Rajak BK, Rani P, Mandal P, Chhokar RS, Singh N, Singh DV. Emerging possibilities in the advancement of herbicides to combat acetyl-CoA carboxylase inhibitor resistance. Front Agron. 2023b;5(1218824):10-3389. doi: 10.3389/fagro.2023.1218824.
Griffiths S, Wingen L, Pietragalla J, Garcia G, Hasan A, Miralles D et al. Genetic dissection of grain size and grain number trade-offs in CIMMYT wheat germplasm. PLoS ONE. 2015; 10: e0118847. https://doi.org/10.1371/journal.pone.0118847.
Malik C, Dwivedi S, Rabuma T, Kumar R, Singh N, Kumar A et al. De novo sequencing, assembly and characterization of Asparagus racemosus transcriptome and analysis of expression profile of genes involved in the flavonoid biosynthesis pathway. Frontiers in Genetics. 2023;14. 10.3389/fgene.2023.1236517.
Brinton J, Simmonds J, Minter F, Leverington-Waite M, Snape J, Uauy C. Increased pericarp cell length underlies a major quantitative trait locus for grain weight in hexaploid wheat. New Phytol. 2017;215(3):1026-38. doi: 10.1111/nph.14624. Epub 2017 Jun 2. PMID: 28574181.
Wang W, Simmonds J, Pan Q, Davidson D, He F, Battal A et al. Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. Theor Appl Genet. 2018;131(11):2463-75. doi: 10.1007/s00122-018-3166-7.
Sahariah P, Bora J, Malik S, Syiem D, Bhan S, Hussain A et al. Therapeutic potential of Dillenia indica L. in attenuating hyperglycemia-induced oxidative stress and apoptosis in alloxan-administered diabetic mice. Frontiers in Bioscience-Landmark. 2023 May 26;28(5):105. https://doi.org/10.31083/j.fbl2805105.
Tillett BJ, Hale CO, Martin JM, Giroux MJ. Genes impacting grain weight and number in wheat (Triticum aestivum L. ssp. aestivum). Plants (Basel). 2022;4:11(13):1772. doi: 10.3390/plants11131772.
Zhang Y, Li D, Zhang D, Zhao X, Cao X, Dong L et al. Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits. Plant J. 2018;94(5):857-66. doi: 10.1111/tpj.13903.
Downloads
Published
Versions
- 16-07-2024 (2)
- 06-07-2024 (1)
How to Cite
Issue
Section
License
Copyright (c) 2024 Saroj Rani, Aanchal Gupta, Deepshikha Kaushik, Sarvesh Rustagi, Sumira Malik, Rajesh Yogi, Nitesh Singh
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright and Licence details of published articles
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
Open Access Policy
Plant Science Today is an open access journal. There is no registration required to read any article. All published articles are distributed under the terms of the Creative Commons Attribution License (CC Attribution 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited (https://creativecommons.org/licenses/by/4.0/). Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
