Abstract
The biochemical basis behind the preferential presence and action of GmITPKs (myo-inositol—1, 3, 4 tris phosphate 5/6 kinases) in regulating the phosphorous flux towards phytate synthesis in soybean is an important, still unresolved question. In this study, context specific expression of GmITPKs in developing seeds was analysed, which found to be maximum at early stages (0–4 mm); while isozyme specificity was observed with varied dynamics till maturity. It is commonly believed that similarity at sequence level will infer similarity in structure as well, but the robust correlation between sequence and structure has not yet been proved. Hence full length coding sequences of GmITPKs were cloned and their sequence comparison revealed a low identity score of about 50% among the isoforms. Creative computational tools were employed to predict and comprehend the structural attributes and to explore the inverse correlation between the structural and sequence similarities of GmITPKs. Homology modeling of GmITPKs, their refinement and superposition validated the functional isoformic nature, with 92–97% similarity in spatial configuration. Ligand docking and energy computations showed ADP, IP6 and IP5 as possible ligands, and interactions were studied using docking and simulation. The homology models of GmITPKs were used as the starting point for nanosecond-duration molecular dynamics and were found to be stable during 20 ns simulation period. Existence of situation-specific functional basis for this isoform multiplicity, at structural and expression levels revealed to be a preferred regulatory mechanism to adapt to the metabolic fluctuations in inositol pathway during seed development.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Explore related subjects
Discover the latest articles and news from researchers in related subjects, suggested using machine learning.Abbreviations
- MIPS:
-
Myo inositol phosphate synthase
- IPK1:
-
myo-inositol 1, 3, 4, 5, 6 pentakisphosphate 2-kinase
- ITPK:
-
myo-inositol 1,3,4 tris phosphate 5/6 kinase
- IP3 :
-
myo-inositol 1, 3, 4 tris phosphate
- IP4 :
-
myo-inositol 1, 3, 4, 5/6 tetra phosphates
- RMSD:
-
Root mean square deviation
- PMDB:
-
Protein model data base
- ORF:
-
Open reading frame
- RMSF:
-
Root mean square fluctuations
References
Basak N, Krishnan V, Pandey V, Punjabi M, Hada A, Marathe A, Jolly M, Sachdev A (2017) Molecular characterization of inositol pentakisphosphate 2-kinase (GmlPk1) from soybean and its expression pattern in the developing seeds. Indian J Genet Plant Breed 77(3):371–378. https://doi.org/10.5958/0975-6906.2017.00050.5
Bhati KK, Aggarwal S, Sharma S, Mantri S, Singh SP, Bhalla S, Kaur J, Tiwari S, Roy JK, Tuli R, Pandey AK (2014) Differential expression of structural genes for the late phase of phytic acid biosynthesis in developing seeds of wheat (Triticum aestivum L.). Plant Sci 224:74–85. https://doi.org/10.1016/j.plantsci.2014.04.009
Chung SY, Subbiah S (1996) A structural explanation for the twilight zone of protein sequence homology. Structure 4(10):1123–1127. https://doi.org/10.1016/S0969-2126(96)00119-0
Courtois S, de Fromentel CC, Hainaut P (2004) p53 protein variants: structural and functional similarities with p63 and p73 isoforms. Oncogene 23(3):631. https://doi.org/10.1038/sj.onc.1206929
Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three dimensional profiles. Methods Enzymol 277:396–404. https://doi.org/10.1016/S0076-6879(97)77022-8
Field J, Wilson MP, Mai Z, Majerus PW, Samuelson J (2000) An Entamoeba histolytica inositol 1, 3, 4-trisphosphate 5/6-kinase has a novel 3-kinase activity. Mol Biochem Parasitol 108(1):119–123. https://doi.org/10.1016/S0166-6851(00)00197-3
Foulkes NS, Borjigin J, Snyder SH, Sassone-Corsi P (1997) Rhythmic transcription: the molecular basis of circadian melatonin synthesis. Trends Neurosci 20(10):487–492. https://doi.org/10.1016/S0166-2236(97)01109-0
Hunter RL, Markert CL (1957) Histochemical demonstration of enzymes separated by zone electrophoresis in starch gels. Science 125(3261):1294–1295. https://doi.org/10.1126/science.125.3261.1294-a
Krishnan V, Jain P, Vinutha T, Hada A, Manickavasagam M, Ganapathi A, Rai RD, Sachdev A (2015) Molecular modeling and ‘in-silico’ characterization of ‘Glycine max’ Inositol (1, 3, 4) tris 5/6 kinase-1 (Gmitpk1)-a potential candidate gene for developing low phytate transgenics. Plant Omics 8(5):381–391
Krishnan V, Singh A, Thimmegowda V, Singh B, Dahuja A, Rai RD, Sachdev A (2016) Low gamma irradiation effects on protein profile, solubility, oxidation, scavenger ability and bioavailability of essential minerals in black and yellow Indian soybean (Glycine max L.) varieties. J Radioanal Nucl Chem 307(1):49–57. https://doi.org/10.1007/s10967-015-4193-3
Kumar S, Krishnan V (2017) Phytochemistry and functional food: the needs of healthy life. J Phytochem Biochem 1:103
Kumari S, Jolly M, Krishnan V, Dahuja A, Sachdev A (2012) Spatial and temporal expression analysis of D-myo-inositol 3-phosphate synthase (MIPS) gene family in Glycine max. Afr J Biotechnol 11(98):16443–16454. https://doi.org/10.5897/AJB12.2811
Kumari S, Krishnan V, Jolly M, Sachdev A (2014) In vivo bioavailability of essential minerals and phytase activity during soaking and germination in soybean (‘Glycine max’ L.). Aust J Crop Sci 8(8):1168–1174
Lovell SC, Davis IW, Arendall WB III, Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Cα geometry: Φ, Ψ and Cβ deviation. Proteins 50:437–450. https://doi.org/10.1002/prot.10286
Marathe A, Krishnan V, Mahajan MM, Thimmegowda V, Dahuja A, Jolly M, Praveen S, Sachdev A (2018) Characterization and molecular modeling of Inositol 1, 3, 4 tris phosphate 5/6 kinase-2 from Glycine max (L) Merr.: comprehending its evolutionary conservancy at functional level. 3 Biotech 8(1):50. https://doi.org/10.1007/s13205-017-1076-z
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera–a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. https://doi.org/10.1002/jcc.20084
Punjabi M, Bharadvaja N, Sachdev A, Krishnan V (2018) Molecular characterization, modeling, and docking analysis of late phytic acid biosynthesis pathway gene, inositol polyphosphate 6-/3-/5-kinase, a potential candidate for developing low phytate crops. 3 Biotech 8(8):344. https://doi.org/10.1007/s13205-018-1343-7
Shi J, Wang H, Wu Y, Hazebroek J, Meeley RB, Ertl DS (2003) The maize low-phytic acid mutant lpa2 is caused by mutation in an inositol phosphate kinase gene. Plant Physiol 131(2):507–515. https://doi.org/10.1104/pp.014258
Stiles AR, Qian X, Shears SB, Grabau EA (2008) Metabolic and signaling properties of an Itpk gene family in Glycine max. FEBS Lett 582(13):1853–1858. https://doi.org/10.1016/j.febslet.2008.04.054
Suzuki M, Tanaka K, Kuwano M, Yoshida KT (2007) Expression pattern of inositol phosphate-related enzymes in rice (Oryza sativa L.): implications for the phytic acid biosynthetic pathway. Gene 405(1):55–64. https://doi.org/10.1016/j.gene.2007.09.006
Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410. https://doi.org/10.1093/nar/gkm290
Acknowledgements
The authors are thankful to ICAR for funding under National Agricultural Science Fund (NASF)—RNAi/2011. Authors also thank the Department of Biotechnology (6242-P104/RGCB/PMD/DBT/ADRO/2015), Govt. of India for the financial assistance in purchasing work station for carrying out the molecular simulation work.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that there is no conflict of interest regarding the publication of this article.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Krishnan, V., Hada, A., Marathe, A. et al. Functional characterization of GmITPK (myo-inositol: 1, 3, 4 tris phosphate 5/6 kinase) isoforms—‘so different yet so similar’. J. Plant Biochem. Biotechnol. 28, 389–396 (2019). https://doi.org/10.1007/s13562-019-00499-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13562-019-00499-y