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Characterization of a Novel Glutelin Subunit OsGluBX by the Experimental Approach and Molecular Dynamics Simulations

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Abstract

Rice glutelin is a multi-subunit storage protein and has high nutritional value. However, many glutelin subunits are still not identified by experiment approach. In this study, a novel subunit (OsGluBX) was discovered by sequence alignment in the UniProtKB database. And then, the OsGluBX of rice from japonica cv. Nipponbare and indica cv. 9311 were cloned and expressed in Escherichia coli system and further identified by Western blotting. The total storage proteins were extracted from the grains of Nipponbare and 9311, and the native OsGluBX were identified. The novel OsGluBX subunit was classified into the subfamily B based on its high homology to the subfamily B members and their immunoblotting identification against the subfamily-specific antibody. Furthermore, two-dimensional electrophoresis analysis showed similarity and difference of the entire glutelin profiles between the two subspecies. Moreover, the atomic coordinate of the OsGluBX was constructed based on homology modeling approach and refined by molecular dynamics simulations. The spatial conformation of the OsGluBX protein was stable during the simulation, and the obvious hydrogen bonds were observed to maintain the integrity and stability of the β-sheets region of the OsGluBX. Research into this novel OsGluBX subunit has improved our understanding of the glutelin family in rice.

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Abbreviations

1-D:

One-dimensional

2-D:

Two-dimensional

Cα RMSD:

α-Carbon root-mean-square deviation

CBB:

Coomassie brilliant blue

ER:

Endoplasmic reticulum

MD:

Molecular dynamics

MW:

Molecular weight

PAGE:

Polyacrylamide gel electrophoresis

PB:

Protein body

PI:

Isoelectric point

PME:

Particle-mesh Ewald

PSV:

Protein storage vacuole

SDS:

Sodium dodecyl sulfate

VDW:

van der Waals

References

  1. Adachi, M., Kanamori, J., Masuda, T., Yagasaki, K., Kitamura, K., Mikami, B., & Utsumi, S. (2003). Crystal structure of soybean 11S globulin: Glycinin A3B4 homohexamer. Proceedings of the National Academy of Sciences of the United States of America, 100, 7395–7400.

    Article  CAS  Google Scholar 

  2. Shewry, P. R., & Halford, N. G. (2002). Cereal seed storage proteins: structures, properties and role in grain utilization. Journal of Experimental Botany, 53, 947–958.

    Article  CAS  Google Scholar 

  3. Katsube-Tanaka, T., Iida, S., Yamaguchi, T., & Nakano, J. (2010). Capillary electrophoresis for analysis of microheterogeneous glutelin subunits in rice (Oryza sativa L.). Electrophoresis, 31, 3566–3572.

    Article  CAS  Google Scholar 

  4. Ufaz, S., & Galili, G. (2008). Improving the content of essential amino acids in crop plants: goals and opportunities. Plant Physiology, 147, 954–961.

    Article  CAS  Google Scholar 

  5. Motoyama, T., Maruyama, N., Amari, Y., Kobayashi, K., Washida, H., Higasa, T., Takaiwa, F., & Utsumi, S. (2009). α' Subunit of soybean β-conglycinin forms complex with rice glutelin via a disulphide bond in transgenic rice seeds. Journal of Experimental Botany, 60, 4015–4027.

    Article  CAS  Google Scholar 

  6. Shewry, P. R. (2007). Improving the protein content and composition of cereal grain. Journal of Cereal Science, 46, 239–250.

    Article  CAS  Google Scholar 

  7. Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T., Fujii, Y., Antonio, B. A., Nagamura, Y., Imanishi, T., Ikeo, K., Itoh, T., Gojobori, T., & Sasaki, T. (2006). The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Research, 34, 741–744.

    Article  Google Scholar 

  8. Qu, L., Xing, Y., Liu, W., Xu, X., & Song, Y. (2008).Expression pattern and activity of six glutelin gene promoters in transgenic rice. Journal of Experimental Botany, 59, 2417–2424.

    Article  CAS  Google Scholar 

  9. Kawakatsu, T., Yamamoto, M., Hirose, S., Yano, M., & Takaiwa, F. (2008). Characterization of a new rice glutelin gene GluD-1 expressed in the starchy endosperm. Journal of Experimental Botany, 59, 4233–4245.

    Article  CAS  Google Scholar 

  10. Katsube-Tanaka, T., Duldulao, J. B. A., Kimura, Y., Iida, S., Yamaguchi, T., Nakano, J., & Utsumi, S. (2004). The two subfamilies of rice glutelin differ in both primary and higher-order structures. BBA Proteins Proteom, 1699, 95–102.

    Article  CAS  Google Scholar 

  11. Takagi, H., Hiroi, T., Hirose, S., Yang, L., & Takaiwa, F. (2010). Rice seed ER-derived protein body as an efficient delivery vehicle for oral tolerogenic peptides. Peptides, 31, 1421–1425.

    Article  CAS  Google Scholar 

  12. Tandang-Silvas, M. R. G., Fukuda, T., Fukuda, C., Prak, K., Cabanos, C., Kimura, A., Itoh, T., Mikami, B., Utsumi, S., & Maruyama, N. (2010). Conservation and divergence on plant seed 11S globulins based on crystal structures. BBA Proteins Proteom, 1804, 1432–1442.

    Article  CAS  Google Scholar 

  13. Borght, A. V. D., Vandeputte, G. E., Derycke, V., Brijs, K., Daenen, G., & Delcour, J. A. (2006). Extractability and chromatographic separation of rice endosperm proteins. Journal of Cereal Science, 44, 68–74.

    Article  Google Scholar 

  14. Khan, N., Katsube-Tanaka, T., Iida, S., Yamaguchi, T., Nakano, J., & Tsujimoto, H. (2008). Identification and variation of glutelin alpha polypeptides in the genus Oryza assessed by two-dimensional electrophoresis and step-by-step immunodetection. Journal of Agricultural and Food Chemistry, 56, 4955–4961.

    Article  CAS  Google Scholar 

  15. Wakasa, Y., Yang, L., Hirose, S., & Takaiwa, F. (2009). Expression of unprocessed glutelin precursor alters polymerization without affecting trafficking and accumulation. Journal of Experimental Botany, 60, 3503–3511.

    Article  CAS  Google Scholar 

  16. Wang, S., Zhang, Y., Liu, H., He, Y., Yan, J., Wu, Z., & Ding, Y. (2012). Molecular cloning and functional analysis of a recombinant ribosome-inactivating protein (alpha-momorcharin) from Momordica charantia. Applied Microbiology and Biotechnology, 96, 939–950.

    Article  Google Scholar 

  17. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28, 235–242.

    Article  CAS  Google Scholar 

  18. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.

    Article  Google Scholar 

  19. Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. Journal of the American Chemical Society, 118, 11225–11236.

    Article  CAS  Google Scholar 

  20. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103, 8577–8593.

    Article  CAS  Google Scholar 

  21. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684–3690.

    Article  CAS  Google Scholar 

  22. Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38.

    Article  CAS  Google Scholar 

  23. Team, R. D. C. (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria.

  24. May, A. C. W. (2002). Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies. Protein Science, 11, 2825–2835.

    Article  CAS  Google Scholar 

  25. Zhang, Y., Baaden, M., Yan, J., Shao, J., Qiu, S., Wu, Y., & Ding, Y. (2010). The molecular recognition mechanism for superoxide dismutase presequence binding to the mitochondrial protein import receptor Tom20 from Oryza sativa involves an LRTLA motif. The Journal of Physical Chemistry. B, 114, 13839–13846.

    Article  CAS  Google Scholar 

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Acknowledgments

This research was supported by the National Basic Research Program (973) of China (2013CB126900) and the National Natural Science Foundation of China (NSFC 30971740), the key project of Hubei Province Natural Science Foundation (2011002923388), and the China Postdoctoral Science Foundation (20100480914).

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China

    Ying He, Yubo Zhang, Shuzhen Wang & Yi Ding

  2. Crop Physiology and Production Center, Key Laboratory of Huazhong Crop Physiology, Ecology and Production, Ministry of Agriculture, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China

    Ying He & Hanlai Zeng

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  1. Ying He
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  2. Yubo Zhang
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  3. Shuzhen Wang
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Correspondence to Hanlai Zeng or Yi Ding.

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He, Y., Zhang, Y., Wang, S. et al. Characterization of a Novel Glutelin Subunit OsGluBX by the Experimental Approach and Molecular Dynamics Simulations. Appl Biochem Biotechnol 169, 1482–1496 (2013). https://doi.org/10.1007/s12010-012-0058-1

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  • DOI: https://doi.org/10.1007/s12010-012-0058-1

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