Skip to main content
SpringerLink
Log in

Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Key message

Our results not only provide a comprehensive overview of the starch biosynthetic pathway in the developing endosperm but also reveal some important protein markers that regulate the synthesis of starch.

Abstract

In human diets, rice (Oryza sativa L.) is an important source of starch, a substantial amount of which is accumulated in developing endosperm. A better understanding of the complicated pathways involved in starch biosynthesis is needed to improve the yield and quality of rice and other cereal crops through breeding. One pure line rice mutant, SA0419, was induced from a wild-type rice, TNG67, by sodium azide mutagenesis; therefore, TNG67 and SA0419 share the same genetic background. SA0419 is, however, a unique glutinous rice with a lower amylose content (8%) than that of TNG67 (20%), and the grains of SA0419 develop earlier and faster than those of TNG67. In this study, we used a comparative proteomic analysis to identify the differentially expressed proteins that may explain the differences in starch biosynthesis and the characteristics of TNG67 and SA0419. A gel-based proteomic approach was applied to profile the expressed proteome in the developing endosperm of these two rice varieties by nano-LC/MS/MS. Several over-expressed proteins were found in SA0419, such as plastidial ADP-glucose pyrophosphorylase (AGPase), phosphoglucomutase (PGM), pyrophosphate–fructose 6-phosphate 1-phosphotransferase (PFP), 6-phosphofructokinase (PFK), pyruvate phosphate dikinase (PPDK), starch branching enzymes (SBE) and starch debranching enzyme (SDBE), with those proteins mainly being involved in the pathways of starch metabolism and PPDK-mediated gluconeogenesis. Those over-expressed enzymes may contribute to the relatively early development, similar starch accumulation and rapid grain filling of SA0419 as compared with TNG67. This study provides a detailed biochemical description of starch biosynthesis and related information regarding a unique starch mutant that may assist future research efforts to improve the yield and quality of grain and starch in rice through breeding.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Abe N, Asai H, Yago H, Oitome NF, Itoh R, Crofts N, Nakamura Y, Fujita N (2014) Relationships between starch synthase I and branching enzyme isozymes determined using double mutant rice lines. BMC Plant Biol 14:80

    Article  PubMed  PubMed Central  Google Scholar 

  • Ahmed Z, Tetlow IJ, Ahmed R, Morell MK, Emes MJ (2015) Protein-protein interactions among enzymes of starch biosynthesis in high-amylose barley genotypes reveal differential roles of heteromeric enzyme complexes in the synthesis of A and B granules. Plant Sci 233:95–106

    Article  CAS  PubMed  Google Scholar 

  • Asai H, Abe N, Matsushima R, Crofts N, Oitome NF, Nakamura Y, Fujita N (2014) Deficiencies in both starch synthase IIIa and branching enzyme IIb lead to a significant increase in amylose in SSIIa-inactive japonica rice seeds. J Exp Bot 65:5497–5507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ballicora MA, Dubay JR, Devillers CH, Preiss J (2005) Resurrecting the ancestral enzymatic role of a modulatory subunit. J Biol Chem 280:10189–10195

    Article  CAS  PubMed  Google Scholar 

  • Barrell D, Dimmer E, Huntley RP, Binns D, O’Donovan C, Apweiler R (2009) The GOA database in 2009—an integrated gene ontology annotation resource. Nucleic Acids Res 37:D396–D403

    Article  CAS  PubMed  Google Scholar 

  • Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  CAS  PubMed  Google Scholar 

  • Chirgwin JM, Przybyla AE, Macdonald RJ, Ratter WJ (1979) Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18:5294–5299

  • Dauvillée D, Chochois V, Steup M, Haebel S, Eckermann N, Ritte G, Ral JP, Colleoni C, Hicks G, Wattebled F, Deschamps P, d’Hulst C, Liénard L, Cournac L, Putaux JL, Dupeyre D, Ball SG (2006) Plastidial phosphorylase is required fornormal starch synthesis in Chlamydomonas reinhardtii. Plant J 48:274–285

    Article  PubMed  Google Scholar 

  • Fageria NK (2007) Yield physiology of rice. J Plant Nutr 30:843–879

    Article  CAS  Google Scholar 

  • Fujita N, Hasegawa H, Taira T (2001) The isolation and characterization of a waxy mutant of diploid wheat (Triticum monococcum L.). Plant Sci 160:595–602

    Article  CAS  PubMed  Google Scholar 

  • Geigenberger P (2011) Regulation of starch biosynthesis in response to a fluctuating environment. Plant Physiol 155:1566–1577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geigenberger P, Kolbe A, Tiessen A (2005) Redox regulation of carbon storage and partitioning in response to light and sugars. J Exp Bot 56:1469–1479

    Article  CAS  PubMed  Google Scholar 

  • Glawischnig E, Gierl A, Tomas A, Bacher A, Eisenreich W (2002) Starch biosynthesis and intermediary metabolism in maize kernels. Quantitative analysis of metabolite flux by nuclear magnetic resonance. Plant Physiol 130:1717–1727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Görg A, Obermaier C, Boguth G, Weiss W (1999) Recent developments in two-dimensional gel electrophoresis with immobilized pH gradients: wide pH gradients up to pH 12, longer separation distances and simplified procedures. Electrophoresis 20:712–717

    Article  PubMed  Google Scholar 

  • Hanashiro I, Itoh K, Kuratomi Y, Yamazaki M, Igarashi T, Matsugasako J, Takeda Y (2008) Granule-bound starch synthase I is responsible for biosynthesis of extra-long unit chains of amylopectin in rice. Plant Cell Physiol 49:925–933

    Article  CAS  PubMed  Google Scholar 

  • Hannah LC, James M (2008) The complexities of starch biosynthesis in cereal endosperms. Curr Opin Biotechnol 19:160–165

    Article  CAS  PubMed  Google Scholar 

  • Hennen-Bierwagen TA, Lin Q, Grimaud F, Planchot V, Keeling PL, James MG, Myers AM (2009) Proteins from multiple metabolic pathways associate with starch biosynthetic enzymes in high molecular weight complexes: a model for regulation of carbon allocation in maize amyloplasts. Plant Physiol 149:1541–1559

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hwang SK, Nishi A, Satoh H, Okita TW (2010) Rice endosperm-specific plastidial alpha-glucanphosphorylase is important for synthesis of short-chain malto-oligosaccharides. Arch Biochem Biophys 495:82–92

    Article  CAS  PubMed  Google Scholar 

  • Jeng TL, Tseng TH, Wang CS, Chen CL, Sung JM (2003) Starch biosynthesizing enzymes in developing grains of ricecultivar Tainung 67 and its sodium azide-induced rice mutant. Field Crop Res 84:261–269

    Article  Google Scholar 

  • Jeng TL, Tseng TH, Wang CS, Chen CL, Sung JM (2006) Nitro-blue tetrazolium staining of starch-synthesizing enzymes in developing rice grains. J Sci Food Agric 86:666–674

    Article  CAS  Google Scholar 

  • Jeng TL, Wang CS, Tseng TH, Sung JM (2007) Expression of granule-bound starch synthase in developing rice grain. J Sci Food Agric 87:2456–2463

    Article  CAS  Google Scholar 

  • Jeon JS, Ryoo N, Hahn TR, Walia H, Nakamura Y (2010) Starch biosynthesis in cereal endosperm. Plant Physiol Biochem 48:383–392

    Article  CAS  PubMed  Google Scholar 

  • Keeling PL, Myers AM (2010) Biochemistry and genetics of starch synthesis. Annu Rev Food Sci Technol 1:271–303

    Article  CAS  PubMed  Google Scholar 

  • Li QF, Zhang GY, Dong ZW, Yu HX, Gu MH, Sun SS, Liu QQ (2009) Characterization of expression of the OsPUL gene encoding a pullulanase-type debranching enzyme during seed development and germination in rice. Plant Physiol Biochem 47:351–358

    Article  CAS  PubMed  Google Scholar 

  • Lin Q, Huang B, Zhang M, Zhang X, Rivenbark J, Lappe RL, James MG, Myers AM, Hennen-Bierwagen TA (2012) Functional interactions between starch synthase III and isoamylase-type starch-debranching enzyme in maize endosperm. Plant Physiol 158:679–692

    Article  CAS  PubMed  Google Scholar 

  • Liu F, Makhmoudova A, Lee EA, Wait R, Emes MJ, Tetlow IJ (2009) The amylose extender mutant of maize conditions novel protein-protein interactions between starch biosynthetic enzymes in amyloplasts. J Exp Bot 60:4423–4440

    Article  CAS  PubMed  Google Scholar 

  • Liu CW, Chang TS, Hsu YK, Wang AZ, Yen HC, Wu YP, Wang CS, Lai CC (2014) Comparative proteomic analysis of early salt stress responsive proteins in roots and leaves of rice. Proteomics 14:1759–1775

    Article  PubMed  Google Scholar 

  • Rabilloud T, Carpentier G, Tarroux P (1988) Improvement and simplification of low-background silver staining of proteins by using sodium dithionite. Electrophoresis 9:288–291

    Article  CAS  PubMed  Google Scholar 

  • Ramesh M, Ali SZ, Bhattacharya KR (1999) Structure of rice starch and its relation to cooked-rice texture. Carbohydr Polym 38:337–347

    Article  CAS  Google Scholar 

  • Satoh H, Shibahara K, Tokunaga T, Nishi A, Tasaki M, Hwang SK, Okita TW, Kaneko N, Fujita N, Yoshida M, Hosaka Y, Sato A, Utsumi Y, Ohdan T, Nakamura Y (2008) Mutation of the plastidial alpha-glucanphosphorylase gene in rice affects the synthesis and structure of starch in the endosperm. Plant Cell 20:1833–1849

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sokolov LN, Dominguez-Solis JR, Allary AL, Buchanan BB, Luan S (2006) A redox-regulated chloroplast protein phosphatase binds to starch diurnally and functions in its accumulation. Proc Natl Acad Sci USA 103:9732–9737

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Streb S, Delatte T, Umhang M, Eicke S, Schorderet M, Reinhardt D, Zeeman SC (2008) Starch granule biosynthesis in Arabidopsis is abolished by removal of all debranching enzymes but restored by the subsequent removal of an endoamylase. Plant Cell 20:3448–3466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tetlow IJ, Morell MK, Emes MJ (2004a) Recent developments in understanding the regulation of starch metabolism in higher plants. J Exp Bot 55:2131–2145

    Article  CAS  PubMed  Google Scholar 

  • Tetlow IJ, Wait R, Lu Z, Akkasaeng R, Bowsher CG, Esposito S, Kosar-Hashemi B, Morell MK, Emes MJ (2004b) Protein phosphorylation in amyloplasts regulates starch branching enzyme activity and protein-protein interactions. Plant Cell 16:694–708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D, Wang Y, Yu J, Gu M, Li J (2007) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765

    Article  Google Scholar 

  • Yamakawa H, Hakata M (2010) Atlas of rice grain filling-related metabolism under high temperature: joint analysis of metabolome and transcriptome demonstrated inhibition of starch accumulation and induction of amino acid accumulation. Plant Cell Physiol 51:795–809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yun MS, Umemoto T, Kawagoe Y (2011) Rice debranching enzyme isoamylase 3 facilitates starch metabolism and affects plastid morphogenesis. Plant Cell Physiol 52:1068–1082

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeeman SC, Thorneycroft D, Schupp N, Chapple A, Weck M, Dunstan H, Haldimann P, Bechtold N, Smith AM, Smith SM (2004) Plastidial alpha-glucanphosphorylase is not required for starch degradation in Arabidopsis leaves but has a role in the tolerance of abiotic stress. Plant Physiol 135:849–858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeeman SC, Kossmann J, Smith AM (2010) Starch: its metabolism, evolution, and biotechnological modification in plants. Annu Rev Plant Biol 61:209–234

    Article  CAS  PubMed  Google Scholar 

  • Zhout Z, Robards K, Helliwell S, Blanchard C (2002) Ageing of stored rice: changes in chemical and physical attributes. J Cereal Sci 35:65–78

    Article  Google Scholar 

Download references

Acknowledgements

The study was funded by a Grant (#MOST-102-2113-M-005-001-MY3) from the Ministry of Science and Technology, R.O.C.

Author information

Author notes

  1. Tao-Shan Chang and Chih-Wei Liu have contributed equally to this work.

Authors and Affiliations

  1. Institute of Molecular Biology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, 40227, Taiwan, Republic of China

    Tao-Shan Chang, Chih-Wei Liu, Chao-Yi Li, Min-Wei Chien & Chien-Chen Lai

  2. Department of Agronomy, National Chung Hsing University, 250, Kuo-Kuang Rd., Taichung, Taiwan, Republic of China

    Yu-Ling Lin, Arthur Z. Wang & Chang-Sheng Wang

  3. Graduate institute of Chinese Medical Science, China Medical University, Taichung, 40402, Taiwan, Republic of China

    Chien-Chen Lai

Authors
  1. Tao-Shan Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chih-Wei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yu-Ling Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chao-Yi Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Arthur Z. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Min-Wei Chien
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chang-Sheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chien-Chen Lai
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: C-SW, C-CL; data curation: T-SC, C-WL; formal analysis: T-SC, C-WL, AZW, M-WC, C-SW and C-CL; funding acquisition: C-CL; investigation: T-SC, C-WL, Y-LL, C-YL, AZW, M-WC, C-SW and C-CL; methodology: T-SC, C-WL, AZW, C-SW and C-C; project administration: C-SW, C-CL; resources: T-SC, C-WL, C-SW, C-CL; supervision: C-SW, C-CL; validation: T-SC, Y-LL, C-YL, C-SW, C-CL; visualization: T-SC, C-WL, and C-CL; writing (original draft preparation): T-SC, C-WL and C-CL; writing (review and editing): T-SC, C-SW and C-CL. All authors made substantive intellectual contributions to the present study and approved the final manuscript.

Corresponding authors

Correspondence to Chang-Sheng Wang or Chien-Chen Lai.

Ethics declarations

Conflict of interest

The authors declare no financial or commercial conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 786 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chang, TS., Liu, CW., Lin, YL. et al. Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS. Plant Mol Biol 95, 333–343 (2017). https://doi.org/10.1007/s11103-017-0652-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11103-017-0652-2

Keywords

Search

Navigation