Skip to main content
SpringerLink
Log in

N-Glycoproteome Reveals That N-Glycosylation Plays Crucial Roles in Photosynthesis and Carbon Metabolism in Young Rice Leaves

  • Research Article
  • Published:
Journal of Plant Biology Aims and scope Submit manuscript

Abstract

N-Glycosylation, one of the most prominent and abundant protein post-translational modifications in eukaryotic cells, is involved in diverse biological processes. To date, large-scale profiling of the N-glycoproteome has been only reported in rice germinating embryos, but that in rice leaves has not been profiled. Here, we report the first rice N-glycoproteome in leaves, determined by combining Concanavalin A (ConA) lectin affinity chromatography enrichment and high-resolution LC–MS/MS. In total, 282 N-glycopeptides, corresponding to 556 proteins and 643 sites, were identified from the leaves of H4 (indica) and LTH (japonica). Two conserved canonical N-glycosylation motifs N-X-T and N-X-S and two more non-canonical motifs N-X-S-X-N and A-X-X-N-X-S were revealed in rice. More than 50% of the identified proteins are localized to the chloroplast, extracellular part, and plasma membrane. Bioinformatics analysis revealed that N-glycosylation occurs on proteins involved in a wide variety of biological processes, especially photosynthesis and carbon metabolism. Protein–protein interaction networks of these proteins provided further evidence that N-glycosylation contributes to a wide range of regulatory functions. In summary, these findings revealed the complexity of the rice N-glycoproteome and provided useful information to further explore the regulatory roles of N-glycosylation in the growth, development, and stress responses of rice.

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.

Institutional subscriptions

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

Similar content being viewed by others

References

  • Akmal MA, Rasool N, Khan YD (2017) Prediction of N-linked glycosylation sites using position relative features and statistical moments. PLoS ONE. https://doi.org/10.1371/journal.pone.0181966

    Article  PubMed  PubMed Central  Google Scholar 

  • Ashikari M, Sakakibara H, Lin SY, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745

    Article  CAS  Google Scholar 

  • Barba-Espin G, Dedvisitsakul P, Hagglund P, Svensson B, Finnie C (2014) Gibberellic acid-induced aleurone layers responding to heat shock or tunicamycin provide insight into the N-glycoproteome, protein secretion, and endoplasmic reticulum stress. Plant Physiol 164:951–965

    Article  CAS  Google Scholar 

  • Bause E, Hettkamp H (1979) Primary structural requirements for N-glycosylation of peptides in rat liver. FEBS Lett 108:341–344

    Article  CAS  Google Scholar 

  • Bu T, Shen J, Chao Q, Shen Z, Yan Z, Zheng H, Wang B (2017) Dynamic N-glycoproteome analysis of maize seedling leaves during de-etiolation using concanavalin A lectin affinity chromatography and a nano-LC–MS/MS-based iTRAQ approach. PLant Cell Rep 36:1943–1958

    Article  CAS  Google Scholar 

  • Cao W, Huang J, Jiang B, Gao X, Yang P (2016) Highly selective enrichment of glycopeptides based on zwitterionically functionalized soluble nanopolymers. Sci Rep. https://doi.org/10.1038/srep29776

    Article  PubMed  PubMed Central  Google Scholar 

  • Catala C, Howe KJ, Hucko S, Rose JKC, Thannhauser TW (2011) Towards characterization of the glycoproteome of tomato (Solanum lycopersicum) fruit using concanavalin A lectin affinity chromatography and LC–MALDI–MS/MS analysis. Proteomics 11:1530–1544

    Article  CAS  Google Scholar 

  • Chen R, Wang F, Tan Y, Sun Z, Song C, Ye M, Wang H, Zou H (2012) Development of a combined chemical and enzymatic approach for the mass spectrometric identification and quantification of aberrant N-glycosylation. J Proteomics 75:1666–1674

    Article  CAS  Google Scholar 

  • Cheng A, Grant CE, Noble WS, Bailey TL (2018) MoMo: discovery of statistically significant post-translational modification motifs. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty1058

    Article  PubMed  PubMed Central  Google Scholar 

  • Childs KL, Davidson RM, Buell CR (2011) Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS ONE. https://doi.org/10.1371/journal.pone.0022196

    Article  PubMed  PubMed Central  Google Scholar 

  • Contessa JN, Bhojani MS, Freeze HH, Rehemtulla A, Lawrence TS (2008) Inhibition of N-linked glycosylation disrupts receptor tyrosine kinase signaling in tumor cells. Cancer Res 68:3803–3809

    Article  CAS  Google Scholar 

  • Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372

    Article  CAS  Google Scholar 

  • Haeweker H, Rips S, Koiwa H, Salomon S, Saijo Y, Chinchilla D, Robatzek S, von Schaewen A (2010) Pattern recognition receptors require N-glycosylation to mediate plant immunity. J Biol Chem 285:4629–4636

    Article  CAS  Google Scholar 

  • Helenius A, Aebi M (2004) Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem 73:1019–1049

    Article  CAS  Google Scholar 

  • Horton P, Park K, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35S:W585–W587

    Article  Google Scholar 

  • Kaji H, Shikanai T, Sasaki-Sawa A, Wen H, Fujita M, Suzuki Y, Sugahara D, Sawaki H, Yamauchi Y, Shinkawa T, Taoka M, Takahashi N, Isobe T, Narimatsu H (2012) Large-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB. J Proteome Res 11:4553–4566

    Article  CAS  Google Scholar 

  • Kumar S, Kumar K, Pandey P, Rajamani V, Padmalatha KV, Dhandapani G, Kanakachari M, Leelavathi S, Kumar PA, Reddy VS (2013) Glycoproteome of elongating cotton fiber cells. Mol Cell Proteomics 12:3677–3689

    Article  CAS  Google Scholar 

  • Ma J, Wang D, She J, Li J, Zhu J, She Y (2016) Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis. New Phytol 212:282–296

    Article  CAS  Google Scholar 

  • Martin C, Zhang Y (2007) Mechanisms of epigenetic inheritance. Curr Opin Cell Biol 19:266–272

    Article  CAS  Google Scholar 

  • Mohnen D, Tierney ML (2011) Plants get hyp to O-glycosylation. Science 332:1393–1394

    Article  CAS  Google Scholar 

  • Mustafa G, Komatsu S (2014) Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress. Front Plant Sci. https://doi.org/10.3389/fpls.2014.00627

    Article  PubMed  PubMed Central  Google Scholar 

  • Parker BL, Palmisano G, Edwards AVG, White MY, Engholm-Keller K, Lee A, Scott NE, Kolarich D, Hambly BD, Packer NH, Larsen MR, Cordwell SJ (2011) Quantitative N-linked glycoproteomics of myocardial ischemia and reperfusion injury reveals early remodeling in the extracellular environment. Mol Cell Proteomics DO I:10. https://doi.org/10.1074/mcp.M110.006833

    Article  CAS  Google Scholar 

  • Phuc VNL, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, Mazumder R (2013) Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes. Genomics Proteomics Bioinform 11:96–104

    Article  Google Scholar 

  • Pless DD, Lennarz WJ (1977) Enzymatic conversion of proteins to glycoproteins. Proc Natl Acad Sci USA 74:134–138

    Article  CAS  Google Scholar 

  • Rose JKC, Lee S (2010) Straying off the highway: trafficking of secreted plant proteins and complexity in the plant cell wall proteome. Plant Physiol 153:433–436

    Article  CAS  Google Scholar 

  • Ruiz-May E, Hucko S, Howe KJ, Zhang S, Sherwood RW, Thannhauser TW, Rose JKC (2014) A comparative study of lectin affinity based plant N-Glycoproteome profiling using tomato fruit as a model. Mol Cell Proteomics 13:566–579

    Article  CAS  Google Scholar 

  • Ruthenburg AJ, Li H, Patel DJ, Allis CD (2007) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8:983–994

    Article  CAS  Google Scholar 

  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504

    Article  CAS  Google Scholar 

  • Song W, Mentink RA, Henquet MGL, Cordewener JHG, van Dijk ADJ, Bosch D, America AHP, van der Krol AR (2013) N-Glycan occupancy of Arabidopsis N-glycoproteins. J Proteomics 93:343–355

    Article  CAS  Google Scholar 

  • Spiro RG (2002) Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12:43R–56R

    Article  CAS  Google Scholar 

  • Strasser R (2014) Biological significance of complex N-glycans in plants and their impact on plant physiology. Front Plant Sci. https://doi.org/10.3389/fpls.2014.00363

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L (2013) N-glycoproteome of E14.Tg2a mouse embryonic stem cells. PLoS ONE 8:2. https://doi.org/10.1371/journal.pone.0055722

    Article  CAS  Google Scholar 

  • Trempel F, Kajiura H, Ranf S, Grimmer J, Westphal L, Zipfel C, Scheel D, Fujiyama K, Lee J (2016) Altered glycosylation of exported proteins, including surface immune receptors, compromises calcium and downstream signaling responses to microbe-associated molecular patterns in Arabidopsis thaliana. BMC Plant Biol. https://doi.org/10.1186/s12870-016-0718-3

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Den Steen P, Rudd PM, Dwek RA, Opdenakker G (1998) Concepts and principles of O-linked glycosylation. Crit Rev Biochem Mol 33:151–208

    Article  Google Scholar 

  • Vasudevan K, Gruissem W, Bhullar NK (2015) Identification of novel alleles of the rice blast resistance gene Pi54. Sci Rep-UK. https://doi.org/10.1038/srep15678

    Article  Google Scholar 

  • Wisniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–360

    Article  CAS  Google Scholar 

  • Xiao W, Yang Q, Wang H, Guo T, Liu Y, Zhu X, Chen Z (2011) Identification and fine mapping of a resistance gene to Magnaporthe oryzae in a space-induced rice mutant. Mol Breed 28:303–312

    Article  CAS  Google Scholar 

  • Xu S, Medzihradszky KF, Wang Z, Burlingame AL, Chalkley RJ (2016) N-Glycopeptide pofiling in Arabidopsis inflorescence. Mol Cell Proteomics 15:048–2054

    Article  Google Scholar 

  • Ying J, Zhao J, Hou Y, Wang Y, Qiu J, Li Z, Tong X, Shi Z, Zhu J, Zhang J (2017) Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS ONE 12:3. https://doi.org/10.1371/journal.pone.0173853

    Article  CAS  Google Scholar 

  • Zaia J (2008) Mass spectrometry and the emerging field of glycomics. Chem Biol 15:881–892

    Article  CAS  Google Scholar 

  • Zhu J, Sun Z, Cheng K, Chen R, Ye M, Xu B, Sun D, Wang L, Liu J, Wang F, Zou H (2014) Comprehensive mapping of protein N-glycosylation in human liver by combining hydrophilic interaction chromatography and hydrazide chemistry. J Proteome Res 13:1713–1721

    Article  CAS  Google Scholar 

  • Zielinska DF, Gnad F, Schropp K, Wisniewski JR, Mann M (2012) Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery. Mol Cell 46:542–548

    Article  CAS  Google Scholar 

  • Zielinska DF, Gnad F, Wisniewski JR, Mann M (2010) Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141:897–907

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by Open Subject of State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (Grant no. SKLCUSA-b201504), Public Welfare Research and Capacity Building Transformation Funds in Guangdong (Grant no. 2015A020209138), and the National Key Technology Research and Development Program of China (Grant no. 2016YFD0102102).

Author information

Authors and Affiliations

  1. National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People’s Republic of China

    Jiafeng Wang, Hui Wen, Ming Li, Tao Guo & Chun Chen

Authors
  1. Jiafeng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hui Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ming Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tao Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chun Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

CC designed the experiments; JFW, HW, ML, and TG performed the experiments; JFW analyzed the data and wrote the manuscript. All the authors agreed on the final submission and posted no conflicting interest.

Corresponding author

Correspondence to Chun Chen.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, J., Wen, H., Li, M. et al. N-Glycoproteome Reveals That N-Glycosylation Plays Crucial Roles in Photosynthesis and Carbon Metabolism in Young Rice Leaves. J. Plant Biol. 63, 165–175 (2020). https://doi.org/10.1007/s12374-020-09243-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12374-020-09243-9

Keywords

Search

Navigation