Quantitative Proteomics Analysis of Sugarcane Ratoon Crop Chlorosis

Sugar Tech (2021)Cite this article

Abstract

Sugarcane is the most important sugar and bioenergy crop. Sugarcane ratoon crop chlorosis, caused by deficiencies of Fe, Ca and Mg because of low soil pH and excessive absorption of Mn, is a major crop production constraint in China and reduces cane yield as much as 40%. The molecular basis of the ratoon crop chlorosis is little understood. In this study, we employed TMT-labeling quantitative proteomics approach to study the proteins associated with sugarcane ratoon crop chlorosis using chlorotic leaves collected from the field. An in-house transcriptome database for sugarcane leaf was also constructed. From the proteome database, 7480 sugarcane proteins were identified; among them, 199 and 80 were found to be up- and down-regulated by the chlorosis. By functional characterization and protein–protein interaction studies, we were able to identify the components and pathways that might play a role in sugarcane chlorosis response. In addition to genes associated with photosynthesis, drought-responsive and jasmonic acid biosynthesis genes were also found to be associated with ratoon crop chlorosis in sugarcane. Data obtained in the presented study provide the molecular details of sugarcane ratoon crop proteome response during chlorosis.

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References

  1. Andrade, J.C., J. Terto, J.V. Silva, and C. Almeida. 2015. Expression profiles of sugarcane under drought conditions: Variation in gene regulation. Genetics and Molecular Biology 38: 465–469.

    Article  Google Scholar 

  2. Barnabas, L., R. Ashwin, A.R. Sundar, P. Malathi, and R. Viswanathan. 2015. Sugarcane proteomics: An update on current status, challenges, and future prospects. Proteomics 15 (10): 1658–1670.

    CAS  Article  Google Scholar 

  3. Baryla, A., P. Carrier, F. Franck, C. Coulomb, C. Sahut, and M. Havaux. 2001. Leaf chlorosis in oilseed rape plants (Brassica napus) grown on cadmium-polluted soil: causes and consequences for photosynthesis and growth. Planta 212: 696–709.

    CAS  Article  Google Scholar 

  4. Chen, G.F., Z. Liu, Y.Y. Huang, L.M. Xiong, Y.M. Tan, Y. Xing, and Q.Z. Tang. 2016. Factors responsible for sugarcane ratoon chlorosis in acid soil and its management in Guangxi Province of China. Sugar Tech 18 (5): 500–504.

    CAS  Article  Google Scholar 

  5. Conesa, A., S. Gotz, J.M. Garcia-Gomez, J. Terol, M. Talon, and M. Robles. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674–3676.

    CAS  Article  Google Scholar 

  6. Dal-Bianco, M., M.S. Carneiro, C.T. Hotta, R.G. Chapola, H.P. Hoffmann, A.A.F. Garcia, and G.M. Souza. 2012. Sugarcane improvement: how far can we go? Current Opinion in Biotechnology 23 (2): 265–270.

    CAS  Article  Google Scholar 

  7. Haas, B.J., A. Papanicolaou, M. Yassour, M. Grabherr, P.D. Blood, J. Bowden, M.B. Couger, D. Eccles, B. Li, M. Lieber, M.D. Macmanes, M. Ott, J. Orvis, N. Pochet, F. Strozzi, N. Weeks, R. Westerman, T. William, C. Dewey, R. Henschel, R.D. Leduc, N. Friedman, and A. Regev. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8: 1494–1512.

    CAS  Article  Google Scholar 

  8. Ham, B.K., G. Li, B.H. Kang, F. Zeng, and W.J. Lucas. 2012. Overexpression of Arabidopsis plasmodesmata germin-like proteins disrupts root growth and development. The Plant Cell 24: 3630–3648.

    CAS  Article  Google Scholar 

  9. Herbik, A., A. Giritch, C. Horstmann, R. Becker, H.J. Balzer, M. Ganal, M.G. Stephan, H. Baumlein, and U.W. Stephan. 1996. Iron and copper nutrition-dependent changes in protein expression in a tomato wild type and the nicotianamine-free mutant chloronerva. Plant Physiology 111: 533–540.

    CAS  Article  Google Scholar 

  10. Hindt, M.N., and M.L. Guerinot. 2012. Getting a sense for signals: regulation of the plant iron deficiency response. Biochimica et Biophysica Acta 1823: 1521–1530.

    CAS  Article  Google Scholar 

  11. Huang, Y.L., S. Yang, G.X. Long, Z.K. Zhao, X.F. Li, and M.H. Gu. 2016. Manganese toxicity in sugarcane plantlets grown on aciditic soils of Southern China. PLoS ONE 11 (3): e0148956.

    Article  Google Scholar 

  12. Laganowsky, A., S.M. Gomez, J.P. Whitelegge, and J.N. Nishio. 2009. Hydroponics on a chip: analysis of the Fe deficient Arabidopsis thylakoid membrane proteome. Journal of Proteomics 72: 397–415.

    CAS  Article  Google Scholar 

  13. Li, Y.R., and L.T. Yang. 2015. Sugarcane agriculture and sugar industry in China. Sugar Tech 17 (1): 1–8.

    Article  Google Scholar 

  14. Li, C., Q. Nong, M.K. Solanki, Q. Liang, J. Xie, X. Liu, Y. Li, W. Wang, L. Yang, and Y. Li. 2016. Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress. Scientific Reports 6: 25698.

    CAS  Article  Google Scholar 

  15. Lü, F., J.W. Guo, F. Yu, T.T. Zhang, S.M. Zhang, H.P. Cui, X.J. Liu, L. Chen, L.Y. Liu, S.F. Liu, and F.W. Xie. 2016. Determination of nine volatile N-nitrosamines in tobacco and smokeless tobacco products by dispersive solid-phase extraction with gas chromatography and tandem mass spectrometry. Journal of Separation Science 39 (11): 2123–2128.

    Article  Google Scholar 

  16. Miller, G.W., J.C. Pushnik, and G.W. Welkie. 1984. Iron chlorosis, a world wide problem, the relation of chlorophyll biosynthesis to iron. Journal of Plant Nutrition 7 (1–5): 1–22.

    CAS  Article  Google Scholar 

  17. Mueller, M.J. 1997. Enzymes involved in jasmonic acid biosynthesis. Physiologia Plantarum 100 (3): 653–663.

    CAS  Article  Google Scholar 

  18. Oberg, A., D. Mahoney, J.E. Eckel-Passow, C. Malone, R. Wolfinger, E.G. Hill, L.T. Cooper, O.K. Onuma, C. Spiro, T.M. Therneau, and H.R. Bergen. 2008. Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVA. Journal of Proteome Research 7: 225–233.

    CAS  Article  Google Scholar 

  19. Orosa, B., S. Üstün, L.I.A.C. Villalobos, P. Genschik, D. Gibbs, M.J. Holdsworth, E. Isono, M. Lois, M. Trujillo, and A. Sadanandom. 2020. New Phytologist 227 (4): 1028–1033.

    Article  Google Scholar 

  20. Shrivastava, A.K., M.K. Srivastava, S.P. Shukla, A. Gaur, and R. Darash. 2004. Chlorosis induced alterations in leaf laminae of sugarcane. Indian Journal of Plant Physiology 9: 429–434.

    Google Scholar 

  21. Su, Y.C., L.P. Xu, Z.Q. Wang, Q. Peng, Y.T. Yang, Y. Chen, and Y.X. Que. 2016. Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane. BMC Genomics 17 (1): 800.

    Article  Google Scholar 

  22. Szklarczyk, D., A. Franceschini, S. Wyder, K. Forslund, D. Heller, J. Huerta-Cepas, M. Simonovic, A. Roth, A. Santos, K.P. Tsafou, M. Kuhn, P. Bork, L.J. Jensen, and C. von Mering. 2015. STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research 43: D447-452.

    CAS  Article  Google Scholar 

  23. Wang, H., F. Ma, and L. Cheng. 2010. Metabolism of organic acids, nitrogen and amino acids in chlorotic leaves of ‘Honeycrisp’ apple (Malus domestica Borkh) with excessive accumulation of carbohydrates. Planta 232: 511–522.

    CAS  Article  Google Scholar 

  24. Xie, C., X. Mao, J. Huang, Y. Ding, J. Wu, S. Dong, L. Kong, G. Gao, C.Y. Li, and L. Wei. 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research 39: W316-322.

    CAS  Article  Google Scholar 

  25. Yang, F., Y.F. Shen, D.G. Camp, and R.D. Smith. 2012. High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Review of Proteomics 9 (2): 129–134.

    CAS  Article  Google Scholar 

  26. Zhang, Y., T.T. Ji, T.T. Li, Y.Y. Tian, L.F. Wang, and W.C. Liu. 2020. Jasmonic acid promotes leaf senescence through MYC2-mediated repression of CATALASE2 expression in Arabidopsis. Plant Science 199: 110604.

    Article  Google Scholar 

  27. Zhao, C., F.Q. Wang, P. Wang, H.J. Ding, X.Y. Huang, and Z.H. Shi. 2015. Early second-trimester plasma protein profiling using multiplexed isobaric tandem mass tag (TMT) labeling predicts gestational diabetes mellitus. Acta Diabetoiogica 52 (6): 1103–1112.

    CAS  Article  Google Scholar 

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Funding

This work was supported in part by National Natural Foundation of China (31360312), Guangxi Nature Science Fund (2015GXNSFDA139011), Guangxi Science and Technology Base and Talents Special Project (Guike AD17195100), National Modern Agriculture Industry Technology System of Guangxi Sugarcane Innovation Team Projects (gjnytxgxcxtd-03), and Guangxi Academy of Agricultural Sciences project (2015YM13, 2015YT03, 2016JM06).

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Affiliations

  1. Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences/ Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/ Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, 530007, China

    Ye-Geng Fan, Rong-Fa Chen, Li-Hang Qiu, Zhong-Feng Zhou, Hui-Wen Zhou, Xiu-Peng Song, Ting Luo, Prakash Lakshmanan, Xing Huang, Jian-Ming Wu & Yang-Rui Li

  2. College of Agriculture, Guangxi University, Nanning, 530005, China

    Ji-Guang Wei & Xing Huang

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  1. Ye-Geng Fan
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  2. Rong-Fa Chen
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  3. Li-Hang Qiu
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Correspondence to Xing Huang or Jian-Ming Wu or Yang-Rui Li.

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Fan, YG., Chen, RF., Qiu, LH. et al. Quantitative Proteomics Analysis of Sugarcane Ratoon Crop Chlorosis. Sugar Tech (2021). https://doi.org/10.1007/s12355-021-00952-0

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Keywords

  • Sugarcane
  • Ratoon
  • Chlorosis
  • Proteins
  • TMT-labeling quantitative proteomics