Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.)

Horticulture Research

Volumn 5, Issue 1, 2018, Pages

  Xie, Yang ^a   Xu, Liang ^a   Wang, Yan ^a   Fan, Lianxue ^a   Chen, Yinglong ^b   Tang, Mingjia ^a   Luo, Xiaobo ^a   Liu, Liwang ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85054125237     PISSN: None     EISSN: 20527276     Source Type: Journal    
DOI: 10.1038/s41438-018-0057-7     Document Type: Article

References (48)

1. Lu, Z. L. et al. Analysis and evaluation of nutritional quality in Chinese radish (Raphanus sativus L.). Agric. Sci. China 7, 823–830 (2008).
2. Curtis, I. S. The noble radish: past, present and future. Trends Plant Sci. 8, 305–307 (2003).
3. Ishida, M., Kakizaki, T., Ohara, T. & Morimitsu, Y. Development of a simple and rapid extraction method of glucosinolates from radish roots. Breed. Sci. 61, 208–211 (2011).
4. Li, G. F. et al. Study on molecular tracking and bioactivity of glucocerebroside isolated from radish (Raphanus sativus L.). J. Food Nutr. Res. 2, 914–917 (2014).
5. You, H. et al. The effect of radish sourced 4-(methylthio)-3-butenyl isothiocyanate on ameliorating the severity of high fat diet inducted nonalcoholic fatty liver disease in rats. Int. J. Clin. Exp. Med. 8, 15910–15919 (2015).
6. Zaki, H. E. M., Takahata, Y. & Yokoi, S. Analysis of the morphological and anatomical characteristics of roots in three radish (Raphanus sativus L.) cultivars that differ in root shape. J. Hortic. Sci. Biotechnol. 87, 172–178 (2012).
7. Jang, G. et al. Cytokinin-dependent secondary growth determines root biomass in radish (Raphanus sativus L.). J. Exp. Bot. 66, 4607–4619 (2015).
8. Wang, Y. et al. De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. BMC Genomics 14, 836 (2013).
9. Yu, R. G. et al. Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.). BMC Plant Biol. 15, 30 (2015).
10. Kitashiba, H. et al. Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res. 21, 481–490 (2014).
11. Mitsui, Y. et al. The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci. Rep. 5, 10835 (2015).
12. Jeong, Y. M. et al. Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes. Theor. Appl. Genet. 129, 1357–1372 (2016).
13. Yu, R. G. et al. De novo taproot transcriptome sequencing and analysis of major genes involved in sucrose metabolism in radish (Raphanus sativus L.). Front. Plant Sci. 7, 585 (2016).
14. Yu, R. G. et al. Transcriptome profiling of taproot reveals complex regulatory networks during taproot thickening in Radish (Raphanus sativus L.). Front. Plant Sci. 7, 1210 (2016).
15. Ndimba, B. K., Chivasa, S., Simon, W. J. & Slabas, A. R. Identification of Arabidopsis salt and osmotic stress responsive proteins using two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 5, 4185–4196 (2005).
16. Agrawal, L. et al. Comparative proteomics of tuber induction, development and maturation reveal the complexity of tuberization process in potato (Solanum tuberosum L.). J. Proteome Res. 7, 3803–3817 (2008).
17. Lee, J. J. et al. A comparative study of proteomic differences between pencil and storage roots of sweetpotato (Ipomoea batatas (L.) Lam.). Plant Physiol. Biochem. 87, 92–101 (2015).
18. Folgado, R. et al. Unravelling the effect of sucrose and cold pretreatment on cryopreservation of potato through sugar analysis and proteomics. Cryobiology 71, 432–441 (2015).
19. Wiese, S., Reidegeld, K. A., Meyer, H. E. & Warscheid, B. Protein labeling by ITRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 7, 340–350 (2007).
20. Wang, Y. et al. Functional and integrative analysis of the proteomic profile of radish root under Pb exposure. Front. Plant Sci. 7, 1871 (2016).
21. Owiti, J. et al. iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration. Plant J. 67, 145–156 (2011).
22. Yang, Y. et al. Evaluation of different multidimensional LC-MS/MS pipelines for isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis of potato tubers in response to cold storage. J. Proteome Res. 10, 4647–4660 (2011).
23. Liu, B. L. et al. Proteomic changes during tuber dormancy release process revealed by iTRAQ quantitative proteomics in potato. Plant Physiol. Biochem. 86, 181–190 (2015).
24. Chu, P. et al. iTRAQ-based quantitative proteomics analysis of Brassica napus leaves reveals pathways associated with chlorophyll deficiency. J. Proteomics 113, 244–259 (2015).
25. Marion, M. B. 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 (1976).
26. Wu, J. X. et al. An integrative analysis of the transcriptome and proteome of the pulp of a spontaneous late-ripening sweet orange mutant and its wild type improves our understanding of fruit ripening in citrus. J. Exp. Bot. 65, 1651–1671 (2014).
27. Chang, H. et al. iTRAQ-based proteomic analysis of myofibrillar contents and relevant synthesis and proteolytic proteins in soleus muscle of hibernating Daurian ground squirrels (Spermophilus dauricus). Proteome Sci. 14, 16 (2016).
28. Zhang, L. L. et al. Proteins differentially expressed during limonene biotransformation by Penicillium digitatum DSM 62840 were examined using iTRAQ labeling coupled with 2D-LC–MS/MS. J. Ind. Microbiol. Biotechnol. 43, 1481–1495 (2016).
29. Meng, Q. G. et al. iTRAQ-based proteomic study of the effects of Spiroplasma eriocheiris on Chinese mitten crab Eriocheir sinensis hemocytes. Fish Shellfish Immunol. 40, 182–189 (2014).
30. 2+ on soybean sprout yield and nutritional qualities. J. Proteomics 143, 161–172 (2016).
31. Wang, L. et al. Complementary transcriptomic and proteomic analyses of a chlorophyll-deficient tea plant cultivar reveal multiple metabolic pathway changes. J. Proteomics 130, 160–169 (2016).
32. Zhao, J. et al. iTRAQ-based comparative proteomic analysis of embryogenic and non-embryogenic tissues of Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr). Plant Cell Tissue Organ Cult. 120, 655–669 (2015).
33. Xu, Y., Dou, D., Ran, X., Liu, C. & Chen, J. Integrative analysis of proteomics and metabolomics of anaphylactoid reaction induced by Xuesaitong injection. J. Chromatogr. A. 1416, 103–111 (2015).
34. Xu, Y. et al. Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR. Biochem. Biophys. Res. Commun. 424, 398–403 (2012).
35. Sun, X. et al. Unraveling the root proteome changes and its relationship to molecular mechanism underlying salt stress response in radish (Raphanus sativus L.). Front. Plant Sci. 8, 1192 (2017).
36. D’Alessandro, S., Golin, S., Hardtke, C. S., Schiavo, F. L. & Zottini, M. The co-chaperone p23 controls root development through the modulation of auxin distribution in the Arabidopsis root meristem. J. Exp. Bot. 66, 5113–5122 (2015).
37. Velasquez, S. M., Barbez, E., Kleine-Vehn, J. & Estevez, J. Auxin and cellular elongation. Plant Physiol. 170, 1206 (2016).
38. Pernisova, M., Kuderova, A. & Hejatko, J. Cytokinin and auxin interactions in plant development: metabolism, signalling, transport and gene expression. Curr. Protein Pept. Sci. 12, 137–147 (2011).
39. Van de Poel, B., Smet, D. & Van Der Straeten, D. Ethylene and hormonal cross talk in vegetative growth and development. Plant Physiol. 169, 61–72 (2015).
40. Baroja-Fernández, E. et al. Enhancing sucrose synthase activity in transgenic potato (Solanum tuberosum L.) tubers results in increased levels of starch, ADP glucose and UDP glucose and total yield. Plant Cell Physiol. 50, 1651–1662 (2009).
41. Sun, Y. Y. & Li, X. X. A review on molecular mechanism of the modified roots or stems development in vegetables. Sci. Agric. Sin. 48, 1162–1176 (2015).
42. Lin, Z. Q. et al. AtCDC5 regulates the G2 to M transition of the cell cycle and is critical for the function of Arabidopsis shoot apical meristem. Cell Res. 17, 815–828 (2007).
43. Zhang, S., Xie, M., Ren, G. & Yu, B. CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts. Proc. Natl. Acad. Sci. U.S.A. 110, 17588–17593 (2013).
44. Ratsima, H., Serrano, D., Pascariu, M. & D’Amours, D. Centrosome-dependent bypass of the DNA damage checkpoint by the polo kinase Cdc5. Cell Rep. 14, 1422–1434 (2016).
45. Cheng, L., Li, S., Yin, J., Li, L. & Chen, X. Genome-wide analysis of differentially expressed genes relevant to rhizome formation in lotus root (Nelumbo nucifera Gaertn). PLoS One 8, e67116 (2013).
46. Noh, S. A. et al. Down-regulation of the IbEXPB1 gene enhanced storage root develoment in sweetpotato. J. Exp. Bot. 64, 129–142 (2013).
47. Claisse, G., Charrier, B. & Kreis, M. The Arabidopsis thaliana GSK3/Shaggy like kinase AtSK3-2 modulates floral cell expansion. Plant Mol. Biol. 64, 113–124 (2007).
48. Wu, X., Sklodowski, K., Encke, B., & Schulze, W. X. A kinase-phosphatase signaling module with BSK8 and BSL2 involved in regulation of sucrose-phosphate synthase. J. Proteome Res. 13, 3397–3409 (2014).