Proteomics dissection of plant responses to mineral nutrient deficiency

Proteomics

Volumn 13, Issue 3-4, 2013, Pages 624-636

  Liang, Cuiyue ^a   Tian, Jiang ^a   Liao, Hong ^a  

^a SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Adaptation; Mass spectrometer; Mineral nutrient deficiency; Plant proteomics

Indexed keywords

CALRETICULIN; CARBON; CHAPERONE; ETHYLENE; HYDROGEN; OXYGEN; PHOSPHATASE; PROTEASOME; VEGETABLE PROTEIN;

ADAPTATION; ARABIDOPSIS; CROP; ENDOSPERM; HUMAN; LIFE CYCLE; LIPID MEMBRANE; MAIZE; MINERAL DEFICIENCY; MITOCHONDRION; MOLECULAR MECHANICS; NUTRITIONAL DEFICIENCY; PHOTOSYNTHESIS; PHOTOSYSTEM II; PLANT; PLANT DEVELOPMENT; PLANT ROOT; PRIORITY JOURNAL; PROTEIN DEFICIENCY; PROTEIN STRUCTURE; PROTEIN TRANSPORT; PROTEOMICS; RAPESEED; REGULATORY MECHANISM; REVIEW; RICE; ROOT GROWTH; SOIL; SOYBEAN;

ADAPTATION, PHYSIOLOGICAL; CROPS, AGRICULTURAL; METABOLIC NETWORKS AND PATHWAYS; MICRONUTRIENTS; MINERALS; PLANT PROTEINS; PLANT ROOTS; PROTEOME; PROTEOMICS; STRESS, PHYSIOLOGICAL;

EID: 84873996440     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200263     Document Type: Review

References (79)

1. Marschner, H. (Eds.), Mineral Nutrition of Higher Plants. Academic Press, London 1995.
2. Gojon, A., Nacry, P., Davidian, J. C., Root uptake regulation: a central process for NPS homeostasis in plants. Curr. Opin. Plant Biol. 2009, 12, 328-338.
3. Tian, J., Wang, X., Tong, Y., Chen, X., Liao, H., Bioengineering and management for efficient phosphorus utilization in crops and pastures. Curr. Opin. Biotech. 2012, 23, 1-6.
4. Lynch, J. P., Root phenes for enhanced soil exploration and phosphorus acquisition: tools for future crops. Plant Physiol. 2011, 156, 1041-1049.
5. Xu, G., Fan, X., Miller, A. J., Plant nitrogen assimilation and use efficiency. Annu. Rev. Plant Biol. 2012, 63, 153-182.
6. Amtmann, A., Armengaud, P., Effects of N, P, K and S on metabolism: new knowledge gained from multi-level analysis. Curr. Opin. Plant Biol. 2009, 12, 275-283.
7. Chiou, T. J., Lin, S. I., Signaling network in sensing phosphate availability in plants. Annu. Rev. Plant Biol. 2011, 62, 185-206.
8. Wang, X., Wang, Y., Tian, J., Lim, B. L. et al., Overexpressing AtPAP15 enhances phosphorus efficiency in soybean. Plant Physiol. 2009, 151, 233-240.
9. Liang, C., Tian, J., Lam, H. M., Lim, B. L. et al., Biochemical and molecular characterization of PvPAP3, a novel purple acid phosphatase isolated from common bean enhancing extracellular ATP utilization. Plant Physiol. 2010, 152, 854-865.
10. Liang, C., Sun, L., Yao, Z., Liao, H. et al., Comparative analysis of PvPAP gene family and their functions in response to phosphorus deficiency in common bean. PloS ONE 2012, 7, e38106.
11. Plaxton, W. C., Tran, H. T., Metabolic adaptations of phosphate-starved plants. Plant Physiol. 2011, 156, 1006-1015.
12. Li, K., Xu, C., Zhang, K., Yang, A., Zhang, J., Proteomic analysis of roots growth and metabolic changes under phosphorus deficit in maize (Zea mays L.) plants. Proteomics 2007, 7, 1501-1512.
13. Li, K., Xu, C., Li, Z., Zhang, K. et al., Comparative proteome analyses of phosphorus responses in maize (Zea mays L.) roots of wild-type and a low-P-tolerant mutant reveal root characteristics associated with phosphorus efficiency. Plant J. 2008, 55, 927-939.
14. Kim, S. G., Wang, Y., Lee, C. H., Mun, B. G. et al., A comparative proteomics survey of proteins responsive to phosphorous starvation in roots of hydroponically-grown rice seedlings. J. Korean Soc. Appl. Biol. Chem. 2011, 54, 667-677.
15. Torabi, S., Wissuwa, M., Heidari, M., Naghavi, M. R. et al., A comparative proteome approach to decipher the mechanism of rice adaptation to phosphorous deficiency. Proteomics 2009, 9, 159-170.
16. Fukuda, T., Saito, A., Wasaki, J., Shinano, T., Osaki, M., Metabolic alterations proposed by proteome in rice roots grown under low P and high Al concentration under low pH. Plant Sci. 2007, 172, 1157-1165.
17. Chevalier, F., Rossignol, M., Proteomic analysis of Arabidopsis thaliana ecotypes with contrasted root architecture in response to phosphate deficiency. J. Plant Physiol. 2011, 168, 1885-1890.
18. Tran, H. T., Plaxton, W. C., Proteomic analysis of alterations in the secretome of Arabidopsis thaliana suspension cells subjected to nutritional phosphate deficiency. Proteomics 2008, 8, 4317-4326.
19. Lan, P., Li, W., Schmidt, W., Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation. Mol. Cell. Proteomics 2012, 11, 1156-1166.
20. Chen, Z., Cui, Q., Liang, C., Sun, L. et al., Identification of differentially expressed proteins in soybean nodules under phosphorus deficiency through proteomic analysis. Proteomics 2011, 11, 4648-4659.
21. Yao, Y., Sun, H., Xu, F., Zhang, X., Liu, S., Comparative proteome analysis of metabolic changes by low phosphorus stress in two Brassica napus genotypes. Planta 2011, 233, 523-537.
22. Feng, W., Li, Z., Guo, B., Peng, H. et al., Identification of differential expressed proteins responding to phosphorus starvation based on proteomic analysis in roots of wheat (Triticum aestivum L.). Acta Agron. Sin. 2012, 38, 780-790.
23. Gilbert, G. A., Knight, J. D., Vance, C. P., Allan, D. L., Proteoid root development of phosphorus deficient lupin is mimicked by auxin and phosphonate. Ann. Bot. 2000, 85, 921-928.
24. Rashotte, A. M., DeLong, A., Muday, G. K., Genetic and chemical reductions in protein phosphatase activity alter auxin transport, gravity response, and lateral root growth. Plant Cell 2001, 13, 1683-1697.
25. Pérez-Torres, C. A., López-Bucio, J., Cruz-Ramírez, A., Ibarra-Laclette, E. et al., Phosphate availability alters lateral root development in Arabidopsis by modulating auxin sensitivity via a mechanism involving the TIR1 auxin receptor. Plant Cell 2008, 20, 3258-3272.
26. Lü, J., Gao, X., Dong, Z., An, L., Expression of mitochondrial malate dehydrogenase in Escherichia coli improves phosphate solubilization. Ann. Microbiol. 2012, 62, 607-614.
27. Tesfaye, M., Temple, S. J., Allan, D. L., Vance, C. P., Samac, D. A., Overexpression of malate dehydrogenase in transgenic alfalfa enhances organic acid synthesis and confers tolerance to aluminum. Plant Physiol. 2001, 127, 1836-1844.
28. Vincent, A. G., Schleucher, J., Gröbner, G., Vestergren, J. et al., Changes in organic phosphorus composition in boreal forest humus soils: the role of iron and aluminium. Biogeochemistry 2012, 1-15.
29. Vance, C. P., Uhde-Stone, C., Allan, D. L., Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytol. 2003, 157, 423-447.
30. Plaxton, W. C., Podestá, F. E., The functional organization and control of plant respiration. Crit. Rev. Plant Sci. 2006, 25, 159-198.
31. Smalle, J., Kurepa, J., Yang, P., Babiychuk, E. et al., Cytokinin growth responses in Arabidopsis involve the 26S proteasome subunit RPN12. Plant Cell 2002, 14, 17-32.
32. Smalle, J., Vierstra, R. D., The ubiquitin 26S proteasome proteolytic pathway. Annu. Rev. Plant Biol. 2004, 55, 555-590.
33. Torres, M. A., Dangl, J. L., Functions of the respiratory burst oxidase in biotic interactions, abiotic stress and development. Curr. Opin. Plant Biol. 2005, 8, 397-403.
34. Bartosz, G., Oxidative stress in plants. Acta Physiol. Plant. 1997, 19, 47-64.
35. Bi, Y. M., Wang, R. L., Zhu, T., Rothstein, S. J., Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis. BMC Genomics 2007, 8, 281-297.
36. Kant, S., Bi, Y. M., Rothstein, S. J., Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency. J. Exp. Bot. 2011, 62, 1499-1509.
37. Bahrman, N., Gouy, A., Devienne-Barret, F., Hirel, B. et al., Differential change in root protein patterns of two wheat varieties under high and low nitrogen nutrition levels. Plant Sci. 2005, 168, 81-87.
38. Bahrman, N., Le Gouis, J., Negroni, L., Amilhat, L. et al., Differential protein expression assessed by two-dimensional gel electrophoresis for two wheat varieties grown at four nitrogen levels. Proteomics 2004, 4, 709-719.
39. Prinsi, B., Negri, A. S., Pesaresi, P., Cocucci, M., Espen, L., Evaluation of protein pattern changes in roots and leaves of Zea mays plants in response to nitrate availability by two-dimensional gel electrophoresis analysis. BMC Plant Biol. 2009, 9, 113-129.
40. Liao, C., Liu, R., Zhang, F., Li, C., Li, X., Nitrogen under- and over-supply induces distinct protein responses in maize xylem sap. J. Integr. Plant Biol. 2012, 54, 374-387.
41. Kim, D. H., Shibato, J., Kim, D. W., Oh, M. K. et al., Gel-based proteomics approach for detecting low nitrogen-responsive proteins in cultivated rice species. Physiol. Mol. Biol. Plants 2009, 15, 31-41.
42. Song, C., Zeng, F., Feibo, W., Ma, W., Zhang, G., Proteomic analysis of nitrogen stress-responsive proteins in two rice cultivars differing in N utilization efficiency. J. Integr. OMICS 2010, 1, 78-87.
43. Ding, C., You, J., Liu, Z., Rehmani, M. I. A. et al., Proteomic analysis of low nitrogen stress-responsive proteins in roots of rice. Plant Mol. Biol. Rep. 2011, 29, 618-625.
44. Ding, C., You, J., Wang, S., Liu, Z. et al., A proteomic approach to analyze nitrogen- and cytokinin-responsive proteins in rice roots. Mol. Biol. Rep. 2012, 39, 1617-1626.
45. Castillejo, M. A., Kirchev, H. K., Jorrin, J. V., Differences in the triticale (X Triticosecale Wittmack) flag leaf 2-DE protein profile between varieties and nitrogen fertilization levels. J. Agric. Food Chem. 2010, 58, 5698-5707.
46. Xu, C., Jiang, Z., Huang, B., Nitrogen deficiency-induced protein changes in immature and mature leaves of creeping bentgrass. J. Am. Soc. Hortic. Sci. 2011, 136, 399-407.
47. Yang, H., Xu, L., Cui, H., Zhong, B. et al., Low nitrogen-induced expression of cyclophilin in Nicotiana tabacum. J. Plant Res. 2012, doi:10.1007/s10265-012-0499-1.
48. Wang, X., Bian, Y., Cheng, K., Zou, H. et al., A comprehensive differential proteomic study of nitrate deprivation in Arabidopsis reveals complex regulatory networks of plant nitrogen responses. J. Proteome Res. 2012, 11, 2301-2315.
49. Moller, A. L., Pedas, P., Andersen, B., Svensson, B. et al., Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium. Plant Cell Environ. 2011, 34, 2024-2037.
50. Hörtensteiner, S., Feller, U., Nitrogen metabolism and remobilization during senescence. J. Exp. Bot. 2002, 53, 927-937.
51. Feller, U., Anders, I., Mae, T., Rubiscolytics: fate of Rubisco after its enzymatic function in a cell is terminated. J. Exp. Bot. 2008, 59, 1615-1624.
52. Shin, R., Berg, R. H., Schachtman, D. P., Reactive oxygen species and root hairs in Arabidopsis root response to nitrogen, phosphorus and potassium deficiency. Plant Cell Physiol. 2005, 46, 1350-1357.
53. Pate, J. S., Uptake, assimilation and transport of nitrogen compounds by plants. Soil Biol. Biochem. 1973, 5, 109-119.
54. Marschner, H., Römheld, V., Kissel, M., Different strategies in higher plants in mobilization and uptake of iron. J. Plant Nutr. 1986, 9, 695-713.
55. Rellan-Alvarez, R., Andaluz, S., Rodriguez-Celma, J., Wohlgemuth, G. et al., Changes in the proteomic and metabolic profiles of Beta vulgaris root tips in response to iron deficiency and resupply. BMC Plant Biol. 2010, 10, 120-134.
56. Andaluz, S., Lopez-Millan, A. F., De Las, R. J., Aro, E. M. et al., Proteomic profiles of thylakoid membranes and changes in response to iron deficiency. Photosynth. Res. 2006, 89, 141-155.
57. Lan, P., Li, W., Wen, T. N., Shiau, J. Y. et al., iTRAQ protein profile analysis of Arabidopsis roots reveals new aspects critical for iron homeostasis. Plant Physiol. 2011, 155, 821-834.
58. Laganowsky, A., Gómez, S. M., Whitelegge, J. P., Nishio, J. N., Hydroponics on a chip: analysis of the Fe deficient Arabidopsis thylakoid membrane proteome. J. Proteomics 2009, 72, 397-415.
59. Wang, J., Ruan, S., Wu, W., Xu, X. et al., Proteomics approach to identify differentially expressed proteins induced by iron deficiency in roots of Malus. Pak. J. Bot. 2010, 42, 3055-3064.
60. Meisrimler, C. N., Planchon, S., Renaut, J., Sergeant, K., Luthje, S., Alteration of plasma membrane-bound redox systems of iron deficient pea roots by chitosan. J. Proteomics 2011, 74, 1437-1449.
61. Brumbarova, T., Matros, A., Mock, H. P., Bauer, P., A proteomic study showing differential regulation of stress, redox regulation and peroxidase proteins by iron supply and the transcription factor FER. Plant J. 2008, 54, 321-334.
62. Li, J., Wu, X., Hao, S., Wang, X., Ling, H., Proteomic response to iron deficiency in tomato root. Proteomics 2008, 8, 2299-2311.
63. Donnini, S., Prinsi, B., Negri, A. S., Vigani, G. et al., Proteomic characterization of iron deficiency responses in Cucumis sativus L. roots. BMC Plant Biol. 2010, 10, 268-282.
64. Rodriguez-Celma, J., Lattanzio, G., Grusak, M. A., Abadia, A. et al., Root responses of Medicago truncatula plants grown in two different iron deficiency conditions: changes in root protein profile and riboflavin biosynthesis. J. Proteome Res. 2011, 10, 2590-2601.
65. Lopez-Bucio, J., Cruz-Ramirez, A., Herrera-Estrella, L., The role of nutrient availability in regulating root architecture. Curr. Opin. Plant Biol. 2003, 6, 280-287.
66. Jin, C., You, G., He, Y., Tang, C. et al., Iron deficiency-induced secretion of phenolics facilitates the reutilization of root apoplastic iron in red clover. Plant Physiol. 2007, 144, 278-285.
67. + deficiency in Arabidopsis thaliana. Proteomics 2004, 4, 3549-3559.
68. Wang, Z., Wang, Z., Shi, L., Wang, L., Xu, F., Proteomic alterations of Brassica napus root in response to boron deficiency. Plant Mol. Biol. 2010, 74, 265-278.
69. Agrawal, G. K., Rakwal, R., Rice proteomics: a move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 2011, 11, 1630-1649.
70. Misson, J., Raghothama, K. G., Jain, A., Jouhet, J. et al., A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc. Natl. Acad. Sci. 2005, 102, 11934-11939.
71. Wu, P., Ma, L., Hou, X., Wang, M. et al., Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol. 2003, 132, 1260-1271.
72. Devaiah, B. N., Nagarajan, V. K., Raghothama, K. G., Phosphate homeostasis and root development in Arabidopsis are synchronized by the zinc finger transcription factor ZAT6. Plant Physiol. 2007, 145, 147-159.
73. Cramer, G. R., Urano, K., Delrot, S., Pezzotti, M., Shinozaki, K., Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol. 2011, 11, 163-176.
74. Yuan, J. S., Galbraith, D. W., Dai, S. Y., Griffin, P., Stewart, C. N., Plant systems biology comes of age. Trends Plant Sci. 2008, 13, 165-171.
75. Baldazzi, V., Bertin, N., de Jong, H., Génard, M., Towards multiscale plant models: integrating cellular networks. Trends Plant Sci. 2012, 17, 728-736.
76. Hirai, M. Y., Yano, M., Goodenowe, D. B., Kanaya, S. et al., Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 2004, 101, 10205-10210.
77. Kaufmann, K., Smaczniak, C., de Vries, S., Angenent, G. C., Karlova, R., Proteomics insights into plant signaling and development. Proteomics 2011, 11, 744-755.
78. Kosov, A. K., Vitámvás, P., Prášil, I. T. A., Plant proteome changes under abiotic stress-contribution of proteomics studies to understanding plant stress response. J. Proteomics 2011, 1, 1301-1322.
79. Engelsberger, W. R., Schulze, W. X., Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings. Plant J. 2012, 69, 978-995.