A digital compendium of genes mediating the reversible phosphorylation of proteins in Fe-deficient Arabidopsis roots

Frontiers in Plant Science

Volumn 4, Issue JUN, 2013, Pages

  Lan, Ping ^a,b   Li, Wenfeng ^b   Schmidt, Wolfgang ^b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

Author keywords

Co expression; Iron deficiency; Potassium homeostasis; Protein phosphorylation; RNA seq

Indexed keywords

EID: 84887260558     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2013.00173     Document Type: Article

References (49)

1. Alexa, A., Rahnenfuhrer, J., and Lengauer, T. (2006). Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600-1607. doi:10.1093/bioinformatics/btl140
2. Aoki, K., Ogata, Y., and Shibata, D. (2007). Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 48, 381-390. doi:10.1093/pcp/pcm013
3. Arnaud, N., Murgia, I., Boucherez, J., Briat, J. F., Cellier, F., and Gaymard, F. (2006). An iron-induced nitric oxide burst precedes ubiquitin-dependent protein degradation for Arabidopsis AtFer1 ferritin gene expression. J. Biol. Chem. 281, 23579-23588. doi:10.1074/jbc.M602135200
4. Arrivault, S., Senger, T., and Kramer, U. (2006). The Arabidopsis metal tolerance protein AtMTP3 maintains metal homeostasis by mediating Zn exclusion from the shoot under Fe deficiency and Zn oversupply. Plant J. 46, 861-879. doi:10.1111/j.1365-313X.2006.02746.x
5. Barak, P., and Chen, Y. (1983). The effect of potassium fertilization on iron deficiency. Commun. Soil Sci. Plant Anal. 14, 945-950. doi:10.1080/00103628309367422
6. Barberon, M., Zelazny, E., Robert, S., Conejero, G., Curie, C., Friml, J., et al. (2011). Monoubiquitin-dependent endocytosis of the iron-regulated transporter 1 (IRT1) transporter controls iron uptake in plants. Proc. Natl. Acad. Sci. U.S.A. 108, E450-458. doi:10.1073/pnas.1100659108
7. Bauer, P., Ling, H. Q., and Guerinot, M. L. (2007). FIT, the FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACTOR in Arabidopsis. Plant Physiol. Biochem. 45, 260-261. doi:10.1016/j.plaphy.2007.03.006
8. Buckhout, T. J., Yang, T. J., and Schmidt, W. (2009). Early iron-deficiency-induced transcriptional changes in Arabidopsis roots as revealed by microarray analyses. BMC Genomics 10:147. doi:10.1186/1471-2164-10-147
9. Colangelo, E. P., and Guerinot, M. L. (2004). The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response. Plant Cell 16, 3400-3412. doi:10.1105/tpc.104.024315
10. Curie, C., Panaviene, Z., Loulergue, C., Dellaporta, S. L., Briat, J. F., and Walker, E. L. (2001). Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake. Nature 409, 346-349. doi:10.1038/35053080
11. Dinneny, J. R., Long, T. A., Wang, J. Y., Jung, J. W., Mace, D., Pointer, S., et al. (2008). Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320, 942-945. doi:10.1126/science.1153795
12. Durrett, T. P., Gassmann, W., and Rogers, E. E. (2007). The FRD3-mediated efflux of citrate into the root vasculature is necessary for efficient iron translocation. Plant Physiol. 144, 197-205. doi:10.1104/pp.107.097162
13. Eide, D., Broderius, M., Fett, J., and Guerinot, M. L. (1996). A novel iron-regulated metal transporter from plants identified by functional expression in yeast. Proc. Natl. Acad. Sci. U.S.A. 93, 5624-5628. doi:10.1073/pnas.93.11.5624
14. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95, 14863-14868. doi:10.1073/pnas.95.25.14863
15. Garcia, M. J., Lucena, C., Romera, F. J., Alcantara, E., and Perez-Vicente, R. (2010). Ethylene and nitric oxide involvement in the up-regulation of key genes related to iron acquisition and homeostasis in Arabidopsis. J. Exp. Bot. 61, 3885-3899. doi:10.1093/jxb/erq203
16. Ho, C. H., Lin, S. H., Hu, H. C., and Tsay, Y. F. (2009). CHL1 functions as a nitrate sensor in plants. Cell 138, 1184-1194. doi:10.1016/j.cell.2009.07.004
17. Ihmels, J., Levy, R., and Barkai, N. (2004). Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat. Biotechnol. 22, 86-92. doi:10.1038/nbt918
18. Ivanov, R., Brumbarova, T., and Bauer, P. (2012). Fitting into the harsh reality: regulation of iron-deficiency responses in dicotyledonous plants. Mol. Plant. 5, 27-42. doi:10.1093/mp/ssr065
19. Kharchenko, P., Church, G. M., and Vitkup, D. (2005). Expression dynamics of a cellular metabolic network. Mol. Syst. Biol. 1:2005.0016. doi:10.1038/msb4100023
20. Lan, P., Li, W., and Schmidt, W. (2012a). Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation. Mol. Cell Proteomics 11, 1156-1166. doi:10.1074/mcp.M112.020461
21. Lan, P., Li, W., Wen, T. N., and Schmidt, W. (2012b). Quantitative phosphoproteome profiling of iron-deficient Arabidopsis roots. Plant Physiol. 159, 403-417. doi:10.1104/pp.112.193987
22. Lin, W.-D., Chen, Y.-C., Ho, J.-M., and Hsiao, C.-D. (2006). GOBU: toward an integration interface for biological objects. J. Inf. Sci. Eng. 22, 19.
23. Lin, W. D., Liao, Y. Y., Yang, T. J., Pan, C. Y., Buckhout, T. J., and Schmidt, W. (2011). Coexpression-based clustering of Arabidopsis root genes predicts functional modules in early phosphate deficiency signaling. Plant Physiol. 155, 1383-1402. doi:10.1104/pp.110.166520
24. Lingam, S., Mohrbacher, J., Brumbarova, T., Potuschak, T., Fink-Straube, C., Blondet, E., et al. (2011). Interaction between the bHLH transcription factor FIT and ETHYLENE INSENSITIVE3/ETHYLENE INSENSITIVE3-LIKE1 reveals molecular linkage between the regulation of iron acquisition and ethylene signaling in Arabidopsis. Plant Cell 23, 1815-1829. doi:10.1105/tpc.111.084715
25. Liu, L. L., Ren, H. M., Chen, L. Q., Wang, Y., and Wu, W. H. (2013). A protein kinase, calcineurin B-like protein-interacting protein Kinase9, interacts with calcium sensor calcineurin B-like Protein3 and regulates potassium homeostasis under low-potassium stress in Arabidopsis. Plant Physiol. 161, 266-277. doi:10.1104/pp.112.206896
26. Long, T. A., Tsukagoshi, H., Busch, W., Lahner, B., Salt, D. E., and Benfey, P. N. (2010). The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell 22, 2219-2236. doi:10.1105/tpc.110.074096
27. Lu, K. P., and Zhou, X. Z. (2007). The prolyl isomerase PIN1: a pivotal new twist in phosphorylation signalling and disease. Nat. Rev. Mol. Cell Biol. 8, 904-916. doi:10.1038/nrm2261
28. Meiser, J., Lingam, S., and Bauer, P. (2011). Posttranslational regulation of the iron deficiency basic helix-loop-helix transcription factor FIT is affected by iron and nitric oxide. Plant Physiol. 157, 2154-2166. doi:10.1104/pp.111.183285
29. Morrissey, J., Baxter, I. R., Lee, J., Li, L., Lahner, B., Grotz, N., et al. (2009). The ferroportin metal efflux proteins function in iron and cobalt homeostasis in Arabidopsis. Plant Cell 21, 3326-3338. doi:10.1105/tpc.109.069401
30. Ozsolak, F., and Milos, P. M. (2011). RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98. doi:10.1038/nrg2934
31. Rellan-Alvarez, R., El-Jendoubi, H., Wohlgemuth, G., Abadia, A., Fiehn, O., Abadia, J., et al. (2011). Metabolite profile changes in xylem sap and leaf extracts of strategy I plants in response to iron deficiency and resupply. Front. Plant Sci. 2:66. doi:10.3389/fpls.2011.00066
32. Robinson, N. J., Procter, C. M., Connolly, E. L., and Guerinot, M. L. (1999). A ferric-chelate reductase for iron uptake from soils. Nature 397, 694-697. doi:10.1038/17800
33. Rogers, E. E., and Guerinot, M. L. (2002). FRD3, a member of the multidrug and toxin efflux family, controls iron deficiency responses in Arabidopsis. Plant Cell 14, 1787-1799. doi:10.1105/tpc.001495
34. Romheld, V., and Marschner, H. (1986). Evidence for a specific uptake system for iron phytosiderophores in roots of grasses. Plant Physiol. 80, 175-180. doi:10.1104/pp.80.1.175
35. Roschzttardtz, H., Seguela-Arnaud, M., Briat, J. F., Vert, G., and Curie, C. (2011). The FRD3 citrate effluxer promotes iron nutrition between symplastically disconnected tissues throughout Arabidopsis development. Plant Cell 23, 2725-2737. doi:10.1105/tpc.111.088088
36. Santi, S., and Schmidt, W. (2009). Dissecting iron deficiency-induced proton extrusion in Arabidopsis roots. New Phytol. 183, 1072-1084. doi:10.1111/j.1469-8137.2009.02908.x
37. Schaaf, G., Honsbein, A., Meda, A. R., Kirchner, S., Wipf, D., and Von Wiren, N. (2006). AtIREG2 encodes a tonoplast transport protein involved in iron-dependent nickel detoxification in Arabidopsis thaliana roots. J. Biol. Chem. 281, 25532-25540. doi:10.1074/jbc.M601062200
38. Schmidt, W., and Buckhout, T. J. (2011). A hitchhiker's guide to the Arabidopsis ferrome. Plant Physiol. Biochem. 49, 462-470. doi:10.1016/j.plaphy.2010.12.001
39. Sivitz, A., Grinvalds, C., Barberon, M., Curie, C., and Vert, G. (2011). Proteasome-mediated turnover of the transcriptional activator FIT is required for plant iron-deficiency responses. Plant J. 66, 1044-1052. doi:10.1111/j.1365-313X.2011.04565.x
40. Sivitz, A. B., Hermand, V., Curie, C., and Vert, G. (2012). Arabidopsis bHLH100 and bHLH101 control iron homeostasis via a FIT-independent pathway. PLoS ONE 7:::e44843. doi:10.1371/journal.pone.0044843
41. Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F. M., Bassel, G. W., Tanimoto, M., et al. (2009). Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32, 1633-1651. doi:10.1111/j.1365-3040.2009.02040.x
42. Vert, G., Grotz, N., Dedaldechamp, F., Gaymard, F., Guerinot, M. L., Briat, J. F., et al. (2002). IRT1, an Arabidopsistransporter essential for iron uptake from the soil and for plant growth. Plant Cell 14, 1223-1233. doi:10.1105/tpc.001388
43. Wang, H., Chevalier, D., Larue, C., Ki Cho, S., and Walker, J. C. (2007). The protein phosphatases and protein kinases of Arabidopsis thaliana. Arabidopsis Book 5, e0106.
44. Wang, N., Cui, Y., Liu, Y., Fan, H., Du, J., Huang, Z., et al. (2013). Requirement and functional redundancy of Ib subgroup bHLH proteins for iron deficiency responses and uptake in Arabidopsis thaliana. Mol. Plant. 6, 503-513. doi:10.1093/mp/sss089
45. Wang, S., Yin, Y., Ma, Q., Tang, X., Hao, D., and Xu, Y. (2012). Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. BMC Plant Biol. 12:138. doi:10.1186/1471-2229-12-138
46. Wang, Y. H., Garvin, D. F., and Kochian, L. V. (2002). Rapid induction of regulatory and transporter genes in response to phosphorus, potassium, and iron deficiencies in tomato roots. Evidence for cross talk and root/rhizosphere-mediated signals. Plant Physiol. 130, 1361-1370.
47. Xu, J., Li, H. D., Chen, L. Q., Wang, Y., Liu, L. L., He, L., et al. (2006). A protein kinase, interacting with two calcineurin B-like proteins, regulates K+ transporter AKT1 in Arabidopsis. Cell 125, 1347-1360. doi:10.1016/j.cell.2006.06.011
48. Yang, T. J., Lin, W. D., and Schmidt, W. (2010). Transcriptional profiling of the Arabidopsis iron deficiency response reveals conserved transition metal homeostasis networks. Plant Physiol. 152, 2130-2141. doi:10.1104/pp.109.152728
49. Yuan, Y., Wu, H., Wang, N., Li, J., Zhao, W., Du, J., et al. (2008). FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis. Cell Res. 18, 385-397. doi:10.1038/cr.2008.26