A systems approach to understanding root development

Canadian Journal of Botany

Volumn 84, Issue 5, 2006, Pages 695-701

  Brady, Siobhan M ^a   Benfey, Philip N ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Development; Root; Systems biology

Indexed keywords

DATABASE SYSTEMS; GENES;

GENE EXPRESSION; ROOT DEVELOPMENT; SYSTEMS BIOLOGY;

PLANTS (BOTANY);

BIOLOGICAL ANALYSIS; DATA SET; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; ROOT SYSTEM;

BIOLOGY; GENES; ROOTS;

EID: 33749326628     PISSN: 00084026     EISSN: None     Source Type: Journal    
DOI: 10.1139/B06-028     Document Type: Review

References (50)

1. Aida, M., Beis, D., Heidstra, R., Willemsen, V., Blilou, I., Galinha, C., Nussaume, L., Noh, Y.-S., Amasino, R., and Scheres, B. 2004. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell, 119: 109-120. doi:10.1016/j.cell.2004.09.018.
2. Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C.C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D.E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W.L., Berry, C.C., and Ecker, J.R. 2003. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301: 653-657. doi:10.1126/science.1086391.
3. An, S., Park, S., Jeong, D.-H., Lee, D.-Y., Kang, H.-G., Yu, J.-H., Hur, J., Kim, S.-R., Kim, Y.-H., Lee, M., Han, S., Kim, S.-J., Yang, J., Kim, E., Wi, S.J., Chung, H.S., Hong, J.-P., Choe, V., Lee, H.-K., Choi, J.-H., Nam, J., Kim, S.-R., Park, P.-B., Park, K.Y., Kim, W.T., Choe, S., Lee, C.-B., and An, G. 2003. Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol. 133: 2040-2047. doi:10.1104/pp.103.030478.
4. Barabasi, A.-L., and Albert, R. 1999. Emergence of scaling in random networks. Science, 286: 509-512.
5. Birnbaum, K., and Benfey, P.N. 2004. Network building: transcriptional circuits in the root. Curr. Opin. Plant Biol. 7: 582-588. doi:10.1016/j.pbi. 2004.07.010.
6. Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., and Benfey, P.N. 2003. A gene expression map of the Arabidopsis root. Science, 302: 1956-1960. doi:10.1126/science.1090022.
7. Bork, P., Jensen, L.J., von Mering, C., Ramani, A.K., Lee, I., and Marcotte, E.M. 2004. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14: 292-299. doi:10.1016/j.sbi.2004.05.003.
8. Chen, K.C., Csikasz-Nagy, A., Gyorffy, B., Val, J., Novak, B., and Tyson, J.J. 2000. Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol. Biol. Cell, 11: 369-391.
9. Dolan, L. 2006. Positional information and mobile transcriptional regulators determine cell pattern in the Arabidopsis root epidermis. J. Exp. Bot. 57: 51-54.
10. Fizames, C., Munos, S., Cazettes, C., Nacry, P., Boucherez, J., Gaymard, F., Piquemal, D., Delorme, V., Commes, T., Doumas, P., Cooke, R., Marti, J., Sentenac, H., and Gojon, A. 2004. The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence. Plant Physiol. 134: 67-80. doi:10.1104/pp.103.030536.
11. Friedman, N., Linial, M., Nachman, I., and Pe'er, D. 2000. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7: 601-620. doi:10.1089/106652700750050961.
12. Goff, S.A., Ricke, D., Lan, T.-H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W.-I., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean, R., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J., Macalma, T., Oliphant, A., and Briggs, S. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296: 92-100. doi:10.1126/science.1068275.
13. Gomez-Mena, C., de Folter, S., Costa, M.M.R., Angenent, G.C., and Sablowski, R. 2005. Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis. Development, 132: 429-438. doi:10.1242/dev.01600.
14. Hartemink, A.J., Gifford, D.K., Jaakkola, T.S., Young, R.A. 2002. Combining location and expression data for principled discovery of genetic regulatory network models. Pacif. Symp. Biocomput 7: 437-449.
15. Hatzimanikatis, V., Li, C., Ionita, J.A., and Broadbelt, L.J. 2004. Metabolic networks: enzyme function and metabolite structure. Curr. Opin. Struct. Biol. 14: 300-306. doi:10.1016/j.sbi.2004.04.004.
16. Himanen, K., Vuylsteke, M., Vanneste, S., Vercruysse, S., Boucheron, E., Alard, P., Chriqui, D., Van Montagu, M., Inze, D., and Beeckman, T. 2004. Transcript profiling of early lateral root initiation. Proc. Natl. Acad. Sci. U.S.A. 101: 5146-5151. doi:10.1073/pnas.0308702101.
17. Ideker, T., Galitski, T., and Hood, L. 2001. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2: 343-372. doi:10.1146/annurev.genom.2.1.343.
18. Initiative, T.A.G. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408: 796-815.
19. Kauffman, S., Peterson, C., Samuelsson, B., and Troein, C. 2003. Random Boolean network models and the yeast transcriptional network. Proc. Natl. Acad. Sci. U.S.A. 100: 14796-14799. doi:10.1073/pnas.2036429100.
20. Keller, E.F. 2005. Revisiting "scale-free" networks. Bioessays, 27: 1060-1068.
21. Kohn, K.W. 1999. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell, 10: 2703-2734.
22. Kohn, K.W., and Pommier, Y. 2005. Molecular interaction map of the p53 and Mdm2 logic elements, which control the off-on switch of p53 in response to DNA damage. Biochem. Biophys. Res. Commun. 331: 816-827. doi:10.1016/j.bbrc. 2005.03.186.
23. Lange, B.M., and Ghassemian, M. 2005. Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps. Phytochemistry, 66: 413-451.
24. Li, L., Alderson, D., Willinger, W., and Doyle, J. 2004. A first-principles approach to understanding the Internet's router-level topology. In Proceedings of ACM SIGCOMM, Portland, Oregon, 30 August - 2 September 2004. ACM Press, New York. pp. 3-14.
25. Locke, J.C.W., Millar, A.J., and Turner, M.S. 2005. Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. J. Theor. Biol. 234: 383-393. doi:10.1016/j.jtbi.2004.11. 038.
26. May, B.P., Liu, H., Vollbrecht, E., Senior, L., Rabinowicz, P.D., Roh, D., Pan, X., Stein, L., Freeling, M., Alexander, D., and Martienssen, R. 2003. Maize-targeted mutagenesis: A knockout resource for maize. Proc. Natl. Acad. Sci. U.S.A. 100: 11541-11546. doi:10.1073/pnas.1831119100.
27. Mendoza, L., Thieffry, D., and Alvarez-Buylla, E.R. 1999. Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinformatics, 15: 593-606. doi:10.1093/bioinformatics/15.7.593.
28. Montiel, G., Gantet, P., Jay-Allemand, C., and Breton, C. 2004. Transcription factor networks. Pathways to the knowledge of root development. Plant Physiol. 136: 3478-3485. doi:10.1104/pp.104.051029.
29. Nawy, T., Lee, J.-Y., Colinas, J., Wang, J.Y., Thongrod, S.C., Malamy, J.E., Birnbaum, K., and Benfey, P.N. 2005. Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell, 17: 1908-1925. doi:10.1105/tpc.105.031724.
30. Nikiforova, V.J., Gakiere, B., Kempa, S., Adamik, M., Willmitzer, L., Hesse, H., and Hoefgen, R. 2004. Towards dissecting nutrient metabolism in plants: a systems biology case study on sulphur metabolism. J. Exp. Bot. 55: 1861-1870. doi.10.1093/jxb/erh177.
31. Nikiforova, V.J., Kopka, J., Tolstikov, V., Fiehn, O., Hopkins, L., Hawkesford, M.J., Hesse, H., and Hoefgen, R. 2005. Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol. 138: 304-318. doi:10.1104/pp.104.053793.
32. Nuhse, T.S., Stensballe, A., Jensen, O.N., and Peck, S.C. 2004. Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell, 16: 2394-2405. doi:10.1105/tpc.104.023150.
33. Palenchar, P., Kouranov, A., Lejay, L., and Coruzzi, G. 2004. Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol. 5: R91.1-R91.15.
34. Poroyko, V., Hejlek, L.G., Spollen, W.G., Springer, G.K., Nguyen, H.T., Sharp, R.E., and Bohnert, H.J. 2005. The maize root transcriptome by serial analysis of gene expression. Plant Physiol. 138: 1700-1710. doi:10.1104/pp.104. 057638.
35. Provart, N.J., and McCourt, P. 2004. Systems approaches to understanding cell signaling and gene regulation. Curr. Opin. Plant Biol. 7: 605-609. doi:10.1016/j.pbi.2004.07.001.
36. Rabinowicz, P.D., Citek, R., Budiman, M.A., Nunberg, A., Bedell, J.A., Lakey, N., O'Shaughnessy, A.L., Nascimento, L.U., McCombie, W.R., and Martienssen, R.A. 2005. Differential methylation of genes and repeats in land plants. Genome Res. 15: 1431-1440. doi:10.1101/gr.4100405.
37. Rives, A.W., and Galitski, T. 2003. Modular organization of cellular networks. Proc. Natl. Acad. Sci. U.S.A. 100: 1128-1133. doi:10.1073/pnas. 0237338100.
38. Schiefelbein, J. 2003. Cell-fate specification in the epidermis: a common patterning mechanism in the root and shoot. Curr. Opin. Plant Biol. 6: 74-78. doi:10.1016/S136952660200002X.
39. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D., and Lohmann, J.U. 2005. A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37: 501-506. doi:10.1038/ng1543.
40. Sessions, A., Burke, E., Presting, G., Aux, G., McElver, J., Patton, D., Dietrich, B., Ho, P., Bacwaden, J., Ko, C., Clarke, J.D., Cotton, D., Bullis, D., Snell, J., Miguel, T., Hutchison, D., Kimmerly, B., Mitzel, T., Katagiri, F., Glazebrook, J., Law, M., and Goff, S.A. 2002. A high-throughput Arabidopsis reverse genetics system. Plant Cell, 14: 2985-2994. doi:10.1105/tpc.004630.
41. Swidzinski, J.A., Leaver, C.J., and Sweetlove, L.J. 2004. A proteomic analysis of plant programmed cell death. Phytochemistry, 65: 1829-1838. doi:10.1016/j.phytochem.2004.04.020.
42. Thum, K., Shin, M., Palenchar, P., Kouranov, A., and Coruzzi, G. 2004. Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol. 5: R10.1-R10.20. doi:10.1186/gb-2004-5-2-r10.
43. Vanneste, S., De Rybel, B., Beemster, G.T.S., Ljung, K., De Smet, I., Van Isterdael, G., Naudts, M., Iida, R., Gruissem, W., Tasaka, M., Inze, D., Fukaki, H., and Beeckman, T. 2005. Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana. Plant Cell, 17: 3035-3050. doi:10.1105/tpc.105.035493.
44. Vilar, J.M.G., Kueh, H.Y., Barkai, N., and Leibler, S. 2002. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl. Acad. Sci. U.S.A. 99: 5988-5992. doi:10.1073/pnas.092133899.
45. William, D.A., Su, Y., Smith, M.R., Lu, M., Baldwin, D.A., and Wagner, D. 2004. Genomic identification of direct target genes of LEAFY. Proc. Natl. Acad. Sci. U.S.A. 101: 1775-1780. doi:10.1073/pnas.0307842100.
46. Wolf, Y.I., Karev, G., and Koonin, E.V. 2002. Scale-free networks in biology: new insights into the fundamentals of evolution? Bioessays, 24: 105-109. doi:10.1002/bies.10059.
47. Woll, K., Borsuk, L.A., Stransky, H., Nettleton, D., Schnable, P.S., and Hochholdinger, F. 2005. Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1. Plant Physiol. 139: 1255-1257. doi:10.1104/pp.105.067330.
48. Wuchty, S. 2004. Evolution and topology in the yeast protein interaction network. Genome Res. 14: 1310-1314. doi:10.1101/gr.2300204.
49. Xia, Y., Yu, H., Jansen, R., Seringhaus, M., Baxter, S., Greenbaum, D., Zhao, H., and Gerstein, M. 2004. Analyzing cellular biochemistry in terms of molecular networks. Annu. Rev. Biochem. 73: 1051-1087. doi:10.1146/annurev. biochem.73.011303.073950.
50. Yu, J., Hu, S., Wang, J., Wong, G.K.-S., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., Cao, M., Liu, J., Sun, J., Tang, J., Chen, Y., Huang, X., Lin, W., Ye, C., Tong, W., Cong, L., Geng, J., Han, Y., Li, L., Li, W., Hu, G., Huang, X., Li, W., Li, J., Liu, Z., Li, L., Liu, J., Qi, Q., Liu, J., Li, L., Li, T., Wang, X., Lu, H., Wu, T., Zhu, M., Ni, P., Han, H., Dong, W., Ren, X., Feng, X., Cui, P., Li, X., Wang, H., Xu, X., Zhai, W., Xu, Z., Zhang, J., He, S., Zhang, J., Xu, J., Zhang, K., Zheng, X., Dong, J., Zeng, W., Tao, L., Ye, J., Tan, J., Ren, X., Chen, X., He, J., Liu, D., Tian, W., Tian, C., Xia, H., Bao, Q., Li, G., Gao, H., Cao, T., Wang, J., Zhao, W., Li, P., Chen, W., Wang, X., Zhang, Y., Hu, J., Wang, J., Liu, S., Yang, J., Zhang, G., Xiong, Y., Li, Z., Mao, L., Zhou, C., Zhu, Z., Chen, R., Hao, B., Zheng, W., Chen, S., Guo, W., Li, G., Liu, S., Tao, M., Wang, J., Zhu, L., Yuan, L., and Yang, H. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296: 79-92. doi:10.1126/science.1068037.