Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root

Developmental Cell

Volumn 21, Issue 4, 2011, Pages 770-782

  Iyer Pascuzzi, Anjali S ^a   Jackson, Terry ^a   Cui, Hongchang ^b   Petricka, Jalean J ^a   Busch, Wolfgang ^a   Tsukagoshi, Hironaka ^a   Benfey, Philip N ^a  

^a DUKE UNIVERSITY   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CELLULAR STRESS RESPONSE; GENOME ANALYSIS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN EXPRESSION;

ABSCISIC ACID; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOLOGICAL MARKERS; CELL LINEAGE; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT GROWTH REGULATORS; PLANT ROOTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC;

ARABIDOPSIS;

EID: 80054733290     PISSN: 15345807     EISSN: 18781551     Source Type: Journal    
DOI: 10.1016/j.devcel.2011.09.009     Document Type: Article

References (53)

1. Aida M., Beis D., Heidstra R., Willemsen V., Blilou I., Galinha C., Nussaume L., Noh Y.S., Amasino R., Scheres B. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 2004, 119:109-120.
2. Birnbaum K., Shasha D.E., Wang J.Y., Jung J.W., Lambert G.M., Galbraith D.W., Benfey P.N. A gene expression map of the Arabidopsis root. Science 2003, 302:1956-1960.
3. Brady S.M., Orlando D.A., Lee J.Y., Wang J.Y., Koch J., Dinneny J.R., Mace D., Ohler U., Benfey P.N. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 2007, 318:801-806.
4. Brown D.M., Zeef L.A., Ellis J., Goodacre R., Turner S.R. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 2005, 17:2281-2295.
5. Burguillo F.J., Martin J., Barrera I., Bardsley W.G. Meta-analysis of microarray data: the case of imatinib resistance in chronic myelogenous leukemia. Comput. Biol. Chem. 2010, 34:184-192.
6. Busch W., Miotk A., Ariel F.D., Zhao Z., Forner J., Daum G., Suzaki T., Schuster C., Schultheiss S.J., Leibfried A., et al. Transcriptional control of a plant stem cell niche. Dev. Cell 2010, 18:849-861.
7. Carlsbecker A., Lee J.Y., Roberts C.J., Dettmer J., Lehesranta S., Zhou J., Lindgren O., Moreno-Risueno M.A., Vatén A., Thitamadee S., et al. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature 2010, 465:316-321.
8. Chen R., Guan C., Boonsirichai K., Masson P.H. Complex physiological and molecular processes underlying root gravitropism. Plant Mol. Biol. 2002, 49:305-317.
9. Cui H., Levesque M.P., Vernoux T., Jung J.W., Paquette A.J., Gallagher K.L., Wang J.Y., Blilou I., Scheres B., Benfey P.N. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 2007, 316:421-425.
10. Cutler S.R., Rodriguez P.L., Finkelstein R.R., Abrams S.R. Abscisic acid: emergence of a core signaling network. Annu. Rev. Plant Biol. 2010, 61:651-679.
11. Dinneny J.R., Long T.A., Wang J.Y., Jung J.W., Mace D., Pointer S., Barron C., Brady S.M., Schiefelbein J., Benfey P.N. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 2008, 320:942-945.
12. Fisher R.A. Statistical Methods for Research Workers 1932, Oliver and Boyd, Edinburgh.
13. Fujita M., Fujita Y., Noutoshi Y., Takahashi F., Narusaka Y., Yamaguchi-Shinozaki K., Shinozaki K. Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr. Opin. Plant Biol. 2006, 9:436-442.
14. Gifford M.L., Dean A., Gutierrez R.A., Coruzzi G.M., Birnbaum K.D. Cell-specific nitrogen responses mediate developmental plasticity. Proc. Natl. Acad. Sci. USA 2008, 105:803-808.
15. Hirayama T., Shinozaki K. Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J. 2010, 61:1041-1052.
16. Hong F., Breitling R., McEntee C.W., Wittner B.S., Nemhauser J.L., Chory J. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 2006, 22:2825-2827.
17. Inoue T., Higuchi M., Hashimoto Y., Seki M., Kobayashi M., Kato T., Tabata S., Shinozaki K., Kakimoto T. Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature 2001, 409:1060-1063.
18. Karas B., Amyot L., Johansen C., Sato S., Tabata S., Kawaguchi M., Szczyglowski K. Conservation of lotus and Arabidopsis basic helix-loop-helix proteins reveals new players in root hair development. Plant Physiol. 2009, 151:1175-1185.
19. Kilian J., Whitehead D., Horak J., Wanke D., Weinl S., Batistic O., D'Angelo C., Bornberg-Bauer E., Kudla J., Harter K. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 2007, 50:347-363.
20. Kreps J.A., Wu Y., Chang H.S., Zhu T., Wang X., Harper J.F. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 2002, 130:2129-2141.
21. Kubo M., Udagawa M., Nishikubo N., Horiguchi G., Yamaguchi M., Ito J., Mimura T., Fukuda H., Demura T. Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev. 2005, 19:1855-1860.
22. Kültz D. Molecular and evolutionary basis of the cellular stress response. Annu. Rev. Physiol. 2005, 67:225-257.
23. Levesque M.P., Vernoux T., Busch W., Cui H., Wang J.Y., Blilou I., Hassan H., Nakajima K., Matsumoto N., Lohmann J.U., et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 2006, 4:e143.
24. Liu Q., Yao X., Pi L., Wang H., Cui X., Huang H. The ARGONAUTE10 gene modulates shoot apical meristem maintenance and leaf polarity establishment by repressing miR165/166 in Arabidopsis. Plant J. 2008, 58:27-40.
25. Long T.A., Tsukagoshi H., Busch W., Lahner B., Salt D.E., Benfey P.N. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell 2010, 22:2219-2236.
26. Ma S., Bohnert H.J. Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol. 2007, 8:R49.
27. Mallory A.C., Elmayan T., Vaucheret H. MicroRNA maturation and action-the expanding roles of ARGONAUTEs. Curr. Opin. Plant Biol. 2008, 11:560-566.
28. Miyashima S., Hashimoto T., Nakajima K. ARGONAUTE1 acts in Arabidopsis root radial pattern formation independently of the SHR/SCR pathway. Plant Cell Physiol. 2009, 50:626-634.
29. Nemhauser J.L., Hong F., Chory J. Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell 2006, 126:467-475.
30. Ochando I., Jover-Gil S., Ripoll J.J., Candela H., Vera A., Ponce M.R., Martínez-Laborda A., Micol J.L. Mutations in the microRNA complementarity site of the INCURVATA4 gene perturb meristem function and adaxialize lateral organs in Arabidopsis. Plant Physiol. 2006, 141:607-619.
31. Ohashi-Ito K., Bergmann D.C. Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY. Development 2007, 134:2959-2968.
32. Orlando D.A., Brady S.M., Koch J.D., Dinneny J.R., Benfey P.N. Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods Mol. Biol. 2009, 553:57-77.
33. Pernas M., Ryan E., Dolan L. SCHIZORIZA controls tissue system complexity in plants. Curr. Biol. 2010, 20:818-823.
34. Persson S., Wei H., Milne J., Page G.P., Somerville C.R. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc. Natl. Acad. Sci. USA 2005, 102:8633-8638.
35. Rabbani M.A., Maruyama K., Abe H., Khan M.A., Katsura K., Ito Y., Yoshiwara K., Seki M., Shinozaki K., Yamaguchi-Shinozaki K. Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol. 2003, 133:1755-1767.
36. Sakuma Y., Maruyama K., Osakabe Y., Qin F., Seki M., Shinozaki K., Yamaguchi-Shinozaki K. Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 2006, 18:1292-1309.
37. Sato A., Yamamoto K.T. Overexpression of the non-canonical Aux/IAA genes causes auxin-related aberrant phenotypes in Arabidopsis. Physiol. Plant. 2008, 133:397-405.
38. Sozzani R., Cui H., Moreno-Risueno M.A., Busch W., Van Norman J.M., Vernoux T., Brady S.M., Dewitte W., Murray J.A., Benfey P.N. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 2010, 466:128-132.
39. Storey J.D., Tibshirani R. Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol. Biol. 2003, 224:149-157.
40. Swindell W.R. The association among gene expression responses to nine abiotic stress treatments in Arabidopsis thaliana. Genetics 2006, 174:1811-1824.
41. ten Hove C.A., Willemsen V., de Vries W.J., van Dijken A., Scheres B., Heidstra R. SCHIZORIZA encodes a nuclear factor regulating asymmetry of stem cell divisions in the Arabidopsis root. Curr. Biol. 2010, 20:452-457.
42. Ticconi C.A., Lucero R.D., Sakhonwasee S., Adamson A.W., Creff A., Nussaume L., Desnos T., Abel S. ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability. Proc. Natl. Acad. Sci. USA 2009, 106:14174-14179.
43. Tominaga-Wada R., Iwata M., Sugiyama J., Kotake T., Ishida T., Yokoyama R., Nishitani K., Okada K., Wada T. The GLABRA2 homeodomain protein directly regulates CESA5 and XTH17 gene expression in Arabidopsis roots. Plant J. 2009, 60:564-574.
44. Tran L.S., Urao T., Qin F., Maruyama K., Kakimoto T., Shinozaki K., Yamaguchi-Shinozaki K. Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in Arabidopsis. Proc. Natl. Acad. Sci. USA 2007, 104:20623-20628.
45. Tsukagoshi H., Busch W., Benfey P.N. Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root. Cell 2010, 143:606-616.
46. Tucker M.R., Hinze A., Tucker E.J., Takada S., Jürgens G., Laux T. Vascular signalling mediated by ZWILLE potentiates WUSCHEL function during shoot meristem stem cell development in the Arabidopsis embryo. Development 2008, 135:2839-2843.
47. Tuteja N. Abscisic acid and abiotic stress signaling. Plant Signal. Behav. 2007, 2:135-138.
48. Walley J.W., Dehesh K. Molecular mechanisms regulating rapid stress signaling networks in Arabidopsis. J. Integr. Plant Biol. 2010, 52:354-359.
49. Walley J.W., Coughlan S., Hudson M.E., Covington M.F., Kaspi R., Banu G., Harmer S.L., Dehesh K. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet. 2007, 3:1800-1812.
50. Walther D., Brunnemann R., Selbig J. The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana. PLoS Genet. 2007, 3:e11.
51. Wang J.W., Wang L.J., Mao Y.B., Cai W.J., Xue H.W., Chen X.Y. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 2005, 17:2204-2216.
52. Zaykin D.V., Zhivotovsky L.A., Westfall P.H., Weir B.S. Truncated product method for combining P-values. Genet. Epidemiol. 2002, 22:170-185.
53. Zeller G., Henz S.R., Widmer C.K., Sachsenberg T., Rätsch G., Weigel D., Laubinger S. Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J. 2009, 58:1068-1082.