Double-filter identification of vascular-expressed genes using Arabidopsis plants with vascular hypertrophy and hypotrophy

Plant Science

Volumn 181, Issue 2, 2011, Pages 96-104

  Ckurshumova, Wenzislava ^a   Scarpella, Enrico ^b   Goldstein, Rochelle S ^a   Berleth, Thomas ^a  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Arabidopsis; Full transcriptome expression profiling; Gene expression markers; Microarray; Plant vascular development; Procambium

Indexed keywords

ARABIDOPSIS PROTEIN; COMPLEMENTARY DNA; COMPLEMENTARY RNA; INDOLEACETIC ACID DERIVATIVE; PLANT RNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARABIDOPSIS; ARTICLE; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT LEAF; TRANSGENIC PLANT; TRANSPORT AT THE CELLULAR LEVEL; UPREGULATION; VASCULAR BUNDLE (PLANT);

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOLOGICAL TRANSPORT; DNA, COMPLEMENTARY; DOWN-REGULATION; GENE EXPRESSION; GENE EXPRESSION REGULATION, PLANT; INDOLEACETIC ACIDS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT LEAVES; PLANT VASCULAR BUNDLE; PLANTS, GENETICALLY MODIFIED; RNA, COMPLEMENTARY; RNA, PLANT; TRANSCRIPTION FACTORS; TRANSCRIPTOME; UP-REGULATION;

ARABIDOPSIS;

EID: 79959199491     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2011.04.008     Document Type: Article

References (64)

1. Scarpella E., Meijer A.H. Pattern formation in the vascular system of monocot and dicot plant species. New Phytol. 2004, 164:209-242.
2. Sticklen M. Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol. Nat. Rev. Genet. 2008, 9:433-443.
3. Roberts K., McCann M.C. Xylogenesis: the birth of a corpse. Curr. Opin. Plant Biol. 2000, 3:517-522.
4. Dengler N.G. Regulation of vascular development. J. Plant Growth Regul. 2001, 20:113-120.
5. Ye Z.H. Vascular tissue differentiation and pattern formation in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2002, 53:183-202.
6. Fukuda H. Signals that control plant vascular cell differentiation. Nat. Rev. Mol. Cell Biol. 2004, 5:379-391.
7. Dinneny J.R., Yanofsky M.F. Vascular patterning: xylem or phloem. Curr. Biol. 2004, 14:112-114.
8. Esau K. Vascular Differentiation in Plants 1965, Rinehart and Winston, Inc., USA: Holt.
9. Scarpella E., Francis P., Berleth T. Stage specific markers define early steps of procambium development in Arabidopsis leaves and correlate termination of vein formation with mesophyl differentiation. Development 2004, 131:3445-3455.
10. Hertzberg M., Aspeborg H., Schrader J., et al. A transcriptional roadmap to woodformation. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:14732-14737.
11. Vilaine F., Palauqui J.C., Amselem J., Kusiak C., Lemoine R., Dinant S. Towards deciphering phloem: a transcriptome analysis of the phloem of Apium graveolens. Plant J. 2003, 36:67-81.
12. Ehlting J., Mattheus N., Aeschliman D.S., Li E., Hamberger B., Cullis I.F., Zhuang J., Kaneda M., Mansfield S.D., Samuels L., Ritland K., Ellis B.E., Bohlmann J., Douglas C.J. Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J. 2005, 42:618-640.
13. Kerk N.M., Ceserani T., Tausta S.L., Sussex I.M., Nelson T.M. Laser capture microdissection of cells from plant tissues. Plant Physiol. 2003, 132:27-35.
14. Asano T., Masumura T., Kusano H., Kikuchi S., Kurita A., Shimada H., Kadowaki K. Construction of a specialized cDNA library from plant cells isolated by laser capture microdissection: toward comprehensive analysis of the genes expressed in the rice phloem. Plant J. 2002, 32:401-408.
15. Nakazono M., Qiu F., Borsuk L.A., Schnable P.S. Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 2003, 15:583-596.
16. 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.
17. Brady S.M., Orlando D.A., Lee J.Y., Wang J.Y., Koch J., et al. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 2007, 318:801-806.
18. Nagawa S., Sawa S., Sato S., Kato T., Tabata S., Fukuda H. Gene trapping in Arabidopsis reveals genes involved in vascular development. Plant Cell Physiol. 2006, 47:1394-1405.
19. Ckurshumova W., Koizumi K., Chatfield S.P., Sanchez-Buelna S.U., Gangaeva A.E., McKenzie R., Berleth T. Tissue-specific GAL4 expression patterns as a resource enabling targeted gene expression, cell type-specific transcript profiling and gene function characterization in the Arabidopsis vascular system. Plant Cell Physiol. 2009, 50:141-150.
20. Demura T., Tashiro G., Horiguchi G., Kishimoto N., Kubo M., et al. Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:15794-15799.
21. Milioni D., Sado P.E., Stacey N.J., Roberts K., McCann M.C. Early gene expression associated with the commitment and differentiation of a plant tracheary element is revealed by cDNA-amplified fragment length polymorphism analysis. Plant Cell 2002, 14:2813-2824.
22. Kubo M., Udagawa M., Nishikubo N., Horiguchi G., Yamaguchi M., et al. Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev. 2005, 19:1855-1860.
23. Lev-Yadun S. Induction of sclereid differentiation in the pith of Arabidopsis thaliana (L.) Heynh. J. Exp. Bot. 1994, 45:1845-1849.
24. Zhao C., Johnson B.J., Kositsup B., Beers E.P. Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases. Plant Physiol. 2000, 123:1185-1196.
25. Little C.H.A., MacDonald J.E., Olsson O. Involvement of indole-3-acetic acid in fascicular and interfascicular cambial growth and interfascicular extraxylary fiber differentiation in Arabidopsis thaliana inflorescence stems. Int. J. Plant Sci. 2002, 163:519-529.
26. Oh S., Park S., Han K.-H. Transcriptional regulation of secondary growth in Arabidopsis thaliana. J. Exp. Bot. 2003, 54:2709-2722.
27. Ko J.-H., Han K.-H., Park S., Yang J. Plant body weight-Induced secondary growth in Arabidopsis and its transcription phenotype revealed by whole-transcriptome profiling. Plant Physiol. 2004, 135:1069-1083.
28. Mattsson J., Sung R.Z., Berleth T. Responses of plant vascular systems to auxin transport inhibition. Development 1999, 126:2979-2991.
29. Wenzel C.L., Hester Q., Mattsson J. Identification of genes expressed in vascular tissues using NPA-induced vascular overgrowth in Arabidopsis. Plant Cell Physiol. 2008, 49:457-468.
30. Mattsson J., Ckurshumova W., Berleth T. Auxin signaling in Arabidopsis leaf vascular development. Plant Physiol. 2003, 131:1327-1339.
31. Kang J., Dengler N. Cell cycling frequency and expression of the homeobox gene ATHB-8 during leaf vein development in Arabidopsis. Planta 2002, 216:212-219.
32. Baucher M., El Jaziri M., Vanderputte O. From primary to secondary growth: origin and development of the vascular system. J. Exp. Bot. 2007, 58:3485-3501.
33. Lincoln C., Britton J.H., Estelle M. Growth and development of the axr1 mutants of Arabidopsis. Plant Cell 1990, 2:1071-1080.
34. Prezemeck G.K.H., Mattsson J., Hardtke C.S., Sung Z.R., Berleth T. Studies of the role of the Arabidopsis gene MONOPTEROS in vascular development and plant cell axialisation. Planta 1996, 200:229-237.
35. Gälweiler L., Changhui G., Müller A., Wisman E., Mendgen K., Yephremov A., Palme K. Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue. Science 1998, 282:2226-2230.
36. Sieburth L.E. Auxin is required for leaf vein pattern in Arabidopsis. Plant Physiol. 1999, 121:1179-1190.
37. Redman J.C., Haas B.J., Tanimoto G., Town C.D. Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J. 2004, 38:545-561.
38. Desikan A.H., Mackerness S., Hancock J.T., Neill S.J. Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiol. 2001, 127:159-172.
39. Kawasaki S., Borchert C., Deyholos M., Wang H., Brazille S., Kawai K., Galbraith D., Bohnert H.J. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 2001, 13:889-906.
40. Perez-Amador M.A., Lidder P., Johnson M.A., Landgraf J., Wisman E., Green P.J. New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis. Plant Cell 2001, 13:2703-2717.
41. Swidzinski J.A., Sweetlove L.J., Leaver C. A custom microarray analysis of gene expression during programmed cell death in Arabidopsis thaliana. Plant J. 2002, 30:431-446.
42. Beeckman T., Przemeck G.K., Stamatiou G., Lau R., Terryn N., De Rycke R., Inzé D., Berleth T. Genetic complexity of cellulose synthase a gene function in Arabidopsis embryogenesis. Plant Physiol. 2002, 130:1883-1893.
43. Zachgo S., Perbal M.C., Saedler H., Schwarz-Sommer Z. In situ analysis of RNA and protein expression in whole mounts facilitates detection of floral gene expression dynamics. Plant J. 2000, 23:697-702.
44. Nieminen K.M., Kauppinen L., Helariutta Y. A weed for wood? Arabidopsis as a genetic model for xylem development. Plant Physiol. 2004, 135:653-659.
45. Hardtke C.S., Berleth T. The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J. 1998, 17:1405-1411.
46. Baima S., Possenti M., Matteucci A., Wisman E., Altamura M.M., Ruberti I., Morelli G. The Arabidopsis ATHB-8 HD-zip protein acts as a differentiation-promoting transcription factor of the vascular meristems. Plant Physiol. 2001, 126:643-655.
47. Mouchel C.F., Osmont K.S., Hardtke C.S. BRX mediates feedback between brassinosteroid levels and auxin signalling in root growth. Nature 2006, 28:458-461.
48. Kim S.J., Kim M.R., Bedgar D.L., Moinuddin S.G., Cardenas C.L., Davin L.B., Kang C., Lewis N.G. Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2004, 6:1455-1459.
49. Riechmann J.L., Ratcliffe O.J. A genomic perspective on plant transcription factors. Curr. Opin. Plant Biol. 2000, 3:423-434.
50. Koshino-Kimura Y., Wada T., Tachibana T., Tsugeki R., Ishiguro S., Okada K. Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis. Plant Cell Physiol. 2005, 46:817-826.
51. Lee J.Y., Colinas J., Wang J.Y., Mace D., Ohler U., Benfey P.N. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:6055-6060.
52. Kurata T., Kawabata-Awai C., Sakuradani E., Shimizu S., Okada K., Wada T. The YORE-YORE gene regulates multiple aspects of epidermal cell differentiation in Arabidopsis. Plant J. 2003, 36:55-66.
53. Scarpella E., Marcos D., Friml J., Berleth T. Control of leaf vascular patterning by polar auxin transport. Genes Dev. 2006, 20:1015-1027.
54. Kerstetter R.A., Bollman K., Taylor R.A., Bomblies K., Poethig R.S. KANADI regulates organ polarity in Arabidopsis. Nature 2001, 7:706-709.
55. McConnell J.R., Emery J., Eshed Y., Bao N., Bowman J., Barton M.K. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 2001, 7:709-713.
56. Emery J.F., Floyd S.K., Alvarez J., Eshed Y., Hawker N.P., Izhaki A., Baum S.F., Bowman J.L. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 2003, 13:1768-1774.
57. Hawker N.P., Bowman J.L. Roles for Class III HD-Zip and KANADI genes in Arabidopsis root development. Plant Physiol. 2004, 135:2261-2270.
58. Zhong R., Ye Z.H. IFL1, a gene regulating interfascicular fiber differentiation in Arabidopsis, encodes a homeodomain-leucine zipper protein. Plant Cell 1999, 11:2139-2152.
59. Helariutta Y., Fukaki H., Wysocka-Diller J., Nakajima K., Jung J., Sena G., Hauser M.T., Benfey P.N. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 2000, 101:555-567.
60. Nakajima K., Sena G., Nawy T., Benfey P.N. Intercellular movement of the putative transcription factor SHR in root patterning. Nature 2001, 413:307-311.
61. Gardiner J., Donner T.J., Scarpella E Simultaneous activation of SHR and ATHB8 expression defines switch to preprocambial cell state in Arabidopsis leaf development. Dev. Dyn. 2011, 240(1):261-270.
62. Gardiner J., Sherr I., Scarpella E. Expression of DOF genes identifies early stages of vascular development in Arabidopsis leaves. Int. J. Dev. Biol. 2010, 54:1389-1396.
63. Konishi M., Yanagisawa S. Sequential activation of two Dof transcription factor gene promoters during vascular development in Arabidopsis thaliana. Plant Physiol. Biochem. 2007, 45:623-629.
64. Skirycz A., Radziejwoski A., Busch W., Hannah M.A., Czeszejko J., Kwaśniewski M., Zanor M.I., Lohmann J.U., De Veylder L., Witt I., Mueller-Roeber B. The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana. Plant J. 2008, 56:779-792.