The auxin-induced transcriptome for etiolated Arabidopsis seedlings using a structure/function approach

Functional and Integrative Genomics

Volumn 3, Issue 4, 2003, Pages 135-143

  Pufky, John ^a   Qiu, Yang ^a   Rao, Mulpuri V ^a   Hurban, Patrick ^a   Jones, Alan M ^b  

^a Clinical Data Inc   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Abscisic acid; Arabidopsis; Auxenic herbicides; Auxin; Gene expression

Indexed keywords

ABSCISIC ACID; AUXIN; AUXIN RESPONSE FACTOR; INDOLEACETIC ACID; PROTEIN ARFAT; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG; INDOLEACETIC ACID DERIVATIVE; PHYTOHORMONE;

ARABIDOPSIS; ARTICLE; CONCENTRATION RESPONSE; DNA BINDING MOTIF; DNA MICROARRAY; DNA RESPONSIVE ELEMENT; DNA STRUCTURE; ETIOLATION; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE IDENTIFICATION; GENE LIBRARY; GENOME ANALYSIS; HORMONE ACTION; HORMONE STRUCTURE; MODULATION; NONHUMAN; ONCOGENE MYC; PRIORITY JOURNAL; PROMOTER REGION; SEEDLING; SILENCER ELEMENT; 5' UNTRANSLATED REGION; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; COMPARATIVE STUDY; DRUG EFFECT; GENE; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; REGULATORY SEQUENCE; STRUCTURE ACTIVITY RELATION; TIME;

5' UNTRANSLATED REGIONS; ARABIDOPSIS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; INDOLEACETIC ACIDS; MOLECULAR STRUCTURE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT GROWTH REGULATORS; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; SEEDLING; STRUCTURE-ACTIVITY RELATIONSHIP; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 2642525271     PISSN: 1438793X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10142-003-0093-7     Document Type: Article

References (38)

1. Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9:1859-1868 1:CAS:528:DyaK2sXntFaks7s%3D
2. Abel S, Theologis A (1996) Early genes and auxin action. Plant Physiol 111:9-17 8685277
3. Abel S, Nguyen MD, Theologis A (1995) The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J Mol Biol 251:533-549 10.1006/jmbi.1995.0454
4. Boerjan W, Cervera MT, Delarue M, Beeckman T, Dewitte W, Bellini C, Caboche M, Van Oncklen H, Inze D (1995) superroot, a recessive mutation in Arabidopsis, confers auxin overproduction. Plant Cell 7:1405-1419 1:CAS:528:DyaK2MXot1Ogurs%3D
5. Boyle B, Brisson N (2001) Repression of the defense gene PR-10a by the single-stranded DNA binding protein SEBF. Plant Cell 13:2525-2537 10.1105/tpc.13.11.2525
6. Busk PK, Pages M (1998) Regulation of abscisic acid-induced transcription. Plant Mol Biol 37:425-443 1:CAS:528:DyaK1cXjtlKqtbo%3D
7. Che P, Gingerich DJ, Lall S, Howell SH (2002) Global and hormone-induced gene expression changes during shoot development in Arabidopsis. Plant Cell 14:2771-2785
8. Edgerton MD, Tropsha A, Jones AM (1994) The auxin-binding site of auxin-binding protein 1. Phytochemistry 35:1111-1123 10.1016/ S0031-9422(00)94807-6
9. Finkelstein RR, Lynch TJ (2000) The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell 12:599-609
10. Giraudat J, Hauge BM, Valon C, Smalle J, Parcy F, Goodman HM (1992) Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell 4:1251-1261 1359917
11. Guilfoyle TJ, Ulmasov T, Hagen G (1998) The ARF family of transcription factors and their role in plant hormone responsive transcription. Cell Mol Life Sci 54:619-627 10.1007/s000180050190
12. Hagen G, Guilfoyle T (2002) Auxin-responsive gene expression: Genes, promoters and regulatory factors. Plant Mol Biol 49:373-385 10.1023/ A:1015207114117
13. Hagen G, Kleinschmidt A, Guilfoyle T (1984) Auxin regulated gene expression in intact soybean hypocotyl and excised hypocotyl sections. Planta 162:147-153 1:CAS:528:DyaL2cXmt1ersbY%3D
14. Hansen H, Grossmann K (2000) Auxin-induced ethylene triggers abscisic acid biosynthesis and growth inhibition. Plant Physiol 124:1437-1448 1:CAS:528:DC%2BD3cXotlWqsLY%3D
15. Higo K, Ugawa Y, Iwamoto M, Korennaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res 27:297-300 1:CAS:528:DyaK1MXpsVKgug%3D%3D
16. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342-347 10.1038/86730
17. Imamura H, Tanaka K, Hihara T, Umikawa M, Kamei T, Takahashi K, Sasaki T, Takai Y (1997) Bni1p and Bnr1p: Downstream targets of the Rho family small G-proteins which interact with profilin and regulate actin cytoskeleton in Saccharomyces cerevisiae. EMBO J 16:2745-2755 1:CAS:528:DyaK2sXjsF2nurc%3D
18. Jiang C, Iu B, Singh J (1996) Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol Biol 30:679-684 1:CAS:528:DyaK28XhvFygsrY%3D
19. Jones AM (1994) Auxin-binding proteins. Annu Rev Plant Physiol Plant Mol Biol 45:393-420
20. Kim SY, Chung HJ, Thomas TL (1997) Isolation of a novel class of bZIP transcription factors that interact with ABA-responsive and embryo-specification elements in the Dc3 promoter using a modified yeast one-hybrid system. Plant J 11:1237-1251 10.1046/ j.1365-313X.1997.11061237.x
21. Melhado LL, Jones AM, Ho T-HD, Leonard NJ (1981) Azido auxins: Synthesis and biological activity of fluorescent labeling agents. Plant Physiol 68:469-475 1:CAS:528:DyaL3MXlvFyhsrg%3D
22. Napier R (1995) Towards an understanding of ABP1. J. Exp Bot 46:1787-1795 1:CAS:528:DyaK28XlsFegsA%3D%3D
23. Overbeek J van (1964) Survey of mechanism of herbicide action. Academic Press, London
24. Reed JW, Elumalai RP, Chory J (1998) Suppressors of an Arabidopsis thaliana phyB mutation identify genes that control light signaling and hypocotyl elongation. Genetics 148:1295-1310 1:CAS:528:DyaK1cXks1eitLg%3D
25. Seki M, Ishida J, Narusaka M, Fujita M, Nanjo T, Umezawa T, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002) Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genom 2(6):282-291 10.1007/s10142-002-0070-6
26. Shuai B, Reynaga-Pena CG, Springer PS (2002). The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol. 129:747-761
27. Singh KB, Foley RC, Onate-Sanchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430-436 10.1016/S1369-5266(02)00289-3
28. Staswick P, Tiryaki I, Rowe M (2002) Jasmonate response locus, JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation. Plant Cell 14:1405-1415
29. Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci USA 94:1035-1040 1:CAS:528:DyaK2sXhtVyhsLc%3D
30. Theologis A, Huynh TV, Davis RW (1985) Rapid induction of specific mRNAs by auxin in pea epicotyl tissue. J Mol Biol 183:53-68 1:CAS:528:DyaL2MXktlaqtLg%3D
31. Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouze P, Moreau Y (2001) A higher order background model improves the detection of regulatory elements by Gibbs sampling. Bioinformatics 17:1113-1122 10.1093/bioinformatics/17.12.1113
32. Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouze P, Moreau Y (2002) A Gibbs sampling method to detect over-represented motifs in upstream regions of coexpressed genes. J Comp Biol 9:447-464 10.1089/ 10665270252935566
33. Tiwari SB, Hagen G, Guilfoyle T (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15:533-543 10.1105/tpc.008417
34. Ulmasov T, Hagan G, Guilfoyle T (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276:1865-1868 1:CAS:528:DyaK2sXksVCnu7k%3D
35. Ulmasov T, Hagen G, Guilfoyle TJ (1999) Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci USA 96:5844-5849 1:CAS:528:DyaK1MXjtFCnu7s%3D
36. Watahiki MK, Yamamoto KT (1997) The massugu1 mutation of Arabidopsis identified with failure of auxin-induced growth curvature of hypocotyl confers auxin insensitivity to hypocotyl and leaf. Plant Physiol 115:419-426 10.1104/pp.115.2.419
37. Weed Society of America (eds) (1989) Herbicide handbook. Weed Society of America, Champaign, Ill.
38. Woo EJ, Marshall J, Bauly JM, Chen J-G, Venis MA, Napier RM, Pickersgill RW (2002) Crystal structure of auxin-binding protein 1 in complex with auxin. EMBO J 21:2877-2885 10.1093/emboj/cdf291