The Arabidopsis basic/helix-loop-helix transcription factor family

Plant Cell

Volumn 15, Issue 8, 2003, Pages 1749-1770

  Toledo Ortiz, Gabriela ^b   Huq, Enamul ^a   Quail, Peter H ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

DIMERS; DNA; GENES;

PHYLOGENETIC ANALYSIS;

PROTEINS;

ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA;

EID: 0042421751     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.013839     Document Type: Article

References (66)

1. Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2003). Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15, 63-78.
2. Abe, H., Yamaguchi-Shinozaki, K., Urao, T., Iwasaki, T., Hosokawa, D., and Shinozaki, K. (1997). Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9, 1859-1868.
3. Atchley, W.R., and Fitch, W.M. (1997). A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. USA 94, 5172-5176.
4. Atchley, W.R., Therhalle, W., and Dress, A. (1999). Positional dependence, cliques and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48, 501-516.
5. Baudino, T.A., and Cleveland, J.L. (2001). The Max network gone mad. Mol. Cell. Biol. 21, 691-702.
6. Beischlag, T.V., Wang, S., Rose, D.W., Torchia, J., Reisz-Porszasz, S., Muhammad, K., Nelson, W.E., Probst, M.R., Rosenfeld, M.G., and Hankinson, O. (2002). Recruitment of the NcoA/SRC-1/p160 family of transcriptional coactivators by the aryl hydrocarbon receptor/aryl hydrocarbon receptor nuclear translocator complex. Mol. Cell. Biol. 22, 4319-4333.
7. Bornberg-Bauer, E., Rivals, E., and Vingron, M. (1998). Computational approaches to identify leucine zippers. Nucleic Acids Res. 26, 2740-2746.
8. Brownlie, P., Ceska, T., Lamers, M., Romier, C., Stier, G., Teo, H., and Suck, D. (1997). The crystal structure of an intact human Max-DNA complex: New insights into mechanisms of transcriptional control. Structure 5, 509-520.
9. Brunak, S., Engelbrecht, J., and Knudsen, S. (1991). Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol. 220, 49-65.
10. Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.-H., Hong, X., Agarwal, M., and Zhu, J.-K. (2003). ICE: A regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 1043-1054.
11. Ciarapica, R., Rosati, J., Cesareni, G., and Nasi, S. (2003). Molecular recognition in helix-loop-helix and helix-loop-helix leucine zipper domains. J. Biol. Chem. 278, 12182-12190.
12. Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16, 10881-10890.
13. Crozatier, M., Valle, D., Dubois, L., Ibnsouda, S., and Vincent, A. (1996). collier, a novel regulator of Drosophila head development, is expressed in a single mitotic domain. Curr. Biol. 6, 707-718.
14. Dang, C.V., Dolde, C., Gillison, M.L., and Kato, G.J. (1992). Discrimination between related DNA sites by a single amino acid residue of Myc-related basic-helix-loop-helix proteins. Proc. Natl. Acad. Sci. USA 89, 599-602.
15. Dhordain, P., Lin, R.J., Quief, S., Lantoine, D., Kerckaert, J.P., Evans, R.M., and Albagli, O. (1998). The LAZ3 (BCL-6) oncoprotein recruits SMRT/mSIN3A/histone deacetylase containing complex to mediate transcription. Nucleic Acids Res. 26, 4645-4651.
16. Dubois, L., and Vincent, A. (2001). The COE-Collier /Olf1/EBF transcription factors: Structural conservation and diversity of developmental functions. Mech. Dev. 108, 3-12.
17. Ellenberg, T., Fass, D., Arnaud, M., and Harrison, S. (1994). Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 8, 970-980.
18. Eulgem, T., Rushton, P.J., Robatzek, S., and Somssich, I.E. (2000). The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5, 199-206.
19. Fairchild, C.D., Schumaker, M.A., and Quail, P.H. (2000). HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction. Genes Dev. 14, 2377-2391.
20. Fairman, R., Beran-Steed, R.K., Anthony-Cahill, S.J., Lear, J.D., Strafford, W.F., 3rd, DeGrado, W.F., Benfield, P.A., and Brenner, S.L. (1993). Multiple oligomeric states regulate the DNA binding of helix-loop-helix peptides. Proc. Natl. Acad. Sci. USA 90, 10429-10433.
21. Ferre-D'Amare, A.R., Pognonec, P., Roeder, R.G., and Burley, S.K. (1994). Structure and function of the b/HLH/Z domain of USF. EMBO J. 13, 180-189.
22. Fisher, A., and Caudy, M. (1998). The function of hairy-related bHLH represser proteins in cell fate decisions. Bioessays 20, 298-306.
23. Fisher, F., and Goding, C.R. (1992). Single amino acid substitutions alter helix-loop-helix protein specificity for bases flanking the core CANNTG motif. EMBO J. 11, 4103-4109.
24. Friedrichsen, D.M., Nemhauser, J., Muramitsu, T., Maloof, J.N., Alonso, J., Ecker, J.R., Furuya, M., and Chory, J. (2002). Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics 162, 1445-1456.
25. Fuji, Y., Shimizu, T., Toda, T., Yaganida, M., and Hakoshima, T. (2000). Structural basis for the diversity of DNA recognition by bZip transcription factors. Nat. Struct. Biol. 7, 889-893.
26. Grandori, C., Cowley, S.M., James, L.P., and Eisenman, R.N. (2000). The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu. Rev. Cell Dev. Biol. 16, 653-699.
27. Hebsgaard, S.M., Korning, P.G., Tolstrup, N., Engelbrecht, J., Rouze, P., and Brunak, S. (1996). Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information. Nucleic Acids Res. 24, 3439-3452.
28. Heim, M.A., Jacoby, M., Werber, M., Martin, C., Weisshaar, B., and Bailey, P.C. (2003). The basic helix-loop-helix transcription factor family in plants: A genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20, 735-747.
29. Heisler, M.G.B., Atkinson, A., Bylstra, Y.H., Walsh, R., and Smith, D.R. (2001). SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein. Development 128, 1089-1098.
30. Hua, X., Yokoyama, C., Wu, J., Briggs, M.R., Brown, M.S., Goldstein, J.L., and Wang, X. (1993). SREBP-2, a second basic-helix-loop-helix leucine zipper protein that stimulates transcription by binding to a sterol regulatory element. Proc. Natl. Acad. Sci. USA 90, 11603-11607.
31. Huq, E., and Quail, P.H. (2002). PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J. 21, 2441-2450.
32. Iyer, L.M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B., and Koonin, E.V. (2003). Quoderat demostrandum? The mystery of experimental validation of apparent erroneous computational analyses of protein sequences. Genome Biol. 2, RESEARCH0051.1-RESEARCH0051.11.
33. Jakoby, M., Weisshaar, B., Droge-Laser, W., Vicente-Carbajosa, J., Tiedmann, J., Kroi, T., and Parcy, F. (2002). bZIP transcription factors in Arabidopsis. Trends Plant Sci. 7, 106-111.
34. Ledent, V., and Vervoort, M. (2001). The basic helix-loop-helix protein family: Comparative genomics and phylogenetic analysis. Genome Res. 11, 754-770.
35. Levens, D.L. (2003). Reconstructing MYC. Genes Dev. 17, 1071-1077.
36. Littlewood, T., and Evan, G.I. (1998). Helix-Loop-Helix Transcription Factors, 3rd ed. (New York: Oxford University Press).
37. Ludwig, S.R., Habera, L.F., Dellaporta, S.L., and Wessier, S.R. (1989). Lc, a member of the maize R gene family responsible for tissue specific anthocyanin production, encodes a protein similar to transcriptional activators and contains a myc-homology region. Proc. Natl. Acad. Sci. USA 86, 7092-7096.
38. Ma, P.C.M., Rould, M.A., Weintraub, H., and Pabo, C.O. (1994). Crystal structure of MyoD bHLH domain-DMA recognition and implications for transcriptional activation. Cell 77, 451-459.
39. Martinez-Garcia, J., Huq, E., and Quail, P.M. (2000). Direct targeting of light signals to a promoter element-bound transcription factor. Science 288, 859-863.
40. Massari, M.E., and Murre, C. (2000). Helix-loop-helix proteins: Regulators of transcription in eukaryotic organisms. Mol. Cell. Biol. 20, 429-440.
41. Mewes, H.W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S., and Weil, B. (2002). MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30, 31-34.
42. Morgenstern, B., and Atchley, W.R. (1999). Evolution of bHLH transcription factors: Modular evolution by domain shuffling? Mol. Biol. Evol. 16, 1654-1663.
43. Murre, C., McCaw, P.S., and Baltimore, D. (1989). A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD and myc proteins. Cell 56, 777-783.
44. Nair, S.K., and Burley, S.K. (2000). Recognizing DNA in the library. Nature 404, 715-717.
45. Nesi, N., Debeaujon, I., Jond, C., Pelletier, G., Caboche, M., and Lepiniec, L. (2000). The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques. Plant Cell 12, 1863-1878.
46. Ni, M., Tepperman, J.M., and Quail, P.M. (1998). PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95, 657-667.
47. Ni, M., Tepperman, J.M., and Quail, P.M. (1999). Binding of phytochrome B to its nuclear signalling partner PIF3 is reversibly induced by light. Nature 400, 781-784.
48. Paroush, Z., Finley, R.L., Jr., Kidd, T., Wainwright, S.M., Ingham, P.W., Brent, R., and Ish-Horowicz, D. (1994). Groucho is required for-Drosophila neurogenesis, segmentation, and sex determination and interacts directly with hairy-related bHLH proteins. Cell 79, 5805-5815.
49. Payne, C.T., Zhang, F., and Lloyd, A.M. (2000). GL3 encodes a bHLH protein that regulates trichome development in Arabidopsis through the interaction with GL1 and TTG1. Genetics 156, 1349-1362.
50. Pscherer, A., Dorflinger, U., Kifel, J., Gawas, K., Ruschoff, J., Buettner, R., and Schule, R. (1996). The helix-loop-helix transcription factor SEF-2 regulates the activity of a novel initiator element in the promoter of the human somatostatin receptor II gene. EMBO J. 15, 6680-6690.
51. Puri, P.L., Avantaggiati, M.L., Balsano, C., Sang, N., Graessmann, A., Giordano, A., and Levrero, M. (1997). p300 is required for MyoD-dependent cell cycle arrest and muscle-specific gene transcription. EMBO J. 16, 369-383.
52. Quail, P.M. (2000). Phytochrome interacting factors. Semin. Cell Dev. Biol. 11, 457-466.
53. Rajani, S., and Sundaresan, V. (2001). The Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence. Curr. Biol. 11, 1914-1922.
54. Riechmann, J.L., et al. (2000). Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science 290, 2105-2109.
55. Robinson, K.A., Koepke, J.I., Kharodawala, M., and Lopes, J.M. (2000). A network of yeast basic helix-loop-helix interactions. Nucleic Acids Res. 28, 4460-4466.
56. Roy, A.L., Meisterernst, M., Pognonec, P., and Roeder, R.G. (1991). Cooperative interaction of an initiator-binding transcription factor and the basic-helix-loop-helix activator USF. Nature 354, 245-248.
57. Shimizu, T., Toumoto, A., Ihara, K., Shimizu, M., Kyogoku, Y., Ogawa, N., Oshima, Y., and Hakoshima, T. (1997). Crystal structure of PHO4 bHLH domain-DNA complex: Flanking base recognition. EMBO J. 16,4689-4697.
58. Shirakata, M., Friedman, F.K., Wei, Q., and Patterson, B. (1993). Dimerization specificity of myogenic helix-loop-helix DNA bindingfactors directed by nonconserved hydrophilic residues. Genes Dev. 7, 2456-2470.
59. Smolen, G.A., Pawlowski, L., Wilensky, S.E., and Bender, J. (2002). Dominant alleles of the basic helix-loop-helix transcription factor ATR2 activate stress-responsive genes in Arabidopsis. Genetics 161, 1235-1246.
60. Sorensen, A.M., Krober, S., Unte, U.S., Hujser, P., Dekker, K., and Saedler, H. (2003). The Arabidopsis Aborted Microspores (AMS) gene encodes a MYC class transcription factor. Plant J. 33, 413-423.
61. Stracke, R., Werber, M., and Weisshaar, B. (2001). The R2R3-MYB gene family in Arabidopsis thaliana. Curr. Opin. Plant Biol. 4, 447-456.
62. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
63. Venter, J.C., et al. (2001). The sequence of the human genome. The Celera Genomics Human Genome Sequencing Consortium. Science 291, 1304-1350.
64. Waterston, R.H., et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Mouse Genome Sequencing Consortium. Nature 420, 520-562.
65. Winston, R.L., and Gottesfeld, J.M. (2000). Rapid identification of key amino-acid-DNA contacts through combinatorial peptide synthesis. Chem. Biol. 7, 245-251.
66. Zhu, Y., Tepperman, J.M., Fairchild, C.D., and Quail, P.M. (2000). Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3. Proc. Natl. Acad. Sci. USA 21, 13419-13424.