Identification of a consensus DNA-binding site for the Arabidopsis thaliana SBP domain transcription factor, AtSPL14, and binding kinetics by surface plasmon resonance

Biochemistry

Volumn 47, Issue 12, 2008, Pages 3645-3653

  Liang, Xinwen ^a   Nazarenus, Tara J ^a   Stone, Julie M ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA ATSPL14 SBP DOMAIN GENE; BINDING KINETICS; DNA-BINDING SITE;

BINDING ENERGY; DNA SEQUENCES; PHOTOSYNTHESIS; TRANSCRIPTION;

PROTEINS;

BINDING PROTEIN; SQUAMOSA PROMOTER BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SPL14; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; BINDING KINETICS; BINDING SITE; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; DNA BINDING; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; SURFACE PLASMON RESONANCE;

ARABIDOPSIS PROTEINS; BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; KINETICS; PROTEIN STRUCTURE, TERTIARY; SELEX APTAMER TECHNIQUE; SURFACE PLASMON RESONANCE;

ARABIDOPSIS THALIANA;

EID: 41149092953     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701431y     Document Type: Article

References (45)

1. Deyhle, F., Sarkar, A. K., Tucker, E. J., and Laux, T. (2007) WUSCHEL regulates cell differentiation during anther development. Dev. Biol. 302, 154-159.
2. van Doorn, W. G., and Woltering, E. J. (2005) Many ways to exit? Cell death categories in plants. Trends Plant Sci. 10, 117-122.
3. Groover, A., and Jones, A. M. (1999) Tracheary element differentiation uses a novel mechanism coordinating programmed cell death and secondary cell wall synthesis. Plant Physiol. 119, 375-384.
4. Demura, T., Tashiro, G., Horiguchi, G., Kishimoto, N., Kubo, M., Matsuoka, N., Minami, A., Nagata-Hiwatashi, M., Nakamura, K., Okamura, Y., Sassa, N., Suzuki, S., Yazaki, J., Kikuchi, S., and Fukuda, H. (2002) Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl. Acad. Sci. U.S.A. 99, 15794-15799.
5. Fukuda, H. (2000) Programmed cell death of tracheary elements as a paradigm in plants. Plant Mol. Biol. 44, 245-253.
6. Gechev, T. S., Van Breusegem, F., Stone, J. M., Denev, I., and Laloi, C. (2006) Reactive oxygen species as signals that modulate plant stress responses and programmed cell death. BioEssays 28, 1091-1101.
7. Gilchrist, D. G. (1998) Programmed cell death in plant disease: the purpose and promise of cellular suicide. Annu. Rev. Phytopathol. 36, 393-414.
8. Beers, E. P., and McDowell, J. M. (2001) Regulation and execution of programmed cell death in response to pathogens, stress and developmental cues. Curr. Opin. Plant Biol. 4, 561-567.
9. Stone, J. M., Liang, X., Nekl, E. R., and Stiers, J. J. (2005) Arabidopsis AtSPL14, a plant-specific SBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1. Plant J. 41, 744-754.
10. Stone, J. M., Heard, J. E., Asai, T., and Ausubel, F. M. (2000) Simulation of fungal-mediated cell death by fumonisin B1 and selection of fumonisin B1-resistant (fbr) Arabidopsis mutants. Plant Cell 12, 1811-1822.
11. Asai, T., Stone, J. M., Heard, J. E., Kovtun, Y., Yorgey, P., Sheen, J., and Ausubel, F. M. (2000) Fumonisin B1-induced cell death in Arabidopsis protoplasts requires jasmonate-, ethylene-, and salicylate-dependent signaling pathways. Plant Cell 12, 1823-1836.
12. Xie, K., Wu, C., and Xiong, L. (2006) Genomic organization, differential expression and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol. 142, 280-293.
13. Cardon, G., Hohmann, S., Klein, J., Nettesheim, K., Saedler, H., and Huijser, P. (1999) Molecular characterisation of the Arabidopsis SBP-box genes. Gene 237, 91-104.
14. Moreno, M. A., Harper, L. C., Krueger, R. W., Dellaporta, S. L., and Freeling, M. (1997) liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis. Genes Dev. 11, 616-628.
15. Wang, H., Nussbaum-Wagler, T., Li, B., Zhao, Q., Vigouroux, Y., Faller, M., Bomblies, K., Lukens, L., and Doebley, J. F. (2005) The origin of the naked grains of maize. Nature 436, 714-719.
16. Unte, U. S., Sorensen, A. M., Pesaresi, P., Gandikota, M., Leister, D., Saedler, H., and Huijser, P. (2003) SPL8, an SBP-box gene that affects pollen sac development in Arabidopsis. Plant Cell 15, 1009-1019.
17. Cardon, G. H., Hohmann, S., Nettesheim, K., Saedler, H., and Huijser, P. (1997) Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J. 12, 367-377.
18. Kropat, J., Tottey, S., Birkenbihl, R. P., Depege, N., Huijser, P., and Merchant, S. (2005) A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc. Natl. Acad. Sci. U.S.A. 102, 18730-18735.
19. Merchant, S. S., Allen, M. D., Kropat, J., Moseley, J. L., Long, J. C., Tottey, S., and Terauchi, A. M. (2006) Between a rock and a hard place: trace element nutrition in Chlamydomonas. Biochim. Biophys. Acta 1763, 578-594.
20. Zhang, Y., Schwarz, S., Saedler, H., and Huijser, P. (2007) SPL8, a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol. Biol. 63, 429-439.
21. Manning, K., Tor, M., Poole, M., Hong, Y., Thompson, A. J., King, G. J., Giovannoni, J. J., and Seymour, G. B. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38, 948-952.
22. Lee, J., Park, J. J., Kim, S. L., Yim, J., and An, G. (2007) Mutations in the rice liguleless gene result in a complete loss of the auricle, ligule, and laminar joint. Plant Mol. Biol. 65, 487-499.
23. Jones-Rhoades, M. W., and Battel, D. P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787-799.
24. Xie, Z., Allen, E., Fahlgren, N., Calamar, A., Givan, S. A., and Carrington, J. C. (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol. 138, 2145-2154.
25. Gandikota, M., Birkenbihl, R. P., Hohmann, S., Cardon, G. H., Saedler, H., and Huijser, P. (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 49, 683-693.
26. Yamasaki, K., Kigawa, T., Inoue, M., Tateno, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Nunokawa, E., Ishizuka, Y., Terada, T., Shirouzu, M., Osanai, T., Tanaka, A., Seki, M., Shinozaki, K., and Yokoyama, S. (2004) A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J. Mol. Biol. 337, 49-63.
27. Yamasaki, K., Kigawa, T., Inoue, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Tomo, Y., Terada, T., Shirouzu, M., Tanaka, A., Seki, M., Shinozaki, K., and Yokoyama, S. (2006) An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure. FEBS Lett. 580, 2109-2116.
28. Birkenbihl, R. P., Jach, G., Saedler, H., and Huijser, P. (2005) Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J. Mol. Biol. 352, 585-596.
29. Klein, J., Saedler, H., and Huijser, P. (1996) A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 250, 7-16.
30. Sambrook, J., and Russell, D. W. (2001) Molecular cloning: a laboratory manual, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Watson, D. K., Kitching, R., Vary, C., Kola, I., and Seth, A. (2000) Isolation of target gene promoter/enhancer sequences by whole genome PCR method, in Transcription Factor Protocols (Tymms, M. J., Ed.) pp 1-11, Humana Press, Totowa, NJ.
32. Karlsson, R. (1999) Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology. J. Mol. Recognit. 12, 285-292.
33. Kalifa, Y., Gilad, A., Konrad, Z., Zaccai, M., Scolnik, P. A., and Bar-Zvi, D. (2004) The water- and salt-stress-regulated Asr1 (abscisic acid stress ripening) gene encodes a zinc-dependent DNA-binding protein. Biochem. J. 381, 373-378.
34. Manuel, M., Rallu, M., Loones, M. T., Zimarino, V., Mezger, V., and Morange, M. (2002) Determination of the consensus binding sequence for the purified embryonic heat shock factor 2. Eur. J. Biochem. 269, 2527-2537.
35. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K., Eds. (2006) Current Protocols in Molecular Biology, John Wiley and Sons, New York, NY.
36. Grundy, W. N., Bailey, T. L., Elkan, C. P., and Baker, M. E. (1997) Meta-MEME: motif-based hidden Markov models of protein families. Comput. Appl. Biosci. 13, 397-406.
37. Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004) WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190.
38. Desai, K., Sullards, M. C., Allegood, J., Wang, E., Schmelz, E. M., Hartl, M., Humpf, H. U., Liotta, D. C., Peng, Q., and Merrill, A. H., Jr. (2002) Fumonisins and fumonisin analogs as inhibitors of ceramide synthase and inducers of apoptosis. Biochim. Biophys. Acta 1585, 188-192.
39. Chen, L. (1999) Combinatorial gene regulation by eukaryotic transcription factors. Curr. Opin. Struct. Biol. 9, 48-55.
40. Robbins, J., Dilworth, S. M., Laskey, R. A., and Dingwall, C. (1991) Two interdependent basic domains in nucleoplasmin nuclear targeting sequence: identification of a class of bipartite nuclear targeting sequence. Cell 64, 615-623.
41. Luscombe, N. M., Laskowski, R. A., and Thornton, J. M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29, 2860-2874.
42. Lejeune, D., Delsaux, N., Charloteaux, B., Thomas, A., and Brasseur, R. (2005) Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. Proteins 61, 258-271.
43. 13Cβ chemical shift data. J. Biomol. NMR 34, 259-269.
44. Seimiya, M., and Kurosawa, Y. (1996) Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance. FEBS Lett. 398, 279-284.
45. Oda, M., Furukawa, K., Sarai, A., and Nakamura, H. (1999) Kinetic analysis of DNA binding by the c-Myb DNA-binding domain using surface plasmon resonance. FEBS Lett. 454, 288-292.