Solution Structure of the B3 DNA Binding Domain of the Arabidopsis Cold-responsive Transcription Factor RAV1

Overview

Journal Plant Cell

Publisher Oxford University Press

Specialties Biology
Cell Biology

Date 2004 Nov 19

PMID 15548737

Citations 67

Authors

Kazuhiko Yamasaki

Takanori Kigawa

Makoto Inoue

Masaru Tateno

Tomoko Yamasaki

Takashi Yabuki

Masaaki Aoki

Eiko Seki

Takayoshi Matsuda

Yasuko Tomo

Nobuhiro Hayami

Takaho Terada

Mikako Shirouzu

Takashi Osanai

Akiko Tanaka

Motoaki Seki

Kazuo Shinozaki

Shigeyuki Yokoyama

Affiliations

Soon will be listed here.

Abstract

The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid-regulated transcription. Herein, we report the NMR solution structure of the B3 domain of the Arabidopsis thaliana cold-responsive transcription factor RAV1. The structure consists of a seven-stranded open beta-barrel and two alpha-helices located at the ends of the barrel and is significantly similar to the structure of the noncatalytic DNA binding domain of the restriction enzyme EcoRII. An NMR titration experiment revealed a DNA recognition interface that enabled us to propose a structural model of the protein-DNA complex. The locations of the DNA-contacting residues are also likely to be similar to those of the EcoRII DNA binding domain.

Citing Articles

Evolutionary origins and functional diversification of Auxin Response Factors.

Hernandez-Garcia J, Carrillo-Carrasco V, Rienstra J, Tanaka K, de Roij M, Dipp-Alvarez M Nat Commun. 2024; 15(1):10909.

PMID: 39738167 PMC: 11685440. DOI: 10.1038/s41467-024-55278-8.

Comprehensive analysis of pepper (Capsicum annuum) RAV genes family and functional identification of CaRAV1 under chilling stress.

Pei M, Yang P, Li J, Wang Y, Li J, Xu H BMC Genomics. 2024; 25(1):731.

PMID: 39075389 PMC: 11285464. DOI: 10.1186/s12864-024-10639-x.

Genome-Wide Characterization and Expression Profiling of the AP2/ERF Gene Family in L.

Wei Y, Kong Y, Li H, Yao A, Han J, Zhang W Int J Mol Sci. 2024; 25(14).

PMID: 39062854 PMC: 11277216. DOI: 10.3390/ijms25147614.

Genome-Wide Identification and Expression Analysis Reveals the B3 Superfamily Involved in Embryogenesis and Hormone Responses in Lour.

Tang M, Zhao G, Awais M, Gao X, Meng W, Lin J Int J Mol Sci. 2024; 25(1).

PMID: 38203301 PMC: 10779397. DOI: 10.3390/ijms25010127.

Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans.

Cui T, Zang S, Sun X, Zhang J, Su Y, Wang D BMC Genomics. 2024; 25(1):22.

PMID: 38166591 PMC: 10759518. DOI: 10.1186/s12864-023-09919-9.

References

Pabo C, Sauer R . Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem. 1992; 61:1053-95. DOI: 10.1146/annurev.bi.61.070192.005201. View

Fowler S, Thomashow M . Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell. 2002; 14(8):1675-90. PMC: 151458. DOI: 10.1105/tpc.003483. View

Tiwari S, Hagen G, Guilfoyle T . The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell. 2003; 15(2):533-43. PMC: 141219. DOI: 10.1105/tpc.008417. View

Wagner G, Braun W, Havel T, Schaumann T, Go N, Wuthrich K . Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J Mol Biol. 1987; 196(3):611-39. DOI: 10.1016/0022-2836(87)90037-4. View

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

Koradi R, Billeter M, Wuthrich K . MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph. 1996; 14(1):51-5, 29-32. DOI: 10.1016/0263-7855(96)00009-4. View

Leung J, Giraudat J . ABSCISIC ACID SIGNAL TRANSDUCTION. Annu Rev Plant Physiol Plant Mol Biol. 2004; 49:199-222. DOI: 10.1146/annurev.arplant.49.1.199. View

Seimiya M, Kurosawa Y . Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance. FEBS Lett. 1996; 398(2-3):279-84. DOI: 10.1016/s0014-5793(96)01246-x. View

Kigawa T, Yabuki T, Matsuda N, Matsuda T, Nakajima R, Tanaka A . Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J Struct Funct Genomics. 2004; 5(1-2):63-8. DOI: 10.1023/B:JSFG.0000029204.57846.7d. View

10.

McCarty D, Hattori T, Carson C, Vasil V, Lazar M, Vasil I . The Viviparous-1 developmental gene of maize encodes a novel transcriptional activator. Cell. 1991; 66(5):895-905. DOI: 10.1016/0092-8674(91)90436-3. View

11.

Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T . Structural genomics projects in Japan. Nat Struct Biol. 2000; 7 Suppl:943-5. DOI: 10.1038/80712. View

12.

Suzuki M, Kao C, McCarty D . The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell. 1997; 9(5):799-807. PMC: 156957. DOI: 10.1105/tpc.9.5.799. View

13.

Mucke M, Grelle G, Behlke J, Kraft R, Kruger D, Reuter M . EcoRII: a restriction enzyme evolving recombination functions?. EMBO J. 2002; 21(19):5262-8. PMC: 129036. DOI: 10.1093/emboj/cdf514. View

14.

Bondeson K, Frostell-Karlsson A, Fagerstam L, Magnusson G . Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor. Anal Biochem. 1993; 214(1):245-51. DOI: 10.1006/abio.1993.1484. View

15.

Nilges M . A calculation strategy for the structure determination of symmetric dimers by 1H NMR. Proteins. 1993; 17(3):297-309. DOI: 10.1002/prot.340170307. View

16.

Ulmasov T, Hagen G, Guilfoyle T . Dimerization and DNA binding of auxin response factors. Plant J. 1999; 19(3):309-19. DOI: 10.1046/j.1365-313x.1999.00538.x. View

17.

Giraudat J, Hauge B, Valon C, Smalle J, Parcy F, Goodman H . Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell. 1992; 4(10):1251-61. PMC: 160212. DOI: 10.1105/tpc.4.10.1251. View

18.

Kigawa T, Yabuki T, Yoshida Y, Tsutsui M, Ito Y, Shibata T . Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Lett. 1999; 442(1):15-9. DOI: 10.1016/s0014-5793(98)01620-2. View

19.

Wojciak J, Connolly K, Clubb R . NMR structure of the Tn916 integrase-DNA complex. Nat Struct Biol. 1999; 6(4):366-73. DOI: 10.1038/7603. View

20.

Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T . Functional annotation of a full-length Arabidopsis cDNA collection. Science. 2002; 296(5565):141-5. DOI: 10.1126/science.1071006. View