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. 1998 Jan 15;26(2):608–615. doi: 10.1093/nar/26.2.608

Cys2/His2 zinc-finger protein family of petunia: evolution and general mechanism of target-sequence recognition.

K i Kubo 1, A Sakamoto 1, A Kobayashi 1, Z Rybka 1, Y Kanno 1, H Nakagawa 1, H Takatsuji 1
PMCID: PMC147284  PMID: 9421523

Abstract

The EPF family is a group of Cys2/His2zinc-finger proteins in petunia. In these proteins, characteristically long spacer regions have been found to separate the zinc fingers. Our previous DNA-binding studies demonstrated that two-fingered proteins (ZPT2-1 and ZPT2-2), which have spacers of different lengths, bind to two separate AGT core motifs in a spacing specific manner. To investigate the possibility that these proteins might distinguish between the target sequences on the basis of spacing between the core motifs, we screened petunia cDNA library for other proteins belonging to this family. Initial screening by PCR and subsequent cloning of full-length cDNAs allowed us to identify the genes for 10 new proteins that had two, three or four zinc fingers. Among the two-fingered proteins the spacing between zinc fingers varied from 19 to 65 amino acids. The variation in the length of spacers was even more extensive in three- and four-fingered proteins. The presence of such proteins is consistent with our hypothesis that the spacing between the core motifs might be important for target sequence recognition. Furthermore, comparison of diverse protein structures suggests that three- and two-fingered proteins might have resulted due to successive loss of fingers from a four-fingered protein during molecular evolution. We also demonstrate that a highly conserved motif (QALGGH) among the members of EPF family and other Cys2/His2 zinc-finger proteins in plants is critical for the DNA-binding activity.

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Selected References

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  1. Agarie S., Kai M., Takatsuji H., Ueno O. Expression of C3 and C4 photosynthetic characteristics in the amphibious plant Eleocharis vivipara: structure and analysis of the expression of isogenes for pyruvate, orthophosphate dikinase. Plant Mol Biol. 1997 May;34(2):363–369. doi: 10.1023/a:1005897118660. [DOI] [PubMed] [Google Scholar]
  2. Boutry M., Chua N. H. A nuclear gene encoding the beta subunit of the mitochondrial ATP synthase in Nicotiana plumbaginifolia. EMBO J. 1985 Sep;4(9):2159–2165. doi: 10.1002/j.1460-2075.1985.tb03910.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Braun T., Schofield P. R., Sprengel R. Amino-terminal leucine-rich repeats in gonadotropin receptors determine hormone selectivity. EMBO J. 1991 Jul;10(7):1885–1890. doi: 10.1002/j.1460-2075.1991.tb07714.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bray P., Lichter P., Thiesen H. J., Ward D. C., Dawid I. B. Characterization and mapping of human genes encoding zinc finger proteins. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9563–9567. doi: 10.1073/pnas.88.21.9563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Choo Y., Klug A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11168–11172. doi: 10.1073/pnas.91.23.11168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Desjarlais J. R., Berg J. M. Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach. Proteins. 1992 Feb;12(2):101–104. doi: 10.1002/prot.340120202. [DOI] [PubMed] [Google Scholar]
  7. Desjarlais J. R., Berg J. M. Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7345–7349. doi: 10.1073/pnas.89.16.7345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fairall L., Schwabe J. W., Chapman L., Finch J. T., Rhodes D. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature. 1993 Dec 2;366(6454):483–487. doi: 10.1038/366483a0. [DOI] [PubMed] [Google Scholar]
  9. Gill G., Pascal E., Tseng Z. H., Tjian R. A glutamine-rich hydrophobic patch in transcription factor Sp1 contacts the dTAFII110 component of the Drosophila TFIID complex and mediates transcriptional activation. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):192–196. doi: 10.1073/pnas.91.1.192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Jacobs G. H. Determination of the base recognition positions of zinc fingers from sequence analysis. EMBO J. 1992 Dec;11(12):4507–4517. doi: 10.1002/j.1460-2075.1992.tb05552.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kühn C., Frommer W. B. A novel zinc finger protein encoded by a couch potato homologue from Solanum tuberosum enables a sucrose transport-deficient yeast strain to grow on sucrose. Mol Gen Genet. 1995 Jun 25;247(6):759–763. doi: 10.1007/BF00290408. [DOI] [PubMed] [Google Scholar]
  12. Lippuner V., Cyert M. S., Gasser C. S. Two classes of plant cDNA clones differentially complement yeast calcineurin mutants and increase salt tolerance of wild-type yeast. J Biol Chem. 1996 May 31;271(22):12859–12866. doi: 10.1074/jbc.271.22.12859. [DOI] [PubMed] [Google Scholar]
  13. Meissner R., Michael A. J. Isolation and characterisation of a diverse family of Arabidopsis two and three-fingered C2H2 zinc finger protein genes and cDNAs. Plant Mol Biol. 1997 Mar;33(4):615–624. doi: 10.1023/a:1005746803089. [DOI] [PubMed] [Google Scholar]
  14. Michael A. J., Hofer J. M., Ellis T. H. Isolation by PCR of a cDNA clone from pea petals with similarity to petunia and wheat zinc finger proteins. Plant Mol Biol. 1996 Mar;30(5):1051–1058. doi: 10.1007/BF00020815. [DOI] [PubMed] [Google Scholar]
  15. Michael S. F., Kilfoil V. J., Schmidt M. H., Amann B. T., Berg J. M. Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4796–4800. doi: 10.1073/pnas.89.11.4796. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Muriel W. J., Cole J., Lehmann A. R. Molecular analysis of ouabain-resistant mutants of the mouse lymphoma cell line L5178Y. Mutagenesis. 1987 Sep;2(5):383–389. doi: 10.1093/mutage/2.5.383. [DOI] [PubMed] [Google Scholar]
  18. Nardelli J., Gibson T. J., Vesque C., Charnay P. Base sequence discrimination by zinc-finger DNA-binding domains. Nature. 1991 Jan 10;349(6305):175–178. doi: 10.1038/349175a0. [DOI] [PubMed] [Google Scholar]
  19. Nardelli J., Gibson T., Charnay P. Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis. Nucleic Acids Res. 1992 Aug 25;20(16):4137–4144. doi: 10.1093/nar/20.16.4137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Omichinski J. G., Clore G. M., Schaad O., Felsenfeld G., Trainor C., Appella E., Stahl S. J., Gronenborn A. M. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science. 1993 Jul 23;261(5120):438–446. doi: 10.1126/science.8332909. [DOI] [PubMed] [Google Scholar]
  21. Pavletich N. P., Pabo C. O. Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science. 1993 Sep 24;261(5129):1701–1707. doi: 10.1126/science.8378770. [DOI] [PubMed] [Google Scholar]
  22. Pavletich N. P., Pabo C. O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science. 1991 May 10;252(5007):809–817. doi: 10.1126/science.2028256. [DOI] [PubMed] [Google Scholar]
  23. Sakai H., Medrano L. J., Meyerowitz E. M. Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature. 1995 Nov 9;378(6553):199–203. doi: 10.1038/378199a0. [DOI] [PubMed] [Google Scholar]
  24. Sakamoto A., Minami M., Huh G. H., Iwabuchi M. The putative zinc-finger protein WZF1 interacts with a cis-acting element of wheat histone genes. Eur J Biochem. 1993 Nov 1;217(3):1049–1056. doi: 10.1111/j.1432-1033.1993.tb18336.x. [DOI] [PubMed] [Google Scholar]
  25. Schuh R., Aicher W., Gaul U., Côté S., Preiss A., Maier D., Seifert E., Nauber U., Schröder C., Kemler R. A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Krüppel, a Drosophila segmentation gene. Cell. 1986 Dec 26;47(6):1025–1032. doi: 10.1016/0092-8674(86)90817-2. [DOI] [PubMed] [Google Scholar]
  26. Tague B. W., Goodman H. M. Characterization of a family of Arabidopsis zinc finger protein cDNAs. Plant Mol Biol. 1995 May;28(2):267–279. doi: 10.1007/BF00020246. [DOI] [PubMed] [Google Scholar]
  27. Takatsuji H. A single amino acid determines the specificity for the target sequence of two zinc-finger proteins in plants. Biochem Biophys Res Commun. 1996 Jul 5;224(1):219–223. doi: 10.1006/bbrc.1996.1010. [DOI] [PubMed] [Google Scholar]
  28. Takatsuji H., Matsumoto T. Target-sequence recognition by separate-type Cys2/His2 zinc finger proteins in plants. J Biol Chem. 1996 Sep 20;271(38):23368–23373. doi: 10.1074/jbc.271.38.23368. [DOI] [PubMed] [Google Scholar]
  29. Takatsuji H., Mori M., Benfey P. N., Ren L., Chua N. H. Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings. EMBO J. 1992 Jan;11(1):241–249. doi: 10.1002/j.1460-2075.1992.tb05047.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Takatsuji H., Nakamura N., Katsumoto Y. A new family of zinc finger proteins in petunia: structure, DNA sequence recognition, and floral organ-specific expression. Plant Cell. 1994 Jul;6(7):947–958. doi: 10.1105/tpc.6.7.947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Tso J. Y., Van Den Berg D. J., Korn L. J. Structure of the gene for Xenopus transcription factor TFIIIA. Nucleic Acids Res. 1986 Mar 11;14(5):2187–2200. doi: 10.1093/nar/14.5.2187. [DOI] [PMC free article] [PubMed] [Google Scholar]

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