Skip to main content
NCBI home page
The Plant Cell logoLink to The Plant Cell
. 1992 Apr;4(4):485–496. doi: 10.1105/tpc.4.4.485

Sequences flanking the hexameric G-box core CACGTG affect the specificity of protein binding.

M E Williams 1, R Foster 1, N H Chua 1
PMCID: PMC160147  PMID: 1498606

Abstract

The CACGTG G-box motif is a highly conserved DNA sequence that has been identified in the 5' upstream region of plant genes exhibiting regulation by a variety of environmental signals and physiological cues. Gel mobility shift assays using a panel of G-box oligonucleotides differing in their flanking sequences identified two types of binding activity (A and B) in a cauliflower nuclear extract. Competition gel retardation assays demonstrated that the two types of binding activity were distinct. Type A binding activity interacted with oligonucleotides designated as class I elements, whereas type B binding activity interacted strongly with class II elements and weakly with class I elements. A third class of elements, null elements, did not exhibit any detectable binding under our assay conditions. Gel retardation analysis of nonpalindromic hybrid G-box oligonucleotides indicated that hybrid elements of the same class exhibited binding affinity commensurate with the affinity of the weaker element, hybrid class I/II elements exhibited only type B binding, and hybrid class I/null and class II/null elements did not show any detectable binding activity. These binding activities can be explained by the affinity of bZip G-box binding homo- or heterodimer subunits for G-box half sites. These experiments led to a set of classification rules that can predict the binding activity of all reported plant G-box motifs containing the consensus hexameric core. Tissue- and/or development-specific expression of genes containing G-box motifs may be regulated by the affinity of G-box proteins for the different classes of G-box elements.

Full Text

The Full Text of this article is available as a PDF (2.2 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ainley W. M., Walker J. C., Nagao R. T., Key J. L. Sequence and characterization of two auxin-regulated genes from soybean. J Biol Chem. 1988 Aug 5;263(22):10658–10666. [PubMed] [Google Scholar]
  2. Baszczynski C. L., Fallis L. Isolation and nucleotide sequence of a genomic clone encoding a new Brassica napus napin gene. Plant Mol Biol. 1990 Apr;14(4):633–635. doi: 10.1007/BF00027511. [DOI] [PubMed] [Google Scholar]
  3. Bouchez D., Tokuhisa J. G., Llewellyn D. J., Dennis E. S., Ellis J. G. The ocs-element is a component of the promoters of several T-DNA and plant viral genes. EMBO J. 1989 Dec 20;8(13):4197–4204. doi: 10.1002/j.1460-2075.1989.tb08605.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Busch S. J., Sassone-Corsi P. Dimers, leucine zippers and DNA-binding domains. Trends Genet. 1990 Feb;6(2):36–40. doi: 10.1016/0168-9525(90)90071-d. [DOI] [PubMed] [Google Scholar]
  5. Bäumlein H., Wobus U., Pustell J., Kafatos F. C. The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element. Nucleic Acids Res. 1986 Mar 25;14(6):2707–2720. doi: 10.1093/nar/14.6.2707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Coen E. S., Carpenter R., Martin C. Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus. Cell. 1986 Oct 24;47(2):285–296. doi: 10.1016/0092-8674(86)90451-4. [DOI] [PubMed] [Google Scholar]
  7. Coruzzi G., Broglie R., Edwards C., Chua N. H. Tissue-specific and light-regulated expression of a pea nuclear gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. EMBO J. 1984 Aug;3(8):1671–1679. doi: 10.1002/j.1460-2075.1984.tb02031.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. DeLisle A. J., Ferl R. J. Characterization of the Arabidopsis Adh G-box binding factor. Plant Cell. 1990 Jun;2(6):547–557. doi: 10.1105/tpc.2.6.547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dean C., Elzen P., Tamaki S., Dunsmuir P., Bedbrook J. Differential expression of the eight genes of the petunia ribulose bisphosphate carboxylase small subunit multi-gene family. EMBO J. 1985 Dec 1;4(12):3055–3061. doi: 10.1002/j.1460-2075.1985.tb04045.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dennis E. S., Gerlach W. L., Pryor A. J., Bennetzen J. L., Inglis A., Llewellyn D., Sachs M. M., Ferl R. J., Peacock W. J. Molecular analysis of the alcohol dehydrogenase (Adh1) gene of maize. Nucleic Acids Res. 1984 May 11;12(9):3983–4000. doi: 10.1093/nar/12.9.3983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Donald R. G., Cashmore A. R. Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. EMBO J. 1990 Jun;9(6):1717–1726. doi: 10.1002/j.1460-2075.1990.tb08295.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Doyle J. J., Schuler M. A., Godette W. D., Zenger V., Beachy R. N., Slightom J. L. The glycosylated seed storage proteins of Glycine max and Phaseolus vulgaris. Structural homologies of genes and proteins. J Biol Chem. 1986 Jul 15;261(20):9228–9238. [PubMed] [Google Scholar]
  13. Ellison N. W., Yu P. L., White D. W. Nucleotide sequence of a white clover ribulose bisphosphate carboxylase small subunit gene. Nucleic Acids Res. 1990 Aug 25;18(16):4914–4914. [PMC free article] [PubMed] [Google Scholar]
  14. Feinbaum R. L., Ausubel F. M. Transcriptional regulation of the Arabidopsis thaliana chalcone synthase gene. Mol Cell Biol. 1988 May;8(5):1985–1992. doi: 10.1128/mcb.8.5.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fluhr Robert, Moses Phyllis, Morelli Giorgio, Coruzzi Gloria, Chua Nam-Hai. Expression dynamics of the pea rbcS multigene family and organ distribution of the transcripts. EMBO J. 1986 Sep;5(9):2063–2071. doi: 10.1002/j.1460-2075.1986.tb04467.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Fromm H., Katagiri F., Chua N. H. An octopine synthase enhancer element directs tissue-specific expression and binds ASF-1, a factor from tobacco nuclear extracts. Plant Cell. 1989 Oct;1(10):977–984. doi: 10.1105/tpc.1.10.977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gatehouse J. A., Bown D., Gilroy J., Levasseur M., Castleton J., Ellis T. H. Two genes encoding 'minor' legumin polypeptides in pea (Pisum sativum L.). Characterization and complete sequence of the LegJ gene. Biochem J. 1988 Feb 15;250(1):15–24. doi: 10.1042/bj2500015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Giuliano G., Pichersky E., Malik V. S., Timko M. P., Scolnik P. A., Cashmore A. R. An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7089–7093. doi: 10.1073/pnas.85.19.7089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Green P. J., Kay S. A., Chua N. H. Sequence-specific interactions of a pea nuclear factor with light-responsive elements upstream of the rbcS-3A gene. EMBO J. 1987 Sep;6(9):2543–2549. doi: 10.1002/j.1460-2075.1987.tb02542.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Guiltinan M. J., Marcotte W. R., Jr, Quatrano R. S. A plant leucine zipper protein that recognizes an abscisic acid response element. Science. 1990 Oct 12;250(4978):267–271. doi: 10.1126/science.2145628. [DOI] [PubMed] [Google Scholar]
  21. Harada J. J., Spadoro-Tank J., Maxwell J. C., Schnell D. J., Etzler M. E. Two lectin genes differentially expressed in Dolichos biflorus differ primarily by a 116-base pair sequence in their 5' flanking regions. J Biol Chem. 1990 Mar 25;265(9):4997–5001. [PubMed] [Google Scholar]
  22. Herrmann A., Schulz W., Hahlbrock K. Two alleles of the single-copy chalcone synthase gene in parsley differ by a transposon-like element. Mol Gen Genet. 1988 Apr;212(1):93–98. doi: 10.1007/BF00322449. [DOI] [PubMed] [Google Scholar]
  23. Huttly A. K., Martienssen R. A., Baulcombe D. C. Sequence heterogeneity and differential expression of the alpha-Amy2 gene family in wheat. Mol Gen Genet. 1988 Oct;214(2):232–240. doi: 10.1007/BF00337716. [DOI] [PubMed] [Google Scholar]
  24. Josefsson L. G., Lenman M., Ericson M. L., Rask L. Structure of a gene encoding the 1.7 S storage protein, napin, from Brassica napus. J Biol Chem. 1987 Sep 5;262(25):12196–12201. [PubMed] [Google Scholar]
  25. Keil M., Sanchez-Serrano J., Schell J., Willmitzer L. Primary structure of a proteinase inhibitor II gene from potato (Solanum tuberosum). Nucleic Acids Res. 1986 Jul 25;14(14):5641–5650. doi: 10.1093/nar/14.14.5641. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Klee H. J., Muskopf Y. M., Gasser C. S. Cloning of an Arabidopsis thaliana gene encoding 5-enolpyruvylshikimate-3-phosphate synthase: sequence analysis and manipulation to obtain glyphosate-tolerant plants. Mol Gen Genet. 1987 Dec;210(3):437–442. doi: 10.1007/BF00327194. [DOI] [PubMed] [Google Scholar]
  27. Krebbers E., Herdies L., De Clercq A., Seurinck J., Leemans J., Van Damme J., Segura M., Gheysen G., Van Montagu M., Vandekerckhove J. Determination of the Processing Sites of an Arabidopsis 2S Albumin and Characterization of the Complete Gene Family. Plant Physiol. 1988 Aug;87(4):859–866. doi: 10.1104/pp.87.4.859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Köster-Töpfer M., Frommer W. B., Rocha-Sosa M., Willmitzer L. Presence of a transposon-like element in the promoter region of an inactive patatin gene in Solanum tuberosum L. Plant Mol Biol. 1990 Feb;14(2):239–247. doi: 10.1007/BF00018564. [DOI] [PubMed] [Google Scholar]
  29. Lam E., Benfey P. N., Gilmartin P. M., Fang R. X., Chua N. H. Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7890–7894. doi: 10.1073/pnas.86.20.7890. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lam E., Katagiri F., Chua N. H. Plant nuclear factor ASF-1 binds to an essential region of the nopaline synthase promoter. J Biol Chem. 1990 Jun 15;265(17):9909–9913. [PubMed] [Google Scholar]
  31. Lycett G. W., Croy R. R., Shirsat A. H., Richards D. M., Boulter D. The 5'-flanking regions of three pea legumin genes: comparison of the DNA sequences. Nucleic Acids Res. 1985 Sep 25;13(18):6733–6743. doi: 10.1093/nar/13.18.6733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Maddaloni M., Di Fonzo N., Hartings H., Lazzaroni N., Salamini F., Thompson R., Motto M. The sequence of the zein regulatory gene opaque-2 (O2) of Zea Mays. Nucleic Acids Res. 1989 Sep 25;17(18):7532–7532. doi: 10.1093/nar/17.18.7532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Marcotte W. R., Jr, Russell S. H., Quatrano R. S. Abscisic acid-responsive sequences from the em gene of wheat. Plant Cell. 1989 Oct;1(10):969–976. doi: 10.1105/tpc.1.10.969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Mazur B. J., Chui C. F. Sequence of a genomic DNA clone for the small subunit of ribulose bis-phosphate carboxylase-oxygenase from tobacco. Nucleic Acids Res. 1985 Apr 11;13(7):2373–2386. doi: 10.1093/nar/13.7.2373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Mundy J., Yamaguchi-Shinozaki K., Chua N. H. Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1406–1410. doi: 10.1073/pnas.87.4.1406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Oeda K., Salinas J., Chua N. H. A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes. EMBO J. 1991 Jul;10(7):1793–1802. doi: 10.1002/j.1460-2075.1991.tb07704.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Oliphant A. R., Brandl C. J., Struhl K. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol. 1989 Jul;9(7):2944–2949. doi: 10.1128/mcb.9.7.2944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Pichersky E., Soltis D., Soltis P. Defective chlorophyll a/b-binding protein genes in the genome of a homosporous fern. Proc Natl Acad Sci U S A. 1990 Jan;87(1):195–199. doi: 10.1073/pnas.87.1.195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Post-Beittenmiller M. A., Hlousek-Radojcić A., Ohlrogge J. B. DNA sequence of a genomic clone encoding an Arabidopsis acyl carrier protein (ACP). Nucleic Acids Res. 1989 Feb 25;17(4):1777–1777. doi: 10.1093/nar/17.4.1777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ralston E. J., English J. J., Dooner H. K. Sequence of three bronze alleles of maize and correlation with the genetic fine structure. Genetics. 1988 May;119(1):185–197. doi: 10.1093/genetics/119.1.185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sathasivan K., Haughn G. W., Murai N. Nucleotide sequence of a mutant acetolactate synthase gene from an imidazolinone-resistant Arabidopsis thaliana var. Columbia. Nucleic Acids Res. 1990 Apr 25;18(8):2188–2188. doi: 10.1093/nar/18.8.2188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Sawadogo M., Roeder R. G. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell. 1985 Nov;43(1):165–175. doi: 10.1016/0092-8674(85)90021-2. [DOI] [PubMed] [Google Scholar]
  43. Schleif R. DNA binding by proteins. Science. 1988 Sep 2;241(4870):1182–1187. doi: 10.1126/science.2842864. [DOI] [PubMed] [Google Scholar]
  44. Schulze-Lefert P., Dangl J. L., Becker-André M., Hahlbrock K., Schulz W. Inducible in vivo DNA footprints define sequences necessary for UV light activation of the parsley chalcone synthase gene. EMBO J. 1989 Mar;8(3):651–656. doi: 10.1002/j.1460-2075.1989.tb03422.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Scofield S. R., Crouch M. L. Nucleotide sequence of a member of the napin storage protein family from Brassica napus. J Biol Chem. 1987 Sep 5;262(25):12202–12208. [PubMed] [Google Scholar]
  46. Seurinck J., Truettner J., Goldberg R. B. The nucleotide sequence of an anther-specific gene. Nucleic Acids Res. 1990 Jun 11;18(11):3403–3403. doi: 10.1093/nar/18.11.3403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Staiger D., Becker F., Schell J., Koncz C., Palme K. Purification of tobacco nuclear proteins binding to a CACGTG motif of the chalcone synthase promoter by DNA affinity chromatography. Eur J Biochem. 1991 Aug 1;199(3):519–527. doi: 10.1111/j.1432-1033.1991.tb16150.x. [DOI] [PubMed] [Google Scholar]
  48. Stanford A., Bevan M., Northcote D. Differential expression within a family of novel wound-induced genes in potato. Mol Gen Genet. 1989 Jan;215(2):200–208. doi: 10.1007/BF00339718. [DOI] [PubMed] [Google Scholar]
  49. Sugita M., Manzara T., Pichersky E., Cashmore A., Gruissem W. Genomic organization, sequence analysis and expression of all five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from tomato. Mol Gen Genet. 1987 Sep;209(2):247–256. doi: 10.1007/BF00329650. [DOI] [PubMed] [Google Scholar]
  50. Tabata T., Takase H., Takayama S., Mikami K., Nakatsuka A., Kawata T., Nakayama T., Iwabuchi M. A protein that binds to a cis-acting element of wheat histone genes has a leucine zipper motif. Science. 1989 Sep 1;245(4921):965–967. doi: 10.1126/science.2772648. [DOI] [PubMed] [Google Scholar]
  51. Takahashi T., Komeda Y. Characterization of two genes encoding small heat-shock proteins in Arabidopsis thaliana. Mol Gen Genet. 1989 Nov;219(3):365–372. doi: 10.1007/BF00259608. [DOI] [PubMed] [Google Scholar]
  52. Tokuhisa J. G., Singh K., Dennis E. S., Peacock W. J. A DNA-binding protein factor recognizes two binding domains within the octopine synthase enhancer element. Plant Cell. 1990 Mar;2(3):215–224. doi: 10.1105/tpc.2.3.215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Tumer N. E., Clark W. G., Tabor G. J., Hironaka C. M., Fraley R. T., Shah D. M. The genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase are expressed differentially in petunia leaves. Nucleic Acids Res. 1986 Apr 25;14(8):3325–3342. doi: 10.1093/nar/14.8.3325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Twell D., Ooms G. Structural diversity of the patatin gene family in potato cv. Desiree. Mol Gen Genet. 1988 May;212(2):325–336. doi: 10.1007/BF00334703. [DOI] [PubMed] [Google Scholar]
  55. Vinson C. R., Sigler P. B., McKnight S. L. Scissors-grip model for DNA recognition by a family of leucine zipper proteins. Science. 1989 Nov 17;246(4932):911–916. doi: 10.1126/science.2683088. [DOI] [PubMed] [Google Scholar]
  56. Vorst O., van Dam F., Oosterhoff-Teertstra R., Smeekens S., Weisbeek P. Tissue-specific expression directed by an Arabidopsis thaliana pre-ferredoxin promoter in transgenic tobacco plants. Plant Mol Biol. 1990 Apr;14(4):491–499. doi: 10.1007/BF00027495. [DOI] [PubMed] [Google Scholar]
  57. Waksman G., Lebrun M., Freyssinet G. Nucleotide sequence of a gene encoding sunflower ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcs). Nucleic Acids Res. 1987 Sep 11;15(17):7181–7181. doi: 10.1093/nar/15.17.7181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wandelt C., Feix G. Sequence of a 21 kd zein gene from maize containing an in-frame stop codon. Nucleic Acids Res. 1989 Mar 25;17(6):2354–2354. doi: 10.1093/nar/17.6.2354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Williams M. E., Mundy J., Kay S. A., Chua N. H. Differential expression of two related organ-specific genes in pea. Plant Mol Biol. 1990 May;14(5):765–774. doi: 10.1007/BF00016509. [DOI] [PubMed] [Google Scholar]
  60. Wu C. H., Caspar T., Browse J., Lindquist S., Somerville C. Characterization of an HSP70 Cognate Gene Family in Arabidopsis. Plant Physiol. 1988 Nov;88(3):731–740. doi: 10.1104/pp.88.3.731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Ziff E. B. Transcription factors: a new family gathers at the cAMP response site. Trends Genet. 1990 Mar;6(3):69–72. doi: 10.1016/0168-9525(90)90081-g. [DOI] [PubMed] [Google Scholar]

Articles from The Plant Cell are provided here courtesy of Oxford University Press

RESOURCES