Skip to main content
PMC home page
Plant Physiology logoLink to Plant Physiology
. 1993 Mar;101(3):915–924. doi: 10.1104/pp.101.3.915

Analysis of genes negatively regulated by phytochrome action in Lemna gibba and identification of a promoter region required for phytochrome responsiveness.

P A Okubara 1, S A Williams 1, R A Doxsee 1, E M Tobin 1
PMCID: PMC158707  PMID: 8310060

Abstract

As a step to understanding how the photoreceptor phytochrome acts to change the transcription of specific nuclear genes in Lemna gibba, we wish to compare promoter elements involved in negative regulation by phytochrome with those involved in positive regulation. We have isolated three genes negatively regulated by phytochrome, designated NR (negatively phytochrome regulated) genes (P.A. Okubara, E.M. Tobin [1991] Plant Physiol 96:1237-1245), and we have now sequenced two of these. The promoters of both contain some sequence motifs that are identical with motifs from other genes. We used a transient assay in L. gibba to demonstrate that approximately 1.7 kb pairs of the NPR1 promoter and 1.1 kb pairs of the NPR2 promoter could confer negative phytochrome regulation to a luciferase reporter gene. Deletion analysis of the NPR2 promoter showed that sequences between -208 and -82 from the transcription start were necessary for negative phytochrome regulation. However, this region was not sufficient to confer negative regulation by phytochrome to another promoter. Additionally, we noted that this region showed no similarity to a region identified as important for the negative regulation of the oat phyA promoter (W.B. Bruce, X.-W. Deng, P.H. Quail [1991] EMBO J 10:3015-3024), but it does contain a sequence element found in several other kinds of genes, including ones positively regulated by phytochrome. The deduced amino acid sequences of NPR1 and NPR2 were found to share similarities with many abscisic acid-induced or seed-abundant proteins. Thus, these genes, like other phytochrome-regulated genes, might respond to multiple regulatory signals.

Full Text

The Full Text of this article is available as a PDF (1.6 MB).

Selected References

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

  1. Buzby J. S., Yamada T., Tobin E. M. A light-regulated DNA-binding activity interacts with a conserved region of a Lemna gibba rbcS promoter. Plant Cell. 1990 Aug;2(8):805–814. doi: 10.1105/tpc.2.8.805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Castresana C., Garcia-Luque I., Alonso E., Malik V. S., Cashmore A. R. Both positive and negative regulatory elements mediate expression of a photoregulated CAB gene from Nicotiana plumbaginifolia. EMBO J. 1988 Jul;7(7):1929–1936. doi: 10.1002/j.1460-2075.1988.tb03030.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen Z. Y., Hsing Y. I., Lee P. F., Chow T. Y. Nucleotide sequences of a soybean cDNA encoding an 18 kilodalton late embryogenesis abundant protein. Plant Physiol. 1992 Jun;99(2):773–774. doi: 10.1104/pp.99.2.773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Close T. J., Kortt A. A., Chandler P. M. A cDNA-based comparison of dehydration-induced proteins (dehydrins) in barley and corn. Plant Mol Biol. 1989 Jul;13(1):95–108. doi: 10.1007/BF00027338. [DOI] [PubMed] [Google Scholar]
  5. Colbert J. T., Costigan S. A., Zhao Z. Photoregulation of beta-Tubulin mRNA Abundance in Etiolated Oat and Barley Seedlings. Plant Physiol. 1990 Jul;93(3):1196–1202. doi: 10.1104/pp.93.3.1196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Datta N., Cashmore A. R. Binding of a pea nuclear protein to promoters of certain photoregulated genes is modulated by phosphorylation. Plant Cell. 1989 Nov;1(11):1069–1077. doi: 10.1105/tpc.1.11.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Davidson I., Fromental C., Augereau P., Wildeman A., Zenke M., Chambon P. Cell-type specific protein binding to the enhancer of simian virus 40 in nuclear extracts. Nature. 1986 Oct 9;323(6088):544–548. doi: 10.1038/323544a0. [DOI] [PubMed] [Google Scholar]
  8. Eyal Y., Sagee O., Fluhr R. Dark-induced accumulation of a basic pathogenesis-related (PR-1) transcript and a light requirement for its induction by ethylene. Plant Mol Biol. 1992 Jul;19(4):589–599. doi: 10.1007/BF00026785. [DOI] [PubMed] [Google Scholar]
  9. Gilmartin P. M., Chua N. H. Spacing between GT-1 binding sites within a light-responsive element is critical for transcriptional activity. Plant Cell. 1990 May;2(5):447–455. doi: 10.1105/tpc.2.5.447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gilmartin P. M., Sarokin L., Memelink J., Chua N. H. Molecular light switches for plant genes. Plant Cell. 1990 May;2(5):369–378. doi: 10.1105/tpc.2.5.369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Godoy J. A., Pardo J. M., Pintor-Toro J. A. A tomato cDNA inducible by salt stress and abscisic acid: nucleotide sequence and expression pattern. Plant Mol Biol. 1990 Nov;15(5):695–705. doi: 10.1007/BF00016120. [DOI] [PubMed] [Google Scholar]
  13. Joshi C. P. An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucleic Acids Res. 1987 Aug 25;15(16):6643–6653. doi: 10.1093/nar/15.16.6643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kay S. A., Keith B., Shinozaki K., Chye M. L., Chua N. H. The rice phytochrome gene: structure, autoregulated expression, and binding of GT-1 to a conserved site in the 5' upstream region. Plant Cell. 1989 Mar;1(3):351–360. doi: 10.1105/tpc.1.3.351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kozak M. An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 1987 Oct 26;15(20):8125–8148. doi: 10.1093/nar/15.20.8125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lam E., Chua N. H. ASF-2: a factor that binds to the cauliflower mosaic virus 35S promoter and a conserved GATA motif in Cab promoters. Plant Cell. 1989 Dec;1(12):1147–1156. doi: 10.1105/tpc.1.12.1147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Manzara T., Carrasco P., Gruissem W. Developmental and organ-specific changes in promoter DNA-protein interactions in the tomato rbcS gene family. Plant Cell. 1991 Dec;3(12):1305–1316. doi: 10.1105/tpc.3.12.1305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Ohme M., Tanaka M., Chunwongse J., Shinozaki K., Sugiura M. A tobacco chloroplast DNA sequence possibly coding for a polypeptide similar to E. coli RNA polymerase beta-subunit. FEBS Lett. 1986 May 5;200(1):87–90. doi: 10.1016/0014-5793(86)80516-6. [DOI] [PubMed] [Google Scholar]
  21. Okubara P. A., Tobin E. M. Isolation and Characterization of Three Genes Negatively Regulated by Phytochrome Action in Lemna gibba. Plant Physiol. 1991 Aug;96(4):1237–1245. doi: 10.1104/pp.96.4.1237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pustell J., Kafatos F. C. A convenient and adaptable package of DNA sequence analysis programs for microcomputers. Nucleic Acids Res. 1982 Jan 11;10(1):51–59. doi: 10.1093/nar/10.1.51. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Raynal M., Gaubier P., Grellet F., Delseny M. Nucleotide sequence of a radish cDNA clone coding for a late embryogenesis abundant (LEA) protein. Nucleic Acids Res. 1990 Oct 25;18(20):6132–6132. doi: 10.1093/nar/18.20.6132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Riggs C. D., Chrispeels M. J. Luciferase reporter gene cassettes for plant gene expression studies. Nucleic Acids Res. 1987 Oct 12;15(19):8115–8115. doi: 10.1093/nar/15.19.8115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Rolfe S. A., Tobin E. M. Deletion analysis of a phytochrome-regulated monocot rbcS promoter in a transient assay system. Proc Natl Acad Sci U S A. 1991 Apr 1;88(7):2683–2686. doi: 10.1073/pnas.88.7.2683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Shapiro M. B., Senapathy P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 1987 Sep 11;15(17):7155–7174. doi: 10.1093/nar/15.17.7155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Skriver K., Mundy J. Gene expression in response to abscisic acid and osmotic stress. Plant Cell. 1990 Jun;2(6):503–512. doi: 10.1105/tpc.2.6.503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Tsai F. Y., Coruzzi G. Light represses transcription of asparagine synthetase genes in photosynthetic and nonphotosynthetic organs of plants. Mol Cell Biol. 1991 Oct;11(10):4966–4972. doi: 10.1128/mcb.11.10.4966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Weisshaar B., Armstrong G. A., Block A., da Costa e Silva O., Hahlbrock K. Light-inducible and constitutively expressed DNA-binding proteins recognizing a plant promoter element with functional relevance in light responsiveness. EMBO J. 1991 Jul;10(7):1777–1786. doi: 10.1002/j.1460-2075.1991.tb07702.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Zinn K., DiMaio D., Maniatis T. Identification of two distinct regulatory regions adjacent to the human beta-interferon gene. Cell. 1983 Oct;34(3):865–879. doi: 10.1016/0092-8674(83)90544-5. [DOI] [PubMed] [Google Scholar]
  33. de Wet J. R., Wood K. V., DeLuca M., Helinski D. R., Subramani S. Firefly luciferase gene: structure and expression in mammalian cells. Mol Cell Biol. 1987 Feb;7(2):725–737. doi: 10.1128/mcb.7.2.725. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Plant Physiology are provided here courtesy of Oxford University Press

RESOURCES