Skip to main content
NCBI home page
The Plant Cell logoLink to The Plant Cell
. 1997 Aug;9(8):1317–1326. doi: 10.1105/tpc.9.8.1317

A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing.

M J Aukerman 1, M Hirschfeld 1, L Wester 1, M Weaver 1, T Clack 1, R M Amasino 1, R A Sharrock 1
PMCID: PMC157000  PMID: 9286109

Abstract

The PHYD gene of the Wassilewskija (Ws) ecotype of Arabidopsis contains a 14-bp deletion (the phyD-1 mutation) beginning at amino acid 29 of the reading frame, resulting in translation termination at a nonsense codon 138 nucleotides downstream of the deletion end point. Immunoblot analyses showed that Ws lacks phyD but contains normal levels of phyA, phyB, and phyC. By backcrossing into the Ws and Landsberg erecta genetic backgrounds, we constructed sibling pairs of PHYD+ and phyD-1 lines and of phyB- PHYD+ and phyB- phyD- lines. Hypocotyl lengths after growth under white or red light increased sequentially in strains that were B+D+, B+D-, B-D+, and B-D-. In the Ws genetic background, an increase in petiole length, a reduction in cotyledon area and in anthocyanin accumulation in seedling stems, a diminished effect of an end-of-day pulse of far-red light on hypocotyl elongation, and a decrease in the number of rosette leaves at the onset of flowering were also seen sequentially in these lines. Thus, phyD, which is approximately 80% identical in amino acid sequence to phyB, acts in conjunction with phyB in regulating many shade avoidance responses. The existence of the apparently naturally occurring phyD-1 mutation indicates that phyD is not essential in some natural environments.

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. Adam E., Deak M., Kay S., Chua N. H., Nagy F. Sequence of a tobacco (Nicotiana tabacum) gene coding for type A phytochrome. Plant Physiol. 1993 Apr;101(4):1407–1408. doi: 10.1104/pp.101.4.1407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bell C. J., Ecker J. R. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 1994 Jan 1;19(1):137–144. doi: 10.1006/geno.1994.1023. [DOI] [PubMed] [Google Scholar]
  3. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  4. Chory J., Cook R. K., Dixon R., Elich T., Li H. M., Lopez E., Mochizuki N., Nagpal P., Pepper A., Poole D. Signal-transduction pathways controlling light-regulated development in Arabidopsis. Philos Trans R Soc Lond B Biol Sci. 1995 Oct 30;350(1331):59–65. doi: 10.1098/rstb.1995.0138. [DOI] [PubMed] [Google Scholar]
  5. Clack T., Mathews S., Sharrock R. A. The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE. Plant Mol Biol. 1994 Jun;25(3):413–427. doi: 10.1007/BF00043870. [DOI] [PubMed] [Google Scholar]
  6. Devlin P. F., Halliday K. J., Harberd N. P., Whitelam G. C. The rosette habit of Arabidopsis thaliana is dependent upon phytochrome action: novel phytochromes control internode elongation and flowering time. Plant J. 1996 Dec;10(6):1127–1134. doi: 10.1046/j.1365-313x.1996.10061127.x. [DOI] [PubMed] [Google Scholar]
  7. Devlin P. F., Rood S. B., Somers D. E., Quail P. H., Whitelam G. C. Photophysiology of the Elongated Internode (ein) Mutant of Brassica rapa: ein Mutant Lacks a Detectable Phytochrome B-Like Polypeptide. Plant Physiol. 1992 Nov;100(3):1442–1447. doi: 10.1104/pp.100.3.1442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Edwards K., Johnstone C., Thompson C. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res. 1991 Mar 25;19(6):1349–1349. doi: 10.1093/nar/19.6.1349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Halliday K. J., Koornneef M., Whitelam G. C. Phytochrome B and at Least One Other Phytochrome Mediate the Accelerated Flowering Response of Arabidopsis thaliana L. to Low Red/Far-Red Ratio. Plant Physiol. 1994 Apr;104(4):1311–1315. doi: 10.1104/pp.104.4.1311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Isaacson Peter G. Primary Gastric Lymphoma. Pathol Oncol Res. 1996;2(1-2):5–10. doi: 10.1007/BF02893940. [DOI] [PubMed] [Google Scholar]
  11. Kehoe D. M., Grossman A. R. Similarity of a chromatic adaptation sensor to phytochrome and ethylene receptors. Science. 1996 Sep 6;273(5280):1409–1412. doi: 10.1126/science.273.5280.1409. [DOI] [PubMed] [Google Scholar]
  12. Klimyuk V. I., Carroll B. J., Thomas C. M., Jones J. D. Alkali treatment for rapid preparation of plant material for reliable PCR analysis. Plant J. 1993 Mar;3(3):493–494. doi: 10.1111/j.1365-313x.1993.tb00169.x. [DOI] [PubMed] [Google Scholar]
  13. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  14. López-Juez E., Nagatani A., Tomizawa K., Deak M., Kern R., Kendrick R. E., Furuya M. The cucumber long hypocotyl mutant lacks a light-stable PHYB-like phytochrome. Plant Cell. 1992 Mar;4(3):241–251. [PMC free article] [PubMed] [Google Scholar]
  15. Mathews S., Sharrock R. A. The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. Mol Biol Evol. 1996 Oct;13(8):1141–1150. doi: 10.1093/oxfordjournals.molbev.a025677. [DOI] [PubMed] [Google Scholar]
  16. Millar A. J., McGrath R. B., Chua N. H. Phytochrome phototransduction pathways. Annu Rev Genet. 1994;28:325–349. doi: 10.1146/annurev.ge.28.120194.001545. [DOI] [PubMed] [Google Scholar]
  17. Nagatani A., Reed J. W., Chory J. Isolation and Initial Characterization of Arabidopsis Mutants That Are Deficient in Phytochrome A. Plant Physiol. 1993 May;102(1):269–277. doi: 10.1104/pp.102.1.269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Parks B. M., Quail P. H. hy8, a new class of arabidopsis long hypocotyl mutants deficient in functional phytochrome A. Plant Cell. 1993 Jan;5(1):39–48. doi: 10.1105/tpc.5.1.39. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pratt L. H., Cordonnier-Pratt M. M., Hauser B., Caboche M. Tomato contains two differentially expressed genes encoding B-type phytochromes, neither of which can be considered an ortholog of Arabidopsis phytochrome B. Planta. 1995;197(1):203–206. doi: 10.1007/BF00239958. [DOI] [PubMed] [Google Scholar]
  20. Quail P. H., Boylan M. T., Parks B. M., Short T. W., Xu Y., Wagner D. Phytochromes: photosensory perception and signal transduction. Science. 1995 May 5;268(5211):675–680. doi: 10.1126/science.7732376. [DOI] [PubMed] [Google Scholar]
  21. Reed J. W., Nagpal P., Poole D. S., Furuya M., Chory J. Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell. 1993 Feb;5(2):147–157. doi: 10.1105/tpc.5.2.147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Robson PRH., Whitelam G. C., Smith H. Selected Components of the Shade-Avoidance Syndrome Are Displayed in a Normal Manner in Mutants of Arabidopsis thaliana and Brassica rapa Deficient in Phytochrome B. Plant Physiol. 1993 Aug;102(4):1179–1184. doi: 10.1104/pp.102.4.1179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Sharrock R. A., Quail P. H. Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 1989 Nov;3(11):1745–1757. doi: 10.1101/gad.3.11.1745. [DOI] [PubMed] [Google Scholar]
  24. Somers D. E., Sharrock R. A., Tepperman J. M., Quail P. H. The hy3 Long Hypocotyl Mutant of Arabidopsis Is Deficient in Phytochrome B. Plant Cell. 1991 Dec;3(12):1263–1274. doi: 10.1105/tpc.3.12.1263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Valvekens D., Van Montagu M., Van Lijsebettens M. Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Natl Acad Sci U S A. 1988 Aug;85(15):5536–5540. doi: 10.1073/pnas.85.15.5536. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Van Tuinen A., Kerckhoffs LHJ., Nagatani A., Kendrick R. E., Koornneef M. A Temporarily Red Light-Insensitive Mutant of Tomato Lacks a Light-Stable, B-Like Phytochrome. Plant Physiol. 1995 Jul;108(3):939–947. doi: 10.1104/pp.108.3.939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wagner D., Quail P. H. Mutational analysis of phytochrome B identifies a small COOH-terminal-domain region critical for regulatory activity. Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8596–8600. doi: 10.1073/pnas.92.19.8596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Weller J. L., Nagatani A., Kendrick R. E., Murfet I. C., Reid J. B. New lv Mutants of Pea Are Deficient in Phytochrome B. Plant Physiol. 1995 Jun;108(2):525–532. doi: 10.1104/pp.108.2.525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Whitelam G. C., Johnson E., Peng J., Carol P., Anderson M. L., Cowl J. S., Harberd N. P. Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. Plant Cell. 1993 Jul;5(7):757–768. doi: 10.1105/tpc.5.7.757. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES