Skip to main content
PMC home page
The Plant Cell logoLink to The Plant Cell
. 1992 Mar;4(3):333–347. doi: 10.1105/tpc.4.3.333

Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations.

B W Shirley 1, S Hanley 1, H M Goodman 1
PMCID: PMC160133  PMID: 1354004

Abstract

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and has been used extensively for inducing mutations. In Arabidopsis, two methods for the isolation of genes identified on the basis of mutant phenotypes--genomic subtraction and chromosome walking--either rely on or are greatly facilitated by the availability of these types of mutations. This article gives a detailed characterization of ionizing radiation-induced mutations in plants. The Arabidopsis genes encoding chalcone flavanone isomerase (CHI) and dihydroflavonol 4-reductase (DFR) were cloned and found to correspond to two transparent testa loci. A CHI allele, generated by fast-neutron irradiation, consisted of an inversion within the gene. A 272-bp fragment from 38 centimorgans away on the same chromosome was transferred to one end of this inversion. A DFR allele, induced by x-irradiation, contained two deletions and an inversion of the 2.8-centimorgan intervening region. Sequence analysis of the break points in both mutants indicate that repair of radiation-induced damage involves mechanisms similar or identical to those that mediate the integration of foreign sequences into the genome. The chromosome rearrangements found in these mutants have important implications for the use of ionizing radiation-induced alleles in classical and molecular genetic experiments in plants.

Full Text

The Full Text of this article is available as a PDF (3.2 MB).

Selected References

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

  1. Bednar R. A., Fried W. B., Lock Y. W., Pramanik B. Chemical modification of chalcone isomerase by mercurials and tetrathionate. Evidence for a single cysteine residue in the active site. J Biol Chem. 1989 Aug 25;264(24):14272–14276. [PubMed] [Google Scholar]
  2. Begley C. G., Aplan P. D., Denning S. M., Haynes B. F., Waldmann T. A., Kirsch I. R. The gene SCL is expressed during early hematopoiesis and encodes a differentiation-related DNA-binding motif. Proc Natl Acad Sci U S A. 1989 Dec;86(24):10128–10132. doi: 10.1073/pnas.86.24.10128. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beld M., Martin C., Huits H., Stuitje A. R., Gerats A. G. Flavonoid synthesis in Petunia hybrida: partial characterization of dihydroflavonol-4-reductase genes. Plant Mol Biol. 1989 Nov;13(5):491–502. doi: 10.1007/BF00027309. [DOI] [PubMed] [Google Scholar]
  4. Blyden E. R., Doerner P. W., Lamb C. J., Dixon R. A. Sequence analysis of a chalcone isomerase cDNA of Phaseolus vulgaris L. Plant Mol Biol. 1991 Jan;16(1):167–169. doi: 10.1007/BF00017927. [DOI] [PubMed] [Google Scholar]
  5. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Coen E. S., Romero J. M., Doyle S., Elliott R., Murphy G., Carpenter R. floricaula: a homeotic gene required for flower development in antirrhinum majus. Cell. 1990 Dec 21;63(6):1311–1322. doi: 10.1016/0092-8674(90)90426-f. [DOI] [PubMed] [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  10. Goff S. A., Klein T. M., Roth B. A., Fromm M. E., Cone K. C., Radicella J. P., Chandler V. L. Transactivation of anthocyanin biosynthetic genes following transfer of B regulatory genes into maize tissues. EMBO J. 1990 Aug;9(8):2517–2522. doi: 10.1002/j.1460-2075.1990.tb07431.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gould S. J., Subramani S., Scheffler I. E. Use of the DNA polymerase chain reaction for homology probing: isolation of partial cDNA or genomic clones encoding the iron-sulfur protein of succinate dehydrogenase from several species. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1934–1938. doi: 10.1073/pnas.86.6.1934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Grossberger D. Minipreps of DNA from bacteriophage lambda. Nucleic Acids Res. 1987 Aug 25;15(16):6737–6737. doi: 10.1093/nar/15.16.6737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Hawkins R. B. Double strand-breaks and DNA-to-protein cross-links induced by fast neutrons in bacteriophage DNA. Int J Radiat Biol Relat Stud Phys Chem Med. 1979 Jan;35(1):1–13. doi: 10.1080/09553007914550011. [DOI] [PubMed] [Google Scholar]
  15. Herman P. L., Marks M. D. Trichome Development in Arabidopsis thaliana. II. Isolation and Complementation of the GLABROUS1 Gene. Plant Cell. 1989 Nov;1(11):1051–1055. doi: 10.1105/tpc.1.11.1051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Jordan B. R. Megabase methods: a quantum jump in recombinant DNA techniques. Bioessays. 1988 May;8(5):140–145. doi: 10.1002/bies.950080503. [DOI] [PubMed] [Google Scholar]
  17. Käs E., Chasin L. A. Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol. 1987 Dec 20;198(4):677–692. doi: 10.1016/0022-2836(87)90209-9. [DOI] [PubMed] [Google Scholar]
  18. Liang X. W., Dron M., Schmid J., Dixon R. A., Lamb C. J. Developmental and environmental regulation of a phenylalanine ammonia-lyase-beta-glucuronidase gene fusion in transgenic tobacco plants. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9284–9288. doi: 10.1073/pnas.86.23.9284. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Luo D., Coen E. S., Doyle S., Carpenter R. Pigmentation mutants produced by transposon mutagenesis in Antirrhinum majus. Plant J. 1991 Jul;1(1):59–69. [PubMed] [Google Scholar]
  20. Martin C., Prescott A., Mackay S., Bartlett J., Vrijlandt E. Control of anthocyanin biosynthesis in flowers of Antirrhinum majus. Plant J. 1991 Jul;1(1):37–49. doi: 10.1111/j.1365-313x.1991.00037.x. [DOI] [PubMed] [Google Scholar]
  21. Mayerhofer R., Koncz-Kalman Z., Nawrath C., Bakkeren G., Crameri A., Angelis K., Redei G. P., Schell J., Hohn B., Koncz C. T-DNA integration: a mode of illegitimate recombination in plants. EMBO J. 1991 Mar;10(3):697–704. doi: 10.1002/j.1460-2075.1991.tb07999.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. McClintock B. The significance of responses of the genome to challenge. Science. 1984 Nov 16;226(4676):792–801. doi: 10.1126/science.15739260. [DOI] [PubMed] [Google Scholar]
  23. Meyer P., Heidmann I., Forkmann G., Saedler H. A new petunia flower colour generated by transformation of a mutant with a maize gene. Nature. 1987 Dec 17;330(6149):677–678. doi: 10.1038/330677a0. [DOI] [PubMed] [Google Scholar]
  24. O'Reilly C., Shepherd N. S., Pereira A., Schwarz-Sommer Z., Bertram I., Robertson D. S., Peterson P. A., Saedler H. Molecular cloning of the a1 locus of Zea mays using the transposable elements En and Mu1. EMBO J. 1985 Apr;4(4):877–882. doi: 10.1002/j.1460-2075.1985.tb03713.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Oppenheimer D. G., Herman P. L., Sivakumaran S., Esch J., Marks M. D. A myb gene required for leaf trichome differentiation in Arabidopsis is expressed in stipules. Cell. 1991 Nov 1;67(3):483–493. doi: 10.1016/0092-8674(91)90523-2. [DOI] [PubMed] [Google Scholar]
  26. Roth D. B., Wilson J. H. Relative rates of homologous and nonhomologous recombination in transfected DNA. Proc Natl Acad Sci U S A. 1985 May;82(10):3355–3359. doi: 10.1073/pnas.82.10.3355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sankaranarayanan K. Ionizing radiation and genetic risks. III. Nature of spontaneous and radiation-induced mutations in mammalian in vitro systems and mechanisms of induction of mutations by radiation. Mutat Res. 1991 Jul;258(1):75–97. doi: 10.1016/0165-1110(91)90029-u. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Schwarz-Sommer Z., Shepherd N., Tacke E., Gierl A., Rohde W., Leclercq L., Mattes M., Berndtgen R., Peterson P. A., Saedler H. Influence of transposable elements on the structure and function of the A1 gene of Zea mays. EMBO J. 1987 Feb;6(2):287–294. doi: 10.1002/j.1460-2075.1987.tb04752.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sperry A. O., Blasquez V. C., Garrard W. T. Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci U S A. 1989 Jul;86(14):5497–5501. doi: 10.1073/pnas.86.14.5497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Staiger D., Kaulen H., Schell J. A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein. Proc Natl Acad Sci U S A. 1989 Sep;86(18):6930–6934. doi: 10.1073/pnas.86.18.6930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Sun Tp., Goodman H. M., Ausubel F. M. Cloning the Arabidopsis GA1 Locus by Genomic Subtraction. Plant Cell. 1992 Feb;4(2):119–128. doi: 10.1105/tpc.4.2.119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Underbrink A. G., Sparrow R. C., Sparrow A. H., Rossi H. H. Relative biological effectiveness of x-rays and 0.43-MeV monoenergetic neutrons on somatic mutations and loss of reproductive integrity in Tradescantia stamen hairs. Radiat Res. 1970 Oct;44(1):187–203. [PubMed] [Google Scholar]
  34. Wilkinson J. Q., Crawford N. M. Identification of the Arabidopsis CHL3 gene as the nitrate reductase structural gene NIA2. Plant Cell. 1991 May;3(5):461–471. doi: 10.1105/tpc.3.5.461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Yang R., Lis J., Wu R. Elution of DNA from agarose gels after electrophoresis. Methods Enzymol. 1979;68:176–182. doi: 10.1016/0076-6879(79)68012-6. [DOI] [PubMed] [Google Scholar]
  36. van der Krol A. R., Mur L. A., Beld M., Mol J. N., Stuitje A. R. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell. 1990 Apr;2(4):291–299. doi: 10.1105/tpc.2.4.291. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES