Nonsense-mediated mRNA decay in barley mutants allows the cloning of mutated genes by a microarray approach - PubMed

Nonsense-mediated mRNA decay in barley mutants allows the cloning of mutated genes by a microarray approach

Rena Gadjieva et al. Plant Physiol Biochem. 2004 Jul-Aug.

Abstract

We have previously described a microarray approach to identify and clone genes from mutants of higher organisms. In the method cDNA of two mutants with similar phenotype are competitively hybridized to DNA clones arrayed on a glass slide. Clones corresponding to an mRNA that is not expressed in one of the strains due to a mutation will be specifically highlighted in the hybridization, which provides a possibility to identify and eventually clone the mutated gene. The approach is dependent on mutations that affect the amount of mRNA. Nonsense mutations, which prematurely terminate translation, can be such mutations as a surveillance system known as nonsense-mediated decay (NMD) has been developed by organisms to reduce the abundance of mRNA with nonsense codons. In the present study, we have analysed the barley (Hordeum vulgare L.) magnesium chelatase mutants xantha-f26, xantha-f27 and xantha-f40 in order to investigate the presence of NMD in barley, as well as the importance of the position of the stop codon for NMD. Both nonsense-mutants xantha-f27 and xantha-f40, but not the missense mutant xantha-f26, showed NMD. This was not expected for xantha-f27 as its mutation is in the last exon of the gene. We conclude the NMD expands the number of mutants that can be used for gene cloning by our described microarray approach.

Similar articles

• Comparing two microarray platforms for identifying mutated genes in barley (Hordeum vulgare L.).

  Zakhrabekova S, Gough SP, Lundqvist U, Hansson M. Zakhrabekova S, et al. Plant Physiol Biochem. 2007 Aug;45(8):617-22. doi: 10.1016/j.plaphy.2007.05.004. Epub 2007 May 31. Plant Physiol Biochem. 2007. PMID: 17606380

• Structural genes for Mg-chelatase subunits in barley: Xantha-f, -g and -h.

  Jensen PE, Willows RD, Petersen BL, Vothknecht UC, Stummann BM, Kannangara CG, von Wettstein D, Henningsen KW. Jensen PE, et al. Mol Gen Genet. 1996 Mar 7;250(4):383-94. doi: 10.1007/BF02174026. Mol Gen Genet. 1996. PMID: 8602155

• Characterization of eight barley xantha-f mutants deficient in magnesium chelatase.

  Olsson U, Sirijovski N, Hansson M. Olsson U, et al. Plant Physiol Biochem. 2004 Jun;42(6):557-64. doi: 10.1016/j.plaphy.2004.05.011. Plant Physiol Biochem. 2004. PMID: 15246070

• NMD microarray analysis for rapid genome-wide screen of mutated genes in cancer.

  Wolf M, Edgren H, Muggerud A, Kilpinen S, Huusko P, Sørlie T, Mousses S, Kallioniemi O. Wolf M, et al. Cell Oncol. 2005;27(3):169-73. doi: 10.1155/2005/478316. Cell Oncol. 2005. PMID: 16037637 Free PMC article. Review.

• Nonsense-mediated mRNA decay of collagen -emerging complexity in RNA surveillance mechanisms.

  Fang Y, Bateman JF, Mercer JF, Lamandé SR. Fang Y, et al. J Cell Sci. 2013 Jun 15;126(Pt 12):2551-60. doi: 10.1242/jcs.120220. Epub 2013 May 31. J Cell Sci. 2013. PMID: 23729740 Review.

Cited by

• Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley.

  Zhang L, Fetch T, Nirmala J, Schmierer D, Brueggeman R, Steffenson B, Kleinhofs A. Zhang L, et al. Theor Appl Genet. 2006 Sep;113(5):847-55. doi: 10.1007/s00122-006-0342-y. Epub 2006 Jul 11. Theor Appl Genet. 2006. PMID: 16832646

• Both introns and long 3'-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants.

  Kertész S, Kerényi Z, Mérai Z, Bartos I, Pálfy T, Barta E, Silhavy D. Kertész S, et al. Nucleic Acids Res. 2006;34(21):6147-57. doi: 10.1093/nar/gkl737. Epub 2006 Nov 6. Nucleic Acids Res. 2006. PMID: 17088291 Free PMC article.

• Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.

  Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR. Campbell MA, et al. BMC Genomics. 2006 Dec 28;7:327. doi: 10.1186/1471-2164-7-327. BMC Genomics. 2006. PMID: 17194304 Free PMC article.

• Recessiveness and dominance in barley mutants deficient in Mg-chelatase subunit D, an AAA protein involved in chlorophyll biosynthesis.

  Axelsson E, Lundqvist J, Sawicki A, Nilsson S, Schröder I, Al-Karadaghi S, Willows RD, Hansson M. Axelsson E, et al. Plant Cell. 2006 Dec;18(12):3606-16. doi: 10.1105/tpc.106.042374. Epub 2006 Dec 8. Plant Cell. 2006. PMID: 17158606 Free PMC article.

• An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.).

  Shah S, Karunarathna NL, Jung C, Emrani N. Shah S, et al. BMC Plant Biol. 2018 Dec 29;18(1):380. doi: 10.1186/s12870-018-1606-9. BMC Plant Biol. 2018. PMID: 30594150 Free PMC article.

Publication types

MeSH terms

Substances