Skip to main content
SpringerLink
Log in

The Arabidopsis AUX1 gene: a model system to study mRNA processing in plants

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

It is advantageous for an organism to be able to remove aberrant mRNAs that have either been incorrectly transcribed or processed in order to prevent the accumulation of potentially harmful proteins. The selective degradation of nonsense containing transcripts has been described in yeast, Caenorhabiditis elegans and plants. The ease of identification of new mutant alleles in the AUX1 gene of Arabidopsis thaliana has provided a useful system to study novel mutations affecting mRNA stability and pre-mRNA splicing. To date 50 alleles of AUX1 have been identified of which 14 have been characterised at the sequence level. Eight of the characterised alleles encode missense mutations while the others cause nonsense mutations or splicing defects. The 2 splicing mutants identified affect the 5′ or 3′ splice sites and lead to cryptic splicing events resulting in premature stop codons. The AUX1 mRNA levels of the nonsense containing mutants are reduced compared to the wild-type or missense mutants whereas those of a control transcript (SecY) are unaltered. This provides further evidence for a nonsense-mediated mRNA degradation mechanism in plants and provides a system to study the phenomenon further in Arabidopsis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Bennett MJ, Marchant A, Green HG, May ST, Ward SP, Millner PA, Walker AR, Schultz B, Feldmann KA: Arabidopsis AUX1 gene: a permease-like regulator of root gravitropism. Science 273: 948–950 (1996).

    PubMed  Google Scholar 

  2. Bradley JM, Whitelam GC, Harberd NP: Impaired splicing of phytochrome B pre-mRNA in a novel phyB mutant of Arabidopsis. Plant Mol Biol 27: 1133–1142 (1995).

    PubMed  Google Scholar 

  3. Brown JWS: A catalogue of splice site junction and putative branch point sequences from plant introns. Nucl Acids Res 14: 9549–9559 (1996).

    Google Scholar 

  4. Brown JWS: Arabidopsis intron mutations and pre-mRNA splicing. Plant J 10: 771–780 (1996).

    PubMed  Google Scholar 

  5. Brown JWS, Simpson CG, Simpson GG, Turnbull-Ross AD, Clark GP: Plant prem-RNA splicing and splicing components. Phil Trans R Soc Lond B 342: 217–224 (1993).

    Google Scholar 

  6. Brown JWS, Smith P, Simpson CG: Arabidopsis consensus intron sequences. Plant Mol Biol 32: 531–535 (1996).

    PubMed  Google Scholar 

  7. Carle-Urioste JC, Ko CH, Benito MI, Walbot V. In vivo analysis of intron processing using splicing-dependent reporter gene assays. Plant Mol. Biol. 26: 1785–1795 (1994).

    PubMed  Google Scholar 

  8. Cheng J, Fogel-Petrovic M, Maquat LE: Translation to near the distal end of the penultimate exon is required for normal levels of spliced thiosephosphate isomerase mRNA. Mol Cell Biol 10: 5215–5225 (1990).

    PubMed  Google Scholar 

  9. Czaplinski K, Weng Y, Hagan KW, Peltz SW: Purification and characterisation of the Upf1 protein: a factor involved in translation and mRNA degradation. RNA 1: 610–623 (1995).

    PubMed  Google Scholar 

  10. Forsthoefel NR, Wu Y, Schultz B, Bennett MJ, Feldmann KA: T-DNA insertion mutagenesis in Arabidopsis: prospects and perspectives. Aust J Plant Physiol 19: 353–366 (1992).

    Google Scholar 

  11. Golde TE, Estus S, Usiak M, Younkin LH, Younkin SG: Expression of β amyloid protein precursor mRNAs: recognition of a novel alternatively spliced form and quantitation in Alzheimer's disease using PCR. Neuron 4: 253–267 (1990).

    PubMed  Google Scholar 

  12. Goodall GJ, Filipowicz W: The AUrich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58: 473–483 (1989).

    Article  PubMed  Google Scholar 

  13. Goodall GJ, Filipowicz W: Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants. EMBO J 10: 2635–2644 (1991).

    PubMed  Google Scholar 

  14. Hagan KW, Ruiz-Echevarria MJ, Quan Y, Peltz SW: Characterisation of cis-acting sequences and decay intermediates involved in nonsensemediated mRNA turnover. Mol Cell Biol 15: 809–823 (1995).

    PubMed  Google Scholar 

  15. Hartley MR, Wheeler A, Ellis RJ: Protein synthesis in chloroplasts. J Mol Biol 91: 67–77 (1975).

    PubMed  Google Scholar 

  16. He F, Brown AH, Jacobsen A: Identification of a novel component of the nonsensemediated mRNAdecay pathway by use of an interacting protein screen. Genes & Devel 9: 437–454 (1997).

    Google Scholar 

  17. He F, Jacobson A: Upf1p, Nmd2p and Upf3p are interacting components of the yeast nonsensemediated mRNA decay pathway. Mol Cell Biol 17: 1580–1594 (1995).

    Google Scholar 

  18. Hobbie L, Estelle M: The axr4 auxin-resistant mutants of Arabidopsis thaliana define a gene important for root gravitropism and lateral root initiation. Plant J 7: 211–220 (1995).

    PubMed  Google Scholar 

  19. Hoffmann LM, Donaldson DD: Characterisation of two Phaseolus vulgaris phytohemagglutinin genes closely linked on the chromosome. EMBO J 4: 883–889 (1985).

    PubMed  Google Scholar 

  20. Jacobsen SE, Binkowski K, Olszewski NE: SPINDLY – a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis. Proc Natl Acad Sci USA 93: 9292–9296 (1996).

    PubMed  Google Scholar 

  21. Jofuku KD, Schipper RD, Goldberg RB: A frameshift mutation prevents Kunitz trypsin inhibitor mRNA accumulation in soybean embryos. Plant Cell 1: 427–435 (1989).

    PubMed  Google Scholar 

  22. Khorana S, Gagel RF, Cote GJ: Direct sequencing of PCR products in agarose gel slices. Nucl Acids Res 22: 3425–3426 (1994).

    PubMed  Google Scholar 

  23. Laidler V, Chaddock AM, Knott TG, Walker D, Robinson C: A SecY homolog in Arabidopsis thaliana: sequence of a full-length cDNA clone and import of the precursor protein into chloroplasts. J Biol Chem 270: 17664–17667 (1995).

    PubMed  Google Scholar 

  24. Leeds P, Wood JM, Lee BS, Culbertson MR: Gene products that promote mRNA turnover in Saccharomyces cerevisiae. Mol Cell Biol 12: 2165–2177 (1992).

    PubMed  Google Scholar 

  25. Leeds P, Peltz SW, Jacobson A, Culbertson MR: The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes & Devel 5: 2303–2314 (1991).

    Google Scholar 

  26. Liu H-X, Filipowicz W: Mapping of branchpoint nucleotides in mutant pre-mRNAs expressed in plant cells. Plant J 9: 381–389 (1996).

    PubMed  Google Scholar 

  27. Logemann J, Schell J, Willmitzer L: Improved method for the isolation of RNA from plant tissues. Anal Biochem 163: 16–20 (1987).

    PubMed  Google Scholar 

  28. Lou H, McCullough AJ, Schuler MA: 3′ splice site selection in dicot plant nuclei is position dependent. Mol Cell Biol 13: 4485–4493 (1993).

    PubMed  Google Scholar 

  29. Maher EP, Martindale SJB: Mutants of Arabidopsis thaliana with altered responses to auxins and gravity. Biochem Genet 18: 1041–1053 (1980).

    PubMed  Google Scholar 

  30. McCullough A, Lou H, Schuler MA: Factors affecting authentic 5′splice site selection in plant nuclei. Mol Cell Biol 13: 1323–1331 (1993).

    PubMed  Google Scholar 

  31. McNellis TW, von Arnim AG, Araki T, Komeda Y, Miséra S, Deng XW: Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6: 487–500 (1994).

    PubMed  Google Scholar 

  32. Mirza JI, Olsen GM, Iversen TH, Maher EP: The growth and gravitropic responses of wild-type and auxin-resistant mutants of Arabidopsis thaliana. Physiol Plant 60: 516–522 (1984).

    Google Scholar 

  33. Muhlrad D, Parker R: Premature translation termination triggers mRNA decapping. Nature 370: 578–581 (1994).

    PubMed  Google Scholar 

  34. Okada K, Shimura Y: Reversible root tip rotation in Arabidopsis seedlings induced by obstacle-touching stimulus. Science 250: 274–276 (1990).

    Google Scholar 

  35. Peltz SW, Brown AH, Jacobsen A: mRNA destabilisation triggered by premature translational termination depends on at least three cis-acting sequence elements and one transacting factor. Genes & Devel 7: 1737–1754 (1993).

    Google Scholar 

  36. Pickett BF, Wilson AK, Estelle M: The aux1 mutation of Arabidopsis confers both auxin and ethylene resistance. Plant Physiol 94: 1462–1466 (1990).

    Google Scholar 

  37. Pulak R, Anderson P: mRNA surveillance by the Caenorhabditis elegans smg genes. Genes & Devel 10: 1885–1897 (1993).

    Google Scholar 

  38. Roman G, Lubarsky B, Kieber JJ, Rothenberg M, Ecker JR: Genetic analysis of ethylene signal transduction in Arabidopsis thaliana: five novel mutant loci integrated into a stress response pathway. Genetics 139: 1393–1409 (1995).

    PubMed  Google Scholar 

  39. Simpson CG, Clark G, Davidson D, Smith P, Brown JWS: Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency. Plant J 9: 369–380 (1996).

    PubMed  Google Scholar 

  40. Simpson GG, Filipowicz W: Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery. Plant Mol Biol 32: 1–41 (1996).

    PubMed  Google Scholar 

  41. Sullivan ML, Green PJ: Posttranscriptional regulation of nuclear-encoded genes in higher plants: the roles of mRNA stability and translation. Plant Mol Biol 23: 1091–1104 (1993).

    PubMed  Google Scholar 

  42. van Hoof A, Green PJ: Premature nonsense codons decrease the stability of phytohemagglutininmRNAin a position-dependent manner. Plant J 10: 415–424 (1996).

    PubMed  Google Scholar 

  43. Voelker TA, Moreno J, Chrispeels MJ: Expression of a pseudogene in transgenic tobacco: a frameshift mutation prevents mRNA accumulation. Plant Cell 2: 255–261 (1990).

    PubMed  Google Scholar 

  44. Voelker TA, Staswick P, Chrispeels MJ: Molecular analysis of two phtohemagglutinin genes and their expression in Phaseolus vulgaris cv. Pinto, a lectin-deficient cultivar of the bean. EMBO J 5: 3075–3082 (1986).

    Google Scholar 

  45. Zhang J, Maquat LE: Evidence that the decay of nucleusassociated nonsense mRNA for human triosephosphate isomerase involves nonsense codon recognition after splicing. RNA 2: 235–243 (1996).

    PubMed  Google Scholar 

  46. Zhang S, Ruiz-Echevarria MJ, Quan Y, Peltz SW: Identification and characterisation of a sequence motif involved in nonsensemediated mRNA decay. Mol Cell Biol 15: 2231–2244 (1995).

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK

    Alan Marchant & Malcolm J. Bennett

Authors
  1. Alan Marchant
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Malcolm J. Bennett
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Marchant, A., Bennett, M.J. The Arabidopsis AUX1 gene: a model system to study mRNA processing in plants. Plant Mol Biol 36, 463–471 (1998). https://doi.org/10.1023/A:1005961303167

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1005961303167

Search

Navigation