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Analysis of Arabidopsis genome sequence reveals a large new gene family in plants

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Abstract

A detailed analysis of the currently available Arabidopsis thaliana genomic sequence has revealed the presence of a large number of open reading frames with homology to the stigmatic self-incompatibility (S) genes of Papaver rhoeas. The products of these potential genes are all predicted to be relatively small, basic, secreted proteins with similar predicted secondary structures. We have named these potential genes SPH (S-protein homologues). Their presence appears to have been largely missed by the prediction methods currently used on the genomic sequence. Equivalent homologues could not be detected in the human, microbial, Drosophila or C. elegans genomic databases, suggesting a function specific to plants. Preliminary RT-PCR analysis indicates that at least two members of the family (SPH1, SPH8) are expressed, with expression being greatest in floral tissues. The gene family may total more than 100 members, and its discovery not only illustrates the importance of the genome sequencing efforts, but also indicates the extent of information which remains hidden after the initial trawl for potential genes.

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References

  1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389–3402 (1997).

    PubMed  Google Scholar 

  2. An YQ, McDowell JM, Huang SR, McKinney EC, Chambliss S, Meagher RB: Strong, constitutive expression of the Arabidopsis ACT2/ACT8 actin subclass in vegetative tissues. Plant J 10: 107–121 (1996).

    Article  PubMed  Google Scholar 

  3. Bevan M, Others AN: Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391: 485–488 (1998).

    PubMed  Google Scholar 

  4. Dickinson HG, C rabbe MJC, Gaude T: Sporophytic selfincompatibility systems: S gene products. Int Rev Cytol 140: 525–561 (1992).

    PubMed  Google Scholar 

  5. Foote HCC, Ride JP, Franklin-Tong VE, Walker EA, Lawrence MJ, Franklin FCH: Cloning and expression of a distinctive class of self-incompatibility (S) gene from Papaver rhoeas L. Proc Natl Acad Sci USA 91: 2265–2269 (1994).

    Google Scholar 

  6. Franklin FCH, Lawrence MJ, Franklin-Tong VE: Cell and molecular biology of self-incompatibility in flowering plants. Int Rev Cytol 158: 1–64 (1995).

    Google Scholar 

  7. Hearn MJ, Franklin FCH, Ride JP: Identification of a membrane glycoprotein in pollen of Papaver rhoeas which binds stigmatic self-incompatibility (S-) proteins. Plant J 9: 467–475 (1996).

    Google Scholar 

  8. King RD, Saqi M, Sayle R, Sternberg MJE: DSC: public domain protein secondary structure prediction. Comp Appl Biosci 13: 473–474 (1997).

    PubMed  Google Scholar 

  9. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wooton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262: 208–214 (1993).

    PubMed  Google Scholar 

  10. Lawrence MJ, Afzal M, Kenrick J: The genetical control of self-incompatibility in Papaver rhoeas L. Heredity 40: 239–253 (1978).

    Google Scholar 

  11. Nielsen H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Prot Engng 10: 1–6 (1997).

    Google Scholar 

  12. Rost B, Sander C: Prediction of protein structure at better than 70% accuracy. J Mol Biol 232: 584–599 (1993).

    Article  PubMed  Google Scholar 

  13. Rost B, Sander C, Schneider R: PHD-an automatic mail server for protein secodary structure prediction. CABIOS 10: 53–60 (1994).

    PubMed  Google Scholar 

  14. Schuler GD, Altschul SF, Lipman DG: A workbench for multiple alignment construction and analysis. Prot Struct Funct Genet 9: 180–190 (1991).

    Google Scholar 

  15. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22: 4673–4680 (1994).

    PubMed  Google Scholar 

  16. Walker EA, Ride JP, Kurup S, Franklin-Tong VE, Lawrence MJ, Franklin FCH: Molecular analysis of two functional homologues of the S3 allele of the Papaver rhoeas selfincompatibility gene isolated from different populations. Plant Mol Biol 30: 983–994 (1996).

    PubMed  Google Scholar 

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Authors and Affiliations

  1. University of Birmingham, P.O. Box 363, Birmingham, B15 2TT, UK

    J.P. Ride & E.M. Davies

  2. Bioinformatics & IT Research Unit, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

    D.F. Marshall

Authors
  1. J.P. Ride
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  2. E.M. Davies
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  3. F.C.H. Franklin
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  4. D.F. Marshall
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Ride, J., Davies, E., Franklin, F. et al. Analysis of Arabidopsis genome sequence reveals a large new gene family in plants. Plant Mol Biol 39, 927–932 (1999). https://doi.org/10.1023/A:1006178511787

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  • DOI: https://doi.org/10.1023/A:1006178511787

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