Skip to main content
SpringerLink
Log in

Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1 locus on chromosome III

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

The Arabidopsis thaliana Em1 gene has been mapped to the lower arm of chromosome III. Fine analysis of 60 kb around this gene, based largely on identification and sequencing of cognate cDNAs, has allowed us to identify 15 genes or putative genes. Cognate cDNAs exist for ten of these genes, indicating that they are effectively expressed. Analysis by sequence alignment and intracellular localization prediction programs allows attribution of a potential protein product to these genes which show no obvious functional relationship. Comparison of the true exon/intron structure based on cDNA sequences with that proposed by three commonly used prediction programs shows that, in the absence of further information, the results of these predictions on anonymous genomic sequences should be interpreted with caution. Examination of the non-coding sequence showed the presence of a novel repeated, palindromic element. The results of this detailed analysis show that in-depth studies will be necessary to exploit correctly the complete A. thaliana genome sequence.

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

  • Altschul, S.F., Gish, W., Miller, W., Myers, E. and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.

    Article  PubMed  Google Scholar 

  • Aubourg, S., Takvorian, A., Chéron, A., Kreis, M. and Lecharny, A. 1997. Structure, organization and putative function of the genes identified within a 23.9 kb fragment from Arabidopsis thaliana chromosome IV. Gene 199: 241–253.

    PubMed  Google Scholar 

  • Bevan, M. 1997. Objective: the complete sequence of a plant genome. Plant Cell 9: 476–478.

    PubMed  Google Scholar 

  • Bevan, M., Bancroft, I., Bent, E., Love, K., Goodman, H., Dean, C., Bergkamp, R., Dirkse, W., van Staveren, M., Stiekem, W., Drost, L., Ridley, P., Hudson, S.A., Patel, K., Murphy, G., Piffanelli, P., Wedler, H., Wedler, E., Wambutt, R., Weitzenegger, T., Pohl, T.M., Terryn, N., Gielen, J., Villarroel, R., De Clerck, R., Van Montagu, M., Lecharny, A., Aubourg, S., Gy, I., Kreis, M., Lao, N., Kavanagh, T., Hempel, S., Kotter, P., Entian, K.D., Rieger, M., Schaeffer, M., Funk, B., Mueller-Auer, S., Silvey, M., James, R., Montfort, A., Pons, A., Puigdomenech, P., Douka, A., Voukelatou, E., Milioni, D., Hatzopoulos, P., Piravandi, E., Obermaier, B., Hilbert, H., Dusterhoft, A., Moores, T., Jones, J.D.G., Eneva, T., Palme, K., Benes, V., Rechman, S., Ansorge, W., Cooke, R., Berger, C., Delseny, M., Voet, M., Volekaert, G., Mewes, H.-W., Klosterman, S., Schueller, C. and Chalwatzis, N. 1998. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391: 485–488.

    PubMed  Google Scholar 

  • Bies, N., Aspart L., Carles, C., Gallois, P. and Delseny, M. 1998. Accumulation and degradation of Em proteins in Arabidopsis thaliana: evidence for post-transcriptional controls. J. Exp. Bot. 49: 1925–1933.

    Google Scholar 

  • Bollivar, D.W., Wang, S., Allen, J.P. and Bauer, C.E. 1994. Molecular genetic analysis of terminal steps in bacteriochlorophyll a biosynthesis: characterization of a Rhodobacter capsulatus strain that synthesizes geranylgeraniol-esterified bacteriochlorophyll a. Biochemistry 33: 12763–12768.

    PubMed  Google Scholar 

  • Borodovsky, M. and McInnich, J. 1993. GeneMark: parallel gene recognition for both DNA strands. Comp. Chem. 17: 123–133.

    Google Scholar 

  • Burge, C.B. and Karlin, S. 1998. Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8: 346–354.

    PubMed  Google Scholar 

  • Camilleri, C., Lafleuriel, J., Macadre, C., Varoquaux, F., Parmen-tier, Y., Picard, G., Caboche, M. and Bouchez, D. 1998. A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J. 14: 633–642.

    PubMed  Google Scholar 

  • Chelsky, D., Ralph, R. and Jonak, G. 1989. Sequence requirements for synthetic peptide-mediated translocation to the nucleus. Mol. Cell Biol. 9: 2487–2492.

    PubMed  Google Scholar 

  • Cleves, A.E., Novick, P.J. and Bankaitis, V.A. 1989. Mutations in the Sac1 gene suppress defects in yeast golgi and yeast actin function. J. Cell Biol. 109: 2939–2950.

    PubMed  Google Scholar 

  • Cooke, R., Raynal, M., Laudie, M., Grellet, F., Delseny, M., Morris, P.C., Guerrier, D., Giraudat, J., Quigley, F., Clabault, G., Li, Y., Mache, R., Krivitzky, M., Gy, I.J.J., Kreis, M., Lecharny, A., Parmentier, Y., Marbach, J., Fleck, J., Clement, B., Philipps, G., Herve, C., Bardet, C., Tremousaygue, D., Lescure, B., Laccome, C., Roby, D., Jourjon, M.F., Chabrier, P., Charpenteau, J., Desprez, T., Amselem, J., Chiapello, H., Hofte, H. and Li, Y.F. 1996. Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTS. Plant J. 91: 101–124.

    Google Scholar 

  • Creusot, F., Fouilloux, E., Dron, M., Lafleuriel, J., Picard, G., Bil-lault, A., LePaslier, D., Cohen, D., Chabouté, M.E. and Durr, A. 1995. The CIC library: a large insert Yac library for genome mapping in A. thaliana. Plant J. 85: 763–770.

    Google Scholar 

  • Delseny, M., Cooke, R., Comella, P., Wu, H.J, Raynal, M. and Grellet, F. 1997. The Arabidopsis thaliana genome project. C. R. Acad. Sci. Paris 320: 589–599.

    Google Scholar 

  • Desprez, T., Amselem, J., Caboche, M. and Hofte, H. 1998. Differential gene expression in Arabidopsis monitored using cDNA arrays. Plant J. 14: 643–652.

    PubMed  Google Scholar 

  • Fiermonte, G., Runswick, M.J., Walker, J.E. and Palmieri, F. 1992. Sequence and pattern of expression of a bovine homologue of a human mitochondrial transport protein associated with Grave's disease. DNA Seq. 3: 71–78.

    PubMed  Google Scholar 

  • Finkelstein, R.R., Wang, M.L., Lynch, T.J., Rao, S., Goodman, H.M. 1998. The Arabidopsis abscisic acid response locus AB14 encodes an APETALA 2 domain protein. Plant Cell 10: 1043–1054.

    PubMed  Google Scholar 

  • Gaubier, P., Raynal, M., Hull, G., Huestis, G.M., Grellet, F., Arenas, C., Pagès, M. and Delseny, M. 1993. Two different Em-like genes are expressed in Arabidopsis thaliana seeds during maturation. Mol. Gen. Genet. 238: 409–418.

    PubMed  Google Scholar 

  • Gaubier, P., Wu, H.J., Laudie, M., Delseny, M. and Grellet, F. 1995. A chlorophyll synthetase gene from Arabidopsis thaliana.Mol. Gen. Genet. 249: 58–64.

    Google Scholar 

  • Harmon, A.C., Yoo, B.C. and McCaffery, C. 1994. Pseudosubstrate inhibition of CDPK, a protein kinase with a calmodulin-like domain. Biochemistry 33: 7278–7287.

    PubMed  Google Scholar 

  • Heinemeyer, T., Wingender, E., Reuter, I., Hermjakob, H., Kel, A.E., Kel, O.V., Ignatieva, E.V., Ananko, E.A., Podkolodnaya, O.A., Kolpakov, F.A., Podkolodny, N.L. and Kolchanov, N.A. 1998. Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL. Nucl. Acids Res. 26: 364–370.

    Google Scholar 

  • Higo, K., Ugawa, Y., lwamoto, M. and Higo, H. 1998. PLACE: a database of plant cis-acting regulatory DNA elements. Nucl. Acids Res. 26: 358–359.

    PubMed  Google Scholar 

  • Hirschi, K.D., Zhen, R.G., Cunningham, K.W., Rea, P.A. and Fink, G.R. 1996. CAX1, an H C /Ca 2 C antiporter from Arabidopsis. Proc. Natl. Acad. Sci. USA 93: 8782–8786.

    PubMed  Google Scholar 

  • Hull, G., Bies, N., Twell, D. and Delseny, M. 1996. Analysis of the promoter of an abscisic acid responsive late embryogenesis abundant gene of Arabidopsis thaliana. Plant Sci. 114: 181–192.

    Google Scholar 

  • Kotani, H., Nakamura, Y., Sato, S., Kaneko, T., Asamizu, E., Miyajima, and Tabata, S. 1997. Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones. DNA Res. 4: 291–300.

    PubMed  Google Scholar 

  • Lister, C. and Dean, C. 1993. Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J. 4: 745–750.

    Google Scholar 

  • Marck, C. 1988. 'DNA Strider': a ‘C’ program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers. Nucl. Acids Res. 16: 1829–1836.

    PubMed  Google Scholar 

  • Mayinger, P., Bankaitis, V.A. and Meyer, D.I. 1995. Sac1p mediates the adenosine triphosphate transport into yeast endoplasmic reticulum that is required for protein translocation. J. Cell Biol. 131: 1377–1386.

    PubMed  Google Scholar 

  • McPherson, P.S., Garcia, E.P., Slepnev, V.I., David, C., Zhang, X., Grabs, D., Sossin, W.S., Bauerfeind, R., Nemoto, Y. and De Camilli, P. 1996. A presynaptic inositol-5-phosphatase. Nature 379: 353–357.

    PubMed  Google Scholar 

  • Nakai, K. and Kanehisa, M. 1992. A knowledge base for predicting protein localization sites in eucaryotic cells. Genomics 14: 897–911.

    Google Scholar 

  • Nakamura, Y., Sato, S., Kaneko, T., Kotani, H., Asamizu, E., Miyajima, N. and Tabata, S. 1997. Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones. DNA Res. 4: 401–414.

    PubMed  Google Scholar 

  • Newman, T., de Bruijn, F.J., Green, P., Keegstra, K., Kende, H., McIntosh, L., Ohlrogge, J., Raikhel, N., Somerville, S., Thomashow, M., Retzel, E. and Somerville, C. 1994. Genes galore: a summary of the methods for accessing results from large scale partial sequencing of anonymous Arabidopsis thaliana cDNA clones. Plant Physiol. 106: 1241–1255.

    PubMed  Google Scholar 

  • Öster, U. and Rüdiger, W. 1997. The G4 gene of Arabidopsis thaliana encodes a chlorophyll synthase of etiolated plants. Bot. Acta 110: 420–423.

    Google Scholar 

  • Parcy, F., Valon, C., Raynal, M., Gaubier-Comella, P., Delseny, M. and Giraudat, J. 1994. Regulation of gene expression programs during Arabidopsis seed development: roles of the ABI3 locus and of exogenous abscisic acid. Plant Cell 6: 1567–1582.

    Article  PubMed  Google Scholar 

  • Quigley, F., Dao, P., Cottet, A. and Mache, R. 1996. Sequence analysis of an 81 kbp contig from Arabidopsis thaliana chro-mosome III. Nucl. Acids Res. 24: 4313–4318.

    Google Scholar 

  • Radomski, N. and Jost, E. 1995. Molecular cloning of a murine cDNA encoding a novel protein, p38-2G4, which varies with the cell cycle. Exp. Cell Res. 22: 434–445.

    Google Scholar 

  • Reiter, R.S., Williams, J.G.K., Feldman, K.A., Rafalski, J.A., Tingey, S.V. and Scolnick, P.A. 1992. Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAS. Proc. Natl. Acad. Sci. USA 89: 1477–1481.

    PubMed  Google Scholar 

  • Ritz, D., Thony-Meyer, L. and Hennecke, H. 1995. The cycHJKL gene cluster plays an essential role in the biogenesis of c-type cytochromes in Bradyrhizobium japonicum. Mol. Gen. Genet. 247: 27–38.

    PubMed  Google Scholar 

  • Ruan, Y., Gilmore, J., Conner, T. 1998. Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15: 821–833.

    Article  PubMed  Google Scholar 

  • Sadowski, J., Gaubier, P., Delseny, M. and Quiros, C.F. 1996. Genetic and physical mapping in Brassica diploid species of a gene cluster defined in Arabidopsis thaliana. Mol. Gen. Genet. 251: 298–306.

    PubMed  Google Scholar 

  • Sato, S., Kotani, H., Nakamura, Y., Kaneko, T., Asamizu, E., Fukami, M., Miyajima, N. and Tabata, S. 1997. Structural analy-sis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones. DNA Res. 4: 215–230.

    PubMed  Google Scholar 

  • Schmidt, R., Cnops, G., Bancroft, I. and Dean, C. 1992. Construction of an overlapping YAC library of Arabidopsis thaliana genome. Aust. J. Plant Physiol. 19: 341–351.

    Google Scholar 

  • Smith, F.W., Ealing, P.M., Hawkesford, M.J. and Clarkson, D.T. 1995. Plant members of a family of sulfate transporters reveal functional subtypes. Proc. Natl. Acad. Sci. USA 92: 9373–9377.

    PubMed  Google Scholar 

  • Strynadka, N.C.J. and James, M.N.G. 1989. Crystal structure of the helix-loop-helix calcium-binding proteins. Annu. Rev. Biochem. 58: 951–998.

    PubMed  Google Scholar 

  • Takahashi, H., Yamazaki, M., Sasakura, N., Watanabe, A., Leustek, T., Engler, J.A., Engler, G., Van Montagu, M. and Saito, K. 1997. Regulation of sulfur assimilation in higher plants: a sulfate transporter induced in sulfate-starved roots plays a central role in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 94: 11102–11107.

    PubMed  Google Scholar 

  • Terryn, N., Gielen, J., De Keyser, A., Van Den Daele, H., Ardiles, W., Neyt, P., De Clercq, R., Coppieters, J., Dehais, P., Villarroel, R., Rouze, P. and Van Montagu, M. 1998. Sequence analysis of a 40 kbArabidopsis thaliana genomic region located at the top of chromosome I. Gene 215: 11–17.

    PubMed  Google Scholar 

  • Terzaghi, W.B. and Cashmore, A.R. 1995. Light-regulated tran-scription. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46: 445–474.

    Google Scholar 

  • Tremousaygue, D., Bardet, C., Dabos, P., Regad, F., Pelese, F., Nazer, R., Gander, E. and Lescure, B. 1997. Genome DNA se-quencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high density and a shuffling of non coding regions. Genome Res. 7: 198–209.

    PubMed  Google Scholar 

  • Wu, H.J., Gaubier-Comella, P., Delseny, M., Grellet, F., Van Montagu, M. and Rouze, P. 1996. Non-canonical introns are at least 10 9 years old. Nature Genet. 14: 383–384.

    PubMed  Google Scholar 

  • Yamada, H., Mori, H., Momoi, H., Nakagawa, Y., Ueguchi, C. and Mizuno, T. 1994. A fission yeast gene encoding a protein that preferentially associates with curved DNA. Yeast 10: 883–894.

    PubMed  Google Scholar 

  • Zhang, M.Q. 1997. Identification of protein coding regions in the human genome based on quadratic discriminant analysis. Proc. Natl. Acad. Sci. USA 94: 565–568.

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratoire de Physiologie et Biologie Moléculaire des Plantes, UMR CNRS 5545, Université de Perpignan, 52 Avenue de Villeneuve, 66860, Perpignan, France

    Pascale Comella, Hui-Ju Wu, Michèle Laudie, Christel Berger, Richard Cooke, Michel Delseny & Françoise Grellet

Authors
  1. Pascale Comella
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hui-Ju Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michèle Laudie
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Christel Berger
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Richard Cooke
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Michel Delseny
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Françoise Grellet
    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

Comella, P., Wu, HJ., Laudie, M. et al. Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1 locus on chromosome III. Plant Mol Biol 41, 687–700 (1999). https://doi.org/10.1023/A:1006395324818

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1006395324818

Search

Navigation