Analysis of a 14-kb fragment containing a putative cell wall gene and a candidate for the ARA1, arabinose kinase, gene from chromosome IV of Arabidopsis thaliana

Gene

Volumn 209, Issue 1-2, 1998, Pages 201-210

  Gy, Isabelle ^a   Aubourg, Sébastien ^a   Sherson, Sarah ^b   Cobbett, Christopher S ^b   Cheron, Angélique ^a   Kreis, Martin ^a   Lecharny, Alain ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Ara1 locus; E.S.S.A; Galactose kinase; GPI anchored protein

Indexed keywords

CELL MEMBRANE PROTEIN; COMPLEMENTARY DNA; DNA FRAGMENT;

AMINO TERMINAL SEQUENCE; ARABIDOPSIS; ARTICLE; CELL WALL; CHROMOSOME; CODON USAGE; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC ORGANIZATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL WALL; CHROMOSOME MAPPING; CLONING, MOLECULAR; CODON; COSMIDS; DNA PRIMERS; EXONS; GALACTOKINASE; GENES, PLANT; HUMANS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); POLYMERASE CHAIN REACTION; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

ARABIDOPSIS THALIANA;

EID: 0032536893     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(98)00049-3     Document Type: Article

References (52)

1. Altschul S.F., Stephen F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Aubourg S., Takvorian A., Chéron A., Kreis M., Lecharny A. Structure, organization and putative function of the genes identified within a 23.9 kb fragment from Arabidopsis thaliana chromosome IV. Gene. 199:1997;241-253.
3. Axelos M., Curie C., Mazzolini L., Bardet C., Lescure B. A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures. Plant Physiol. Biochem. 30:1992;1-6.
4. Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res. 20:1992;2013-2018.
5. Bergsma D.J., Ai Y., Skatch W.R., Nesburn K., Anoia E., Van Horn S., Stambolian D. Fine structure of the human galactokinase GALK1 gene. Genome Res. 6:1996;980-985.
6. Bevan, M., Bancroft, I., Bent, E., Love, K., Piffanelli, P., Goodman, H., Dean, C., Bergkamp, R., Dirkse, W., Van Staveren, M., Stiekema, W., Drost, L., Ridley, P., Hudson, S.-A., Patel, K., Murphy, G., Wedler, H., Wedler, E., Wambutt, R., Weitzenegger, T., Pohl, T., 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., Scholfer, M., Funk, B., Muller-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., Duesterhoeft, A., Moores, T., Jones, J., Eneva, T., Palme, K., Benes, V., Rechman, S., Ansorge, W., Cooke, R., Berger, C., Delseny, M., Volckaert, G., Mewes, H.-W., Schueller, C. and Chalwatzis, N., 1997. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature, in press.
7. Bianchi M.W., Guivarc'h D., Thomas M., Woodgett J.R., Kreis M. Arabidopsis homologs of the shaggy and GSK-3 protein kinases / molecular cloning and functional expression in E. coli. Mol. Gen. Genet. 242:1994;337-345.
8. Bork P., Sander C., Valencia A. Convergent evolution of similar function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases. Prot. Sci. 2:1993;31-40.
9. Boutry M., Chua N.H. A nuclear gene encoding the beta subunit of the mitochondrial ATP synthase in Nicotiana plumbaginifolia. EMBO J. 9:1985;2159-2163.
10. Chan P.H., Hassid W.Z. One step purification of D-galactose and L-arabinose kinase from Phaseolus aureus seedlings by ATP-Sepharose affinity chromatography. Analyt. Biochem. 64:1975;372-379.
11. Citron B.A., Donelson J.E. Sequence of the Saccharomyces Gal region and its transcription in vivo. J. Bacteriol. 158:1984;269-278.
12. Cobbett C.S., Medd J.M., Dolezal O. Suppressors of an Arabinose-sensitive mutant of Arabidopsis thaliana. Aust. J. Plant Physiol. 19:1992;367-375.
13. Cooke R., Raynal M., Laudié M., Grellet F., Delseny M., Morris P-C., Guerrier D., Giraudat J., Quigley F., Clabaut G., Li Y-F., Mache R., Krivitzki M., Jean-Jacques Gy I., Kreis M., Lecharny A., Parmentier Y., Marbach J., Fleck J., Clement B., Philipps G., Hervé C., Bardet C., tremousaygues D., Lescure B., Lacomme C., Roby D., Jourjon M-F., Chabrier P., Charpenteau J-L., Desprez T., Amselme J., Chiapello H., Höfte H. Further progress towards a catalague of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J. 9:1996;101-124.
14. Dean C., Schmidt R. Plant genomes. A current molecular description. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:1995;395-418.
15. Dellaporta S., Wood L.J., Hicks J.B. A plant DNA minipreparation: 'version II'. Plant Mol. Biol. Rep. 1:1983;19-21.
16. Dolezal O., Cobbett C.S. Arabinose kinase-deficient mutant of Arabidopsis thaliana. Plant Physiol. 96:1991;1255-1260.
17. Dopico B., Nicolas G., Labrador E. Partial purification of cell wall α-arabinosidases from Cicer arietinum epicotyls. Relationship with cell wall autolytic processes. Physiol. Plant. 75:1989;465-468.
18. Englund P.T. The structure and biosynthesis of glycosyl phosphatidylinositol protein anchors. Annu. Rev. Biochem. 62:1993;121-138.
19. Feingold, D.S., Avigad, G., 1980. Sugar nucleotide transformations in plant. In: Stumpf, P.K., Conn, E.E. (Eds.), The Biochemistry of Plants, Vol. 3, Academic Press, New York, pp 101-170.
20. Giraudat J., Hauge B.M., Valon C., Smalle J., Parcy F., Goodman H.M. Isolation of the Arabidopsis ABI3 gene positional cloning. Plant Cell. 4:1992;1251-1261.
21. Gomord V., Faye L. Signals and mechanisms involved in intracellular transport of secreted proteins in plants. Plant Physiol. Biochem. 34:1996;165-181.
22. Hanks S.K., Quinn A.M., Hunter T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science. 241:1988;42-52.
23. Haouazine-Takvorian N., Tymowska-Lalanne Z., Takvorian A., Tregear J., Lejeune B., Lecharny A., Kreis M. Characterization of two members of the Arabidopsis thaliana gene family, Atbfruct3 and Atbfruct4, coding for vacuolar invertases. Gene. 197:1997;239-251.
24. Harpster M.H., Taylor W.C. Differential expression of the maize PEPc gene family. J. Biol. Chem. 261:1986;6132-6136.
25. Hebsgaard S.M., Korning P.G., Tolstrup N., Engelbrecht J., Rouzé P., Brunak S. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 24:1986;3439-3452.
26. von Heijne G. A new method for predicting signal sequence cleavage sites. Nucleic Acids Res. 14:1986;4683-4690.
27. Henikoff J.G., Pietrokovski S., Henikoff S. Recent enhancements to the Blocks Database servers. Nucleic Acids Res. 25:1997;222-225.
28. Hillier L., Green P. OSP: a computer program for choosing PCR and DNA sequencing primers. PCR Meth. Appl. 1:1991;124-128.
29. Joshi C.P. An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucleic Acids Res. 15:1987;6643-6653.
30. Kaplan C.P., Tugal H.B., Baker A. Isolation of a cDNA encoding an Arabidopsis galactokinase by functional expression in yeast. Plant Mol. Biol. 34:1997;497-506.
31. Klein P., Kanehisa M., DeLisi C. The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta. 815:1985;468-476.
32. Koornneef M., Hanhart C.J., Van Der Veen J.H. A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol. Gen. Genet. 229:1991;57-66.
33. Kunze M., Riedel J., Lange U., Hurwitz R., Tischner R. Evidence for the presence of GPI-anchored PM-NR in leaves of Beta vulgaris and for PM-NR in barley leaves. Plant Physiol. Biochem. 35:1997;507-512.
34. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132.
35. Lee R.T., Peterson C.L., Calman A.F., Herskowitz I., O'Donnell J. Cloning of a human galactokinase gene (GK2) on chromosome 15 by complementation in yeast. Proc. Natl. Acad. Sci. USA. 89:1992;10887-10891.
36. Le Guen L., Thomas M., Kreis M. Gene density and organization in a small region of the Arabidopsis thaliana genome. Mol. Gen. Genet. 245:1994;390-396.
37. Macknight R., Bancroft I., Page T., Lister C., Schmidt R., Love K., Westphal L., Murphy G., Sherson S., Cobbett C., Dean C. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell. 88:1997;737-745.
38. McClure B.A., Hagen G., Brown C.S., Gee M.A., Guilfoyle T.J. Transcription, organization, and sequence of an auxin-regulated gene cluster in soybean. Plant Cell. 1:1989;229-239.
39. Meyer J., Walker-Jonah A., Hollenberg C. Galactokinase encoded by GAL1 is a bifunctional protein required for induction of the Gal genes in Kluyveromyces lactis and is able to suppress the gal3 phenotype in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:1991;5454-5461.
40. Nakaï K., Kanehisa M. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics. 14:1992;897-911.
41. Newman T., de Bruijn F.J., Green P., Keegstra K., Kende H., McIntosh L., Ohlrogge J., Raikhel N., Somerville S., Thomashow M., Retzel E., Somerville C.R. Genes galore: a summary for acessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106:1994;1241-1255.
42. Quigley F., Dao P., Cottet A., Mache R. Sequence analysis of an 81 kb contig from Arabidopsis thaliana chromosome III. Nucleic Acids Res. 24:1996;4313-4318.
43. Rothnie H.M. Plant mRNA 3′-end formation. Plant Mol. Biol. 32:1996;43-61.
44. Seetharaman J., Srinivasan R. Analysis of codon usage: positional preference in various organisms. Ind. J. Biochem. Biophys. 32:1995;156-160.
45. Solovyev V.V., Salamov A.A., Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22:1994;5156-5163.
46. Stöhr C., Schuler F., Tischner R. Glycosyl-phosphatidylinositol-anchored proteins exist in the plasma membrane of Chlorella saccharophila (Krüger) Nadson: Plasma-membrane-bound nitrate reductase as an example. Planta. 196:1995;284-287.
47. Takos A.M., Dry I.B., Soole K.L. Detection of glycosyl-phosphatidylinositol-anchored proteins on the surface of Nicotiana tabacum protoplasts. FEBS Lett. 405:1997;1-4.
48. Takumi T., Lodish H.F. Rapid cDNA cloning by PCR sequences. Biotechniques. 17:1994;443-444.
49. Tremousaygue D., Bardet C., Dabos P., Regad F., Pelese F., Nazer R., Gander E., Lescure B. Genome DNA sequencing around the EF-1α multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions. Genome Res. 7:1997;198-209.
50. Tsay Y.H., Robinson G.W. Cloning and characterization of ERG8, an essential gene of Saccharomyces cerevisiae that encodes phosphomevalonate kinase. Mol. Cell. Biol. 11:1991;620-631.
51. Weigel D., Meyerowitz E.M. Activation of floral homeotic genes in Arabidopsis. Science. 261:1993;1723-1726.
52. White O., Soderlund C., Shanmugan P., Fields C. Information contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin. Plant Mol. Biol. 19:1992;1057-1064.