Unraveling plant metabolism by EST analysis

Current Opinion in Plant Biology

Volumn 3, Issue 3, 2000, Pages 224-228

  Ohlrogge, John ^a   Benning, Christoph ^b  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0034068685     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(00)00068-6     Document Type: Review

References (26)

1. Boguski M.S., Lowe T.M., Tolstoshev C.M. dbEST - database for 'expressed sequence tags'. Nat Genet. 4:1993;332-333.
2. Cooke R., Raynal M., Laudie M., Grellet F., Delseny M., Morris P.C., Guerrier D., Giraudat J., Quigley F., Clabault G.et al. Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J. 9:1996;101-124.
3. Newman T., de Bruijn F.J., Green P., Keegstra K., Kende H., McIntosh L., Ohlrogge J., Raikhel N., Somerville S., Thomashow M. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106:1994;1241-1255.
4. Sasaki T., Song J., Koga Ban Y., Matsui E., Fang F., Higo H., Nagasaki H., Hori M., Miya M., Murayama-Kayano E.et al. Toward cataloging all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J. 6:1994;615-624.
5. Van de Loo F.J., Broun P., Turner S., Somerville C. An oleate 12-hydroxylase from Ricinus communis L. is a fatty acyl desaturase homolog. Proc Natl Acad Sci USA. 92:1995;6743-6747.
6. Cahoon E.B., Carlson T.J., Ripp K.G., Schweiger B.J., Cook G.A., Hall S.E., Kinney A.J. Biosynthetic origin of conjugated double bonds: production of fatty acid components of high-value drying oils in transgenic soybean embryos. Proc Natl Acad Sci USA. 96:1999;12935-12940. The authors describe the isolation of genes that encode fatty-acid conjugase using an EST approach. Fatty-acid conjugases, a term coined in this paper, introduce conjugated double bonds into fatty acids, generating high-value conjugated products.
7. Shanklin J., Cahoon E.B. Desaturation and related modifications of fatty acids. Annu Rev Plant Physiol Plant Mol Biol. 49:1998;611-641.
8. Broun P., Shanklin J., Whittle E., Somerville C. Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids. Science. 282:1998;1315-1317. The authors of this paper demonstrate the close structural relationship between different fatty-acid-modifying enzymes. The principle that different enzymatic activities can be converted into each other by protein engineering is proved.
9. Arondel V., Lemieux B., Hwang I., Gibson S., Goodman H.M., Somerville C.R. Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis. Science. 258:1992;1353-1355.
10. Van de Loo F.J., Turner S., Somerville C. Expressed sequence tags from developing castor seeds. Plant Physiol. 108:1995;1141-1150.
11. Crock J., Wildung M., Croteau R. Isolation and bacterial expression of a sesquiterpene synthase cDNA clone from peppermint (Mentha x piperita, L.) that produces the aphid alarm pheromone (E)-beta-farnesene. Proc Natl Acad Sci USA. 94:1997;12833-12838.
12. Lange B.M., Croteau R. Genetic engineering of essential oil production in mint. Curr Opin Plant Biol. 2:1999;139-144.
13. Lange B.M., Wildung M.R., McCaskill D., Croteau R. A family of transketolases that directs isoprenoid biosynthesis via a mevalonate-independent pathway. Proc Natl Acad Sci USA. 95:1998;2100-2104. This paper describes the isolation of a cDNA that encodes the enzymes involved in the first reaction of the recently discovered mevalonate-independent pathway of isoprenoid biosynthesis. The authors demonstrate that the recently described Arabidopsis cla1 mutant is deficient in isoprenoid biosynthesis.
14. Lichtenthaler H. The 1-deoxy-D-xylose-5-phosphate pathway of isoprenoid biosynthesis in plants. Annu Rev Plant Physiol Plant Mol Biol. 50:1999;47-65.
15. Mandel M.A., Feldmann K.A., Herrera-Estrella L., Rocha-Sosa M., Leon P. CLA1, a novel gene required for chloroplast development, is highly conserved in evolution. Plant J. 9:1996;649-658.
16. Pear J.R., Kawagoe Y., Schreckengost W.E., Delmer D.P., Stalker D.M. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Proc Natl Acad Sci USA. 93:1996;12637-12642.
17. Kimura S., Laosinchai W., Itoh T., Cui X., Linder C.R., Brown R.M.J. Immunogold labeling of rosette terminal cellulose-synthesizing complexes in the vascular plant Vigna angularis. Plant Cell. 11:1999;2075-2086. The authors demonstrate that the terminal rosette complex observed by electron microscopy does indeed contain cellulose synthase, as had been speculated for a long time.
18. Cutler S., Somerville C. Cloning in silico. Curr Biol. 7:1997;R108-R111.
19. Allona I., Quinn M., Shoop E., Swope K., Cyr S.S., Carlis J., Riedl J., Retzel E., Campbell M.M., Sederoff R., Whetten R.W. Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci USA. 95:1998;9693-9698.
20. Sterky F., Regan S., Karlsson J., Hertzberg M., Rohde A., Holmberg A., Amini B., Bhalerao R., Larsson M., Villarroel R.et al. Gene discovery in the wood-forming tissues of poplar: analysis of 5,692 expressed sequence tags. Proc Natl Acad Sci USA. 95:1998;13330-13335.
21. Ewing R.M., Kahla A.B., Poirot O., Lopez F., Audic S., Claverie J.M. Large scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9:1999;950-959. This is an important technical paper describing the bioinformatic procedures behind the cluster analysis of large EST data sets. Several tissue-specific EST data sets from rice were analyzed. A 'digital' analysis of the data is provided.
22. Mekhedov S., Martinez de Ilarduya O., Ohlrogge J. Towards a functional catalog of the plant genome: a survey of genes for lipid biosynthesis. Plant Physiol. 2000;. in press. The authors provide an extensive in silico analysis of publicly available plant ESTs encoding lipid-metabolizing enzymes. The validity of the approach is demonstrated with reference to existing knowledge of the underlying biochemistry.
23. Audic S., Claverie J.M. The significance of digital gene expression profiles. Genome Res. 7:1997;986-995.
24. Schmitt A.O., Specht T., Beckmann G., Dahl E., Pilarsky C.P., Hinzmann B., Rosenthal A. Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues. Nucleic Acids Res. 27:1999;4251-4260.
25. Rezvani M., Barrans J.D., Dai K.S., Liew C.C. Apoptosis-related genes expressed in cardiovascular development and disease an EST approach. Cardiovasc Res. 45:2000;621-629.
26. Ladunga I. Large-scale predictions of secretory proteins from mammalian genomic and EST sequences. Curr Opin Biotechnol. 11:2000;13-18.