Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database

Plant Physiology

Volumn 132, Issue 2, 2003, Pages 681-697

  Beisson, Frédéric ^a   Koo, Abraham J K ^a   Ruuska, Sari ^a   Schwender, Jörg ^a   Pollard, Mike ^a   Thelen, Jay J ^a,b   Paddock, Troy ^a,c   Salas, Joaquín J ^a,d   Savage, Linda ^a   Milcamps, Anne ^a,e   Mhaske, Vandana B ^a   Cho, Younghee ^a,f   Ohlrogge, John B ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

^c OHIO STATE UNIVERSITY   (United States)

^d INSTITUTO DE LA GRASA   (Spain)

^e JOINT RESEARCH CENTRE   (Italy)

^f MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; GENES; LIPIDS; METABOLISM; PROTEINS; WEBSITES;

EXPRESSED SEQUENCE TAG (EST);

PLANTS (BOTANY);

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0038460019     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.022988     Document Type: Article

References (50)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
3. Arondel V, Vergnolle C, Cantrel C, Kader JC (2000) Lipid transfer proteins are encoded by a small multigene family in Arabidopsis thaliana. Plant Sci 157: 1-12
4. Audic S, Claverie JM (1997) The significance of digital expression profiles. Genome Res 7: 986-995
5. Beisson F, Tiss A, Rivière C, Verger R (2000) Methods for lipase detection and assay: a critical review. Eur J Lipid Sci Technol 2: 133-153
6. Blein J-P, Coutos-Thévenot P, Marion D, Ponchet M (2002) From elicitins to lipid-transfer proteins: a new insight in cell signalling involved in plant defence mechanisms. Trends Plant Sci 7: 293-296
7. Bouché N, Bouchez D (2001) Arabidopsis gene knockout: phenotypes wanted. Curr Opin Plant Biol 4: 111-117
8. Brick DJ, Brumlik MJ, Buckley JT, Cao JX, Davies PC, Misra S, Tranbarger TJ, Upton C (1995) A new family of lipolytic plant enzymes with members in rice, Arabidopsis and maize. FEBS Lett 377: 475-480
9. Browse J, Somerville C (1994) Glycerolipids. In EM Meyerowitz, CR Somerville, eds, Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 881-912
10. Cahoon EB, Ohlrogge JB (1994) Apparent role of phosphatidylcholine in the metabolism of petroselinic acid in developing Umbelliferae endosperm. Plant Physiol 104: 845-855
11. Douliez JP, Pato C, Rabesona H, Molle H, Marion D (2001) Disulfide bond assignment, lipid transfer activity and secondary structure of a 7-kDa plant lipid transfer protein, LTP2. Eur J Biochem 268: 1400-1403
12. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
13. Fatland B, Anderson M, Nikolau BJ, Wurtele ES (2000) Molecular biology of cytosolic acetyl-CoA generation. Biochem Soc Trans 28: 593-595
14. Gerlt JA, Babbitt PC (2000) Can sequence determine function? Genome Biol 1: 5.1-5.10
15. Ghanevati M, Jaworski JG (2001) Active-site residues of a plant membrane-bound fatty acid elongase β-ketoacyl-CoA synthase FAE1 KCS. Biochim Biophys Acta 1530: 77-85
16. Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J (2000) Microarray analysis of developing Arabidopsis seeds. Plant Physiol 124: 1570-1581
17. Gunstone FD, Pollard M (2001) Vegetable oils with fatty acid changed by plant breeding or genetic modification. In FD Gunstone, ed, Structured and Modified Lipids. Marcel Dekker, New-York, pp 155-184
18. Henrissat B, Countinho PM, Davies GJ (2001) A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol Biol 47: 55-72
19. Hooker TS, Millar AA, Kunst L (2002) Significance of the expression of the CER6 condensing enzyme for cuticular wax production in Arabidopsis. Plant Physiol 129: 1568-1580
20. Ishiguro S, Kawai-Oda A, Ueda J, Nishida I, Okada K (2001) The DEFECTIVE IN ANTHER DEHISCIENCE gene encodes a novel phospholipase A1 catalyzing the initial step of jasmonic acid biosynthesis, which synchronizes pollen maturation, anther dehiscence, and flower opening in Arabidopsis. Plant Cell 13: 2191-2209
21. Kader JC (1996) Lipid-transfer proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 47: 627-654
22. Karlsson M, Contreras JA, Hellman U, Tornqvist H, Holm C (1997) cDNA cloning, tissue distribution, and identification of the catalytic triad of monoglyceride lipase: evolutionary relationship to esterases, lysophospholipases, and haloperoxidases. J Biol Chem 272: 27218-27223
23. Ke J, Behal RH, Back SL, Nikolau BJ, Wurtele ES, Oliver DJ (2000) The role of pyruvate dehydrogenase and acetyl-CoA synthetase in fatty acid synthesis in developing Arabidopsis seeds. Plant Physiol 123: 497-508
24. Koo AJK, Ohlrogge JB (2002) The predicted candidates of Arabidopsis plastid envelope membrane proteins and their expression profiles. Plant Physiol 130: 823-836
25. Lacey DJ, Hills MJ (1996) Heterogeneity of the endoplasmic reticulum with respect to lipid synthesis in developing seeds of Brassica napus L. Planta 199: 545-551
26. Lee JM, Williams ME, Tingey SV, Rafalski JA (2001) DNA array profiling of gene expression changes during maize embryo development. Funct Integr Genomics 2: 13-27
27. Maldonado AM, Doerner P, Dixon RA, Lamb CJ, Cameron RK (2002) A putative lipid transfer protein involved in systemic resistance in Arabidopsis. Nature 419: 399-403
28. Mekhedov S, Martfnez de Llárduya, Ohlrogge JB (2000) Toward a functional catalog of the plant genome: a survey of genes for lipid biosynthesis. Plant Physiol 122: 389-401
29. Millar AA, Clemens S, Zachgo S, Giblin EM, Taylor DC, Kunst L (1999) CUT1, an Arabidopsis gene required for cuticular wax biosynthesis and pollen fertility, encodes a very-long-chain fatty acid condensing enzyme. Plant Cell 11: 825-838
30. Mou Z, Wang X, Fu Z, Dai Y, Han C, Ouyang J, Bao F, Hu Y, Li J (2002) Silencing of phosphoethanolamine N-methyltransferase results in temperature-sensitive male sterility and salt hypersensitivity in Arabidopsis. Plant Cell 14: 2031-2043
31. Newman T, de Bruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M et al. (1994) Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 106: 1241-1256
32. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217
33. O'Hara P, Slabas AR, Fawcett T (2002) Fatty acid and lipid biosynthetic genes are expressed at constant molar ratios but different absolute levels during embryogenesis. Plant Physiol 129: 310-320
34. Ohlrogge J, Browse J (1995) Lipid Biosynthesis. Plant Cell 7: 957-970
35. Okubo K, Hori N, Matoba R, Niiyama T, Fukushima A, Kojima Y, Matsubara K (1992) Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nat Genet 2: 173-179
36. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J et al. (1992) The alpha/beta hydrolase fold. Protein Eng 5: 197-211
37. Peeters N, Small I (2001) Dual targeting to mitochondria and chloroplasts. Biochim Biophys Acta 1541: 54-63
38. Pruitt RE, Vielle-Calzada JP, Ploense SE, Grossniklaus U, Lolle SJ (2000) FIDDLEHEAD, a gene required to suppress epidermal cell interactions in Arabidopsis, encodes a putative lipid biosynthetic enzyme. Proc Natl Acad Sci USA 1: 1311-1316
39. Romualdi C, Bortoluzzi S, Danieli GA (2001) Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Hum Mol Genet 10: 2133-2141
40. Schwender J, Ohlrogge JB (2002) Probing in vivo metabolism by stable isotope labeling of storage lipids and proteins in developing Brassica napus embryos. Plant Physiol 130: 347-361
41. Sprong H, van der Sluijs P, van Meet G (2001) How proteins move lipids and lipids move proteins. Nat Rev Mol Cell Biol 2: 504-513
42. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637
43. Thelen JJ, Ohlrogge JB (2002) Metabolic Engineering of fatty acid biosynthesis in plants. Metab Eng 4: 12-21
44. Thoma S, Kaneko Y, Somerville C (1993) A non-specific lipid transfer protein from Arabidopsis is a cell wall protein. Plant J 3: 427-436
45. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
46. Vogel G, Browse J (1996) Cholinephosphhotransferase and diacylglycerol acyltransferase: substrate specificities at a key branch point in seed lipid metabolism. Plant Physiol 110: 923-931
47. Wallis JG, Browse J (2002) Mutants of Arabidopsis reveal many roles for membrane lipids. Prog Lipid Res 41: 254-278
48. Ward JM (2001) Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics 17: 560-563
49. White JA, Todd J, Newman T, Focks N, Girke T, de Ilarduya OM, Jaworski JG, Ohlrogge JB, Benning C (2000) A new set of Arabidopsis expressed sequence tags from developing seeds: the metabolic pathway from carbohydrates to seed oil. Plant Physiol 124: 1582-1594
50. Yephremov A, Wisman E, Huijser P, Huijser C, Wellesen K, Saedler H (1999) Characterization of the FIDDLEHEAD gene of Arabidopsis reveals a link between adhesion response and cell differentiation in the epidermis. Plant Cell 11: 2187-2202