Predicting the function and subcellular location of Caenorhabditis elegans proteins similar to Saccharomyces cerevisiae β-oxidation enzymes

Yeast

Volumn 17, Issue 3, 2000, Pages 188-200

  Gurvitz, Aner ^a   Langer, Sigrid ^a   Piskacek, Martin ^a   Hamilton, Barbara ^a   Ruis, Helmut ^a   Hartig, Andreas ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

Caenorhabditis clegans; Peroxisome; PEX 5; PTS1; Saccharomyces cercrisiae; Tetratricopeptide repeat (TPR); Two hybrid; oxidation

Indexed keywords

EID: 33749199662     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0061(20000930)17:3<188::AID-YEA27>3.3.CO;2-5     Document Type: Article

References (59)

1. Altschul SF, Madden TL, Schaffer AA, cl al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Bartel P, Chien CT, Sternglanz R, Fields S. 1993. Elimination of false positives that arise in using the two-hybrid system. Biotechniques 14: 920-924.
3. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochcm 72: 248-254.
4. Brown GK, Hunt SM, Scholem R, et al. 1982. β-Hydroxyisobutyryl-coenzyme A deacylase deficiency: a defect in valine metabolism associated with physical malformations. Pediatrics 70: 532-538.
5. Bun-Ya M, Maebuchi M, Hashimoto T, Yokota S, Kamiryo T. 1997. A second isoform of 3-ketoacyl-CoA thiolase found in Caenorhabditis elegans, which is similar to sterol carrier protein x but lacks the sequence of sterol carrier protein 2. Eur J Biochcm 245: 252-259.
6. Chen D-C, Yang B-C, Kuo T-T. 1992. One-step transformation of yeast in stationary phase. Curr Genet 21: 83-84.
7. Chervitz SA, Aravind L, Sherlock G, et al. 1998. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282: 2022-2028.
8. Chevray PM, Nathans D. 1992. Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc Nail Acad Sci US AW: 5789-5793.
9. Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
10. Costanzo MC, Hogan JD, Cusick ME, et al. 2000. The yeast proteome database. YPD and Caenorhabditis elegans proteome database. WormPD: comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res 28: 73-76.
11. de Duve C, Baudhuin P. 1966. Peroxisomes. Microbodies and related particles. Physiol Rev 46: 323-357.
12. Didion T, Roggenkamp R. 1992. Targeting signal of the peroxisomal catalase in the methylotrophic yeast Hanscnula polymorpha. FEES Lett 303: 113-116.
13. Dmochowska A, Dignard D, Maleszka R, Thomas DY. 1990. Structure and transcriptional control of the Saccharoniyces cererisiae POX1 gene encoding acyl-coenzyme A oxidase. Gene 88: 247-252.
14. Einerhand AW, Voorn-Brouwer TM, Erdmann R, Kunau W-H, Tabak HF. 1991. Regulation of transcription of the gene coding for peroxisomal 3-oxoacyl-CoA thiolase of Saccharomyces cererisiae. Eur J Biochcm 200: 113-122.
15. Elgersma Y, van Roermund CW, Wanders RJ, Tabak HF. 1995. Peroxisomal and mitochondrial carnitine acetyltransferases of Saccharomyces cererisiae are encoded by a single gene. EMBO J 14: 3472-3479.
16. Elgersma Y, Vos A, van den Berg M, van Roermund CW, et al. 1996. Analysis of the carboxy-terminal peroxisomal targeting signal 1 in a homologous context in Saccharomyces cererisiae. J Biol Chem 271: 26375-26382.
17. 2,4-Dienoyl-CoA isomerase from rat liver. Molecular characterization. J Biol Chem 273: 349-355.
18. Fransen M, Van Veldhoven PP, Subramani S. 1999. Identification of peroxisomal proteins by using M13 phage protein VI phage display: molecular evidence that mammalian peroxisomes contain a 2,4-dienoyl-CoA reductase. Biochem J 340: 561-568.
19. 2-enoyl-CoA isomerase. J Biol Chem 273: 33184-33191.
20. Geisbrecht BV, Schulz K, Nau K, et al. 1999a. Preliminary characterization of YorlSOCp: identification of a novel peroxisomal protein of Saccharomyces cerevisiae involved in fatty acid metabolism. Biochem Biophys Res Coniiiiiin 260: 28-34.
21. 4-dienoyICoA reductase. J Biol Chem 27-1: 25814-25820.
22. Gould SJ, Keller GA, Subramani S. 1987. Identification of a peroxisomal targeting signal at the carboxy-terminus of firefly lueiferase. J Cell Biol 105: 2923-2931.
23. Gould SJ, Keller GA, Schneider M, et al. 1990. Peroxisomal protein import is conserved between yeast, plants, insects and mammals. EMBO J 9: 85-90.
24. Gurvitz A, Rottensteiner H, KilpelUinen SH, cl al. 1997. The Saccharomyces cercrisiac peroxisomal 2,4-dienoyl-CoA reductase is encoded by the oleate-inducible gene SPS19. J Biol Chem 272: 22140-22147.
25. 2-trans-enoyl-CoA isomerase encoded by ECH is required for growth of the yeast Saccharomyces ccrevisiae on unsaturated fatty acids. J Biol Chem 273: 31366-31374.
26. 2,4-dienoylCoA isomerase. J Biol Chem 274: 24514-24521.
27. 2-enoyl-CoA isomerase during peroxisomal β-oxidation in Saccharomyces cerevisiae. Biochem J 344: 903-914.
28. Hakkola EH, Autio-Harmainen HI, Sormunen RT, Hassinen IE, Hiltunen JK. 1989. The known purified mammalian 2,4-dienoyl-CoA reductases are mitochondrial isoenzymes. J Histochcm Cytochcm 37: 1863-1867.
29. Hakkola EH, Hiltunen JK. 1993. The existence of two mitochondrial isoforms of 2,4-dienoyl-CoA reductase in the rat. Eur J Biochem 215: 199-204.
30. Hawes JW, Jaskicwicz J, Shimomura Y, et al. 1996. Primary structure and tissue-specific expression of human -hydroxyisobutyryl-coenzyme A hydrolase. J Biol Chem 271: 26430-26434.
31. Hiltunen JK, Wenzel B, Beyer A, Erdmann R, Fossa A, Kunau W-H. 1992. Peroxisomal multifunctional /5-oxidation protein of Saccharomyces cercvisiae. Molecular analysis of the FOX2 gene and gene product. J Biol Chem 267: 6646-6653.
32. Igual JC, Matallana E, Gonzalez-Bosch C, Franco L, PerezOrtin JE. 1991. A new glucose-repressible gene identified from the analysis of chromatin structure in deletion mutants of yeast SUC2 locus. Yeast 7: 379-389.
33. Itoh M, Suzuki Y, Akaboshi S, Zhang Z, Miyabara S, Takashima S. 2000. Developmental and pathological expression of peroxisomal enzymes: their relationship of o-bifunctional protein deficiency and Zellweger syndrome. Brain Res 858: 40-47.
34. Jardim A, Liu W, Zheleznova E, Ullman B. 2000. Peroxisomal targeting signal-1 receptor protein PEX5 from Leislimania donovani. Molecular, biochemical, and immunocytochemical characterization. J Biol Chem 275: 13637-13644.
35. Karpichev IV, Small GM. 2000. Evidence for a novel pathway for the targeting of a Saccharomyces cerevisiae peroxisomal protein belonging to the isomerase/hydratasc family. J Cell Sci 113:533-544.
36. Koivuranta KT, Hakkola EH, Hiltunen JK. 1994. Isolation and characterization of cDNA for human 120kDa mitochondrial 2,4-dienoyl-coenzyme A reductase. Biochcm J 304: 787-792.
37. Kragler F, Lametschwandtner G, Christmann J, Hartig A, Harada JJ. 1998. Identification and analysis of the plant peroxisomal targeting signal 1 receptor NtPEXS. Proc Nail AcadSci USA 95: 13336-13341.
38. Kragler F, Langcder A, Raupachova J, Binder M, Hartig A. 1993. Two independent peroxisomal targeting signals in catalase A of Saccliaromyccs ccrevisiae. J Cell Biol 120: 665-673.
39. Kunau W-H, Dommes V, Schulz H. 1995. β-Oxidation of fatty acids in mitochondria, peroxisomes, and bacteria: a century of continued progress. Prog Lipicl Res 34: 267-342.
40. Lametschwandtner G, Brocard C, Fransen M, Van Veldhoven P, Berger J, Hartig A. 1998. The difference in recognition of terminal tripeptides as peroxisomal targeting signal 1 between yeast and human is due to different affinities of their receptor PexSp to the cognate signal and to residues adjacent to it. J Biol Clicm 273: 33635-33643.
41. Maebuchi M, Togo SH, Yokota S, Ghenea S, Bun-Ya M, Kamiryo T, Kawahara A. 1999. Typc-II 3-oxoacyl-CoA thiolase of the nematode Cacnorhabditis elegans is located in peroxisomes, highly expressed during larval stages and induced by clofibrate. EUT J Biochcm 264: 509-515.
42. Marzioch M, Erdmann R, Vcenhuis M, Kunau W-H. 1994. PAS7 encodes a novel yeast member of the WD-40 protein family essential for import of 3-oxoacyl-CoA thiolase, a PTS2containing protein, into peroxisomes. EMBO J 13: 4908-4918.
43. McNew JA, Goodman JM. 1996. The targeting and assembly of peroxisomal proteins: some old rules do not apply. Trends Biochcm Sci 21: 54-58.
44. Miller JH. 1972. Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press: New York.
45. Müller-Newen G, Janssen U, Stoffel W. 1995. Enoyl-CoA hydratase and isomerase form a superfamily with a common active-site glutamate residue. Eur J Biochem 228: 68-73.
46. 2-enoyl-CoA isomerase activities. J Biol Cltcm 265: 2446-2449.
47. Rehling P, Marzioch M, Niesen F, Wittke E, Veenhuis M, Kunau W-H. 1996. The import receptor for the peroxisomal targeting signal 2. PTS2 in Saccharomyccs cerevisiae is encoded by the PAS7 gene. EMBO J 15: 2901-2913.
48. Roe CR, Millington DS, Norwood DL, et al. 1990. 2,4-Dienoylcoenzyme A reductase deficiency: a possible new disorder of fatty acid oxidation. J Clin Invest 85: 1703-1707.
49. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, 2nd cdn. Cold Spring Harbor Laboratory Press: New York.
50. Smeland TE, Nada M, Cuebas D, Schulz H. 1992. NADPHdependent β-oxidation of unsaturated fatty acids with double bonds extending from odd-numbered carbon atoms. Proc Natl AcadSci USA 89: 6673-6677.
51. Sommer JM, Cheng QL, Keller G-A, Wang CC. 1992. In vivo import of firefly luciferase into the glycosomes of Trypanosoma brucci and mutational analysis of the C-terminal targeting signal. Mol Biol Cell 3: 749-759.
52. Subramani S. 1993. Protein import into pcroxisomes and biogenesis of the organelle. Ann Rev Cell Biol 9: 445-478.
53. Subramani S. 1997. PEX genes on the rise. Nature Genet 15: 331-333.
54. Sulston JE, Schierenberg E, White JG, Thomson JN. 1983. The embryonic cell lineage of the nematodc Caenorhabditis elegans. Dev Biol 100: 64-119.
55. Taniguchi K, Nonami T, Nakao A, et al. 1996. The valine catabolic pathway in human liver: effect of cirrhosis on enzyme activities. Hepatology 24: 1395-1398.
56. Togo SH, Maebuchi M, Yokota S, Bun-Ya M, Kawahara A, Kamiryo T. 2000. Immunological detection of alkalinediaminobenzidine-negative peroxisomes of the nematode Caenorhabdilis elegans. Purification and unique pH optima of peroxisomal catalase. Eur J Biocheni 267: 1307-1312.
57. Van der Leij I, Franse MM, Elgersma Y, Distel B, Tabak HF. 1993. PAS10 is a tetratricopcptide-repeat protein that is essential for the import of most matrix proteins into peroxisomes of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 90: 11782-11786.
58. Wang H, Le Dali MT, Wache Y, Laroche C, Belin JM, Nicaud JM. 1999. Cloning, sequencing, and characterization of five genes coding for acyl-CoA oxidase isozymes in the yeast Yarronïa lipolytica. Cell Biochem Biophys 31: 165-174.
59. Yang M, Wu Z, Fields S. 1995. Protein-peptide interactions analyzed with the yeast two-hybrid system. Nucleic Acids Res 23: 1152-1156.