The yeast GID complex, a novel ubiquitin ligase (E3) involved in the regulation of carbohydrate metabolism

Molecular Biology of the Cell

Volumn 19, Issue 8, 2008, Pages 3323-3333

  Santt, Olivier ^a   Pfirrmann, Thorsten ^a,c   Braun, Bernhard ^a   Juretschke, Jeannette ^a   Kimmig, Philipp ^a   Scheel, Hartmut ^b   Hofmann, Kay ^b   Thumm, Michael ^a,d   Wolf, Dieter H ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

^b MILTENYI BIOTEC GMBH   (Germany)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FRUCTOSE BISPHOSPHATASE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PROTEIN RMD5; PROTEIN VID24; PROTEIN VID30; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

ARTICLE; CARBOHYDRATE METABOLISM; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME DEGRADATION; GLUCONEOGENESIS; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN INTERACTION; YEAST;

CARBOHYDRATE METABOLISM; FRUCTOSE-BISPHOSPHATASE; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, FUNGAL; GLUCONEOGENESIS; GLUCOSE; MODELS, BIOLOGICAL; MUTATION; PHOSPHOENOLPYRUVATE CARBOXYKINASE (ATP); PLASMIDS; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; UBIQUITIN-PROTEIN LIGASES;

EID: 54249111115     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E08-03-0328     Document Type: Article

References (55)

1. Amerik, A., Swaminathan, S., Krantz, B. A., Wilkinson, K. D., and Hochstrasser, M. (1997). In vivo disassembly of free polyubiquitin chains by yeast Ubp14 modulates rates of protein degradation by the proteasome. EMBO J. 16, 4826-4838.
2. Ausubel, F. M., Kingston, R. E., Seidman, F. G., Struhl, K., Moore, D. D., Brent, R., and Smith, F. A. (1992). Current Protocols in Molecular Biology, New York: Greene.
3. Bairoch, A., and Apweiler, R. (1997). The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res. 25, 31-36.
4. Balzi, E., Wang, M., Leterme, S., Van Dyck, L., and Goffeau, A. (1994). PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1. J. Biol. Chem. 269, 2206-2214.
5. Benton, D. (1990). Recent changes in the GenBank On-line Service. Nucleic Acids Res. 18, 1517-1520.
6. Bissinger, P. H., and Kuchler, K. (1994). Molecular cloning and expression of the Saccharomyces cerevisiae STS1 gene product. A yeast ABC transporter conferring mycotoxin resistance. J. Biol. Chem. 269, 4180-4186.
7. Bucher, P., Karplus, K., Moeri, N., and Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Comput. Chem. 20, 3-23.
8. Chiang, M. C., and Chiang, H. L. (1998). Vid24p, a novel protein localized to the fructose-1, 6-bisphosphatase-containing vesicles, regulates targeting of fructose-1,6-bisphosphatase from the vesicles to the vacuole for degradation. J. Cell Biol. 140, 1347-1356.
9. Cottarel, G. (1995). The Saccharomyces cerevisiae HIS3 and LYS2 genes complement the Schizosaccharomyces pombe his5-303 and lys1-131 mutations, respectively: new selectable markers and new multi-purpose multicopy shuttle vectors, pSP3 and pSP4. Curr. Genet. 28, 380-383.
10. de la Guerra, R., Valdes-Hevia, M. D., and Gancedo, J. M. (1988). Regulation of yeast fructose-1,6-bisphosphatase in strains containing multicopy plasmids coding for this enzyme. FEBS Lett. 242, 149-152.
11. DeRisi, J. L., Iyer, V. R., and Brown, P. O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
12. Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
13. Eisele, F., Braun, B., Pfirrmann, T., and Wolf, D. H. (2006). Mutants of the deubiquitinating enzyme Ubp14 decipher pathway diversity of ubiquitin-proteasome linked protein degradation. Biochem. Biophys. Res. Commun. 350, 329-333.
14. Fang, S., and Weissman, A. M. (2004). A field guide to ubiquitylation. Cell Mol. Life Sci. 61, 1546-1561.
15. Gancedo, C. (1971). Inactivation of fructose-1,6-diphosphatase by glucose in yeast. J. Bacteriol. 107, 401-405.
16. Gancedo, J. M. (1998). Yeast carbon catabolite repression. Microbiol. Mol. Biol. Rev. 62, 334-361.
17. Gauss, R., Trautwein, M., Sommer, T., and Spang, A. (2005). New modules for the repeated internal and N-terminal epitope tagging of genes in Saccharomyces cerevisiae. Yeast 22, 1-12.
18. Guthrie, C., and Fink, G. R. (1991). Guide to yeast genetics and molecular biology. Methods Enzymol. 194, 21-37.
19. Hatakeyama, S., Yada, M., Matsumoto, M., Ishida, N., and Nakayama, K. I. (2001). U box proteins as a new family of ubiquitin-protein ligases. J. Biol. Chem. 276, 33111-33120.
20. Henikoff, S., and Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.
21. Ho, Y. et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
22. Hoffman, M., and Chiang, H. L. (1996). Isolation of degradation-deficient mutants defective in the targeting of fructose-1,6-bisphosphatase into the vacuole for degradation in Saccharomyces cerevisiae. Genetics 143, 1555-1566.
23. Hofmann, K. (2000). Sensitive protein comparisons with profiles and hidden Markov models. Brief. Bioinform. 1, 167-178.
24. Holzer, H. (1976). Catabolite inactivation in yeast. Trends Biochem. Sci. 1, 178-181.
25. Holzer, H. (1989). Proteolytic catabolite inactivation in Saccharomyces cerevisiae. Revis. Biol. Celular 21, 305-319.
26. Hung, G. C., Brown, C. R., Wolfe, A. B., Liu, J., and Chiang, H. L. (2004). Degradation of the gluconeogenic enzymes fructose-1,6-bisphosphatase and malate dehydrogenase is mediated by distinct proteolytic pathways and signaling events. J. Biol. Chem. 279, 49138-49150.
27. Hämmerle, M., Bauer, J., Rose, M., Szallies, A., Thumm, M., Dusterhus, S., Mecke, D., Entian, K. D., and Wolf, D. H. (1998). Proteins of newly isolated mutants and the amino-terminal proline are essential for ubiquitin-proteasome-catalyzed catabolite degradation of fructose-1,6- bisphosphatase of Saccharomyces cerevisiae. J. Biol. Chem. 273, 25000-25005.
28. Kobayashi, N., Yang, J., Ueda, A., Suzuki, T., Tomaru, K., Takeno, M., Okuda, K., and Ishigatsubo, Y. (2007). RanBPM, Muskelin, p48EMLP, p44CTLH, and the armadillo-repeat proteins ARMC8alpha and ARMC8beta are components of the CTLH complex. Gene 396, 236-247.
29. Krogan, N. J. et al. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643.
30. Longtine, M. S., McKenzie, A., 3rd, Demarini, D. J., Shah, N. G., Wach, A., Brachat, A., Philippsen, P., and Pringle, J. R. (1998). Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953-961.
31. Lorick, K. L., Jensen, J. P., Fang, S., Ong, A. M., Hatakeyama, S., and Weissman, A. M. (1999). RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination. Proc. Natl. Acad. Sci. USA 96, 11364-11369.
32. Marcus, F., Rittenhouse, J., Moberly, L., Edelstein, I., Hiller, E., and Rogers, D. T. (1988). Yeast (Saccharomyces cerevisiae) fructose-1,6-bisphosphatase. Properties of phospho and dephospho forms and of two mutants in which serine 11 has been changed by site-directed mutagenesis. J. Biol. Chem. 263, 6058-6062.
33. Mazon, M. J., Gancedo, J. M., and Gancedo, C. (1982). Inactivation of yeast fructose-1,6-bisphosphatase. In vivo phosphorylation of the enzyme. J. Biol. Chem. 257, 1128-1130.
34. Mercado, J. J., and Gancedo, J. M. (1992). Regulatory regions in the yeast FBP1 and PCK1 genes. FEBS Lett. 311, 110-114.
35. Muller, M., Muller, H., and Holzer, H. (1981). Immunochemical studies on catabolite inactivation of phosphoenolpyruvate carboxykinase in Saccharomyces cerevisiae. J. Biol. Chem. 256, 723-727.
36. Ohi, M. D., Vander Kooi, C. W., Rosenberg, J. A., Chazin, W. J., and Gould, K. L. (2003). Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat. Struct. Biol. 10, 250-255.
37. Pitre, S. et al. (2006). PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics 7, 365.
38. Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M., and Seraphin, B. (2001). The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229.
39. Regelmann, J., Schüle, T., Josupeit, F. S., Horak, J., Rose, M., Entian, K. D., Thumm, M., and Wolf, D. H. (2003). Catabolite degradation of fructose-1,6-bisphosphatase in the yeast Saccharomyces cerevisiae: a genome-wide screen identifies eight novel GID genes and indicates the existence of two degradation pathways. Mol. Biol. Cell 14, 1652-1663.
40. Rose, M. D., Novick, P., Thomas, J. H., Botstein, D., and Fink, G. R. (1987). A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene 60, 237-243.
41. Schork, S., Bee, G., Thumm, M., and Wolf, D. H. (1994a). Catabolite inactivation of fructose-1,6-bisphosphatase in yeast is mediated by the proteasome. FEBS Lett. 349, 270-274.
42. Schork, S., Bee, G., Thumm, M., and Wolf, D. H. (1994b). Site of catabolite inactivation. Nature 369, 283-284.
43. Schork, S. M., Thumm, M., and Wolf, D. H. (1995). Catabolite inactivation of fructose-1,6-bisphosphatase of Saccharomyces cerevisiae. Degradation occurs via the ubiquitin pathway. J. Biol. Chem. 270, 26446-26450.
44. Schüle, T., Rose, M., Entian, K. D., Thumm, M., and Wolf, D. H. (2000). Ubc8p functions in catabolite degradation of fructose-1,6-bisphosphatase in yeast. EMBO J. 19, 2161-2167.
45. Sikorski, R. S., and Hieter, P. (1989). A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19-27.
46. Suzuki, T., Ueda, A., Kobayashi, N., Yang, J., Tomaru, K., Yamamoto, M., Takeno, M., and Ishigatsubo, Y. (2008). Proteasome-dependent degradation of alpha-catenin is regulated by interaction with ARMc8alpha. Biochem. J. 411, 581-591.
47. Umeda, M., Nishitani, H., and Nishimoto, T. (2003). A novel nuclear protein, Twa1, and Muskelin comprise a complex with RanBPM. Gene 303, 47-54.
48. Vaulont, S., Vasseur-Cognet, M., and Kahn, A. (2000). Glucose regulation of gene transcription. J. Biol. Chem. 275, 31555-31558.
49. von Herrath, M., and Holzer, H. (1988). Sensitivity of fructose-1,6-biphosphatase from yeast, liver and skeletal muscle to fructose-2,6-biphosphate and 5′-adenosine monophosphate. Z. Lebensm. Unters. Forsch. 186, 427-430.
50. Wahren, J., and Ekberg, K. (2007). Splanchnic Regulation of Glucose Production. Annu. Rev. Nutr. 27, 329-345.
51. Wolf, D. H. (2004). From lysosome to proteasome: the power of yeast in the dissection of proteinase function in cellular regulation and waste disposal. Cell Mol. Life Sci. 61, 1601-1614.
52. Yaffe, M. P., and Schatz, G. (1984). Two nuclear mutations that block mitochondrial protein import in yeast. Proc. Natl. Acad. Sci. USA 81, 4819-4823.
53. Yin, Z., Hatton, L., and Brown, A. J. (2000). Differential post-transcriptional regulation of yeast mRNAs in response to high and low glucose concentrations. Mol. Microbiol. 35, 553-565.
54. Zaragoza, O., and Gancedo, J. M. (2001). Elements from the cAMP signaling pathway are involved in the control of expression of the yeast gluconeogenic gene FBP1. FEBS Lett. 506, 262-266.
55. Zheng, N., Wang, P., Jeffrey, P. D., and Pavletich, N. P. (2000). Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases. Cell 102, 533-539.