Global control of gene expression in yeast by the Ccr4-Not complex

Gene

Volumn 313, Issue 1-2, 2003, Pages 1-16

  Collart, Martine A ^a  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

Author keywords

Ccr4 Not complex; Deadenylation; Gene expression; TFIID; Transcription; Yeast

Indexed keywords

CARBON CATABOLITE REPRESSION 4 PROTEIN; CHROMATIN ASSEMBLY FACTOR 1 PROTEIN; CHROMATIN ASSEMBLY FACTOR 130 PROTEIN; CHROMATIN ASSEMBLY FACTOR 40 PROTEIN; DBF2 PROTEIN; DHH1 PROTEIN; MOB1 PROTEIN; MUTANT PROTEIN; NEGATIVE ON TATA LESS 1 PROTEIN; NEGATIVE ON TATA LESS 2 PROTEIN; NEGATIVE ON TATA LESS 3 PROTEIN; NEGATIVE ON TATA LESS 4 PROTEIN; NEGATIVE ON TATA LESS 5 PROTEIN; NEGATIVE ON TATA LESS PROTEIN; PROTEIN; PROTEIN SUBUNIT; SRB10 PROTEIN; SRB11 PROTEIN; SRB9 PROTEIN; TAF1 PROTEIN; TAF13 PROTEIN; TBP PROTEIN; UNCLASSIFIED DRUG; CCR4 PROTEIN, S CEREVISIAE; CDC39 PROTEIN, S CEREVISIAE; CELL CYCLE PROTEIN; RIBONUCLEASE; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

AMINO TERMINAL SEQUENCE; CARBOXY TERMINAL SEQUENCE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE MUTATION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; NONHUMAN; NUTRITIONAL DEFICIENCY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; REVIEW; RNA DEGRADATION; SACCHAROMYCES CEREVISIAE; STRESS; TRANSCRIPTION INITIATION; YEAST; GENETICS; METABOLISM; PROTEIN BINDING;

CELL CYCLE PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; PROTEIN BINDING; RIBONUCLEASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 0242285769     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(03)00672-3     Document Type: Review

References (81)

1. Albert T.K., Lemaire M., van Berkum N.L., Gentz R., Collart M.A., Timmers M.H.T. Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits. Nucleic Acids Res. 28:2000;809-817.
2. Albert T., Hanzawa H., Legtenberg Y.I.A., et al. Identification of a ubiquitin-protein ligase subunit within the CCR4-NOT transcription repressor complex. EMBO J. 21:2002;355-364.
3. Badarinarayana V., Chiang Y.-C., Denis C.L. Functional interaction of CCR4-NOT proteins with TATAAA-binding protein (TBP) and its associated factors in yeast. Genetics. 155:2000;1045-1054.
4. Bai Y., Salvadore C., Chiang Y.-C., Collart M.A., Liu H.-Y., Denis C.L. The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4 and NOT5. Mol. Cell. Biol. 19:1999;6642-6651.
5. Banik U., Beechem J.M., Klebanow E., Schroeder S., Weil A.P. Fluorescence-based analyses of the effects of full-length recombinant TAF130p on the interaction of TATA Box-binding protein with TATA Box DNA. J. Biol. Chem. 276:2001;49100-49109.
6. Bennett C.B., Lewis K.L., Karthikeyan G., Lobachev K.S., Jin Y.H., Sterling J.F., Snipe J.R., Resnick M.A. Genes required for ionising radiation resistance in yeast. Nat. Genet. 29:2001;426-434.
7. Benson J.D., Benson M., Howley P.M., Struhl K. Association of distinct yeast NOT2 functional domains with components of GCN5 histone acetylase and CCR4 transcriptional regulatory complexes. EMBO J. 17:1998;6714-6722.
8. Bogdan J.A., Adams-Burton C., Pedicord D.L., Sukovich D.A., Benfield P.A., Corjay M.H., Stoltenborg J.K., Dicker I.B. Human carbon catabolite repressor protein (CCR4)-associative factor 1: cloning, expression and characterization of its interaction with the B-cell translocation protein BTG1. Biochem. J. 336:1998;471-481.
9. Bortvin A., Winston F. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science. 272:1996;1473-1476.
10. Cade R.M., Errede B. MOT2 encodes a negative regulator of gene expression that affects basal expression of pheromone-responsive genes in Saccharmyces cerevisiae. Mol. Cell. Biol. 14:1994;3139-3149.
11. Chang M., French-Cormay D., Fan H.-Y., Klein H., Denis C.L., Jaehning J. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol. Cell. Biol. 19:1999;1056-1067.
12. Chang-Hui S., Leblanc B.P., Neal C., Akhavan R., Clark D.J. Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10. Mol. Cell. Biol. 22:2002;6406-6416.
13. Chen J., Rappsilber J., Chiang Y.-C., Russell P., Mann M., Denis C.D. Purification and characterization of the 1.0 MDa Ccr4-Not complex identifies two novel components of the complex. J. Mol. Biol. 314:2001;683-694.
14. Chen J., Chiang Y.-C., Denis C.L. CCR4, a 3′-5′ poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. EMBO J. 21:2002;1414-1426.
15. Collart M.A. The NOT, SPT3, and MOT1 genes functionally interact to regulate transcription at core promoters. Mol. Cell. Biol. 16:1996;6668-6676.
16. Collart M.A., Struhl K. CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters. EMBO J. 12:1993;177-186.
17. Collart M.A., Struhl K. NOT1 (CDC39), NOT2 (CDC36), NOT3, and NOT4 encode a global negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev. 8:1994;525-537.
18. Coller J.M., Tucker M., Sheth U., Valencia-Sanchez M.A., Parker R. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA. 12:2001;1717-1727.
19. Croft L., Beatson S.A., Whitchurch C.B., Huang B., Blakeley R.L., Mattick J.S. An interactive web-based Pseudomonas aeruginosa genome database: discovery of new genes, pathways and structures. Mol. Microbiol. 146:2000;2351-2364.
20. Daugeron M.-C., Mauxion F., Séraphin B. The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation. Nucleic Acids Res. 29:2001;2448-2455.
21. de Barros Lopes M., Ho J.-Y., Reed S.I. Mutations in cell division cycle genes CDC36 and CDC39 activate the Saccharomyces cerevisiae mating phermone response pathway. Mol. Cell. Biol. 10:1990;2966-2972.
22. Deluen C., James N., Maillet L., Molinete M., Theiler G., Lemaire M., Paquet N., Collart M.A. The Ccr4-Not complex and yTAF1 (yTaf(II)130p/yTaf(II) 145p) present physical and functional interactions. Mol. Cell. Biol. 22:2002;6735-6749.
23. Denis C.L. Identification of new genes involved in the regulation of yeast alcohol dehydrogenase II. Genetics. 108:1984;833-834.
24. Denis C.L., Malvar T. The CCR4 gene from Saccharomyces cerevisiae is required for both nonfermentative and spt-mediated gene expression. Genetics. 124:1990;283-291.
25. Denis C.L., Chiang Y.-C., Cui Y., Chen J. Genetic evidence supports a role for the yeast Ccr4-Not complex in transcriptional elongation. Genetics. 158:2001;627-634.
26. Dlakic M. Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases. Trends Biochem. Sci. 25:2000;272-273.
27. Draper D.E. Themes in RNA-protein recognition. J. Mol. Biol. 293:1999;255-270.
28. Draper M.P., Liu H.-Y., Nelsbach A.H., Mosley S.P., Denis C.L. CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context. Mol. Cell. Biol. 14:1994;4522-4531.
29. Draper M.P., Salvadore C., Denis C.L. Identification of a mouse protein whose homolog in Saccharomyces cerevisiae is a component of the CCR4 transcriptional regulatory complex. Mol. Cell. Biol. 15:1995;3487-3495.
30. Ferguson J., Ho T.A., Peterson T.A., Reed S.I. Nucleotide sequence of the yeast cell division cycle start genes CDC28, CDC36, CDC37 and CDC39, and a structural analysis of the predicted proteins. Nucleic Acids Res. 14:1986;6681-6697.
31. Fidler C., Wainscoat J.S., Boultwood J. The human POP2 gene: identification, sequencing, and mapping to the critical region of the 5q-syndrome. Genomics. 56:1999;134-136.
32. Fischer N., Weis K. The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1. EMBO J. 21:2002;2788-2797.
33. Gavin A.-C., Bosche M., Krause R., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147.
34. Goppelt A., Stelzer G., Lottspeich F., Meisterernst M. A mechanism for repression of class II gene transcription through specific binding of NC2 to TBP-promoter complexes via heterodimeric histone fold domains. EMBO J. 15:1996;3105-3116.
35. Grandin N., Charbonneau M. Dbf2 is implicated in a Cbt1-dependent pathway following a shift from glucose to galactose or non-fermentable carbon sources in Saccharomyces cerevisiae. Mol. Gen. Genet. 261:1999;402-407.
36. Hanzawa H., de Ruwe M.J., Albert T.K., Van de Vliet P.C., Timmers M.H.T., Boelens R. The structure of the C4C4 Ring finger of human NOT4 reveals features distinct from those of C3HC4 ring fingers. J. Biol. Chem. 276:2001;10185-10190.
37. Holstege F.C.P., Jennings E.G., Wyrick J.J., et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 95:1998;717-728.
38. Hope I., Struhl K. Functional dissection of a eukaryotic transcriptional activator protein. Cell. 46:1986;885-894.
39. Ikematsu N., Yoshida Y., Kawamura-Tsuzuku Y., Ohsugi M., Onda M., Hirai M., Fujimoto M., Yamamoto T. Tob2, a novel anti-proliferative Tob/BTG1 family member, associates with a component of the CCR4 transcriptional regulatory complex capable of binding cyclin-dependent kinases. Oncogene. 18:1999;7432-7441.
40. Irie K., Yamaguchi K., Kawase K., Matsumoto K. The yeast MOT2 gene encodes a putative zinc finger protein that serves as a global negative regulator affecting expression of several categories of genes, including mating-pheromone-responsive genes. Mol. Cell. Biol. 14:1994;3150-3157.
41. Jensess D.D., Goldman B.S., Hartwell L.H. Saccharomyces cerevisiae mutants unresponsive to alpha-factor binding and extragenic suppression. Mol. Cell. Biol. 7:1987;1311-1319.
42. Johnston L.H., Eberly S.L., Chapman J.W., Araki H., Sugino A. The product of the Saccharomyces cerevisiae cell cycle gene DBF2 has homology with protein kinases and is periodically expressed in the cell cycle. Mol. Cell. Biol. 10:1990;1358-1366.
43. Johnson R.D., Cok S.J., Feldmann H., Gordon J.I. Suppressors of nmt1-181, a conditional lethal allele of the Saccharomyces cerevisiae myristoyl-CoA:protein N-myristoyltransferase gene, reveal proteins involved in regulating protein N-myristoylation. Proc. Natl. Acad. Sci. USA. 91:1994;10158-10162.
44. Khodursky A.B., Bernstein J.A. Life after transcription-revisiting the fate of messenger RNA. Trends Genet. 19:2003;113-115.
45. Komarnitsky S.I., Chiang Y.-C., Luca F.C., Chen J., Toyn J.H., Winey M., Johnston L.H., Denis C.L. DBF2 protein kinase binds to and acts through the cell cycle-regulated MOB1 protein. Mol. Cell. Biol. 18:1998;2100-2107.
46. II145 that are functionally interchangeable for inhibiting TBP-DNA interactions in vitro and in promoting yeast cell growth in vivo. J. Biol. Chem. 273:1998;32254-32264.
47. Leberer E., Dignard D., Whiteway M., Thomas D.Y. Molecular characterization of SIG1, a Saccharomyces cerevisiae gene involved in negative regulation of G-protein mediated signal transduction. EMBO J. 13:1994;3050-3054.
48. Lee T.I., Wyrick J.J., Koh S.S., Jennings E.G., Gadbois E.L., Young R.A. Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme. Mol. Cell. Biol. 18:1998;4455-4462.
49. II19p functionally interacts with components of the global transcriptional regulator Ccr4-Not complex and physically interacts with the Not5 subunit. J. Biol. Chem. 275:2000;26925-26934.
50. Lemaire M., Xie J., Meisterernst M., Collart M.A. The NC2 repressor is dispensable in yeast mutated for the Sin4p component of the holoenzyme and plays roles similar to Mot1p in vivo. Mol. Microbiol. 36:2000;163-173.
51. Lenssen E., Oberholzer U., Labarre J., de Virgilio C., Collart M.A. Saccharomyces cerevisiae Ccr4-Not complex contributes to the control of Msn2p-dependent transcription by the Ras/cAMP pathway. Mol. Microbiol. 43:2002;1023-1037.
52. Liao S.-M., Zhang J., Jeffery D.A., Koleske A.J., Thompson C.M., Chao D.M., Vijoen M., van Vuuren H.J.J., Young R.A. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 374:1995;193-196.
53. Liu H.-Y., Toyn J.H., Chiang Y.-C., Draper M.P., Johnston L.H., Denis C.L. DBF2, a cell cycle-regulated protein kinase, is physically and functionally associated with the CCR4 transcriptional regulatory complex. EMBO J. 16:1997;5289-5298.
54. Liu H.-Y., Badarinarayana V., Audino D.C., Rappsilber J., Mann M., Denis C.L. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 17:1998;1096-1106.
55. Liu H.-Y., Chiang Y.-C., Pan J., et al. Characterization of CAF4 and CAF16 Reveals a Functional Connection between the CCR4-NOT Complex and a Subset of SRB Proteins of the RNA Polymerase II Holoenzyme. J. Biol. Chem. 276:2001;7541-7548.
56. C, an unusual promoter element required for constitutive transcription of the yeast HIS3 gene. Mol. Cell. Biol. 10:1990;4447-4455.
57. Maillet L., Collart M.A. Interaction between Not1p, a component of the Ccr4-Not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase. J. Biol. Chem. 277:2002;2835-2842.
58. Maillet L., Tu C., Hong Y.K., Shuster E.O., Collart M.A. The essential function of NOT1 lies within the CCR4-NOT complex. J. Mol. Biol. 303:2000;131-143.
59. McKenzie E.A., Kent N.A., Dowell S.J., Moreno F., Bird L.E., Mellor J. The centromere and promoter factor 1, CPF1, of Saccharomyces cerevisiae, modulates gene activity through a family of factors including SPT21, RPD1 (SIN3), RPD3 and CCR4. Mol. Gen. Genet. 240:1993;374-386.
60. Moqtaderi Z., Bai Y., Poon D., Weil A.P., Struhl K. TBP-associated factors are not generally required for transcriptional activation in yeast. Nature. 383:1996;188-191.
61. Moriya H., Shimizu-Yoshida Y., Omori A., Iwashita S., Katoh M., Sakai A. Yak1p, a DYRK family kinase, traslocates to the nucleus and phosphorylates yeast Pop2p in response to a glucose signal. Genes Dev. 15:2001;1217-1228.
62. Mosch H.-U., Fink G.R. Dissection of Filamentous Growth by Transposon Mutagenesis in Saccharomyces cerevisiae. Genetics. 145:1997;671-684.
63. Neiman A.M., Chang F., Komachi K., Herskowitz I. CDC36 and CDC39 are negative elements in the signal transduction pathway of yeast. Cell. Regul. 5:1990;391-401.
64. Oberholzer U., Collart M.A. Characterization of NOT5 that encodes a new component of the NOT protein complex. Gene. 207:1998;61-69.
65. Oberholzer U., Collart M.A. In vitro transcription of a TATA-less promoter: negative regulation by the Not1 protein. Biol. Chem. 380:1999;1365-1370.
66. Palmer R.H., Ridden J., Parker P.J. Cloning and expression patterns of two members of a novel protein-kinase-C-related kinase family. Eur. J. Biochem. 227:1995;344-351.
67. Prévôt D., Morel A.-P., Voeltzel T., Rostan M.-C., Rimokh R., Magaud J.-P., Corbo L. Relationships of the antiproliferative proteins Btg1 and Btg2 with CAF1, the human homolog of a component of the yeast CCR4 transcription complex. J. Biol. Chem. 276:2001;9640-9648.
68. Reed S.I. The selection of S. cerevisiae mutants defective in the start event of cell division. Genetics. 95:1980;561-577.
69. Rouault J.-P., Prévot D., Berthet C., Birot A.-M., Billaud M., Magaud J.-P., Corbo L. Interaction of BTG1 and p53-regulated BTG2 gene products with mCaf1, the Murine Homolog of a Component of the Yeast CCR4 Transcriptional Regulatory Complex. J. Biol. Chem. 273:1998;22563-22569.
70. Russell P., Benson J.D., Denis C.L. Characterization of mutations in NOT2 indicates that it plays an important role in maintaining the integrity of the Ccr4-Not complex. J. Mol. Biol. 322:2002;27-39.
71. Sakai A., Chibazakura Y., Shimizu Y., Hishinuma F. Molecular analysis of the POP2 gene, a gene required for glucose repression of Saccharomyces cerevisiae. Nucleic Acids Res. 20:1992;6227-6233.
72. Sanders S.L., Jennings J., Canutescu A., Link A.J., Weil A.P. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22:2002;4723-4738.
73. Schild D. Suppression of a new allele of the yeast RAD52 gene by overexpression of RAD51, mutations in srs2 and ccr4, or mating-type heterozygosity. Genetics. 140:1995;115-127.
74. Schmitz H.-P., Lorberg A., Heinisch J.J. Regulation of yeast protein kinase C activity by interaction with the small GTPase Rho1p through its amino-terminal HR1 domain. Mol. Microbiol. 44:2002;829-840.
75. Seufert W., Jentsch S. Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation of short-lived and abnormal proteins. EMBO J. 9:1990;543-550.
76. Shimizu-Yoshida Y., Sasamoto M., Yoshida A., Yoshioka T., Matsumoto A., Sakai A. Mouse CAF1, a mouse homologue of the yeast POP2 gene, complements the yeast pop2 null mutation. Yeast. 15:1999;1357-1364.
77. Shuster E.O., Byers B. Pachytene arrest and other meiotic effects of the start mutations in Saccharomyces cerevisiae. Genetics. 123:1989;29-43.
78. Smith A., Ward M.P., Garrett S. Yeast PKA represses Msn2p/ Msn4p-dependent gene expression to regulate growth, stress response and glycogen accumulation. EMBO J. 17:1998;3556-3564.
79. Tucker M., Valencia-Sanchez M.A., Staples R.R., Chen J., Denis C.L., Parker R. The transcription factor associated proteins, Ccr4p and Caf1p, are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell. 104:2001;377-386.
80. Tucker M., Staples R.R., Valencia-Sanchez M.A., Muhlrad D., Parker R. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J. 21:2002;1427-1436.
81. Viswanathan P., Chen J., Chiang Y.-C., Denis C.L. Identification of multiple RNA features that influence CCR4 deadenylation activity. J. Biol. Chem. 278:2003;14949-14955.