Gene recruitment of the activated INO1 locus to the nuclear membrane

PLoS Biology

Volumn 2, Issue 11, 2004, Pages

  Brickner, Jason H ^a   Walter, Peter ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; INTEGRAL MEMBRANE PROTEIN SCS 2; MEMBRANE PROTEIN; MYOINOSITOL 1 PHOSPHATE SYNTHASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HAC1; TRANSCRIPTION FACTOR OPI1; UNCLASSIFIED DRUG; GREEN FLUORESCENT PROTEIN; INO2 PROTEIN, S CEREVISIAE; INO4 PROTEIN, S CEREVISIAE; OPI1 PROTEIN, S CEREVISIAE; REPRESSOR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; SCS2 PROTEIN, S CEREVISIAE; TRANSACTIVATOR PROTEIN;

ARTICLE; CELL NUCLEUS MEMBRANE; CHROMATIN; CONTROLLED STUDY; ENDOPLASMIC RETICULUM; GENE ACTIVATION; GENE LOCATION; GENE LOCUS; GENE TRANSFER; INTRACELLULAR SPACE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INDUCTION; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION; BIOLOGICAL MODEL; CELL NUCLEUS; CHEMISTRY; CYTOPLASM; ESCHERICHIA COLI; FLUORESCENCE MICROSCOPY; GENE EXPRESSION REGULATION; GENETICS; IMMUNOBLOTTING; IMMUNOPRECIPITATION; METABOLISM; MOLECULAR GENETICS; NORTHERN BLOTTING; PHENOTYPE; PLASMID; PROMOTER REGION; PROTEIN BINDING; PROTEIN DENATURATION; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; TRANSACTIVATION;

BLOTTING, NORTHERN; CELL NUCLEUS; CHROMATIN; CYTOPLASM; ENDOPLASMIC RETICULUM; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, FUNGAL; GREEN FLUORESCENT PROTEINS; IMMUNOBLOTTING; IMMUNOPRECIPITATION; MEMBRANE PROTEINS; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; MYO-INOSITOL-1-PHOSPHATE SYNTHASE; NUCLEAR ENVELOPE; PHENOTYPE; PLASMIDS; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING; REPRESSOR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SCHIZOSACCHAROMYCES; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 14044266853     PISSN: 15449173     EISSN: None     Source Type: Journal    
DOI: 10.1371/journal.pbio.0020342     Document Type: Article

References (73)

1. Ambroziak J, Henry SA (1994) INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 269: 15344-15349.
2. Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394: 592-595.
3. Andrulis ED, Zappulla DC, Ansari A, Perrod S, Laiosa CV, et al. (2002) Esc1, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Mol Cell Biol 22: 8292-8301.
4. Ashburner BP, Lopes JM (1995a) Regulation of yeast phospholipid biosynthetic gene expression in response to inositol involves two superimposed mechanisms. Proc Natl Acad Sci U S A 92: 9722-9726.
5. Ashburner BP, Lopes JM (1995b) Autoregulated expression of the yeast INO2 and INO4 helix-loop-helix activator genes effects cooperative regulation on their target genes. Mol Cell Biol 15: 1709-1715.
6. Bachhawat N, Ouyang Q, Henry SA (1995) Functional characterization of an inositol-sensitive upstream activation sequence in yeast. A cis-regulatory element responsible for inositol-choline mediated regulation of phospholipid biosynthesis. J Biol Chem 270: 25087-25095.
7. Blobel G (1985) Gene gating: A hypothesis. Proc Natl Acad Sci U S A 82: 8527-8529.
8. Boveri T (1909) Die blastermerenkerne von Ascaris megalocephala und die theorie der chromosomenindividualität. Arch Zellforschung 3: 181.
9. Bressan DA, Vazquez J, Haber JE (2004) Mating type-dependent constraints on the mobility of the left arm of yeast chromosome III. J Cell Biol 164: 361-371.
10. Brown KE, Baxter J, Graf D, Merkenschlager M, Fisher AG (1999) Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol Cell 3: 207-217.
11. Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, et al. (1997) Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91: 845-854.
12. Casolari JM, Brown CR, Komili S, West J, Hieronymous H, et al. (2004) Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117: 427-439.
13. Cobb BS, Morales-Alcelay S, Kleiger G, Brown KE, Fisher AG, et al. (2000) Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding. Genes Dev 14: 2146-2160.
14. Cockell M, Gasser SM (1999) Nuclear compartments and gene regulation. Curr Opin Genet Dev 9: 199-205.
15. Cox JS, Walter P (1996) A novel mechanism for regulating activity of a transcription factor that controls the unfolded protein response. Cell 87: 391-404.
16. Cox JS, Shamu CE, Walter P (1993) Transcriptional induction of genes encoding endoplasmic reticulum resident proteins requires a transmembrane protein kinase. Cell 73: 1197-1206.
17. Cox JS, Chapman RE, Walter P (1997) The unfolded protein response coordinates the production of endoplasmic reticulum protein and endoplasmic reticulum membrane. Mol Biol Cell 8: 1805-1814.
18. Craven RJ, Petes TD (2001) The Saccharomyces cerevisiae suppressor of choline sensitivity (SCS2) gene is a multicopy Suppressor of mec1 telomeric silencing defects. Genetics 158: 145-154.
19. Csink AK, Henikoff S (1996) Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381: 529-531.
20. Cuperus G, Shore D (2002) Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics 162: 633-645.
21. Dedon PC, Soults JA, Allis CD, Gorovsky MA (1991) A simplified formaldehyde fixation and immunoprecipitation technique for studying protein-DNA interactions. Anal Biochem 197: 83-90.
22. Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, et al. (1996) Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745-759.
23. Dietz M, Heyken WT, Hoppen J, Geburtig S, Schuller HJ (2003) TFIIB and subunits of the SAGA complex are involved in transcriptional activation of phospholipid biosynthetic genes by the regulatory protein Ino2 in the yeast Saccharomyces cerevisiae. Mol Microbiol 48: 1119-1130.
24. Ebbert R, Birkmann A, Schuller HJ (1999) The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecularweight protein complex. Mol Microbiol 32: 741-751.
25. Feuerbach F, Galy V, Trelles-Sticken E, Fromont-Racine M, Jacquier A, et al. (2002) Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast. Nat Cell Biol 4: 214-221.
26. Galy V, Olivo-Marin JC, Scherthan H, Doye V, Rascalou N, et al. (2000) Nuclear pore complexes in the organization of silent telomeric chromatin. Nature 403: 108-112.
27. Gasser SM (2002) Visualizing chromatin dynamics in interphase nuclei. Science 296: 1412-1416.
28. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
29. Gotta M, Laroche T, Formenton A, Maillet L, Scherthan H, et al. (1996) The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol 134: 1349-1363.
30. Gottschling DE, Aparicio OM, Billington BL, Zakian VA (1990) Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63: 751-762.
31. Greenberg ML, Goldwasser P, Henry SA (1982) Characterization of a yeast regulatory mutant constitutive for synthesis of inositol-1-phosphate synthase. Mol Gen Genet 186: 157-163.
32. Griac P (1997) Regulation of yeast phospholipid biosynthetic genes in phosphatidylserine decarboxylase mutants. J Bacteriol 179: 5843-5848.
33. Griac P, Swede MJ, Henry SA (1996) The role of phosphatidylcholine biosynthesis in the regulation of the INO1 gene of yeast. J Biol Chem 271: 25692-25698.
34. Hudak KA, Lopes JM, Henry SA (1994) A pleiotropic phospholipid biosynthetic regulatory mutation in Saccharomyces cerevisiae is allelic to sin3 (sdi1, ume4, rpd1). Genetics 136: 475-483.
35. Isogai Y, Tjian R (2003) Targeting genes and transcription factors to segregated nuclear compartments. Curr Opin Cell Biol 15: 296-303.
36. Kagiwada S, Zen R (2003) Role of the yeast VAP homolog, Scs2p, in INO1 expression and phospholipid metabolism. J Biochem (Tokyo) 133: 515-522.
37. Kagiwada S, Hosaka K, Murata M, Nikawa J, Takatsuki A (1998) The Saccharomyces cerevisiae SCS2 gene product, a homolog of a synaptobrevin- associated protein, is an integral membrane protein of the endoplasmic reticulum and is required for inositol metabolism. J Bacteriol 180: 1700-1708.
38. Kawahara T, Yanagi H, Yura T, Mori K (1997) Endoplasmic reticulum stress-induced mRNA splicing permits synthesis of transcription factor Hac1p/Ern4p that activates the unfolded protein response. Mol Biol Cell 8: 1845-1862.
39. Kodaki T, Hosaka K, Nikawa J, Yamashita S (1995) The SNF2/SWI2/ GAM1/TYE3/RIC1 gene is involved in the coordinate regulation of phospholipid synthesis in Saccharomyces cerevisiae. J Biochem (Tokyo) 117: 362-368.
40. Laroche T, Martin SG, Gotta M, Gorham HC, Pryde FE, et al. (1998) Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curr Biol 8: 653-656.
41. Loewen CJ, Roy A, Levine TP (2003) A conserved ER targeting motif in three families of lipid binding proteins and in Opi1p binds VAP. EMBO J 22: 2025-2035.
42. Loewy BS, Henry SA (1984) The INO2 and INO4 loci of Saccharomyces cerevisiae are pleiotropic regulatory genes. Mol Cell Biol 4: 2479-2485.
43. Longtine MS, McKenzie A, 3rd, Demarini DJ, Shah NG, Wach A, et al. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953-961.
44. Lopes JM, Henry SA (1991) Interaction of trans and cis regulatory elements in the INO1 promoter of Saccharomyces cerevisiae. Nucleic Acids Res 19: 3987-3994.
45. Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, et al. (1996) Evidence for silencing compartments within the yeast nucleus: A role for telomere proximity and Sir protein concentration in silencer- mediated repression. Genes Dev 10: 1796-1811.
46. McGraw P, Henry SA (1989) Mutations in the Saccharomyces cerevisiae opi3 gene: Effects on phospholipid methylation, growth and cross-pathway regulation of inositol synthesis. Genetics 122: 317-330.
47. Mori K, Ma W, Gething MJ, Sambrook J (1993) A transmembrane protein with a cdc2+/CDC28-related kinase activity is required for signaling from the ER to the nucleus. Cell 74: 743-756.
48. Nikawa J, Murakami A, Esumi E, Hosaka K (1995) Cloning and sequence of the SCS2 gene, which can suppress the defect of INO1 expression in an inositol auxotrophic mutant of Saccharomyces cerevisiae. J Biochem (Tokyo) 118: 39-45.
49. Patil C, Li H, Walter P (2004) Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response. PLoS Biology 2: e246.
50. Pollard KJ, Peterson CL (1997) Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol Cell Biol 17: 6212-6222.
51. Rabl C (1885) Über Zeillteilung. Morphol Jahrbuch 10: 214-330.
52. Redding K, Holcomb C, Fuller RS (1991) Immunolocalization of Kex2 protease identifies a putative late Golgi compartment in the yeast Saccharomyces cerevisiae. J Cell Biol 113: 527-538.
53. Robinett CC, Straight A, Li G, Willhelm C, Sudlow G, et al. (1996) In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol 135: 1685-1700.
54. Rodriguez-Navarro S, Fischer T, Luo MJ, Antunez O, Brettschneider S, et al. (2004) Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell 116: 75-86.
55. Rogatsky I, Wang JC, Derynck MK, Nonaka DF, Khodabakhsh DB, et al. (2003) Target-specific utilization of transcriptional regulatory surfaces by the glucocorticoid receptor. Proc Natl Acad Sci U S A 100: 13845-13850.
56. Ruegsegger U, Leber JH, Walter P (2001) Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell 107: 103-114.
57. Rusche LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72: 481-516.
58. Schwank S, Hoffmann B, Schuller HJ (1997) Influence of gene dosage and autoregulation of the regulatory genes INO2 and INO4 on inositol/ cholinerepressible gene transcription in the yeast Saccharomyces cerevisiae. Curr Genet 31: 462-468.
59. Schwank S, Ebbert R, Rautenstrauss K, Schweizer E, Schuller HJ (1995) Yeast transcriptional activator INO2 interacts as an Ino2p/Ino4p basic helixloop-helix heteromeric complex with the inositol/choline-responsive element necessary for expression of phospholipid biosynthetic genes in Saccharomyces cerevisiae. Nucleic Acids Res 23: 230-237.
60. Shamu CE, Walter P (1996) Oligomerization and phosphorylation of the Ire1p kinase during intracellular signaling from the endoplasmic reticulum to the nucleus. EMBO J 15: 3028-3039.
61. Shen X, Mizuguchi G, Hamiche A, Wu C (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406: 541-544.
62. Shen X, Xiao H, Ranallo R, Wu WH, Wu C (2003) Modulation of ATPdependent chromatin-remodeling complexes by inositol polyphosphates. Science 299: 112-114.
63. Shirra MK, Patton-Vogt J, Ulrich A, Liuta-Tehlivets O, Kohlwein SD, et al. (2001) Inhibition of acetyl coenzyme A carboxylase activity restores expression of the INO1 gene in a snf1 mutant strain of Saccharomyces cerevisiae. Mol Cell Biol 21: 5710-5722.
64. Sidrauski C, Walter P (1997) The transmembrane kinase Ire1p is a sitespecific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell 90: 1031-1039.
65. Sidrauski C, Cox JS, Walter P (1996) tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell 87: 405-413.
66. Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene. Cell 53: 937-947.
67. Steger DJ, Haswell ES, Miller AL, Wente SR, O'Shea EK (2003) Regulation of chromatin remodeling by inositol polyphosphates. Science 299: 114-116.
68. Strahl-Bolsinger S, Hecht A, Luo K, Grunstein M (1997) SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev 11: 83-93.
69. Straight AF, Belmont AS, Robinett CC, Murray AW (1996) GFP tagging of budding yeast chromosomes reveals that protein-protein interactions can mediate sister chromatid cohesion. Curr Biol 6: 1599-1608.
70. Sugiyama M, Nikawa J (2001) The Saccharomyces cerevisiae Isw2p-Itc1p complex represses INO1 expression and maintains cell morphology. J Bacteriol 183: 4985-4993.
71. Sukegawa J, Blobel G (1993) A nuclear pore complex protein that contains zinc finger motifs, binds DNA, and faces the nucleoplasm. Cell 72: 29-38.
72. Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, et al. (2000) Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101: 249-258.
73. Wagner C, Blank M, Strohmann B, Schuller HJ (1999) Overproduction of the Opi1 repressor inhibits transcriptional activation of structural genes required for phospholipid biosynthesis in the yeast Saccharomyces cerevisiae. Yeast 15: 843-854.