The jmjN and jmjC domains of the yeast zinc finger protein Gis1 interact with 19 proteins involved in transcription, sumoylation and DNA repair

Molecular Genetics and Genomics

Volumn 277, Issue 1, 2007, Pages 57-70

  Tronnersjö, Susanna ^a,b   Hanefalk, Christine ^a   Balciunas, Darius ^a,b,c   Hu, Guo Zhen ^a,b   Nordberg, Niklas ^b   Murén, Eva ^a,b   Ronne, Hans ^a,b  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Bud27; Gis1; jmjC; Sgs1; Sumoylation

Indexed keywords

DNA; HISTONE; RECQ HELICASE; SUMO PROTEIN; TRANSCRIPTION FACTOR; ZINC FINGER PROTEIN;

ARTICLE; DNA REPAIR; ENZYME ACTIVITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; SUMOYLATION;

HUMANS; MOLECULAR CHAPERONES; NUCLEAR PROTEINS; PROTEIN BINDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; RECQ HELICASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; SMALL UBIQUITIN-RELATED MODIFIER PROTEINS; TRANSCRIPTION, GENETIC; TWO-HYBRID SYSTEM TECHNIQUES;

EUKARYOTA; MAMMALIA;

EID: 33845895736     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-006-0171-3     Document Type: Article

References (75)

1. Andrulis AD, Zappulla DC, Ansari A, Perrod S, Laiosa CV, Gartenberg MR, Sternglanz R (2002) Esc1, a nuclear protein required for Sir4-based plasmid anchoring and partitioning. Mol Cell Biol 22:8292-8301
2. Balciunas D, Ronne H (1999) Yeast genes GIS1-4: multicopy suppressors of the Gal- phenotype of snf1 mig1 srb8/10/11 cells. Mol Gen Genet 262:589-599
3. Balciunas D, Ronne H (2000) Evidence of domain swapping within the jumonji family of transcription factors. Trends Biochem Sci 25:274-276
4. Balciunas D, Gälman C, Ronne H, Björklund S (1999) The Med1 subunit of the yeast mediator complex is involved in both transcriptional activation and repression. Proc Natl Acad Sci USA 96:376-381
5. Bennett RJ, Sharp JA, Wang JC (1998) Purification and characterization of the Sgs1 DNA helicase activity of Saccharomyces cerevisiae. J Biol Chem 273:9644-9650
6. Blander G, Zalle N, Daniely Y, Taplick J, Gray MD, Oren M (2002) DNA damage-induced translocation of the Werner helicase is regulated by acetylation. J Biol Chem 277:50934-50940
7. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123:581-592
8. Cheng C, Huang D, Roach PJ (1997) Yeast PIG genes: PIG1 encodes a putative type 1 phosphatase subunit that interacts with the yeast glycogen synthase Gsy2p. Yeast 13:1-8
9. Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G (2006) Structural insights into histone demethylation by JMJD2 family members. Cell 125:1-12
10. Clissold PM, Ponting CP (2001) JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta. Trends Biochem Sci 26:7-9
11. Enomoto T (2001) Function of RecQ family helicases: possible involvement of Bloom's and Werner's syndrome gene products in guarding genome integrity during DNA replication. J Biochem (Tokyo) 129:501-507
12. Estojak J, Brent R, Golemis EA (1995) Correlation of two-hybrid affinity data with in vitro measurements. Mol Cell Biol 15:5820-5829
13. Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245-246
14. Gangloff S, McDonald JP, Bendixen C, Arthur L, Rothstein R (1994) The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol Cell Biol 14:8391-8398
15. Gasser SM, Cockell MM (2001) The molecular biology of the SIR proteins. Gene 279:1-16
16. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631-636
17. Gstaiger M, Luke B, Hess D, Oakeley EJ, Wirbelauer C, Blondel M, Vigneron M, Peter M, Krek W (2003) Control of nutrient-sensitive transcription programs by the unconventional prefoldin URI. Science 302:1208-1212
18. Gyuris J, Zervos AS, Brent R (1993) Mxi1, a protein that specifically interacts with Max to bind Myc-Max recognition sites. Cell 72:223-232
19. Hannich JT, Lewis A, Kroetz MB, Li SJ, Heide H, Emili A, Hochstrasser M (2005) Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem 250:4102-4110
20. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183
21. Hu F, Alcasabas AA, Elledge SJ (2001) Asf1 links Rad53 to control of chromatin assembly. Genes Dev 15:1061-1066
22. Ivy JM, Hicks JB, Klar AJ (1985) Map positions of yeast genes SIR1, SIR3 and SIR4. Genetics 111:735-744
23. Iwase M, Toh-e A (2001) Nis1 encoded by YNL078W: a neck protein of Saccharomyces cerevisiae. Gen Gen Sys 76:335-343
24. Jang YK, Wang L, Sancar GB (1999) RPH1 and GIS1 are damage-responsive repressors of PHR1. Mol Cell Biol 19:7630-7638
25. Johnson ES (2004) Protein modification by SUMO. Annu Rev Biochem 73:355-382
26. Johnson ES, Gupta AA (2001) An E3-like factor that promotes SUMO conjugation to the yeast septins. Cell 106:735-744
27. Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell 20:971-978
28. Kamens J, Brent R (1991) A yeast transcription assay defines distinct rel and dorsal DNA recognition sequences. New Biol 3:1005-1013
29. Kawabe Y, Seki M, Seki T, Wang WS, Imamura O, Furuichi Y, Saitoh H, Enomoto T (2000) Covalent modification of the Werner's syndrome gene product with the ubiquitin-related protein SUMO-1. J Biol Chem 275:20963-20966
30. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123:593-605
31. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 12:4207-4318
32. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637-643
33. Kurischko C, Weiss G, Ottey M, Luca FC (2005) A role for the Saccharomyces cerevisiae regulation of Ace2 and polarized morphogenesis signaling network in cell integrity. Genetics 171:443-455
34. Li B, Howe L, Anderson S, Yates JR III, Workman JL (2003) The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 278:8897-8903
35. Lisby M, Rothstein R (2004) DNA damage checkpoint and repair centers. Curr Opin Cell Biol 16:328-334
36. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6:838-849
37. Metzger E, Wissmann M, Yin N, Muller JM, Schneider R, Peters AH, Gunther T, Buettner R, Schule R (2005) LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437:436-439
38. Müller S, Ledl A, Schmidt D (2004) SUMO: a regulator of gene expression and genome integrity. Oncogene 23:1998-2008
39. Nathan D, Ingvarsdottir K, Sterner DE, Bylebyl GR, Dokmanovic M, Dorsey JA, Whelan KA, Krsmanovic M, Lane WS, Meluh PB, Johnson ES, Berger SL (2006) Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev 20:966-976
40. Negorev D, Maul GG (2001) Cellular proteins localized at and interacting with ND10/PML nuclear bodies/PODs suggest a functions of a nuclear depot. Oncogene 20:7234-7242
41. Ni L, Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12:2147-2170
42. Oshiro J, Han G-S, Iwanyshyn WM, Conover K, Carman GM (2003) Regulation of the yeast DPP1-encoded diacylglycerol pyrophosphate phosphatase by transcription factor Gis1p. J Biol Chem 278:31495-31503
43. Panse VG, Hardeland U, Werner T, Kuster B, Hurt E (2004) A proteome-wide approach identifies sumoylated substrate proteins in yeast. J Biol Chem 279:41346-41351
44. Pedruzzi I, Bürckert N, Egger P, De Virgilio C (2000) Saccharomyces cerevisiae Ras/cAMP pathway controls post-diauxic shift element-dependent transcription through the zinc finger protein Gis1. EMBO J 19:2569-2579
45. Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, Bragado-Nilsson E, Wilm M, Seraphin B (2001) The tandem affinity purification (TAP) method: a general procedure of protein complexes. Methods 24:218-229
46. Rabitsch KP, Toth A, Galova M, Schleiffer A, Schaffner G, Aigner E, Rupp C, Penkner AM, Moreno-Borchart AC, Primig M, Esposito RE, Klein F, Knop M, Nasmyth K (2001) A screen for genes required for meiosis and spore formation based on whole-genome expression. Curr Biol 11:1001-1009
47. Redon C, Pilch DR, Bonner WM (2006) Genetic analysis of Saccharomyces cerevisiae H2A serine 129 mutant suggests a functional relationship between H2A and the sister-chromatid cohesion partners Csm3-Tof1 for the repair of topoisomerase I-induced DNA damage. Genetics 172:67-76
48. Rondon AG, Jimeno S, Garcia-Rubio M, Aguilera A (2003) Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation. J Biol Chem 278:39037-39043
49. Russnak R, Pereira S, Platt T (1996) RNA binding analysis of yeast REF2 and its two-hybrid interaction with a new gene product, FIR1. Gene Expr 6:241-258
50. Sachdev S, Bruhn L, Sieber H, Pichler A, Melchior F, Grosschedl R (2001) PIASy, a nuclear matrix-associated SUMO E3 ligase, represses LEF1 activity by sequestration into nuclear bodies. Genes Dev 15:3088-3103
51. Sanders SL, Weil PA (2000) Identification of two novel TAF subunits of the yeast Saccharomyces cerevisiae TFIID complex. J Biol Chem 18:13895-13900
52. Schmidt D, Müller S (2003) PIAS/SUMO: new partners in transcriptional regulation. Cell Mol Life Sci 60:2561-2574
53. Seeler J-S, Dejean A (1999) The PML nuclear bodies: actors or extras? Curr Opin Genet Dev 9:362-367
54. Seeler J-S, Dejean A (2003) Nuclear and unclear functions of SUMO. Nat Rev Mol Cell Biol 4:690-699
55. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-953
56. Strasser K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondon AG, Aguilera A, Struhl K, Reed R, Hurt E (2002) TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417:304-308
57. Takahashi Y, Toh-e A, Kikuchi Y (2001) A novel factor for the SUMO/Smt3 conjugation of yeast septins. Gene 275:223-231
58. Takahashi Y, Toh-e A, Kikuchi Y (2003) Comparative analysis of yeast PIAS-type SUMO ligases in vivo and in vitro. J Biochem 133:415-422
59. Takeuchi T, Yamazaki Y, Katoh-Fukui Y, Tsuchiya R, Kondo S, Motoyama J, Higashinakagawa T (1995) Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. Genes Dev 9:1211-1222
60. Tang HY, Xu J, Cai M (2000) Pan1p, End3p, and Sla1p, three yeast proteins required for normal cortical actin cytoskeleton organization, associate with each other and play essential roles in cell wall morphogenesis. Mol Cell Biol 20:12-25
61. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y (2006) Histone demethylation by a family of jmjC domain-containing proteins. Nature 439:811-816
62. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomycescerevisiae. Nature 403:623-627
63. Wang XW, Tseng A, Ellis NA, Spillare EA, Linke SP, Robles AI, Seker H, Yang Q, Hu P, Beresten S, Bemmels NA, Garfield S, Harris CC (2001) Functional interaction of p53 and BLM DNA helicase in apoptosis. J Biol Chem 276:32948-32955
64. Wegierski T, Billy E, Nasr R, Filipowicz W (2001) Bms1p, a G-domain containing protein, associates with Rvl1p and is required for 18S rDNA biogenesis in yeast. RNA 7:1254-1267
65. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:1-15
66. Wohlschlegel JA, Johnson ES, Reed SI, Yates JA III (2004) Global analysis of protein sumoylation in Saccharomyces cerevisiae. J Biol Chem 279:45662-45668
67. Woods A, Cheung PC, Smith FC, Davison MD, Scott J, Beri RK, Carling D (1996) Characterization of AMP-activated protein kinase β and γ subunits: assembly of the heterotrimeric complex in vitro. J Biol Chem 271:10282-10290
68. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, Strahl BD (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 17:654-663
69. 2-catenin-dependent activation of Tcf-4. EMBO J 22:2047-2059
70. Yamane K, Toumazou C, Tsukada Y, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (2006) JHDM2A, a jmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125:1-13
71. Yuan DS (2000) Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging. Genetics 156:45-58
72. Zhang S, Skalsky Y, Garfinkel DJ (1999) MGA2 or SPT23 is required for transcription of the delta 9 fatty acid desaturase gene, OLE1, and nuclear membrane integrity in Saccharomyces cerevisiae. Genetics 151:473-483
73. Zhong S, Hu P, Ye TZ, Stan R, Ellis NA, Pandolfi PP (1999) A role for PML and the nuclear body in genomic stability. Oncogene 18:7941-7947
74. Zhong S, Salomoni P, Pandolfi PP (2000) The transcriptional role of PML and the nuclear body. Nat Cell Biol 2:E85-E90
75. Zhou W, Ryan JJ, Zhou H (2004) Global analyses of sumoylated proteins in Saccharomyces cerevisiae. J Biol Chem 279:32262-32268