Sir3-nucleosome interactions in spreading of silent chromatin in Saccharomyces cerevisiae.
Silent chromatin in Saccharomyces cerevisiae is established in a stepwise process involving the SIR complex, comprised of the histone deacetylase Sir2 and the structural components Sir3 and Sir4. The Sir3 protein, which is the primary histone-binding component of the SIR complex, forms oligomers in vitro and has been proposed to mediate the spreading of the SIR complex along the chromatin fiber. In order to analyze the role of Sir3 in the spreading of the SIR complex, we performed a targeted genetic screen for alleles of SIR3 that dominantly disrupt silencing. Most mutations mapped to a single surface in the conserved N-terminal BAH domain, while one, L738P, localized to the AAA ATPase-like domain within the C-terminal half of Sir3. The BAH point mutants, but not the L738P mutant, disrupted the interaction between Sir3 and nucleosomes. In contrast, Sir3-L738P bound the N-terminal tail of histone H4 more strongly than wild-type Sir3, indicating that misregulation of the Sir3 C-terminal histone-binding activity also disrupted spreading. Our results underscore the importance of proper interactions between Sir3 and the nucleosome in silent chromatin assembly. We propose a model for the spreading of the SIR complex along the chromatin fiber through the two distinct histone-binding domains in Sir3.
Buchberger
Johannes R
JR
Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA.
Onishi
Megumi
M
Li
Geng
G
Seebacher
Jan
J
Rudner
Adam D
AD
Gygi
Steven P
SP
Moazed
Danesh
D
D000595:Amino Acid Sequence; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D020868:Gene Silencing; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009707:Nucleosomes / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
D002843:Chromatin; D046911:Macromolecular Substances; D009707:Nucleosomes; C084122:SIR3 protein, S cerevisiae; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae
Mol Cell Biol. 2006 Apr;26(8):3256-65
16581798
Genetics. 2004 Sep;168(1):547-51
15454564
Science. 1994 Oct 21;266(5184):404-9
7545955
Nature. 2000 Feb 17;403(6771):795-800
10693811
Protein Sci. 2006 May;15(5):1182-6
16641491
Proc Natl Acad Sci U S A. 1990 Aug;87(16):6286-90
2201024
Cell. 1995 Feb 24;80(4):583-92
7867066
Genetics. 1997 Mar;145(3):605-14
9055071
Nat Struct Mol Biol. 2007 Mar;14(3):200-7
17310250
Mol Cell. 2007 Dec 28;28(6):1002-14
18158898
Bioessays. 1998 Jan;20(1):30-40
9504045
J Biol Chem. 2006 Jul 21;281(29):20107-19
16717101
EMBO J. 1992 Jun;11(6):2201-9
1600945
Nature. 1996 Sep 5;383(6595):92-6
8779721
J Cell Biol. 1980 Jun;85(3):811-22
6993497
Cell. 2002 Feb 22;108(4):489-500
11909520
Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6658-63
10841563
Genome Res. 1999 Jan;9(1):27-43
9927482
Mol Cell. 2001 Aug;8(2):473-9
11545749
Mol Cell. 2001 Sep;8(3):489-98
11583612
Cell. 1999 Dec 23;99(7):735-45
10619427
Biochem Biophys Res Commun. 2000 Nov 30;278(3):685-90
11095969
EMBO J. 2001 Sep 17;20(18):5207-18
11566884
EMBO J. 2002 Sep 2;21(17):4600-11
12198162
Cell. 1990 Nov 16;63(4):751-62
2225075
Genes Dev. 1993 Jul;7(7A):1133-45
8319906
Mol Biol Cell. 2002 Jul;13(7):2207-22
12134062
Genes Dev. 2003 Sep 1;17(17):2162-76
12923057
Genes Dev. 1994 Oct 1;8(19):2257-69
7958893
Mol Cell Biol. 1991 Apr;11(4):2253-62
2005909
Mol Cell. 2007 Dec 28;28(6):1015-28
18158899
Gene. 1992 Jan 2;110(1):119-22
1544568
Cell. 1995 Nov 17;83(4):563-8
7585959
Nucleic Acids Res. 2004 Aug 10;32(14):e115
15304544
Genetics. 2000 Jun;155(2):509-22
10835377
Mol Cell Biol. 2006 Oct;26(20):7616-31
16908543
Cell. 2005 May 20;121(4):515-527
15907466
Mol Cell Biol. 1998 Oct;18(10):6110-20
9742128
Nat Struct Mol Biol. 2006 Aug;13(8):676-83
16829961
Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14178-82
11106374
Science. 2003 Aug 8;301(5634):798-802
12907790
Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):415-20
11134535
Genes Dev. 2002 Jun 15;16(12):1528-39
12080091
Genetics. 1987 May;116(1):9-22
3297920
Annu Rev Biophys Biomol Struct. 2006;35:93-114
16689629
Mol Cell Biol. 2002 Jun;22(12):4167-80
12024030
Genetics. 1989 May;122(1):19-27
2659436
Mol Cell Biol. 2005 Jun;25(11):4514-28
15899856
Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2186-91
9122169
Yeast. 1997 Sep 15;13(11):1029-42
9290207
Biochemistry. 2006 Dec 26;45(51):15941-8
17176117
Annu Rev Biochem. 2003;72:481-516
12676793
J Biol Chem. 2002 May 24;277(21):18535-44
11893743