Processing Mechanism and Substrate Selectivity of the Core NuA4 Histone Acetyltransferase Complex

Overview

Journal Biochemistry

Specialty Biochemistry

Date 2010 Dec 25

PMID 21182309

Citations 8

Authors

Kevin M Arnold

Susan Lee

John M Denu

Affiliations

Soon will be listed here.

Abstract

Esa1, an essential MYST histone acetyltransferase found in the yeast piccolo NuA4 complex (picNuA4), is responsible for genome-wide histone H4 and histone H2A acetylation. picNuA4 uniquely catalyzes the rapid tetra-acetylation of nucleosomal H4, though the molecular determinants driving picNuA4 efficiency and specificity have not been defined. Here, we show through rapid substrate trapping experiments that picNuA4 utilizes a nonprocessive mechanism in which picNuA4 dissociates from the substrate after each acetylation event. Quantitative mass spectral analyses indicate that picNuA4 randomly acetylates free and nucleosomal H4, with a small preference for lysines 5, 8, and 12 over lysine 16. Using a series of 24 histone mutants of H4 and H2A, we investigated the parameters affecting catalytic efficiency. Most strikingly, removal of lysine residues did not substantially affect the ability of picNuA4 to acetylate remaining sites, and insertion of an additional lysine into the H4 tail led to rapid quintuple acetylation. Conversion of the native H2A tail to an H4-like sequence resulted in enhanced multisite acetylation. Collectively, the results suggest picNuA4's site selectivity is dictated by accessibility on the nucleosome surface, the relative proximity from the histone fold domain, and a preference for intervening glycine residues with a minimal (n + 2) spacing between lysines. Functionally distinct from other HAT families, the proposed model for picNuA4 represents a unique mechanism of substrate recognition and multisite acetylation.

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References

Ruiz-Garcia A, Sendra R, Pamblanco M, Tordera V . Gcn5p is involved in the acetylation of histone H3 in nucleosomes. FEBS Lett. 1997; 403(2):186-90. DOI: 10.1016/s0014-5793(97)00049-5. View

Pray-Grant M, Daniel J, Schieltz D, Yates 3rd J, Grant P . Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature. 2005; 433(7024):434-8. DOI: 10.1038/nature03242. View

Pena P, Davrazou F, Shi X, Walter K, Verkhusha V, Gozani O . Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature. 2006; 442(7098):100-3. PMC: 3190580. DOI: 10.1038/nature04814. View

Tan S, Kern R, Selleck W . The pST44 polycistronic expression system for producing protein complexes in Escherichia coli. Protein Expr Purif. 2005; 40(2):385-95. DOI: 10.1016/j.pep.2004.12.002. View

Smith C . Quantification of acetylation at proximal lysine residues using isotopic labeling and tandem mass spectrometry. Methods. 2005; 36(4):395-403. DOI: 10.1016/j.ymeth.2005.03.007. View

Yan Y, Barlev N, Haley R, Berger S, Marmorstein R . Crystal structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate binding by histone acetyltransferases. Mol Cell. 2000; 6(5):1195-205. DOI: 10.1016/s1097-2765(00)00116-7. View

Wang H, Huang Z, Xia L, Feng Q, Erdjument-Bromage H, Strahl B . Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science. 2001; 293(5531):853-7. DOI: 10.1126/science.1060781. View

Galarneau L, Nourani A, Boudreault A, Zhang Y, Heliot L, Allard S . Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell. 2000; 5(6):927-37. DOI: 10.1016/s1097-2765(00)80258-0. View

Poux A, Cebrat M, Kim C, Cole P, Marmorstein R . Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor. Proc Natl Acad Sci U S A. 2002; 99(22):14065-70. PMC: 137837. DOI: 10.1073/pnas.222373899. View

10.

Luger K, Rechsteiner T, Richmond T . Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 1999; 304:3-19. DOI: 10.1016/s0076-6879(99)04003-3. View

11.

Berndsen C, Albaugh B, Tan S, Denu J . Catalytic mechanism of a MYST family histone acetyltransferase. Biochemistry. 2007; 46(3):623-9. PMC: 2752042. DOI: 10.1021/bi602513x. View

12.

Smith E, Eisen A, Gu W, Sattah M, Pannuti A, Zhou J . ESA1 is a histone acetyltransferase that is essential for growth in yeast. Proc Natl Acad Sci U S A. 1998; 95(7):3561-5. PMC: 19875. DOI: 10.1073/pnas.95.7.3561. View

13.

Jenuwein T, Allis C . Translating the histone code. Science. 2001; 293(5532):1074-80. DOI: 10.1126/science.1063127. View

14.

Nourani A, Utley R, Allard S, Cote J . Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J. 2004; 23(13):2597-607. PMC: 449761. DOI: 10.1038/sj.emboj.7600230. View

15.

Iizuka M, Takahashi Y, Mizzen C, Cook R, Fujita M, Allis C . Histone acetyltransferase Hbo1: catalytic activity, cellular abundance, and links to primary cancers. Gene. 2009; 436(1-2):108-14. PMC: 2674512. DOI: 10.1016/j.gene.2009.01.020. View

16.

Suka N, Suka Y, Carmen A, Wu J, Grunstein M . Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell. 2001; 8(2):473-9. DOI: 10.1016/s1097-2765(01)00301-x. View

17.

Downs J, Allard S, Jobin-Robitaille O, Javaheri A, Auger A, Bouchard N . Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol Cell. 2004; 16(6):979-90. DOI: 10.1016/j.molcel.2004.12.003. View

18.

Grant P, Duggan L, Cote J, Roberts S, Brownell J, Candau R . Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997; 11(13):1640-50. DOI: 10.1101/gad.11.13.1640. View

19.

Blanchetot C, Chagnon M, Dube N, Halle M, Tremblay M . Substrate-trapping techniques in the identification of cellular PTP targets. Methods. 2004; 35(1):44-53. DOI: 10.1016/j.ymeth.2004.07.007. View

20.

Clements A, Poux A, Lo W, Pillus L, Berger S, Marmorstein R . Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. Mol Cell. 2003; 12(2):461-73. DOI: 10.1016/s1097-2765(03)00288-0. View