Functional Dissection of the NuA4 Histone Acetyltransferase Reveals Its Role as a Genetic Hub and that Eaf1 Is Essential for Complex Integrity

Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Roger Guidon Hall, 451 Smyth Rd., Ottawa, ONT K1H 8M5, Canada.
Molecular and Cellular Biology (Impact Factor: 4.78). 05/2008; 28(7):2244-56. DOI: 10.1128/MCB.01653-07
Source: PubMed


The Saccharomyces cerevisiae NuA4 histone acetyltransferase complex catalyzes the acetylation of histone H4 and the histone variant Htz1 to regulate key
cellular events, including transcription, DNA repair, and faithful chromosome segregation. To further investigate the cellular
processes impacted by NuA4, we exploited the nonessential subunits of the complex to build an extensive NuA4 genetic-interaction
network map. The map reveals that NuA4 is a genetic hub whose function buffers a diverse range of cellular processes, many
not previously linked to the complex, including Golgi complex-to-vacuole vesicle-mediated transport. Further, we probe the
role that nonessential subunits play in NuA4 complex integrity. We find that most nonessential subunits have little impact
on NuA4 complex integrity and display between 12 and 42 genetic interactions. In contrast, the deletion of EAF1 causes the collapse of the NuA4 complex and displays 148 genetic interactions. Our study indicates that Eaf1 plays a crucial
function in NuA4 complex integrity. Further, we determine that Eaf5 and Eaf7 form a subcomplex, which reflects their similar
genetic interaction profiles and phenotypes. Our integrative study demonstrates that genetic interaction maps are valuable
in dissecting complex structure and provides insight into why the human NuA4 complex, Tip60, has been associated with a diverse
range of pathologies.

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    • " a platform for the process to occur , and perhaps protect the C - terminal domains from proteolysis . A requirement for membrane interactions provides a rationale for the large number of synthetic interactions observed between membrane traffick - ing components and either tra1 - SRR 3413 or deletions of NuA4 component genes ( Hoke et al . 2008a ; Mitchell et al . 2008"
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    ABSTRACT: Tra1 is a 3744-residue component of the Saccharomyces cerevisiae SAGA, NuA4, and ASTRA complexes. Tra1 contains essential C-terminal PI3K and FATC domains, but unlike other PIKK (phosphoinositide three-kinase-related kinase) family members, lacks kinase activity. To analyze functions of the FATC domain, we selected for suppressors of tra1-F3744A, an allele that results in slow growth under numerous conditions of stress. Two alleles of TTI2, tti2-F328S and tti2-I336F, acted in a partially dominant fashion to suppress the growth-related phenotypes associated with tra1-F3744A as well as its resulting defects in transcription. tti2-F328S suppressed an additional FATC domain mutation (tra1-L3733A), but not a mutation in the PI3K domain or deletions of SAGA or NuA4 components. We find eGFP-tagged Tti2 distributed throughout the cell. Tti2 is a component of the ASTRA complex, and in mammalian cells associates with molecular chaperones in complex with Tti1 and Tel2. Consistent with this finding, Tra1 levels are reduced in a strain with a temperature-sensitive allele of tel2. Further agreeing with a possible role for Tti2 in the folding or stabilization of Tra1, tra1-F3744A was mislocalized to the cytoplasm, particularly under conditions of stress. Since an intragenic mutation of tra1-R3590I also suppressed F3744A, we propose that Tti2 is required for the folding/stability of the C-terminal FATC and PI3K domains of Tra1 into their functionally active form.
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    • "Its direct human counterpart is unclear. Eaf5 protein forms subcomplex with Eaf7, and Eaf5 interacts with NuA4 complex (Mitchell et al., 2008). Eaf5 deletion strain is viable, and shows resistance to chemicals such as acetic acid and lactic acid (Kawahata et al., 2006). "

    Full-text · Chapter · Feb 2012
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    • "Both these modifications are associated with active transcription, consistent with the idea that, since the intercomplex interactions are negative, the complexes may provide supportive or redundant roles during gene expression. Interestingly, two recent studies linking the function of the NuA4 complex to other chromatin modification complexes, including SWR1-C, highlight a coordinating role for EAF1 [40,41]. The Bub1p spindle checkpoint protein provides another example of NNP triplets spanning protein complexes with aligned roles (Figure 5B). "
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    ABSTRACT: Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.
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