The packaging of DNA into chromatin has profound implications for all cellular processes that require access to the DNA substrate. Numerous activities have been identified that make compacted chromatin more amenable to the complex machinery responsible for transcription, replication and repair. These activities include histone chaperone–mediated nucleosome assembly and disassembly, post-translational modifications of histones, incorporation of histone variants and ATP-dependent chromatin remodeling. Evidence is emerging that all of these activities are tightly interwoven and cooperate in complex ways to achieve the delicate balance of chromatin compaction and decompaction.
Histone chaperones have been recognized as important players in regulating DNA accessibility and chromatin fluidity (recently reviewed in refs. 1
). Many histone chaperones are found in complex with histone modification enzymes or ATP-dependent chromatin-remodeling proteins. For example, human nucleosome assembly proteins 1 and 2 (NAP1 and NAP2) physically interact with p300 (ref. 3
); yeast Nap1 and other histone chaperones collaborate with the remodeling factor SWR1 in the replacement of histone H2A with the histone variant H2A.Z (ref. 4
), and the putative Nap1 family member Vps75 forms a complex with the newly discovered histone acetyltransferase (HAT) Rtt109 (refs. 4
Yeast Rtt109 acetylates H3K56, a modification that is likely to have a role in DNA replication and in maintaining genome stability in fungi7
. Recent findings have demonstrated that Rtt109 also acetylates H3K911
. Rtt109 is only the second-known HAT that seems to require a histone chaperone for its activity6
; the first documented case was the complex of Hat1 (the catalytic component) and Hat2 (the ortholog of the human histone binding protein RBAP48 (ref. 13
)). In vitro
, the reaction catalyzed by recombinant Rtt109 alone is slow and inefficient9
, and Vps75 serves to activate Rtt109's HAT activity6
. Vps75 is a bona fide histone chaperone on the basis of its ability to bind histones and to assemble chromatin in vitro
and to associate with chromatin in vivo14
. Vps75 has approximately 24% sequence homology with yeast Nap1, a multifunctional histone chaperone with pleotropic roles in chromatin metabolism and cell-cycle regulation (reviewed in refs. 15
). The unrelated histone chaperone Asf1 also stimulates Rtt109 activity in vitro6
. Notably, a deletion of VPS75
has only minor effects on global H3K56 acetylation (H3K56ac) in yeast cells, also supporting redundant functions in vivo for the chaperones and Rtt109 stimulation12
. Asf1 may be a good candidate for these redundant functions, because deletion of ASF1
does lead to loss of H3K56ac, but it also leads to loss of H3K9ac, a modification that is performed by a different HAT, Gcn5 (ref. 17
). Moreover, Asf1 is not a member of the Nap1 family. Thus, the relationships between these chaperones and their roles in Rtt109 stimulation are unclear.
Here we describe the crystal structure of Saccharomyces cerevisiae Vps75 and compare its structural and functional properties to those of S. cerevisiae Nap1. Both chaperones (the only two known Nap1 family members in yeast) bind histones with similarly high affinities, and both proteins stably interact with Rtt109; however, only Vps75 is capable of stimulating Rtt109 HAT activity. In addition, deletion of VPS75 results in dramatic and diverse mutant phenotypes, in contrast to the lack of effects observed for the deletion of NAP1. The flexible C-terminal domain of Vps75 is important for the in vivo functions of Vps75 and modulates Rtt109 activity in vitro. Together, our data demonstrate a remarkable specialization of Vps75 for the interaction with and stimulation of Rtt109.