Gene name - Pcaf
Synonyms - Gcn5, dGcn5
Cytological map position - 69C8--12
Symbol - Pcaf
FlyBase ID: FBgn0020388
Genetic map position - 3L
Classification - histone acetyltransferase, bromodomain, PCAF (N-terminal)
Cellular location - nuclear
Although it has been well established that histone acetyltransferases (HATs) are involved in the modulation of chromatin structure and gene transcription, there is only little information on their developmental role in higher organisms. Pcaf, alternatively called Gcn5, was the first transcription factor with HAT activity identified in eukaryotes. Null alleles of Drosophila Gcn5 block the onset of both oogenesis and metamorphosis, while hypomorphic Gcn5 alleles impair the formation of adult appendages and cuticle. Strikingly, the dramatic loss of acetylation of the K9 and K14 lysine residues of histone H3 in Gcn5 mutants has no noticeable effect on larval tissues. In contrast, strong cell proliferation defects in imaginal tissues are observed. In vivo complementation experiments have revealed that Gcn5 integrates specific functions in addition to chromosome binding and acetylation. Defects displayed by Gcn5 mutant adults rescued by the Gcn5DeltaPcaf variant (deficient in the N-terminal Pcaf specific motif) suggest a role of Gcn5 in the ecdysone regulatory hierarchy during metamorphosis, possibly through interactions with nuclear receptors. Surprisingly, a Gcn5 variant protein with a deletion of the bromodomain, which has been shown to recognize acetylated histones, appears to be fully functional. These results establish Gcn5 as a major histone H3 acetylase in Drosophila that plays a key role in the control of specific morphogenetic cascades during developmental transitions (Carré, 2005).
Gene expression in eukaryotes has to accommodate the presence of nucleosomes and the packaging of DNA into higher-order chromatin structures. Nucleosomes are composed of octamers of histone proteins H2a, H2b, H3, and H4, whose N-terminal tails project outward from the nucleosomal core and are subjected to covalentmodifications such as acetylation, methylation, phosphorylation, and ubiquitination. The variety of these modifications and their association with distinct states of gene transcription suggested that they may act as a combinatorial code to specify downstream events such as the recruitment of transcription factors or modifications of the chromatin structure (Carré, 2005).
The acetylation of lysine residues is one of the most studied histone modifications and has long been linked to gene activation. For instance, a twofold up-regulation of transcription from the male X chromosome in Drosophila is correlated with histone hyperacetylation, while gene silencing in heterochromatin or X chromosome inactivation in mammals is correlated with histone hypoacetylation. Numerous sequence-specific activators, such as the nuclear receptors MyoD and CREB, have been shown to recruit coactivator complexes with histone acetyltransferase (HAT) activity, while transcriptional repressors have been found associated with corepressor complexes with histone deacetylase activity. HAT activity is also associated with more general transcription factors, such as TATA-binding protein-associated factor 1 (TAF1) and yeast elongation factor 3. Collectively, these data point to a causal role of histone acetylation in transcriptional activation. In support of this hypothesis, the acetylation of lysine 8 in histone H4 (H4-AcK8) and lysine 14 in histone H3 (H3-AcK14) has been implicated in the sequential recruitment of transcription factors leading to the activation of the human beta interferon gene in vitro, and distinct patterns of histone acetylation have been associated with groups of coexpressed genes in genome-wide studies (Carré, 2005).
The yeast adaptor Gcn5 was the first transcription factor identified as a bona fide HAT. It defines a family of evolutionarily conserved Gcn5-related N-acetyltransferases (GNATs) whose members were purified as essential subunits of ADA and SAGA (Spt-Ada-Gcn5 acetyltransferase) complexes in yeast and of PCAF, STAGA, and TFTC complexes in mammals. The GNAT complexes contain Ada transcriptional adapters, Spt proteins, and a set of TATA-binding protein-associated factors, and they are structurally related, suggesting that they perform similar functions in transcription. In vitro, Gcn5 acetylates lysine 14 of free, but not nucleosomal, histone H3. In contrast, Gcn5 acetylates an expanded set of lysines of nucleosomal histone H3 when copurified with native ADA or SAGA complexes (Grant, 1999), suggesting that one function of these complexes in vivo is to modulate the activity and specificity of Gcn5 (Carré, 2005).
Two distinct genes, hGCN5 and hPCAF, encode Gcn5 homologues in humans. Both hGCN5 isoforms, GCN5S and GCN5L, and hPCAF (P300/CBP-associated factor) share a close similarity with the complete yeast Gcn5 sequence, including more matches within the HAT catalytic domain as well as the bromodomain, which has been shown to bind acetylated histone lysines. PCAF and GCN5L share an additional N-terminal domain (Pcaf homology domain) of about 350 amino acids involved in binding to CBP/p300 and to several nuclear receptors. While the GCN5 gene knockout results in early embryonic lethality, the PCAF gene knockout has no detectable consequences on mouse development (Xu, 2000). However, GCN5-PCAF double mutants die earlier than single GCN5 mutants, indicating that PCAF and GCN5 functions are not completely redundant (Carré, 2005).
Although the Gcn5 HAT has been clearly involved in the control of Arabidopsis growth, development, and homeostasis (Bertrand, 2003; Vlachonasios, 2003), its contribution to the control of specific morphogenetic events during animal development remains poorly understood. There is only one Gcn5 homologue in Drosophila (Smith, 1998), which thus provides a simplified model for the study of the function of a GNAT in the context of a whole organism. Drosophila Gcn5 (dGcn5) has been isolated in at least two GNAT complexes that contain distinct Ada2 variants (Kusch, 2003; Muratoglu, 2003). A 1.8-MDa SAGA-like complex includes the Ada2b variant, the Ada3 and Spt3 homologues, and several TAFs. An Ada2b loss-of-function mutation is lethal and suppresses the histone H3 acetylation of polytene chromosomes (Qi, 2004), indicating that the SAGA-like complex plays an essential role in gene expression in Drosophila. In addition, Gcn5 associates with the Ada2a variant and with Ada3 in a 440-kDa non-SAGA-like complex. Interestingly, Ada2a and Ada2b mainly localize to different bands on polytene chromosomes, suggesting that GNAT complexes may play distinct functions depending on their composition (Carré, 2005).
In order to characterize the function of Drosophila Gcn5 and GNAT complexes during Drosophila development, two complementary approaches have been undertaken. Gcn5 loss-of-function mutants were isolated from a genetic screen, and in vivo targeting of Gcn5-specific RNA interference was performed, using inverted repeat transgenes. Gcn5 is shown to be the major HAT for the lysine residues K9 and K14 of histone H3, while the acetylation of histone H4 involves other HATs. These data indicate that Gcn5 is required for larva-to-adult metamorphosis and suggest an essential function of Gcn5 in the control of the cell cycle in imaginal tissues. An analysis of Gcn5 variant proteins revealed that the Pcaf homology domain, the domain of interaction with the Ada proteins, and the catalytic domain are all required for the function of the Gcn5 protein. In contrast, the bromodomain appears to be dispensable (Carré, 2005).
Gcn5 mutants have no discernible phenotype before the onset of metamorphosis. The considerable Gcn5 maternal stock may be sufficient to fulfill Gcn5 functions in mutant embryos. However, the Gcn5 protein is undetectable in Gcn5 mutant mid-third-instar larvae, and the proliferation of imaginal discs is already strongly impaired in such mutants at this stage. In addition, mutant larvae keep wandering when control animals have already formed a puparium, dramatically extending the duration of their third larval instar by 4 to 5 days before they die. Ada2b mutants die during pupal development (Qi, 2004), while Ada2a mutants fail to form a puparium in a manner very similar to that of Gcn5 mutant larvae (Pankotai, 2005). Together with these observations, the results strongly suggest that the function of the GNAT complexes is not required for Drosophila larval life (Carré, 2005).
The absence of normal induction of the three early puffs at 2B, 74EF, and 75B in Gcn5 mutants is indicative of a major failure in the regulatory hierarchy controlled by the steroid hormone ecdysone at the end of the third larval instar. The extended duration of this stage in Gcn5 null mutants is also characteristic of defects in pathways controlled by ecdysone. For instance, it is observed with EcR-B1-specific alleles of the ecdysone receptor gene and with mutant alleles of the broad gene. The Pcaf homology domain has been involved in interactions of human Pcaf with various nuclear receptors. Two Gcn5 hypomorphic alleles isolated in this work change amino acids in the Pcaf homology domain, resulting in a partial loss of function of the protein. Heteroallelic combination with the null Gcn5E333st allele led to impaired metamorphosis, with strong defects in adult appendage formation. Gcn5 adult mutant escapers rescued by the Gcn5DeltaPcaf variant consistently display very similar defects of leg elongation and blistered wings. These defects are also highly suggestive of an impaired ecdysone regulatory cascade during metamorphosis. From these observations, it is proposed that Gcn5 acts as a nuclear receptor coactivator at metamorphosis. The finding that the EcR protein is coimmunoprecipitated from embryonic nuclear extracts with Gcn5 in an ecdysone-dependent manner (A. Mazo, personal communication to Carré, 2005) points to the ecdysone receptor itself as a Gcn5 target. However, no interactions were detected between Gcn5 alleles and EcR mutant alleles in a trans-heterozygous genetic test. Although these results do not rule out a functional interaction between Gcn5 and the ecdysone receptor, they may also indicate that Gcn5 acts in the metamorphic ecdysone regulatory hierarchy through interactions with other Drosophila nuclear receptors (Carré, 2005).
This study shows that the lack of Gcn5 in the female germ line arrests oogenesis at an early stage. In addition, somatic Gcn5 mutant clones in ovarian follicles induce the formation of compound egg chambers indicative of an oocyte packaging defect (J. R. Huynh, personal communication to Carré, 2005). Together, these results indicate a strict requirement for Gcn5 during oogenesis, in both the germ line and the somatic line. In light of the role of Gcn5 during ecdysone-triggered metamorphosis, it is noteworthy that ecdysone regulatory hierarchies have also been shown to regulate Drosophila oogenesis (Carré, 2005).
Gcn5 mutant imaginal discs, as well as imaginal tissues silenced by Gcn5 RNAi, display slower cell proliferation. The role of CBP in the cell cycle has been documented for vertebrates, and a domain of interaction of CBP with the Gcn5 homologue Pcaf is targeted by viral and cellular factors (Schiltz, 2000) to regulate cell cycle progression (Carré, 2005).
The acetylation of E2F1 by Pcaf also results in cell cycle modulation (Martinez-Balbas, 2000). In yeast, Gcn5 regulates genes required for mitotic exit (Krebs, 2000). Together, these data suggest that functions of Gcn5 in cell cycle regulation have been conserved throughout evolution. Interestingly, a mouse knock-in mutant for Trrap, a conserved component of GNAT complexes, results in aberrant mitosis. Similarly, the higher mitotic index, together with the increased BrdU incorporation, of Gcn5-silenced imaginal cells suggests that they undergo an aberrant cell cycle. It has been shown that apoptosis induced in imaginal tissues by the loss of Gcn5 function may contribute to the net reduction in cell number. The Drosophila SAGA-like complex interacts in vitro with Dmp53 (Kusch, 2003), and several authors reported a role of dAda2b in DNA damage-induced p53-dependent apoptosis (Qi, 2003; Pankotai, 2005). However, this is the first time that apoptosis in a mutant with a deletion of a component of the Drosophila SAGA-like complex has been observed in the absence of X-ray-induced DNA damage. Strikingly, Gcn5 mouse mutants also display apoptosis in the absence of any exogenous inducers (Xu, 2000). Although further analysis is required to understand the complex roles of Gcn5 in cell proliferation, it is proposed that apoptosis in the Gcn5 mutant might be a consequence of cell cycle defects (Carré, 2005).
The data demonstrate that Gcn5 is the major acetylase for two distinct histone residues, H3 K9 and H3 K14, in Drosophila. In contrast, its contribution to histone H4 acetylation could not be detected in a global analysis. The loss of Ada2b results in a partial loss of H3 K9 and H3 K14 acetylation on polytene chromosomes, while the loss of Ada2a has no detectable effect on chromosome acetylation (Qi, 2004, Pankotai, 2005). In light of the results, these data suggest that the Drosophila GNAT complexes may retain partial Gcn5 HAT activity in the absence of the Ada2 components. Alternatively, Gcn5 could exert its HAT activity in other complexes which remain to be characterized. The substrate specificities of Drosophila and yeast Gcn5 proteins appear to be identical (Grant, 1999). However, it is interesting that in contrast to what was found for Drosophila, both the Gcn5 and Elp3 HATs must be invalidated in yeast to significantly impair histone H3 K9 and K14 acetylation (Wittschieben, 2000). Recent studies have extensively documented the relationship between histone H3 acetylation and gene transcription, but whether or not patterns of histone modification constitute a true code for the control of gene activity in eukaryotes is still a matter of debate. In either case, the results strongly suggest that specific histone acetylation profiles may be established in vivo through the activity of a very limited set of substrate-specific enzymes. The observation that Gcn5 mutant larvae survive for several days without detectable acetylation of H3 K9 and H3 K14 residues is striking and suggests that transcriptional regulation in larval versus embryonic or adult insect tissues involves distinct mechanisms (Carré, 2005).
Numerous data indicate that histone modifications can influence each other. The loss of H3 K9 and H3 K14 acetylation in imaginal discs or salivary glands has no detectable effect either on the levels of H3 S10 phosphorylation and H3 K4 methylation, both of which have been associated with transcriptional activation, or on the level of H3 K9 methylation, which marks HP1 recruitment and silencing. These results suggest that histone H3 acetylation is either a terminal or independent process in the cascade of histone H3 modifications (Carré, 2005).
Using transgenic Gcn5 variants, this study investigated the functions of the conserved regions in the Gcn5 protein. The deletion of the HAT domain completely abolishes the ability of Gcn5 to acetylate histones and to rescue Gcn5 mutant larvae. This result provides the first demonstration that Gcn5 in metazoans exerts its regulatory function during development through its histone acetylase activity. Defects displayed by Gcn5 mutant adults rescued by the Gcn5DeltaPcaf variant suggest a role of Gcn5 in the ecdysone regulatory hierarchy during metamorphosis, possibly through interactions with nuclear receptors. However, it is noteworthy that Gcn5DeltaPcaf retains important functions. The variant protein was distributed along polytene chromosomes similar to the dGcn5 wild-type protein and provided apparently normal H3 K9 and K14 acetylation. This suggests that the core functions of chromatin binding and substrate acetylation may be performed by the ancestral portion of Gcn5, which has been conserved throughout evolution from yeast to humans, and that the Pcaf homology domain has evolved to perform more specific functions in metazoans. The Ada2 interaction domain has been mapped in Gcn5 to an evolutionarily conserved region between the HAT domain and the bromodomain (Candau, 1996; Candau, 1997; Marcus, 1994). A direct interaction in vitro between dGcn5 and Ada2b was recently shown for Drosophila (Qi, 2004). The finding that the Gcn5DeltaAda variant was completely unable to rescue the lethality of the Gcn5 mutants at the time of puparium formation provides strong evidence that the interaction of dGcn5 with Ada2 proteins is crucial for the function of the Drosophila GNAT complexes. Strikingly, however, in Gcn5 mutants Gcn5DeltaAda could bind to polytene chromosomes and restore H3 K9 and H3 K14 acetylation patterns that were indistinguishable from those provided by the wild-type dGcn5 protein. This result is at odds with the finding that histone H3 acetylation is strongly reduced in Ada2b null mutant polytene chromosomes (Qi, 2004). It is possible that the loss of interaction between Ada2b and dGcn5 is deleterious for a specific function of the multiprotein SAGA-like complex but is not sufficient to disrupt the architecture of this complex as well as its ability to acetylate histones (Carré, 2005).
The bromodomain is conserved in a large number of transcription factors and has been shown to bind to acetylated lysines on histone tails. The yeast Gcn5 bromodomain has been shown to be involved in the stabilization of the SWI/SNF remodeling complex through interactions with acetylated nucleosomes at the PHO5 promoter (Syntichaki, 2000). The bromodomain-containing complexes SWI/SNF and TFIID have been shown to be targeted to acetylated histone H3 and H4 tails on the beta interferon promoter in vitro. Collectively, these findings suggest that the bromodomain is essential for targeting a large set of transcription factors to acetylated nucleosomes. In this context, the apparently normal chromosome acetylation by the Gcn5DeltaBromo variant, and most significantly, the complete rescue of Gcn5 mutant viability by this protein, raises a number of questions. The possibility cannot be excluded that the overexpression of the Gcn5DeltaBromo variant may overcome the lack of an essential Gcn5 function or that Gcn5DeltaBromo may be unable to supply an essential function under particular stress conditions. However, the observations clearly indicate that the Gcn5 bromodomain is not as strictly required as the other domains of the protein, since variants with truncations of these domains were expressed under the same conditions. Interestingly, others have reported a minor contribution of the bromodomain to the functions of various transcription factors. Notably, in yeast the deletion of the bromodomain of Drosophila Gcn5 has little consequence on its transcriptional activity (Candau, 1967; Sterner, 1999), while deletion of the bromodomain of Swi2/Snf2 or Spt7 has no phenotypic effect. Similarly, the Brahma protein with a deletion of its bromodomain binds normally to chromosomes in Drosophila and fully rescues brahma null mutants. The apparent lack of requirement for the bromodomain in Drosophila Gcn5 may be due to a functional redundancy of various components of Gcn5 complexes in targeting chromatin. This role has been proposed for the Spt7 factor and the large Tra1 protein, which are both components of the SAGA complex. The recent demonstration that a chromodomain of the yeast SAGA component Chd1 (see Drosophila Chd1) interacts with methylated lysine 4 of histone H3 also raises the interesting possibility that different factors in GNAT complexes interact with different histone modifications (Carré, 2005).
In summary, the deletion of the HAT domain in Gcn5 abolished both its HAT activity and its ability to rescue Gcn5 mutants. Gcn5 variants deleted in either the Pcaf homology domain or the Ada2 interaction domain acetylate chromosomes. However, Gcn5DeltaPcaf is able to partially rescue the Gcn5 mutants, while Gcn5DeltaAda is not. Finally, the deletion of the Gcn5 bromodomain has no noticeable consequences. This remarkable variety of effects revealed in complementation experiments strongly suggests that Gcn5 integrates multiple functions during development (Carré, 2005).
PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcriptional co-activator p300/CBP. Adenoviral protein E1a can disrupt PCAF-CBP interactions and prevent PCAF-dependent cellular differentiation. This report describes the cloning and initial characterization of a Drosophila homolog of yGCN5. In addition to the homology to yGCN5, the Drosophila protein shares sequence similarity with the N-terminal portion of human PCAF that is involved in binding to CBP. In the course of characterizing dGCN5, it was discovered that hGCN5 also contains an N-terminal extension with significant similarity to PCAF. Interestingly, in the case of the h GCN5 gene, alternative splicing may regulate the production of full-length hGCN5. The presence of the N-terminal domain in a Drosophila GCN5 homolog and both human homologs suggests that it was part of the ancestral form of metazoan GCN5 (Smith, 1998).
To demonstrate that dGCN5 possesses HAT activity, both full-length dGCN5 and a fragment corresponding to the catalytic domain of dGCN5 (amino acids 469-634) were expressed as 6×His N-terminal tagged fusion proteins in E.coli and purified on Ni+-agarose. As expected and in excellent agreement with other GCN5 family members, each protein acetylates histone H3 when presented with a mixture of core histones. The similar substrate specificity between the full-length and catalytic fragment is consistent with evidence that a corresponding catalytic fragment from yGCN5 contains all of the sequences required for full HAT activity. An additional substrate utilized by hPCAF is nucleosomal histones; the ability to weakly acetylate nucleosomal substrates was attributed to the N-terminal domain. However, despite sequence similarities between the N-termini of hPCAF and dGCN5, no significant acetylation of nucleosomal histones by dGCN5 was detected (Smith, 1998).
date revised: 10 December 2005
Home page: The Interactive Fly © 1995, 1996 Thomas B. Brody, Ph.D.
The Interactive Fly resides on the
Society for Developmental Biology's Web server.