Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710,1 Gene Expression Laboratory, The Salk Institute for Biological Studies, and Howard Hughes Medical Institute, La Jolla, California 920372
Received 28 February 2005/ Returned for modification 11 April 2005/ Accepted 6 June 2005
| ABSTRACT |
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| INTRODUCTION |
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Among HDAC family members involved in transcriptional regulation, HDAC4 and HDAC5 are closely related and belong to a subfamily that also includes HDAC7 and HDAC9 (reviewed in reference 37). This subfamily of HDACs share several unique properties. First, they all contain the N-terminal noncatalytic MITR (MEF2-interacting transcription repressor) homology domain (37). Second, they are all regulated by phosphorylation-dependent cytoplasmic-nuclear trafficking (18, 23, 45). Third, and most importantly, they are all critical regulators of MEF2, a family of transcription factors important in muscle cell differentiation and apoptosis (reviewed in reference 24). In skeletal muscle cells, MEF2 members collaborate with the basic helix-loop-helix (bHLH) protein MyoD to activate the genes critical for muscle cell differentiation (reviewed in reference 2). It was found that HDAC4 and related members bind to MEF2 via the MITR homology domain and potently repress MEF2-induced gene transcription (5, 22, 26, 39). Supporting the importance of this repression activity, the overexpression of HDAC4 and -5 can suppress skeletal muscle cell differentiation in a cell culture model (22), and the ablation of HDAC9 in mice leads to inappropriate and ectopic activation of MEF2-mediated gene transcription in cardiac muscle (43). These results identify members of the HDAC4 subfamily as critical negative regulators of MEF2. Because HDAC4 is a member of the histone deacetylase family, the transcriptional repression effect of HDAC4 on MEF2 has been naturally attributed to its ability to induce histone deacetylation (22, 26). However, deacetylase-independent transcription repression by HDAC4 has also been reported (3, 44; X. Zhao and T.-P. Yao, unpublished observation). This observation suggests that HDAC4 might control MEF2 activity by some other mechanisms that have yet to be characterized.
SUMO (small ubiquitin-related modifier) is a small polypeptide related to ubiquitin. Like ubiquitin, SUMO can be covalently attached to a target protein at specific lysine residues by the activities of an activating enzyme (E1), a conjugating enzyme (E2) (Ubc9), and a growing number of SUMO E3 ligases (reviewed in reference 35). Although the understanding of the function of protein sumoylation remains poor, recent studies have suggested that it might play a role in transcriptional regulation (reviewed in reference 9). Several reports indicate that lysine sumoylation negatively regulates transcription factors (reviewed in references 7 and 38), a function that is also dominantly associated with members of the HDAC family. However, it has not been determined previously whether HDAC members are functionally connected to transcription factor sumoylation.
In this report, we provide evidence that HDAC4 has a novel SUMO E3 ligase activity that regulates MEF2 sumoylation. We show that HDAC4 binds the SUMO-conjugating enzyme Ubc9 and potently stimulates MEF2 sumoylation in both cultured cells and an in vitro reconstituted system. Furthermore, we show that the MEF2 lysine acceptor for SUMO is also subject to dynamic acetylation mediated by a MEF2 coactivator, the acetyltransferase CBP (6, 33), and a NAD+-dependent class III deacetylase, SIRT1. Functionally, we found that a MEF2 sumoylation-deficient mutant is more potent than wild-type MEF2 in activating target gene transcription and promoting muscle cell differentiation, whereas a MEF2-SUMO fusion protein is transcriptionally inactive. Our results uncover the unexpected complexity of the regulation of MEF2 function by two different classes of deacetylases and reveal a novel mode of transcriptional regulation whereby the deacetylase HDAC4 controls MEF2 activity by promoting its sumoylation with SUMO E3 ligase activity.
| MATERIALS AND METHODS |
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Tissue culture, transfections, and Western blots. 293T and 10T1/2 cells were maintained in Dulbecco's modified Eagle medium (DMEM) with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. Calcium phosphate-mediated transfections were performed as described previously to transfect 293T cells (41). Thirty-six hours after transfection, cells were harvested and lysed with RIPA buffer containing 100 mM N-ethylmaleimide. Five-hundred-microgram aliquots of protein were immunoprecipitated with anti-MEF2D antibody overnight, followed by immunoblotting using anti-SUMO or anti-acetylated lysine antibody. Endogenous MEF2 sumoylation was detected as described previously (17). Briefly, C2C12 cells were lysed in RIPA buffer containing 1% SDS. After a quick sonication, cell lysates were diluted 10-fold for immunoprecipitation with an anti-MEF2 antibody. For the endogenous MEF2 acetylation assay, C2C12 cells were induced to differentiate by serum withdrawal for different time periods, as indicated. The cells were treated with nicotinamide for 4 h before being harvested. The cells were lysed in 170 mM NETN (0.5% NP-40, 1 mM EDTA, 20 mM Tris-HCl, 170 mM NaCl), and MEF2 was immunoprecipitated and analyzed by Western blotting as stated above.
Coimmunoprecipitation assays. For the interaction of HDAC4 and Ubc9, HDAC4 and Ubc9 were coexpressed in U2OS cells, which were then lysed in RIPA buffer. After a brief sonication, cell lysates were precleared with protein G beads for 1 h. The supernatants were then incubated with anti-Myc (9E10) antibody and protein G beads overnight. For the interaction of HDAC4 and SIRT1, 293T cells coexpressing SIRT1 and HDAC4 were lysed in 170 mM NETN and incubated with 9E10 antibody and protein G beads. In both cases, the immunoprecipitation products were analyzed by Western blotting using an anti-FLAG antibody to detect immunoprecipitated HDAC4.
Myogenic conversion assay. Polyamine-based transfection (Genejammer; Stratagene) was carried out to transiently transfect 10T1/2 cells using company-provided instructions. Twenty-four hours after transfection, the growth medium (GM) was switched to differentiation medium (DM) (DMEM with 2% horse serum). Four days later, the cells were harvested and lysed in cracking buffer containing 4 M urea (27). The muscle cell differentiation marker myosin heavy chain (MHC) was detected in 30-µg aliquots of protein by a Western blot using anti-MHC antibody (MF20).
In vitro sumoylation assay. Recombinant SUMO-1, SAE-1, and SAE-2 were expressed as glutathione S-transferase (GST) fusion proteins using the pGEX series of plasmids. H6-tagged Ubc9 was expressed from plasmid pET15b-Ubc9, which contains the Ubc9 cDNA as an XhoI/BamHI fragment. Recombinant HDAC4 was purified from a baculovirus expression system. In vitro sumoylation reactions were carried out in 20 µl of reaction buffer as described previously (36), supplemented with 2 mM ATP. One hundred nanograms of GST-SAE1, 150 ng of GST-SAE2, 50 ng of H6-Ubc9, 1 to 2 µg of SUMO-1, and 1 to 2 µl of in vitro-translated, 35S-labeled MEF2D were added to the reaction mix. Reactions were carried out for 45 min at 30°C and analyzed by SDS-polyacrylamide gel electrophoresis. Quantitation was performed using a PhosphorImager (Molecular Dynamics). After subtraction of the background, the sum of the signal for modified plus unmodified MEF2 in each lane was set to 100%, and the relative values are given accordingly.
Luciferase reporter assay. 10T1/2 cells were transfected by using the Genejammer transfection reagent (Stratagene) in 24-well plates with plasmids for the MCK-Luc reporter (0.4 µg), MEF2D or the MEF2D K424R (I423A) mutant (0.2 µg), MyoD (10 ng), and pCMX-ßGal (0.1 µg). Twenty-four hours after transfection, cells were collected, and the luciferase activity was measured and normalized by the ß-galactosidase activity as previously described (45).
| RESULTS |
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To determine whether HDAC4 has the activity to promote MEF2 sumoylation directly, we examined the effect of recombinant HDAC4 on MEF2 sumoylation in a reconstituted system in vitro. To this end, in vitro-translated MEF2D was incubated with purified recombinant SUMO E1-activating enzymes (SAE1/SAE2), E2 Ubc9, and SUMO-1 in the presence or absence of recombinant HDAC4. As shown in Fig. 2C, a small population of MEF2D becomes sumoylated after incubation with the reconstituted SUMO machinery (upper panel, lanes 1 and 2). Significantly, the addition of purified recombinant HDAC4 to the reaction dramatically increases the production of sumoylated MEF2D, with a concomitant reduction in the unmodified species (Fig. 2C, lanes 3 to 5). Quantification of these experiments revealed that recombinant HDAC4 can stimulate MEF2D sumoylation more than fivefold in a dose-dependent manner (Fig. 2C, lower panel). These results strongly support a direct role for HDAC4 in promoting MEF2 sumoylation.
A sequence analysis of MEF2D revealed the presence of one consensus sumoylation motif surrounding lysine 424. Notably, this motif is highly conserved and can be found in most isoforms of MEF2 from different animal species (Fig. 2D). Supporting the hypothesis that lysine 424 is the key SUMO acceptor, the conversion of lysine 424 to arginine (K424R) completely abrogates HDAC4-dependent MEF2D sumoylation in cells (Fig. 2E) and in the in vitro assay (data not shown). Together, these results demonstrate that HDAC4 can stimulate MEF2 sumoylation on lysine 424 both in vivo and in vitro.
MEF2D lysine 424 is subject to reversible acetylation catalyzed by CBP and SIRT1. Recently, several lysine-targeting modifications, such as acetylation, sumoylation, and ubiquitination, have been reported as important modulators of transcription (7). Our observation that HDAC4, a protein deacetylase, can stimulate MEF2 sumoylation prompted us to ask whether MEF2 is also subject to lysine acetylation. To test this, we first determined whether MEF2 can be acetylated by the acetyltransferase CBP, which has been shown to promote MEF2 activity and is essential for C2C12 cell differentiation (6, 33). As shown in Fig. 3A, we found that wild-type CBP can potently induce MEF2D acetylation. An enzymatically deficient mutant of CBP fails to do so. Importantly, mutation of the SUMO acceptor lysine 424 dramatically reduces CBP-induced MEF2 acetylation (Fig. 3B), revealing lysine 424 as the major acceptor for both acetylation and sumoylation and suggesting a potential interplay of these two lysine-targeting modifications in regulating MEF2 function.
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SUMO modification negatively regulates MEF2 activity. Since acetylation and sumoylation both target lysine 424 (Fig. 2E and 3B) and since acetylation positively correlates with MEF2 activity during the muscle cell differentiation process (Fig. 4C), we hypothesized that HDAC4-induced sumoylation negatively regulates MEF2 activity. To examine this, we coexpressed MyoD with wild-type or sumoylation-deficient mutant (MEF2D K424R) MEF2D and assessed their ability to activate a luciferase reporter controlled by the muscle creatine kinase (MCK) enhancer. Consistent with previous reports, wild-type MEF2D and MyoD activate the MCK reporter cooperatively (Fig. 5A, upper panel). Importantly, the sumoylation-deficient mutant MEF2D K424R is consistently more active than wild-type MEF2D in collaborating with MyoD to activate the MCK reporter (Fig. 5A, upper panel), suggesting that sumoylation negatively regulates MEF2 activity. A similar conclusion was made by assessing the transcriptional activity of another sumoylation-deficient mutant, MEF2D I423A (Fig. 5A, upper panel), in which the sumoylation consensus site (IKSE) was destroyed in order to eliminate only MEF2 sumoylation but still keep acetylation (Fig. 5A, lower panel). To further confirm that sumoylation negatively regulates MEF2D activity, we fused SUMO to MEF2D to mimic sumoylated MEF2. Both the SUMO-MEF2D and SUMO-MEF2DK424R fusion proteins fail to synergize with MyoD in activating the MCK-luciferase reporter (Fig. 5B) or a reporter driven by tandem MEF2 binding sites (data not shown). These data support the idea that sumoylated MEF2 is transcriptionally inactive. Lastly, we examined the activity of sumoylation-deficient MEF2 in converting 10T1/2 fibroblasts to myocytes. As shown in Fig. 5C, coexpression of the sumoylation-deficient MEF2D mutant with MyoD induces MHC in 10T1/2 fibroblasts more potently than that of wild-type MEF2. Together, our data indicate that the conjugation of SUMO down-regulates MEF2 activity.
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| DISCUSSION |
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Supporting the idea that the interaction between HDAC4 and Ubc9 is functional, we found that HDAC4 can be sumoylated (Fig. 1C). This observation is consistent with two earlier reports (19, 36). However, unlike a previous report (19), our analysis of an HDAC4 sumoylation-deficient mutant did not uncover obvious defects, indicating that the sumoylation of HDAC4 itself might not be important (Fig. 1D and data not shown). Instead, we found that the HDAC4-Ubc9 interaction efficiently stimulates MEF2 sumoylation (Fig. 2B and C). Consistent with this notion, HDAC5, which also interacts with Ubc9 but is not itself sumoylated, can stimulate MEF2 sumoylation effectively (Fig. 2B). Importantly, HDAC members without the Ubc9-interactive coiled-coil domain, such as HDAC6 and HDAC1, cannot promote MEF2 sumoylation (Fig. 2B, lanes 5 and 7). Furthermore, well-characterized SUMO E3s, such as PIAS1 and PIASy, do not increase MEF2 sumoylation either (Fig. 2B and data not shown). Together, these data demonstrate that HDAC4 and its related family member HDAC5 can specifically stimulate MEF2 sumoylation.
Like protein ubiquitination, the efficient conjugation of SUMO to its protein substrates usually employs three enzymes. While the E1 activating enzyme and the E2 conjugating enzyme Ubc9 are sufficient to link SUMO to certain target proteins, an E3 ligase can significantly facilitate this process by simultaneously binding to both the E2 enzyme and the substrate protein (reviewed in reference 15). Thus, as with the RING finger E3 ubiquitination ligases, SUMO E3 enzymes function as adaptors to physically bring the E2 and substrate proteins together. In this report, we show that HDAC4 interacts with both SUMO E2 Ubc9 and MEF2. HDAC4 can significantly stimulate MEF2 SUMO modification both in vivo and in vitro (Fig. 2B and C). Like other SUMO E3 ligases, such as PIAS and RanBP2, HDAC4 itself is also sumoylated, probably as a by-product of its association with Ubc9 (19, 20, 30). These data reveal that HDAC4, a histone deacetylase, has all the properties expected for a MEF2 SUMO E3 ligase. These surprising findings suggest that HDAC4 and related members, such as HDAC5, possess SUMO E3 ligase activity and could regulate gene transcription via a novel mechanism by promoting protein sumoylation.
Recently, Gregoire and Yang described that HDAC4 can promote the modification of MEF2 by two other SUMO family members, SUMO-2 and -3 (10). However, the exact role of HDAC4 in this process is not known. Our study supports the conclusion that HDAC4 functions as a SUMO-1 E3 ligase, which can also be true for SUMO-2/3 conjugation. However, we have looked for a SUMO-2/3 modification of endogenous MEF2 but have not observed it in either undifferentiated or differentiated C2C12 cells. This discrepancy may be due to tissue type-specific modifications of MEF2 by different SUMO family members. Different signals could regulate the activity of HDAC4 to preferentially conjugate either SUMO-1 or SUMO-2/3 on MEF2 in different tissues. Alternatively, the desumoylation machinery may also be tissue specific. Regardless of the details, our observations suggest a complex regulation of MEF2 by sumoylation.
We have observed an inhibitory effect of SUMO modification on MEF2 activity. This is consistent with the role of HDAC4 as a transcription repressor. Similar results have also been reported by Gregoire and Yang for a Gal-4-MEF2D fusion protein (10). The exact mechanism(s) by which sumoylation regulates protein function remains unclear. Sumoylation has been shown to affect protein stability and to direct target proteins to promyelocytic leukemia nuclear bodies (reviewed in references 28 and 35). Our analysis, however, did not detect a significant effect of sumoylation on either the stability or subcellular localization of MEF2 (data not shown). SUMO has also been shown to recruit HDAC2 (40), and a similar mechanism could be involved in regulating MEF2 activity. For this report, we found that MEF2 is subject to both sumoylation and acetylation. MEF2 acetylation is positively correlated with its activation upon muscle cell differentiation and is catalyzed by its coactivator, CBP (Fig. 3A and 4C). In contrast to acetylation, sumoylation appears to inhibit MEF2 activity (Fig. 5). Importantly, we have found that both sumoylation and acetylation target lysine 424 of MEF2 (Fig. 2E and 3B). Together, these observations raise the possibility of a competition between these two modifications for this lysine residue, and this interplay might result in activation or repression of MEF2 activity. However, we have also found that both acetylation and sumoylation are very transient and dynamic processes. For example, endogenous MEF2 acetylation could only be detected when we treated C2C12 cells with the SIRT1 inhibitor nicotinamide (Fig. 4C). To detect the endogenous SUMO-1 modification of MEF2 in C2C12 cells, large amounts of cell lysates were needed (Fig. 2A). These observations argue that a sustained modification may not be required for the biological functions of acetylation or sumoylation. A similar concept has been proposed in several reports (9, 13, 35). Recently, it has also been suggested that SUMO can regulate the long-term fate of its target proteins despite being rapidly deconjugated from them (14). We believe that this potentially transient nature makes it technically very difficult to detect an inverse relationship between MEF2 acetylation and sumoylation. Nevertheless, on the biochemical level, since both acetylation and sumoylation are conjugated on the
-amino group of the lysine side chain, once this lysine is occupied by one of these modifications, it cannot be available for others at any given time. Indeed, a recent report on Sp3 sumoylation reached a similar conclusion (31). In conjunction with the proposed competition between acetylation and ubiquitination on specific lysine residues in p53 and Smad7 (11, 16, 31), our study provides evidence further supporting the importance of the interplay between these lysine-targeting modifications in regulating gene transcription.
How acetylation changes MEF2 activity is not clear. It has been demonstrated that acetylation can modify transcription factor activity by increasing the DNA binding activity, stability, or interaction with other transcription components. While not excluding these possibilities, it is interesting that while the MEF2 K424R mutation affects both sumoylation and acetylation, another SUMO-deficient MEF2D mutant (I423A) can still be acetylated by CBP (Fig. 5A). However, the transcriptional activities of I423A and K424R mutant MEF2D are comparable (Fig. 5A), suggesting that acetylation on lysine 424 is not essential for full MEF2D transcriptional activity. We speculate that the main function of MEF2 lysine 424 acetylation might be to block sumoylation and prevent MEF2 from entering a repressed state.
Surprisingly, we found that HDAC4 cannot catalyze MEF2 deacetylation efficiently. Instead, we identified a class III deacetylase, SIRT1, as a potent MEF2 deacetylase that dynamically catalyzes MEF2 deacetylation during muscle cell differentiation (Fig. 4C). These observations could provide a potential mechanism by which SIRT1 negatively regulates myogenesis (8). Interestingly, we found that SIRT1 can form a complex with HDAC4, suggesting the possibility that MEF2-dependent myogenesis could be controlled by a dual-deacetylase complex. It is reasonable to speculate that HDAC4 might function to integrate sumoylation and deacetylation signals via its interaction with Ubc9 and SIRT1 (Fig. 5D).
Overall, our data uncover a new biological property of a deacetylase to act as a SUMO E3 ligase for MEF2. In addition, we have described CBP-induced acetylation as another novel modification of MEF2 and identified SIRT1 as the MEF2 deacetylase. Furthermore, our data showing that acetylation and sumoylation occupy the same lysine residue provide a potential mechanistic framework for understanding the interplay between sumoylation and acetylation in regulating MEF2 activity. Taken together, our results have provided a comprehensive understanding of the regulation of MEF2 function by two distinct classes of deacetylases. Given the potential roles of class II and class III HDACs in the pathogenesis of cardiac hypertrophy and muscle cell differentiation (4, 8, 43), it will be of great interest to explore the significance and therapeutic implications of these different regulatory mechanisms of MEF2 in the future.
| ACKNOWLEDGMENTS |
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T.S. was supported by a grant from the Deutsche Forschungsgemeinschaft (Ste 1003/1) and the Howard Hughes Medical Institute (HHMI). X.Z. is supported by a Department of Defense Breast Cancer Research grant (DAMD 17-02-1-0380). T.A.B. is supported by a National Science Foundation graduate research fellowship. R.M.E. is an Investigator of the Howard Hughes Medical Institute at the Salk Institute and the March of Dimes Chair in Molecular and Developmental Biology. T.P.Y. is a Leukemia & Lymphoma Society Scholar.
| FOOTNOTES |
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