Myc-nick is a truncated form of Myc localized predominantly in the cytoplasm
While studying regulation of c-Myc degradation we noticed an inverse correlation between the levels of full-length c-Myc and a cytoplasmic 42KDa protein in anti-Myc immunoblots derived from confluent fibroblast cultures (). As described below, this protein, which we have named Myc-nick, is a cytoplasmic cleavage product of full-length c-Myc generated at high cell density (). Myc-nick is recognized by three antibodies against the N-terminal two-thirds of c-Myc (anti-Myc N262, 274, 143; and Fig. S1A) but not by anti- C-terminal antibodies (anti-Myc 9E10, C19; ). Furthermore, an anti-HA antibody immunoprecipitates Myc-nick from cytoplasmic extracts of cells expressing N-terminally HA-tagged c-Myc (). In addition, cytoplasmic Myc bearing N-terminal but not C-terminal epitopes is detected by imunofluorescence in confluent cultures (see below, ). Together, these results indicate that Myc-nick is a truncated protein lacking the C-terminal portion of c-Myc while preserving an intact N-terminus comprising Myc boxes I–III (). This makes Myc-nick distinct from any other previously identified form of Myc (see Introduction).
We have detected endogenously expressed Myc-nick in the cytoplasm of a large number of cell lines including HFF, Wi38, L-cells, HCT116, SW480, Hela (Fig. S1B), C2C12 (), 293T, A431, Rat1, U2OS, ES cells, mouse neurospheres (not shown), in addition to mouse tissues such as muscle, brain, cerebellum, ( and Fig. S7A). We also observed Myc cytoplasmic localization by immunofluorescence of confluent cultures of HFFs (, and Fig. S5A) and Rat1 myc-null cells (not shown) expressing c-myc. Therefore a protein with the size and properties of Myc-nick is very widely expressed. In some settings we observe relatively low and variable amounts of Myc-nick in the nucleus (e.g. ).
Myc-nick accelerates muscle cell differentiation
Myc-nick is product of c-Myc cytoplasmic cleavage independent of the proteasome
Myc-nick is generated by proteolytic cleavage of c-Myc in the cytoplasm
We considered the possibility that Myc-nick is generated in the cytoplasm because the nuclear export inhibitor Leptomycin B had no effect on the production or cytoplasmic localization of Myc-nick (). To determine whether a cytoplasmic activity could convert full-length c-Myc into Myc-nick we incubated in vitro translated [35S]-methionine labeled c-Myc or purified full-length recombinant c-Myc with nuclear or cytoplasmic extracts from Rat1 myc-null cells. Only cytoplasmic extracts (CE) were capable of producing a protein () having the same apparent molecular weight as Myc-nick that was recognized by antibodies against the N-terminus, but not C-terminus of c-Myc (Fig. S2A). Increasing the incubation time with CE augmented Myc-nick production and decreased the amounts of full-length c-Myc input (). In agreement with our observations made in vivo, CE of dense cultures were more efficient in cleaving c-Myc than CE of sparse cultures (Fig. S2B). In experiments designed to characterize the cytoplasmic activity responsible for formation of Myc-nick we found that inhibitors of transcription or translation had no effect on Myc-nick formation () while heating or adding protease inhibitors to the CE blocked Myc-nick, consistent with proteolysis (). While MG132, an inhibitor of proteasome (and other cysteine proteases) blocked Myc nick formation, specific proteasome inhibitors such as Epoxomycin and Lactacystein failed to block the formation of Myc-nick in vitro and in vivo (). In addition, inhibition of either the Fbw7 or Skp2 degradation pathways, known to be responsible for proteasomal Myc turnover, had no effect on Myc-nick formation (data not shown). Moreover, incubation of Myc with 20S and 26S proteasomes failed to produce Myc-nick (not shown). These results indicate that full-length c-Myc is converted into Myc-nick by a cytoplasmic protease that is independent of the proteasome.
Myc is cleaved by a calcium-activated calpain to produce Myc-nick
In a systematic search for the proteases mediating cytoplasmic cleavage of Myc we ruled out both caspases and lysosomal proteases on the basis of inhibitors and cleavage conditions (Fig. S2C). However, we found that all calpain inhibitors tested including calpeptin, calpain inhibitor XII () and Calpain inhibitor VI () blocked the formation of Myc-nick in vitro and in vivo. Moreover, MG132, while well known as a proteasome inhibitor has also been shown to inhibit calpains (Mailhes et al., 2002
). Calpains had been linked to Myc stability earlier, but the antibodies used in those studies would not have detected Myc-nick (Gonen et al., 1997
; Small et al., 2002
). Calpains comprise a large family of calcium-dependent cytoplasmic cysteine proteases that function at neutral pH and are primarily associated with partial protein cleavage rather than complete protein degradation. The most well studied members of this family are mcalpain and μcalpain. These ubiquitously expressed catalytic subunits form functional heterodimers with a calpain regulatory subunit (calpain r) to bind calcium. To determine whether Myc-cleavage is regulated by calcium-activated calpains, we employed siRNA to knockdown calpain r in cells expressing c-Myc either endogenously or under control of a retroviral vector. In both settings a partial silencing of calpain r correlated with decreased Myc-nick and increased full-length c-Myc (). Knockdown of m or μcalpains alone did not block the formation of Myc-nick, most likely due to the presence of other redundant calpains (not shown). Because calpain activity is calcium dependent we next examined the effects on Myc-nick of modulating calcium levels. Treatment with the calcium chelators Bapta or EGTA reduced the ability of CEs to cleave c-Myc (). Incubation of either IVT c-Myc () or recombinant c-Myc () with purified m or μ calpain (together with calpain r) produced Myc-nick. These results demonstrate that Myc-nick is directly generated by calcium dependant calpain cleavage of full-length c-Myc.
Myc-nick is generated by calpain cleavage of full-length Myc
Lysine 298 is the primary calpain cleavage site in c-Myc
To map the calpain cleavage region on c-Myc, we used a series of internal deletion mutants lacking 60 residue segments (c-Myc ΔA-ΔG) (Tworkowski et al., 2002
) () and determined whether any failed to generate a shorter c-Myc protein. Only the deletion of residues 252–315 (ΔE) resulted in loss of a Myc-nick-like product (). This region contains a high scoring PEST domain, often present in unstable proteins and frequently associated with calpain cleavage sites. We further narrowed our search to residues 270–315, based on the ability of antibody 274 to detect Myc-nick (Fig. S1A and ). While there is no universal consensus for a calpain cleavage site, a comparison of 106 sites present in 49 known calpain substrates indicated a preference for calpain cleavage after K or R, and to lesser extent Y especially when these amino acids are flanked by P, V, and L () (Tompa et al., 2004
). We noted a region localized C-terminal to the PEST domain containing the sequence PLVLKRC (, marked in red). This region is evolutionarily conserved in c-Myc and N-Myc but not L-Myc (Fig. S3A), consistent with the fact that c-Myc and N-Myc, but not L-Myc, are cleaved (Fig. S3B,C). To determine whether this region functions as a calpain cleavage site we synthesized a 10 amino acid peptide corresponding to the putative c-Myc calpain cleavage region (291–300) and to another a nearby region of c-Myc (236–245) (, in red and blue respectively) and asked whether they could act as competitive inhibitors of Myc-nick formation in vitro. Addition of increasing amounts of the peptide containing the putative calpain cleavage site blocked the formation of Myc-nick in vitro while the control peptide had no effect (). Next, we generated a deletion mutant of Myc lacking residues 291–300 and found it to be resistant to cleavage by CE (). When this mutant was ectopically expressed in 293T cells the cleavage was also reduced in comparison to the wild type c-Myc (), indicating that this is the major calpain cleavage site within c-Myc. Next, we made point mutations in the calpain cleavage region (labeled with asterisks in ), and assessed their cleavage. We found that the K298A mutation reduced the cleavage of c-Myc in vitro () and in vivo when ectopically expressed in 293T cells (). Although K298 appears to be the major calpain cleavage site, a K298A mutant was still cleaved in vivo most likely because when this residue is mutated the cleavage is shifted to R299 (and perhaps L297, V296). We also identified weaker calpain cleavage sites localized in the C-terminus of Myc that become more pronounced in the cleavage deficient mutants.
Expression of Myc-nick alters cell morphology and increases acetylation of α-tubulin
To study Myc-nick function we generated a truncated form of Myc containing amino acids 1–298 (referred to as Myc-nick*). We found that ectopically expressed Myc-nick* is localized predominantly to the cytoplasm and migrates on SDS-PAGE with the same apparent molecular weight as Myc-nick generated by cleavage of full-length c-Myc (). Myc-nick is degraded at a comparable rate to full-length c-Myc with a half-life of about 30 minutes (data not shown). Because Myc-nick contains the MBI phosphodegron, with its GSK3β phosphorylation and Fbw7 binding sites, we would expect Myc-nick to be degraded through similar proteasomal pathways as full-length Myc. Indeed, blocking proteasome activity by pharmacological inhibitors or by silencing E3 ligases and components of the proteasome induced the stabilization of both full-length Myc and Myc-nick (data not shown). Calpain inhibitors are incapable of inducing accumulation of Myc-nick, indicating that calpains are unlikely to play a major role in Myc-nick turnover in vivo.
The expression of Myc-nick* promotes changes in cell morphology
While overexpression of full-length c-Myc in Rat1a myc-null fibroblasts is associated with increased proliferation and apoptosis, the ectopic expression of Myc-nick* had no detectable effect on either cell doubling time or survival (data not shown). However, Myc-nick* expressing cells displayed dramatic morphological changes - they appeared spindle-like with long protrusions that occasionally formed intercellular contacts (, Fig. S4, Fig. S5C). This morphology was specific for Myc-nick* expression and could not be produced by expressing the C-terminal 100 residues of c-Myc (not shown). Introducing a scratch wound across a confluent cell monolayer showed that while control cells migrated into the wound by extending lamellipodia, Myc-nick* expressing cells aligned parallel to each other and extended long protrusions into the wound ().
The morphological changes induced by Myc-nick* are suggestive of altered cell-cell contacts and/or major cytoskeletal reorganization. The elongated cellular protrusions present in Myc-nick expressing cells resemble specialized structures formed by stable microtubules. Because stable microtubules display increased acetylation of α-tubulin on Lysine 40 (Hubbert et al., 2002
) we stained Myc-nick* expressing cells with antibodies against α-tubulin and acetylated α-tubulin. shows that while acetylated α-tubulin immunostaining in vector and c-Myc expressing cells is low, Myc-nick* cells display intense staining of elongated structures (). This was confirmed by immunoblotting for acetylated α-tubulin in Rat1 myc-null or 293T cells expressing Myc-nick* (; Fig. S6B). Importantly neither the levels of total cellular acetylated lysine (Fig. S6A) nor the levels of tyrosinated tubulin (not shown), were affected. To ask whether Myc-nick* expression increased microtubule stability, we treated cells expressing Myc-nick*, c-Myc or vector with nocodozole for 15’. This treatment disrupts unstable microtubules with a half-life of about 10 minutes, but not stable microtubules with a half-life >2 hours. Only Myc-nick* expressing cells possessed microtubules that survived nocodozole treatment and these stained strongly with anti-acetylated α-tubulin ().
Myc-nick* cells display increased levels of acetylated (-tubulin and microtubule stabilization
Myc-nick interacts with α- and β- tubulins
We observed partial cytoplasmic co-localization between Myc and α-tubulin in several cell types expressing c-Myc or Myc-nick (; Fig. S5A–C). Using 293T cells expressing GFP-tubulin and Myc-nick we performed immunoprecipitation with anti-GFP and immunobloted with anti-Myc. Myc-nick was co-immunoprecipitated with GFP-tubulin but not GFP-EB1, a microtubule binding protein (Fig. S5D). In addition, immunoprecipitation of either c-Myc or endogenous α-tubulin from cytoplasmic extracts indicated that Myc-nick interacts with α-tubulin in vivo (). To examine in vitro interactions we incubated 35
[S]-methionine labeled IVT c-Myc with purified brain tubulins for 1h, then immunoprecipitated α, β, γ, pIII and acetylated α-tubulin and exposed the gel to detect radioactive Myc. Full-length c-Myc was co-immunoprecipitated mostly with β-tubulin (Fig. S5E middle panel). We also incubated IVT c-Myc with CE for 1h to produce Myc-nick and then performed immunoprecipitation for tubulins as above. The results showed that Myc-nick interacts with α- and β-tubulin (Fig. S5E upper panel). The binding of Myc-nick to tubulin is consistent with the previous report of an N-terminal region of Myc capable of associating with tubulin (Alexandrova et al., 1995
Myc-nick directly regulates α-tubulin acetylation through GCN5
Because Myc-nick lacks the Myc C-terminal dimerization and DNA binding domains, we surmised that the increase in acetylated α-tubulin induced by Myc-nick* expression is independent of Myc transcriptional activity. One possibility is that Myc-nick recruits an acetyltransferase microtubules. We observed marked acetylation of α-tubulin in cytoplasmic extracts incubated in the presence of either recombinant c-Myc () or of IVT c-Myc ( and Fig. S6C). Importantly, Myc proteins are known to associate with the acetyltransferases GCN5, and TIP60 (Frank et al., 2003
; Sterner and Berger, 2000
) via TRRAP that interacts with MBII (residues 106–143) (McMahon et al., 1998
). We therefore tested a Myc-nick deletion mutant lacking Myc box II (ΔMBII) and found that its ability to promote α-tubulin acetylation was reduced (). In addition, the ΔMBII Myc-nick* mutant failed to induce the cell morphological changes that we had detected with WT Myc-nick* while a comparably sized deletion in a region adjacent to MBII was similar to wild type ().
c-Myc and the HAT GCN5 promote α-tubulin acetylation
The dependence on MBII for tubulin acetylation and altered cell morphology suggests involvement of the acetyltranferases known to bind this region. We detected substantial amounts of GCN5 and TRRAP in the cytoplasm (Fig. S6D), while Tip60 was predominantly nuclear (not shown). To test GCN5’s involvement in α-tubulin acetylation we performed siRNA-mediated knockdown of TRRAP and GCN5 in Myc-nick* expressing cells and found that decreasing either one of these proteins reduced the levels of acetylated α-tubulin () and reverted the changes in cell morphology induced by Myc-nick to that of vector infected cells (). Moreover, GCN5 co-immunoprecipated with α-tubulin and Myc in cytoplasmic extracts of 293T cells transfected with GCN5 ().
Both ectopic expression of GCN5 in 293T cells (), and addition of full-length recombinant GCN5 to cytoplasmic extracts ( upper panel), resulted in increased levels of acetylated α-tubulin. The addition of Myc further increased the levels of α- tubulin acetylation induced by GCN5 in cytoplasmic extracts (). Full-length recombinant GCN5 also induced the acetylation of α-tubulin present in assembled microtubules () and synergized with c-Myc to promote further acetylation (, compare lanes 1 to 4 and 2 to 5). The GCN5 catalytic domain alone was sufficient to induce α- tubulin acetylation, but no synergy with Myc was detected, most likely because association between these two proteins occurs outside of GCN5’s active site (). As a further control we tested p300, a HAT that binds the C-terminus of Myc (Faiola et al., 2005
). P300 neither induced tubulin acetylation nor did it synergize with Myc ( bottom panels). These data indicate that GCN5 can specifically acetylate tubulin and that Myc augments tubulin acetylation by binding to tubulin and recruiting GCN5.
Myc-nick is produced in differentiating cells and tissues
When examining the expression of Myc-nick in adult mouse tissues, we found that brain, cerebellum and skeletal muscle express significantly higher levels of Myc-nick than any other tissue (, Fig. S7A). Interestingly, both neuronal and muscle differentiation require major cytoskeletal rearrangements that have been associated with increased microtubule stability and elevated levels of acetylated α-tubulin. For example it has been demonstrated that the acetylation of α-tubulin by the Elp3 acetyltransferase is required for proper cortical neuronal migration and differentiation (Creppe et al., 2009
). Increased levels of acetylated α-tubulin are found during myogenic differentiation (Gundersen et al., 1989
). Importantly, inhibiting the activity of the deacetylases HDAC6 and Sirt2 (known to deacetylate α-tubulin) generates augmented levels of acetylated α-tubulin, promotes differentiation of myoblasts (Iezi et al., 2004). Furthermore, the presence of the primary cilium, a microtubule based antenna-like structure composed of acetylated α-tubulin, is essential for cardiomiocyte differentiation (Clement et al., 2009
The extensive cytoskeletal changes that occur during muscle differentiation are regulated by calcium and calpains (Dedieu et al., 2004
). The inhibition of calpain activity either by pharmacological inhibitors or by overexpression of Calpastatin (an endogenous inhibitor of calpains) blocks muscle cell differentiation (Dedieu et al., 2004
). In addition, both types of ubiquitous calpains (m and μ) were shown to regulate muscle cell differentiation in vitro (Moyen et al., 2004
). Moreover, mutations in the Calpain 3 gene (the muscle specific Calpain) cause limb girdle muscle dystrophy 2A (LGMD2A) (Richard et al., 1995
). Finally, knocking out Calpain r (the regulatory subunit shared by all calcium dependent calpains) is lethal due to impaired cardiovascular development (Arthur et al., 2000
To study the cleavage of Myc to Myc-nick during the process of muscle differentiation, we employed human primary myoblasts purified from pectoral girdle, mouse myoblasts purified from hindlimb muscles, and C2C12 cultured mouse myoblasts. When stimulated to differentiate, these cells displayed low levels of full-length c-Myc and high levels of Myc-nick when compared to undifferentiated cycling cells (; Fig. S7B). Interestingly, Myc-nick levels were higher in a Rhabdomyosarcoma cell line from the alveolar subtype (), a very aggressive tumor derived from partially differentiated muscle cells.
The increased levels of Myc-nick in differentiated primary mouse myoblasts correlates with an increase in Calpain 3 levels (; Fig. S7B) and in total calpain activity (). Similarly, when C2C12 cells were stimulated to differentiate they also displayed an increase in total calpain activity (Fig. S7C) and in the ability to cleave Myc in vitro (Fig. S7D). Importantly, the levels of acetylated α-tubulin were also elevated during the process of differentiation (; Fig. S7B, F). Acetylation of α-tubulin is accompanied by myoblast fusion to form multinucleated myotubes (; Fig. S7F). When myoblasts are stimulated to differentiate they fuse into multinucleated myotubes. In addition to displaying increased levels of acetylated α-tubulin, these myotubes show decreased immunostaining for nuclear Myc and increased cytoplasmic Myc staining (). Conversely, undifferentiated satellite cells in the same culture display nuclear staining for Myc (Fig. S7E). This is consistent with our results showing conversion of full-length Myc into predominantly cytoplasmic Myc-nick.
In C2C12 cells, concomitant with increased Myc-nick abundance we observed a decrease in Myc-nick phosphorylation at threonine 58 (T58) after the switch to differentiation conditions (). Phospho-T58 mediates Fbw7-dependent degradation of Myc by the proteasome. Decreased phosphorylation at this site is consistent with the notion that stabilization of Myc-nick contributes to its elevated levels. Interestingly we found that Myc-nick phosphorylation at T58 is also reduced in adult muscle, brain and cerebellum (Fig. S7A and data not shown).
In summary, we found that during muscle differentiation there is an increase in Myc-nick, concomitant with an elevation in calpain activity and tubulin acetylation (; ; Fig. S7B–D; Fig. S7F).
Myc-nick accelerates muscle differentiation
We examined the effects of ectopic expression of Myc-nick* in human primary myoblasts isolated from the pectoral girdle () and rectus abdominus (), the human rhabdomyosarcoma cell line RD (), and in C2C12 cells (). In all cells we found that Myc-nick* expression accelerated muscle cell differentiation, augmented α-tubulin acetylation, and elevated expression of muscle specific proteins (). The expression of Myc-nick* in C2C12 myoblasts promoted an increase in cell fusion not only in confluent cultures (; Fig. S7H), but also in sparse cultures (Fig. S7G). The role of Myc-nick in promoting muscle cell differentiation is partially dependent on MBII, since the differentiation of RD and C2C12 cells by Myc-nick can be delayed, but not inhibited by the deletion of MBII (; Fig. S7I).
To examine the requirement for Myc-nick production during differentiation further, we first tested calpain inhibitor XII and found that it reduces differentiation and tubulin acetylation (Fig. S7J). Next we employed c-Myc mutant (Δ291–300) which is deficient in cleavage to Myc-nick. Similar to full-length wt c-Myc, this mutant can induce proliferation, apoptosis, fibrillarin expression, and phosphorylated H2AX in Rat1 myc-null cells (Fig. S7L–M). However the Δ291–300 c-Myc mutant significantly reduces C2C12 cell differentiation when compared to c-Myc, even though the proteins are expressed at equal levels. While full-length c-Myc only blocks the fusion of C2C12 myoblasts, the c-Myc mutant (Δ291–300) with reduced ability to generate Myc-nick, dramatically reduces the expression of muscle markers in addition to blocking fusion (Fig. S7N–O).
Myc-nick renders Rat1 myc-null cells competent to differentiate
MyoD has been long known to induce the transdifferentiation in diverse cell types. We found that MyoD induces expression of muscle-specific markers in Rat1 fibroblasts but not in Rat1 myc-null fibroblasts (), indicating that myc is necessary for the transdifferentiation process. Expressing Myc-nick together with MyoD in myc+/+ Rat1 fibroblasts further elevated the levels of muscle specific markers and promoted cell fusion compared to MyoD alone (). Importantly, we find that in Rat1 myc-null cells, the co-expression of Myc-nick (Fig. S7K) permitted transdifferentiation to muscle in response to MyoD (). This experiment indicates that Myc-nick is sufficient for Myo-D induced transdifferentiation supporting the idea that conversion of full-length Myc to Myc-nick is important in MyoD induced differentiation.