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J. Biol. Chem., Vol. 276, Issue 35, 33111-33120, August 31, 2001
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From the Department of Molecular and Cellular Biology, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582 and CREST, Japan Science and Technology
Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
Received for publication, March 28, 2001, and in revised form, June 6, 2001
The U box is a domain of ~70 amino acids that
is present in proteins from yeast to humans. The prototype U box
protein, yeast Ufd2, was identified as a ubiquitin chain assembly
factor that cooperates with a ubiquitin-activating enzyme (E1), a
ubiquitin-conjugating enzyme (E2), and a ubiquitin-protein ligase (E3)
to catalyze ubiquitin chain formation on artificial substrates. E3
enzymes are thought to determine the substrate specificity of
ubiquitination and have been classified into two families, the HECT and
RING finger families. Six mammalian U box proteins have now been shown
to mediate polyubiquitination in the presence of E1 and E2 and in the
absence of E3. These U box proteins exhibited different specificities
for E2 enzymes in this reaction. Deletion of the U box or mutation of
conserved amino acids within it abolished ubiquitination activity. Some U box proteins catalyzed polyubiquitination by targeting lysine residues of ubiquitin other than lysine 48, which is utilized by HECT
and RING finger E3 enzymes for polyubiquitination that serves as a
signal for proteolysis by the 26 S proteasome. These data suggest that
U box proteins constitute a third family of E3 enzymes and that E4
activity may reflect a specialized type of E3 activity.
The abundance of cellular proteins is regulated by a balance
between their synthesis and degradation, and such regulation is central
to many cellular functions. Two predominant pathways for the
degradation of cellular proteins have been identified: the vacuolar
pathway (mediated by lysosomes, endosomes, and the endoplasmic
reticulum, for example) and the cytoplasmic ubiquitin-mediated pathway.
The ubiquitin proteolytic pathway plays an important role in the
degradation of short lived regulatory proteins (1), including those
that participate in the cell cycle, cellular signaling in response to
stress and to extracellular signals, morphogenesis, the secretory
pathway, DNA repair, and organelle biogenesis (2, 3). This pathway
includes two distinct steps as follows: the covalent attachment of
multiple ubiquitin molecules to the protein substrate, and the
degradation of the ubiquitinated protein by the 26 S proteasome
complex. The system responsible for ubiquitin attachment consists of
several components that act in concert (4, 5). A ubiquitin-activating
enzyme (E1),1 with ATP as a
substrate, catalyzes the formation of a thioester bond between itself
and ubiquitin and then transfers the activated ubiquitin to a
ubiquitin-conjugating enzyme (E2). Whereas some E2s transfer ubiquitin
directly to a substrate, others require the participation of a third
component, termed a ubiquitin-protein ligase (E3). E3 is thought to be
the component of the ubiquitin conjugation system that is most directly
responsible for substrate recognition (5, 6).
Despite the large number of protein substrates for the ubiquitin
proteolytic pathway, relatively few E3s have been characterized at the
molecular level. The amino acid sequences of E3s are known include
members of the homologous to E6-AP COOH terminus (HECT) family (7) and
members of the RING finger-containing family (8-10). HECT family E3s
include E6-AP, which targets p53 for ubiquitination in the presence of
human papilloma virus E6 (11), and Nedd4, which ubiquitinates
epithelial Na+ channel subunits (12). E3s that contain a
RING finger, a motif defined by a total of eight cysteine and histidine
residues that coordinate two zinc ions, include those that mediate
protein degradation according to the N end rule (13); Mdm2, which
catalyzes both its own ubiquitination and that of p53 (14, 15); c-IAP1
and XIAP, which prevent apoptosis (16); Cbl, which targets the receptor for epidermal growth factor (17, 18); the anaphase-promoting complex/cyclosome (APC/C), which ubiquitinates mitotic cyclins and
anaphase inhibitors (securins) (19, 20); and the SCF complexes, whose
substrates include G1 cyclins, cyclin-dependent
kinase inhibitors, I A new class of ubiquitination enzyme (termed E4), the prototype of
which is yeast Ufd2, was recently identified (35). Together with E1
(Uba1), E2 (Ubc4), and a HECT-type E3 (Ufd4), E4 (Ufd2) is required for
the assembly of a polyubiquitin chain on artificial substrates that
consist of proteins fused to ubiquitin at their NH2 termini
and that are preferentially targeted for degradation. In yeast, Ufd2 is
implicated in cell survival under stress conditions and is associated
with Cdc48, which belongs to the large family of AAA-type ATPases that
are thought to possess protein folding activity. Ufd2 and its homologs
in other eukaryotes share a conserved domain designated the U box (35).
The U box of Ufd2 mediates the interaction of this protein with
ubiquitin-conjugated targets and therefore appears to be an essential
functional unit of E4 enzymes. The predicted three-dimensional
structure of the U box is similar to that of the RING finger, despite
the lack in the former of the hallmark metal-chelating residues of the
latter (36). This observation prompted us to investigate the
possibility that U box proteins in general possess the ability to
function as E3s in E2-dependent ubiquitination and that E4
activity might reflect a specialized type of E3 activity that targets
the ubiquitinated ubiquitin moiety fused to other proteins for further ubiquitination.
We now show that all six mammalian U box proteins tested mediate
ubiquitination in conjunction with E1 and E2 and in the absence of
other E3 components. Deletion of the U box domain or mutation of its
most conserved amino acid resulted in the loss of
E2-dependent ubiquitination activity, suggesting that this
activity depends on an intact U box. The U box proteins appeared to
catalyze their own ubiquitination as well as that of heterologous
substrates. One of these proteins, UFD2a, attached ubiquitin to lysine
residues of ubiquitin other than those at positions 29, 48, or 63, a
property that is not usually exhibited by HECT or RING
finger-containing E3s. These observations suggest that U box proteins
are indeed E3s, some of which may function as E4s to mediate the
assembly of polyubiquitin chains on proteins ubiquitinated by another
E3 enzyme.
Cloning of Mammalian U Box Protein cDNAs--
The sequences
of mouse UFD2a (accession number AI593754), UFD2b (accession number
AI390103), CHIP (accession number NM019719), and KIAA0860 (accession
numbers AB020667 and AW476623) cDNAs as well as those of human CYC4
(accession number HSU37219) and PRP19 (accession number XM006045)
cDNAs were obtained from the GenBankTM data base. The
cDNAs for UFD2a, UFD2b, CHIP, and KIAA0860 were amplified by the
polymerase chain reaction (PCR) with Taq polymerase (Takara,
Tokyo, Japan) from mouse testis cDNA (CLONTECH,
Palo Alto, CA), whereas those for CYC4 and PRP19 were amplified from human thymus cDNA or human brain cDNA, respectively. The PCR
primers were as follows: 5'-CAG TCA CTA CAG CAT TAC CTG GAG-3' and
5'-AGC GAC GAC AAC TAG GCA GAA TAG-3' for UFD2a; 5'-CCT TTT GGT CGC TGT AGC TGT GA-3' and 5'-TTC CAA GTA CAC ACA ACG GCT GGG-3' for UFD2b; 5'-GGC TGC GAG ATC TAG GTG-3' and 5'-CTT CCG TCT CCA GAT CCT-3' for
CHIP; 5'-TGC TTG GAA GCT ATT GTT CCA GTT-3' and 5'-TGG CCT GGC TTG GAA
GCC CCT GTG-3' for KIAA0860; 5'-GGC GCC ATG TCC CTA ATC TGC TCC-3' and
5'-GGC CTA CAG GCT GTA GAA CTT GAG-3' for CYC4; and 5'-GGC GCC ATG TCC
CTA ATC TGC TCC-3' and 5'-GGC CTA CAG GCT GTA GAA CTT GAG-3' for PRP19.
The amplified fragments were phosphorylated with T4 polynucleotide
kinase (New England Biolabs, Beverly, MA), subcloned into pBluescriptII
SK+ (Stratagene, La Jolla, CA), and sequenced. In the case
of UFD2a, UFD2b, and KIAA0860, the cDNA fragments were used as
probes to isolate full-length clones from a mouse T cell cDNA
library in Construction of Expression Plasmids and Mutagenesis--
The
entire coding regions of the U box protein cDNAs were subcloned
into pGEX-6P-1 (Amersham Pharmacia Biotech), pBacPAC9 (CLONTECH), pFASTBAC HTa (Life Technologies, Inc.),
or pcDNA3 (Invitrogen, Groningen, The Netherlands).
To generate U box deletion mutants of UFD2a or CHIP, we performed PCR
with pBluescriptII SK+ containing UFD2a or CHIP cDNA as
a template and with a sense primer beginning at the start codon and an
antisense primer beginning proximal to the U box. To generate a U box
deletion mutant (
Complementary DNAs encoding mouse UFD2a, UFD2b, CHIP, and KIAA0860 as
well as human CYC4 and PRP19 tagged at their NH2 termini with the FLAG epitope were generated by PCR, sequenced, and subcloned into pcDNA3 (Invitrogen). The plasmids pT7-7-Ubc2A, -Ubc2B, -Ubc3, -Ubc4, -UbcH5C, -UbcH6, -UbcH7, and -UbcH8 (Novagen, Madison, WI) were
kindly provided by H. Yasuda (Tokyo Pharmaceutical University), and
pCGN-HA-Ub was kindly provided by M. Nakao (Kumamoto University). A
cDNA encoding hemagglutinin epitope (HA)-tagged ubiquitin was generated by PCR with pCGN-HA-Ub as template, with a sense primer that
includes an EcoRI site, the HA tag sequence, and the
beginning of the ubiquitin coding region and with an antisense primer
that includes the ubiquitin stop codon and a XhoI site. The
resulting PCR product was subcloned into pGEX-6P-1. To generate the
various lysine residue mutants of ubiquitin, we performed site-directed mutagenesis with a Quick Change kit (Stratagene) and with mutated oligonucleotide primers corresponding to each lysine site.
Production of Recombinant Proteins in Bacteria--
Glutathione
S-transferase (GST) fusion proteins were expressed in
Escherichia coli strain DH5
His6-tagged proteins were expressed in E. coli strain BL21(DE3)pLysS (Novagen) incubated in the presence of
0.1 mM isopropyl- Baculovirus Expression System--
Baculoviruses were generated
in Sf9 cells with the use of BacPAK6 virus DNA and pBacPAK9-GST
containing the relevant cDNA (23). The recombinant proteins were
purified from Sf9 cell lysates according to the protocol
described for bacterially expressed GST fusion proteins. The plasmid
pFASTBAC HTa containing the relevant cDNA was subjected to
recombination with the baculoviral genome in HB10BAC, and the resulting
recombinant viral genome was introduced into Sf9 cells by
transfection in order to generate recombinant baculovirus. The infected
Sf9 cells were lysed, and the recombinant proteins were purified
by the protocol described for bacterially expressed
His6-tagged proteins. Only the purified recombinant proteins were detected by electrophoresis and Coomassie Blue staining.
Northern Blot Analysis--
Mouse and human multiple-tissue
Northern blots (CLONTECH) were subjected to
hybridization with U box protein or Production of Antibodies--
Polyclonal antibodies to UFD2a
were generated in rabbits by standard procedures with the use of a
synthetic peptide corresponding to residues 129-142 of mouse UFD2a
(MEVDENDRREKRSL) coupled to keyhole limpet hemocyanin.
Immunofluorescence Staining--
HeLa cells grown on glass
coverslips were transfected by calcium phosphate precipitation and
prepared for immunostaining as described (37). In brief, the cells were
fixed for 20 min at room temperature with 4% formaldehyde in PBS and
then incubated for 1 h at room temperature with a mouse monoclonal
antibody (M5) to the FLAG epitope (1 µg/ml) (Sigma) in PBS containing
0.1% bovine serum albumin and 0.1% saponin. They were then incubated
for 1 h at room temperature with Alexa 546-labeled goat polyclonal
antibodies to mouse immunoglobulin (Molecular Probes, Eugene, OR) at a
dilution of 1:500 and stained with Hoechst 33258 (Wako, Osaka, Japan). Cells were covered with a drop of GEL/MOUNT (Biomeda, Foster City, CA)
and then viewed and photographed with a Nikon Eclipse E800M microscope
equipped with a color chilled 3CCD camera (model C5810; Hamamatsu
Photonics, Hamamatsu, Japan).
Ubiquitination Assay--
The in vitro ubiquitination
assay was performed as described (8) with some modifications. In brief,
reaction mixtures (20 µl) containing 1 µg of GST-UFD2a, -UFD2b,
-CHIP, or -KIAA0860, or of His6-CYC4 or -PRP19, 0.1 µg of
recombinant rabbit E1 (Boston Biomedica, Cambridge, MA), 1 µl of
crude lysate of E. coli expressing UbcH5C or 1 µg of
purified UbcH5C, 0.5 units of phosphocreatine kinase, 1 µg of
ubiquitin (Sigma), 25 mM Tris-HCl (pH 7.5), 120 mM NaCl, 2 mM ATP, 1 mM
MgCl2, 0.3 mM dithiothreitol, and 1 mM creatine phosphate were incubated for 2 h at
30 °C. The reaction was terminated by the addition of SDS sample
buffer containing 4%
In some experiments, the ubiquitination reaction was terminated by the
addition of 400 µl of a solution containing 10 mM
Tris-HCl (pH 7.4), 150 mM NaCl, 1% Nonidet P-40, 0.1%
sodium deoxycholate, 0.1% SDS, 1 mM EDTA, 10 mM NaF, and 10 mM sodium pyrophosphate. After
incubation for 1 h at 4 °C with 50 µl of protein G-Sepharose beads (Amersham Pharmacia Biotech) and removal of the beads, the mixture was incubated first for 4 h at 4 °C with 5 µg of
mouse monoclonal antibodies to GST (kindly provided by S. Tanaka,
Hokkaido University) or antibodies to the FLAG epitope (M5) and then
for 4 h at 4 °C with protein G-Sepharose beads. The
immunoprecipitates were washed four times with an ice-cold solution
containing 50 mM Tris-HCl (pH 7.6), 300 mM
NaCl, 0.1% Triton X-100, aprotinin (10 µg/ml), leupeptin (10 µg/ml), 10 mM iodoacetamide, 1 mM
phenylmethylsulfonyl fluoride, 0.4 mM
Na3VO4, 0.4 mM EDTA, 10 mM NaF, and 10 mM sodium pyrophosphate and were
then subjected to immunoblot analysis with antibodies to ubiquitin,
horseradish peroxidase-conjugated antibodies to mouse immunoglobulin,
and ECL reagents.
For chelation experiments, glutathione-bound proteins were incubated
for 18 h at 4 °C with three changes of PBS containing 5 mM TPEN (Sigma). The TPEN-chelated GST fusion proteins were then washed with PBS and eluted from the glutathione-Sepharose 4B beads
with 50 mM Tris-HCl (pH 8.0) containing 10 mM
reduced glutathione (8).
In Vitro Transcription and
Translation--
35S-Labeled FLAG-Nedd4, -UFD2a, and
-KIAA0860 were synthesized with the use of a TNT Quick-coupled
Transcription/Translation System (Promega) and
[35S]methionine (ICN, Costa Mesa, CA). Translation was
performed in a 100-µl reaction mixture containing 98 µl of
reticulocyte extract and 2 µg of circular plasmid containing the
relevant cDNA. To remove ubiquitin and potential fraction
I-containing E2 enzymes, we applied the translation mixture containing
the labeled protein to DEAE-cellulose (Amersham Pharmacia Biotech) in a
solution containing 10 mM Tris-HCl (pH 7.5) and 0.1 mM dithiothreitol. After extensive washing of the resin
with 100 mM NaCl, the labeled protein was eluted with 400 mM NaCl and subjected to in vitro assay of
self-ubiquitination.
Identification of Mammalian U Box Proteins--
A search of the
GenBankTM data base for mammalian proteins that contain a U
box domain identified six molecules as follows: mouse UFD2a, UFD2b,
CHIP, and KIAA0860 and human CYC4 and PRP19 (Fig.
1A). UFD2a and UFD2b appear to
be mammalian homologs of Saccharomyces cerevisiae Ufd2; they
contain the U box domain at their COOH termini and, unlike the other
four proteins identified, do not possess other known motifs. In
addition to their U box domains, CHIP contains three tandem
tetratricopeptide repeats (TPRs), KIAA0860 contains a RING finger, CYC4
contains a cyclophilin-like motif, and PRP19 contains six WD40 repeats.
Alignment of their amino acid sequences revealed a marked similarity
among the U box domains of the yeast and mammalian proteins (Fig.
1B). The U box sequences of UFD2a, UFD2b, CHIP, and KIAA0860
are more closely related to each other than to those of CYC4 and PRP19.
The proline residue corresponding to proline 924 of S. cerevisiae Ufd2 is perfectly conserved not only in the six
mammalian U box proteins but also in all U box proteins from other
organisms that are present in the data base (data not shown).
Expression Analysis of Mammalian U Box Proteins--
The tissue
specificity of expression of the genes for these mammalian U box
proteins was examined by Northern blot analysis of polyadenylated RNA
from a variety of mouse or human tissues (Fig.
2A). The genes for UFD2a,
UFD2b, and KIAA0860 are expressed in liver, heart, brain, kidney, and
testis. CHIP mRNA was most abundant in skeletal muscle but was also
present in smaller amounts in heart, liver, kidney, and pancreas.
CYC4 gene transcripts were detected in heart, brain,
placenta, skeletal muscle, kidney, and pancreas, and PRP19 mRNA was
present in all tissues examined.
The subcellular localization of the mammalian U box proteins was
examined by immunofluorescence analysis of HeLa cells transfected with
vectors encoding FLAG epitope-tagged versions of these proteins. Cells
were also transfected with plasmids encoding FLAG-tagged versions of
Skp2 and IKK2 (I Ubiquitin-Protein Ligase Activities of Mammalian U Box
Proteins--
To determine whether the mammalian U box proteins
mediate ubiquitination, we subjected them to an in vitro
assay with recombinant proteins produced in E. coli, which
does not express components of the ubiquitin-conjugating system,
thereby avoiding contamination with or copurification of eukaryotic
proteins such as E3s (8). The U box proteins were expressed as GST or
histidine (His6)-tagged fusion constructs and were isolated
by affinity chromatography. Recombinant ubiquitin, recombinant E1, and
E. coli lysate containing recombinant E2 (UbcH5C) were added
to the assay. Potential substrates included the added fusion proteins
and bacterial proteins. UFD2a and Nedd4 (an E3 of the HECT family) each
mediated polyubiquitination in the presence of both E1 and E2 (Fig.
3A). To examine the
requirements for E1, E2, UFD2a, and ubiquitin in the ubiquitination
reaction, we performed in vitro ubiquitination assays with
the various combinations thereof in which one component (E1, E2, UFD2a,
or ubiquitin) was missing from the reaction mixture (Fig.
3B). All components were required for polyubiquitination.
Some of the ubiquitinated species detected were smaller than UFD2a
(GST-FLAG-UFD2a, 162 kDa), suggesting that they were derived from
bacterial proteins, although it remains possible that the recombinant
protein might be degraded during the reaction. Given that immunoblot
analysis with antibodies to the FLAG epitope revealed a shift in the
mobility of the band corresponding to GST-FLAG-UFD2a, UFD2a was itself
likely a target of polyubiquitination (Fig. 3B; see also
Figs. 6B and 7). To confirm that bacterial proteins were
ubiquitinated in the reaction, we subjected the reaction mixture after
completion of the incubation to immunodepletion with antibodies to GST
(for GST-FLAG-UFD2a), and the resulting supernatant was then subjected
to immunoblot analysis with antibodies to ubiquitin (Fig.
3C). Although the GST-FLAG-UFD2a protein was almost
completely removed by the immunodepletion procedure, the remaining
supernatant still contained a substantial amount of ubiquitinated
protein. We thus conclude that the ubiquitinated species detected in
the assay are derived from both bacterial proteins and UFD2a itself. On
the other hand, the autoubiquitination of E2 (UbcH5C) was not apparent
(Fig. 3B; see also Fig.
4B). Like UFD2a, UFD2b (see
Fig. 4A), CHIP (Fig. 3, D-F), KIAA0860 (Fig. 3,
E and F), as well as CYC4 and PRP19 (see Fig.
4A) also mediated polyubiquitination in a manner dependent
on the presence of both E1 and E2. Given the absence of other E3
factors from the assay mixture, these U box proteins, like Nedd4 and
Mdm2 (RING finger-containing E3) (Fig. 3F), by definition
function as E3 enzymes.
To exclude the possibility that the apparent E3 activity of the U box
proteins was nonspecific and attributable to their presence at
physiologically irrelevant concentrations, we compared the ubiquitination activities of UFD2a, CHIP, and KIAA0860 with those of
equimolar amounts of Nedd4 (Fig. 3E). The E3 activities of these U box proteins were similar to (CHIP and KIAA0860) or greater than (UFD2a) that of Nedd4.
The ubiquitination activity of the RING finger-containing Mdm2 requires
divalent cations, as revealed by the loss of activity induced by
chelation with TPEN, a potent chelator for Zn2+ (Fig.
3F). Such chelation did not inhibit the activities of Nedd4 (a HECT family E3) or E3s containing a U box domain (Fig.
3F), even though the predicted structure of this
domain resembles that of the RING finger (36). The observation
that KIAA0860, which contains both a U box and a RING finger, was
resistant to TPEN treatment suggested that the RING finger domain of
this protein is dispensable for ubiquitination activity.
E2 Preference of Mammalian U Box Proteins--
The variety of the
possible combinations of E2 and E3 may be relevant to the diversity of
substrate specificity for ubiquitination. However, most E3s exhibit
specificity for a relatively narrow range of E2 enzymes. We thus
examined the preference of the mammalian U box proteins for eight
different E2 enzymes in the presence of E1 (Fig. 4A). The
ubiquination activity of UFD2a, UFD2b, CHIP, and KIAA0860 was greatest
with Ubc4 or UbcH5C, whereas only Ubc3 cooperated with PRP19. CYC4
exhibited greatest activity with Ubc2B or Ubc3 but was also active with UbcH7.
To rule out the possibility of ubiquitination of E2 in the in
vitro ubiquination reaction, we performed immunoblot analysis with
antibodies to the His6 tag. Only a low level of E2
ubiquitination was apparent, with Ubc4 and UbcH5C showing virtually no
susceptibility to ubiquitination; in contrast, as shown above (Fig. 3,
C and D), immunoblot analysis with antibodies to
the FLAG epitope revealed a marked mobility shift for UFD2a (Fig.
4B), resulting from the self-ubiquitination of this protein.
Requirement of the U Box Domain for E3 Activity--
To determine
whether the U box is essential for ubiquitination by mammalian U box
proteins, we introduced deletions or point mutations into UFD2a (Fig.
5A) and CHIP (Fig.
5C). Deletion of the U box domain (
To determine whether the U box in its middle portion or the RING finger
at its COOH terminus is responsible for the E3 activity of KIAA0860, we
generated a series of mutants of this protein (Fig. 5E).
Whereas deletion of the U box domain ( Polyubiquitination by U Box Proteins of Themselves, as Well as of
Heterologous Targets--
Proteins that catalyze ubiquitination often
undergo automodification. With the use of immunoprecipitation and
immunoblot analysis, we first examined the ability of the mammalian U
box proteins to facilitate E2-dependent ubiquitination of
heterologous substrates (Fig.
6A). After in vitro
ubiquitination reactions, the U box proteins were immunoprecipitated
and then subjected, together with the intact reaction mixture, to
immunoblot analysis with antibodies to ubiquitin. The distinct patterns
and extents of ubiquitination apparent between the intact reaction
mixture and the U box protein immunoprecipitates suggested that the U
box proteins are indeed able to catalyze the ubiquitination of
heterologous substrates. To assess further whether the U box proteins
themselves also undergo ubiquitination, we prepared
35S-labeled versions of these proteins by in
vitro translation in a reticulocyte lysate and then tested them in
the ubiquitination assay (Fig. 6B). As with Nedd4, a
substantial proportion of UFD2a and KIAA0860 exhibited a shift in
electrophoretic mobility toward the top of the gel, indicative of
automodification by polyubiquitination. These results thus indicated
that U box proteins serve as E3s to mediate ubiquitination of
themselves as well as of heterologous substrates.
Unusual Lysine Residue Specificity for Polyubiquitination by
Mammalian U Box Proteins--
Given that yeast Ufd4 and Ufd2 require
lysine residues 29 and 48 of the ubiquitin moiety of the substrate to
mediate its polyubiquitination (35), we examined which lysine residues
of ubiquitin are required for polyubiquitination by mammalian U box
proteins. Neither Nedd4 nor Mdm2 was able to mediate ubiquitination
with a ubiquitin mutant (K48R) in which lysine 48 was replaced with
arginine (Fig. 7A), consistent
with the notion that these E3s conjugated the COOH-terminal glycine of
one ubiquitin molecule to the internal lysine 48 of the adjacent
ubiquitin molecule. The dependence on lysine 48 of ubiquitin appeared
to differ among the mammalian U box proteins. Whereas UFD2b, CYC4, and
PRP19 were not able to function with the K48R mutant of ubiquitin (Fig.
7A), the extent of ubiquitination mediated by UFD2a appeared
unaffected or even slightly increased with the K48R mutant. CHIP and
KIAA0860 were each able to mediate ubiquitination with the K48R mutant
ubiquitin, although with a markedly reduced efficiency (Fig.
7A).
The lysine residue specificity of UFD2a was further characterized. The
ubiquitination of 35S-labeled UFD2a was thus monitored with
ubiquitin mutants in which the lysine residues at positions 6, 11, 27, 29, 33, 48, or 63 were individually substituted with arginine (Fig.
7B). All of the ubiquitin mutants supported
polyubiquitination of UFD2a, although the extent of polyubiquitination
with K6R and K27R mutants was slightly reduced compared with that
apparent with the wild-type protein (Fig. 7C). Given that
the roles of lysines at positions 29, 48, and 63 of ubiquitin have been
extensively analyzed, we next generated ubiquitin mutants in which two
or all three of these residues were replaced with arginine. UFD2a
mediated polyubiquitination even with these double and triple mutants
of ubiquitin (data not shown). The lysine residues at positions 6 and
11 of ubiquitin have been implicated previously (38) in
polyubiquitination. We therefore generated mutant ubiquitins in which
four or five lysine residues, including lysine 6 or lysine 11, were
replaced with arginine. Again, a substantial extent of
polyubiquitination by UFD2a remained apparent with these ubiquitin
mutants, including the K6R/K11R/K29R/K48R/K63R mutant (data not
shown). To exclude the possibility that several ubiquitin monomers are
attached at more than one site of UFD2a (referred to here as
multiubiquitination), we prepared a recombinant ubiquitin (K0) in which
all lysines are substituted with arginines (Fig. 7D), and we
included this mutant in the ubiquitination assay. Only the
monoubiquitinated form of UFD2a was generated with the K0 mutant of
ubiquitin (Fig. 7E), suggesting that the ladder pattern of
ubiquitination observed with wild-type ubiquitin is indeed due to
polyubiquitination (not multiubiquitination) of UFD2a.
To determine which lysine residues of ubiquitin support
polyubiquitination by UFD2a, we prepared a series (K1) of ubiquitin mutants in which all but one lysine residue are replaced with arginine
(Fig. 7D). The extent of UFD2a-mediated polyubiquitination with the K1 ubiquitin mutant with an intact lysine 33 (K1(33)) was
similar to that apparent with wild-type ubiquitin (Fig. 7E). In addition, a reduced extent of polyubiquitination was also observed with the mutant K1(27). These data do not necessarily rule out the
possibility that other lysines at positions 6, 11, 29, 48, and 63 support polyubiquitination because of possible structural changes
induced by the replacement of multiple lysine residues with arginine.
We finally examined whether the ubiquitin mutant K27R/K33R is
functional with UFD2a (Fig. 7F). This mutant supported polyubiquitination of UFD2a to almost the same extent as that observed
with K1(27) (Fig. 7G), suggesting that lysines at positions other than 27 and 33 can be used by UFD2a. Collectively, these experiments with various ubiquitin mutants indicate that UFD2a is able
to utilize multiple lysine residues of ubiquitin in addition to lysine
48 to mediate the formation of polyubiquitin chains.
Our results indicate that the U box domain, in the appropriate
molecular context, facilitates E2-dependent ubiquitination. The U box proteins thus define a third family of E3 enzymes, in addition to the HECT and RING finger families of E3s. This observation is somewhat unexpected, given that yeast Ufd2, the prototype U box
protein, was originally described as a factor (designated E4) that
promotes polyubiquitination of artificial ubiquitin fusion proteins in
conjunction with E1, E2, and E3 (35, 39). In this scenario, the E3
(Ufd4, a HECT-type E3) catalyzes oligo-ubiquitination, but not
polyubiquitination; E4 is required for elongation of the oligo-ubiquitin chain and consequent recognition of the substrate by
the 26 S proteasome. We have now shown, however, that six unrelated mammalian U box proteins, including the yeast Ufd2 homologs UFD2a and
UFD2b, mediate polyubiquitination in the presence of E1 and E2 in a
manner that is independent of other E3s. Thus, we propose that E4
activity is a specialized type of E3 activity that recognizes oligo-ubiquitinated artificial fusion proteins as substrates. Whether
the mammalian U box proteins also possess E4 activity and whether E4
activity is physiologically relevant remain to be determined.
With regard to the mechanism by which U box proteins function together
with E2s to catalyze ubiquitination, it is possible that, analogous to
HECT family E3s, U box proteins both bind to E2 and form thiol ester
intermediates with ubiquitin. However, no cysteine residue within the U
box is conserved among members of this family, making this possibility
unlikely. Indeed, some U box proteins, such as UFD2a, do not contain
any cysteine residues within the U box domain. Alternatively, the U box
may constitute a site of interaction with E2 that allows the direct
transfer of ubiquitin from E2 to target lysines. This notion is
consistent with the observations that the amino acid sequences of the U
box domains of UFD2a, UFD2b, CHIP, and KIAA0860 (all of which prefer Ubc4 or UbcH5C as an E2) are more similar to each other than they are
to those of the U box domains of CYC4 and PRP19 (neither of which
functions with Ubc4 or UbcH5C) and that the U box is structurally similar to the RING finger (which recruits E2 in RING finger family E3s). However, we failed to detect a physical interaction of U box
proteins with the relevant E2 enzymes either by yeast two-hybrid analysis or with biochemical assays (data not shown), suggesting that
if these proteins do interact they do so with low affinity. In general,
physical E2-E3 interactions are not necessarily detected in other E2-E3 systems.
The formation of a polyubiquitin chain by linkage of the COOH terminus
of one ubiquitin moiety to lysine 48 of the adjacent ubiquitin had been
thought to mark a protein for proteolysis by the 26 S proteasome.
However, recent observations (40) indicate that polyubiquitin chains
can also be assembled through conjugation to lysine residues of
ubiquitin other than lysine 48, and the resulting chains appear to
function in distinct biological processes. A short lysine 29-linked
chain might thus constitute a signal to recruit E4 before proteasomal
proteolysis (35). Polyubiquitination through lysine 63 of ubiquitin
appears to mark proteins that contribute to DNA repair (41), to the
cellular response to stress (42), to inheritance of mitochondrial DNA
(43), to endocytosis of certain plasma membrane proteins (44), or to
ribosomal function (45). In addition, TRAF6, a RING finger-type E3, in
conjunction with the E2 Ubc13 and and the Ubc-like protein Uev1A,
targets lysine 63 of ubiquitin and plays an important role in I In yeast, Ufd2 is implicated in cell survival under stress conditions,
a role that is consistent with the association of Ufd2 with the
AAA-type ATPase Cdc48, which possesses chaperone activity. We have also
shown2 that UFD2a, a
mammalian homolog of yeast Ufd2, interacts with VCP, which appears to
be the mammalian ortholog of yeast Cdc48, suggesting that the
association of AAA-type ATPases with U box proteins has been conserved
through evolution and thus may be functionally important. Furthermore,
the TPR-containing U box protein CHIP binds to the molecular chaperones
HSP70 and HSP90 (47), and CYC4 contains a cyclophilin-like
peptidylprolyl isomerase domain (48). These observations suggest that U
box proteins may serve as E3s that physically and functionally
associate with chaperones. The U box-type E3s may therefore play an
important role in the cellular response to stress or to misfolded or
otherwise damaged proteins. The combination of CHIP with HSP90 induces
ubiquitination of the glucocorticoid receptor (49), and CHIP together
with HSP70 targets immature cystic fibrosis transmembrane conductance regulator for proteasomal degradation (50). The folding of both the
glucocorticoid receptor and cystic fibrosis transmembrane conductance
regulator is controlled by molecular chaperones. In these two
instances, CHIP was proposed to act as a co-chaperone that regulates
the balance between protein folding and degradation by ubiquitination.
However, our present results demonstrate that CHIP itself possesses
ubiquitin ligase activity. Other U box proteins likely play important
roles in the ubiquitination of specific substrates, especially under
conditions of cellular stress, when they may serve to link the
processes of protein folding by molecular chaperones and protein
degradation by the ubiquitin-proteasome pathway.
We thank H. Yasuda, M. Nakao, and S. Tanaka
for plasmids and antibodies used in this study; S. Matsushita, N. Nishimura, R. Yasukochi, and other laboratory members for technical
assistance; and M. Kimura for help in preparing the manuscript.
*
This work was supported in part by a grant from the Ministry
of Education, Science, Sports, and Culture of Japan and by the Human
Frontier Science Program.The costs of publication of this article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
Published, JBC Papers in Press, July 2, 2001, DOI 10.1074/jbc.M102755200
2
M. Matsumoto, S. Hatakeyama, M. Yada, N. Ishida,
M. Kitagawa, and K.-I. Nakayama, manuscript in preparation.
The abbreviations used are:
E1, ubiquitin-activating enzyme;
E2, ubiquitin-conjugating enzyme;
E3, ubiquitin-protein ligase;
E4, ubiquitin-chain assembly factor;
PCR, polymerase chain reaction;
HA, hemagglutinin epitope;
GST, glutathione
S-transferase;
PBS, phosphate-buffered saline;
PAGE, polyacrylamide gel
electrophoresis;
TPR, tetratricopeptide repeat;
TPEN, tetrakis(2-pyridylmethyl)- ethylenediamine.
U Box Proteins as a New Family of Ubiquitin-Protein
Ligases*
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ABSTRACT
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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INTRODUCTION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
B, and
-catenin (21-34). Furthermore, RING
fingers of otherwise unrelated proteins, such as BRCA1, Siah-1, TRC-8,
Praja1, and AO7, activate E2-dependent ubiquitination,
suggesting that this domain plays a general role in the ubiquitin
system (8).
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EXPERIMENTAL PROCEDURES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
ZAP (Stratagene). The positive clones obtained from of
1 × 106 plaques for each screening were isolated, and
the inserts were subcloned into pBluescriptII SK+.
U) of KIAA0860, we performed PCR with pBluescriptII
SK+ containing KIAA0860 cDNA as a template and either
with a sense primer beginning at the start codon and an antisense
primer beginning proximal to the U box, or with a sense primer
beginning distal to the U box and an antisense primer beginning at the
stop codon. Both amplified products were mixed and subjected to a
second PCR with a sense primer beginning at the start codon and an
antisense primer beginning at the stop codon. To generate RING finger
deletion mutants of KIAA0860, we performed PCR with wild-type or
U
mutant KIAA0860 cDNA as a template and with a sense primer
beginning at the start codon and an antisense primer beginning proximal to the RING finger domain.
cultured in the presence of 0.1 mM isopropyl-
-D-thiogalactopyranoside.
Bacterial cells were resuspended in phosphate-buffered saline (PBS) and
lysed by sonication, and cellular debris was removed by centrifugation
for 20 min at 13,000 × g. Glutathione-Sepharose 4B
beads (Amersham Pharmacia Biotech) were added to the resulting
supernatant, and the mixture was rotated at 4 °C overnight. The
beads were washed in PBS, and GST fusion proteins were eluted with 50 mM Tris-HCl (pH 8.0) containing 10 mM reduced
glutathione. To generate the ubiquitin mutants, we subjected the
purified GST fusion proteins attached to the glutathione-Sepharose 4B
beads to digestion for 4 h at 4 °C with PreScission protease
(Amersham Pharmacia Biotech) in a buffer containing 50 mM
Tris-HCl (pH 8.0), 150 mM NaCl, 1 mM EDTA, and 1 mM dithiothreitol. Only the ubiquitin derivatives, not
the GST moiety nor the GST-ubiquitin fusion proteins, were detected in the eluate by electrophoresis and Coomassie Blue staining (data not shown).
-D-thiogalactopyranoside. The recombinant proteins were purified with the use of ProBond resin (Invitrogen).
-actin (mouse or human) cDNA
probes that had been labeled with [
-32P]dCTP. The
blots were washed at 68 °C in 0.2× standard saline citrate
containing 0.1% SDS and were then exposed and analyzed with a BAS-2000
instrument (Fuji Film, Kanagawa, Japan).
-mercaptoethanol and heating at 95 °C for 5 min (37). Samples were resolved by SDS-polyacrylamide gel
electrophoresis (PAGE) on 9 or 12% gels and then subjected to
immunoblot analysis with a mouse monoclonal antibody to ubiquitin
(clone 1B3; MBL, Nagoya, Japan) and horseradish peroxidase-conjugated
rabbit polyclonal antibodies to mouse immunoglobulin (Promega,
Madison, WI). Immune complexes were detected by enhanced
chemiluminescence (ECL kit; Amersham Pharmacia Biotech).
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RESULTS
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EXPERIMENTAL PROCEDURES
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DISCUSSION
REFERENCES

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Fig. 1.
Structural organization of members of the U
box family of proteins. A, schematic representation of
the structures of mammalian U box proteins. The U box domain is
depicted as a filled box. Other protein motifs are
indicated: TPR, tetratricopeptide repeat; RING,
RING finger; Cy-like, cyclophilin-like peptidylprolyl
isomerase domain; WD40, WD40 repeat. The total number of
amino acids (aa) in each protein is shown on the
right. B, alignment of amino acid sequences of
the U box domains of S. cerevisiae Ufd2; Mus
musculus UFD2a, UFD2b, CHIP, and KIAA0860; and Homo
sapiens PRP19 and CYC4. The consensus sequence is shown at the
bottom. Residue numbers are indicated, and dashes
represent gaps introduced to optimize alignment. Identical and similar
residues shared by the various proteins are boxed; the
conserved proline residue is boxed in bold.

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Fig. 2.
Expression of mammalian U box
proteins. A, Northern blot analysis of transcripts
encoding mammalian U box proteins in various mouse (left
panels) and human (right panels) tissues. Hybridization
was performed with 32P-labeled cDNA probes
corresponding to the coding regions of UFD2a,
UFD2b, KIAA0860, CHIP,
CYC4, PRP19, mouse
-actin, and
human
-actin genes. The sizes of hybridizing transcripts
are indicated. B, immunofluorescence analysis of the
subcellular localization of mammalian U box proteins. HeLa cells were
transfected with expression plasmids encoding FLAG-tagged versions of
Skp2 (control for nuclear expression), IKK2 (control for cytoplasmic
expression), UFD2a, UFD2b, KIAA0860, CHIP, CYC4, or PRP19. After
48 h, the cells were fixed and stained with antibodies to the FLAG
epitope and Hoechst 33258 to reveal the subcellular distribution of the
recombinant proteins and nuclei, respectively. Scale bars,
25 µm.
B kinase 2) as controls for nuclear and cytoplasmic
expression, respectively. Whereas KIAA0860 and CYC4 appeared to be
localized to the nucleus of transfected HeLa cells, UFD2b and CHIP were
localized to the cytoplasm (Fig. 2B). UFD2a and PRP19
exhibited a nuclear localization in some cells and a cytoplasmic
localization in others, suggesting that the localization of these
proteins might be regulated in a cell cycle-dependent manner.

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Fig. 3.
E3 activity of mammalian U box proteins.
A, polyubiquitination by UFD2a. Equal amounts of GST-Nedd4
or GST-FLAG-UFD2a were incubated for 2 h at 30 °C in the
presence of rabbit E1 and bacterial lysate containing E2 (UbcH5C). As a
negative control, an E3 component was omitted from the reaction mixture
(mock). The reaction mixture was resolved under reducing
conditions by SDS-PAGE, and the separated proteins were subjected to
immunoblot analysis (IB) with antibodies to ubiquitin
(anti-Ub). B, E1, E2, and ubiquitin dependence of
the polyubiquitination activity of UFD2a. In vitro
ubiquitination assays were performed with the indicated combinations of
E1, E2 (His6-UbcH5C), ubiquitin, and GST-FLAG-UFD2a
(top panel). The reaction mixture was also subjected to
immunoblot analysis with antibodies to the His6 tag
(middle panel) or to the FLAG epitope (bottom
panel) in order to detect UbcH5C and UFD2a proteins, respectively.
C, polyubiquitination of bacterial proteins by UFD2a.
In vitro ubiquitination assays were performed as in
B, after which the reaction mixture was subjected to
immunoprecipitation (IP) with antibodies to GST. The
resulting supernatant (upper right panel) or the intact
reaction mixture (upper left panel) was then subjected to
immunoblot analysis with antibodies to ubiquitin (Ub).
Immunodepletion of GST-FLAG-UFD2a was confirmed by immunoblot analysis
of the corresponding samples with antibodies to the FLAG epitope
(lower panels). D, E1- and
E2-dependent polyubiquitination by CHIP. Equal amounts of
GST-Nedd4, GST-UFD2a, or GST-CHIP were incubated for 2 h at
30 °C in the absence or presence of rabbit E1 or bacterial lysate
containing E2 (UbcH5C), as indicated. As a negative control, an E3
component was not added to the reaction mixture (mock). The
reaction mixture was resolved under reducing conditions by SDS-PAGE,
and the separated proteins were subjected to immunoblot analysis with
antibodies to ubiquitin. E, comparison of the efficiencies
of polyubiquitination mediated by Nedd4, UFD2a, CHIP, and KIAA0860. The
activity of each GST fusion protein (10, 3, and 1 pmol) was assayed in
the presence of E1 and E2 as described in A and
B. Coomassie Blue (CB) staining of the gel is
shown below the immunoblot (IB). Asterisks
indicate the positions of the E3 proteins. F, effect of
divalent cation chelation on the ubiquitination activities of Mdm2,
Nedd4, CHIP, and KIAA0860. Bead-bound GST fusion proteins were
incubated in the absence (
) or presence (+) of 5 mM TPEN
before assay of ubiquitination activity in the presence of E1 and E2.
The positions of the GST-E3 fusion proteins are indicated on the
right of the Coomassie Blue-stained gel.

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Fig. 4.
E2 preference of mammalian U box
proteins. A, in vitro ubiquitination assays
were performed with mammalian U box proteins in the presence of E1 and
in the absence (mock) or presence of bacterial lysates containing the
indicated His6-tagged E2 proteins (1 µl). The reaction
mixture was resolved under reducing conditions by SDS-PAGE, and the
separated proteins were subjected to immunoblot analysis with
antibodies to ubiquitin. Anti-Ub, anti-ubiquitin.
B, in vitro ubiquitination reactions were
performed with UFD2a, after which the reaction mixture was resolved
under reducing conditions by SDS-PAGE, and the separated proteins were
subjected to immunoblot analysis either with antibodies to the
His6 tag for E2s (upper panel) or with
antibodies to the FLAG epitope for UFD2a (lower
panel).
U) or point mutation
(P1140A) of the conserved proline at position 1140 abolished the E3
activity of UFD2a (Fig. 5B). Similarly, CHIP mutants lacking
the U box domain or with a P270A point mutation failed to exhibit
polyubiquitination activity (Fig. 5D). Furthermore,
substitution (H261A) of the histidine residue at position 261 of CHIP,
which corresponds to the residue (tryptophan 408) of Cbl, a RING
finger-type E3, implicated in E2 binding (17), also resulted in the
loss of E3 activity.

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Fig. 5.
Requirement of the U box domain for E3
activity. A, schematic representation of wild-type and
mutant UFD2a proteins. B, equimolar amounts of the indicated
GST (upper left panel) or His6 (upper
right panel) fusion proteins were assayed for ubiquitination
activity in the presence of E1 and bacterial lysate containing E2
(UbcH5C). The same blots were reprobed with antibodies to GST
(lower left panel) or antibodies to UFD2a (lower right
panel). C, schematic representation of wild-type and
mutant CHIP proteins. D, equimolar amounts of the indicated
GST fusion proteins were assayed for ubiquitination activity
(upper panel) as in B. The same blot was reprobed
with antibodies to GST (lower panel). E,
schematic representation of wild-type and mutant KIAA0860 proteins.
F, equimolar amounts of the indicated GST fusion proteins
were assayed for ubiquitination activity (upper panel) as in
B. The same blot was reprobed with antibodies to GST
(lower panel). Anti-Ub, anti-ubiquitin.
U) abolished E3 activity,
deletion of the RING finger (
R) did not affect ubiquitination, indicating that the U box, not the RING finger, is responsible for E3
activity of KIAA0860 (Fig. 5F). This observation is
consistent with the resistance of KIAA0860 to TPEN treatment (Fig.
3F). Mutagenesis (P306A) of the conserved proline at
position 306 of KIAA0860 also abolished E3 activity, whereas activity
was unaffected by substitution (C292A) of cysteine 292. Collectively,
these data indicate that the U box domain is essential for the E3
activity of mammalian U box proteins and that the conserved proline is
indispensable for the function of the U box domain.

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Fig. 6.
Polyubiquitination by mammalian U box
proteins of themselves, as well as of heterologous targets.
A, in vitro ubiquitination assays were performed
with the indicated mammalian U box proteins in the presence of E1 and
purified UbcH5C, after which the U box proteins were immunoprecipitated
(IP) with antibodies to the FLAG epitope (UFD2a)
or to GST (UFD2b, CHIP, and KIAA0860). The
immunoprecipitates (+) and intact reaction mixtures (
) were then
subjected to immunoblot (IB) analysis with antibodies to
ubiquitin (Anti-Ub, upper panel) as well as with
antibodies to the FLAG tag (lower left panel) or to GST
(lower right panel). B, 35S-labeled
UFD2a, KIAA0860, luciferase (negative control), or Nedd4 (positive
control) was resolved directly by SDS-PAGE (
) or first subjected to
the in vitro ubiquitination assay (+) in the presence of E1
and bacterial lysate containing E2 (UbcH5C). The
35S-labeled proteins were then detected by autoradiography.
The positions of ubiquitinated (Ub) Nedd4, UFD2a, and
KIAA0860 are indicated.

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Fig. 7.
Ubiquitin lysine residue specificity of
polyubiquitination by mammalian U box proteins. A, the
ubiquitination activities of Nedd4, Mdm2, and mammalian U box proteins
were assayed in vitro in the absence (mock) or
presence of wild-type (WT) ubiquitin (Ub) or its
K48R mutant. Bacterial lysate containing UbcH5C was used as the E2 for
Nedd4, Mdm2, UFD2a, UFD2b, CHIP, and KIAA0860, whereas bacterial lysate
containing Ubc3 was used for CYC4 and PRP19. The reaction mixtures were
subjected to immunoblot analysis with antibodies to ubiquitin.
B, schematic representation of ubiquitin mutants in which
the lysine residues at positions 6, 11, 27, 29, 33, 48, or 63 were
individually substituted with arginine. The substituted arginines are
indicated in bold. C, in vitro
ubiquitination assays were performed with 35S-labeled UFD2a
and bacterial lysate containing E2 (UbcH5C) in the absence
(mock) or presence of wild-type ubiquitin or the ubiquitin
mutants shown in B. The reaction mixtures were subjected to
SDS-PAGE and autoradiography. D, schematic representations
both of a series (K1) of ubiquitin mutants in which all but the
indicated single lysine residues (shown in bold) are
replaced with arginine and of the K0 mutant of ubiquitin, in which all
lysines are substituted with arginine. E,
35S-labeled UFD2a was subjected to the ubiquitination assay
in the presence of bacterial lysate containing E2 (UbcH5C) and in the
absence (mock) or presence of wild-type ubiquitin or the
ubiquitin mutants shown in D. F, schematic
representation of the K27R/K33R mutant, in which lysines 27 and 33 are
substituted with arginine. G, 35S-labeled UFD2a
was subjected to the ubiquitination assay in the presence of bacterial
lysate containing E2 (UbcH5C) and in the absence (mock) or
presence of wild-type ubiquitin or the ubiquitin mutants shown in
F.
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DISCUSSION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
B
phosphorylation in the NF-
B signaling pathway (46). Our data now
show that some U box E3s catalyze polyubiquitination by targeting
lysine residues other than lysine 48, whereas HECT and RING finger E3s (with the exception of TRAF6) usually target lysine 48 for
polyubiquitination. Moreover, UFD2a exhibits broad specificity for
ubiquitin lysine residues in polyubiquitination. Hence, it is possible
that proteins that have undergone polyubiquitination by UFD2a display
heterogeneous or multiply branched structures that might possess
distinct biological functions. However, it is unclear whether it is
possible for two ubiquitin moieties to be simultaneously conjugated to
different lysine residues of a single ubiquitin molecule or whether
conjugation of the first ubiquitin may physically interfere with the
conjugation of the second ubiquitin on a different lysine. The
formation of multiply branched ubiquitin chains by UFD2a might be
expected to give rise to irregularly spaced ubiquitinated species on
SDS-PAGE; however, we did not observe such electrophoretic patterns.
The structure and function of the unusual polyubiquitin chains formed by UFD2a thus require further characterization.
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ACKNOWLEDGEMENTS
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FOOTNOTES
To whom correspondence should be addressed: Dept. of Molecular and
Cellular Biology, Medical Inst. of Bioregulation, Kyushu University,
3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. Tel.:
81-92-642-6815; Fax: 81-92-642-6819; E-mail:
nakayak1@bioreg.kyushu-u.ac.jp.
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ABBREVIATIONS
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INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
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