The Rab5 effector Rabaptin-5 and its isoform Rabaptin-5d
differ in their ability to interact with the small GTPase
Rab4
Elena Korobko
1,2
, Sergey Kiselev
1
, Sjur Olsnes
3
, Harald Stenmark
3
and Igor Korobko
1
1 Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
2 University of Oslo, Centre for Medical Studies at Moscow, Moscow, Russia
3 Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
Intracellular membrane transport is an important pro-
cess for eukaryotic cells. Intracellular membranes are
organized in compartments, and transport between
compartments requires high specificity and tight regu-
lation. The intercompartmental transport typically
occurs through transport vesicles budding from a
donor compartment and fusing to an acceptor com-
partment. In this process, Rab GTPases were demon-
strated to play a central role by regulating vesicle
budding, motility and fusion [1]. Another group of
molecules, v- and t-SNAREs, were suggested to con-
tribute to specificity of vesicle targeting [2–4] although
the specificity of the transport is also maintained by
Rab GTPases [5]. A large number of Rab GTPases
have been identified in mammalian cells, and each of

encoding the Rabaptin-5 isoform, Rabaptin-5d. To evaluate the interaction
properties of Rabaptin-5 d with the small GTPases Rab4 and Rab5, we
have applied protein interaction assays using the yeast two-hybrid system
and a glutathione S-transferase pull-down assay. We found that unlike
Rabaptin-5, that interacts with both GTPases in GTP-bound conforma-
tions, Rabaptin-5d interacts only with GTP-bound Rab5, and does not
interact with Rab4, presumably due to a disrupted Rab4 binding site.
Immunofluorescence microscopy analysis carried out to address the locali-
zation of Rabaptin-5d relative to GTP-bound Rab4 and Rab5 in BHK-21
cells supported these data. Our data suggests that while Rabaptin-5 was
proposed to act as a molecular linker between Rab5 and Rab4, to coordi-
nate endocytic and recycling traffic, Rabaptin-5d is involved only in the
Rab5-driven events.
Abbreviations
3AT, 3-amino-(1,2,4)-triazole; EGFP, enhanced green fluorescent protein; GEF, guanine nucleotide exchange factor; GAL4AD, GAL4
transcriptional activating domain; GAL4BD, GAL4 DNA-binding domain; GST, glutathione S-transferase; SD, synthetic dextrose;
TGN, trans-Golgi network.
FEBS Journal 272 (2005) 37–46 ª 2004 FEBS 37
these is Rabaptin-5, which is an essential and rate-
limiting factor for homotypic early endosome fusion
and heterotypic fusion between early endosomes and
clatrin-coated vesicles [12–14]. Cytosolic Rabaptin-5 is
complexed with Rabex-5, a Rab5 guanine nucleotide
exchange factor (GEF), and both proteins act syner-
gistically to activate Rab5 in early endosome fusion
events [13,15].
As well as being a Rab5 effector, Rabaptin-5 has
been suggested to play a role in connecting different
steps of the membrane transport process. First,
Rabaptin-5 was demonstrated to interact through a

domain of Rabaptin-5 [14,23] (Fig. 1). The ubiquitous
occurrence of the Rabaptin-5d transcript suggests that
this protein could play a significant role in the cell,
probably through modulation of the Rabaptin-5 func-
tions. In an attempt to clarify this suggestion, and to
better understand the functional role of Rabaptin-5d,
we have characterized this molecule with respect to
its ability to interact with the known Rabaptin-5
interaction partners, Rab4, Rab5 and Rabex-5 as well
as its ability to be recruited to specific endosomal
compartments.
Results
Rabaptin-5d interacts differentially with the small
GTPases Rab4 and Rab5
The interaction of Rabaptin-5 with the small GTPases
Rab4 and Rab5 can be assessed readily in the yeast
two-hybrid system [12,14]. We therefore used this assay
to analyze the interaction of Rabaptin-5d with Rab4
and Rab5.
Similarly to Rabaptin-5, Rabaptin-5d was not able
to bind Rab4 or Rab5 in the inactive, GDP-bound
form as no HIS3 reporter gene trans-activation was
observed upon coexpression of GAL4AD–Rabaptin-5
or -Rabaptin-5d and GAL4BD fused to Rab5S34N or
Rab4S22N, dominant negative mutants of Rab5 and
Rab4 with decreased affinity for guanine nucleotides
(Figs 2 and 3). Likewise, no HIS3 reporter gene trans-
activation was revealed upon coexpression of the wild-
type Rab5 bait and the Rabaptin-5d isoform prey
(Fig. 2), which is consistent with no detectable reporter

140 295
R4BD
Fig. 1. Schematic representation of Rabaptin-5 and its d isoform.
Coiled-coil regions (CC1–1, CC1–2, CC2–1, CC2–2) are shown in
black. Positions of the Rab4 binding domain (R4BD) are marked as
white and black hatched boxes as determined in [14] and [26],
respectively. The Rab5 binding domain (R5BD) is marked as a dot-
filled box. The region deleted in Rabaptin-5d is shown in white.
Positions of coiled-coil regions CC1-1 and CC1-2, Rab4 binding
domain, and the region deleted in Rabaptin-5d are numbered
according to the amino acid sequence of mouse Rabaptin-5 (Gene-
Bank Accession No. D86066).
Rabaptin-5 isoform d is not a Rab4 effector E. Korobko et al.
38 FEBS Journal 272 (2005) 37–46 ª 2004 FEBS
observed a similar pattern of the reporter gene trans-
activations for Rabaptin-5 (Fig. 3). However, when
Rabaptin-5d was assayed as a prey in the yeast two-
hybrid system, no HIS3 reporter gene trans-activation
was observed with neither bait, wild-type Rab4 nor its
GTPase-deficient mutant (Fig. 3) suggesting the lack
of interaction between Rab4 and Rabaptin-5d.
The interaction properties of the Rabaptin-5 iso-
forms with Rab4 and Rab5 were further assayed in
glutathione S-transferase (GST) pull-down assays.
GST–Rab4 preloaded with either GDP or the unhy-
drolyzable GTP analogue, GTPcS, was unable to pull
down enhanced green fluorescent protein (EGFP)-
tagged Rabaptin-5d from cytosol of transiently trans-
fected BHK-21 cells (Fig. 4A). At the same time,
consistent with the data from yeast two-hybrid system,

M 3-amino-
(1,2,4)-triazole (3AT).
Fig. 3. Interaction specificity of Rabaptin-5d with Rab4 in the yeast
two-hybrid system. Y153 reporter yeast cells were cotransformed
with plasmids encoding GAL4BD alone or fused to Rab4 or its
mutants, and GAL4AD alone or fused to Rabaptin-5 (Rn5) or Rabap-
tin-5d (Rn5d). HIS3 reporter gene activation caused by interaction
between GAL4BD- and GAL4AD-fused proteins in yeast was
assessed by spotting yeast onto synthetic minimal medium supple-
mented (bottom) or not supplemented (top) with 25 m
M 3AT.
E. Korobko et al. Rabaptin-5 isoform d is not a Rab4 effector
FEBS Journal 272 (2005) 37–46 ª 2004 FEBS 39
GTP in vitro, Rabaptin-5 alone could not support bio-
logical activity of Rab5 in early endosome fusion [12].
We therefore asked if the Rabaptin-5d isoform is
complexed with Rabex-5 in vivo. As shown in Fig. 5,
Rabex-5 coimmunoprecipitates with EGFP-tagged
Rabaptin-5d from cytosol of transfected BHK-21 cells,
similarly to Rabaptin-5. Thus Rabaptin-5d is associ-
ated with the Rab5 GEF, Rabex-5, in vivo.
Subcellular localization of Rabaptin-5d upon
coexpression with GTPase-deficient mutants of
Rab4 or Rab5 GTPases
The findings based on the yeast two-hybrid system and
GST pull-down analyses suggest that, whereas Rabap-
tin-5 interacts with both Rab4 and Rab5 in their GTP-
bound forms, Rabaptin-5d can interact only with
GTP-bound Rab5 and not with GTP-bound Rab4. To
address the question of how relevant these findings are

clonal antiserum against Rabaptin-5 (A, B) or with anti-FLAGâ-M2
monoclonal Igs (C). Arrows indicate endogenous Rabaptin-5 (Rn5)
and EGFP-fused Rabaptin-5 and its isoform (E-Rn5’s) (A,B), and
FLAGÒ-tagged Rabaptin-5 and its isoform (Rn5-FLAGâ)(C).
AB
DC
Fig. 5. Cytosolic Rabaptin-5d expressed in BHK-21 cells is com-
plexed with Rabex-5. Cytosols were prepared from BHK-21 cells
transiently expressing EGFP alone (E) or EGFP C-terminally fused
with Rabaptin-5 (5) or Rabaptin-5d (5d). Cytosols (A, C) or proteins
immunoprecipitated from cytosols with anti-EGFP Igs (B, D) were
separated by SDS ⁄ PAGE and immunoblotted with polyclonal anti-
sera against Rabaptin-5 (A, B) or against Rabex-5 (C, D). Arrows
indicate endogenous Rabaptin-5 (Rn5) and EGFP-fused Rabaptin-5
and its isoform (E-Rn5’s), Rabex-5 (Rabex-5), and antibody used for
immunoprecipitation (Ab).
Rabaptin-5 isoform d is not a Rab4 effector E. Korobko et al.
40 FEBS Journal 272 (2005) 37–46 ª 2004 FEBS
coexpression of EGFP–Rabaptin-5 and myc-tagged
Rab5Q79L (Fig. 6A,A¢).
When a myc-tagged GTPase-deficient mutant of
Rab4, Rab4Q67L, was coexpressed in BHK-21 cells
with EGFP–Rabaptin-5, we found that the two pro-
teins colocalize on vesicular structures in the perinu-
clear area (Fig. 7A,A¢ and insets), which is consistent
with previous reports [14,24]. Whereas EGFP–Rabap-
tin-5d also concentrated in the perinuclear region when
coexpressed with myc-tagged Rab4Q67L, the two pro-
teins did not show any significant colocalization
(Fig. 7B,B¢ and insets).

EGFP-fused proteins. Panel dimensions are
80 lm  80 lm.
Fig. 7. Confocal immunofluorescence
analysis of BHK-21 cells coexpressing myc-
tagged Rab4Q67L and EGFP-tagged Rabap-
tin-5 or EGFP-tagged Rabaptin-5d. Cells
cotransfected with myc-tagged Rab4Q67L
and EGFP-tagged Rabaptin-5 (A–A¢)or
Rabaptin-5d (B–B¢) were stained with mouse
monoclonal anti-(myc 9E10 Ig) followed by
Alexa546-conjugated anti-mouse secondary
antibodies (A¢,B¢), or EGFP fluorescence
was recorded (A, B). Overlays are shown in
A and B with yellow color indicating colo-
calization, red color indicating myc-
Rab4Q67L, and green color indicating EGFP-
fused proteins. The black-and white insets
in panels A¢ and B¢ shows higher magnifica-
tion of indicated regions for green (left )and
red (right) channels. Panel dimensions are
100 lm  100 lm.
E. Korobko et al. Rabaptin-5 isoform d is not a Rab4 effector
FEBS Journal 272 (2005) 37–46 ª 2004 FEBS 41
portion of the polypeptide chain [23]. Rabaptin-5 was
identified initially as a Rab5 effector protein that specif-
ically interacted with Rab5 in the GTP-bound form and
was an essential component for homotypic early endo-
some fusion and heterotypic fusion between clathrin-
coated vesicles and early endosomes [12–14]. It was pro-
posed that Rabaptin-5 functioned by coupling Rab5

this point, we assayed the interaction properties of dif-
ferent N-terminal fragments of Rabaptin-5 with Rab4
in the yeast two-hybrid system. Consistent with the
data of Deneka et al. [26], amino acids 140–294 of
Rabaptin-5 were sufficient to interact with Rab4 as
judged by trans-activation of the LacZ reporter gene,
while a polypeptide consisting of the first 149 amino
acids was not (Fig. 9). At the same time, a fragment of
Rabaptin-5d corresponding to amino acids 140–294 of
Rabaptin-5, which contains the deleted region, was
unable to bind Rab4. In addition, the first 251 amino
acids of the Rabaptin-5c isoform, bearing a natural
deletion of amino acids 22–64 of Rabaptin-5 [23], was
able to interact with Rab4, thus demonstrating the dis-
pensability of these amino acids for the interaction
(Fig. 9). Taken together, the conclusion can be made
that Rab4 binding site is located between amino acids
140 and 294 of Rabaptin-5. Rabaptin-5d has amino
acids 187–226 deleted from the polypeptide chain,
which is inside the minimal Rab4 binding fragment.
This suggests that the deletion disrupts the Rab4 bind-
ing site of Rabaptin-5, which is further supported by
the demonstrated lack of interaction between Rab4
and Rabaptin-5d.
The colocalization studies in BHK-21 cells support
the assumption that Rabaptin-5 d can interact with
Rab5 but not with Rab4. Accordingly, the recruitment
of EGFP–Rabaptin-5d on the enlarged Rab5Q79L-
positive endosomes was observed whereas no apparent
colocalization with Rab4Q67L was seen. Finally, we

5d is a Rab5 effector but unlike Rabaptin-5, does not
interact with the Rab4, presumably due to a disrupted
Rab4 binding site, and is thus unlikely to provide a link
to a Rab4-positive domain. It is tempting to hypothesize
that selective recruitment of the d Rabaptin-5 isoform
by an early endosome would disfavor it moving along
the early recycling pathway. This model should be veri-
fied experimentally, and if confirmed, it would provide
an example of membrane traffic regulation through
selective recruitment of a minor Rab effector variant.
Experimental procedures
Plasmids
To construct pPC97-Rab5, pPC97-Rab5Q79L and pPC97-
Rab5S34N, the respective cDNAs were excised from
pLexA-Rab5, pLexA-Rab5Q79L and pLexA-Rab5S34N
[12] with EcoRI and NheI. The cDNAs with filled-in EcoRI
site were subcloned between XbaI and filled-in BamHI sites
in pBK-CMV vector (Stratagene, La Jolla, CA, USA), and
subsequently excised and cloned between SalI and NotI
sites in pPC97 vector [27] to obtained in-frame fusion with
GAL4 DNA-binding domain (GAL4BD).
To construct pPC97-Rab4, pPC97-Rab4Q67L and
pPC97-Rab4S22N, the respective cDNAs were excised from
pLexA-Rab4, pLexA-Rab4Q67L and pLexA-Rab4S22N
[14] with EcoRI and SalI and cloned between EcoRI and
XhoI sites in pBK-CMV vector. After digestion with SpeI,
filling-in and self-ligation, the cDNAs were excised and
cloned between the SalI and NotI sites in pPC97 vector to
produce in-frame fusion with GAL4BD. pPC86-Rabaptin-5
plasmid with a pPC86 backbone [27] for expression of the

the respective cDNAs were excised from the pRn5 and
pRn5d plasmids with XhoI and NotI (the NotI site was
blunted after digestion) and cloned between the XhoI and
SmaI sites in pEGFP-C2 vector (Clontech. Palo Alto, CA,
USA). Plasmids for expression of N-terminally FLAGÒ-
tagged Rabaptin-5 and Rabaptin-5d were constructed in a
following way. The 5¢-end of the Rabaptin-5 coding region
from amino acid 2 was amplified from the pRn5 template
with the antisense primer used to construct deletion
mutants of Rabaptin-5 in the pPC86 vector and the
Fig. 9. Mapping of the Rab4 binding site in Rabaptin-5 using the
yeast two-hybrid protein–protein interaction assay. Indicated frag-
ments of Rabaptin-5 (Rn5), Rabaptin-5d (Rn5d) or Rabaptin-5c
(Rn5c) fused to GAL4AD or GAL4AD alone (none) were coex-
pressed with GAL4BD fused to Rab4Q67L in yeast Y153. Amino
aids of Rabaptin-5 or its isoforms fused to GAL4AD are shown in
brackets, and deleted regions in Rabaptin-5 isoforms are presented
as thin lines. LacZ reporter gene activation caused by interaction
between GAL4BD- and GAL4AD-fused proteins (b-gal) in yeast was
assessed by filter a b-galactosidase assay. A similar assay with
GAL4BD alone as a bait revealed no activation of the LacZ reporter
gene (data not shown).
E. Korobko et al. Rabaptin-5 isoform d is not a Rab4 effector
FEBS Journal 272 (2005) 37–46 ª 2004 FEBS 43
sense primer 5¢-ATGGTACCACTAGATCTGGCGCAG
CC-3¢ containing KpnI and BglII sites, and subcloned
between the KpnI and HindIII sites of pBluescript
SK II(+) vector using the internal HindIII site (plasmid
p5Rn5). The 3¢-end of the Rabaptin-5 coding region inclu-
ding the translation termination codon was amplified with

proteins were then excised with SalI and NotI and cloned
between the XhoI and NotI sites of the pEGFP-N1 vector
(Clontech) to produce expression plasmids for FLAGÒ-
tagged Rabaptin-5 and Rabaptin-5d (the EGFP coding
sequence was removed by digestion with XhoI and NotI).
The plasmid for expression of myc-tagged Rab5Q79L
was described previously [28]. For construction of the myc-
Rab4Q67L expression vector, the Rab4Q67L cDNA from
pPC97-Rab4Q67L was excised and cloned between the SalI
and NotI sites into a pBK-CMV vector engineered to con-
tain after the CMV promoter the fragment of the human
preproinsulin cDNA 5¢-untranslated region and ATG
codon (GeneBank Accession No. NM_000207, nucleo-
tides 10–47) linked by an NcoI site with the NcoI-EcoRI
fragment from the pECT plasmid encoding His
6
and myc
tags. To construct plasmids for expression of glutathione
S-transferase (GST)-tagged Rab4 and Rab5, pGEX-Rab4
and pGEX-Rab5, the respective cDNAs were excised with
EcoRI and SalI from pLexA-Rab4 and pLexA-Rab5 and
cloned into the pGEX-4T-1 vector (Amersham Biosciences,
Chalfont St. Giles, UK).
Yeast two-hybrid methods
The protein interaction assay was performed as described
[29]. In brief, the yeast strain Y153 was used to cotrans-
form bait and prey plasmids, and transformants were selec-
ted by plating onto synthetic dextrose (SD) leucine and
tryptophan dropout plate. To evaluate HIS3 reporter gene
trans-activation, yeast from a single colony was spotted

Antibodies
The anti-Rabex-5 rabbit polyclonal antiserum [13] was a
gift from M. Zerial (Max-Plank Institute of Molecular Cell
Biology and Genetics, Dresden, Germany). Mouse anti-
(EGFP 2G7) monoclonal Igs were kindly provided by A.
Surovoy (Moscow, Russia). Mouse anti-(myc 9E10) mono-
clonal Igs were used as supernatant from the respective
hybridoma, and Alexa546-conjugated anti-mouse Igs
(Molecular Probes, . To detect the FLAGÒ-epitope, rabbit
anti-FLAGÒ polyclonal antibodies (Sigma) were used
following Alexa-488-conjugated antirabbit antibodies
(Molecular Probes, Eugene, OR, USA). Rabbit polyclonal
anti-(Rabaptin-5 Ig) antiserum was raised using a His
6
-
tagged mouse Rabaptin-5 fragment (amino acids 407–663)
as the immunogen. To produce and purify recombinant
protein, QIAexpressionist expression and purification
system (Qiagen, Valencia, CA, USA) was used.
Rabaptin-5 isoform d is not a Rab4 effector E. Korobko et al.
44 FEBS Journal 272 (2005) 37–46 ª 2004 FEBS
Confocal immunofluorescence microscopy
Twenty-four hours after transfection, cells on coverslips
were washed in phosphate-buffered saline (PBS) and fixed
with 3% (w ⁄ v) paraformaldehyde. Free aldehyde groups
were quenched with 50 mm ammonium chloride, and cells
were permeabilized with 0.05% (w ⁄ v) saponin (Sigma).
After permeabilization, coverslips were washed with PBS
and incubated with primary antibodies diluted in PBS con-
taining 5% (w ⁄ v) nonfat dry milk and 0.1% (w ⁄ v)

1mm dithiothreitol, 100 mm NaCl, 1 mm EDTA contain-
ing Protease Inhibitor Cocktail (Sigma)].
Recombinant proteins
GST-Rab4 and GST-Rab5 were produced in Escheri-
chia coli BL21 carrying pGEX-Rab4 and pGEX-Rab5 plas-
mids. Production and purification of GST-tagged proteins
were carried out on Gluthatione Sepharose 4B (APBiotech)
according to the manufacturer’s instructions. Eluted pro-
teins were extensively dialyzed against 50 mm tris ⁄ HCl,
pH 8.0, 135 mm NaCl, 1 mm EDTA followed by dialysis
against the same buffer containing 50% (v ⁄ v) glycerol, and
stored at )20 °C. The final protein concentration was about
2mgÆmL
)1
with purity over 95%.
GST pull-down assay
GST pull-down assays with GDP- or GTPcS-loaded GST–
Rab4 and GST–Rab5 were performed essentially as des-
cribed [11]. Binding and washing were performed in batch,
and cytosols prepared from two 100 mm (diam.) dishes of
BHK-21 transiently transfected with plasmids for expression
of EGFP- or FLAGÒ-tagged proteins were used to pull
down EGFP- or FLAGÒ-tagged Rabaptin-5 or Rabaptin-
5d. Before addition of cytosols to immobilized and nucleo-
tide-preloaded GST-Rab4 or GST-Rab5, cytosols were
diluted two-fold to adjust a final binding buffer composition.
After washing, SDS ⁄ PAGE loading buffer was added to
Sepharose beads, samples were boiled and loaded onto a
7.5% SDS ⁄ polyacrylamide gel. After separation, proteins
were transferred onto Immobilon P poly(vinylidene difluo-

Basic Research and the Physical and Chemical Biology
Program of the Russian Academy of Sciences. E.K.
was partially supported by a FEBS Short-Term Travel
Fellowship.
E. Korobko et al. Rabaptin-5 isoform d is not a Rab4 effector
FEBS Journal 272 (2005) 37–46 ª 2004 FEBS 45
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