BioArchitecture, 5:44–53, 2015
Published with license by Taylor and Francis Group, LLC
ISSN: 1949-0992 print / 1949-100X online
DOI: 10.1080/19490992.2015.1102826
COMMENTARIES
High-content analysis of Rab protein function
at the ER-Golgi interface
George Galea and Jeremy C Simpson*
School of Biology and Environmental Science & UCD Conway Institute of Biomolecular
and Biomedical Research; University College Dublin; Dublin, Ireland
ABSTRACT. The Rab family of small GTPases play fundamental roles in the regulation of
trafficking pathways between intracellular membranes in eukaryotic cells. In this short commentary
we highlight a recent high-content screening study that investigates the roles of Rab proteins in
retrograde trafficking from the Golgi complex to the endoplasmic reticulum, and we discuss how the
findings of this work and other literature might influence our thoughts on how the architecture of the
Golgi complex is regulated.
KEYWORDS. ER-Golgi interface, Golgi morphology, high-content screening, Rab proteins,
retrograde traffic
THE RAB PROTEINS AT THE
ER-GOLGI INTERFACE
The Rab GTPases are a large family of small
GTP-binding proteins that regulate distinct
aspects of the endomembrane system, including
vesicle budding, uncoating, motility, fusion,
membrane organization and identity, often
through the recruitment of effectors such as
vesicle tethers, SNAREs, membrane and motor
proteins. Rab proteins accomplish their functions by switching between an inactive GDPbound and an active GTP-bound form, which
determines their ability to bind effectors. In
their inactive state, Rabs are bound to a molecule of GDP dissociation inhibitor (GDI),
Ó George Galea and Jeremy C Simpson
*Correspondence to: Jeremy Simpson; Email: jeremy.simpson@ucd.ie
Submitted: 09/24/2015; Accepted: 09/28/2015.
This is an Open Access article distributed under the terms of the Creative Commons AttributionNon-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted
non-commercial use, distribution, and reproduction in any medium, provided the original work is
properly cited. The moral rights of the named author(s) have been asserted.
Color versions of one or more figures in this article can be found online at www.tandfonline.com/kbia.
44
HIGH-CONTENT ANALYSIS OF RAB PROTEIN FUNCTION AT THE ER-GOLGI INTERFACE
which keeps them in a soluble cytoplasmic
state. The switch of Rab proteins from the
GDP-bound state to the GTP state is mediated
by Rab-specific guanine nucleotide exchange
factors (GEFs), and GTP hydrolysis is
enhanced by GTPase-activating proteins
(GAPs). In addition, so-called GDI displacement factors (GDFs) have been proposed to
play a role in selectively removing Rabs from
GDI and help position the Rab at the appropriate membrane.1,2
Around one third of the »60 members of the
Rab GTPase family found in human cells have
been associated with either the endoplasmic
reticulum (ER) and Golgi complex, or the
membrane intermediates at their interface
(Fig. 1), of which only a handful have been
reasonably well characterized.3 The most
prominent members are Rab1, Rab2, and Rab6
variants; where Rab1 and Rab2 isoforms regulate bi-directional ER-Golgi trafficking and
Rab6 isoforms regulate intra-, early- and postGolgi trafficking.4,5 Other less-characterized
Rabs have been also been associated with the
functionality of the Golgi complex, for example
Rab33b, Rab34, Rab41 and Rab43 have all
been linked with intra-Golgi traffic and to a certain extent Golgi organization. Several Rab
proteins (e.g. Rab8 isoforms, Rab10, Rab11a,
Rab14, and Rab31) function at the trans-Golgi
network (TGN), orchestrating trafficking
events to or from the endosomal system.6,7 At
the ER, close to a dozen Rab proteins (Fig. 1)
perform a diversity of functions, such as organelle maintenance, membrane tubulation, and
control of the lipid environment.8,9
The fact that such a variety different Rab
proteins are found in this part of the endomembrane system suggests that there also must be
numerous and complex molecular mechanisms
in place to ensure their functionality and maintain the local membrane architecture. Surprisingly, despite the field of Rab protein biology
being relatively advanced, we are still adding
to the list of Rab proteins functioning at the
ER-Golgi interface. For example, in the last
3 years, Rab10 and Rab18 have been associated with the regulation of ER structure and
membrane tubule morphology. Complexes containing Rab10 have been found to regulate ER
45
extension and fusion in association with microtubules,10 while Rab18 in conjunction with the
Rab3GAP complex was observed to be
required to maintain normal ER structure.11 Of
additional note is that in recent years the ER
and Golgi complex have become associated
with functions beyond their conventional roles
in protein and lipid synthesis and transport.
One notable example would be a role for these
organelles in autophagy.12-14 Despite the fact
that these 2 sets of membranes engage in such a
variety of tasks, all involving continual loss
and gain of material, remarkably they are able
to retain their unique morphologies in the cell.
Clearly therefore, there is still much to discover
about the ER-Golgi dynamic and how Rab proteins contribute to events here.
GOLGI ORGANIZATION
VS. TRANSPORT
As the Golgi is effectively the meeting point
between the secretory pathway and the endosomal system, maintenance of the morphology of
this organelle at steady-state must at least partially be a consequence of a highly regulated
balance between the amount of membrane that
is internalised at the cell surface and that leaving the ER. Any significant imbalance between
these trafficking pathways would be expected
to affect the structure and therefore function of
the Golgi; similarly alterations in the organization of the Golgi would be expected to result in
the alteration of traffic rates in and out of the
organelle. Therefore, it seems highly likely that
the 2 processes of membrane traffic and organelle maintenance are tightly linked.
Several Rab proteins have been shown to
participate in membrane traffic and organelle
maintenance, such as Rab1, which regulates
COPI-coat mediated transport between the ER
and Golgi through associated interactions with
key effectors such as GBF1. In parallel, it can
interact with and recruit the cis-Golgi matrix
proteins GM130 and giantin, both found to be
crucial for the regulation of Golgi structure and
the tethering of coated vesicles.15-17 Similarly,
Rab2 also promotes the recruitment of the
COPI coat complex to the Golgi membrane and
46
Galea and Simpson
FIGURE 1. Schematic of the Golgi-ER interface illustrating the localization, function and transport
pathways of the Rab proteins according to the literature. Blue and red arrows depict anterograde
and retrograde traffic, respectively.
HIGH-CONTENT ANALYSIS OF RAB PROTEIN FUNCTION AT THE ER-GOLGI INTERFACE
it interacts with GM130 and golgin-45, 2 regulators of Golgi structure.8,18-20 These examples
clearly highlight the linkage between a role for
Rab proteins in organelle structure and trafficking, but when one considers the extensive number of Rab proteins localizing to these
membranes, it seems likely that other family
members will be involved. In order to further
investigate this, we have recently reported the
effects of systematic protein depletion of the
Rab protein family in the context of transport
pathways exiting the Golgi complex, particularly toward the ER.21 This study provides the
first systematic view of the key Rab molecules
operating at the ER-Golgi interface with new
implications for how Golgi architecture is
maintained.
Using a high-content microscopy-based
approach, we systematically assessed and
ranked proteins involved in Golgi-to-ER retrograde transport in cultured mammalian cells.
The screen was performed using a cell line stably expressing a GFP-tagged Golgi enzyme,
which was treated with brefeldin A (BFA) to
stimulate the production of Golgi-to-ER carriers. This allowed us to carry out a population
analysis of the cellular response to the BFA
treatment, specifically to determine the percentage of cells retaining an intact Golgi complex at
each time point after treatment. Loss of this
organelle under these conditions effectively
represents the rate of transport carrier formation and movement of Golgi residents to the
ER, a process which has an absolute requirement for membrane traffic machinery molecules such as Rab proteins. Logarithmic
transformation of the data obtained at each
time point allowed us to apply a linear model
and extract a slope value. The value obtained
for a population of cells treated with negative
control non-silencing small interfering RNA
(siRNA; Neg siRNA), was used to normalize
all subsequent experiments giving us a Golgito-ER trafficking index (GETI). A GETI value
of 1 is considered to represent the Golgi-to-ER
trafficking kinetics of cells in control conditions, while values smaller or larger than 1, represent the inhibition or acceleration of this
transport step.21 Using the same image dataset
we were able to extract various morphological
47
and texture features describing Golgi complex
organization after siRNA treatment, but prior
to BFA addition. The texture features were utilized to classify the cell population into 3 categories (normal, compact and dispersed) based
on their respective Golgi patterns (Fig. 2A),
while at the same time Golgi fragments for
each cell were counted to quantify the extent of
disruption of the organelle. The resulting mean
number of Golgi fragments per cell and per
well were normalized to the values determined
from cells treated with the negative control siRNAs on a plate-by-plate basis, which allowed
the calculation of a ‘Golgi fragmentation index’
(GFI). GFI values greater than 1.0 indicate
Golgi fragmentation whereas values smaller
than 1.0 indicate Golgi compaction (Fig. 2B)
(The image analysis pipeline is presented in
more detail in22).
This quantitative image analysis routine
revealed strong Golgi fragmentation and dispersion phenotypes in cells depleted of Rab1
and Rab2 variants. Rab1a and Rab2a were
found to cause the most significant Golgi fragmentation with GFI values of 1.80 and 1.73
respectively. The depletion also affected the
distribution of the Golgi, with a large percentage of cells in the population exhibiting a
dispersed distribution (29% and 28%, respectively) when compared with the negative control (8%). On the other end of the spectrum,
Rab6a was found to have the lowest GFI value
of 0.68, with 52% of the cells exhibiting a compacted distribution of the Golgi. These parallel
experiments allowed us to rank the proteins
with respect to their influence on Golgi structure as denoted by the GFI values, both in terms
of fragmentation and compaction. The candidates were then further divided into strong and
weak effectors, based on the statistical significance of their effect on the Golgi, when compared to cells treated with negative control
siRNAs. Specifically, depletions with a p-value
of 0.05 to 0.10 were denoted as weak regulators, whereas depletions that had a p-value
smaller than 0.05 were considered strong regulators. In total, 8 Rab proteins (Rab1a, Rab2a,
Rab1b, Rab2b, Rab3d, Rab3c, Rab22a, and
Rab21) were identified as strong disruptors
(and therefore likely regulators) of Golgi
48
Galea and Simpson
FIGURE 2. The effects of Rab protein depletion on Golgi organization and retrograde traffic in
HeLa cells. (A) The heat map indicates the type of Golgi morphology observed in a population of
cells depleted for a specific Rab protein. Texture features were utilized to classify the cell population
into 3 categories (normal, compact and fragmented) based on their respective Golgi patterns. The
results are presented as percentage of the population. (B) The number of Golgi fragments per cell
was measured and a Golgi fragmentation index (GFI) value was calculated for each condition as
described in.22 Asterisks indicate p-values; * (<0 .10 to 0.05), and ** (<0 .05). (C) Graphical representation of the output of the 2 assays carried out in cells systematically depleted for each Rab protein, correlating GFI and Golgi-to-ER trafficking index (GETI) values. Eight proteins displayed
effects on both Golgi structure and Golgi-to-ER trafficking. (A-C) Results are presented as means
from 3 independent experiments.
structure and 6 Rab proteins (Rab24, Rab26,
Rab3b, Rab23, Rab5b, and Rab3a) as weak
disruptors. We also identified one Rab
protein (Rab6a) causing a Golgi compaction
phenotype.
These corresponding experiments therefore
allowed us to directly compare the effect of
Rab protein depletion on Golgi organization
and transport, through the direct comparison of
the GETI and GFI values. Correlation between
effects on Golgi structure and retrograde transport out of the Golgi was observed for many of
the identified regulators, with Rab1, Rab2,
Rab3b, Rab6a, Rab8b and Rab21 being particularly prominent (Fig. 2C). Perhaps unsurprisingly, the primary Rabs associated with the
HIGH-CONTENT ANALYSIS OF RAB PROTEIN FUNCTION AT THE ER-GOLGI INTERFACE
ER-Golgi interface, Rab1 and Rab2, were
found in this group of strongest regulators of
both Golgi organization and transport. As discussed above, Rab1 and Rab2 variants have
long been associated with the regulation of
anterograde and COPI-dependent retrograde
traffic, in addition to linking to Golgi matrix
proteins. Depletion of the COPI-independent
retrograde pathway regulator Rab6a also inhibited Golgi-to-ER traffic in our assay, as well as
inducing a compact Golgi phenotype, similar to
that previously described.23-25 This GTPase has
been shown to interact with various Golgi proteins but one of its binding partners, myosin-II,
is particularly interesting, since it provides a
link between the Rab protein and the actin cytoskeleton.26 Depletion of this myosin using siRNAs also induces a compact Golgi in cells
(Galea & Simpson, unpublished observations),
a phenotype that has been observed by others
on perturbation of the actin network.27,28
Although Rab6a is a fundamental driver of
membrane flow from Golgi cisternae (it is
highly visible on the carriers themselves), these
observations suggest a wider role in maintenance of Golgi architecture perhaps through the
actin cytoskeleton.
Interestingly, the depletion of Rab3 and
Rab21 also resulted in the alteration of Golgi
structure and inhibition of Golgi-to-ER traffic.
This was unexpected, as other studies have suggested that these Rab family members are primarily localized to membranes distal from the
ER-Golgi interface. The individual down-regulation of the 4 Rab3 isoforms revealed that
Rab3a and Rab3d induced strong Golgi fragmentation, whereas Rab3b strongly inhibited
Golgi-to-ER transport along with a mild fragmentation of the organelle. At first glance,
these results are not easily explained, especially
with regard to their influence on retrograde trafficking, as Rab3 isoforms have been associated
principally with the regulation of secretory
vesicles and to a certain extent endosomal compartments.29,30 These GTPases are relatively
poorly characterized and most of the studies
examining their regulatory roles have been carried out in neurons and endocrine cells, in
which they are enriched.31 However, recent
reports have linked Rab3 with multiple
49
effectors which themselves function either in
Golgi organization or Golgi-to-ER trafficking.
Particularly interesting are 2 effectors, the
growth-arrest-specific gene 8 (GAS8), a
microtubule-binding protein found on Golgi
membranes,32 and the Rab3GAP complex
(Rab3GAP1/2) shown to be required for the
recruitment of Rab18 and vesicle-associated
membrane protein (VAMP) associated protein
B (VAPB) to the ER membrane and ER-Golgi
interface, respectively, where both proteins are
needed for the organization,11,33 lipid control
and trafficking activities34-37 of the 2 organelles. Knowledge of these interactions allows
us to postulate that the depletion of Rab3 isoforms might have an upstream effect on early
secretory pathway membranes, either indirectly
by causing an imbalance in trafficking to or
from the TGN, or directly through a change in
recruitment kinetics of these Rab3 effectors
recently found at the ER-Golgi interface.
Another consideration is how Rab3 levels may
influence other Rabs on nearby membranes.
The downregulation of any Rab protein in a
network can result in an increased concentration of its effectors in a soluble pool. This
might have various consequences, including
up- or down-regulation of proteins in complementary networks38 to compensate for the
imbalance, the disruption of Rab cascades due
to higher levels of GAPs or GEFs common to
other Rab proteins leading to uncontrolled budding or fusion of vesicles,9,39 or in the case of
the 2 effectors described above, misregulation
of the lipid environment at the ER and Golgi.
Altogether, Rab3 isoforms and their interactors
seem likely to be playing a wider role in organization of the ER-Golgi interface than previously appreciated.
The second endosomal GTPase identified,
Rab21, predominantly localizes to the early
endocytic pathway, although a small population residing on the Golgi stacks has been
visualized in immuno-electron microscopy
studies.40 This Rab protein has been implicated in numerous functions, including the
trafficking of integrins and receptors responsible for cell adhesion, migration, cell polarity
and cytokinesis.41,42 However, it has also been
shown to interact with various actin and
50
Galea and Simpson
microtubule cytoskeleton regulators, which in
turn coordinate the transport of intracellular
vesicles.43-45 The Rab21 GEF, Varp, has been
shown to interact with the TGN-localized golgin p230,43 a protein important for Golgi positioning and possibly dynein-dynactin directed
transport.46 These interactions therefore implicate Rab21 in a role regulating the cytoskeletal organization of the Golgi, in addition to its
established trafficking role at the TGN and
endosomes.
Our results also revealed certain Rab protein depletions that disrupted only one process
(either trafficking or Golgi architecture) without having an effect on the other. For example,
a number of Golgi-associated Rab proteins
identified in the Golgi-to-ER trafficking
screen, namely Rab10, Rab11a and Rab34,
each showed no detectable effect on Golgi
morphology when depleted. Rab10 and
Rab11a have been shown to mainly reside on
various endosome populations, however in
both cases a small proportion has been
reported to be present on juxta-nuclear Golgi
membranes47 and, as described above, Rab10
has been recently associated with ER membranes.10 We observed fluorescently-tagged
Rab10 and Rab11a on Golgi-derived carriers
induced in the presence of BFA, suggesting
that they might play a more direct role in
transport than previously appreciated. This
will clearly need further in depth analysis to
understand its significance. Rab34 localizes
throughout the Golgi stack, both on Golgi cisternae and on a population of Golgi-associated
vesicles, including cis-Golgi-derived transport
carriers.48 Previous protein depletion studies
have shown that Rab34 is required for anterograde intra-Golgi transport of GFP-tagged
vesicular stomatitis virus glycoprotein (VSVG), a model secretory cargo molecule, but that
its depletion has no effect on Golgi-to-TGN
transport.48 Why the depletion of Rab34 inhibits Golgi-to-ER traffic is also unclear at this
stage. One possibility is that by disrupting
intra-Golgi traffic, there would be a consequential change in the intra-Golgi distribution
of certain membrane-associated molecular
machinery (for example SNAREs and tethering factors) that would need to be assembled
on retrograde-destined carriers prior to their
departure from the Golgi. If this was the case,
it highlights an impressive regulatory mechanism to govern the fidelity of membrane traffic
events from this organelle.
CONCLUSION
A huge number of contributions over the
years allow us now to appreciate that several
Rab proteins, in particular Rab1, Rab2, Rab8,
Rab6, Rab18, Rab33b and Rab43 are fundamental for normal Golgi function in mammalian cells.18,49,50 A number of these proteins
seemingly play a wider role in linking organelle morphology with trafficking at the ERGolgi interface. Cellular depletions of either
Rab1a/b, Rab2a/b or Rab6a all exhibit a strong
influence on Golgi organization as well as
Golgi-export, while comparatively few Rab
proteins known to function in trafficking in or
out of the TGN affect organelle structure
when depleted. This suggests that membrane
flux at the ER-Golgi interface, rather than at
the Golgi/TGN-endosome interface, plays a
more critical role in governing the morphology of this central organelle. Alterations in
trafficking of specific lipids or structurally
important membrane proteins supplied from
the ER are undoubtedly part of the explanation
for many of the observed effects on these
membranes, but further systematic approaches
are needed if we are to fully understand how
the internal architecture of the cell is
maintained.
DISCLOSURE OF POTENTIAL
CONFLICTS OF INTEREST
No potential conflicts of interest were
disclosed.
FUNDING
This work was funded by a Principal Investigator (PI) grant (09/IN.1/B2604) from Science
Foundation Ireland (SFI) to JCS. This work
HIGH-CONTENT ANALYSIS OF RAB PROTEIN FUNCTION AT THE ER-GOLGI INTERFACE
was carried out in the UCD Cell Screening
Laboratory, supported by a grant from the
UCD College of Science.
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