Correspondence to Ian G. Macara: igm9c{at}virginia.edu
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Introduction |
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Imp contains a COOH-terminal region that binds directly to proteins containing an NLS sequence (Conti et al., 1998; Herold et al., 1998). However, Imp
also contains an NH2-terminal auto-inhibitory domain that blocks the NLS-binding site (Kobe, 1999). Binding of Impß to Imp
relieves this auto-inhibitory blockade and allows Imp
to bind cargo proteins with high affinity (Fanara et al., 2000).
Translocation of the ImpImpßcargo complex through the NPC is thought to be mediated by weak hydrophobic interactions between Impß and nucleoporins (Bayliss et al., 2000). On the nuclear side of the NPC, RanGTP dislodges Impß from the complex (Görlich et al., 1996). The Imp
cargo heterodimer then dissociates, assisted by the high affinity binding of CAS to NLS-free Imp
. CAS is a karyopherin that serves to export Imp
in association with RanGTP (Kutay et al., 1997). Both the RanGTPImpß and RanGTPCASImp
complexes translocate back to the cytoplasm where RanGAP (assisted by RanBP1 and Imp
) hydrolyzes the RanGTP to RanGDP (Bischoff and Görlich, 1997; Floer et al., 1997; Petersen et al., 2000). The export complexes disassociate and the transport receptors are recycled for another round of import (Fig. 1).
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Smith et al. (2002) conducted the first in silico analysis of Ran transport. A system of ordinary differential equations (ODEs) was created using the Virtual Cell software to describe reactions and fluxes of proteins involved in Ran Transport (Loew and Schaff, 2001; Smith et al., 2002). These proteins were set at known initial concentrations and allowed to come to steady state. A jump in cytoplasmic Ran concentration was used to simulate the micro-injection of recombinant Ran. Sensitivity analysis showed that RCC1 dominated changes in steady-state Ran flux, whereas NTF2 and the permeability of NTF2RanGDP had smaller effects. Increases in RanBP1, RanGAP, karyopherins, and the permeability of the RanGTPkaryopherin complex had no effect on Ran flux at steady state. A similar analysis to determine rate-limiting components of the initial rate of Ran import after cytoplasmic injection showed that NTF2 was limiting, but that the initial rate of import was insensitive to RCC1.
To compare simulation results with Ran flux in live cells, a fluorescently tagged Ran (RanFl) was injected into BHK21 cells and imaged using confocal microscopy. Time-lapse images were used to quantify nuclear accumulation and import rate of the Ran. Co-injected NTF2 produced positive changes in the initial rate of import and steady-state N/C ratio of Ran, as predicted by the model. RanGAP produced no changes, which also is consistent with the model. RCC1 depletion was tested using tsBN2 cells. These cells possess a temperature-sensitive RCC1 mutation, so that at 39.5°C the mutant RCC1 is rapidly degraded (Uchida et al., 1990). Temperature-shifted tsBN2 cells showed reduced nuclear accumulation of Ran but only small affects on initial rate of Ran import, which is consistent with the model.
Görlich and colleagues (Görlich et al., 2003) developed a model to study how the nuclearcytoplasmic Ran gradient couples to nuclear import through Impß. The authors modified several kinetic parameters in their simulation of the Ran GTPase system. Most significantly, the Michaelis-Menten model of RCC1 used by Smith et al. (2002) was replaced by a four-step reversible series of reactions for GTPGDP exchange, based on a detailed in vitro kinetic analysis by Klebe et al. (1995b). The kcat/Km for RanGAP was also adjusted upward to reflect enzyme activity at 37°C. This simulation predicted that decreases in nuclear RCC1 would reduce RanGTP accumulation, but that RCC1 is not limiting for the system. Conversely, the simulation suggested that RanGAP is limiting. Lastly, nuclear accumulation of RanGTP was shown to be heavily dependent on the GDP/GTP ratio used in the model. The model also predicted a close relationship between the RanGTP gradient and the nuclear/cytoplasmic ratio of cargo concentration at steady state.
In summary, the Smith and Görlich kinetic models show how the RanGTP gradient is established and used to drive a nuclear cargo gradient, and that even a simple system of interacting proteins can generate behavior that would difficult to predict using a static model.
In the current study, we extend the RanGTPase model to show how the Ran gradient couples to nuclear cargo import through the ImpImpß system. Using a compartmental model, we show how the system of known biochemical reactions involved in Imp
Impß import can successfully recapitulate nuclear import seen in vivo. Predictions from the model were tested in vivo by monitoring nuclear import in whole cells. Unexpectedly, the model predicted that increasing the concentrations of RCC1 or Impß would inhibit rather than stimulate the initial rate of cargo import, and these effects were validated experimentally.
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Results |
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Quantitative models of nuclear protein import are necessarily complex, because of the large number of factors involved in a single transport cycle. Moreover, there are multiple pathways for nuclear import and export, all of which use some factors such as Ran and NTF2 in common, but which use different karyopherins (Görlich and Kutay, 1999; Chook and Blobel, 2001; Macara, 2001). The concentrations and even the identities of all the cargoes for each of these karyopherins remain mostly unknown. However, the kinetics of the Ran cycle and of individual components of the Impß pathway have been well studied. Therefore, in our computer model we used experimentally determined parameters for Ran and Imp
ß, and included terms for a generic karyopherin to account for other nuclear transport pathways. The same kinetic parameters were used for the generic karyopherin as for Impß. This approach seems reasonable because karyopherins such as transportin bind Ran with an affinity similar to that of Impß, while karyopherins that have a much lower affinity for Ran will not significantly perturb the system. Another complication is that there are probably hundreds of endogenous cargoes for Imp
ß, most of which have not yet been characterized, and their cytoplasmic concentrations are unknown. Necessarily, therefore, we initially treated the concentration of endogenous cargo as a floating parameter. Endogenous cargo and labeled cargo reactions were modeled with identical but separate reaction pathways (Fig. S1) using the parameters listed in Tables IIII.
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One important limitation of the model is that it does not include terms for competition between different transport pathways at the level of permeability across the nuclear envelope. Thus, permeabilities measured in vitro (using digitonin-treated cells) are likely to be rather higher than permeabilities measured for the same proteins in intact cells where the proteins are competing with other endogenous proteins for access to the pores. However, we know that the NPC has a high capacity and the import rate is, to a first approximation, linear with concentration over the concentration range of GGNLS used in this study. Competition is unlikely, therefore, to be a major source of error in the modeling. Moreover, the sensitivity analysis (see below) suggests that the cargo import rate is not limited by the permeabilities of many of the transport components in the model.
Sensitivity analysis
To identify possible rate-limiting steps in nuclear protein import, we performed a global sensitivity analysis on reactant concentrations in the model (Fig. 3). Reactant concentrations were varied individually over a five log scale from 0.0001 to 10 times the initial concentration. After allowing the system to come to steady state for 1,000 s, the cytoplasmic injection of GGNLS was simulated. Normalized initial rates of GGNLS import were then plotted as a function of initial concentration.
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The initial import rate is also highly sensitive to the concentration of NTF2, which mediates the import of Ran into the nucleus, although the dynamic capacity is not so large as for Imp or Ran. Perturbations in the concentration of NTF2 will alter the import rate because the RanGTP gradient across the nuclear envelope is coupled to the rate at which RanGDP is recycled back into the nucleus.
The sensitivity analysis showed that RanGAP is not limiting for cargo import, and that the concentration of its cofactor, RanBP1, can be reduced at least 10-fold before cargo import is affected. Cytoplasmic RanBP1 forms a RanBP1ImpßRanGTP complex but then is immediately released in the next reaction step when RanGAP triggers GTP hydrolysis, and the complex disassociates (Fig. 1). This rapid recycling of RanBP1 allows it to be effective at submicromolar levels. By contrast, the nucleotide exchange factor for Ran, RCC1, shows an unexpectedly complex relationship to cargo import, in that either a reduction or an increase in the cellular RCC1 concentration relative to the endogenous level strongly inhibits import. A reduction in RCC1 reduces the concentration of free nuclear RanGTP, which leads to a nuclear accumulation of ImpßImpcargo complexes that cannot dissociate, and of Imp
which cannot be exported back to the cytoplasm by CAS. But why would an increase in RCC1 also inhibit cargo? The explanation lies in the four-step kinetic model for nucleotide exchange, described by Wittinghofer and colleagues (Klebe et al., 1995b). In this model, RCC1 has a significant affinity for Ran, and high concentrations of the exchange factor sequester Ran in the nucleus as an RCC1Ran complex. The free concentration of RanGTP available to dissociate import complexes and export Imp
is therefore reduced, with a consequent inhibition of cargo import.
Another unexpected outcome of the sensitivity analysis was the inhibitory effect of high Impß concentrations. Intuitively, one might have predicted that increasing the amount of the transport receptor for GGNLS cargo would stimulate import. However, the receptor and Ran levels are finely balanced in the model and, if in excess, the Impß translocates into the nucleus in an unloaded state, then sequesters free RanGTP, and delivers it to the cytoplasm where it is hydrolyzed. This process is called futile cycling, and it depletes the nucleus of RanGTP, thereby inhibiting cargo import. A similar, but less dramatic effect is seen at high concentrations of CAS, which also reduce import (Fig. 3).
We also performed a sensitivity analysis of the NPC permeability constants for various transport components (Fig. S3, available at http://www.jcb.org/cgi/content/full/jcb.200409024/DC1), which predicts that the system is fairly robust to perturbations in many of these constants. Thus, the predictions of the computer simulations are not dependent on their exact magnitudes. This is important, because we do not have experimental data on the permeabilities of all the components of the model.
Experimental approach
Experimental tests of this type of global sensitivity analysis are complicated by the need to change the endogenous concentration of each factor by a known amount, before the injection of the fluorescent import cargo. Ectopic expression from a plasmid varies from cell to cell, and cannot easily be measured until after the experiment has been completed. Micro-injection is also highly variable from cell to cell, because the injected volume is very sensitive to back pressure and needle diameter. Therefore, we chose in most cases to use co-injection of the GGNLS cargo with known concentrations of recombinant factors. Although the amount of injected cargo and factor will vary from cell to cell, the actual concentrations can be calculated from the total GFP fluorescence intensity within each cell. One advantage of computational modeling is the ease with which effects on transport rate can be calculated and compared with experimental data even when there are two variables for each data point (the cargo concentration and the factor concentration).
Imp is a limiting reactant for nuclear import
To test the predictions of the computer model for nuclear import, we performed co-injection experiments using 20 µM GGNLS as the labeled cargo. The GGNLS was injected together with recombinant transport factors into the cytoplasm of HeLa cells that were maintained at 37°C. The total amount of injected cargo and its initial rate of import were then quantified as described in Materials and methods. The variability in the injected volume from cell to cell generates a range of initial cytoplasmic concentrations that can be plotted against the initial rates. To provide a direct comparison with the model, we generated a series of simulations that directly mirrored the conditions used in the co-injection experiments, over the same range of initial cargo and factor concentrations.
The initial cytoplasmic concentration of cargo varied from 0.5 to 4 µM, and the initial import rate was linear with concentration over this range (Fig. 4 A), showing that, as predicted by our model, the Imp
ß transport system is operating well below maximum capacity in HeLa cells. The concentration at half-maximal import rate (K0.5) for cargo in silico was calculated to be
12 µM.
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Import is insensitive to elevated CAS concentration
During each transport cycle, Imp needs to be recycled back to the cytoplasm. It is exported in a complex with RanGTP and CAS. Therefore, we expected that increasing the concentration of CAS in the cell would increase the availability of cytoplasmic Imp
and therefore increase the cargo import rate. However, the model predicts that CAS is not limiting for import (Fig. 3 and Fig. 5 B). We addressed this possibility using recombinant CAS. To test the functionality of the CAS, we used a permeabilized cell assay, and observed that the recombinant CAS could accumulate in the nuclei of HeLa cells (Fig. 5 C). Second, we conducted binding assays between CAS, Imp
, and RanGTP, using a constitutively active mutant of Ran (RanQ69L) (Fig. 5 D). The recombinant CAS bound Imp
and showed increased binding in the presence of RanGTP. However, when the CAS was co-injected with GGNLS into intact HeLa cells, it had no detectable effect on import. These data show that CAS is not limiting for the initial rate of
ß cargo import into the nucleus.
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Increased nuclear RCC1 inhibits cargo import
One unexpected prediction of the computer simulations was that the endogenous RCC1 concentration is finely balanced to provide the maximum RanGTP gradient. A reduction in the amount of RCC1 in the nucleus will of course reduce the production of RanGTP, but an increase in the amount of RCC1 also is predicted to reduce the free RanGTP concentration, through the formation of an RCC1RanGTP complex.
A small decrease in nuclear RanGTP in response to elevated RCC1 was proposed previously (Görlich et al., 2003), but this decrease was not predicted to alter the dynamic capacity of the system for Ran-driven transport, and no analysis of transport rates was performed. We found that cytoplasmic co-injection of recombinant RCC1 with GGNLS in equimolar ratio did inhibit import (unpublished data) but this result could arise because the RCC1 generates RanGTP in the cytoplasm, which would disassociate import complexes, and it might compete with the GGNLS for binding to Imp (Nemergut and Macara, 2000). Therefore, we tested the effect of RCC1 by transfection of HeLa cells with an mRFP-RCC1 construct, and then compared the import rates for injected GGNLS in cells that expressed the RFP fusion protein versus those that did not. As shown in Fig. 8 A, GGNLS import was dramatically inhibited in those cells that express mRFP-RCC1, as compared with adjacent cells that were injected 1020 s earlier and that do not express the fusion protein. Cells transfected with mRFP alone showed no inhibition of import (Fig. 8 B), confirming that the effect is dependent on RCC1 expression and is not a nonspecific response to the mRFP.
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Excess Impß suppresses the initial rate of nuclear import
Counter-intuitively, the model predicts that the co-injection of Impß with cargo suppresses rather than stimulates the initial rate of GGNLS import (Fig. 3 and Fig. 9 B). Why does this surprising effect occur? The simulation shows that excess Impß undergoes futile cyclingthat is, it translocates into the nucleus without cargo, where it sequesters free RanGTP. Without an available pool of free RanGTP, the ImpImpßcargo heteromer cannot dissociate, so the cargo is not released, and will not accumulate in the nucleus.
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The underlying mechanism for the inhibition of cargo import by increased Impß is the sequestration of nuclear RanGTP, and the model predicts that addition of exogenous Ran can reverse this effect (Fig. 10 A). The additional Ran accumulates in the nucleus in the GTP-bound form, replenishing the free RanGTP pool that has been reduced by the excess Impß, and hence stimulating import (Fig. 10 B). To test this prediction, we first transfected HeLa cells with a fusion protein of Ran and RFP (mRFP-Ran). We then co-injected GGNLS and Impß into those cells that showed nuclear accumulation of mRFP-Ran. Compared with nontransfected cells from the same population, the mRFP-Ran cells showed significant reduction of the Impß effect on initial rate (Fig. 10 B). This result strongly argues that the observed effect of Impß on import rates is not a consequence simply of contamination by inhibitory fragments of Impß, and also validates the computer model.
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Discussion |
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The model was successful in making two unexpected and accurate predictions about the behavior of the nuclear transport system: that elevations in the cellular concentrations of either impß or RCC1 would inhibit rather than stimulate cargo import. The inhibitory effect of Impß demonstrates that futile cycling of transport receptors across the nuclear envelope can significantly deplete the Ran gradient. The levels of Impß and of similar karyopherins must therefore be carefully regulated to reduce the steady-state concentration of free receptors in the cell. We have suggested previously that transport cofactors such as RanBP3 and NPAP60 might also function to reduce futile cycling (Lindsay et al., 2001; Nemergut et al., 2002). We have not included these cofactors in the current model, but expect that they might reduce the inhibitory effect of high Impß levels.
The effect of RCC1 is of interest because it is a consequence of the kinetic model for exchange that was used in the transport model. In our earlier study, virtual cell simulations of Ran transport, we used simple Michaelis-Menten kinetics that did not produce the same outcome (Smith et al., 2002). These results therefore suggest that the four-step in vitro kinetic analysis of exchange by RCC1 provides an accurate reflection of the in vivo kinetics. Our model also predicts that RanGAP is not rate-limiting, and this was validated experimentally.
We believe that our model provides a foundation on which to test other concepts in nuclear transport. For example, it is not apparent why the cell uses the Imp adaptor to bind cargo, rather than allowing all cargo to interact directly with the Impß karyopherin. One speculation is that the coupling of cargo import to the export of Imp
, mediated by CasRanGTP, might drive the creation of a higher nuclearcytoplasmic cargo gradient. The potential effects of competition between karyopherins for binding to the same cargo, or to the NPC, are also complex. In the future we will test these ideas both experimentally and in silico, using a modified transport model.
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Materials and methods |
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After construction of the model, parameter optimization was conducted using a genetic algorithm implemented in the Jarnac scripting language (Bäck and Schwefel, 1993).
Constructs, cell culture, and transfections
The ORFs for human Ran and RCC1 were subcloned into a mammalian vector (pKmRFP1) to generate mRFP-Ran and mRFP-RCC1 fusion proteins (T. Chen, University of Virginia). The mRFP1 was provided by R. Tsien (University of California, San Diego, La Jolla, CA; Campbell et al., 2002) and recombinant Cas by M. Yamada (University of Virginia). HeLa cells were transfected with the mRFP vectors using Effectene (QIAGEN) according to the manufacturer's instructions. The medium was changed to Ringer's solution 1224 h after transfection, and the cells were imaged using confocal microscopy.
Immunofluorescence
HeLa cells were fixed and immunostained with anti-Ran and anti-Imp mAbs (Signal Transduction Laboratories) as described previously (Smith et al., 1998).
Protein binding assays
Proteins were purified as described previously (Plafker and Macara, 2000b; Brownawell and Macara, 2002; Smith et al., 2002). Recombinant Impß was tested for its ability to bind both RanGTP and Imp.
-BindSepharose beads were first blocked with 3% BSA. GST-Imp
and Impß were then added in binding buffer and incubated for 1 h at 4°C (20 mM Tris, pH 7.4, 2 mM MgCl2, 200 mM NaCl, 0.1% BSA, 0.1% Tween, 2 mM DTT). The beads were washed with binding buffer lacking BSA. Proteins were eluted with Laemmli sample buffer, separated by SDS-PAGE and visualized by Coomassie brilliant blue staining. Binding of Impß to the constitutively active Ran mutant, RanGTP(Q69L), and of CAS to GSTImp
and Ran(Q69L), were tested in a similar manner.
Microinjection
HeLa cells were cultured in Bioptek Delta-T dishes. The medium was exchanged to a physiological saline (25 mM Hepes, pH 7.2, 110 mM NaCl, 5 mM KCl, 2 mM CaCl2, 1 mM MgSO4, 10 mM glucose, 1 mM KH2PO4, 1 mg/ml BSA) before microinjection. A fusion protein of GGNLS was used as a cargo to quantify nuclear import. The GGNLS was diluted with microinjection buffer to a final concentration of 20 µM. Co-injected proteins were added to give a final concentration of 5 µM in the injection mixture. Samples were centrifuged at 10,000 g at 4°C for 5 min before injection.
Confocal microscopy
A confocal microscope (model Meta LSM510; Carl Zeiss MicroImaging, Inc.) was used to collect time-lapse images. Cells were imaged using a 20x objective lens (NA = 0.65) at a zoom of 1.0. Detector gain was kept beneath 550 to maintain linearity of pixel intensity to concentration. Cells were kept at 37°C and the medium was changed every 15 min to avoid changes in concentration caused by evaporation. Cells were injected using Femtotips on an Eppendorf Injectman NI 2. After cytoplasmic injection, time-lapse images were taken every 20 s to quantify nuclear import for GGNLS. Average nuclear pixel intensity was related to protein concentration by the use of a standard dilution series of known concentration. Initial rates were calculated as the linear regression of the first three data points of nuclear accumulation. The significance of differences between control and experimental rates over a range of GGNLS concentrations was computed by a two-way ANOVA, using the R statistical package (http://cran.r-project.org/). Differences were assumed to be significant for P < 0.05. To quantify permeability factors, Impß and Imp were first labeled with OGI. After cytoplasmic injection, images were acquired every second. The slope of initial nuclear concentration versus initial rate provided the permeability factor for each protein.
Online supplemental material
Computer model. A complete schematic of the computer model is provided in Fig. S1. A script file containing the model is also included and can be run using the program Jarnac, which can be downloaded from http://64.17.162.114/downloads/ISetup.exe.
Permeability assays. Fig. S2 shows import rate data for recombinant OGI-labeled Imp and Impß, and for GST-GFP.
Sensitivity analysis of permeabilities. Fig. S3 shows the effects of varying permeabilities for various components of the model on the initial rate of GGNLS import. Online supplemental material is available at http://www.jcb.org/cgi/content/full/jcb.200409024/DC1.
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Acknowledgments |
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This work was supported by grants GM50526 and GM064437 from the National Institutes of Health and Department of Health and Human Services.
Submitted: 7 September 2004
Accepted: 16 February 2005
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References |
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