Nucleotide binding is the critical regulator of ABCG2 conformational transitions
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The ABC transporter ABCG2 extrudes chemotherapy reagents and other xenobiotics from a number of different tissues. How ABCG2 operates at the molecular level has been largely derived from structures and dynamics carried out in non-physiological environments. The paper presents convincing cell-based evidence describing the relationship between structural changes of ABCG2 and substrate binding using flow cytometry, confocal microscopy, and fluorescence-correlation spectroscopy methods. Both the mechanistic conclusions and methodology employed offer important insights, which will be of general interest to the biochemistry and transport biology communities.
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Abstract
ABCG2 is an exporter-type ABC protein that can expel numerous chemically unrelated xeno- and endobiotics from cells. When expressed in tumor cells or tumor stem cells, ABCG2 confers multidrug resistance, contributing to the failure of chemotherapy. Molecular details orchestrating substrate translocation and ATP hydrolysis remain elusive. Here, we present methods to concomitantly investigate substrate and nucleotide binding by ABCG2 in cells. Using the conformation-sensitive antibody 5D3, we show that the switch from the inward-facing (IF) to the outward-facing (OF) conformation of ABCG2 is induced by nucleotide binding. IF-OF transition is facilitated by substrates, and hindered by the inhibitor Ko143. Direct measurements of 5D3 and substrate binding to ABCG2 indicate that the high-to-low affinity switch of the drug binding site coincides with the transition from the IF to the OF conformation. Low substrate binding persists in the post-hydrolysis state, supporting that dissociation of the ATP hydrolysis products is required to reset the high substrate affinity IF conformation of ABCG2.
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eLife assessment
The ABC transporter ABCG2 extrudes chemotherapy reagents and other xenobiotics from a number of different tissues. How ABCG2 operates at the molecular level has been largely derived from structures and dynamics carried out in non-physiological environments. The paper presents convincing cell-based evidence describing the relationship between structural changes of ABCG2 and substrate binding using flow cytometry, confocal microscopy, and fluorescence-correlation spectroscopy methods. Both the mechanistic conclusions and methodology employed offer important insights, which will be of general interest to the biochemistry and transport biology communities.
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Reviewer #1 (Public Review):
The ABC transporter ABCG2 exports xenobiotics, including chemotherapy reagents, from a number of different organs. Understanding the mechanism of ATP-dependent transport is of fundamental importance, yet current models have been larger derived from structures and protein dynamics have been carried out in artificial environments. Here the authors have used a fluorescent-labeled antibody specific to the inward-facing conformation and monitored this state in a cell by confocal microscopy and fluorescence-correlation spectroscopy (FSC). They conclude that ATP binding drives substrate efflux and the resetting to an inward-facing conformation requires ATP hydrolysis and the subsequent dissociation of the hydrolysis products. Both the mechanistic insights and methodology employed will be of interest to the …
Reviewer #1 (Public Review):
The ABC transporter ABCG2 exports xenobiotics, including chemotherapy reagents, from a number of different organs. Understanding the mechanism of ATP-dependent transport is of fundamental importance, yet current models have been larger derived from structures and protein dynamics have been carried out in artificial environments. Here the authors have used a fluorescent-labeled antibody specific to the inward-facing conformation and monitored this state in a cell by confocal microscopy and fluorescence-correlation spectroscopy (FSC). They conclude that ATP binding drives substrate efflux and the resetting to an inward-facing conformation requires ATP hydrolysis and the subsequent dissociation of the hydrolysis products. Both the mechanistic insights and methodology employed will be of interest to the biochemistry and transport biology fields.
Strengths: The paper exploits a fluorescent labelled antibody to probe some interesting mechanistic questions in a close-to-native environment. The use of different inhibitors and nucleotides to trap different states is beautifully done and the mechanistic interpretation is convincing. The use of FSC to probe the differences in transporter dynamics in the presence of substrates seems novel and is likely to be of general interest.
Weaknesses. The main weakness is that the probe is only able to detect a signal for the inward state and so a change in conformational state has to be derived from a diminished response, I.e., no probe to specifically monitor the outward-facing state.
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Reviewer #2 (Public Review):
A major challenge to studying the ABC transporter dynamics "in situ" is the lack of precise measurement of various structural conformers that correspond to intermediate states during the ATP-catalytic or substrate-transport cycle. The use of the conformation-specific antibody 5D3 has recently enabled structural biology to experimentally visualize a specific structural fold that corresponds to an apo and inward-facing (IF) state of ABCG2. In this study, Gyöngy et al aimed to develop a mammalian cell-based system for ABCG2 to investigate how nucleotide or drug ligands regulate the transporter's alternating nature of its inward- and outward-facing (OF) conformations. The authors exploited the nature of 5D3 to only recognize ABCG2' IF conformers and combined flow cytometry and confocal microscopy to …
Reviewer #2 (Public Review):
A major challenge to studying the ABC transporter dynamics "in situ" is the lack of precise measurement of various structural conformers that correspond to intermediate states during the ATP-catalytic or substrate-transport cycle. The use of the conformation-specific antibody 5D3 has recently enabled structural biology to experimentally visualize a specific structural fold that corresponds to an apo and inward-facing (IF) state of ABCG2. In this study, Gyöngy et al aimed to develop a mammalian cell-based system for ABCG2 to investigate how nucleotide or drug ligands regulate the transporter's alternating nature of its inward- and outward-facing (OF) conformations. The authors exploited the nature of 5D3 to only recognize ABCG2' IF conformers and combined flow cytometry and confocal microscopy to systematically analyze the IF-OF switches in the presence of nucleotides, drug substrates, ATPase inhibitors, and a known ABCG2 inhibitor Ko143. The authors find that nucleotide binding alone is sufficient to decrease the propensity of IF conformation, as well as to drive the high-to-low drug substrate transformation, and subsequently the drug-induced ATP hydrolysis resets the transporter to the IF and 5D3-bound state. These data provide solid cell-based evidence that adds to the ongoing discussion about the allosteric regulation of ABCG2 by both nucleotide and transport substrate ligands. Most importantly, the results support several lines of functional implications that could not be fully addressed by recent high-profile cryo-EM structures of ABCG2.
Strengths:
The development of the methodology is a tour-de-force effort, as well as the biggest strength of this study. The results and the experimental protocol will likely provide a significant impact on how scientists design experiments to address structural questions without using large-scale purified systems and conventional structural biology approaches.The validity of using the GFP-tagged ABCG2 variant is supported by several lines of functional characterizations, including protein expression, 5D3 reactivity, the responsiveness of nucleotide analogs, and mitoxantrone (MX) accumulation analysis. The application of such a strategy is particularly exemplified by the systematic treatment of various nucleotide analogs, which is sufficient to establish kinetic analysis by looking into apparent nucleotide affinities. These initial works add confidence in performing experiments by using either transport substrates or ABCG2 inhibitors. It is very compelling to see candidly the drug-coupled stimulation of ATP hydrolysis, given that both ATP and ADP decrease the 5D3-bound population.
The development of fluorescence correlation spectroscopy (FCS), the first in such a study, allows the measurement of colocalization of both fluorescence-labeled transporter and transport substrates. As illustrated by MX binding to ABCG2, the data supports the notion that nucleotide binding drives substrate release from the transporters, which in this case, can be explained by the high-to-low substrate binding affinity or IF-OF conformational switch of the transporter. Moreover, such an assay will be likely used as part of a high-throughput pipeline in search of therapeutic drugs against ABCG2.
Weakness:
Although the paper presents solid and compelling cell-based evidence describing the relationship between structural changes of ABCG2 and ligand bindings, the enthusiasm is slightly dampened by the fact that this study seems mostly used to support the hypotheses that were proposed by recent cryo-EM structures. It is unclear from this study whether new insight into ABCG2's working mechanism can be proposed based on the data in this manuscript.In addition, the IF-OF switch represents the transformation of two extreme conformations in ABCG2. The authors do not address the intermediate states, such as occluded conformers, in this study, which makes one wonder whether this is a limitation of the methodology presented in this manuscript. Moreover, interdomain crosstalk is highlighted in this manuscript to address the communication between NBD and TMD. However, it is not clear how the data could say anything about the crosstalk between NBD and TMD. For example, one limitation of recording 5D3 sensitivity on WT proteins may not allow us to pinpoint how structural motifs at the NBD-TMD interface (e.g., Q-loop, triple-helix bundle, polar relay, etc) transmit signals that cause IF-OF switch. The authors do not address how the strategy described here can address such a gap.
Lastly, the authors illustrate the conformational change of 5D3 epitope in the extracellular domain (ECD) by using atomic models in the presence and absence of the antibody. The dynamic information of how the ECD transforms to non-5D3 reactive is limited through this study; for instance, what the timing is to set loose of antibodies upon nucleotide binding, or to what degree of drug binding, IF starts to transit to OF under the physiological condition. Despite this, it is worth noting that 30% of MX-ABCG2 colocalization was still observed in untreated cells, perhaps suggesting a dynamic equilibrium between substrate-bound IF and other conformers.
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Reviewer #3 (Public Review):
The goal of this study was to probe the transition from the IF to OF conformations inside the cells of a multidrug ABC transporter, ABCG2. In order to do so the authors used an antibody that specifically recognized the IF state (the epitope is 'disorganized' in the OF conformation) and this tool was particularly useful to address the conformational changes of ABCG2 that take place inside the permeabilized cells, depleted or not in ATP, and complemented with different combinations of nucleotides, drugs, and inhibitors. This technique was also used to show that the drugs increase the transition from the IF to the OF state.
By using confocal microscopy, the authors showed that ATP depletion led to a majority of ABCG2 that reside in a mitoxantrone-bound IF conformation.
The fluorescence correlation spectroscopy …
Reviewer #3 (Public Review):
The goal of this study was to probe the transition from the IF to OF conformations inside the cells of a multidrug ABC transporter, ABCG2. In order to do so the authors used an antibody that specifically recognized the IF state (the epitope is 'disorganized' in the OF conformation) and this tool was particularly useful to address the conformational changes of ABCG2 that take place inside the permeabilized cells, depleted or not in ATP, and complemented with different combinations of nucleotides, drugs, and inhibitors. This technique was also used to show that the drugs increase the transition from the IF to the OF state.
By using confocal microscopy, the authors showed that ATP depletion led to a majority of ABCG2 that reside in a mitoxantrone-bound IF conformation.
The fluorescence correlation spectroscopy was another powerful approach used by the authors to convincingly demonstrate that the mitoxantrone drug could bind to ABCG2 in the IF conformation only.
Overall, the experiments are sound and the main conclusions drawn by the authors are very well supported by their data. This study unravels the first steps of the catalytic cycle of ABCG2 inside the cells, from drug-binding to a high-affinity site in the IF conformation to drug release from a low-affinity site in the OF conformation. It helps us to better understand how this transporter works in an environment that is physiologically relevant.
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