1
|
Perica T, Mathy CJP, Xu J, Jang GM, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature 2021; 599:152-157. [PMID: 34646016 PMCID: PMC8571063 DOI: 10.1038/s41586-021-03982-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 09/01/2021] [Indexed: 11/10/2022]
Abstract
Molecular switch proteins whose cycling between states is controlled by opposing regulators1,2 are central to biological signal transduction. As switch proteins function within highly connected interaction networks3, the fundamental question arises of how functional specificity is achieved when different processes share common regulators. Here we show that functional specificity of the small GTPase switch protein Gsp1 in Saccharomyces cerevisiae (the homologue of the human protein RAN)4 is linked to differential sensitivity of biological processes to different kinetics of the Gsp1 (RAN) switch cycle. We make 55 targeted point mutations to individual protein interaction interfaces of Gsp1 (RAN) and show through quantitative genetic5 and physical interaction mapping that Gsp1 (RAN) interface perturbations have widespread cellular consequences. Contrary to expectation, the cellular effects of the interface mutations group by their biophysical effects on kinetic parameters of the GTPase switch cycle and not by the targeted interfaces. Instead, we show that interface mutations allosterically tune the GTPase cycle kinetics. These results suggest a model in which protein partner binding, or post-translational modifications at distal sites, could act as allosteric regulators of GTPase switching. Similar mechanisms may underlie regulation by other GTPases, and other biological switches. Furthermore, our integrative platform to determine the quantitative consequences of molecular perturbations may help to explain the effects of disease mutations that target central molecular switches.
Collapse
Affiliation(s)
- Tina Perica
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK,These authors contributed equally
| | - Christopher J. P. Mathy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA,These authors contributed equally
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA,The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gwendolyn M. Jang
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA,The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Robyn Kaake
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA,The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Noah Ollikainen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America
| | - Hannes Braberg
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA,The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA,The J. David Gladstone Institutes, San Francisco, CA, USA
| | - David G. Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mark J. S. Kelly
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA,The J. David Gladstone Institutes, San Francisco, CA, USA,Correspondence and Requests for Materials should be addressed to: Tanja Kortemme () and Nevan Krogan ()
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA. .,Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
2
|
Li G, Segev N. Newer Methods Drive Recent Insights into Rab GTPase Biology: An Overview. Methods Mol Biol 2021; 2293:1-18. [PMID: 34453706 DOI: 10.1007/978-1-0716-1346-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
The conserved Ypt/Rab GTPases regulate all major intracellular protein traffic pathways, including secretion, endocytosis and autophagy. These GTPases undergo distinct changes in conformation between their GTP- and GDP-bound forms and cycle between the cytoplasm and membranes with the aid of their upstream regulators. When activated on the membrane in the GTP-bound form, they recruit their downstream effectors, which include components of vesicular transport. Progress in the past 5 years regarding mechanisms of Rab action, functions, and the effects of disruption of these functions on the well-being of cells and organisms has been propelled by advances in methodologies in molecular and cellular biology. Here, we highlight methods used recently to analyze regulation, localization, interactions, and function of Rab GTPases and their roles in human disease. We discuss contributions of these methods to new insights into Rabs, as well as their future use in addressing open questions in the field of Rab biology.
Collapse
|
3
|
Sun J, Wang X, Lin H, Wan L, Chen J, Yang X, Li D, Zhang Y, He X, Wang B, Dong M, Zhong H, Wei C. Shigella escapes lysosomal degradation through inactivation of Rab31 by IpaH4.5. J Med Microbiol 2021; 70. [PMID: 34296983 DOI: 10.1099/jmm.0.001382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Shigella flexneri is an intracellular bacterial pathogen that utilizes a type III secretion apparatus to inject effector proteins into host cells.Hypothesis/Gap Statement. The T3SS effector IpaH4.5 is important for the virulence of Shigella.Aim. This study aimed to elucidate the molecular mechanism and host target of the IpaH4.5 as well as its roles in S. flexneri infection.Methodology. The GAP assay was used to identify substrate Rab GTPases of IpaH4.5. A coimmunoprecipitation assay was applied to identify the interaction of Rab GTPases with IpaH4.5. A confocal microscopy analysis was used to assess the effects of IpaH4.5 on mannose 6-phosphate receptor (MPR) trafficking. To identify the effects of IpaH4.5 GAP activity on the activity of lysosomal cathepsin B, the Magic Red-RR assay was used. Finally, the intracellular persistence assay was used to identify IpaH4.5 GAP activity in S. flexneri intracellular growth.Results. We found that the effector IpaH4.5 disrupts MPR trafficking and lysosomal function, thereby counteracting host lysosomal degradation. IpaH4.5 harbours TBC-like dual-finger motifs and exhibits potent RabGAP activities towards Rab31. IpaH4.5 disrupts the transport of the cation-dependent mannose 6-phosphate receptor (CD-MPR) from the Golgi to the endosome by targeting Rab31, thereby attenuating lysosomal function. As a result, the intracellular persistence of S. flexneri requires IpaH4.5 TBC-like GAP activity to mediate bacterial escape from host lysosome-mediated elimination.Conclusion. We identified an unknown function of IpaH4.5 and its potential role in S. flexneri infection.
Collapse
Affiliation(s)
- Jin Sun
- Basic Medical College, Qingdao University, Qingdao, PR China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Xiaolin Wang
- Basic Medical College, Qingdao University, Qingdao, PR China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Haotian Lin
- Basic Medical College, Qingdao University, Qingdao, PR China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Luming Wan
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Ji Chen
- Basic Medical College, Qingdao University, Qingdao, PR China
| | - Xiaopan Yang
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Dongyu Li
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Yanhong Zhang
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Xiang He
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Bin Wang
- Basic Medical College, Qingdao University, Qingdao, PR China
| | - Mingxin Dong
- Basic Medical College, Qingdao University, Qingdao, PR China
| | - Hui Zhong
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| | - Congwen Wei
- Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, PR China
| |
Collapse
|
4
|
Mishra AK, Lambright DG. High-Throughput Assay for Profiling the Substrate Specificity of Rab GTPase-Activating Proteins. Methods Mol Biol 2021; 2293:27-43. [PMID: 34453708 DOI: 10.1007/978-1-0716-1346-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Measurement of intrinsic as well as GTPase-activating Protein (GAP) catalyzed GTP hydrolysis is central to understanding the molecular mechanism and function of GTPases in diverse cellular processes. For the Rab GTPase family, which comprises at least 60 distinct proteins in humans, putative GAPs have been identified from both eukaryotic organisms and pathogenic bacteria. A major obstacle has involved identification of target substrates and determination of the specificity for the Rab family. Here, we describe a sensitive, high-throughput method to quantitatively profile GAP activity for Rab GTPases in microplate format based on detection of inorganic phosphate released after GTP hydrolysis. The method takes advantage of a well-characterized fluorescent phosphate sensor, requires relatively low protein concentrations, and can, in principle, be applied to any GAP-GTPase system.
Collapse
Affiliation(s)
- Ashwini K Mishra
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - David G Lambright
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| |
Collapse
|
5
|
Veloria J, Shin M, Devkota AK, Payne SM, Cho EJ, Dalby KN. Developing Colorimetric and Luminescence-Based High-Throughput Screening Platforms for Monitoring the GTPase Activity of Ferrous Iron Transport Protein B (FeoB). SLAS Discov 2019; 24:597-605. [PMID: 31039677 DOI: 10.1177/2472555219844572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Iron is an essential requirement for the survival and virulence for bacteria. The bacterial ferrous iron transporter protein B (FeoB) functions as a major iron transporter in prokaryotes and has an N-terminal domain (NFeoB) with homology to eukaryotic G-proteins. Its GTPase activity is required for ferrous iron uptake, making it a potential target for antivirulence therapies. Here, two assay strategies relying on different spectroscopic readouts are described to monitor NFeoB GTPase activity. The first one is the colorimetric-based platform that utilizes a malachite green reagent to monitor phosphate production from GTP hydrolysis. The absorbance change directly relates to the GTPase activity of NFeoB. The assay was further improved by the addition of Tween-20 and miniaturized in a 384-well plate format with a 10 µL assay volume. The second format is a luminescence-based platform, measuring the GTP depletion by using a modified GTPase-Glo assay from Promega. In this platform, the luminescence signal correlates to the amount of GTP remaining, allowing for the direct calculation of GTP hydrolysis by NFeoB. The colorimetric platform was tested in a high-throughput manner against a custom-assembled library of a~2000 small molecules and was found to be simple, cost-effective, and robust. Additionally, the luminescence-based platform demonstrated its capability as an orthogonal assay to monitor GTPase activity, providing a valid and convenient method to filter false hits. These two assay platforms are proven to offset the limitations of each platform while enhancing overall quality and success rates.
Collapse
Affiliation(s)
- John Veloria
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Minhye Shin
- 2 Department of Molecular Biosciences, College of Natural Science, The University of Texas at Austin, Austin, TX, USA
| | - Ashwini K Devkota
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Shelley M Payne
- 2 Department of Molecular Biosciences, College of Natural Science, The University of Texas at Austin, Austin, TX, USA
| | - Eun Jeong Cho
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Kevin N Dalby
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,3 Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
6
|
Borg Distefano M, Hofstad Haugen L, Wang Y, Perdreau-Dahl H, Kjos I, Jia D, Morth JP, Neefjes J, Bakke O, Progida C. TBC1D5 controls the GTPase cycle of Rab7b. J Cell Sci 2018; 131:jcs.216630. [PMID: 30111580 DOI: 10.1242/jcs.216630] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/02/2018] [Indexed: 01/01/2023] Open
Abstract
Rab GTPases are key regulators of intracellular trafficking, and cycle between a GTP-bound active state and a GDP-bound inactive state. This cycle is regulated by guanine-nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Several efforts have been made in connecting the correct GEFs and GAPs to their specific Rab. Here, we aimed to identify GAPs for Rab7b, the small GTPase involved in transport from late endosomes to the trans-Golgi. An siRNA screen targeting proteins containing TBC domains critical for Rab GAPs was performed and coupled to a phenotypic read-out that visualized the distribution of Rab7b. Silencing of TBC1D5 provided the strongest phenotype and this protein was subsequently validated in various in vitro and cell-based assays. TBC1D5 localizes to Rab7b-positive vesicles, interacts with Rab7b and has GAP activity towards Rab7b in vitro, which is further increased by retromer proteins. Similarly to the constitutively active mutant of Rab7b, inactivation of TBC1D5 also reduces the number of CI-MPR- and sortilin-positive vesicles. Together, the results show that TBC1D5 is a GAP for Rab7b in the control of endosomal transport to the trans-Golgi.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Marita Borg Distefano
- Department of Biosciences, Centre for Immune Regulation, University of Oslo, 0316 Oslo, Norway
| | - Linda Hofstad Haugen
- Department of Biosciences, Centre for Immune Regulation, University of Oslo, 0316 Oslo, Norway
| | - Yan Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Harmonie Perdreau-Dahl
- Norwegian Center of Molecular Medicine, Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Ingrid Kjos
- Department of Biosciences, Centre for Immune Regulation, University of Oslo, 0316 Oslo, Norway
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jens Preben Morth
- Norwegian Center of Molecular Medicine, Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital, 0424 Oslo, Norway
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, 2300 RC Leiden, The Netherlands
| | - Oddmund Bakke
- Department of Biosciences, Centre for Immune Regulation, University of Oslo, 0316 Oslo, Norway
| | - Cinzia Progida
- Department of Biosciences, Centre for Immune Regulation, University of Oslo, 0316 Oslo, Norway
| |
Collapse
|
7
|
Luo X, Li C, Tan R, Xu X, Wu WKK, Satoh A, Wang T, Yu S. A RasGAP, DAB2IP, regulates lipid droplet homeostasis by serving as GAP toward RAB40C. Oncotarget 2017; 8:85415-85427. [PMID: 29156729 PMCID: PMC5689619 DOI: 10.18632/oncotarget.19960] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Lipid droplet (LD) homeostasis involves activities of various RAB small GTPases. Recently, we found RAB40C was one of the RAB proteins regulating LD homeostasis. RAB40C contains a unique SOCS domain that is required for clustering of LDs. However, its precise functional role in LD homeostasis and mechanism of regulation remain largely unknown. In this study, we observed over-accumulation of LDs in cells with RAB40C deleted by Crispr-Cas9 editing. RAB40C appeared to reduce LD accumulation after long term incubation of cells with oleic acid (24 hours). Unexpectedly, we found that Ras GTPase activating protein (GAP), DAB2IP, bound to RAB40C mainly via its GAP domain and could serve as RAB40C GAP. Studies involving overexpression of DAB2IP and its GAP defective mutant and siRNA depletion of DAB2IP all confirmed that DAB2IP negatively regulated the effect of RAB40C on LD homeostasis. These results provide a novel perspective on the regulation of RAB40C and implicate various signalling pathways regulated by DAB2IP, which may play a role in LD homeostasis via RAB40C.
Collapse
Affiliation(s)
- Xiaomin Luo
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, P.R. China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Chunman Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Ran Tan
- Department of Anesthesia, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Xiaohui Xu
- Department of Anesthesia, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - William K K Wu
- School of Pharmaceutical Sciences, Xiamen University, Fujian, P.R. China
| | - Ayano Satoh
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Tuanlao Wang
- Department of Anesthesia, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| | - Sidney Yu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China.,Epithelial Cell Biology Research Centre, The Chinese University of Hong Kong, Hong Kong SAR, P.R. China
| |
Collapse
|
8
|
Abstract
Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 431-448, 2016.
Collapse
Affiliation(s)
- Ashwini K Mishra
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
| | - David G Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605
| |
Collapse
|