1
|
Gingras RM, Sulpizio AM, Park J, Bretscher A. High-resolution secretory timeline from vesicle formation at the Golgi to fusion at the plasma membrane in S. cerevisiae. eLife 2022; 11:e78750. [PMID: 36331188 PMCID: PMC9671497 DOI: 10.7554/elife.78750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Most of the components in the yeast secretory pathway have been studied, yet a high-resolution temporal timeline of their participation is lacking. Here, we define the order of acquisition, lifetime, and release of critical components involved in late secretion from the Golgi to the plasma membrane. Of particular interest is the timing of the many reported effectors of the secretory vesicle Rab protein Sec4, including the myosin-V Myo2, the exocyst complex, the lgl homolog Sro7, and the small yeast-specific protein Mso1. At the trans-Golgi network (TGN) Sec4's GEF, Sec2, is recruited to Ypt31-positive compartments, quickly followed by Sec4 and Myo2 and vesicle formation. While transported to the bud tip, the entire exocyst complex, including Sec3, is assembled on to the vesicle. Before fusion, vesicles tether for 5 s, during which the vesicle retains the exocyst complex and stimulates lateral recruitment of Rho3 on the plasma membrane. Sec2 and Myo2 are rapidly lost, followed by recruitment of cytosolic Sro7, and finally the SM protein Sec1, which appears for just 2 s prior to fusion. Perturbation experiments reveal an ordered and robust series of events during tethering that provide insights into the function of Sec4 and effector exchange.
Collapse
Affiliation(s)
- Robert M Gingras
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Abigail M Sulpizio
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Joelle Park
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Anthony Bretscher
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| |
Collapse
|
2
|
Felline A, Raimondi F, Gentile S, Fanelli F. Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release. Comput Struct Biotechnol J 2022; 20:5162-5180. [PMID: 36187918 PMCID: PMC9508438 DOI: 10.1016/j.csbj.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Ras GTPases are molecular switches that cycle between OFF and ON states depending on the bound nucleotide (i.e. GDP-bound and GTP-bound, respectively). The Rab GTPase, Sec4p, plays regulatory roles in multiple steps of intracellular vesicle trafficking. Nucleotide release is catalyzed by the Guanine Nucleotide Exchange Factor (GEF) Sec2p. Here, the integration of structural information with molecular dynamics (MD) simulations addressed a number of questions concerning the intrinsic and stimulated dynamics of Sec2p and Sec4p as well as the chain of structural deformations leading to GEF-assisted activation of the Rab GTPase. Sec2p holds an intrinsic ability to adopt the conformation found in the crystallographic complexes with Sec4p, thus suggesting that the latter selects and shifts the conformational equilibrium towards a pre-existing bound-like conformation of Sec2p. The anchoring of Sec4p to a suitable conformation of Sec2p favors the Sec2p-assisted pulling on itself of the α1/switch 1 (SWI) loop and of SWI, which loose any contact with GDP. Those deformations of Sec4p would occur earlier. Formation of the final Sec2p-Sec4p hydrophobic interface, accomplishes later. Disruption of the nucleotide cage would cause firstly loss of interactions with the guanine ring and secondly loss of interactions with the phosphates. The ease in sampling the energy landscape and adopting a bound-like conformation likely favors the catalyzing ability of GEFs for Ras GTPases.
Collapse
|
3
|
Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. Molecules 2019; 24:molecules24183308. [PMID: 31514408 PMCID: PMC6767298 DOI: 10.3390/molecules24183308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Small GTPases are key regulators of cellular events, and their dysfunction causes many types of cancer. They serve as molecular switches by cycling between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. GTPases are deactivated by GTPase-activating proteins (GAPs) and are activated by guanine-nucleotide exchange factors (GEFs). The intrinsic GTP hydrolysis activity of small GTPases is generally low and is accelerated by GAPs. GEFs promote GDP dissociation from small GTPases to allow for GTP binding, which results in a conformational change of two highly flexible segments, called switch I and switch II, that enables binding of the gamma phosphate and allows small GTPases to interact with downstream effectors. For several decades, crystal structures of many GEFs and GAPs have been reported and have shown tremendous structural diversity. In this review, we focus on the latest structural studies of GEFs. Detailed pictures of the variety of GEF mechanisms at atomic resolution can provide insights into new approaches for drug discovery.
Collapse
|
4
|
Zheng H, Li L, Miao P, Wu C, Chen X, Yuan M, Fang T, Norvienyeku J, Li G, Zheng W, Wang Z, Zhou J. FgSec2A, a guanine nucleotide exchange factor of FgRab8, is important for polarized growth, pathogenicity and deoxynivalenol production in Fusarium graminearum. Environ Microbiol 2018; 20:3378-3392. [PMID: 30105886 DOI: 10.1111/1462-2920.14373] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/20/2022]
Abstract
Sec4/Rab8 is one of the well-studied members of the Rab GTPase family, previous studies have shown that Sec4/Rab8 crucially promotes the pathogenesis of phytopathogens, but the upstream regulators of Rab8 are still unknown. Here, we have identified two Sec2 homologues FgSec2A and FgSec2B in devastating fungal pathogen Fusarium graminearum and investigated their functions and interactions with FgRab8 by live-cell imaging, genetic and functional analyses. Yeast two-hybrid assay shows that FgSec2A specifically interacts with FgRab8DN(N123I) and itself. Importantly, FgSec2A is required for growth, conidiation, DON production and virulence of F. graminearum. Live-cell imaging shows that FgSec2A and FgSec2B are both localized to the tip region of hyphae and conidia. Both N-terminal region and Sec2 domain of FgSec2A are essential for its function, but not for localization, whereas the C-terminal region is important for its polarized localization. Furthermore, constitutively active FgRab8CA(Q69L) partially rescues the defects of ΔFgsec2A. Consistently, FgSec2A is required for the polarized localization of FgRab8. Finally, FgSec2A and FgSec2B show partial functions, but FgSec2A does not interact and co-localize with FgSec2B. Taken together, these results indicate that FgSec2A acts as a FgRab8 guanine nucleotide exchange factor and is necessary for polarized growth, DON production and pathogenicity in F. graminearum.
Collapse
Affiliation(s)
- Huawei Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingping Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengfei Miao
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Congxian Wu
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingyue Yuan
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,College of Ocean Science, Minjiang University, Fuzhou, 350108, China
| | - Jie Zhou
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| |
Collapse
|
5
|
Eckhardt A, Kulhava L, Miksik I, Pataridis S, Hlavackova M, Vasinova J, Kolar F, Sedmera D, Ostadal B. Proteomic analysis of cardiac ventricles: baso-apical differences. Mol Cell Biochem 2018; 445:211-219. [PMID: 29302836 DOI: 10.1007/s11010-017-3266-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/23/2017] [Indexed: 12/19/2022]
Abstract
The heart is characterized by a remarkable degree of heterogeneity. Since different cardiac pathologies affect different cardiac regions, it is important to understand molecular mechanisms by which these parts respond to pathological stimuli. In addition to already described left ventricular (LV)/right ventricular (RV) and transmural differences, possible baso-apical heterogeneity has to be taken into consideration. The aim of our study has been, therefore, to compare proteomes in the apical and basal parts of the rat RV and LV. Two-dimensional electrophoresis was used for the proteomic analysis. The major result of this study has revealed for the first time significant baso-apical differences in concentration of several proteins, both in the LV and RV. As far as the LV is concerned, five proteins had higher concentration in the apical compared to basal part of the ventricle. Three of them are mitochondrial and belong to the "metabolism and energy pathways" (myofibrillar creatine kinase M-type, L-lactate dehydrogenase, dihydrolipoamide dehydrogenase). Myosin light chain 3 is a contractile protein and HSP60 belongs to heat shock proteins. In the RV, higher concentration in the apical part was observed in two mitochondrial proteins (creatine kinase S-type and proton pumping NADH:ubiquinone oxidoreductase). The described changes were more pronounced in the LV, which is subjected to higher workload. However, in both chambers was the concentration of proteins markedly higher in the apical than that in basal part, which corresponds to the higher energetic demand and contractile activity of these segments of both ventricles.
Collapse
Affiliation(s)
- Adam Eckhardt
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.
| | - Lucie Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague, Czech Republic
| | - Ivan Miksik
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Statis Pataridis
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Marketa Hlavackova
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,Department of Physiology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Jana Vasinova
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Frantisek Kolar
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - David Sedmera
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Kateřinská 32, Prague, Czech Republic
| | - Bohuslav Ostadal
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| |
Collapse
|
6
|
Lepore D, Spassibojko O, Pinto G, Collins RN. Cell cycle-dependent phosphorylation of Sec4p controls membrane deposition during cytokinesis. J Cell Biol 2017; 214:691-703. [PMID: 27621363 PMCID: PMC5021095 DOI: 10.1083/jcb.201602038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 08/04/2016] [Indexed: 11/22/2022] Open
Abstract
The GTPase Sec4p is a critical regulator of polarized membrane traffic. Lepore et al. show that the polo-like kinase Cdc5p phosphorylates Sec4p, which promotes coordinated membrane deposition during cytokinesis. Intracellular trafficking is an essential and conserved eukaryotic process. Rab GTPases are a family of proteins that regulate and provide specificity for discrete membrane trafficking steps by harnessing a nucleotide-bound cycle. Global proteomic screens have revealed many Rab GTPases as phosphoproteins, but the effects of this modification are not well understood. Using the Saccharomyces cerevisiae Rab GTPase Sec4p as a model, we have found that phosphorylation negatively regulates Sec4p function by disrupting the interaction with the exocyst complex via Sec15p. We demonstrate that phosphorylation of Sec4p is a cell cycle–dependent process associated with cytokinesis. Through a genomic kinase screen, we have also identified the polo-like kinase Cdc5p as a positive regulator of Sec4p phosphorylation. Sec4p spatially and temporally localizes with Cdc5p exclusively when Sec4p phosphorylation levels peak during the cell cycle, indicating Sec4p is a direct Cdc5p substrate. Our data suggest the physiological relevance of Sec4p phosphorylation is to facilitate the coordination of membrane-trafficking events during cytokinesis.
Collapse
Affiliation(s)
- Dante Lepore
- Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, NY 14853 Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Olya Spassibojko
- Cornell Undergraduate Biology, Cornell University, Ithaca, NY 14853
| | - Gabrielle Pinto
- Cornell Undergraduate Biology, Cornell University, Ithaca, NY 14853
| | - Ruth N Collins
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| |
Collapse
|
7
|
Choi JY, Shin YC, Yoon JH, Kim CM, Lee JH, Jeon JH, Park HH. Molecular mechanism of constitutively active Rab11A was revealed by crystal structure of Rab11A S20V. FEBS Lett 2016; 590:819-27. [PMID: 26879265 DOI: 10.1002/1873-3468.12100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/02/2016] [Accepted: 02/05/2016] [Indexed: 11/06/2022]
Abstract
Rab11A is a small GTP-binding protein involved in the regulation of vesicle trafficking during recycling of endosomes. Substitution of S20 to V (S20V) at Rab11A inhibits the GTP hydrolysis activity of Rab11A. This mutation is known to be constitutively in an active form. Here, we report the crystal structure of the human Rab11A S20V mutant form complexed with GTP at a resolution of 2.4 Å. Without adding any substrate, Rab11A contained non-hydrolyzed natural substrate GTP in the nucleotide binding pocket with Mg(2+). In our observations, substituted V20 of Rab11A was found to interfere with proper localization of the water molecule, which mediated GTP hydrolysis, resulting in GTP being locked in an active form of Rab11A S20V.
Collapse
Affiliation(s)
- Jae Young Choi
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| | - Young-Cheul Shin
- Department of Physiology, Department of Biomedical Sciences, and Institute of Dermatological Science, Seoul National University College of Medicine, South Korea
| | - Jong Hwan Yoon
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| | - Chang Min Kim
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Inchon, South Korea
| | - Ju-Hong Jeon
- Department of Physiology, Department of Biomedical Sciences, and Institute of Dermatological Science, Seoul National University College of Medicine, South Korea
| | - Hyun Ho Park
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan, South Korea
| |
Collapse
|