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Peterson TA, Piper RC. Deconvolution of Multiple Rab Binding Domains Using the Batch Yeast 2-Hybrid Method DEEPN. Methods Mol Biol 2021; 2293:117-141. [PMID: 34453714 PMCID: PMC8524840 DOI: 10.1007/978-1-0716-1346-7_9] [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] [Indexed: 06/13/2023]
Abstract
A hallmark of functionally significant interactions between Rab proteins and their targets is whether that binding depends on the type of nucleotide bound to the Rab GTPase. A system that can directly compare those sets of interactions mediated by a Rab in its GTP-bound conformation versus its GDP bound conformation would provide a direct route to finding biologically relevant partners. Comprehensive large-scale yeast 2-hybrid assays allow a potential method to compare one interactome against another provided that the same set of potentially interacting partners is interrogated between samples. Here we describe the use of such a yeast 2-hybrid system that lends itself toward comparing pairs of Rab mutants, locked in either their GTP or GDP conformation. Importantly, using a complex library of protein fragments as potential binding ("prey") partners, identification of interacting proteins as well as the domain(s) mediating those interactions can be determined using a series of sequence analyses and binary validation experiments.
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Affiliation(s)
- Tabitha A Peterson
- Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert C Piper
- Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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Ruhl DA, Bomba-Warczak E, Watson ET, Bradberry MM, Peterson TA, Basu T, Frelka A, Evans CS, Briguglio JS, Basta T, Stowell MHB, Savas JN, Roopra A, Pearce RA, Piper RC, Chapman ER. Synaptotagmin 17 controls neurite outgrowth and synaptic physiology via distinct cellular pathways. Nat Commun 2019; 10:3532. [PMID: 31387992 PMCID: PMC6684635 DOI: 10.1038/s41467-019-11459-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/13/2019] [Indexed: 12/28/2022] Open
Abstract
The synaptotagmin (syt) proteins have been widely studied for their role in regulating fusion of intracellular vesicles with the plasma membrane. Here we report that syt-17, an unusual isoform of unknown function, plays no role in exocytosis, and instead plays multiple roles in intracellular membrane trafficking. Syt-17 is localized to the Golgi complex in hippocampal neurons, where it coordinates import of vesicles from the endoplasmic reticulum to support neurite outgrowth and facilitate axon regrowth after injury. Further, we discovered a second pool of syt-17 on early endosomes in neurites. Loss of syt-17 disrupts endocytic trafficking, resulting in the accumulation of excess postsynaptic AMPA receptors and defective synaptic plasticity. Two distinct pools of syt-17 thus control two crucial, independent membrane trafficking pathways in neurons. Function of syt-17 appears to be one mechanism by which neurons have specialized their secretory and endosomal systems to support the demands of synaptic communication over sprawling neurite arbors. The functional role of synaptotagmin-17 (syt-17) has remained unanswered. In this study, authors demonstrate that syt-17 exists in two distinct pools in hippocampal neurons (Golgi complex and early endosomes), where it served two completely independent functions: controlling neurite outgrowth and synaptic physiology
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Affiliation(s)
- David A Ruhl
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Ewa Bomba-Warczak
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emma T Watson
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Mazdak M Bradberry
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Tabitha A Peterson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, 52242, USA
| | - Trina Basu
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Alyssa Frelka
- Department of Anesthesiology, University of Wisconsin, Madison, WI, 53706, USA
| | - Chantell S Evans
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph S Briguglio
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Tamara Basta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Robert A Pearce
- Department of Anesthesiology, University of Wisconsin, Madison, WI, 53706, USA
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, 52242, USA
| | - Edwin R Chapman
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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