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O'Shaughnessy EC, Lam M, Ryken SE, Wiesner T, Lukasik K, Zuchero JB, Leterrier C, Adalsteinsson D, Gupton SL. pHusion: A robust and versatile toolset for automated detection and analysis of exocytosis. J Cell Sci 2024:jcs.261828. [PMID: 38690758 DOI: 10.1242/jcs.261828] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
Exocytosis is a fundamental process used by eukaryotes to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate exocytosis in neuronal morphogenesis, previously we developed computational tools with a graphical user interface to enable the automatic detection and analysis of exocytic events from fluorescence timelapse images. Though these tools were useful, we found the code was brittle and not easily adapted to different experimental conditions. Here we developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested this method using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types, and various exocytic markers to generate a flexible and intuitive package. We show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons.
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Affiliation(s)
- Ellen C O'Shaughnessy
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC, USA
| | - Mable Lam
- Department of Neurosurgery, Stanford University School of Medicine; Stanford, CA, USA
| | - Samantha E Ryken
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC, USA
| | - Theresa Wiesner
- NeuroCyto, Aix Marseille Université, CNRS, INP UMR7051, Marseille, France
| | - Kimberly Lukasik
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC, USA
| | - J Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine; Stanford, CA, USA
| | | | - David Adalsteinsson
- University of North Carolina at Chapel Hill, Department of Mathematics, Chapel Hill, NC, USA
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O'Shaughnessy EC, Lam M, Ryken SE, Wiesner T, Lukasik K, Zuchero BJ, Leterrier C, Adalsteinsson D, Gupton SL. pHusion: A robust and versatile toolset for automated detection and analysis of exocytosis. bioRxiv 2023:2023.07.25.550499. [PMID: 37546865 PMCID: PMC10402102 DOI: 10.1101/2023.07.25.550499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Exocytosis is a fundamental process used by eukaryotic cells to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate the role exocytosis plays in neuronal morphogenesis, previously we developed computational tools with a graphical user interface (GUI) to enable the automatic detection and analysis of exocytic events (ADAE GUI) from fluorescence timelapse images. Though these tools have proven useful, we found that the code was brittle and not easily adapted to different experimental conditions. Here, we have developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested this method using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types, and various exocytic markers to generate a flexible and intuitive package. Using pHusion, we show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons. Summary Statement Exocytosis is an essential process by which cells change shape, alter membrane composition, and communicate with other cells. Though all eukaryotic cells carry out exocytosis, the regulation of vesicle fusion, the cargo of vesicles, and the role exocytosis plays in cell fate differ greatly across cell types. Here, we developed a flexible and robust set of tools to enable automatic identification and analysis of exocytic events across a wide range of cell types, vesicle types, and imaging conditions.
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Wu SZ, Ryken SE, Bezanilla M. CRISPR-Cas9 Genome Editing in the Moss Physcomitrium (Formerly Physcomitrella) patens. Curr Protoc 2023; 3:e725. [PMID: 37021953 DOI: 10.1002/cpz1.725] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Until recently, precise genome editing has been limited to a few organisms. The ability of Cas9 to generate double stranded DNA breaks at specific genomic sites has greatly expanded molecular toolkits in many organisms and cell types. Before CRISPR-Cas9 mediated genome editing, P. patens was unique among plants in its ability to integrate DNA via homologous recombination. However, selection for homologous recombination events was required to obtain edited plants, limiting the types of editing that were possible. Now with CRISPR-Cas9, molecular manipulations in P. patens have greatly expanded. This protocol describes a method to generate a variety of different genome edits. The protocol describes a streamlined method to generate the Cas9/sgRNA expression constructs, design homology templates, transform, and quickly genotype plants. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Constructing the Cas9/sgRNA transient expression vector Alternate Protocol 1: Shortcut to generating single and pooled Cas9/sgRNA expression vectors Basic Protocol 2: Designing the oligonucleotide-based homology-directed repair (HDR) template Alternate Protocol 2: Designing the plasmid-based HDR template Basic Protocol 3: Inducing genome editing by transforming CRISPR vector into P. patens protoplasts Basic Protocol 4: Identifying edited plants.
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Affiliation(s)
- Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Samantha E Ryken
- Current address: Biological and Biomedical Sciences Program, University of North Carolina, Chapel Hill, North Carolina
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
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Chang M, Wu SZ, Ryken SE, O’Sullivan JE, Bezanilla M. COPII Sec23 proteins form isoform-specific endoplasmic reticulum exit sites with differential effects on polarized growth. Plant Cell 2022; 34:333-350. [PMID: 34534343 PMCID: PMC8846183 DOI: 10.1093/plcell/koab229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/07/2021] [Indexed: 05/04/2023]
Abstract
Coat Protein complex II (COPII), a coat protein complex that forms vesicles on the endoplasmic reticulum (ER), mediates trafficking to the Golgi. While metazoans have few genes encoding each COPII component, plants have expanded these gene families, leading to the hypothesis that plant COPII has functionally diversified. In the moss Physcomitrium (Physcomitrella) patens, the Sec23/24 gene families are each composed of seven genes. Silencing Sec23/24 revealed isoform-specific contributions to polarized growth, with the closely related Sec23D/E and Sec24C/D essential for protonemal development. Focusing on Sec23, we discovered that Sec23D/E mediate ER-to Golgi transport and are essential for tip growth, with Sec23D localizing to presumptive ER exit sites. In contrast, Sec23A, B, C, F, and G are dispensable and do not quantitatively affect ER-to-Golgi trafficking. However, Δsec23abcfg plants exhibited reduced secretion of plasma membrane cargo. Of the four highly expressed protonemal Sec23 genes, Sec23F/G are members of a divergent Sec23 clade specifically retained in land plants. Notably, Sec23G accumulates on ER-associated foci that are significantly larger, do not overlap with, and are independent of Sec23D. While Sec23D/E form ER exit sites and function as bona fide COPII components essential for tip-growing protonemata, Sec23G and the closely related Sec23F have likely functionally diversified, forming separate and independent ER exit sites and participating in Golgi-independent trafficking pathways.
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Affiliation(s)
- Mingqin Chang
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
- Plant Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01002, USA
| | - Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Samantha E Ryken
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Jacquelyn E O’Sullivan
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01002, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
- Author for correspondence:
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Lara-Rojas F, Juárez-Verdayes M, Wu HM, Cheung AY, Montiel J, Pascual-Morales E, Ryken SE, Bezanilla M, Cardenas L. Using Hyper as a molecular probe to visualize hydrogen peroxide in living plant cells: An updated method. Methods Enzymol 2022; 683:265-289. [PMID: 37087192 DOI: 10.1016/bs.mie.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Reactive oxygen species (ROS) are highly reactive reduced oxygen molecules that play a myriad of roles in animal and plant cells. In plant cells the production of ROS results from aerobic metabolism during respiration and photosynthesis. Therefore mitochondria, chloroplasts, and peroxisomes constitute an important source of ROS. However, ROS can also be produced in response to many physiological stimuli such as pathogen attack, hormone signaling, abiotic stresses or during cell wall organization and plant morphogenesis. The study of ROS in plant cells has been limited to biochemical assays and use of fluorescent probes, however, the irreversible oxidation of the fluorescent dyes prevents the visualization of dynamic changes. We have previously reported that Hyper 1 is a biosensor for H2O2 and consists of a circularly permutated YFP (cpYFP) inserted into the regulatory domain of the Escherichia coli hydrogen peroxide (H2O2) sensor protein OxyR rendering it an H2O2-specific quantitative probe (Bilan & Belousov, 2018; Hernandez-Barrera et al., 2015). Herein we describe an updated protocol for using the improved new version of Hyper 2 and Hyper 3 as a dynamic biosensor for H2O2 in Arabidopsis with virtually unlimited potential to detect H2O2 throughout the plant and under a broad range of developmental and environmental conditions (Bilan et al., 2013).
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Lara-Rojas F, Sarmiento-López LG, Pascual-Morales E, Ryken SE, Bezanilla M, Cardenas L. Using DCP-Rho1 as a fluorescent probe to visualize sulfenic acid-containing proteins in living plant cells. Methods Enzymol 2022; 683:291-308. [PMID: 37087193 DOI: 10.1016/bs.mie.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among the biologically relevant reactive oxygen species (ROS), hydrogen peroxide (H2O2) has special properties. H2O2 can diffuse across membranes, has a low reactivity, and is very stable. Deprotonated cysteine residues in proteins can be oxidized by H2O2 into a highly reactive sulfenic acid derivative (-SOH), which can react with another cysteine to form a disulfide. Under higher oxidative stress the sulfenic acid undergo further oxidation to sulfinic acid (Cys-SO2H), which can subsequently be reduced. The sulfinic acid can be hyperoxidized to sulfonic acid (Cys-SO3H), whose reduction is irreversible. Formation of sulfenic acids can have a role in sensing oxidative stress, signal transduction, modulating localization and activity to regulate protein functions. Therefore, there is an emerging interest in trying to understand the pool of proteins that result in these sorts of modification in response to oxidative stress. This is known as the sulfenome and several approaches have been developed in animal and plant cells to analyze the sulfenome under different stress responses. These approaches can be proteomic, molecular, immunological (i.e., antibodies), or expressing genetically encoded probes that specifically react to sulfenic modifications. In this chapter, we describe an additional approach that allows visualization of sulfenic modification in vivo. This is newly developed fluorescent probe DCP-Rho1 can be implemented in any plant cell to analyze the sulfenic modification.
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Affiliation(s)
- Fernando Lara-Rojas
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec, Morelos, México
| | | | - Edgar Pascual-Morales
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Samantha E Ryken
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Luis Cardenas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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