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Mironov AA, Beznoussenko GV. Algorithm for Modern Electron Microscopic Examination of the Golgi Complex. Methods Mol Biol 2022; 2557:161-209. [PMID: 36512216 DOI: 10.1007/978-1-0716-2639-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.
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Ruberti C. Mitochondrial GFP-Tagged Protein Localization Using Transient Transformations in Arabidopsis thaliana. Methods Mol Biol 2022; 2363:153-163. [PMID: 34545492 DOI: 10.1007/978-1-0716-1653-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Transient transformation assays for the analysis of protein localization are routinely used as rapid and convenient alternatives to stable transformation. In this chapter, we describe two transient gene expression assays (e.g., isolation and transformation of protoplasts, and agroinfiltration of leaves) optimized for Arabidopsis thaliana, and we combine them with fluorescence microscopy, with the final aim to investigate in vivo the subcellular localization of a mitochondrial protein of interest fused to a fluorescent reporter.
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Affiliation(s)
- Cristina Ruberti
- Department of Biology, University of Padua, Padua, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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Modulation of Expression of PVY NTN RNA-Dependent RNA Polymerase (NIb) and Heat Shock Cognate Host Protein HSC70 in Susceptible and Hypersensitive Potato Cultivars. Vaccines (Basel) 2021; 9:vaccines9111254. [PMID: 34835185 PMCID: PMC8619674 DOI: 10.3390/vaccines9111254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Potato virus Y (PVY) belongs to the genus Potyvirus and is considered to be one of the most harmful and important plant pathogens. Its RNA-dependent RNA polymerase (RdRp) is known as nuclear inclusion protein b (NIb). The recent findings show that the genome of PVY replicates in the cytoplasm of the plant cell by binding the virus replication complex to the membranous structures of different organelles. In some potyviruses, NIb has been found to be localized in the nucleus and associated with the endoplasmic reticulum membranes. Moreover, NIb has been shown to interact with other host proteins that are particularly involved in promoting the virus infection cycle, such as the heat shock proteins (HSPs). HSP70 is the most conserved among the five major HSP families that are known to affect the plant-pathogen interactions. Some plant viruses can induce the production of HSP70 during the development of infection. To understand the molecular mechanisms underlying the interactive response to PVYNTN (necrotic tuber necrosis strain of PVY), the present study focused on StHSC70-8 and PVYNTN-NIb gene expression via localization of HSC70 and NIb proteins during compatible (susceptible) and incompatible (hypersensitive) potato-PVYNTN interactions. Our results demonstrate that NIb and HSC70 are involved in the response to PVYNTN infections and probably cooperate at some stages of the virus infection cycle. Enhanced deposition of HSC70 proteins during the infection cycle was associated with the dynamic induction of PVYNTN-NIb gene expression and NIb localization during susceptible infections. In hypersensitive response (HR), a significant increase in HSC70 expression was observed up to 3 days post-inoculation (dpi) in the nucleus and chloroplasts. Thereafter, between 3 and 21 dpi, the deposition of NIb decreased, which can be attributed to a reduction in the levels of both virus accumulation and PVYNTN-NIb gene expression. Therefore, we postulate that increase in the expression of both StHSC70-8 and PVYNTN-NIb induces the PVY infection during susceptible infections. In contrast, during HRs, HSC70 cooperates with PVYNTN only at the early stages of interaction and mediates the defense response signaling pathway at the later stages of infection.
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The Respiratory Burst Oxidase Homolog D (RbohD) Cell and Tissue Distribution in Potato-Potato Virus Y (PVY NTN) Hypersensitive and Susceptible Reactions. Int J Mol Sci 2019; 20:ijms20112741. [PMID: 31167403 PMCID: PMC6600368 DOI: 10.3390/ijms20112741] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/21/2019] [Accepted: 06/02/2019] [Indexed: 12/12/2022] Open
Abstract
The respiratory burst oxidase homolog D (RbohD) acts as a central driving force of reactive oxygen species signaling in plant cells by integrating many different signal transduction pathways in plants, including incompatible interactions with pathogens. This study demonstrated the localization and distribution of RbohD in two types of potato–potato virus Y (PVY) interactions: Compatible and incompatible (resistant). The results indicated a statistically significant induction of the RbohD antigen signal in both interaction types. In the hypersensitive response (resistant reaction) of potato with a high level of resistance to the potato tuber necrotic strain of PVY (PVYNTN), RbohD localization followed by hydrogen peroxide (H2O2) detection was concentrated in the apoplast. In contrast, in the hypersensitive response of potato with a low resistance level to PVYNTN, the distribution of RbohD was concentrated more in the plant cell organelles than in the apoplast, resulting in the virus particles being present outside the inoculation area. Moreover, when compared to mock-inoculated plants and to the hypersensitive response, the PVYNTN-compatible potato interaction triggered high induction in the RbohD distribution, which was associated with necrotization. Our findings indicated that RbohD and hydrogen peroxide deposition was associated with the hypersensitive response, and both were detected in the vascular tissues and chloroplasts. These results suggest that the RbohD distribution is actively dependent on different types of PVY NTN-potato plant interactions. Additionally, the RbohD may be involved in the PVYNTN tissue limitation during the hypersensitive response, and it could be an active component of the systemic signal transduction in the susceptible host reaction.
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Chemical Fixation, Immunofluorescence, and Immunogold Labeling of Electron Microscopical Sections. Methods Mol Biol 2019. [PMID: 31148030 DOI: 10.1007/978-1-4939-9469-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Knowledge about the spatiotemporal distribution patterns of proteins and other molecules of the cell is essential for understanding their function. A widely used technique is immunolabeling which uses specific antibodies to reveal the distribution of molecular components at various structural levels. Immunofluorescence gives an overview about the distribution of molecules at the level of the fluorescence or confocal laser scanning microscope. Electron microscopy offers the highest resolution of morphological techniques and is thus an indispensable tool for the analysis of molecule distribution patterns at the subcellular level. In this chapter we describe selected routine methods for immunofluorescence and for labeling ultrathin sections of resin-embedded material with antibodies conjugated to colloidal gold, including protocols for chemical fixation, embedding, and sectioning.
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Wawra S, Fesel P, Widmer H, Neumann U, Lahrmann U, Becker S, Hehemann JH, Langen G, Zuccaro A. FGB1 and WSC3 are in planta-induced β-glucan-binding fungal lectins with different functions. THE NEW PHYTOLOGIST 2019; 222:1493-1506. [PMID: 30688363 DOI: 10.1111/nph.15711] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in β-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain β1-3-glucan but has no affinity for shorter β1-3- or β1-6-linked glucose oligomers. Comparative analysis with the previously identified β-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require β1-6-linked glucose for efficient binding to branched β1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two β-glucan-binding lectins. Our results highlight the importance of the β-glucan cell wall component in plant-fungus interactions and the potential of β-glucan-binding lectins as specific detection tools for fungi in vivo.
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Affiliation(s)
- Stephan Wawra
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Philipp Fesel
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Heidi Widmer
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Urs Lahrmann
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Stefan Becker
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Gregor Langen
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
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Kozieł E, Otulak-Kozieł K, Bujarski JJ. Ultrastructural Analysis of Prune DwarfVirus Intercellular Transport and Pathogenesis. Int J Mol Sci 2018; 19:E2570. [PMID: 30158483 PMCID: PMC6163902 DOI: 10.3390/ijms19092570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 08/17/2018] [Accepted: 08/28/2018] [Indexed: 12/25/2022] Open
Abstract
Prune dwarf virus (PDV) is an important viral pathogen of plum, sweet cherry, peach, and many herbaceous test plants. Although PDV has been intensively investigated, mainly in the context of phylogenetic relationship of its genes and proteins, many gaps exist in our knowledge about the mechanism of intercellular transport of this virus. The aim of this work was to investigate alterations in cellular organelles and the cell-to-cell transport of PDV in Cucumis sativus cv. Polan at ultrastructural level. To analyze the role of viral proteins in local transport, double-immunogold assays were applied to localize PDV coat protein (CP) and movement protein (MP). We observe structural changes in chloroplasts, mitochondria, and cellular membranes. We prove that PDV is transported as viral particles via MP-generated tubular structures through plasmodesmata. Moreover, the computer-run 3D modeling reveals structural resemblances between MPs of PDV and of Alfalfa mosaic virus (AMV), implying similarities of transport mechanisms for both viruses.
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Affiliation(s)
- Edmund Kozieł
- Faculty of Agriculture and Biology, Department of Botany, Warsaw University of Life Sciences-SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland.
| | - Katarzyna Otulak-Kozieł
- Faculty of Agriculture and Biology, Department of Botany, Warsaw University of Life Sciences-SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland.
| | - Józef J Bujarski
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA.
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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8
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Spatiotemporal Changes in Xylan-1/Xyloglucan and Xyloglucan Xyloglucosyl Transferase (XTH-Xet5) as a Step-In of Ultrastructural Cell Wall Remodelling in Potato⁻Potato Virus Y (PVY NTN) Hypersensitive and Susceptible Reaction. Int J Mol Sci 2018; 19:ijms19082287. [PMID: 30081556 PMCID: PMC6121353 DOI: 10.3390/ijms19082287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/28/2018] [Accepted: 08/01/2018] [Indexed: 01/25/2023] Open
Abstract
One type of monitoring system in a plant cell is the cell wall, which intensively changes its structure during interaction with pathogen-stress factors. The wall plays a role as a dynamic and controlled structure, although it is not fully understood how relevant these modifications are to the molecular mechanisms during plant–virus interactions. In this work we localise the non-cellulosic polysaccharides such as xyloglucan, xylan (xylan-1) and xyloglucosyl transferase (XTH-Xet5), the enzyme that participates in the metabolism of xyloglucan. This provided us with information about the in situ distribution of the components of the hemicellulotic cell wall matrix in hypersensitive and susceptible potato–PVYNTN interactions. The loosening of the cell wall was accompanied by an increase in xylan depositions during susceptible interactions, whereas, during the hypersensitive response, when the cell wall was reinforced, the xylan content decreased. Moreover, the PVY inoculation significantly redirected XTH-Xet5 depositions, regardless of types of interactions, compared to mock-inoculated tissues. Furthermore, the immunogold localisation clearly revealed the domination of Xet5 in the cell wall and in vesicles in the susceptible host. In contrast, in the resistant host increased levels of Xet5 were observed in cytoplasm, in the cell wall and in the trans-Golgi network. These findings show that the hypersensitive reaction activated XTH-Xet5 in the areas of xyloglucan endo-transglycosylase (XET) synthesis, which was then actively transported to cytoplasm, cell wall and to vacuoles. Our results provide novel insight into cell wall reorganisation during PVYNTN infection as a response to biotic stress factors. These novel findings help us to understand the mechanisms of defence responses that are incorporated into the cell wall signalling network.
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Jacob A, Morley M, Hawkins F, McCauley KB, Jean JC, Heins H, Na CL, Weaver TE, Vedaie M, Hurley K, Hinds A, Russo SJ, Kook S, Zacharias W, Ochs M, Traber K, Quinton LJ, Crane A, Davis BR, White FV, Wambach J, Whitsett JA, Cole FS, Morrisey EE, Guttentag SH, Beers MF, Kotton DN. Differentiation of Human Pluripotent Stem Cells into Functional Lung Alveolar Epithelial Cells. Cell Stem Cell 2017; 21:472-488.e10. [PMID: 28965766 PMCID: PMC5755620 DOI: 10.1016/j.stem.2017.08.014] [Citation(s) in RCA: 335] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/21/2017] [Accepted: 08/18/2017] [Indexed: 02/01/2023]
Abstract
Lung alveoli, which are unique to air-breathing organisms, have been challenging to generate from pluripotent stem cells (PSCs) in part because there are limited model systems available to provide the necessary developmental roadmaps for in vitro differentiation. Here we report the generation of alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli, from human PSCs. Using multicolored fluorescent reporter lines, we track and purify human SFTPC+ alveolar progenitors as they emerge from endodermal precursors in response to stimulation of Wnt and FGF signaling. Purified PSC-derived SFTPC+ cells form monolayered epithelial "alveolospheres" in 3D cultures without the need for mesenchymal support, exhibit self-renewal capacity, and display additional AEC2 functional capacities. Footprint-free CRISPR-based gene correction of PSCs derived from patients carrying a homozygous surfactant mutation (SFTPB121ins2) restores surfactant processing in AEC2s. Thus, PSC-derived AEC2s provide a platform for disease modeling and future functional regeneration of the distal lung.
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Affiliation(s)
- Anjali Jacob
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael Morley
- Penn Center for Pulmonary Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Finn Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Katherine B McCauley
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - J C Jean
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Hillary Heins
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cheng-Lun Na
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Timothy E Weaver
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marall Vedaie
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Killian Hurley
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott J Russo
- Penn Center for Pulmonary Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seunghyi Kook
- Department of Pediatrics, Monroe Carell Jr. Children's Hospital, Vanderbilt University, Nashville, TN 37232, USA
| | - William Zacharias
- Penn Center for Pulmonary Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthias Ochs
- Institute of Functional and Applied Anatomy, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), REBIRTH Cluster of Excellence, 30625 Hannover, Germany
| | - Katrina Traber
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Lee J Quinton
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ana Crane
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Frances V White
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jennifer Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey A Whitsett
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - F Sessions Cole
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Edward E Morrisey
- Penn Center for Pulmonary Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susan H Guttentag
- Department of Pediatrics, Monroe Carell Jr. Children's Hospital, Vanderbilt University, Nashville, TN 37232, USA
| | - Michael F Beers
- Penn Center for Pulmonary Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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Pastorek L, Sobol M, Hozák P. Colocalization coefficients evaluating the distribution of molecular targets in microscopy methods based on pointed patterns. Histochem Cell Biol 2016; 146:391-406. [PMID: 27460592 PMCID: PMC5037163 DOI: 10.1007/s00418-016-1467-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/28/2023]
Abstract
In biomedical studies, the colocalization is commonly understood as the overlap between distinctive labelings in images. This term is usually associated especially with quantitative evaluation of the immunostaining in fluorescence microscopy. On the other hand, the evaluation of the immunolabeling colocalization in the electron microscopy images is still under-investigated and biased by the subjective and non-quantitative interpretation of the image data. We introduce a novel computational technique for quantifying the level of colocalization in pointed patterns. Our approach follows the idea included in the widely used Manders' colocalization coefficients in fluorescence microscopy and represents its counterpart for electron microscopy. In presented methodology, colocalization is understood as the product of the spatial interactions at the single-particle (single-molecule) level. Our approach extends the current significance testing in the immunoelectron microscopy images and establishes the descriptive colocalization coefficients. To demonstrate the performance of the proposed coefficients, we investigated the level of spatial interactions of phosphatidylinositol 4,5-bisphosphate with fibrillarin in nucleoli. We compared the electron microscopy colocalization coefficients with Manders' colocalization coefficients for confocal microscopy and super-resolution structured illumination microscopy. The similar tendency of the values obtained using different colocalization approaches suggests the biological validity of the scientific conclusions. The presented methodology represents a good basis for further development of the quantitative analysis of immunoelectron microscopy data and can be used for studying molecular interactions at the ultrastructural level. Moreover, this methodology can be applied also to the other super-resolution microscopy techniques focused on characterization of discrete pointed structures.
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Affiliation(s)
- Lukáš Pastorek
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
- Microscopy Centre, Institute of Molecular Genetics ASCR v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
- Laboratory of Epigenetics of the Cell Nucleus, Division BIOCEV, Institute of Molecular Genetics of the ASCR v. v. i., Průmyslová 595, 252 50, Vestec, Czech Republic.
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11
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Ono NN, Qin X, Wilson AE, Li G, Tian L. Two UGT84 Family Glycosyltransferases Catalyze a Critical Reaction of Hydrolyzable Tannin Biosynthesis in Pomegranate (Punica granatum). PLoS One 2016; 11:e0156319. [PMID: 27227328 PMCID: PMC4882073 DOI: 10.1371/journal.pone.0156319] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022] Open
Abstract
Hydrolyzable tannins (HTs) play important roles in plant herbivore deterrence and promotion of human health. A critical step in HT production is the formation of 1-O-galloyl-β-D-glucopyranoside (β-glucogallin, ester-linked gallic acid and glucose) by a UDP-glucosyltransferase (UGT) activity. We cloned and biochemically characterized four candidate UGTs from pomegranate (Punica granatum), of which only UGT84A23 and UGT84A24 exhibited β-glucogallin forming activities in enzyme assays. Although overexpression and single RNAi knockdown pomegranate hairy root lines of UGT84A23 or UGT84A24 did not lead to obvious alterations in punicalagin (the prevalent HT in pomegranate) accumulation, double knockdown lines of the two UGTs resulted in largely reduced levels of punicalagins and bis-hexahydroxydiphenyl glucose isomers. An unexpected accumulation of galloyl glucosides (ether-linked gallic acid and glucose) was also detected in the double knockdown lines, suggesting that gallic acid was utilized by an unidentified UGT activity for glucoside formation. Transient expression in Nicotiana benthamiana leaves and immunogold labeling in roots of pomegranate seedlings collectively indicated cytosolic localization of UGT84A23 and UGT84A24. Overall, functional characterization and localization of UGT84A23 and UGT84A24 open up opportunities for further understanding the regulatory control of HT metabolism in plants and its coordination with other biochemical pathways in the metabolic network.
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Affiliation(s)
- Nadia N. Ono
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Xiaoqiong Qin
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Alexander E. Wilson
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Gang Li
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Li Tian
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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12
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Ono NN, Qin X, Wilson AE, Li G, Tian L. Two UGT84 Family Glycosyltransferases Catalyze a Critical Reaction of Hydrolyzable Tannin Biosynthesis in Pomegranate (Punica granatum). PLoS One 2016. [PMID: 27227328 DOI: 10.1371/journal.pgen.100156319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Hydrolyzable tannins (HTs) play important roles in plant herbivore deterrence and promotion of human health. A critical step in HT production is the formation of 1-O-galloyl-β-D-glucopyranoside (β-glucogallin, ester-linked gallic acid and glucose) by a UDP-glucosyltransferase (UGT) activity. We cloned and biochemically characterized four candidate UGTs from pomegranate (Punica granatum), of which only UGT84A23 and UGT84A24 exhibited β-glucogallin forming activities in enzyme assays. Although overexpression and single RNAi knockdown pomegranate hairy root lines of UGT84A23 or UGT84A24 did not lead to obvious alterations in punicalagin (the prevalent HT in pomegranate) accumulation, double knockdown lines of the two UGTs resulted in largely reduced levels of punicalagins and bis-hexahydroxydiphenyl glucose isomers. An unexpected accumulation of galloyl glucosides (ether-linked gallic acid and glucose) was also detected in the double knockdown lines, suggesting that gallic acid was utilized by an unidentified UGT activity for glucoside formation. Transient expression in Nicotiana benthamiana leaves and immunogold labeling in roots of pomegranate seedlings collectively indicated cytosolic localization of UGT84A23 and UGT84A24. Overall, functional characterization and localization of UGT84A23 and UGT84A24 open up opportunities for further understanding the regulatory control of HT metabolism in plants and its coordination with other biochemical pathways in the metabolic network.
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Affiliation(s)
- Nadia N Ono
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Xiaoqiong Qin
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Alexander E Wilson
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Gang Li
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Li Tian
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
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Andrade LR. Evidence for changes in beta- and gamma-actin proportions during inner ear hair cell life. Cytoskeleton (Hoboken) 2015; 72:282-91. [PMID: 26033950 DOI: 10.1002/cm.21227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 12/18/2022]
Abstract
Cytoplasmic actin isoforms beta (β-) and gamma (γ-) perform crucial physiological roles in inner ear hair cells (HC). The stereocilium, which is structured by parallel actin filaments composed of both isoforms, is the responsive organelle to mechanical stimuli such as sound, gravity and head movements. Modifications in isoform proportions affect the function of the stereocilia as previously shown in genetic studies of mutant mice. Here, immunogold labeling TEM studies in mice showed that both β- and γ-actin isoforms colocalize throughout stereocilia actin filaments, adherens junctions and cuticular plates as early as embryonic stage 16.5. Gold-particle quantification indicated that there was 40% more γ- actin than β-actin at E16.5. In contrast, β- and γ-actin were equally concentrated in adult stereocilia of cochlear and vestibular HC. Interestingly, all actin-based structures presented almost five-fold more β-actin than γ-actin in 22 month- old mice, suggesting that γ-actin is probably under-expressed during the aging process. These data provide evidence of dynamic modifications of the actin isoforms in stereocilia, cuticular plates and cell junctions during the whole HC life.
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Affiliation(s)
- Leonardo R Andrade
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA.,Laboratory of Biomineralization, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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Sulpice R, McKeown PC. Moving toward a comprehensive map of central plant metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:187-210. [PMID: 25621519 DOI: 10.1146/annurev-arplant-043014-114720] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Decades of intensive study have led to the discovery of the main pathways involved in central metabolism but only some of the pathways and regulatory networks in which they are embedded. In this review, we discuss techniques used to assemble these pathways into a systems biology framework that can enable accurate modeling of the response of central metabolism to changes, including ways to perturb metabolic systems and assemble the resulting data into a meaningful network. Critically, these networks are of such size and complexity that it is possible to derive them only if data from different groups can be comprehensively and meaningfully combined. We conclude that it is essential to establish common standards for the description of experimental conditions and data collection and to store this information in databases to which the whole community can contribute.
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15
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Abstract
Knowledge about the spatio-temporal distribution patterns of proteins and other molecules of the cell is essential for understanding their function. A widely used technique is immunolabeling which uses specific antibodies to reveal the distribution of molecular components at various structural levels. Electron microscopy offers the highest resolution of morphological techniques and is thus an indispensable tool for the analysis of molecule distribution patterns at the subcellular level. In this chapter we describe a routine method for labeling ultrathin sections of resin-embedded material with antibodies conjugated to colloidal gold.
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Webster P, Webster A. Cryosectioning fixed and cryoprotected biological material for immunocytochemistry. Methods Mol Biol 2014; 1117:273-313. [PMID: 24357368 DOI: 10.1007/978-1-62703-776-1_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Immunocytochemistry for electron microscopy provides important information on the location and relative abundance of proteins inside cells. Gaining access to this information without extracting or disrupting the location of target proteins requires specialized preparation methods. Sectioning frozen blocks of chemically fixed and cryoprotected biological material is one method for obtaining immunocytochemical data. Once the cells or tissues are cut, the cryosections are thawed, mounted onto coated grids, and labeled with specific antibodies and colloidal gold probes. They are then embedded in a thin film of plastic containing a contrasting agent. Subcellular morphology can then be correlated with specific affinity labeling by examination in the transmission electron microscope (TEM). The major advantage of using thawed cryosections for immunolabeling is that the sections remain fully hydrated through the immunolabeling steps, reducing the possibility of dehydration-induced antigen modification. Modern technical advancements both in preparation protocols and equipment design make cryosectioning a routine and rapid approach for immunocytochemistry that may provide increased sensitivity for some antibodies.
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Affiliation(s)
- Paul Webster
- Center for Electron Microscopy and Microanalysis (CEMMA), University of Souther California, Los Angeles, CA, USA
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Woods MW, Kelly JN, Hattlmann CJ, Tong JGK, Xu LS, Coleman MD, Quest GR, Smiley JR, Barr SD. Human HERC5 restricts an early stage of HIV-1 assembly by a mechanism correlating with the ISGylation of Gag. Retrovirology 2011; 8:95. [PMID: 22093708 PMCID: PMC3228677 DOI: 10.1186/1742-4690-8-95] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/17/2011] [Indexed: 11/12/2022] Open
Abstract
Background The identification and characterization of several interferon (IFN)-induced cellular HIV-1 restriction factors, defined as host cellular proteins or factors that restrict or inhibit the HIV-1 life cycle, have provided insight into the IFN response towards HIV-1 infection and identified new therapeutic targets for HIV-1 infection. To further characterize the mechanism underlying restriction of the late stages of HIV-1 replication, we assessed the ability of IFNbeta-induced genes to restrict HIV-1 Gag particle production and have identified a potentially novel host factor called HECT domain and RCC1-like domain-containing protein 5 (HERC5) that blocks a unique late stage of the HIV-1 life cycle. Results HERC5 inhibited the replication of HIV-1 over multiple rounds of infection and was found to target a late stage of HIV-1 particle production. The E3 ligase activity of HERC5 was required for blocking HIV-1 Gag particle production and correlated with the post-translational modification of Gag with ISG15. HERC5 interacted with HIV-1 Gag and did not alter trafficking of HIV-1 Gag to the plasma membrane. Electron microscopy revealed that the assembly of HIV-1 Gag particles was arrested at the plasma membrane, at an early stage of assembly. The mechanism of HERC5-induced restriction of HIV-1 particle production is distinct from the mechanism underlying HIV-1 restriction by the expression of ISG15 alone, which acts at a later step in particle release. Moreover, HERC5 restricted murine leukemia virus (MLV) Gag particle production, showing that HERC5 is effective in restricting Gag particle production of an evolutionarily divergent retrovirus. Conclusions HERC5 represents a potential new host factor that blocks an early stage of retroviral Gag particle assembly. With no apparent HIV-1 protein that directly counteracts it, HERC5 may represent a new candidate for HIV/AIDS therapy.
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Affiliation(s)
- Matthew W Woods
- The University of Western Ontario, Schulich School of Medicine and Dentistry, Center for Human Immunology, Department of Microbiology and Immunology, Dental Sciences Building Room 3006b, London, Ontario, Canada
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