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Article ; Online: Novel approach to measure the size of plasma-membrane nanodomains in single molecule localization microscopy.

Ziomkiewicz, Iwona / Sporring, Jon / Pomorski, Thomas Günther / Schulz, Alexander

Cytometry. Part A : the journal of the International Society for Analytical Cytology

2015 Volume 87, Issue 9, Page(s) 868–877

Abstract: Many membrane proteins are not evenly distributed over the plasma membrane, but gathered in domains assumed to have a particular lipid composition. Using single molecule localization microscopy (SMLM) we have immunolocalized a ... ...

Abstract	Many membrane proteins are not evenly distributed over the plasma membrane, but gathered in domains assumed to have a particular lipid composition. Using single molecule localization microscopy (SMLM) we have immunolocalized a glycosylphosphatidylinositol (GPI)-anchor protein that labels nanodomains in a specialized plant cell type, and compared the suitability of three methods to estimate their size. As conventional methods full width at half maximum (FWHM) and the full diameter (FWMin) of domains were used. A boundary detection method of the domain area (DA) was performed in order to take irregular shapes into account. In order to compare the influence of the chosen measurement methods, we have developed a MatLab program that allows for automated analysis of domain sizes from multiple SMLM images and provides the statistics of three key features of domains: FWHM and FWMin along their long and short axes as well as the DA, derived from the molecular density. Domains formed by the GPI-anchor protein are approximating elliptical shapes. Direct and indirect immunolabeling resulted in a statistically significant difference in apparent domain size, reflecting the fact that the secondary antibody molecules extend the uncertainty along the nanodomain border. FWMin values along the long and short axis give good estimates of regular, geometrically centred domain shapes, while the DA value matches regular as well as irregular shapes best, as derived from computer-generated, irregular point clusters.
MeSH term(s)	Brassica/chemistry ; Brassica/metabolism ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Microscopy, Confocal/methods ; Nanotechnology/methods ; Protein Binding/physiology
Language	English
Publishing date	2015-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2099868-5
ISSN	1552-4930 ; 0196-4763 ; 1552-4922
ISSN (online)	1552-4930
ISSN	0196-4763 ; 1552-4922
DOI	10.1002/cyto.a.22708
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Article ; Online: Doc2B acts as a calcium sensor for vesicle priming requiring synaptotagmin-1, Munc13-2 and SNAREs.

Houy, Sébastien / Groffen, Alexander J / Ziomkiewicz, Iwona / Verhage, Matthijs / Pinheiro, Paulo S / Sørensen, Jakob Balslev

eLife

2017 Volume 6

Abstract: Doc2B is a cytosolic protein with binding sites for Munc13 and Tctex-1 (dynein light chain), and two C2-domains that bind to phospholipids, ... ...

Abstract	Doc2B is a cytosolic protein with binding sites for Munc13 and Tctex-1 (dynein light chain), and two C2-domains that bind to phospholipids, Ca
MeSH term(s)	Animals ; Calcium/metabolism ; Calcium-Binding Proteins/genetics ; Calcium-Binding Proteins/metabolism ; Cells, Cultured ; Chromaffin Cells/metabolism ; Gene Expression ; Gene Knockout Techniques ; Intracellular Signaling Peptides and Proteins/metabolism ; Mice ; Mice, Knockout ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; SNARE Proteins/metabolism ; Secretory Vesicles/metabolism ; Synaptotagmin I/metabolism
Chemical Substances	Calcium-Binding Proteins ; Doc2b protein, mouse ; Intracellular Signaling Peptides and Proteins ; Nerve Tissue Proteins ; SNARE Proteins ; Synaptotagmin I ; Unc13b protein, mouse ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2017-12-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.27000
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Article ; Online: Super-resolution imaging with Pontamine Fast Scarlet 4BS enables direct visualization of cellulose orientation and cell connection architecture in onion epidermis cells.

Liesche, Johannes / Ziomkiewicz, Iwona / Schulz, Alexander

BMC plant biology

2013 Volume 13, Page(s) 226

Abstract: Background: In plants, a complex cell wall protects cells and defines their shape. Cellulose fibrils form a multilayered network inside the cell-wall matrix that plays a direct role in controlling cell expansion. Resolving the structure of this network ... ...

Abstract	Background: In plants, a complex cell wall protects cells and defines their shape. Cellulose fibrils form a multilayered network inside the cell-wall matrix that plays a direct role in controlling cell expansion. Resolving the structure of this network will allow us to comprehend the relationship of cellulose fibril orientation and growth.The fluorescent dye Pontamine Fast Scarlet 4BS (PFS) was shown to stain cellulose with high specificity and could be used to visualize cellulose bundles in cell walls of Arabidopsis root epidermal cells with confocal microscopy. The resolution limit of confocal microscopy of some 200 nm in xy and 550 nm in z for green light, restricts the direct visualization of cellulose to relatively large bundles, whereas the structure of cellulose microfibrils with their diameter below 10 nm remains unresolved. Over the last decade, several so-called super-resolution microscopy approaches have been developed; in this paper we explore the potential of such approaches for the direct visualization of cellulose. Results: To ensure optimal imaging we determined the spectral properties of PFS-stained tissue. PFS was found not to affect cell viability in the onion bulb scale epidermis. We present the first super-resolution images of cellulose bundles in the plant cell wall produced by direct stochastic optical reconstruction microscopy (dSTORM) in combination with total internal reflection fluorescence (TIRF) microscopy. Since TIRF limits observation to the cell surface, we tested as alternatives 3D-structured illumination microscopy (3D-SIM) and confocal microscopy, combined with image deconvolution. Both methods offer lower resolution than STORM, but enable 3D imaging. While 3D-SIM produced strong artifacts, deconvolution gave good results. The resolution was improved over conventional confocal microscopy and the approach could be used to demonstrate differences in fibril orientation in different layers of the cell wall as well as particular cellulose fortifications around plasmodesmata. Conclusions: Super-resolution light microscopy of PFS-stained cellulose fibrils is possible and the increased resolution over conventional approaches makes it a valuable tool for the investigation of the cell-wall structure. This is one step in method developments that will close the gap to more invasive techniques, such as atomic force and electron microscopy.
MeSH term(s)	Azo Compounds/metabolism ; Cell Wall/chemistry ; Cell Wall/metabolism ; Cellulose/chemistry ; Cellulose/metabolism ; Fluorescent Dyes/metabolism ; Microscopy/methods ; Microscopy, Confocal/methods ; Microscopy, Fluorescence/methods ; Onions/cytology ; Onions/metabolism ; Plant Epidermis/cytology ; Plant Epidermis/growth & development ; Plant Epidermis/metabolism
Chemical Substances	Azo Compounds ; Direct Fast Scarlet 4BS ; Fluorescent Dyes ; Cellulose (9004-34-6)
Language	English
Publishing date	2013-12-28
Publishing country	England
Document type	Evaluation Study ; Journal Article
ISSN	1471-2229
ISSN (online)	1471-2229
DOI	10.1186/1471-2229-13-226
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Article ; Online: Syncytin-1 in differentiating human myoblasts: relationship to caveolin-3 and myogenin.

Bjerregard, Bolette / Ziomkiewicz, Iwona / Schulz, Alexander / Larsson, Lars-Inge

Cell and tissue research

2014 Volume 357, Issue 1, Page(s) 355–362

Abstract: Myoblasts fuse to form myotubes, which mature into skeletal muscle fibres. Recent studies indicate that an endogenous retroviral fusion gene, syncytin-1, is important for myoblast fusions in man. We have now expanded these data by examining the ... ...

Abstract	Myoblasts fuse to form myotubes, which mature into skeletal muscle fibres. Recent studies indicate that an endogenous retroviral fusion gene, syncytin-1, is important for myoblast fusions in man. We have now expanded these data by examining the immunolocalization of syncytin in human myoblasts induced to fuse. Additionally, we have compared the localization of syncytin with the localization of caveolin-3 and of myogenin, which are also involved in myoblast fusion and maturation. Syncytin was localized to areas of the cell membrane and to filopodial structures connecting myoblasts to each other and to myotubes. Weaker staining was present over intracellular vesicles and tubules. Caveolin-3 was detected in the sarcolemma and in vesicles and tubules in a subset of myoblasts and myotubes. The strongest staining occurred in multinucleated myotubes. Wide-field fluorescence microscopy indicated a partial colocalization of syncytin and caveolin-3 in a subset of myoblasts. Super-resolution microscopy showed such colocalization to occur in the sarcolemma. Myogenin was restricted to nuclei of myoblasts and myotubes and the strongest staining occurred in multinucleated myotubes. Syncytin staining was observed in both myogenin-positive and myogenin-negative cells. Antisense treatment downmodulated syncytin-1 expression and inhibited myoblast cell fusions. Importantly, syncytin-1 antisense significantly decreased the frequency of multinucleated myotubes demonstrating that the treatment inhibited secondary myoblast fusions. Thus, syncytin is involved in human myoblast fusions and is localized in areas of contact between fusing cells. Moreover, syncytin and caveolin-3 might interact at the level of the sarcolemma.
MeSH term(s)	Caveolin 3/genetics ; Caveolin 3/metabolism ; Cell Differentiation/physiology ; Cells, Cultured ; Gene Products, env/metabolism ; Humans ; Male ; Muscle, Skeletal/cytology ; Muscle, Skeletal/metabolism ; Myoblasts/cytology ; Myoblasts/metabolism ; Myogenin/genetics ; Myogenin/metabolism ; Pregnancy Proteins/metabolism ; Transfection
Chemical Substances	Caveolin 3 ; Gene Products, env ; Myogenin ; Pregnancy Proteins ; syncytin
Language	English
Publishing date	2014-07
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	125067-x
ISSN	1432-0878 ; 0302-766X
ISSN (online)	1432-0878
ISSN	0302-766X
DOI	10.1007/s00441-014-1930-9
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Article ; Online: Regulation of Ca2+ channels by SNAP-25 via recruitment of syntaxin-1 from plasma membrane clusters.

Toft-Bertelsen, Trine Lisberg / Ziomkiewicz, Iwona / Houy, Sébastien / Pinheiro, Paulo S / Sørensen, Jakob B

Molecular biology of the cell

2016 Volume 27, Issue 21, Page(s) 3329–3341

Abstract: SNAP-25 regulates ... ...

Abstract	SNAP-25 regulates Ca
MeSH term(s)	Animals ; Calcium/metabolism ; Calcium Channels/metabolism ; Calcium Channels/physiology ; Cell Membrane ; Exocytosis/physiology ; Membrane Proteins/metabolism ; Mice ; Mice, Knockout ; Nerve Tissue Proteins/metabolism ; Patch-Clamp Techniques ; Primary Cell Culture ; Protein Binding ; Synaptosomal-Associated Protein 25/metabolism ; Syntaxin 1/metabolism
Chemical Substances	Calcium Channels ; Membrane Proteins ; Nerve Tissue Proteins ; Snap25 protein, mouse ; Synaptosomal-Associated Protein 25 ; Syntaxin 1 ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2016--01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E16-03-0184
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Article: Syncytin-1 in differentiating human myoblasts: relationship to caveolin-3 and myogenin

Bjerregard, Bolette / Ziomkiewicz, Iwona / Schulz, Alexander / Larsson, Lars-Inge

Cell and tissue research. 2014 July, v. 357, no. 1

2014

Abstract	Myoblasts fuse to form myotubes, which mature into skeletal muscle fibres. Recent studies indicate that an endogenous retroviral fusion gene, syncytin-1, is important for myoblast fusions in man. We have now expanded these data by examining the immunolocalization of syncytin in human myoblasts induced to fuse. Additionally, we have compared the localization of syncytin with the localization of caveolin-3 and of myogenin, which are also involved in myoblast fusion and maturation. Syncytin was localized to areas of the cell membrane and to filopodial structures connecting myoblasts to each other and to myotubes. Weaker staining was present over intracellular vesicles and tubules. Caveolin-3 was detected in the sarcolemma and in vesicles and tubules in a subset of myoblasts and myotubes. The strongest staining occurred in multinucleated myotubes. Wide-field fluorescence microscopy indicated a partial colocalization of syncytin and caveolin-3 in a subset of myoblasts. Super-resolution microscopy showed such colocalization to occur in the sarcolemma. Myogenin was restricted to nuclei of myoblasts and myotubes and the strongest staining occurred in multinucleated myotubes. Syncytin staining was observed in both myogenin-positive and myogenin-negative cells. Antisense treatment downmodulated syncytin-1 expression and inhibited myoblast cell fusions. Importantly, syncytin-1 antisense significantly decreased the frequency of multinucleated myotubes demonstrating that the treatment inhibited secondary myoblast fusions. Thus, syncytin is involved in human myoblast fusions and is localized in areas of contact between fusing cells. Moreover, syncytin and caveolin-3 might interact at the level of the sarcolemma.
Keywords	cell membranes ; fluorescence microscopy ; gene fusion ; humans ; muscle fibers ; myoblasts ; skeletal muscle
Language	English
Dates of publication	2014-07
Size	p. 355-362.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	125067-x
ISSN	1432-0878 ; 0302-766X
ISSN (online)	1432-0878
ISSN	0302-766X
DOI	10.1007/s00441-014-1930-9
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Article ; Online: Dynamic conformational transitions of the EGF receptor in living mammalian cells determined by FRET and fluorescence lifetime imaging microscopy.

Ziomkiewicz, Iwona / Loman, Anastasia / Klement, Reinhard / Fritsch, Cornelia / Klymchenko, Andrey S / Bunt, Gertrude / Jovin, Thomas M / Arndt-Jovin, Donna J

Cytometry. Part A : the journal of the International Society for Analytical Cytology

2013 Volume 83, Issue 9, Page(s) 794–805

Abstract: We have revealed a reorientation of ectodomain I of the epidermal growth factor receptor (EGFR; ErbB1; Her1) in living CHO cells expressing the receptor, upon binding of the native ligand EGF. The state of the unliganded, nonactivated EGFR was compared ... ...

Abstract	We have revealed a reorientation of ectodomain I of the epidermal growth factor receptor (EGFR; ErbB1; Her1) in living CHO cells expressing the receptor, upon binding of the native ligand EGF. The state of the unliganded, nonactivated EGFR was compared to that exhibited after ligand addition in the presence of a kinase inhibitor that prevents endocytosis but does not interfere with binding or the ensuing conformational rearrangements. To perform these experiments, we constructed a transgene EGFR with an acyl carrier protein sequence between the signal peptide and the EGFR mature protein sequence. This protein, which behaves similarly to wild-type EGFR with respect to EGF binding, activation, and internalization, can be labeled at a specific serine in the acyl carrier tag with a fluorophore incorporated into a 4'-phosphopantetheine (P-pant) conjugate transferred enzymatically from the corresponding CoA derivative. By measuring Förster resonance energy transfer between a molecule of Atto390 covalently attached to EGFR in this manner and a novel lipid probe NR12S distributed exclusively in the outer leaflet of the plasma membrane, we determined the apparent relative separation of ectodomain I from the membrane under nonactivating and activating conditions. The data indicate that the unliganded domain I of the EGFR receptor is situated much closer to the membrane before EGF addition, supporting the model of a self-inhibited configuration of the inactive receptor in quiescent cells.
MeSH term(s)	Animals ; CHO Cells ; Cell Membrane/metabolism ; Cricetulus ; Endocytosis/drug effects ; Epidermal Growth Factor/chemistry ; Epidermal Growth Factor/metabolism ; Fluorescence Resonance Energy Transfer/methods ; Fluorescent Dyes/metabolism ; Humans ; Microscopy, Fluorescence/methods ; Models, Molecular ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Quinazolines/pharmacology ; Receptor, Epidermal Growth Factor/antagonists & inhibitors ; Receptor, Epidermal Growth Factor/chemistry ; Recombinant Proteins/analysis
Chemical Substances	4-((3-bromophenyl)amino)-6,7-dimethoxyquinazoline ; Fluorescent Dyes ; Quinazolines ; Recombinant Proteins ; Epidermal Growth Factor (62229-50-9) ; EGFR protein, human (EC 2.7.10.1) ; Receptor, Epidermal Growth Factor (EC 2.7.10.1)
Language	English
Publishing date	2013-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2099868-5
ISSN	1552-4930 ; 0196-4763 ; 1552-4922
ISSN (online)	1552-4930
ISSN	0196-4763 ; 1552-4922
DOI	10.1002/cyto.a.22311
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Article ; Online: Phosphatidylinositol 4,5-bisphosphate optical uncaging potentiates exocytosis.

Walter, Alexander M / Müller, Rainer / Tawfik, Bassam / Wierda, Keimpe Db / Pinheiro, Paulo S / Nadler, André / McCarthy, Anthony W / Ziomkiewicz, Iwona / Kruse, Martin / Reither, Gregor / Rettig, Jens / Lehmann, Martin / Haucke, Volker / Hille, Bertil / Schultz, Carsten / Sørensen, Jakob Balslev

eLife

2017 Volume 6

Abstract: Phosphatidylinositol-4,5-bisphosphate [PI(4,5) ... ...

Abstract	Phosphatidylinositol-4,5-bisphosphate [PI(4,5)P
MeSH term(s)	Animals ; Carrier Proteins/metabolism ; Cell Line ; Chromaffin Cells/metabolism ; Cytological Techniques/methods ; Exocytosis ; Intracellular Signaling Peptides and Proteins/metabolism ; Membrane Proteins/metabolism ; Mice ; Nerve Tissue Proteins/metabolism ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Synaptotagmin I/metabolism
Chemical Substances	Carrier Proteins ; Cybr protein, mouse ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins ; Nerve Tissue Proteins ; Phosphatidylinositol 4,5-Diphosphate ; Synaptotagmin I ; Syt1 protein, mouse ; Unc13b protein, mouse
Language	English
Publishing date	2017-10-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.30203
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Article ; Online: The SNARE protein vti1a functions in dense-core vesicle biogenesis.

Walter, Alexander M / Kurps, Julia / de Wit, Heidi / Schöning, Susanne / Toft-Bertelsen, Trine L / Lauks, Juliane / Ziomkiewicz, Iwona / Weiss, Annita N / Schulz, Alexander / Fischer von Mollard, Gabriele / Verhage, Matthijs / Sørensen, Jakob B

The EMBO journal

2014 Volume 33, Issue 15, Page(s) 1681–1697

Abstract: The SNARE protein vti1a is proposed to drive fusion of intracellular organelles, but recent data also implicated vti1a in exocytosis. Here we show that vti1a is absent from mature secretory vesicles in adrenal chromaffin cells, but localizes to a ... ...

Abstract	The SNARE protein vti1a is proposed to drive fusion of intracellular organelles, but recent data also implicated vti1a in exocytosis. Here we show that vti1a is absent from mature secretory vesicles in adrenal chromaffin cells, but localizes to a compartment near the trans-Golgi network, partially overlapping with syntaxin-6. Exocytosis is impaired in vti1a null cells, partly due to fewer Ca(2+)-channels at the plasma membrane, partly due to fewer vesicles of reduced size and synaptobrevin-2 content. In contrast, release kinetics and Ca(2+)-sensitivity remain unchanged, indicating that the final fusion reaction leading to transmitter release is unperturbed. Additional deletion of the closest related SNARE, vti1b, does not exacerbate the vti1a phenotype, and vti1b null cells show no secretion defects, indicating that vti1b does not participate in exocytosis. Long-term re-expression of vti1a (days) was necessary for restoration of secretory capacity, whereas strong short-term expression (hours) was ineffective, consistent with vti1a involvement in an upstream step related to vesicle generation, rather than in fusion. We conclude that vti1a functions in vesicle generation and Ca(2+)-channel trafficking, but is dispensable for transmitter release.
MeSH term(s)	Animals ; Calcium Channels/metabolism ; Cell Nucleus Structures/metabolism ; Chromaffin Cells/metabolism ; Exocytosis/physiology ; Mice ; Mice, Mutant Strains ; Qa-SNARE Proteins/metabolism ; Qb-SNARE Proteins/genetics ; Qb-SNARE Proteins/metabolism ; Secretory Vesicles/metabolism ; Vesicle-Associated Membrane Protein 2/metabolism
Chemical Substances	Calcium Channels ; Qa-SNARE Proteins ; Qb-SNARE Proteins ; Vesicle-Associated Membrane Protein 2 ; Vti1a protein, mouse ; Vti1b protein, mouse
Language	English
Publishing date	2014-06-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.201387549
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Book ; Online: Phosphatidylinositol 4,5-bisphosphate optical uncaging potentiates exocytosis

Walter, Alexander / Müller, Rainer / Tawfik, Bassam / Wierda, Keimpe / Pinheiro, Paulo S / Nadler, André / McCarthy, Anthony / Ziomkiewicz, Iwona / Kruse, Martin / Reither, Gregor / Rettig, Jens / Lehmann, Martin / Haucke, Volker / Hille Bertil / Schultz, Carsten / Sørensen, Jakob Balslev

eLife, 6:e30203

2017

Abstract: Phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] is essential for exocytosis. Classical ways of manipulating PI(4,5)P2 levels are slower than its metabolism, making it difficult to distinguish effects of PI(4,5)P2 from those of its metabolites. We ... ...

Abstract	Phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] is essential for exocytosis. Classical ways of manipulating PI(4,5)P2 levels are slower than its metabolism, making it difficult to distinguish effects of PI(4,5)P2 from those of its metabolites. We developed a membrane-permeant, photoactivatable PI(4,5)P2, which is loaded into cells in an inactive form and activated by light, allowing sub-second increases in PI(4,5)P2 levels. By combining this compound with electrophysiological measurements in mouse adrenal chromaffin cells, we show that PI(4,5)P2 uncaging potentiates exocytosis and identify synaptotagmin-1 (the Ca2+ sensor for exocytosis) and Munc13-2 (a vesicle priming protein) as the relevant effector proteins. PI(4,5)P2 activation of exocytosis did not depend on the PI(4,5)P2-binding CAPS-proteins, suggesting that PI(4,5)P2 uncaging may bypass CAPS-function. Finally, PI(4,5)P2 uncaging triggered the rapid fusion of a subset of readily-releasable vesicles, revealing a rapid role of PI(4,5)P2 in fusion triggering. Thus, optical uncaging of signaling lipids can uncover their rapid effects on cellular processes and identify lipid effectors.
Keywords	mouse ; adrenal chromaffin cell ; cell biology ; Munc13 ; neuroscience ; optical uncaging ; exocytosis ; synaptotagmin ; phosphatidylinositols
Subject code	571
Language	English
Publishing country	de
Document type	Book ; Online
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