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Bourigault Y, Chane A, Barbey C, Jafra S, Czajkowski R, Latour X. Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol. Microorganisms 2021; 9:microorganisms9020295. [PMID: 33535657 PMCID: PMC7912877 DOI: 10.3390/microorganisms9020295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.
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Affiliation(s)
- Yvann Bourigault
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Andrea Chane
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
| | - Corinne Barbey
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Sylwia Jafra
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, ul. A. Abrahama 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Division of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, ul. A. Abrahama 58, 80-307 Gdansk, Poland
- Correspondence: (R.C.); (X.L.); Tel.: +48-58-523-63-33 (R.C.); +33-235-146-000 (X.L.)
| | - Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, 55 rue Saint-Germain, F-27000 Evreux, France; (Y.B.); (A.C.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
- Correspondence: (R.C.); (X.L.); Tel.: +48-58-523-63-33 (R.C.); +33-235-146-000 (X.L.)
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102
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DNA origami signposts for identifying proteins on cell membranes by electron cryotomography. Cell 2021; 184:1110-1121.e16. [PMID: 33606980 PMCID: PMC7895908 DOI: 10.1016/j.cell.2021.01.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/14/2020] [Accepted: 01/20/2021] [Indexed: 12/21/2022]
Abstract
Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual molecules within tomograms from cryoET is challenging because of sample crowding and low signal-to-noise ratios. Here, we present a tagging strategy for cryoET that precisely identifies individual protein complexes in tomograms without relying on metal clusters. Our method makes use of DNA origami to produce “molecular signposts” that target molecules of interest, here via fluorescent fusion proteins, providing a platform generally applicable to biological surfaces. We demonstrate the specificity of signpost origami tags (SPOTs) in vitro as well as their suitability for cryoET of membrane vesicles, enveloped viruses, and the exterior of intact mammalian cells. Asymmetric DNA signpost origami tags (SPOTs) precisely localize proteins SPOTs identify specific proteins in electron cryomicroscopy SPOTs have a high contrast “sign” and functionalized “post” base for targeting SPOTs recognize fluorescent fusion proteins on vesicles, viruses, and cell surfaces
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103
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Shahraki A, Işbilir A, Dogan B, Lohse MJ, Durdagi S, Birgul-Iyison N. Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents. J Chem Inf Model 2021; 61:715-728. [PMID: 33476150 DOI: 10.1021/acs.jcim.0c00985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a common pest in Mediterranean countries, by employing resonance energy transfer-based methods, we showed Gαi/o coupling and β-arrestin recruitment of the receptor at sub-nanomolar and nanomolar ranges of the endogenous ligand, AST-C, respectively. Molecular docking and molecular dynamics simulation studies revealed the importance of extracellular loop 2 in AstRC/AST-C interaction, and a combination of in silico and in vitro approaches showed the substantial role of Q2716.55 in G protein-dependent activation of AstR-C possibly via contributing to the flexibility of the receptor's structure. The functional and structural insights obtained on T. pit AstR-C positively assist future efforts in developing environmentally friendly pest control agents that are needed urgently.
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Affiliation(s)
- Aida Shahraki
- Department of Molecular Biology and Genetics, Bogazici University, 34342 Istanbul, Turkey.,Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey
| | - Ali Işbilir
- Max Delbrück Center for Molecular Medicine in Helmholz Association, 13125 Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany
| | - Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine in Helmholz Association, 13125 Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany.,ISAR Bioscience Institute, Planegg, 82152 Munich, Germany
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 Istanbul, Turkey
| | - Necla Birgul-Iyison
- Department of Molecular Biology and Genetics, Bogazici University, 34342 Istanbul, Turkey
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104
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Poque E, Ruigrok HJ, Arnaud-Cormos D, Habauzit D, Chappe Y, Martin C, De Gannes FP, Hurtier A, Garenne A, Lagroye I, Le Dréan Y, Lévêque P, Percherancier Y. Effects of radiofrequency field exposure on proteotoxic-induced and heat-induced HSF1 response in live cells using the bioluminescence resonance energy transfer technique. Cell Stress Chaperones 2021; 26:241-251. [PMID: 33067759 PMCID: PMC7736596 DOI: 10.1007/s12192-020-01172-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 01/09/2023] Open
Abstract
As of today, only acute effects of RF fields have been confirmed to represent a potential health hazard and they are attributed to non-specific heating (≥ 1 °C) under high-level exposure. Yet, the possibility that environmental RF impact living matter in the absence of temperature elevation needs further investigation. Since HSF1 is both a thermosensor and the master regulator of heat-shock stress response in eukaryotes, it remains to assess HSF1 activation in live cells under exposure to low-level RF signals. We thus measured basal, temperature-induced, and chemically induced HSF1 trimerization, a mandatory step on the cascade of HSF1 activation, under RF exposure to continuous wave (CW), Global System for Mobile (GSM), and Wi-Fi-modulated 1800 MHz signals, using a bioluminescence resonance energy transfer technique (BRET) probe. Our results show that, as expected, HSF1 is heat-activated by acute exposure of transiently transfected HEK293T cells to a CW RF field at a specific absorption rate of 24 W/kg for 30 min. However, we found no evidence of HSF1 activation under the same RF exposure condition when the cell culture medium temperature was fixed. We also found no experimental evidence that, at a fixed temperature, chronic RF exposure for 24 h at a SAR of 1.5 and 6 W/kg altered the potency or the maximal capability of the proteasome inhibitor MG132 to activate HSF1, whatever signal used. We only found that RF exposure to CW signals (1.5 and 6 W/kg) and GSM signals (1.5 W/kg) for 24 h marginally decreased basal HSF1 activity.
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Affiliation(s)
- Emmanuelle Poque
- CNRS, Bordeaux INP, CBMN laboratory, UMR5248, Bordeaux University, F-33607, Pessac, France
| | - Hermanus J Ruigrok
- CNRS, IMS laboratory, UMR5218, Bordeaux University, F-33400, Talence, France
| | - Delia Arnaud-Cormos
- CNRS, XLIM, UMR 7252, Limoges University, F-87000, Limoges, France
- Institut Universitaire de France (IUF), F-75005, Paris, France
| | - Denis Habauzit
- Institut de Recherche en Santé, Environnement et Travail (IRSET) - UMR_S 1085, Rennes University, F-35000, Rennes, France
| | - Yann Chappe
- CNRS, IMS laboratory, UMR5218, Bordeaux University, F-33400, Talence, France
| | - Catherine Martin
- Institut de Recherche en Santé, Environnement et Travail (IRSET) - UMR_S 1085, Rennes University, F-35000, Rennes, France
| | | | - Annabelle Hurtier
- CNRS, IMS laboratory, UMR5218, Bordeaux University, F-33400, Talence, France
| | - André Garenne
- CNRS, IMS laboratory, UMR5218, Bordeaux University, F-33400, Talence, France
| | - Isabelle Lagroye
- CNRS, IMS laboratory, UMR5218, Bordeaux University, F-33400, Talence, France
- Paris Sciences et Lettres Research University, F-75006, Paris, France
| | - Yves Le Dréan
- Institut de Recherche en Santé, Environnement et Travail (IRSET) - UMR_S 1085, Rennes University, F-35000, Rennes, France
| | - Philippe Lévêque
- CNRS, XLIM, UMR 7252, Limoges University, F-87000, Limoges, France
| | - Yann Percherancier
- CNRS, IMS laboratory, UMR5218, Bordeaux University, F-33400, Talence, France.
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105
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Abstract
A novel tool for the presentation of peptides and small proteins on the surface of human cells has been developed. Our tANCHOR system utilizes tetraspanin anchors containing heterologous amino acid sequences inserted instead of the large extracellular loop. This technology allows a highly effective extracellular display of epitopes for antibody binding studies and many other potential applications.
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106
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Ohshima S, Matsubara T, Miyamoto A, Shigenari A, Imaeda N, Takasu M, Tanaka M, Shiina T, Suzuki S, Hirayama N, Kitagawa H, Kulski JK, Ando A, Kametani Y. Preparation and characterization of monoclonal antibodies recognizing two CD4 isotypes of Microminipigs. PLoS One 2020; 15:e0242572. [PMID: 33237936 PMCID: PMC7688132 DOI: 10.1371/journal.pone.0242572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Cluster of differentiation 4 (CD4) molecule expressed on the leukocytes is known to function as a co-receptor for class II major histocompatibility complex (MHC) binding to T cell receptor (TCR) on helper T cells. We previously identified two CD4 alleles (CD4.A and CD4.B) in a Microminipig population based on nucleotide sequencing and PCR detection of their gene sequences. However, CD4.B protein expression was not examined because of the unavailability of a reactive antibody to a CD4.B epitope. In this study, we have produced two swine-specific monoclonal antibodies (mAbs) against CD4.B molecules, one that recognizes only CD4.B (b1D7) and the other that recognizes both the CD4.A and CD4.B alleles (x1E10) and that can be used to distinguish CD4 T cell subsets by flow cytometry and immunohistochemistry. Using these two mAbs, we identified CD4.A and CD4.B allele-specific proteins on the surface of CD4.A (+/+) and CD4.B (+/+) T cells at a similar level of expression. Moreover, stimulation of peripheral blood mononuclear cells (PBMCs) derived from CD4.A (+/+) and CD4.B (+/+) swine with toxic shock syndrome toxin-1 (TSST-1) in vitro similarly activated both groups of cells that exhibited a slight increase in the CD4/CD8 double positive (DP) cell ratio. A large portion of the DP cells from the allelic CD4.A (+/+) and CD4.B (+/+) groups enhanced the total CD4 and class I swine leukocyte antigen (SLA) expression. The x1E10 mAb delayed and reduced the TSST-1-induced activation of CD4 T cells. Thus, CD4.B appears to be a functional protein whose expression on activated T cells is analogous to CD4.A.
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Affiliation(s)
- Shino Ohshima
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Tatsuya Matsubara
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Asuka Miyamoto
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Atsuko Shigenari
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Noriaki Imaeda
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Masafumi Tanaka
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takashi Shiina
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Shingo Suzuki
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Noriaki Hirayama
- Institute of Advanced Biosciences, Tokai University, Hiratsuka, Kanagawa, Japan
| | - Hitoshi Kitagawa
- Department of Veterinary Medicine, Faculty of Veterinary Medicine Okayama University of Science, Imabari, Ehime, Japan
| | - Jerzy K. Kulski
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA, Australia
| | - Asako Ando
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Yoshie Kametani
- Division of Basic Medical Science, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Institute of Advanced Biosciences, Tokai University, Hiratsuka, Kanagawa, Japan
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107
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Mamontova AV, Shakhov AM, Grigoryev AP, Lukyanov KA, Bogdanov AM. Increasing the Fluorescence Brightness of Superphotostable EGFP Mutant by Introducing Mutations That Block Chromophore Protonation. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020060187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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108
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Lee J, Liu Z, Suzuki PH, Ahrens JF, Lai S, Lu X, Guan S, St-Pierre F. Versatile phenotype-activated cell sorting. SCIENCE ADVANCES 2020; 6:6/43/eabb7438. [PMID: 33097540 PMCID: PMC7608836 DOI: 10.1126/sciadv.abb7438] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/10/2020] [Indexed: 05/02/2023]
Abstract
Unraveling the genetic and epigenetic determinants of phenotypes is critical for understanding and re-engineering biology and would benefit from improved methods to separate cells based on phenotypes. Here, we report SPOTlight, a versatile high-throughput technique to isolate individual yeast or human cells with unique spatiotemporal profiles from heterogeneous populations. SPOTlight relies on imaging visual phenotypes by microscopy, precise optical tagging of single target cells, and retrieval of tagged cells by fluorescence-activated cell sorting. To illustrate SPOTlight's ability to screen cells based on temporal properties, we chose to develop a photostable yellow fluorescent protein for extended imaging experiments. We screened 3 million cells expressing mutagenesis libraries and identified a bright new variant, mGold, that is the most photostable yellow fluorescent protein reported to date. We anticipate that the versatility of SPOTlight will facilitate its deployment to decipher the rules of life, understand diseases, and engineer new molecules and cells.
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Affiliation(s)
- Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Peter H Suzuki
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - John F Ahrens
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Sihui Guan
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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109
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Abstract
Posttranscriptional regulation is a major level of gene expression control in any cell. In bacteria, multiprotein machines called RNA degradosomes are central for RNA processing and degradation, and some were reported to be compartmentalized inside these organelleless cells. The minimal RNA degradosome of the important gastric pathogen Helicobacter pylori is composed of the essential ribonuclease RNase J and RhpA, its sole DEAD box RNA helicase, and plays a major role in the regulation of mRNA decay and adaptation to gastric colonization. Here, the subcellular localization of the H. pylori RNA degradosome was investigated using cellular fractionation and both confocal and superresolution microscopy. We established that RNase J and RhpA are peripheral inner membrane proteins and that this association was mediated neither by ribosomes nor by RNA nor by the RNase Y membrane protein. In live H. pylori cells, we observed that fluorescent RNase J and RhpA protein fusions assemble into nonpolar foci. We identified factors that regulate the formation of these foci without affecting the degradosome membrane association. Flotillin, a bacterial membrane scaffolding protein, and free RNA promote focus formation in H. pylori Finally, RNase J-GFP (RNase J-green fluorescent protein) molecules and foci in cells were quantified by three-dimensional (3D) single-molecule fluorescence localization microscopy. The number and size of the RNase J foci were found to be scaled with growth phase and cell volume as previously reported for eukaryotic ribonucleoprotein granules. In conclusion, we propose that membrane compartmentalization and the regulated clustering of RNase J-based degradosome hubs represent important levels of control of their activity and specificity.IMPORTANCE Helicobacter pylori is a bacterial pathogen that chronically colonizes the stomach of half of the human population worldwide. Infection by H. pylori can lead to the development of gastric pathologies such as ulcers and adenocarcinoma, which causes up to 800,000 deaths in the world each year. Persistent colonization by H. pylori relies on regulation of the expression of adaptation-related genes. One major level of such control is posttranscriptional regulation, which, in H. pylori, largely relies on a multiprotein molecular machine, an RNA degradosome, that we previously discovered. In this study, we established that the two protein partners of this machine are associated with the membrane of H. pylori Using cutting-edge microscopy, we showed that these complexes assemble into hubs whose formation is regulated by free RNA and scaled with bacterial size and growth phase. Organelleless cellular compartmentalization of molecular machines into hubs emerges as an important regulatory level in bacteria.
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110
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von der Heyde B, Hallmann A. Targeted migration of pherophorin-S indicates extensive extracellular matrix dynamics in Volvox carteri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2301-2317. [PMID: 32603539 DOI: 10.1111/tpj.14901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Hydroxyproline-rich glycoproteins (HRGPs) constitute a major group of proteins of the extracellular matrix (ECM). The multicellular green alga Volvox carteri is a suitable model organism in which to study the evolutionary transition to multicellularity, including the basic principles and characteristics of an ECM. In Volvox, the ECM is dominated by a single HRGP family: the pherophorins. Our inventory amounts to 117 pherophorin-related genes in V. carteri. We focused on a pherophorin with an unexpected characteristic: pherophorin-S is a soluble, non-cross-linked ECM protein. Using transformants expressing a YFP-tagged pherophorin-S we observed the synthesis and secretion of pherophorin-S by somatic cells in vivo, and we then traced the protein during its conspicuous migration to the ECM around prehatching juveniles and its localized concentration there. Our results provide insights into how an ECM zone surrounding the progeny is remotely affected by distantly located parental somatic cells. In view of the properties and migration of pherophorin-S, we conclude that pherophorin-S is likely to act as an ECM plasticizer to allow for dynamic ECM remodeling.
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Affiliation(s)
- Benjamin von der Heyde
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, Bielefeld, 33615, Germany
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, Bielefeld, 33615, Germany
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111
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Menaesse A, Sumetsky D, Emanuely N, Stein JL, Gates EM, Hoffman BD, Boustany NN. Simplified Instrument Calibration for Wide-Field Fluorescence Resonance Energy Transfer (FRET) Measured by the Sensitized Emission Method. Cytometry A 2020; 99:407-416. [PMID: 32700451 DOI: 10.1002/cyto.a.24194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/30/2020] [Accepted: 07/17/2020] [Indexed: 12/21/2022]
Abstract
Fӧrster (or fluorescence) resonance energy transfer (FRET) is a quantifiable energy transfer in which a donor fluorophore nonradiatively transfers its excitation energy to an acceptor fluorophore. A change in FRET efficiency indicates a change of proximity and environment of these fluorophores, which enables the study of intermolecular interactions. Measurement of FRET efficiency using the sensitized emission method requires a donor-acceptor calibrated system. One of these calibration factors named the G factor, which depends on instrument parameters related to the donor and acceptor measurement channels and on the fluorophores quantum efficiencies, can be determined in several different ways and allows for conversion of the raw donor and acceptor emission signals to FRET efficiency. However, the calculated value of the G factor from experimental data can fluctuate significantly depending on the chosen experimental method and the size of the sample. In this technical note, we extend the results of Gates et al. (Cytometry Part A 95A (2018) 201-213) by refining the calibration method used for calibration of FRET from image pixel data. Instead of using the pixel histograms of two constructs with high and low FRET efficiency to determine the G factor, we use pixel histogram data from one construct of known efficiency. We validate this method by determining the G factor with the same constructs developed and used by Gates et al. and comparing the results from the two approaches. While the two approaches are equivalent theoretically, we demonstrate that the use of a single construct with known efficiency provides a more precise experimental measurement of the G factor that can be attained by collecting a smaller number of images. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Audrey Menaesse
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,School of Life Sciences Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Daniel Sumetsky
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Nicolas Emanuely
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,Institut d'Optique Graduate School, Palaiseau, France
| | - Jeremy L Stein
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Evan M Gates
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Brenton D Hoffman
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Nada N Boustany
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
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112
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Al-Sabah S, Adi L, Bünemann M, Krasel C. The Effect of Cell Surface Expression and Linker Sequence on the Recruitment of Arrestin to the GIP Receptor. Front Pharmacol 2020; 11:1271. [PMID: 32903502 PMCID: PMC7438548 DOI: 10.3389/fphar.2020.01271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/31/2020] [Indexed: 01/28/2023] Open
Abstract
The glucose-dependent insulinotropic polypeptide (GIP) and the glucagon-like peptide-1 (GLP-1) receptor are important targets in the treatment of both type 2 diabetes mellitus (T2DM) and obesity. Originally identified for their role in desensitization, internalization and recycling of G protein-coupled receptors (GPCRs), arrestins have since been shown to act as scaffolding proteins that allow GPCRs to signal in a G protein-independent manner. While GLP-1R has been reported to interact with arrestins, this aspect of cell signaling remains controversial for GIPR. Using a (FRET)-based assay we have previously shown that yellow fluorescent protein (YFP)-labeled GIPR does not recruit arrestin. This GIPR-YFP construct contained a 10 amino acid linker between the receptor and a XbaI restriction site upstream of the YFP. This linker was not present in the modified GIPR-SYFP2 used in subsequent FRET and bioluminescence resonance energy transfer (BRET) assays. However, its removal results in the introduction of a serine residue adjacent to the end of GIPR’s C-terminal tail which could potentially be a phosphorylation site. The resulting receptor was indeed able to recruit arrestin. To find out whether the serine/arginine (SR) coded by the XbaI site was indeed the source of the problem, it was substituted with glycine/glycine (GG) by site-directed mutagenesis. This substitution abolished arrestin recruitment in the BRET assay but only significantly reduced it in the FRET assay. In addition, we show that the presence of a N-terminal FLAG epitope and influenza hemagglutinin signal peptide were also required to detect arrestin recruitment to the GIPR, most likely by increasing receptor cell surface expression. These results demonstrate how arrestin recruitment assay configuration can dramatically alter the result. This becomes relevant when drug discovery programs aim to identify ligands with “biased agonist” properties.
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Affiliation(s)
- Suleiman Al-Sabah
- Department of Pharmacology and Toxicology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Lobna Adi
- Department of Pharmacology and Toxicology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Moritz Bünemann
- School of Pharmacy, Institute for Pharmacology and Toxicology, The Philipps University of Marburg, Marburg, Germany
| | - Cornelius Krasel
- School of Pharmacy, Institute for Pharmacology and Toxicology, The Philipps University of Marburg, Marburg, Germany
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113
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Prasai A, Schmidt Cernohorska M, Ruppova K, Niederlova V, Andelova M, Draber P, Stepanek O, Huranova M. The BBSome assembly is spatially controlled by BBS1 and BBS4 in human cells. J Biol Chem 2020; 295:14279-14290. [PMID: 32759308 DOI: 10.1074/jbc.ra120.013905] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/04/2020] [Indexed: 12/18/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a pleiotropic ciliopathy caused by dysfunction of primary cilia. More than half of BBS patients carry mutations in one of eight genes encoding for subunits of a protein complex, the BBSome, which mediates trafficking of ciliary cargoes. In this study, we elucidated the mechanisms of the BBSome assembly in living cells and how this process is spatially regulated. We generated a large library of human cell lines deficient in a particular BBSome subunit and expressing another subunit tagged with a fluorescent protein. We analyzed these cell lines utilizing biochemical assays, conventional and expansion microscopy, and quantitative fluorescence microscopy techniques: fluorescence recovery after photobleaching and fluorescence correlation spectroscopy. Our data revealed that the BBSome formation is a sequential process. We show that the pre-BBSome is nucleated by BBS4 and assembled at pericentriolar satellites, followed by the translocation of the BBSome into the ciliary base mediated by BBS1. Our results provide a framework for elucidating how BBS-causative mutations interfere with the biogenesis of the BBSome.
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Affiliation(s)
- Avishek Prasai
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marketa Schmidt Cernohorska
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Klara Ruppova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Veronika Niederlova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Andelova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Peter Draber
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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114
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Alnahhas RN, Sadeghpour M, Chen Y, Frey AA, Ott W, Josić K, Bennett MR. Majority sensing in synthetic microbial consortia. Nat Commun 2020; 11:3659. [PMID: 32694598 PMCID: PMC7374166 DOI: 10.1038/s41467-020-17475-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/25/2020] [Indexed: 01/26/2023] Open
Abstract
As synthetic biocircuits become more complex, distributing computations within multi-strain microbial consortia becomes increasingly beneficial. However, designing distributed circuits that respond predictably to variation in consortium composition remains a challenge. Here we develop a two-strain gene circuit that senses and responds to which strain is in the majority. This involves a co-repressive system in which each strain produces a signaling molecule that signals the other strain to down-regulate production of its own, orthogonal signaling molecule. This co-repressive consortium links gene expression to ratio of the strains rather than population size. Further, we control the cross-over point for majority via external induction. We elucidate the mechanisms driving these dynamics by developing a mathematical model that captures consortia response as strain fractions and external induction are varied. These results show that simple gene circuits can be used within multicellular synthetic systems to sense and respond to the state of the population.
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Affiliation(s)
| | - Mehdi Sadeghpour
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Mathematics, University of Houston, Houston, TX, USA
| | - Ye Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Alexis A Frey
- Department of Biosciences, Rice University, Houston, TX, USA
| | - William Ott
- Department of Mathematics, University of Houston, Houston, TX, USA
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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115
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A Sensitive Magnetic Arsenite-Specific Biosensor Hosted in Magnetotactic Bacteria. Appl Environ Microbiol 2020; 86:AEM.00803-20. [PMID: 32385084 DOI: 10.1128/aem.00803-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/01/2020] [Indexed: 01/22/2023] Open
Abstract
According to the World Health Organization, arsenic is the water contaminant that affects the largest number of people worldwide. To limit its impact on the population, inexpensive, quick, and easy-to-use systems of detection are required. One promising solution could be the use of whole-cell biosensors, which have been extensively studied and could meet all these criteria even though they often lack sensitivity. Here, we investigated the benefit of using magnetotactic bacteria as cellular chassis to design and build sensitive magnetic bacterial biosensors. Promoters potentially inducible by arsenic were first identified in silico within the genomes of two magnetotactic bacteria strains, Magnetospirillum magneticum AMB-1 and Magnetospirillum gryphiswaldense MSR-1. The ArsR-dependent regulation was confirmed by reverse transcription-PCR experiments. Biosensors built by transcriptional fusion between the arsenic-inducible promoters and the bacterial luciferase luxCDABE operon gave an element-specific response in 30 min with an arsenite detection limit of 0.5 μM. After magnetic concentration, we improved the sensitivity of the biosensor by a factor of 50 to reach 10 nM, more than 1 order of magnitude below the recommended guidelines for arsenic in drinking water (0.13 μM). Finally, we demonstrated the successful preservation of the magnetic bacterium biosensors by freeze-drying.IMPORTANCE Whole-cell biosensors based on reporter genes can be designed for heavy metal detection but often require the optimization of their sensitivity and specific adaptations for practical use in the field. Magnetotactic bacteria as cellular hosts for biosensors are interesting models, as their intrinsic magnetism permits them to be easily concentrated and entrapped to increase the arsenic-response signal. This paves the way for the development of sensitive and immobilized whole-cell biosensors tailored for use in the field.
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116
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George J, Kahlke T, Abbriano RM, Kuzhiumparambil U, Ralph PJ, Fabris M. Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology. Front Bioeng Biotechnol 2020; 8:513. [PMID: 32582656 PMCID: PMC7290003 DOI: 10.3389/fbioe.2020.00513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
Diatoms are photosynthetic microeukaryotes that dominate phytoplankton populations and have increasing applicability in biotechnology. Uncovering their complex biology and elevating strains to commercial standards depends heavily on robust genetic engineering tools. However, engineering microalgal genomes predominantly relies on random integration of transgenes into nuclear DNA, often resulting in detrimental “position-effects” such as transgene silencing, integration into transcriptionally-inactive regions, and endogenous sequence disruption. With the recent development of extrachromosomal transgene expression via independent episomes, it is timely to investigate both strategies at the phenotypic and genomic level. Here, we engineered the model diatom Phaeodactylum tricornutum to produce the high-value heterologous monoterpenoid geraniol, which, besides applications as fragrance and insect repellent, is a key intermediate of high-value pharmaceuticals. Using high-throughput phenotyping we confirmed the suitability of episomes for synthetic biology applications and identified superior geraniol-yielding strains following random integration. We used third generation long-read sequencing technology to generate a complete analysis of all transgene integration events including their genomic locations and arrangements associated with high-performing strains at a genome-wide scale with subchromosomal detail, never before reported in any microalga. This revealed very large, highly concatenated insertion islands, offering profound implications on diatom functional genetics and next generation genome editing technologies, and is key for developing more precise genome engineering approaches in diatoms, including possible genomic safe harbour locations to support high transgene expression for targeted integration approaches. Furthermore, we have demonstrated that exogenous DNA is not integrated inadvertently into the nuclear genome of extrachromosomal-expression clones, an important characterisation of this novel engineering approach that paves the road to synthetic biology applications.
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Affiliation(s)
- Jestin George
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Raffaela M Abbriano
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | | | - Peter J Ralph
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Michele Fabris
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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117
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Xu Y, Caldo KMP, Falarz L, Jayawardhane K, Chen G. Kinetic improvement of an algal diacylglycerol acyltransferase 1 via fusion with an acyl-CoA binding protein. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:856-871. [PMID: 31991039 DOI: 10.1111/tpj.14708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/26/2019] [Accepted: 01/21/2020] [Indexed: 05/03/2023]
Abstract
Microalgal oils in the form of triacylglycerols (TAGs) are broadly used as nutritional supplements and biofuels. Diacylglycerol acyltransferase (DGAT) catalyzes the final step of acyl-CoA-dependent biosynthesis of TAG, and is considered a key target for manipulating oil production. Although a growing number of DGAT1s have been identified and over-expressed in some algal species, the detailed structure-function relationship, as well as the improvement of DGAT1 performance via protein engineering, remain largely untapped. Here, we explored the structure-function features of the hydrophilic N-terminal domain of DGAT1 from the green microalga Chromochloris zofingiensis (CzDGAT1). The results indicated that the N-terminal domain of CzDGAT1 was less disordered than those of the higher eukaryotic enzymes and its partial truncation or complete removal could substantially decrease enzyme activity, suggesting its possible role in maintaining enzyme performance. Although the N-terminal domains of animal and plant DGAT1s were previously found to bind acyl-CoAs, replacement of CzDGAT1 N-terminus by an acyl-CoA binding protein (ACBP) could not restore enzyme activity. Interestingly, the fusion of ACBP to the N-terminus of the full-length CzDGAT1 could enhance the enzyme affinity for acyl-CoAs and augment protein accumulation levels, which ultimately drove oil accumulation in yeast cells and tobacco leaves to higher levels than the full-length CzDGAT1. Overall, our findings unravel the distinct features of the N-terminus of algal DGAT1 and provide a strategy to engineer enhanced performance in DGAT1 via protein fusion, which may open a vista in generating improved membrane-bound acyl-CoA-dependent enzymes and boosting oil biosynthesis in plants and oleaginous microorganisms.
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Affiliation(s)
- Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Kristian Mark P Caldo
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Lucas Falarz
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Kethmi Jayawardhane
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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118
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Theruvath J, Sotillo E, Mount CW, Graef CM, Delaidelli A, Heitzeneder S, Labanieh L, Dhingra S, Leruste A, Majzner RG, Xu P, Mueller S, Yecies DW, Finetti MA, Williamson D, Johann PD, Kool M, Pfister S, Hasselblatt M, Frühwald MC, Delattre O, Surdez D, Bourdeaut F, Puget S, Zaidi S, Mitra SS, Cheshier S, Sorensen PH, Monje M, Mackall CL. Locoregionally administered B7-H3-targeted CAR T cells for treatment of atypical teratoid/rhabdoid tumors. Nat Med 2020; 26:712-719. [PMID: 32341579 DOI: 10.1038/s41591-020-0821-8] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/06/2020] [Indexed: 01/01/2023]
Abstract
Atypical teratoid/rhabdoid tumors (ATRTs) typically arise in the central nervous system (CNS) of children under 3 years of age. Despite intensive multimodal therapy (surgery, chemotherapy and, if age permits, radiotherapy), median survival is 17 months1,2. We show that ATRTs robustly express B7-H3/CD276 that does not result from the inactivating mutations in SMARCB1 (refs. 3,4), which drive oncogenesis in ATRT, but requires residual SWItch/Sucrose Non-Fermentable (SWI/SNF) activity mediated by BRG1/SMARCA4. Consistent with the embryonic origin of ATRT5,6, B7-H3 is highly expressed on the prenatal, but not postnatal, brain. B7-H3.BB.z-chimeric antigen receptor (CAR) T cells administered intracerebroventricularly or intratumorally mediate potent antitumor effects against cerebral ATRT xenografts in mice, with faster kinetics, greater potency and reduced systemic levels of inflammatory cytokines compared to CAR T cells administered intravenously. CAR T cells administered ICV also traffic from the CNS into the periphery; following clearance of ATRT xenografts, B7-H3.BB.z-CAR T cells administered intracerebroventricularly or intravenously mediate antigen-specific protection from tumor rechallenge, both in the brain and periphery. These results identify B7-H3 as a compelling therapeutic target for this largely incurable pediatric tumor and demonstrate important advantages of locoregional compared to systemic delivery of CAR T cells for the treatment of CNS malignancies.
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Affiliation(s)
- Johanna Theruvath
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Elena Sotillo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Mount
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Claus Moritz Graef
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sabine Heitzeneder
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Louai Labanieh
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Shaurya Dhingra
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Amaury Leruste
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Robbie G Majzner
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Peng Xu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabine Mueller
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Derek W Yecies
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Pascal D Johann
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, Münster University Hospital, Münster, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg, Germany.,EU-RHAB Registry Center, Augsburg, Germany
| | - Olivier Delattre
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Didier Surdez
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Franck Bourdeaut
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Stephanie Puget
- Paris University, Necker-Enfants Malades Hospital, Department of Neurosurgery, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sakina Zaidi
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Siddhartha S Mitra
- Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Samuel Cheshier
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Primary Children's Hospital and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Michelle Monje
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Institute for Stem Cell and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Crystal L Mackall
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA. .,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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119
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Single-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling. Nat Commun 2020; 11:1942. [PMID: 32327645 PMCID: PMC7181598 DOI: 10.1038/s41467-020-15693-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/20/2020] [Indexed: 01/09/2023] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is a pivotal compound in marine biogeochemical cycles and a key chemical currency in microbial interactions. Marine bacteria transform DMSP via two competing pathways with considerably different biogeochemical implications: demethylation channels sulfur into the microbial food web, whereas cleavage releases sulfur into the atmosphere. Here, we present single-cell measurements of the expression of these two pathways using engineered fluorescent reporter strains of Ruegeria pomeroyi DSS-3, and find that external DMSP concentration dictates the relative expression of the two pathways. DMSP induces an upregulation of both pathways, but only at high concentrations (>1 μM for demethylation; >35 nM for cleavage), characteristic of microscale hotspots such as the vicinity of phytoplankton cells. Co-incubations between DMSP-producing microalgae and bacteria revealed an increase in cleavage pathway expression close to the microalgae’s surface. These results indicate that bacterial utilization of microscale DMSP hotspots is an important determinant of the fate of sulfur in the ocean. DMSP is a ubiquitous organosulfur compound in the ocean that, once degraded by bacteria, plays key roles in global biogeochemical cycles and climate regulation. Here, the authors use single-cell measurements of transcription to investigate the intricate dynamics of bacterial DMSP degradation.
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120
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Senarisoy M, Barette C, Lacroix F, De Bonis S, Stelter M, Hans F, Kleman JP, Fauvarque MO, Timmins J. Förster Resonance Energy Transfer Based Biosensor for Targeting the hNTH1-YB1 Interface as a Potential Anticancer Drug Target. ACS Chem Biol 2020; 15:990-1003. [PMID: 32125823 DOI: 10.1021/acschembio.9b01023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Y-box binding protein 1 (YB1) is an established metastatic marker: high expression and nuclear localization of YB1 correlate with tumor aggressiveness, drug resistance, and poor patient survival in various tumors. In the nucleus, YB1 interacts with and regulates the activities of several nuclear proteins, including the DNA glycosylase, human endonuclease III (hNTH1). In the present study, we used Förster resonance energy transfer (FRET) and AlphaLISA technologies to further characterize this interaction and define the minimal regions of hNTH1 and YB1 required for complex formation. This work led us to design an original and cost-effective FRET-based biosensor for the rapid in vitro high-throughput screening for potential inhibitors of the hNTH1-YB1 complex. Two pilot screens were carried out, allowing the selection of several promising compounds exhibiting IC50 values in the low micromolar range. Interestingly, two of these compounds bind to YB1 and sensitize drug-resistant breast tumor cells to the chemotherapeutic agent, cisplatin. Taken together, these findings demonstrate that the hNTH1-YB1 interface is a druggable target for the development of new therapeutic strategies for the treatment of drug-resistant tumors. Moreover, beyond this study, the simple design of our biosensor defines an innovative and efficient strategy for the screening of inhibitors of therapeutically relevant protein-protein interfaces.
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Affiliation(s)
- Muge Senarisoy
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Caroline Barette
- Univ. Grenoble Alpes, CEA, INSERM, BGE, F-38000 Grenoble, France
| | | | | | - Meike Stelter
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Fabienne Hans
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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121
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Sauret-Güeto S, Frangedakis E, Silvestri L, Rebmann M, Tomaselli M, Markel K, Delmans M, West A, Patron NJ, Haseloff J. Systematic Tools for Reprogramming Plant Gene Expression in a Simple Model, Marchantia polymorpha. ACS Synth Biol 2020; 9:864-882. [PMID: 32163700 DOI: 10.1021/acssynbio.9b00511] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present the OpenPlant toolkit, a set of interlinked resources and techniques to develop Marchantia as testbed for bioengineering in plants. Marchantia is a liverwort, a simple plant with an open form of development that allows direct visualization of gene expression and dynamics of cellular growth in living tissues. We describe new techniques for simple and efficient axenic propagation and maintenance of Marchantia lines with no requirement for glasshouse facilities. Marchantia plants spontaneously produce clonal propagules within a few weeks of regeneration, and lines can be amplified million-fold in a single generation by induction of the sexual phase of growth, crossing, and harvesting of progeny spores. The plant has a simple morphology and genome with reduced gene redundancy, and the dominant phase of its life cycle is haploid, making genetic analysis easier. We have built robust Loop assembly vector systems for nuclear and chloroplast transformation and genome editing. These have provided the basis for building and testing a modular library of standardized DNA elements with highly desirable properties. We have screened transcriptomic data to identify a range of candidate genes, extracted putative promoter sequences, and tested them in vivo to identify new constitutive promoter elements. The resources have been combined into a toolkit for plant bioengineering that is accessible for laboratories without access to traditional facilities for plant biology research. The toolkit is being made available under the terms of the OpenMTA and will facilitate the establishment of common standards and the use of this simple plant as testbed for synthetic biology.
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Affiliation(s)
- Susanna Sauret-Güeto
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Eftychios Frangedakis
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Linda Silvestri
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, U.K
| | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Kasey Markel
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | | | | | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
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122
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Behle A, Saake P, Germann AT, Dienst D, Axmann IM. Comparative Dose-Response Analysis of Inducible Promoters in Cyanobacteria. ACS Synth Biol 2020; 9:843-855. [PMID: 32134640 DOI: 10.1021/acssynbio.9b00505] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Design and implementation of synthetic biological circuits highly depends on well-characterized, robust promoters with predictable input-output responses. While great progress has been made with heterotrophic model organisms such as Escherichia coli, the available variety of tunable promoter parts for phototrophic cyanobacteria is still limited. Commonly used synthetic and semisynthetic promoters show weak dynamic ranges or no regulation at all in cyanobacterial models. Well-controlled alternatives such as native metal-responsive promoters, however, pose the problems of inducer toxicity and lacking orthogonality. Here, we present the comparative assessment of dose-response functions of four different inducible promoter systems in the model cyanobacterium Synechocystis sp. PCC 6803. Using the novel bimodular reporter plasmid pSHDY, dose-response dynamics of the re-established vanillate-inducible promoter PvanCC was compared to the previously described rhamnose-inducible Prha, the anhydrotetracycline-inducible PL03, and the Co2+-inducible PcoaT. We estimate individual advantages and disadvantages regarding dynamic range and strength of each promoter, also in comparison with well-established constitutive systems. We observed a delicate balance between transcription factor toxicity and sufficient expression to obtain a dose-dependent response to the inducer. In summary, we expand the current understanding and employability of inducible promoters in cyanobacteria, facilitating the scalability and robustness of synthetic regulatory network designs and of complex metabolic pathway engineering strategies.
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Affiliation(s)
- Anna Behle
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Pia Saake
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Anna T. Germann
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Dennis Dienst
- Department of Chemistry − Ångström, Uppsala University, 75120 Uppsala, Sweden
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
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123
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Van Geel O, Cheung S, Gadella TWJ. Combining optogenetics with sensitive FRET imaging to monitor local microtubule manipulations. Sci Rep 2020; 10:6034. [PMID: 32265472 PMCID: PMC7138840 DOI: 10.1038/s41598-020-62874-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/06/2020] [Indexed: 11/09/2022] Open
Abstract
Optogenetic methods for switching molecular states in cells are increasingly prominent tools in life sciences. Förster Resonance Energy Transfer (FRET)-based sensors can provide quantitative and sensitive readouts of altered cellular biochemistry, e.g. from optogenetics. However, most of the light-inducible domains respond to the same wavelength as is required for excitation of popular CFP/YFP-based FRET pairs, rendering the techniques incompatible with each other. In order to overcome this limitation, we red-shifted an existing CFP/YFP-based OP18 FRET sensor (COPY) by employing an sYFP2 donor and mScarlet-I acceptor. Their favorable quantum yield and brightness result in a red-shifted FRET pair with an optimized dynamic range, which could be further enhanced by an R125I point mutation that stimulates intramolecular interactions. The new sensor was named ROPY and it visualizes the interaction between the microtubule regulator stathmin/OP18 and free tubulin heterodimers. We show that through phosphorylation of the ROPY sensor, its tubulin sequestering ability can be locally regulated by photo-activatable Rac1 (PARac1), independent of the FRET readout. Together, ROPY and PARac1 provide spatiotemporal control over free tubulin levels. ROPY/PARac1-based optogenetic regulation of free tubulin levels allowed us to demonstrate that depletion of free tubulin prevents the formation of pioneer microtubules, while local upregulation of tubulin concentration allows localized microtubule extensions to support the lamellipodia.
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Affiliation(s)
- Orry Van Geel
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Stephanie Cheung
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.,Developmental Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.
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124
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Dienst D, Wichmann J, Mantovani O, Rodrigues JS, Lindberg P. High density cultivation for efficient sesquiterpenoid biosynthesis in Synechocystis sp. PCC 6803. Sci Rep 2020; 10:5932. [PMID: 32246065 PMCID: PMC7125158 DOI: 10.1038/s41598-020-62681-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Cyanobacteria and microalgae are attractive photoautotrophic host systems for climate-friendly production of fuels and other value-added biochemicals. However, for economic applications further development and implementation of efficient and sustainable cultivation strategies are essential. Here, we present a comparative study on cyanobacterial sesquiterpenoid biosynthesis in Synechocystis sp. PCC 6803 using a commercial lab-scale High Density Cultivation (HDC) platform in the presence of dodecane as in-situ extractant. Operating in a two-step semi-batch mode over a period of eight days, volumetric yields of (E)-α-bisabolene were more than two orders of magnitude higher than previously reported for cyanobacteria, with final titers of 179.4 ± 20.7 mg * L−1. Likewise, yields of the sesquiterpene alcohols (−)-patchoulol and (−)-α-bisabolol were many times higher than under reference conditions, with final titers of 17.3 ± 1.85 mg * L−1 and 96.3 ± 2.2 mg * L−1, respectively. While specific productivity was compromised particularly for (E)-α-bisabolene in the HDC system during phases of high biomass accumulation rates, volumetric productivity enhancements during linear growth at high densities were more pronounced for (E)-α-bisabolene than for the hydroxylated terpenoids. Together, this study provides additional insights into cell density-related process characteristics, introducing HDC as highly efficient strategy for phototrophic terpenoid production in cyanobacteria.
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Affiliation(s)
- Dennis Dienst
- Department of Chemistry - Ångström, Uppsala University, Box 523, Uppsala, 75120, Sweden
| | - Julian Wichmann
- Faculty of Biology - Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Oliver Mantovani
- Department of Chemistry - Ångström, Uppsala University, Box 523, Uppsala, 75120, Sweden
| | - João S Rodrigues
- Department of Chemistry - Ångström, Uppsala University, Box 523, Uppsala, 75120, Sweden
| | - Pia Lindberg
- Department of Chemistry - Ångström, Uppsala University, Box 523, Uppsala, 75120, Sweden.
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125
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von der Heyde EL, Hallmann A. Babo1, formerly Vop1 and Cop1/2, is no eyespot photoreceptor but a basal body protein illuminating cell division in Volvox carteri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:276-298. [PMID: 31778231 DOI: 10.1111/tpj.14623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/29/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
In photosynthetic organisms many processes are light dependent and sensing of light requires light-sensitive proteins. The supposed eyespot photoreceptor protein Babo1 (formerly Vop1) has previously been classified as an opsin due to the capacity for binding retinal. Here, we analyze Babo1 and provide evidence that it is no opsin. Due to the localization at the basal bodies, the former Vop1 and Cop1/2 proteins were renamed V.c. Babo1 and C.r. Babo1. We reveal a large family of more than 60 Babo1-related proteins from a wide range of species. The detailed subcellular localization of fluorescence-tagged Babo1 shows that it accumulates at the basal apparatus. More precisely, it is located predominantly at the basal bodies and to a lesser extent at the four strands of rootlet microtubules. We trace Babo1 during basal body separation and cell division. Dynamic structural rearrangements of Babo1 particularly occur right before the first cell division. In four-celled embryos Babo1 was exclusively found at the oldest basal bodies of the embryo and on the corresponding d-roots. The unequal distribution of Babo1 in four-celled embryos could be an integral part of a geometrical system in early embryogenesis, which establishes the anterior-posterior polarity and influences the spatial arrangement of all embryonic structures and characteristics. Due to its retinal-binding capacity, Babo1 could also be responsible for the unequal distribution of retinoids, knowing that such concentration gradients of retinoids can be essential for the correct patterning during embryogenesis of more complex organisms. Thus, our findings push the Babo1 research in another direction.
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Affiliation(s)
- Eva L von der Heyde
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr 25, 33615, Bielefeld, Germany
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr 25, 33615, Bielefeld, Germany
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126
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Grant BMM, Enomoto M, Back SI, Lee KY, Gebregiworgis T, Ishiyama N, Ikura M, Marshall CB. Calmodulin disrupts plasma membrane localization of farnesylated KRAS4b by sequestering its lipid moiety. Sci Signal 2020; 13:13/625/eaaz0344. [PMID: 32234958 DOI: 10.1126/scisignal.aaz0344] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
KRAS4b is a small guanosine triphosphatase (GTPase) protein that regulates several signal transduction pathways that underlie cell proliferation, differentiation, and survival. KRAS4b function requires prenylation of its C terminus and recruitment to the plasma membrane, where KRAS4b activates effector proteins including the RAF family of kinases. The Ca2+-sensing protein calmodulin (CaM) has been suggested to regulate the localization of KRAS4b through direct, Ca2+-dependent interaction, but how CaM and KRAS4b functionally interact is controversial. Here, we determined a crystal structure, which was supported by solution nuclear magnetic resonance (NMR), that revealed the sequestration of the prenyl moiety of KRAS4b in the hydrophobic pocket of the C-terminal lobe of Ca2+-bound CaM. Our engineered fluorescence resonance energy transfer (FRET)-based biosensor probes (CaMeRAS) showed that, upon stimulation of Ca2+ influx by extracellular ligands, KRAS4b reversibly translocated in a Ca2+-CaM-dependent manner from the plasma membrane to the cytoplasm in live HeLa and HEK293 cells. These results reveal a mechanism underlying the inhibition of KRAS4b activity by Ca2+ signaling pathways.
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Affiliation(s)
- Benjamin M M Grant
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Sung-In Back
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Noboru Ishiyama
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada.
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127
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Watabe T, Terai K, Sumiyama K, Matsuda M. Booster, a Red-Shifted Genetically Encoded Förster Resonance Energy Transfer (FRET) Biosensor Compatible with Cyan Fluorescent Protein/Yellow Fluorescent Protein-Based FRET Biosensors and Blue Light-Responsive Optogenetic Tools. ACS Sens 2020; 5:719-730. [PMID: 32101394 DOI: 10.1021/acssensors.9b01941] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been developed for the visualization of signaling molecule activities. Currently, most of them are comprised of cyan and yellow fluorescent proteins (CFP and YFP), precluding the use of multiple FRET biosensors within a single cell. Moreover, the FRET biosensors based on CFP and YFP are incompatible with the optogenetic tools that operate at blue light. To overcome these problems, here, we have developed FRET biosensors with red-shifted excitation and emission wavelengths. We chose mKOκ and mKate2 as the favorable donor and acceptor pair by calculating the Förster distance. By optimizing the order of fluorescent proteins and modulatory domains of the FRET biosensors, we developed a FRET biosensor backbone named "Booster". The performance of the protein kinase A (PKA) biosensor based on the Booster backbone (Booster-PKA) was comparable to that of AKAR3EV, a previously developed FRET biosensor comprising CFP and YFP. For the proof of concept, we first showed simultaneous monitoring of activities of two protein kinases with Booster-PKA and ERK FRET biosensors based on CFP and YFP. Second, we showed monitoring of PKA activation by Beggiatoa photoactivated adenylyl cyclase, an optogenetic generator of cyclic AMP. Finally, we presented PKA activity in living tissues of transgenic mice expressing Booster-PKA. Collectively, the results demonstrate the effectiveness and versatility of Booster biosensors as an imaging tool in vitro and in vivo.
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Affiliation(s)
- Tetsuya Watabe
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Kenta Terai
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0874, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
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128
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Knöppel A, Andersson DI, Näsvall J. Synonymous Mutations in rpsT Lead to Ribosomal Assembly Defects That Can Be Compensated by Mutations in fis and rpoA. Front Microbiol 2020; 11:340. [PMID: 32210939 PMCID: PMC7069363 DOI: 10.3389/fmicb.2020.00340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/17/2020] [Indexed: 11/21/2022] Open
Abstract
We previously described how four deleterious synonymous mutations in the Salmonella enterica rpsT gene (encoding ribosomal protein S20) result in low S20 levels that can be compensated by mutations that restore [S20]. Here, we have further studied the cause for the deleterious effects of S20 deficiency and found that the S20 mutants were also deficient in four other 30S proteins (S1, S2, S12, and S21), which is likely due to an assembly defect of the S20 deficient 30S subunits. We examined the compensatory effect by six additional mutations affecting the global regulator Fis and the C-terminal domain of the α subunit of RNA polymerase (encoded by rpoA). The fis and rpoA mutations restored the S20 levels, concomitantly restoring the assembly defect and the levels of S1, S2, S12, and S21. These results illustrate the complexity of compensatory evolution and how the negative effects of deleterious mutations can be suppressed by a multitude of mechanisms. Additionally, we found that the mutations in fis and rpoA caused reduced expression of other ribosomal components. Notably, some of the fis mutations and the rpoA mutation corrected the fitness of the rpsT mutants to wild-type levels, although expression of other ribosomal components was reduced compared to wild-type. This finding raises new questions regarding the relation between translation capacity and growth rate.
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129
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Soleja N, Agrawal N, Nazir R, Ahmad M, Mohsin M. Enhanced sensitivity and detection range of FRET-based vitamin B 12 nanosensor. 3 Biotech 2020; 10:87. [PMID: 32089982 DOI: 10.1007/s13205-020-2073-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/18/2020] [Indexed: 11/29/2022] Open
Abstract
Vitamin B12 (cobalamin) is a cobalt-containing compound that acts as an essential co-factor for various enzymes involved in the metabolic processes of the living cells. The constructed FRET Sensor for Vitamin Anemia Linked (SenVitAL) displayed marginal FRET efficiency. Here, we report the development of a molecular SenVitAL containing enhanced cyan fluorescent protein (ECFP) and venus as FRET pair to improve the FRET efficiency for optical imaging and screening of already developed sensor by our group. The sensor is the improved version of previously reported SenVitAL and consists of ECFP/venus as FRET pair instead of the originally used pair CFP/YFP. To increase the physiological range of vitamin B12 measurement, affinity mutants were created. Compared to the wild type, SenVitAL-5 with W44Q mutation has higher affinity and displayed large dynamic detection range (0.10-480 µM) in response to vitamin B12 binding. For cell-based monitoring and dynamic measurement of vitamin B12 flux rates, SenVitAL-5 was successfully expressed in cytosol of yeast and mammalian cells. Changes in the emission intensities of the two fluorophores were detected using confocal microscopy in both cell types in response to vitamin B12. With the addition of 50 µM extracellular vitamin B12 to the cells, the emission intensity of venus increased and that of ECFP decreased over the time. Furthermore, the results show that the variant SenVitAL-5 measures the vitamin B12 in a concentration-dependent manner, showing the resulting increase in the FRET ratio and thus confirming its utility as an ideal fluorescent indicator for the detection of vitamin B12 in eukaryotic systems in real time.
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Affiliation(s)
- Neha Soleja
- 1Department of Biosciences, Metabolic Engineering Laboratory, Jamia Millia Islamia, New Delhi, 110025 India
| | - Neha Agrawal
- 1Department of Biosciences, Metabolic Engineering Laboratory, Jamia Millia Islamia, New Delhi, 110025 India
| | - Rahila Nazir
- 1Department of Biosciences, Metabolic Engineering Laboratory, Jamia Millia Islamia, New Delhi, 110025 India
| | - Mohd Ahmad
- 2Department of Physics, Syracuse University, New York, NY USA
| | - Mohd Mohsin
- 1Department of Biosciences, Metabolic Engineering Laboratory, Jamia Millia Islamia, New Delhi, 110025 India
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130
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Futamata R, Ogasawara F, Ichikawa T, Kodan A, Kimura Y, Kioka N, Ueda K. In vivo FRET analyses reveal a role of ATP hydrolysis-associated conformational changes in human P-glycoprotein. J Biol Chem 2020; 295:5002-5011. [PMID: 32111736 DOI: 10.1074/jbc.ra119.012042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/27/2020] [Indexed: 12/29/2022] Open
Abstract
P-glycoprotein (P-gp; also known as MDR1 or ABCB1) is an ATP-driven multidrug transporter that extrudes various hydrophobic toxic compounds to the extracellular space. P-gp consists of two transmembrane domains (TMDs) that form the substrate translocation pathway and two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP. At least two P-gp states are required for transport. In the inward-facing (pre-drug transport) conformation, the two NBDs are separated, and the two TMDs are open to the intracellular side; in the outward-facing (post-drug transport) conformation, the NBDs are dimerized, and the TMDs are slightly open to the extracellular side. ATP binding and hydrolysis cause conformational changes between the inward-facing and the outward-facing conformations, and these changes help translocate substrates across the membrane. However, how ATP hydrolysis is coupled to these conformational changes remains unclear. In this study, we used a new FRET sensor that detects conformational changes in P-gp to investigate the role of ATP binding and hydrolysis during the conformational changes of human P-gp in living HEK293 cells. We show that ATP binding causes the conformational change to the outward-facing state and that ATP hydrolysis and subsequent release of γ-phosphate from both NBDs allow the outward-facing state to return to the original inward-facing state. The findings of our study underscore the utility of using FRET analysis in living cells to elucidate the function of membrane proteins such as multidrug transporters.
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Affiliation(s)
- Ryota Futamata
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Fumihiko Ogasawara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), KUIAS, Kyoto University, Kyoto 606-8501, Japan
| | - Takafumi Ichikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Atsushi Kodan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), KUIAS, Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhisa Kimura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Noriyuki Kioka
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kazumitsu Ueda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), KUIAS, Kyoto University, Kyoto 606-8501, Japan
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131
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Deal J, Annamdevula N, Pleshinger DJ, Griswold JR, Odom A, Tayara A, Lall M, Browning C, Parker M, Rich TC, Leavesley SJ. Comparison of spectral FRET microscopy approaches for single-cell analysis. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2020; 11243:112430Y. [PMID: 34035557 PMCID: PMC8142325 DOI: 10.1117/12.2546308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Förster resonance energy transfer (FRET) is a valuable tool for measuring molecular distances and the effects of biological processes such as cyclic nucleotide messenger signaling and protein localization. Most FRET techniques require two fluorescent proteins with overlapping excitation/emission spectral pairing to maximize detection sensitivity and FRET efficiency. FRET microscopy often utilizes differing peak intensities of the selected fluorophores measured through different optical filter sets to estimate the FRET index or efficiency. Microscopy platforms used to make these measurements include wide-field, laser scanning confocal, and fluorescence lifetime imaging. Each platform has associated advantages and disadvantages, such as speed, sensitivity, specificity, out-of-focus fluorescence, and Z-resolution. In this study, we report comparisons among multiple microscopy and spectral filtering platforms such as standard 2-filter FRET, emission-scanning hyperspectral imaging, and excitation-scanning hyperspectral imaging. Samples of human embryonic kidney (HEK293) cells were grown on laminin-coated 28 mm round gridded glass coverslips (10816, Ibidi, Fitchburg, Wisconsin) and transfected with adenovirus encoding a cAMP-sensing FRET probe composed of a FRET donor (Turquoise) and acceptor (Venus). Additionally, 3 FRET "controls" with fixed linker lengths between Turquoise and Venus proteins were used for inter-platform validation. Grid locations were logged, recorded with light micrographs, and used to ensure that whole-cell FRET was compared on a cell-by-cell basis among the different microscopy platforms. FRET efficiencies were also calculated and compared for each method. Preliminary results indicate that hyperspectral methods increase the signal-to-noise ratio compared to a standard 2-filter approach.
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Affiliation(s)
- Joshua Deal
- Department of Chemical & Biomolecular Engineering, University of South Alabama
- Center for Lung Biology, University of South Alabama
- Department of Pharmacology, University of South Alabama
| | - Naga Annamdevula
- Center for Lung Biology, University of South Alabama
- Department of Pharmacology, University of South Alabama
| | - Donald John Pleshinger
- Center for Lung Biology, University of South Alabama
- Department of Pharmacology, University of South Alabama
| | | | - Aliyah Odom
- Department of Chemical & Biomolecular Engineering, University of South Alabama
| | - Alia Tayara
- Department of Chemical & Biomolecular Engineering, University of South Alabama
| | - Malvika Lall
- College of Medicine, University of South Alabama
| | - Craig Browning
- Department of Chemical & Biomolecular Engineering, University of South Alabama
- Systems Engineering, University of South Alabama
| | - Marina Parker
- Department of Chemical & Biomolecular Engineering, University of South Alabama
- Systems Engineering, University of South Alabama
| | - Thomas C Rich
- Center for Lung Biology, University of South Alabama
- Department of Pharmacology, University of South Alabama
| | - Silas J Leavesley
- Department of Chemical & Biomolecular Engineering, University of South Alabama
- Center for Lung Biology, University of South Alabama
- Department of Pharmacology, University of South Alabama
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132
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Ehtesabi H, Hallaji Z, Najafi Nobar S, Bagheri Z. Carbon dots with pH-responsive fluorescence: a review on synthesis and cell biological applications. Mikrochim Acta 2020; 187:150. [PMID: 31989317 DOI: 10.1007/s00604-019-4091-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022]
Abstract
This review summarizes state of the art synthesis and applications of carbon dots (CDs) with pH-responsive fluorescence. Following an introduction, the first section covers methods for the preparation of pH-responsive CDs, with subsections on general methods for preparing CDs (by hydrothermal, solvothermal, electrochemical, microwave, laser ablation, pyrolysis or chemical oxidation polymerization methods), and on precursors for synthesis. This is followed by a section on the mechanisms of pH-responsivity (by creating new functional groups, change of energy levels, protonation and deprotonation, aggregation, or by introduction shells). Several Tables are presented that give an overview of the wealth of methods and materials. A final section covers applications of carbon dots (CDs) with pH-responsive fluorescence for sensing, drug delivery, and imaging. The conclusion summarizes the current status, addresses challenges, and gives an outlook on potential future trends. Graphical abstract The synthesis and biological applications of carbon dots(CDs) with pH-responsive fluorescence are summarized. Precursors and methods for preparation of pH-responsive CDs, mechanisms of pH-responsivity, and biological applications of CDs with pH-responsive fluorescence for sensing, drug delivery, and imaging are discussed.
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Affiliation(s)
- Hamide Ehtesabi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, 19839-69411, Iran
| | - Zahra Hallaji
- Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14117-13116, Iran
| | - Shima Najafi Nobar
- Faculty of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19697-64499, Iran
| | - Zeinab Bagheri
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, 19839-69411, Iran.
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133
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Goetz A, Mader A, von Bronk B, Weiss AS, Opitz M. Gene expression noise in a complex artificial toxin expression system. PLoS One 2020; 15:e0227249. [PMID: 31961890 PMCID: PMC6974158 DOI: 10.1371/journal.pone.0227249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/16/2019] [Indexed: 01/29/2023] Open
Abstract
Gene expression is an intrinsically stochastic process. Fluctuations in transcription and translation lead to cell-to-cell variations in mRNA and protein levels affecting cellular function and cell fate. Here, using fluorescence time-lapse microscopy, we quantify noise dynamics in an artificial operon in Escherichia coli, which is based on the native operon of ColicinE2, a toxin. In the natural system, toxin expression is controlled by a complex regulatory network; upon induction of the bacterial SOS response, ColicinE2 is produced (cea gene) and released (cel gene) by cell lysis. Using this ColicinE2-based operon, we demonstrate that upon induction of the SOS response noise of cells expressing the operon is significantly lower for the (mainly) transcriptionally regulated gene cea compared to the additionally post-transcriptionally regulated gene cel. Likewise, we find that mutations affecting the transcriptional regulation by the repressor LexA do not significantly alter the population noise, whereas specific mutations to post-transcriptionally regulating units, strongly influence noise levels of both genes. Furthermore, our data indicate that global factors, such as the plasmid copy number of the operon encoding plasmid, affect gene expression noise of the entire operon. Taken together, our results provide insights on how noise in a native toxin-producing operon is controlled and underline the importance of post-transcriptional regulation for noise control in this system.
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Affiliation(s)
- Alexandra Goetz
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Andreas Mader
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Benedikt von Bronk
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Anna S. Weiss
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
| | - Madeleine Opitz
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, Munich, Germany
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134
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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135
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Castellani CM, Torres-Ocampo AP, Breffke J, White AB, Chambers JJ, Stratton MM, Maresca TJ. Live-cell FLIM-FRET using a commercially available system. Methods Cell Biol 2020; 158:63-89. [PMID: 32423651 PMCID: PMC8006575 DOI: 10.1016/bs.mcb.2020.02.002] [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: 03/03/2023]
Abstract
Förster resonance energy transfer (FRET)-based sensors have been powerful tools in cell biologists' toolkit for decades. Informed by fundamental understanding of fluorescent proteins, protein-protein interactions, and the structural biology of reporter components, researchers have been able to employ creative design approaches to build sensors that are uniquely capable of probing a wide range of phenomena in living cells including visualization of localized calcium signaling, sub-cellular activity gradients, and tension generation to name but a few. While FRET sensors have significantly impacted many fields, one must also be cognizant of the limitations to conventional, intensity-based FRET measurements stemming from variation in probe concentration, sensitivity to photobleaching, and bleed-through between the FRET fluorophores. Fluorescence lifetime imaging microscopy (FLIM) largely overcomes the limitations of intensity-based FRET measurements. In general terms, FLIM measures the time, which for the reporters described in this chapter is nanoseconds (ns), between photon absorption and emission by a fluorophore. When FLIM is applied to FRET sensors (FLIM-FRET), measurement of the donor fluorophore lifetime provides valuable information such as FRET efficiency and the percentage of reporters engaged in FRET. This chapter introduces fundamental principles of FLIM-FRET toward informing the practical application of the technique and, using two established FRET reporters as proofs of concept, outlines how to use a commercially available FLIM system.
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Affiliation(s)
| | - Ana P. Torres-Ocampo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
| | | | | | - James J. Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA
| | - Margaret M. Stratton
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
| | - Thomas J. Maresca
- Biology Department, University of Massachusetts, Amherst, MA,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA
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136
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Wasano K, Takahashi S, Rosenberg SK, Kojima T, Mutai H, Matsunaga T, Ogawa K, Homma K. Systematic quantification of the anion transport function of pendrin (SLC26A4) and its disease-associated variants. Hum Mutat 2020; 41:316-331. [PMID: 31599023 PMCID: PMC6930342 DOI: 10.1002/humu.23930] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/14/2023]
Abstract
Thanks to the advent of rapid DNA sequencing technology and its prevalence, many disease-associated genetic variants are rapidly identified in many genes from patient samples. However, the subsequent effort to experimentally validate and define their pathological roles is extremely slow. Consequently, the pathogenicity of most disease-associated genetic variants is solely speculated in silico, which is no longer deemed compelling. We developed an experimental approach to efficiently quantify the pathogenic effects of disease-associated genetic variants with a focus on SLC26A4, which is essential for normal inner ear function. Alterations of this gene are associated with both syndromic and nonsyndromic hereditary hearing loss with various degrees of severity. We established HEK293T-based stable cell lines that express pendrin missense variants in a doxycycline-dependent manner, and systematically determined their anion transport activities with high accuracy in a 96-well plate format using a high throughput plate reader. Our doxycycline dosage-dependent transport assay objectively distinguishes missense variants that indeed impair the function of pendrin from those that do not (functional variants). We also found that some of these putative missense variants disrupt normal messenger RNA splicing. Our comprehensive experimental approach helps determine the pathogenicity of each pendrin variant, which should guide future efforts to benefit patients.
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Affiliation(s)
- Koichiro Wasano
- Department of Otolaryngology – Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Laboratory of Auditory Disorders, Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
| | - Satoe Takahashi
- Department of Otolaryngology – Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Samuel K. Rosenberg
- Department of Otolaryngology – Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Takashi Kojima
- Department of Otolaryngology – Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hideki Mutai
- Laboratory of Auditory Disorders, Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
| | - Tatsuo Matsunaga
- Laboratory of Auditory Disorders, Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan
| | - Kaoru Ogawa
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuaki Homma
- Department of Otolaryngology – Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, IL 60608, USA
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137
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Denay G, Schultz P, Hänsch S, Weidtkamp‐Peters S, Simon R. Over the rainbow: A practical guide for fluorescent protein selection in plant FRET experiments. PLANT DIRECT 2019; 3:e00189. [PMID: 31844834 PMCID: PMC6898725 DOI: 10.1002/pld3.189] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 05/29/2023]
Abstract
Receptor-like kinases (RLK) and receptor-like proteins (RLP) often interact in a combinatorial manner depending on tissue identity, membrane domains, or endo- and exogenous cues, and the same RLKs or RLPs can generate different signaling outputs depending on the composition of the receptor complexes they are involved in. Investigation of their interaction partners in a spatial and dynamic way is therefore of prime interest to understand their functions. This is, however, limited by the technical complexity of assessing it in endogenous conditions. A solution to close this gap is to determine protein interaction directly in the relevant tissues at endogenous expression levels using Förster resonance energy transfer (FRET). The ideal fluorophore pair for FRET must, however, fulfil specific requirements: (a) The emission and excitation spectra of the donor and acceptor, respectively, must overlap; (b) they should not interfere with proper folding, activity, or localization of the fusion proteins; (c) they should be sufficiently photostable in plant cells. Furthermore, the donor must yield sufficient photon counts at near-endogenous protein expression levels. Although many fluorescent proteins were reported to be suitable for FRET experiments, only a handful were already described for applications in plants. Herein, we compare a range of fluorophores, assess their usability to study RLK interactions by FRET-based fluorescence lifetime imaging (FLIM) and explore their differences in FRET efficiency. Our analysis will help to select the optimal fluorophore pair for diverse FRET applications.
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Affiliation(s)
- Grégoire Denay
- Institute for Developmental GeneticsHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Patrick Schultz
- Institute for Developmental GeneticsHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sebastian Hänsch
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
| | | | - Rüdiger Simon
- Institute for Developmental GeneticsHeinrich Heine University DüsseldorfDüsseldorfGermany
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138
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Wen S, Yao D, Liu X, Wang F. A Novel Fluorescence Resonance Energy Transfer-Based High-Throughput Screening Method for Generation of Lysozyme with Improved Antimicrobial Activity against Escherichia coli Strains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12584-12589. [PMID: 31640344 DOI: 10.1021/acs.jafc.9b05364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lysozyme has emerged to be a promising alternative to traditional antibiotics to deal with the increasing antibiotic resistance of bacteria. However, its application is hampered by its inferior bactericidal activity against Gram-negative bacteria. To address this problem, a novel "enzyme-cascade fluorescent high-throughput screening (HTS) method" was designed and constructed based on detection of fluorescence resonance energy transfer (FRET) and enzyme-cascade reaction of lysozyme and protease. As a proof of concept, site-saturation mutagenesis libraries targeting at residues of the unstructured stretch at the N-terminus of Antheraea pernyi lysozyme were constructed and screened by the proposed HTS method. The isolated lysozyme variants proved to exhibit higher antibacterial activity against Escherichia coli K12, demonstrating the significance of this region for the bactericidal function of lysozyme. The presented cell-based fluorescent HTS method is a new tool for screening lysozyme variants with improved bactericidal efficacy against Gram-negative bacteria and for exploring the sequence-structure-function relationship of lysozyme.
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Affiliation(s)
- Sai Wen
- Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, School of Light Industry , Beijing Technology and Business University , Beijing 100048 , China
| | - Dongmei Yao
- Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, School of Light Industry , Beijing Technology and Business University , Beijing 100048 , China
| | - Xiaoyu Liu
- Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, School of Light Industry , Beijing Technology and Business University , Beijing 100048 , China
| | - Fenghuan Wang
- Beijing Higher Institution Engineering Research Center of Food Additives and Ingredients, School of Light Industry , Beijing Technology and Business University , Beijing 100048 , China
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139
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Piszczek L, Memoli S, Raggioli A, Viosca J, Rientjes J, Hublitz P, Czaban W, Wyrzykowska A, Gross C. Mouse model of the human serotonin transporter-linked polymorphic region. Mamm Genome 2019; 30:319-328. [PMID: 31667540 PMCID: PMC6884432 DOI: 10.1007/s00335-019-09815-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/21/2019] [Indexed: 11/27/2022]
Abstract
Genetic factors play a significant role in risk for mood and anxiety disorders. Polymorphisms in genes that regulate the brain monoamine systems, such as catabolic enzymes and transporters, are attractive candidates for being risk factors for emotional disorders given the weight of evidence implicating monoamines involvement in these conditions. Several common genetic variants have been identified in the human serotonin transporter (5-HTT) gene, including a repetitive sequence located in the promoter region of the locus called the serotonin transporter-linked polymorphic region (5-HTT-LPR). This polymorphism has been associated with a number of mental traits in both humans and primates, including depression, neuroticism, and harm avoidance. Some, but not all, studies found a link between the polymorphism and 5-HTT levels, leaving open the question of whether the polymorphism affects risk for mental traits via changes in 5-HTT expression. To investigate the impact of the polymorphism on gene expression, serotonin homeostasis, and behavioral traits, we set out to develop a mouse model of the human 5-HTT-LPR. Here we describe the creation and characterization of a set of mouse lines with single-copy human transgenes carrying the short and long 5-HTT-LPR variants. Although we were not able to detect differences in expression between the short and long variants, we encountered several technical issues concerning the design of our humanized mice that are likely to have influenced our findings. Our study serves as a cautionary note for future studies aimed at studying human transgene regulation in the context of the living mouse.
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Affiliation(s)
- Lukasz Piszczek
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
- Research Institute of Molecular Pathology, Vienna, Austria.
| | - Simone Memoli
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Angelo Raggioli
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - José Viosca
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
- Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Jeanette Rientjes
- Monash Genome Modification Platform (MGMP), Monash University, Clayton, Australia
| | - Philip Hublitz
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Weronika Czaban
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Anna Wyrzykowska
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Cornelius Gross
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
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140
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Neubert P, Weichselbaum A, Reitinger C, Schatz V, Schröder A, Ferdinand JR, Simon M, Bär AL, Brochhausen C, Gerlach RG, Tomiuk S, Hammer K, Wagner S, van Zandbergen G, Binger KJ, Müller DN, Kitada K, Clatworthy MR, Kurts C, Titze J, Abdullah Z, Jantsch J. HIF1A and NFAT5 coordinate Na +-boosted antibacterial defense via enhanced autophagy and autolysosomal targeting. Autophagy 2019; 15:1899-1916. [PMID: 30982460 PMCID: PMC6844503 DOI: 10.1080/15548627.2019.1596483] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 12/17/2022] Open
Abstract
Infection and inflammation are able to induce diet-independent Na+-accumulation without commensurate water retention in afflicted tissues, which favors the pro-inflammatory activation of mouse macrophages and augments their antibacterial and antiparasitic activity. While Na+-boosted host defense against the protozoan parasite Leishmania major is mediated by increased expression of the leishmanicidal NOS2 (nitric oxide synthase 2, inducible), the molecular mechanisms underpinning this enhanced antibacterial defense of mouse macrophages with high Na+ (HS) exposure are unknown. Here, we provide evidence that HS-increased antibacterial activity against E. coli was neither dependent on NOS2 nor on the phagocyte oxidase. In contrast, HS-augmented antibacterial defense hinged on HIF1A (hypoxia inducible factor 1, alpha subunit)-dependent increased autophagy, and NFAT5 (nuclear factor of activated T cells 5)-dependent targeting of intracellular E. coli to acidic autolysosomal compartments. Overall, these findings suggest that the autolysosomal compartment is a novel target of Na+-modulated cell autonomous innate immunity. Abbreviations: ACT: actins; AKT: AKT serine/threonine kinase 1; ATG2A: autophagy related 2A; ATG4C: autophagy related 4C, cysteine peptidase; ATG7: autophagy related 7; ATG12: autophagy related 12; BECN1: beclin 1; BMDM: bone marrow-derived macrophages; BNIP3: BCL2/adenovirus E1B interacting protein 3; CFU: colony forming units; CM-H2DCFDA: 5-(and-6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate, acetyl ester; CTSB: cathepsin B; CYBB: cytochrome b-245 beta chain; DAPI: 4,6-diamidino-2-phenylindole; DMOG: dimethyloxallyl glycine; DPI: diphenyleneiodonium chloride; E. coli: Escherichia coli; FDR: false discovery rate; GFP: green fluorescent protein; GSEA: gene set enrichment analysis; GO: gene ontology; HIF1A: hypoxia inducible factor 1, alpha subunit; HUGO: human genome organization; HS: high salt (+ 40 mM of NaCl to standard cell culture conditions); HSP90: heat shock 90 kDa proteins; LDH: lactate dehydrogenase; LPS: lipopolysaccharide; Lyz2/LysM: lysozyme 2; NFAT5/TonEBP: nuclear factor of activated T cells 5; MΦ: macrophages; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFI: mean fluorescence intensity; MIC: minimum inhibitory concentration; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; NaCl: sodium chloride; NES: normalized enrichment score; n.s.: not significant; NO: nitric oxide; NOS2/iNOS: nitric oxide synthase 2, inducible; NS: normal salt; PCR: polymerase chain reaction; PGK1: phosphoglycerate kinase 1; PHOX: phagocyte oxidase; RFP: red fluorescent protein; RNA: ribonucleic acid; ROS: reactive oxygen species; sCFP3A: super cyan fluorescent protein 3A; SBFI: sodium-binding benzofuran isophthalate; SLC2A1/GLUT1: solute carrier family 2 (facilitated glucose transporter), member 1; SQSTM1/p62: sequestosome 1; ULK1: unc-51 like kinase 1; v-ATPase: vacuolar-type H+-ATPase; WT: wild type.
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Affiliation(s)
- Patrick Neubert
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | - Andrea Weichselbaum
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | - Carmen Reitinger
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | - Valentin Schatz
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | - Agnes Schröder
- Institute of Orthodontics, University Hospital of Regensburg, Regensburg, Germany
| | - John R. Ferdinand
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Michaela Simon
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | - Anna-Lorena Bär
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | | | | | | | - Karin Hammer
- Department of Internal Medicine II, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | - Stefan Wagner
- Department of Internal Medicine II, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
| | | | - Katrina J. Binger
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Dominik N. Müller
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kento Kitada
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Christian Kurts
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Jens Titze
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Zeinab Abdullah
- Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, Regensburg, Germany
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141
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Fluorescence-Based Quantitative Synapse Analysis for Cell Type-Specific Connectomics. eNeuro 2019; 6:ENEURO.0193-19.2019. [PMID: 31548370 PMCID: PMC6873163 DOI: 10.1523/eneuro.0193-19.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/08/2019] [Accepted: 09/11/2019] [Indexed: 12/20/2022] Open
Abstract
Anatomical methods for determining cell type-specific connectivity are essential to inspire and constrain our understanding of neural circuit function. We developed genetically-encoded reagents for fluorescence-synapse labeling and connectivity analysis in brain tissue, using a fluorogen-activating protein (FAP)-coupled or YFP-coupled, postsynaptically-localized neuroligin-1 (NL-1) targeting sequence (FAP/YFPpost). FAPpost expression did not alter mEPSC or mIPSC properties. Sparse AAV-mediated expression of FAP/YFPpost with the cell-filling, red fluorophore dTomato (dTom) enabled high-throughput, compartment-specific detection of putative synapses across diverse neuron types in mouse somatosensory cortex. We took advantage of the bright, far-red emission of FAPpost puncta for multichannel fluorescence alignment of dendrites, FAPpost puncta, and presynaptic neurites in transgenic mice with saturated labeling of parvalbumin (PV), somatostatin (SST), or vasoactive intestinal peptide (VIP)-expressing neurons using Cre-reporter driven expression of YFP. Subtype-specific inhibitory connectivity onto layer 2/3 (L2/3) neocortical pyramidal (Pyr) neurons was assessed using automated puncta detection and neurite apposition. Quantitative and compartment-specific comparisons show that PV inputs are the predominant source of inhibition at both the soma and the dendrites and were particularly concentrated at the primary apical dendrite. SST inputs were interleaved with PV inputs at all secondary-order and higher-order dendritic branches. These fluorescence-based synapse labeling reagents can facilitate large-scale and cell-type specific quantitation of changes in synaptic connectivity across development, learning, and disease states.
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142
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Klein CA, Emde L, Kuijpers A, Sobetzko P. MoCloFlex: A Modular Yet Flexible Cloning System. Front Bioeng Biotechnol 2019; 7:271. [PMID: 31750294 PMCID: PMC6843054 DOI: 10.3389/fbioe.2019.00271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/30/2019] [Indexed: 02/04/2023] Open
Abstract
Modern cloning solutions are gradually replacing classical cloning methods. Current systems make use of libraries with predefined DNA parts that are joined by Golden-Gate reactions. However, these systems still suffer from specific inflexibilities and the lack of inter-compatibility. Here, we present Flexible Modular Cloning (MoCloFlex) which overcomes this inflexibility by introducing a set of linker- and position-vectors allowing free unit arrangement. Our system, therefore, provides a convenient way to design and build custom plasmids, and iterative assembly of large constructs. To support standardization in synthetic biology, MoCloFlex is compatible with the well-established Modular Cloning standard. Here, we present and characterize MoCloFlex for various applications with up to 12 fragments in a single restriction-ligation reaction.
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Affiliation(s)
- Carlo A. Klein
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Leonie Emde
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Aaron Kuijpers
- Department of Biology, University of Kassel, Kassel, Germany
| | - Patrick Sobetzko
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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143
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Reuven N, Adler J, Broennimann K, Myers N, Shaul Y. Recruitment of DNA Repair MRN Complex by Intrinsically Disordered Protein Domain Fused to Cas9 Improves Efficiency of CRISPR-Mediated Genome Editing. Biomolecules 2019; 9:E584. [PMID: 31597252 PMCID: PMC6843829 DOI: 10.3390/biom9100584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 is a powerful tool for genome editing in cells and organisms. Nevertheless, introducing directed templated changes by homology-directed repair (HDR) requires the cellular DNA repair machinery, such as the MRN complex (Mre11/Rad50/Nbs1). To improve the process, we tailored chimeric constructs of Cas9, in which SpCas9 was fused at its N- or C-terminus to a 126aa intrinsically disordered domain from HSV-1 alkaline nuclease (UL12) that recruits the MRN complex. The chimeric Cas9 constructs were two times more efficient in homology-directed editing of endogenous loci in tissue culture cells. This effect was dependent upon the MRN-recruiting activity of the domain and required lower amounts of the chimeric Cas9 in comparison with unmodified Cas9. The new constructs improved the yield of edited cells when making endogenous point mutations or inserting small tags encoded by oligonucleotide donor DNA (ssODN), and also with larger insertions encoded by plasmid DNA donor templates. Improved editing was achieved with both transfected plasmid-encoded Cas9 constructs as well as recombinant Cas9 protein transfected as ribonucleoprotein complexes. Our strategy was highly efficient in restoring a genetic defect in a cell line, exemplifying the possible implementation of our strategy in gene therapy. These constructs provide a simple approach to improve directed editing.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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144
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Minard A, Bauer CC, Chuntharpursat‐Bon E, Pickles IB, Wright DJ, Ludlow MJ, Burnham MP, Warriner SL, Beech DJ, Muraki K, Bon RS. Potent, selective, and subunit-dependent activation of TRPC5 channels by a xanthine derivative. Br J Pharmacol 2019; 176:3924-3938. [PMID: 31277085 PMCID: PMC6811774 DOI: 10.1111/bph.14791] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND PURPOSE The TRPC1, TRPC4, and TRPC5 proteins form homotetrameric or heterotetrameric, calcium-permeable cation channels that are involved in various disease states. Recent research has yielded specific and potent xanthine-based TRPC1/4/5 inhibitors. Here, we investigated the possibility of xanthine-based activators of these channels. EXPERIMENTAL APPROACH An analogue of the TRPC1/4/5 inhibitor Pico145, AM237, was synthesized and its activity was investigated using HEK cells overexpressing TRPC4, TRPC5, TRPC4-C1, TRPC5-C1, TRPC1:C4 or TRPC1:C5 channels, and in A498 cells expressing native TRPC1:C4 channels. TRPC1/4/5 channel activities were assayed by measuring intracellular concentration of Ca2+ ([Ca2+ ]i ) and by patch-clamp electrophysiology. Selectivity of AM237 was tested against TRPC3, TRPC6, TRPV4, or TRPM2 channels. KEY RESULTS AM237 potently activated TRPC5:C5 channels (EC50 15-20 nM in [Ca2+ ]i assay) and potentiated their activation by sphingosine-1-phosphate but suppressed activation evoked by (-)-englerin A (EA). In patch-clamp studies, AM237 activated TRPC5:C5 channels, with greater effect at positive voltages, but with lower efficacy than EA. Pico145 competitively inhibited AM237-induced TRPC5:C5 activation. AM237 did not activate TRPC4:C4, TRPC4-C1, TRPC5-C1, TRPC1:C5, and TRPC1:C4 channels, or native TRPC1:C4 channels in A498 cells, but potently inhibited EA-dependent activation of these channels with IC50 values ranging from 0.9 to 7 nM. AM237 (300 nM) did not activate or inhibit TRPC3, TRPC6, TRPV4, or TRPM2 channels. CONCLUSIONS AND IMPLICATIONS This study suggests the possibility for selective activation of TRPC5 channels by xanthine derivatives and supports the general principle that xanthine-based compounds can activate, potentiate, or inhibit these channels depending on subunit composition.
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Affiliation(s)
- Aisling Minard
- School of ChemistryUniversity of LeedsLeedsUK
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Claudia C. Bauer
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Eulashini Chuntharpursat‐Bon
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Isabelle B. Pickles
- School of ChemistryUniversity of LeedsLeedsUK
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - David J. Wright
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Melanie J. Ludlow
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | | | | | - David J. Beech
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Katsuhiko Muraki
- Laboratory of Cellular Pharmacology, School of PharmacyAichi‐Gakuin UniversityNagoyaJapan
| | - Robin S. Bon
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
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145
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Alnahhas RN, Winkle JJ, Hirning AJ, Karamched B, Ott W, Josić K, Bennett MR. Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices. ACS Synth Biol 2019; 8:2051-2058. [PMID: 31361464 PMCID: PMC6754295 DOI: 10.1021/acssynbio.9b00146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell-cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia cocultured in microfluidic devices. To do this, we grew two different strains of Escherichia coli in microfluidic devices with cell-trapping regions (traps) of several different designs. We found that the size of the traps is a critical determinant of spatiotemporal dynamics. In small traps, cells can easily signal one another, but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by increasing the initial seeding of cells in larger traps. We also built a mathematical model, which suggests that increasing the number of seed cells can also increase the strain ratio variability due to an increased number of strain interfaces in the trap. These results help elucidate the complex behaviors of synthetic microbial consortia in microfluidic traps and provide a means of analysis to help remedy the spatial heterogeneity inherent to different trap types.
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Affiliation(s)
- Razan N Alnahhas
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - James J Winkle
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Andrew J Hirning
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Bhargav Karamched
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - William Ott
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - Krešimir Josić
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
- Department of Biology and Biochemistry , University of Houston , Houston , Texas 77004 , United States
| | - Matthew R Bennett
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
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146
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Dissecting the cytochrome c 2-reaction centre interaction in bacterial photosynthesis using single molecule force spectroscopy. Biochem J 2019; 476:2173-2190. [PMID: 31320503 PMCID: PMC6688529 DOI: 10.1042/bcj20170519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022]
Abstract
The reversible docking of small, diffusible redox proteins onto a membrane protein complex is a common feature of bacterial, mitochondrial and photosynthetic electron transfer (ET) chains. Spectroscopic studies of ensembles of such redox partners have been used to determine ET rates and dissociation constants. Here, we report a single-molecule analysis of the forces that stabilise transient ET complexes. We examined the interaction of two components of bacterial photosynthesis, cytochrome c 2 and the reaction centre (RC) complex, using dynamic force spectroscopy and PeakForce quantitative nanomechanical imaging. RC-LH1-PufX complexes, attached to silicon nitride AFM probes and maintained in a photo-oxidised state, were lowered onto a silicon oxide substrate bearing dispersed, immobilised and reduced cytochrome c 2 molecules. Microscale patterns of cytochrome c 2 and the cyan fluorescent protein were used to validate the specificity of recognition between tip-attached RCs and surface-tethered cytochrome c 2 Following the transient association of photo-oxidised RC and reduced cytochrome c 2 molecules, retraction of the RC-functionalised probe met with resistance, and forces between 112 and 887 pN were required to disrupt the post-ET RC-c 2 complex, depending on the retraction velocities used. If tip-attached RCs were reduced instead, the probability of interaction with reduced cytochrome c 2 molecules decreased 5-fold. Thus, the redox states of the cytochrome c 2 haem cofactor and RC 'special pair' bacteriochlorophyll dimer are important for establishing a productive ET complex. The millisecond persistence of the post-ET cytochrome c 2[oxidised]-RC[reduced] 'product' state is compatible with rates of cyclic photosynthetic ET, at physiologically relevant light intensities.
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147
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Winkler M, Wrensch F, Bosch P, Knoth M, Schindler M, Gärtner S, Pöhlmann S. Analysis of IFITM-IFITM Interactions by a Flow Cytometry-Based FRET Assay. Int J Mol Sci 2019; 20:ijms20163859. [PMID: 31398796 PMCID: PMC6719045 DOI: 10.3390/ijms20163859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/26/2019] [Accepted: 08/03/2019] [Indexed: 12/14/2022] Open
Abstract
The interferon-induced transmembrane proteins 1–3 (IFITM1–3) inhibit host cell entry of several viruses. However, it is incompletely understood how IFITM1–3 exert antiviral activity. Two phenylalanine residues, F75 and F78, within the intramembrane domain 1 (IM1) were previously shown to be required for IFITM3/IFITM3 interactions and for inhibition of viral entry, suggesting that IFITM/IFITM interactions might be pivotal to antiviral activity. Here, we employed a fluorescence resonance energy transfer (FRET) assay to analyze IFITM/IFITM interactions. For assay calibration, we equipped two cytosolic, non-interacting proteins, super yellow fluorescent protein (SYFP) and super cyan fluorescent protein (SCFP), with signals that target proteins to membrane rafts and also analyzed a SCFP-SYFP fusion protein. This strategy allowed us to discriminate background signals resulting from colocalization of proteins at membrane subdomains from signals elicited by protein–protein interactions. Coexpression of IFITM1–3 and IFITM5 fused to fluorescent proteins elicited strong FRET signals, and mutation of F75 and F78 in IFITM3 (mutant IFITM3-FF) abrogated antiviral activity, as expected, but did not alter cellular localization and FRET signals. Moreover, IFITM3-FF co-immunoprecipitated efficiently with wild type (wt) IFITM3, lending further support to the finding that lack of antiviral activity of IFITM3-FF was not due to altered membrane targeting or abrogated IFITM3-IFITM3 interactions. Collectively, we report an assay that allows quantifying IFITM/IFITM interactions. Moreover, we confirm residues F75 and F78 as critical for antiviral activity but also show that these residues are dispensable for IFITM3 membrane localization and IFITM3/IFITM3 interactions.
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Affiliation(s)
- Michael Winkler
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany.
| | - Florian Wrensch
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Pascale Bosch
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Maike Knoth
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Sabine Gärtner
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany.
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany.
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148
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Stortz JF, Del Rosario M, Singer M, Wilkes JM, Meissner M, Das S. Formin-2 drives polymerisation of actin filaments enabling segregation of apicoplasts and cytokinesis in Plasmodium falciparum. eLife 2019; 8:e49030. [PMID: 31322501 PMCID: PMC6688858 DOI: 10.7554/elife.49030] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
In addition to its role in erythrocyte invasion, Plasmodium falciparum actin is implicated in endocytosis, cytokinesis and inheritance of the chloroplast-like organelle called the apicoplast. Previously, the inability to visualise filamentous actin (F-actin) dynamics had restricted the characterisation of both F-actin and actin regulatory proteins, a limitation we recently overcame for Toxoplasma (Periz et al, 2017). Here, we have expressed and validated actin-binding chromobodies as F-actin-sensors in Plasmodium falciparum and characterised in-vivo actin dynamics. F-actin could be chemically modulated, and genetically disrupted upon conditionally deleting actin-1. In a comparative approach, we demonstrate that Formin-2, a predicted nucleator of F-actin, is responsible for apicoplast inheritance in both Plasmodium and Toxoplasma, and additionally mediates efficient cytokinesis in Plasmodium. Finally, time-averaged local intensity measurements of F-actin in Toxoplasma conditional mutants revealed molecular determinants of spatiotemporally regulated F-actin flow. Together, our data indicate that Formin-2 is the primary F-actin nucleator during apicomplexan intracellular growth, mediating multiple essential functions.
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Affiliation(s)
- Johannes Felix Stortz
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Mario Del Rosario
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Mirko Singer
- Faculty of Veterinary Medicine, Experimental ParasitologyLudwig Maximilian UniversityMunichGermany
| | - Jonathan M Wilkes
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Markus Meissner
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
- Faculty of Veterinary Medicine, Experimental ParasitologyLudwig Maximilian UniversityMunichGermany
| | - Sujaan Das
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity & InflammationUniversity of GlasgowGlasgowUnited Kingdom
- Faculty of Veterinary Medicine, Experimental ParasitologyLudwig Maximilian UniversityMunichGermany
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149
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Al-Zamel N, Al-Sabah S, Luqmani Y, Adi L, Chacko S, Schneider TD, Krasel C. A Dual GLP-1/GIP Receptor Agonist Does Not Antagonize Glucagon at Its Receptor but May Act as a Biased Agonist at the GLP-1 Receptor. Int J Mol Sci 2019; 20:ijms20143532. [PMID: 31330984 PMCID: PMC6678630 DOI: 10.3390/ijms20143532] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/06/2019] [Accepted: 07/12/2019] [Indexed: 12/25/2022] Open
Abstract
Glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) are important regulators of metabolism, making their receptors (GLP-1R and GIPR) attractive targets in the treatment of type 2 diabetes mellitus (T2DM). GLP-1R agonists are used clinically to treat T2DM but the use of GIPR agonists remains controversial. Recent studies suggest that simultaneous activation of GLP-1R and GIPR with a single peptide provides superior glycemic control with fewer adverse effects than activation of GLP-1R alone. We investigated the signaling properties of a recently reported dual-incretin receptor agonist (P18). GLP-1R, GIPR, and the closely related glucagon receptor (GCGR) were expressed in HEK-293 cells. Activation of adenylate cyclase via Gαs was monitored using a luciferase-linked reporter gene (CRE-Luc) assay. Arrestin recruitment was monitored using a bioluminescence resonance energy transfer (BRET) assay. GLP-1, GIP, and glucagon displayed exquisite selectivity for their receptors in the CRE-Luc assay. P18 activated GLP-1R with similar potency to GLP-1 and GIPR with higher potency than GIP. Interestingly, P18 was less effective than GLP-1 at recruiting arrestin to GLP-1R and was inactive at GCGR. These data suggest that P18 can act as both a dual-incretin receptor agonist, and as a G protein-biased agonist at GLP-1R.
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Affiliation(s)
- Noura Al-Zamel
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, PO Box 24923, 13110 Safat, Kuwait
| | - Suleiman Al-Sabah
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, PO Box 24923, 13110 Safat, Kuwait.
| | - Yunus Luqmani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, PO Box 24923, 13110 Safat, Kuwait
| | - Lobna Adi
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, PO Box 24923, 13110 Safat, Kuwait
| | - Siby Chacko
- Department of Pharmacology & Toxicology, Faculty of Medicine, Kuwait University, PO Box 24923, 13110 Safat, Kuwait
| | - Tom Dario Schneider
- Institute of Forensic Medicine, Department of Forensic Pharmacology and Toxicology, University of Zurich, 190/52 CH-8057 Zurich, Switzerland
| | - Cornelius Krasel
- School of Pharmacy, Institute for Pharmacology and Toxicology, The Philipps University of Marburg, Karl-von-Frisch-Straße, 135033 Marburg, Germany
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150
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Manzoor O, Soleja N, Khan P, Imtaiyaz Hassan M, Mohsin M. Visualization of thiamine in living cells using genetically encoded fluorescent nanosensor. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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