1
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Zhu Y, Ackers-Johnson M, Shanmugam MK, Pakkiri LS, Drum CL, Yanpu C, Kim J, Paltzer WG, Mahmoud AI, Wen Tan WL, Lee MCJ, Jianming J, Luu DAT, Ng SL, Li PYQ, Anhui W, Rong Q, Ong GJX, Ng Yu T, Haigh JJ, Tiang Z, Richards AM, Foo R. Asparagine Synthetase Marks a Distinct Dependency Threshold for Cardiomyocyte Dedifferentiation. Circulation 2024; 149:1833-1851. [PMID: 38586957 PMCID: PMC11147732 DOI: 10.1161/circulationaha.123.063965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 01/23/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND Adult mammalian cardiomyocytes have limited proliferative capacity, but in specifically induced contexts they traverse through cell-cycle reentry, offering the potential for heart regeneration. Endogenous cardiomyocyte proliferation is preceded by cardiomyocyte dedifferentiation (CMDD), wherein adult cardiomyocytes revert to a less matured state that is distinct from the classical myocardial fetal stress gene response associated with heart failure. However, very little is known about CMDD as a defined cardiomyocyte cell state in transition. METHODS Here, we leveraged 2 models of in vitro cultured adult mouse cardiomyocytes and in vivo adeno-associated virus serotype 9 cardiomyocyte-targeted delivery of reprogramming factors (Oct4, Sox2, Klf4, and Myc) in adult mice to study CMDD. We profiled their transcriptomes using RNA sequencing, in combination with multiple published data sets, with the aim of identifying a common denominator for tracking CMDD. RESULTS RNA sequencing and integrated analysis identified Asparagine Synthetase (Asns) as a unique molecular marker gene well correlated with CMDD, required for increased asparagine and also for distinct fluxes in other amino acids. Although Asns overexpression in Oct4, Sox2, Klf4, and Myc cardiomyocytes augmented hallmarks of CMDD, Asns deficiency led to defective regeneration in the neonatal mouse myocardial infarction model, increased cell death of cultured adult cardiomyocytes, and reduced cell cycle in Oct4, Sox2, Klf4, and Myc cardiomyocytes, at least in part through disrupting the mammalian target of rapamycin complex 1 pathway. CONCLUSIONS We discovered a novel gene Asns as both a molecular marker and an essential mediator, marking a distinct threshold that appears in common for at least 4 models of CMDD, and revealing an Asns/mammalian target of rapamycin complex 1 axis dependency for dedifferentiating cardiomyocytes. Further study will be needed to extrapolate and assess its relevance to other cell state transitions as well as in heart regeneration.
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Affiliation(s)
- Yike Zhu
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Matthew Ackers-Johnson
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Muthu K Shanmugam
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Leroy Sivappiragasam Pakkiri
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Chester Lee Drum
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Chen Yanpu
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Johnny Kim
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Rhein/Main, Bad Nauheim, Germany
| | - Wyatt G. Paltzer
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ahmed I. Mahmoud
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Wilson Lek Wen Tan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Mick Chang Jie Lee
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Jiang Jianming
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Danh Anh Tuan Luu
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Shi Ling Ng
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Peter Yi Qing Li
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Wang Anhui
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Centre, Peking University
- State Key Laboratory of Vascular Homeostasis and Remodelling, Peking University
| | - Qi Rong
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Centre, Peking University
- State Key Laboratory of Vascular Homeostasis and Remodelling, Peking University
| | - Gabriel Jing Xiang Ong
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Timothy Ng Yu
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - Jody J. Haigh
- CancerCare Manitoba Research Institute, Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- VIB, Flanders Institute for Biotechnology, Ghent University, Ghent, Belgium
| | - Zenia Tiang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
| | - A. Mark Richards
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
- Christchurch Heart Institute, University of Otago, New Zealand
| | - Roger Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore
- Cardiovascular Metabolic Disease Translational Research Programme, National University Health Systems, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore
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2
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Zuo F, Jiang L, Su N, Zhang Y, Bao B, Wang L, Shi Y, Yang H, Huang X, Li R, Zeng Q, Chen Z, Lin Q, Zhuang Y, Zhao Y, Chen X, Zhu L, Yang Y. Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA. Nat Chem Biol 2024:10.1038/s41589-024-01629-x. [PMID: 38783134 DOI: 10.1038/s41589-024-01629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.
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Affiliation(s)
- Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yaqiang Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Limei Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yajie Shi
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huimin Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinyi Huang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ruilong Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qingmei Zeng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yingping Zhuang
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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3
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Baleeva NS, Bogdanova YA, Goncharuk MV, Sokolov AI, Myasnyanko IN, Kublitski VS, Smirnov AY, Gilvanov AR, Goncharuk SA, Mineev KS, Baranov MS. A Combination of Library Screening and Rational Mutagenesis Expands the Available Color Palette of the Smallest Fluorogen-Activating Protein Tag nanoFAST. Int J Mol Sci 2024; 25:3054. [PMID: 38474299 DOI: 10.3390/ijms25053054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
NanoFAST is the smallest fluorogen-activating protein, consisting of only 98 amino acids, used as a genetically encoded fluorescent tag. Previously, only a single fluorogen with an orange color was revealed for this protein. In the present paper, using rational mutagenesis and in vitro screening of fluorogens libraries, we expanded the color palette of this tag. We discovered that E46Q is one of the key substitutions enabling the range of possible fluorogens to be expanded. The introduction of this and several other substitutions has made it possible to use not only orange but also red and green fluorogens with the modified protein.
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Affiliation(s)
- Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
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4
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Shoyer TC, Collins KL, Ham TR, Blanchard AT, Malavade JN, West JL, Hoffman BD. Detection of Fluorescent Protein Mechanical Switching in Cellulo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575065. [PMID: 38260589 PMCID: PMC10802509 DOI: 10.1101/2024.01.10.575065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The ability of cells to sense and respond to mechanical forces is critical in many physiological and pathological processes. However, the mechanisms by which forces affect protein function inside cells remain unclear. Motivated by in vitro demonstrations of fluorescent proteins (FPs) undergoing reversible mechanical switching of fluorescence, we investigated if force-sensitive changes in FP function could be visualized in cells. Guided by a computational model of FP mechanical switching, we develop a formalism for its detection in Förster resonance energy transfer (FRET)-based biosensors and demonstrate its occurrence in cellulo in a synthetic actin-crosslinker and the mechanical linker protein vinculin. We find that in cellulo mechanical switching is reversible and altered by manipulation of cellular force generation as well as force-sensitive bond dynamics of the biosensor. Together, this work describes a new framework for assessing FP mechanical stability and provides a means of probing force-sensitive protein function inside cells. MOTIVATION The ability of cells to sense mechanical forces is critical in developmental, physiological, and pathological processes. Cells sense mechanical cues via force-induced alterations in protein structure and function, but elucidation of the molecular mechanisms is hindered by the lack of approaches to directly probe the effect of forces on protein structure and function inside cells. Motivated by in vitro observations of reversible fluorescent protein mechanical switching, we developed an approach for detecting fluorescent protein mechanical switching in cellulo . This enables the visualization of force-sensitive protein function inside living cells.
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5
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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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6
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Roennfeldt AE, Allen TP, Trowbridge BN, Beard MR, Whitelaw ML, Russell DL, Bersten DC, Peet DJ. NanoFIRE: A NanoLuciferase and Fluorescent Integrated Reporter Element for Robust and Sensitive Investigation of HIF and Other Signalling Pathways. Biomolecules 2023; 13:1545. [PMID: 37892227 PMCID: PMC10605489 DOI: 10.3390/biom13101545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The Hypoxia Inducible Factor (HIF) transcription factors are imperative for cell adaption to low oxygen conditions and development; however, they also contribute to ischaemic disease and cancer. To identify novel genetic regulators which target the HIF pathway or small molecules for therapeutic use, cell-based reporter systems are commonly used. Here, we present a new, highly sensitive and versatile reporter system, NanoFIRE: a NanoLuciferase and Fluorescent Integrated Reporter Element. Under the control of a Hypoxic Response Element (HRE-NanoFIRE), this system is a robust sensor of HIF activity within cells and potently responds to both hypoxia and chemical inducers of the HIF pathway in a highly reproducible and sensitive manner, consistently achieving 20 to 150-fold induction across different cell types and a Z' score > 0.5. We demonstrate that the NanoFIRE system is adaptable via substitution of the response element controlling NanoLuciferase and show that it can report on the activity of the transcriptional regulator Factor Inhibiting HIF, and an unrelated transcription factor, the Progesterone Receptor. Furthermore, the lentivirus-mediated stable integration of NanoFIRE highlights the versatility of this system across a wide range of cell types, including primary cells. Together, these findings demonstrate that NanoFIRE is a robust reporter system for the investigation of HIF and other transcription factor-mediated signalling pathways in cells, with applications in high throughput screening for the identification of novel small molecule and genetic regulators.
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Affiliation(s)
- Alison E. Roennfeldt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA 5006, Australia;
| | - Timothy P. Allen
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
| | - Brooke N. Trowbridge
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Michael R. Beard
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Murray L. Whitelaw
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
- ASEAN Microbiome Nutrition Centre, National Neuroscience Institute, Singapore 169857, Singapore
| | - Darryl L. Russell
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA 5006, Australia;
| | - David C. Bersten
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, SA 5006, Australia;
| | - Daniel J. Peet
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (A.E.R.); (T.P.A.); (B.N.T.); (M.R.B.); (M.L.W.)
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7
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Nooti S, Naylor M, Long T, Groll B, Manu. LucFlow: A method to measure Luciferase reporter expression in single cells. PLoS One 2023; 18:e0292317. [PMID: 37792708 PMCID: PMC10550117 DOI: 10.1371/journal.pone.0292317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Reporter assays, in which the expression of an inert protein is driven by gene regulatory elements such as promoters and enhancers, are a workhorse for investigating gene regulation. Techniques for measuring reporter gene expression vary from single-cell or single-molecule approaches having low throughput to bulk Luciferase assays that have high throughput. We developed a Luciferase Reporter Assay using Flow-Cytometry (LucFlow), which measures reporter expression in single cells immunostained for Luciferase. We optimized and tested LucFlow with a murine cell line that can be differentiated into neutrophils, into which promoter-reporter and enhancer-promoter-reporter constructs have been integrated in a site-specific manner. The single-cell measurements are comparable to bulk ones but we found that dead cells have no detectable Luciferase protein, so that bulk assays underestimate reporter expression. LucFlow is able to achieve a higher accuracy than bulk methods by excluding dead cells during flow cytometry. Prior to fixation and staining, the samples are spiked with stained cells that can be discriminated during flow cytometry and control for tube-to-tube variation in experimental conditions. Computing fold change relative to control cells allows LucFlow to achieve a high level of precision. LucFlow, therefore, enables the accurate and precise measurement of reporter expression in a high throughput manner.
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Affiliation(s)
- Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Brayden Groll
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
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8
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Suyama A, Devlin KL, Macias-Contreras M, Doh JK, Shinde U, Beatty KE. Orthogonal Versatile Interacting Peptide Tags for Imaging Cellular Proteins. Biochemistry 2023; 62:1735-1743. [PMID: 37167569 PMCID: PMC10249344 DOI: 10.1021/acs.biochem.2c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/26/2023] [Indexed: 05/13/2023]
Abstract
Genetic tags are transformative tools for investigating the function, localization, and interactions of cellular proteins. Most studies today are reliant on selective labeling of more than one protein to obtain comprehensive information on a protein's behavior in situ. Some proteins can be analyzed by fusion to a protein tag, such as green fluorescent protein, HaloTag, or SNAP-Tag. Other proteins benefit from labeling via small peptide tags, such as the recently reported versatile interacting peptide (VIP) tags. VIP tags enable observations of protein localization and trafficking with bright fluorophores or nanoparticles. Here, we expand the VIP toolkit by presenting two new tags: TinyVIPER and PunyVIPER. These two tags were designed for use with MiniVIPER for labeling up to three distinct proteins at once in cells. Labeling is mediated by the formation of a high-affinity, biocompatible heterodimeric coiled coil. Each tag was validated by fluorescence microscopy, including observation of transferrin receptor 1 trafficking in live cells. We verified that labeling via each tag is highly specific for one- or two-color imaging. Last, the self-sorting tags were used for simultaneous labeling of three protein targets (i.e., TOMM20, histone 2B, and actin) in fixed cells, highlighting their utility for multicolor microscopy. MiniVIPER, TinyVIPER, and PunyVIPER are small and robust peptide tags for selective labeling of cellular proteins.
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Affiliation(s)
| | | | - Miguel Macias-Contreras
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Julia K. Doh
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Ujwal Shinde
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Kimberly E. Beatty
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
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9
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Gangemi CG, Sabapathy RT, Janovjak H. CDK6 activity in a recurring convergent kinase network motif. FASEB J 2023; 37:e22845. [PMID: 36884374 DOI: 10.1096/fj.202201344r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/30/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
In humans, more than 500 kinases phosphorylate ~15% of all proteins in an emerging phosphorylation network. Convergent local interaction motifs, in which ≥two kinases phosphorylate the same substrate, underlie feedback loops and signal amplification events but have not been systematically analyzed. Here, we first report a network-wide computational analysis of convergent kinase-substrate relationships (cKSRs). In experimentally validated phosphorylation sites, we find that cKSRs are common and involve >80% of all human kinases and >24% of all substrates. We show that cKSRs occur over a wide range of stoichiometries, in many instances harnessing co-expressed kinases from family subgroups. We then experimentally demonstrate for the prototypical convergent CDK4/6 kinase pair how multiple inputs phosphorylate the tumor suppressor retinoblastoma protein (RB) and thereby hamper in situ analysis of the individual kinases. We hypothesize that overexpression of one kinase combined with a CDK4/6 inhibitor can dissect convergence. In breast cancer cells expressing high levels of CDK4, we confirm this hypothesis and develop a high-throughput compatible assay that quantifies genetically modified CDK6 variants and inhibitors. Collectively, our work reveals the occurrence, topology, and experimental dissection of convergent interactions toward a deeper understanding of kinase networks and functions.
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Affiliation(s)
- Christina G Gangemi
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Clayton/Melbourne, Australia.,European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Victoria, Clayton/Melbourne, Australia.,Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Bedford Park/Adelaide, Australia
| | - Rahkesh T Sabapathy
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Bedford Park/Adelaide, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Clayton/Melbourne, Australia.,European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Victoria, Clayton/Melbourne, Australia.,Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Bedford Park/Adelaide, Australia
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10
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Zhu YH, Liu XX, Fang Q, Liu XY, Fang WH, Cui G. Multiple Photoisomerization Pathways of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein: Insights from Quantum Mechanics/Molecular Mechanics Simulations. J Phys Chem Lett 2023; 14:2588-2598. [PMID: 36881005 DOI: 10.1021/acs.jpclett.3c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Herein, we have employed a combined CASPT2//CASSCF approach within the quantum mechanics/molecular mechanics (QM/MM) framework to explore the early time photoisomerization of rsEGFP2 starting from its two OFF trans states, i.e., Trans1 and Trans2. The results show similar vertical excitation energies to the S1 state in their Franck-Condon regions. Considering the clockwise and counterclockwise rotations of the C11-C9 bond, four pairs of the S1 excited-state minima and low-lying S1/S0 conical intersections were optimized, based on which we determined four S1 photoisomerization paths that are essentially barrierless to the relevant S1/S0 conical intersections leading to efficient excited-state deactivation to the S0 state. Most importantly, our work first identified multiple photoisomerization and excited-state decay paths, which must be seriously considered in the future. This work not only sheds significant light on the primary trans-cis photoisomerization of rsEGFP2 but also aids in the understanding of the microscopic mechanism of GFP-like RSFPs and the design of novel GFP-like fluorescent proteins.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xin-Xin Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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11
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Huang S, Yonglun Z. Fluorescent Fusion Protein Expression in Plant Cells. Methods Mol Biol 2023; 2652:119-127. [PMID: 37093472 DOI: 10.1007/978-1-0716-3147-8_6] [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: 04/25/2023]
Abstract
Fluorescent proteins (FPs) revolutionized the cell biology research by visualizing the dynamics of cellular events. In fusion with the targeted proteins, the FPs can be utilized to monitor the protein dynamics and localization in cells. Recently, FPs have been used as reporters for live cell imaging to study the protein localization or organelles dynamics in plants, allowing cell biologists to explore the plant cell function by obtaining tremendous details of cell structures and functions in combination with confocal imaging. To facilitate the usage of fluorescent proteins for protein localization and dynamic analysis in plant cell biology research, here we describe the updated protocol of Agrobacterium-mediated transformation of Arabidopsis thaliana using fluorescent proteins to generate the stable expression transgenic plants for protein trafficking and localization study. We further use the GFP-tagged SDP1 (sugar-dependent protein) lipase, mCherry-tagged peroxisome marker, and BODYPY or Nile Red (lipid droplet staining dye) as examples to introduce the method for the protein localization analysis in plants.
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Affiliation(s)
- Shuxian Huang
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zeng Yonglun
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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12
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Bandla A, Melancon E, Taylor CR, Davidson AE, Eisen JS, Ganz J. A New Transgenic Tool to Study the Ret Signaling Pathway in the Enteric Nervous System. Int J Mol Sci 2022; 23:ijms232415667. [PMID: 36555308 PMCID: PMC9779438 DOI: 10.3390/ijms232415667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The receptor tyrosine kinase Ret plays a critical role in regulating enteric nervous system (ENS) development. Ret is important for proliferation, migration, and survival of enteric progenitor cells (EPCs). Ret also promotes neuronal fate, but its role during neuronal differentiation and in the adult ENS is less well understood. Inactivating RET mutations are associated with ENS diseases, e.g., Hirschsprung Disease, in which distal bowel lacks ENS cells. Zebrafish is an established model system for studying ENS development and modeling human ENS diseases. One advantage of the zebrafish model system is that their embryos are transparent, allowing visualization of developmental phenotypes in live animals. However, we lack tools to monitor Ret expression in live zebrafish. Here, we developed a new BAC transgenic line that expresses GFP under the ret promoter. We find that EPCs and the majority of ENS neurons express ret:GFP during ENS development. In the adult ENS, GFP+ neurons are equally present in females and males. In homozygous mutants of ret and sox10-another important ENS developmental regulator gene-GFP+ ENS cells are absent. In summary, we characterize a ret:GFP transgenic line as a new tool to visualize and study the Ret signaling pathway from early development through adulthood.
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Affiliation(s)
- Ashoka Bandla
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Ellie Melancon
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Charlotte R. Taylor
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ann E. Davidson
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Judith S. Eisen
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Julia Ganz
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence:
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13
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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14
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Tau isoform-specific enhancement of L-type calcium current and augmentation of afterhyperpolarization in rat hippocampal neurons. Sci Rep 2022; 12:15231. [PMID: 36075936 PMCID: PMC9458744 DOI: 10.1038/s41598-022-18648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/17/2022] [Indexed: 11/08/2022] Open
Abstract
Accumulation of tau is observed in dementia, with human tau displaying 6 isoforms grouped by whether they display either 3 or 4 C-terminal repeat domains (3R or 4R) and exhibit no (0N), one (1N) or two (2N) N terminal repeats. Overexpression of 4R0N-tau in rat hippocampal slices enhanced the L-type calcium (Ca2+) current-dependent components of the medium and slow afterhyperpolarizations (AHPs). Overexpression of both 4R0N-tau and 4R2N-tau augmented CaV1.2-mediated L-type currents when expressed in tsA-201 cells, an effect not observed with the third 4R isoform, 4R1N-tau. Current enhancement was only observed when the pore-forming subunit was co-expressed with CaVβ3 and not CaVβ2a subunits. Non-stationary noise analysis indicated that enhanced Ca2+ channel current arose from a larger number of functional channels. 4R0N-tau and CaVβ3 were found to be physically associated by co-immunoprecipitation. In contrast, the 4R1N-tau isoform that did not augment expressed macroscopic L-type Ca2+ current exhibited greatly reduced binding to CaVβ3. These data suggest that physical association between tau and the CaVβ3 subunit stabilises functional L-type channels in the membrane, increasing channel number and Ca2+ influx. Enhancing the Ca2+-dependent component of AHPs would produce cognitive impairment that underlie those seen in the early phases of tauopathies.
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15
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Wen Y, Xie D, Liu Z. Advances in protein analysis in single live cells: principle, instrumentation and applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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16
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Guerra P, Vuillemenot LA, Rae B, Ladyhina V, Milias-Argeitis A. Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synth Biol 2022; 11:1129-1141. [PMID: 35180343 PMCID: PMC8938947 DOI: 10.1021/acssynbio.1c00387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Fluorescent protein
(FP) maturation can limit the accuracy with
which dynamic intracellular processes are captured and reduce the in vivo brightness of a given FP in fast-dividing cells.
The knowledge of maturation timescales can therefore help users determine
the appropriate FP for each application. However, in vivo maturation rates can greatly deviate from in vitro estimates that are mostly available. In this work, we present the
first systematic study of in vivo maturation for
12 FPs in budding yeast. To overcome the technical limitations of
translation inhibitors commonly used to study FP maturation, we implemented
a new approach based on the optogenetic stimulations of FP expression
in cells grown under constant nutrient conditions. Combining the rapid
and orthogonal induction of FP transcription with a mathematical model
of expression and maturation allowed us to accurately estimate maturation
rates from microscopy data in a minimally invasive manner. Besides
providing a useful resource for the budding yeast community, we present
a new joint experimental and computational approach for characterizing
FP maturation, which is applicable to a wide range of organisms.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Brady Rae
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Valeriia Ladyhina
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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17
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Lawrence M, Elhendawi M, Morlock M, Liu W, Liu S, Palakkan A, Seidl L, Hohenstein P, Sjögren A, Davies J. Human iPSC-derived renal organoids engineered to report oxidative stress can predict drug-induced toxicity. iScience 2022; 25:103884. [PMID: 35243244 PMCID: PMC8861638 DOI: 10.1016/j.isci.2022.103884] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/10/2021] [Accepted: 02/03/2022] [Indexed: 01/08/2023] Open
Abstract
Advances in regenerative medicine have led to the construction of many types of organoids, which reproduce important aspects of endogenous organs but may be limited or disorganized in nature. While their usefulness for restoring function remains unclear, they have undoubted usefulness in research, diagnostics, and toxicology. In toxicology, there is an urgent need for better models for human kidneys. We used human iPS-cell (hiPSC)-derived renal organoids to identify HMOX1 as a useful marker of toxic stress via the oxidative stress pathway, and then constructed an HMOX1 reporter in hiPSCs. We used two forms of hiPSC-derived HMOX1-reporter renal organoids to probe their ability to detect nephrotoxicants in a panel of blind-coded compounds. Our results highlight the potential usefulness, and some limitations, of HMOX1-reporter renal organoids as screening tools. The results may guide development of similar stress-reporting organoid assays for other stem-cell-derived organs and tissues.
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Affiliation(s)
- M.L. Lawrence
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD UK
| | - M. Elhendawi
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD UK
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - M. Morlock
- R&D Graduate, R&D, AstraZeneca, Gothenburg, Sweden
| | - W. Liu
- SynthSys Centre for Synthetic and Systems Biology, UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, C.H Waddington Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - S. Liu
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD UK
| | - A. Palakkan
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD UK
| | - L.F. Seidl
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD UK
| | - P. Hohenstein
- Leiden University Medical Center, Leiden University, Leiden, the Netherlands
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - A.K. Sjögren
- CVRM Safety, Clinical Pharmacology and Safety Science, R&D, AstraZeneca, Gothenburg, Sweden
| | - J.A. Davies
- Deanery of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD UK
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18
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Kyeong M, Lee JS. Endogenous BiP reporter system for simultaneous identification of ER stress and antibody production in Chinese hamster ovary cells. Metab Eng 2022; 72:35-45. [PMID: 35182754 DOI: 10.1016/j.ymben.2022.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 02/07/2022] [Indexed: 12/28/2022]
Abstract
As the biopharmaceutical industry expands, improving the production of therapeutic proteins using Chinese hamster ovary (CHO) cells is important. However, excessive and complicated protein production causes protein misfolding and triggers endoplasmic reticulum (ER) stress. When ER stress occurs, cells mediate the unfolded protein response (UPR) pathway to restore protein homeostasis and folding capacity of the ER. However, when the cells fail to control prolonged ER stress, UPR induces apoptosis. Therefore, monitoring the degree of UPR is required to achieve high productivity and the desired quality. In this study, we developed a fluorescence-based UPR monitoring system for CHO cells. We integrated mGFP into endogenous HSPA5 encoding BiP, a major ER chaperone, and the primary ER stress activation sensor, using CRISPR/Cas9-mediated targeted integration. The mGFP expression level changed according to the ER stress induced by chemical treatment and batch culture in the engineered cell line. Using this monitoring system, we demonstrated that host cells and recombinant CHO cell lines with different mean fluorescence intensities (MFI; basal expression levels of BiP) possess a distinct capacity for stress culture conditions induced by recombinant protein production. Antibody-producing recombinant CHO cell lines were generated using site-specific integration based on host cells equipped with the BiP reporter system. Targeted integrants showed a strong correlation between productivity and MFI, reflecting the potential of this monitoring system as a screening readout for high producers. Taken together, these data demonstrate the utility of the endogenous BiP reporter system for the detection of real-time dynamic changes in endogenous UPR and its potential for applications in recombinant protein production during CHO cell line development.
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Affiliation(s)
- Minji Kyeong
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
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19
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KIAA0319 influences cilia length, cell migration and mechanical cell-substrate interaction. Sci Rep 2022; 12:722. [PMID: 35031635 PMCID: PMC8760330 DOI: 10.1038/s41598-021-04539-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/17/2021] [Indexed: 01/11/2023] Open
Abstract
Following its association with dyslexia in multiple genetic studies, the KIAA0319 gene has been extensively investigated in different animal models but its function in neurodevelopment remains poorly understood. We developed the first human cellular knockout model for KIAA0319 in RPE1 retinal pigment epithelia cells via CRISPR-Cas9n to investigate its role in processes suggested but not confirmed in previous studies, including cilia formation and cell migration. We observed in the KIAA0319 knockout increased cilia length and accelerated cell migration. Using Elastic Resonator Interference Stress Microscopy (ERISM), we detected an increase in cellular force for the knockout cells that was restored by a rescue experiment. Combining ERISM and immunostaining we show that RPE1 cells exert highly dynamic, piconewton vertical pushing forces through actin-rich protrusions that are surrounded by vinculin-rich pulling sites. This protein arrangement and force pattern has previously been associated to podosomes in other cells. KIAA0319 depletion reduces the fraction of cells forming these actin-rich protrusions. Our results suggest an involvement of KIAA0319 in cilia biology and cell-substrate force regulation.
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20
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Fagbadebo FO, Rothbauer U. Peptide-Tag Specific Nanobodies for Studying Proteins in Live Cells. Methods Mol Biol 2022; 2446:555-579. [PMID: 35157294 DOI: 10.1007/978-1-0716-2075-5_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-domain antibodies such as nanobodies (Nbs) have substantially expanded the possibilities of advanced cellular imaging. In comparison to conventional antibodies, Nbs are characterized by small size, high stability, and solubility in many environments, including the cytoplasm. Nbs can be efficiently functionalized or modified according to the needs of the imaging approach. Target-specific Nbs can be easily converted into genetically encoded fluorescently labeled intrabodies, also known as chromobodies (CBs), which represent powerful tools to study the dynamics of different proteins of interest within living cells. In this context, CBs specific for a short peptide epitope provide a versatile alternative to bypass the limitations observed with larger fluorescent protein fusions and can be readily used to visualize and monitor peptide-tagged proteins for which specific Nbs are not available. Here, we present our novel detection system comprising a 15 amino acid peptide-tag (PepTag) in combination with a peptide-tag specific CB (PepCB). We provide protocols for adding the PepTag to different proteins of interest, reformatting the peptide-specific Nb (PepNb) into a CB for expression in mammalian cells, and establishment of stable cell lines expressing the PepCB for protein interaction assays and compound screenings.
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Affiliation(s)
- Funmilayo O Fagbadebo
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany.
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
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21
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Chen P, Wang R, Wang K, Han JN, Kuang S, Nie Z, Huang Y. Multifunctional stimuli-responsive chemogenetic platform for conditional multicolor cell-selective labeling. Chem Sci 2022; 13:12187-12197. [PMID: 36349109 PMCID: PMC9601257 DOI: 10.1039/d2sc03100k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Multicolor conditional labeling is a powerful tool that can simultaneously and selectively visualize multiple targets for bioimaging analysis of complex biological processes and cellular features. We herein report a multifunctional stimuli-responsive Fluorescence-Activating and absorption-Shifting Tag (srFAST) chemogenetic platform for multicolor cell-selective labeling. This platform comprises stimuli-responsive fluorogenic ligands and the organelle-localizable FAST. The physicochemical properties of the srFAST ligands can be tailored by modifying the optical-tunable hydroxyl group with diverse reactive groups, and their chemical decaging process caused by cell-specific stimuli induces a conditionally activatable fluorescent labeling upon binding with the FAST. Thus, the resulting switch-on srFASTs were designed for on-demand labeling of cells of interest by spatiotemporally precise photo-stimulation or unique cellular feature-dependent activation, including specific endogenous metabolites or enzyme profiles. Furthermore, diverse enzyme-activatable srFAST ligands with distinct colors were constructed and simultaneously exploited for multicolor cell-selective labeling, which allow discriminating and orthogonal labeling of three different cell types with the same protein tag. Our method provides a promising strategy for designing a stimuli-responsive chemogenetic labeling platform via facile molecular engineering of the synthetic ligands, which has great potential for conditional multicolor cell-selective labeling and cellular heterogeneity evaluation. Comparison of the stimuli-responsive FAST platform (srFAST) proposed in this work with the reported original FAST system (O-FAST). The srFAST could achieve not only conditional selective labeling, but also multicolor selective labeling.![]()
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Affiliation(s)
- Pengfei Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Rui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ke Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jiao-Na Han
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
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22
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Hickey SM, Ung B, Bader C, Brooks R, Lazniewska J, Johnson IRD, Sorvina A, Logan J, Martini C, Moore CR, Karageorgos L, Sweetman MJ, Brooks DA. Fluorescence Microscopy-An Outline of Hardware, Biological Handling, and Fluorophore Considerations. Cells 2021; 11:35. [PMID: 35011596 PMCID: PMC8750338 DOI: 10.3390/cells11010035] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
Fluorescence microscopy has become a critical tool for researchers to understand biological processes at the cellular level. Micrographs from fixed and live-cell imaging procedures feature in a plethora of scientific articles for the field of cell biology, but the complexities of fluorescence microscopy as an imaging tool can sometimes be overlooked or misunderstood. This review seeks to cover the three fundamental considerations when designing fluorescence microscopy experiments: (1) hardware availability; (2) amenability of biological models to fluorescence microscopy; and (3) suitability of imaging agents for intended applications. This review will help equip the reader to make judicious decisions when designing fluorescence microscopy experiments that deliver high-resolution and informative images for cell biology.
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Affiliation(s)
- Shane M. Hickey
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
| | - Ben Ung
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
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Localization of Native Mms13 to the Magnetosome Chain of Magnetospirillum magneticum AMB-1 Using Immunogold Electron Microscopy, Immunofluorescence Microscopy and Biochemical Analysis. CRYSTALS 2021. [DOI: 10.3390/cryst11080874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Magnetotactic bacteria (MTB) biomineralize intracellular magnetite (Fe3O4) crystals surrounded by a magnetosome membrane (MM). The MM contains membrane-specific proteins that control Fe3O4 mineralization in MTB. Previous studies have demonstrated that Mms13 is a critical protein within the MM. Mms13 can be isolated from the MM fraction of Magnetospirillum magneticum AMB-1 and a Mms13 homolog, MamC, has been shown to control the size and shape of magnetite nanocrystals synthesized in-vitro. The objective of this study was to use several independent methods to definitively determine the localization of native Mms13 in M. magneticum AMB-1. Using Mms13-immunogold labeling and transmission electron microscopy (TEM), we found that Mms13 is localized to the magnetosome chain of M. magneticum AMB-1 cells. Mms13 was detected in direct contact with magnetite crystals or within the MM. Immunofluorescence detection of Mms13 in M. magneticum AMB-1 cells by confocal laser scanning microscopy (CLSM) showed Mms13 localization along the length of the magnetosome chain. Proteins contained within the MM were resolved by SDS-PAGE for Western blot analysis and LC-MS/MS (liquid chromatography with tandem mass spectrometry) protein sequencing. Using Anti-Mms13 antibody, a protein band with a molecular mass of ~14 kDa was detected in the MM fraction only. This polypeptide was digested with trypsin, sequenced by LC-MS/MS and identified as magnetosome protein Mms13. Peptides corresponding to the protein’s putative MM domain and catalytic domain were both identified by LC-MS/MS. Our results (Immunogold TEM, Immunofluorescence CLSM, Western blot, LC-MS/MS), combined with results from previous studies, demonstrate that Mms13 and homolog proteins MamC and Mam12, are localized to the magnetosome chain in MTB belonging to the class Alphaproteobacteria. Because of their shared localization in the MM and highly conserved amino acid sequences, it is likely that MamC, Mam12, and Mms13 share similar roles in the biomineralization of Fe3O4 nanocrystals.
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Emenecker RJ, Holehouse AS, Strader LC. Biological Phase Separation and Biomolecular Condensates in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:17-46. [PMID: 33684296 PMCID: PMC8221409 DOI: 10.1146/annurev-arplant-081720-015238] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA;
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Elucidating Recombination Mediator Function Using Biophysical Tools. BIOLOGY 2021; 10:biology10040288. [PMID: 33916151 PMCID: PMC8066028 DOI: 10.3390/biology10040288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary This review recapitulates the initial knowledge acquired with genetics and biochemical experiments on Recombination mediator proteins in different domains of life. We further address how recent in vivo and in vitro biophysical tools were critical to deepen the understanding of RMPs molecular mechanisms in DNA and replication repair, and unveiled unexpected features. For instance, in bacteria, genetic and biochemical studies suggest a close proximity and coordination of action of the RecF, RecR and RecO proteins in order to ensure their RMP function, which is to overcome the single-strand binding protein (SSB) and facilitate the loading of the recombinase RecA onto ssDNA. In contrary to this expectation, using single-molecule fluorescent imaging in living cells, we showed recently that RecO and RecF do not colocalize and moreover harbor different spatiotemporal behavior relative to the replication machinery, suggesting distinct functions. Finally, we address how new biophysics tools could be used to answer outstanding questions about RMP function. Abstract The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context.
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Abstract
Flow cytometry and sorting represents a valuable and mature experimental platform for the analysis of cellular populations. Applications involving higher plants started to emerge around 40 years ago and are now widely employed both to provide unique information regarding basic and applied questions in the biosciences and to advance agricultural productivity in practical ways. Further development of this platform is being actively pursued, and this promises additional progress in our understanding of the interactions of cells within complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types held together by tough cell walls, and, second, because individual plant cells are generally larger than those of mammals.This chapter, which updates work last reviewed in 2014 [Galbraith DW (2014) Flow cytometry and sorting in Arabidopsis. In: Sanchez Serrano JJ, Salinas J (eds) Arabidopsis Protocols, 3rd ed. Methods in molecular biology, vol 1062. Humana Press, Totowa, pp 509-537], describes the application of techniques of flow cytometry and sorting to the model plant species Arabidopsis thaliana, in particular emphasizing (a) fluorescence labeling in vivo of specific cell types and of subcellular components, (b) analysis using both conventional cytometers and spectral analyzers, (c) fluorescence-activated sorting of protoplasts and nuclei, and (d) transcriptome analyses using sorted protoplasts and nuclei, focusing on population analyses at the level of single protoplasts and nuclei. Since this is an update, details of new experimental methods are emphasized.
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Affiliation(s)
- David W Galbraith
- University of Arizona, School of Plant Sciences and Bio5 Institute, Tucson, AZ, USA. .,Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China.
| | - Guiling Sun
- Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China
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Wagner TR, Rothbauer U. Nanobodies Right in the Middle: Intrabodies as Toolbox to Visualize and Modulate Antigens in the Living Cell. Biomolecules 2020; 10:biom10121701. [PMID: 33371447 PMCID: PMC7767433 DOI: 10.3390/biom10121701] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023] Open
Abstract
In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.
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Affiliation(s)
- Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
- Correspondence: ; Tel.: +49-7121-5153-0415; Fax: +49-7121-5153-0816
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Wan J, Lu H. Enabling high-throughput single-animal gene-expression studies with molecular and micro-scale technologies. LAB ON A CHIP 2020; 20:4528-4538. [PMID: 33237042 PMCID: PMC7769683 DOI: 10.1039/d0lc00881h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene expression and regulation play diverse and important roles across all living systems. By quantifying the expression, whether in a sample of single cells, a specific tissue, or in a whole animal, one can gain insights into the underlying biology. Many biological questions now require single-animal and tissue-specific resolution, such as why individuals, even within an isogenic population, have variations in development and aging across different tissues and organs. The popular techniques that quantify the transcriptome (e.g. RNA-sequencing) process populations of animals and cells together and thus, have limitations in both individual and spatial resolution. There are single-animal assays available (e.g. fluorescent reporters); however, they suffer other technical bottlenecks, such as a lack of robust sample-handling methods. Microfluidic technologies have demonstrated various improvements throughout the years, and it is likely they can enhance the impact of these single-animal gene-expression assays. In this perspective, we aim to highlight how the engineering/method-development field have unique opportunities to create new tools that can enable us to robustly answer the next set of important questions in biology that require high-density, high-quality gene expression data.
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Affiliation(s)
- Jason Wan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA.
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Charubin K, Streett H, Papoutsakis ET. Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins. Appl Environ Microbiol 2020; 86:e01271-20. [PMID: 32769192 PMCID: PMC7531948 DOI: 10.1128/aem.01271-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
One of the biggest limitations in the study and engineering of anaerobic Clostridium organisms is the lack of strong fluorescent reporters capable of strong and real-time fluorescence. Recently, we developed a strong fluorescent reporter system for Clostridium organisms based on the FAST protein. Here, we report the development of two new strong fluorescent reporter systems for Clostridium organisms based on the HaloTag and SNAP-tag proteins, which produce strong fluorescent signals when covalently bound to fluorogenic ligands. These new fluorescent reporters are orthogonal to the FAST ligands and to each other, allowing for simultaneous labeling and visualization. We used HaloTag and SNAP-tag to label the strictly anaerobic organisms Clostridium acetobutylicum and Clostridium ljungdahlii We have also identified a new strong promoter for protein expression in C. acetobutylicum, based on the phosphotransacetylase gene (pta) from C. ljungdahlii Furthermore, the HaloTag and the SNAP-tag, in combination with the previously described FAST system, were successfully used to measure cell populations in bacterial mixed cultures and showed the simultaneous orthogonal labeling of HaloTag and SNAP-tag together with the FAST protein reporter. Finally, we show the expression of recombinant fusion protein of FAST and the ZapA division protein (from C. acetobutylicum) in C. ljungdahlii. The availability of multiple strong fluorescent reporters is a major addition to the genetic toolkit of Clostridium and other anaerobes that will lead to better understanding of these unique organisms.IMPORTANCE Up to this point, assays and methods involving fluorescent reporter proteins were unavailable or limited in Clostridium organisms and other strict anaerobes. Green fluorescent protein (GFP), mCherry, and flavin-binding proteins (and their derivatives) have been used only in a few clostridia with limited success and yielded low fluorescence compared to aerobic microbial systems. Recently, we reported a new strong fluorescent reporter system based on the FAST protein as a first step in expanding the fluorescence-based reporters for Clostridium and other anaerobic microbial platforms. Additional strong orthogonal fluorescent proteins, with distinct emission spectra are needed to allow for (i) multispecies tracking within the growing field of microbial cocultures and microbiomes, (ii) protein localization and tracking in anaerobes, and (iii) identification and development of natural and synthetic promoters, ribosome-binding sites (RBS), and terminators for optimal protein expression in anaerobes. Here, we present two new strong fluorescent reporter systems based on the HaloTag and SNAP-tag proteins.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Hannah Streett
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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30
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Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
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31
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Traenkle B, Segan S, Fagbadebo FO, Kaiser PD, Rothbauer U. A novel epitope tagging system to visualize and monitor antigens in live cells with chromobodies. Sci Rep 2020; 10:14267. [PMID: 32868807 PMCID: PMC7459311 DOI: 10.1038/s41598-020-71091-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Epitope tagging is a versatile approach to study different proteins using a well-defined and established methodology. To date, most epitope tags such as myc, HA, V5 and FLAG tags are recognized by antibodies, which limits their use to fixed cells, tissues or protein samples. Here we introduce a broadly applicable tagging strategy utilizing a short peptide tag (PepTag) which is specifically recognized by a nanobody (PepNB). We demonstrated that the PepNB can be easily functionalized for immunoprecipitation or direct immunofluorescence staining of Pep-tagged proteins in vitro. For in cellulo studies we converted the PepNB into a fluorescently labeled Pep-chromobody (PepCB) which is functionally expressed in living cells. The addition of the small PepTag does not interfere with the examined structures in different cellular compartments and its detection with the PepCB enables optical antigen tracing in real time. By employing the phenomenon of antigen-mediated chromobody stabilization (AMCBS) using a turnover-accelerated PepCB we demonstrated that the system is suitable to visualize and quantify changes in Pep-tagged antigen concentration by quantitative live-cell imaging. We expect that this novel tagging strategy offers new opportunities to study the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
- Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Sören Segan
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | | | - Philipp D Kaiser
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany. .,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany.
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Wiechert J, Gätgens C, Wirtz A, Frunzke J. Inducible Expression Systems Based on Xenogeneic Silencing and Counter-Silencing and Design of a Metabolic Toggle Switch. ACS Synth Biol 2020; 9:2023-2038. [PMID: 32649183 DOI: 10.1021/acssynbio.0c00111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inducible expression systems represent key modules in regulatory circuit design and metabolic engineering approaches. However, established systems are often limited in terms of applications due to high background expression levels and inducer toxicity. In bacteria, xenogeneic silencing (XS) proteins are involved in the tight control of horizontally acquired, AT-rich DNA. The action of XS proteins may be opposed by interference with a specific transcription factor, resulting in the phenomenon of counter-silencing, thereby activating gene expression. In this study, we harnessed this principle for the construction of a synthetic promoter library consisting of phage promoters targeted by the Lsr2-like XS protein CgpS of Corynebacterium glutamicum. Counter-silencing was achieved by inserting the operator sequence of the gluconate-responsive transcription factor GntR. The GntR-dependent promoter library is comprised of 28 activated and 16 repressed regulatory elements featuring effector-dependent tunability. For selected candidates, background expression levels were confirmed to be significantly reduced in comparison to established heterologous expression systems. Finally, a GntR-dependent metabolic toggle switch was implemented in a C. glutamicum l-valine production strain allowing the dynamic redirection of carbon flux between biomass and product formation.
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Affiliation(s)
- Johanna Wiechert
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cornelia Gätgens
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Astrid Wirtz
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Frunzke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
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33
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Marshall AP, Shirley JD, Carlson EE. Enzyme-targeted fluorescent small-molecule probes for bacterial imaging. Curr Opin Chem Biol 2020; 57:155-165. [PMID: 32799037 DOI: 10.1016/j.cbpa.2020.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Abstract
Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.
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Affiliation(s)
- Andrew P Marshall
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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Majc B, Sever T, Zarić M, Breznik B, Turk B, Lah TT. Epithelial-to-mesenchymal transition as the driver of changing carcinoma and glioblastoma microenvironment. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118782. [PMID: 32554164 DOI: 10.1016/j.bbamcr.2020.118782] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is an essential molecular and cellular process that is part of normal embryogenesis and wound healing, and also has a ubiquitous role in various types of carcinoma and glioblastoma. EMT is activated and regulated by specific microenvironmental endogenous triggers and a complex network of signalling pathways. These mostly include epigenetic events that affect protein translation-controlling factors and proteases, altogether orchestrated by the switching on and off of oncogenes and tumour-suppressor genes in cancer cells. The hallmark of cancer-linked EMT is that the process is incomplete, as it is opposed by the reverse process of mesenchymal-to-epithelial transition, which results in a hybrid epithelial/mesenchymal phenotype that shows notable cell plasticity. This is a characteristic of cancer stem cells (CSCs), and it is of the utmost importance in their niche microenvironment, where it governs CSC migratory and invasive properties, thereby creating metastatic CSCs. These cells have high resistance to therapeutic treatments, in particular in glioblastoma.
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Affiliation(s)
- Bernarda Majc
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Tilen Sever
- Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia; Department of Biochemistry, Molecular and Structural Biology, Josef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Miki Zarić
- Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia; Department of Biochemistry, Molecular and Structural Biology, Josef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Barbara Breznik
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Josef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia; Institute of Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Bol'shaya Pirogovskaya Ulitsa, 19с1, Moscow 119146, Russia
| | - Tamara T Lah
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000 Ljubljana, Slovenia.
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35
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Kesavan G, Machate A, Hans S, Brand M. Cell-fate plasticity, adhesion and cell sorting complementarily establish a sharp midbrain-hindbrain boundary. Development 2020; 147:dev186882. [PMID: 32439756 DOI: 10.1242/dev.186882] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/30/2020] [Indexed: 01/22/2023]
Abstract
The formation and maintenance of sharp boundaries between groups of cells play a vital role during embryonic development as they serve to compartmentalize cells with similar fates. Some of these boundaries also act as organizers, with the ability to induce specific cell fates and morphogenesis in the surrounding cells. The midbrain-hindbrain boundary (MHB) is such an organizer: it acts as a lineage restriction boundary to prevent the intermingling of cells with different developmental fates. However, the mechanisms underlying the lineage restriction process remain unclear. Here, using novel fluorescent knock-in reporters, live imaging, Cre/lox-mediated lineage tracing, atomic force microscopy-based cell adhesion assays and mutant analysis, we analyze the process of lineage restriction at the MHB and provide mechanistic details. Specifically, we show that lineage restriction occurs by the end of gastrulation, and that the subsequent formation of sharp gene expression boundaries in the developing MHB occur through complementary mechanisms, i.e. cell-fate plasticity and cell sorting. Furthermore, we show that cell sorting at the MHB involves differential adhesion among midbrain and hindbrain cells that is mediated by N-cadherin and Eph-ephrin signaling.
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Affiliation(s)
- Gokul Kesavan
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Anja Machate
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Stefan Hans
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Michael Brand
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
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Gao J, Qian H, Guo X, Mi Y, Guo J, Zhao J, Xu C, Zheng T, Duan M, Tang Z, Lin C, Shen Z, Jiang Y, Wang X. The signal peptide of Cry1Ia can improve the expression of eGFP or mCherry in Escherichia coli and Bacillus thuringiensis and enhance the host's fluorescent intensity. Microb Cell Fact 2020; 19:112. [PMID: 32448275 PMCID: PMC7247199 DOI: 10.1186/s12934-020-01371-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 05/16/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The signal peptides (SPs) of secretory proteins are frequently used or modified to guide recombinant proteins outside the cytoplasm of prokaryotic cells. In the periplasmic space and extracellular environment, recombinant proteins are kept away from the intracellular proteases and often they can fold correctly and efficiently. Consequently, expression levels of the recombinant protein can be enhanced by the presence of a SP. However, little attention has been paid to the use of SPs with low translocation efficiency for recombinant protein production. In this paper, the function of the signal peptide of Bacillus thuringiensis (Bt) Cry1Ia toxin (Iasp), which is speculated to be a weak translocation signal, on regulation of protein expression was investigated using fluorescent proteins as reporters. RESULTS When fused to the N-terminal of eGFP or mCherry, the Iasp can improve the expression of the fluorescent proteins and as a consequence enhance the fluorescent intensity of both Escherichia coli and Bt host cells. Real-time quantitative PCR analysis revealed the higher transcript levels of Iegfp over those of egfp gene in E. coli TG1 cells. By immunoblot analysis and confocal microscope observation, lower translocation efficiency of IeGFP was demonstrated. The novel fluorescent fusion protein IeGFP was then used to compare the relative strengths of cry1Ia (Pi) and cry1Ac (Pac) gene promoters in Bt strain, the latter promoter proving the stronger. The eGFP reporter, by contrast, cannot indicate unambiguously the regulation pattern of Pi at the same level of sensitivity. The fluorescent signals of E. coli and Bt cells expressing the Iasp fused mCherry (ImCherry) were also enhanced. Importantly, the Iasp can also enhanced the expression of two difficult-to-express proteins, matrix metalloprotease-13 (MMP13) and myostatin (growth differentiating factor-8, GDF8) in E. coli BL21-star (DE3) strain. CONCLUSIONS We identified the positive effects of a weak signal peptide, Iasp, on the expression of fluorescent proteins and other recombinant proteins in bacteria. The produced IeGFP and ImCherry can be used as novel fluorescent protein variants in prokaryotic cells. The results suggested the potential application of Iasp as a novel fusion tag for improving the recombinant protein expression.
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Affiliation(s)
- Jianhua Gao
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
| | - Hongmei Qian
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaoqin Guo
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Yi Mi
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Junpei Guo
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Juanli Zhao
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Chao Xu
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ting Zheng
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ming Duan
- Experimental Teaching Center, Shanxi Agricultural University, Taigu, 030801, China
| | - Zhongwei Tang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Chaoyang Lin
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhicheng Shen
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Xingchun Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
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Recovery and Reusability of ApoUnaG Fluorescence Protein from the Unconjugated Bilirubin Complex Structure. J Fluoresc 2020; 30:497-503. [DOI: 10.1007/s10895-020-02519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/14/2020] [Indexed: 10/24/2022]
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Liu J, Hebbrecht T, Brans T, Parthoens E, Lippens S, Li C, De Keersmaecker H, De Vos WH, De Smedt SC, Boukherroub R, Gettemans J, Xiong R, Braeckmans K. Long-term live-cell microscopy with labeled nanobodies delivered by laser-induced photoporation. NANO RESEARCH 2020; 13:485-495. [PMID: 33154805 PMCID: PMC7116313 DOI: 10.1007/s12274-020-2633-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fluorescence microscopy is the method of choice for studying intracellular dynamics. However, its success depends on the availability of specific and stable markers. A prominent example of markers that are rapidly gaining interest are nanobodies (Nbs, ~ 15 kDa), which can be functionalized with bright and photostable organic fluorophores. Due to their relatively small size and high specificity, Nbs offer great potential for high-quality long-term subcellular imaging, but suffer from the fact that they cannot spontaneously cross the plasma membrane of live cells. We have recently discovered that laser-induced photoporation is well suited to deliver extrinsic labels to living cells without compromising their viability. Being a laser-based technology, it is readily compatible with light microscopy and the typical cell recipients used for that. Spurred by these promising initial results, we demonstrate here for the first time successful long-term imaging of specific subcellular structures with labeled nanobodies in living cells. We illustrate this using Nbs that target GFP/YFP-protein constructs accessible in the cytoplasm, actin-bundling protein Fascin, and the histone H2A/H2B heterodimers. With an efficiency of more than 80% labeled cells and minimal toxicity (~ 2%), photoporation proved to be an excellent intracellular delivery method for Nbs. Time-lapse microscopy revealed that cell division rate and migration remained unaffected, confirming excellent cell viability and functionality. We conclude that laser-induced photoporation labeled Nbs can be easily delivered into living cells, laying the foundation for further development of a broad range of Nbs with intracellular targets as a toolbox for long-term live-cell microscopy.
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Affiliation(s)
- Jing Liu
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
| | - Tim Hebbrecht
- Department of Biomolecular medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Toon Brans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
| | - Eef Parthoens
- VIB-UGent Center for Inflammation Research, VIB, Ghent B-9000, Belgium
- VIB Bioimaging Core Ghent, VIB, Ghent B-9000, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent B-9000, Belgium
| | - Saskia Lippens
- VIB-UGent Center for Inflammation Research, VIB, Ghent B-9000, Belgium
- VIB Bioimaging Core Ghent, VIB, Ghent B-9000, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent B-9000, Belgium
| | - Chengnan Li
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille F-59000, France
| | - Herlinde De Keersmaecker
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
| | - Rabah Boukherroub
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille F-59000, France
| | - Jan Gettemans
- Department of Biomolecular medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
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Wan J, Sun G, Dicent J, Patel DS, Lu H. smFISH in chips: a microfluidic-based pipeline to quantify in situ gene expression in whole organisms. LAB ON A CHIP 2020; 20:266-273. [PMID: 31788681 PMCID: PMC8146400 DOI: 10.1039/c9lc00896a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-sequencing and RT-PCR) to compare gene expression levels in hypo- or hyper-morphic mutant animals (e.g. gain-of-function or knockout). This approach is limited, especially in complex gene networks, as these genetic mutations may affect the expressions of related genes in unforseen ways. In contrast, we developed a microfluidic-based pipeline to discover gene relationships in a single genetic background. The microfluidic device provides efficient reagent exchange and the ability to track individual animals. By automating a robust microfluidic reagent exchange strategy, we adapted and validated single molecule fluorescent in situ hybridization (smFISH) on-chip and combined this technology with live-imaging of fluorescent transcriptional reporters. Together, this multi-level information enabled us to quantify a gene expression relationship with single-animal resolution. While this microfluidic-based pipeline is optimized for live-imaging and smFISH C. elegans studies, the strategy is highly-adaptable to other biological models as well as combining other live and end-point biological assays, such as behavior-based toxicology screening and immunohistochemistry.
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Affiliation(s)
- Jason Wan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Jocelyn Dicent
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Radoeva T, Albrecht C, Piepers M, de Vries S, Weijers D. Suspensor-derived somatic embryogenesis in Arabidopsis. Development 2020; 147:dev.188912. [DOI: 10.1242/dev.188912] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/08/2020] [Indexed: 01/16/2023]
Abstract
In many flowering plants, asymmetric division of the zygote generates apical and basal cells with different fates. In Arabidopsis thaliana, the apical cell generates the embryo while the basal cell divides anticlinally, leading to a suspensor of 6-9 cells that remain extra-embryonic and eventually senesce. In some genetic backgrounds, or upon ablation of the embryo, suspensor cells can undergo periclinal cell divisions and eventually form a second, twin embryo. Likewise, embryogenesis can be induced from somatic cells by various genes, but the relation to suspensor-derived embryos is unclear. Here, we addressed the nature of the suspensor to embryo fate transformation, and its genetic triggers. We expressed most known embryogenesis-inducing genes specifically in suspensor cells. We next analyzed morphology and fate marker expression in embryos in which suspensor division were activated by different triggers to address the developmental paths towards reprogramming. Our results show that reprogramming of Arabidopsis suspensor cells towards embryonic identity is a specific cellular response that is triggered by defined regulators, follows a conserved developmental trajectory and shares similarity to the process of somatic embryogenesis from post-embryonic tissues.
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Affiliation(s)
- Tatyana Radoeva
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Catherine Albrecht
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marcel Piepers
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Sacco de Vries
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dolf Weijers
- Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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41
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Doh JK, Enns CA, Beatty KE. Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy. Bio Protoc 2019; 9:e3413. [PMID: 32665966 PMCID: PMC7360171 DOI: 10.21769/bioprotoc.3413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
Genetically-encoded tags are useful tools for multicolor and multi-scale cellular imaging. Versatile Interacting Peptide (VIP) tags, such as VIPER, are new genetically-encoded tags that can be used in various imaging applications. VIP tags consist of a coiled-coil heterodimer, with one peptide serving as the genetic tag and the other ("probe peptide") delivering a reporter compatible with imaging. Heterodimer formation is rapid and specific, allowing proteins to be selectively labeled for live-cell and fixed-cell imaging. In this Bio-Protocol, we include a detailed guide for implementing the VIPER technology for imaging receptors on live cells and intracellular targets in fixed cells. This protocol is complemented by two other Bio-Protocols outlining the use of VIPER (Doh et al., 2019a and 2019b).
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Affiliation(s)
- Julia K. Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Caroline A. Enns
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Kimberly E. Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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Hoffman HK, Fernandez MV, Groves NS, Freed EO, van Engelenburg SB. Genomic tagging of endogenous human ESCRT-I complex preserves ESCRT-mediated membrane-remodeling functions. J Biol Chem 2019; 294:16266-16281. [PMID: 31519756 PMCID: PMC6827313 DOI: 10.1074/jbc.ra119.009372] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
The endosomal sorting complexes required for transport (ESCRT) machinery drives membrane scission for diverse cellular functions that require budding away from the cytosol, including cell division and transmembrane receptor trafficking and degradation. The ESCRT machinery is also hijacked by retroviruses, such as HIV-1, to release virions from infected cells. The crucial roles of the ESCRTs in cellular physiology and viral disease make it imperative to understand the membrane scission mechanism. Current methodological limitations, namely artifacts caused by overexpression of ESCRT subunits, obstruct our understanding of the spatiotemporal organization of the endogenous human ESCRT machinery. Here, we used CRISPR/Cas9-mediated knock-in to tag the critical ESCRT-I component tumor susceptibility 101 (Tsg101) with GFP at its native locus in two widely used human cell types, HeLa epithelial cells and Jurkat T cells. We validated this approach by assessing the function of these knock-in cell lines in cytokinesis, receptor degradation, and virus budding. Using this probe, we measured the incorporation of endogenous Tsg101 in released HIV-1 particles, supporting the notion that the ESCRT machinery initiates virus abscission by scaffolding early-acting ESCRT-I within the head of the budding virus. We anticipate that these validated cell lines will be a valuable tool for interrogating dynamics of the native human ESCRT machinery.
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Affiliation(s)
- Huxley K Hoffman
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, Colorado 80210
| | - Melissa V Fernandez
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nicholas S Groves
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, Colorado 80210
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Schuyler B van Engelenburg
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, Colorado 80210
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Jost APT, Waters JC. Designing a rigorous microscopy experiment: Validating methods and avoiding bias. J Cell Biol 2019; 218:1452-1466. [PMID: 30894402 PMCID: PMC6504886 DOI: 10.1083/jcb.201812109] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/06/2023] Open
Abstract
Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.
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Saady A, Böttner V, Meng M, Varon E, Shav-Tal Y, Ducho C, Fischer B. An oligonucleotide probe incorporating the chromophore of green fluorescent protein is useful for the detection of HER-2 mRNA breast cancer marker. Eur J Med Chem 2019; 173:99-106. [PMID: 30991278 DOI: 10.1016/j.ejmech.2019.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/05/2019] [Accepted: 04/04/2019] [Indexed: 01/15/2023]
Abstract
Diagnosis and treatment of breast cancer can be greatly enhanced and personalized based on the quantitative detection of mRNA markers. Here, we targeted the development of a fluorescent oligonucleotide probe to detect specifically the HER-2 mRNA breast cancer marker. We have selected the chromophore of the Green Fluorescent Protein (GFP), 4-hydroxybenzylidene imidazolinone (HBI), as a fluorophore covalently bound to an oligonucleotide probe and potentially capable of intercalating within a probe-mRNA duplex. We first synthesized the two-ring scaffold of the HBI chromophore 5 and coupled it to 2'-deoxyuridine at C5-position via a 7-atom-spacer, to give 4. Indeed, in the highly viscous glycerol used to mimic the reduced conformational flexibility of the intercalated HBI, chromophore 4 displayed a quantum yield of 0.29 and brightness of 20600 M-1cm-1, while no fluorescent signal was observed in methanol. Next, we synthesized a 20-mer oligonucleotide probe incorporating 4 at position 6 (5'-CCCGTUTCAACAGGAGTTTC-3'), ONHBI, targeting nucleotides 1233-1253 of HER-2 mRNA. A 16-fold enhancement of ONHBI emission intensity upon hybridization with the complementary RNA vs that of the oligonucleotide probe alone indicated the presence of target oligonucleotide and proved the intercalation of the chromophore (quantum yield 0.52; brightness 23500 M-1cm-1). Even more, an 11-fold enhancement of ONHBI emission (quantum yield 0.50; brightness 23200 M-1cm-1) was observed when the probe was mixed with total RNA extract from a human cell line that has high levels of HER2 mRNA expression. Thus, we propose ONHBI as a promising probe potentially useful for the sensitive and specific detection of HER2 mRNA breast cancer marker.
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Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Verena Böttner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Eli Varon
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Yaron Shav-Tal
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel.
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Himmelstoß SF, Hirsch T. A critical comparison of lanthanide based upconversion nanoparticles to fluorescent proteins, semiconductor quantum dots, and carbon dots for use in optical sensing and imaging. Methods Appl Fluoresc 2019; 7:022002. [PMID: 30822759 DOI: 10.1088/2050-6120/ab0bfa] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The right choice of a fluorescent probe is essential for successful luminescence imaging and sensing and especially concerning in vivo and in vitro applications, the development of new classes have gained more and more attention in the last years. One of the most promising class are upconversion nanoparticles (UCNPs)-inorganic nanocrystals capable to convert near-infrared light in high energy radiation. In this review we will compare UCNPs with other fluorescent probes in terms of (a) the optical properties of the probes, such as their brightness, photostability and excitation wavelength; (b) their chemical properties such as the dispersibility, stability under experimental or physiological conditions, availability of chemical modification strategies for labelling; and (c) the potential toxicity and biocompatibility of the probe. Thereby we want to provide a better understanding of the advantages and drawbacks of UCNPs and address future challenges in the design of the nanocrystals.
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Affiliation(s)
- Sandy F Himmelstoß
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
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A Strategy to Optimize the Generation of Stable Chromobody Cell Lines for Visualization and Quantification of Endogenous Proteins in Living Cells. Antibodies (Basel) 2019; 8:antib8010010. [PMID: 31544816 PMCID: PMC6640688 DOI: 10.3390/antib8010010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 02/07/2023] Open
Abstract
Single-domain antibodies have emerged as highly versatile nanoprobes for advanced cellular imaging. For real-time visualization of endogenous antigens, fluorescently labelled nanobodies (chromobodies, CBs) are introduced as DNA-encoded expression constructs in living cells. Commonly, CB expression is driven from strong, constitutively active promoters. However, high expression levels are sometimes accompanied by misfolding and aggregation of those intracellular nanoprobes. Moreover, stable cell lines derived from random genomic insertion of CB-encoding transgenes bear the risk of disturbed cellular processes and inhomogeneous CB signal intensities due to gene positioning effects and epigenetic silencing. In this study we propose a strategy to generate optimized CB expressing cell lines. We demonstrate that expression as ubiquitin fusion increases the fraction of intracellularly functional CBs and identified the elongation factor 1α (EF1-α) promoter as highly suited for constitutive CB expression upon long-term cell line cultivation. Finally, we applied a CRISPR/Cas9-based gene editing approach for targeted insertion of CB expression constructs into the adeno-associated virus integration site 1 (AAVS1) safe harbour locus of human cells. Our results indicate that this combinatorial approach facilitates the generation of fully functional and stable CB cell lines for quantitative live-cell imaging of endogenous antigens.
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47
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Li L, Liang J, Luo H, Tam KM, Tse ECM, Li Y. A new chemical approach for proximity labelling of chromatin-associated RNAs and proteins with visible light irradiation. Chem Commun (Camb) 2019; 55:12340-12343. [DOI: 10.1039/c9cc06251c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new nucleus-localized singlet oxygen generator was designed and synthesized.
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Affiliation(s)
- Lan Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Jiying Liang
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Hao Luo
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - K. Ming Tam
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Edmund C. M. Tse
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Ying Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
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Keller BM, Maier J, Secker KA, Egetemaier SM, Parfyonova Y, Rothbauer U, Traenkle B. Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells. Mol Cell Proteomics 2018; 17:2518-2533. [PMID: 30228193 DOI: 10.1074/mcp.tir118.000914] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/04/2018] [Indexed: 11/06/2022] Open
Abstract
Understanding cellular processes requires the determination of dynamic changes in the concentration of genetically nonmodified, endogenous proteins, which, to date, is commonly accomplished by end-point assays in vitro Molecular probes such as fluorescently labeled nanobodies (chromobodies, CBs) are powerful tools to visualize the dynamic subcellular localization of endogenous proteins in living cells. Here, we employed the dependence of intracellular levels of chromobodies on the amount of their endogenous antigens, a phenomenon, which we termed antigen-mediated CB stabilization (AMCBS), for simultaneous monitoring of time-resolved changes in the concentration and localization of native proteins. To improve the dynamic range of AMCBS we generated turnover-accelerated CBs and demonstrated their application in visualization and quantification of fast reversible changes in antigen concentration upon compound treatment by quantitative live-cell imaging. We expect that this broadly applicable strategy will enable unprecedented insights into the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
| | - Julia Maier
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Kathy-Ann Secker
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | | | - Yana Parfyonova
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany; Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany.
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Albakri MB, Jiang Y, Genereaux J, Lajoie P. Polyglutamine toxicity assays highlight the advantages of mScarlet for imaging in Saccharomyces cerevisiae. F1000Res 2018; 7:1242. [PMID: 30631438 PMCID: PMC6290977 DOI: 10.12688/f1000research.15829.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2018] [Indexed: 11/20/2022] Open
Abstract
Development of fluorescent proteins (FPs) enabled researchers to visualize protein localization and trafficking in living cells and organisms. The extended palette of available FPs allows simultaneous detection of multiple fluorescent fusion proteins. Importantly, FPs are originally derived from different organisms from jelly fish to corals and each FP displays its own biophysical properties. Among these properties, the tendency of FPs to oligomerize inherently affects the behavior of its fusion partner. Here we employed the budding yeast Saccharomyces cerevisiae to determine the impact of the latest generation of red FPs on their binding partner. We used a yeast assay based on the aggregation and toxicity of misfolded polyQ expansion proteins linked to Huntington's disease. Since polyQ aggregation and toxicity are highly dependent on the sequences flanking the polyQ region, polyQ expansions provide an ideal tool to assess the impact of FPs on their fusion partners. We found that unlike what is observed for green FP variants, yemRFP and yFusionRed-tagged polyQ expansions show reduced toxicity. However, polyQ expansions tagged with the bright synthetically engineered ymScarlet displayed severe polyQ toxicity. Our data indicate that ymScarlet might have significant advantages over the previous generation of red FPs for use in fluorescent fusions in yeast.
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Affiliation(s)
- Maram B. Albakri
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
| | - Yuwei Jiang
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A5C1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
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50
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Albakri MB, Jiang Y, Genereaux J, Lajoie P. Polyglutamine toxicity assays highlight the advantages of mScarlet for imaging in Saccharomyces cerevisiae. F1000Res 2018; 7:1242. [PMID: 30631438 PMCID: PMC6290977 DOI: 10.12688/f1000research.15829.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/03/2018] [Indexed: 10/05/2023] Open
Abstract
Development of fluorescent proteins (FPs) enabled researchers to visualize protein localization and trafficking in living cells and organisms. The extended palette of available FPs allows simultaneous detection of multiples fluorescent fusion proteins. Importantly, FPs are originally derived from different organisms from jelly fish to corals and each FP display its own biophysical properties. Among these properties, the tendency of FPs to oligomerize inherently affects the behavior of its fusion partner. Here we employed the budding yeast Saccharomyces cerevisiae to determine the impact of the latest generation of red FPs on their binding partner. We used a yeast assay based on the aggregation and toxicity of misfolded polyQ expansion proteins linked to Huntington's disease. Since polyQ aggregation and toxicity are highly dependent on the sequences flanking the polyQ region, polyQ expansions provide an ideal tool to assess the impact of FPs on their fusion partners. We found that unlike yemRFP and yFusionRed, the synthetically engineered ymScarlet displayed severe polyQ toxicity and aggregation similar to what is observed for green FP variants. Our data indicate that ymScarlet might have significant advantages over the previous generation of red FPs for use in fluorescent fusions in yeast.
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Affiliation(s)
- Maram B. Albakri
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
| | - Yuwei Jiang
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A5C1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A5C1, Canada
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