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Nishida H, Albero AB, Onoue K, Ikegawa Y, Sulekh S, Sakizli U, Minami Y, Yonemura S, Wang YC, Yoo SK. Necrosensor: a genetically encoded fluorescent sensor for visualizing necrosis in Drosophila. Biol Open 2024; 13:bio060104. [PMID: 38156558 PMCID: PMC10836653 DOI: 10.1242/bio.060104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Historically, necrosis has been considered a passive process, which is induced by extreme stress or damage. However, recent findings of necroptosis, a programmed form of necrosis, shed a new light on necrosis. It has been challenging to detect necrosis reliably in vivo, partly due to the lack of genetically encoded sensors to detect necrosis. This is in stark contrast with the availability of many genetically encoded biosensors for apoptosis. Here we developed Necrosensor, a genetically encoded fluorescent sensor that detects necrosis in Drosophila, by utilizing HMGB1, which is released from the nucleus as a damage-associated molecular pattern (DAMP). We demonstrate that Necrosensor is able to detect necrosis induced by various stresses in multiple tissues in both live and fixed conditions. Necrosensor also detects physiological necrosis that occurs during spermatogenesis in the testis. Using Necrosensor, we discovered previously unidentified, physiological necrosis of hemocyte progenitors in the hematopoietic lymph gland of developing larvae. This work provides a new transgenic system that enables in vivo detection of necrosis in real time without any intervention.
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Affiliation(s)
- Hiroshi Nishida
- Division of Cell Physiology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, 650-0047, Japan
| | | | - Kenta Onoue
- Laboratory for Ultrastructural Research, RIKEN BDR, Kobe, 650-0047, Japan
| | - Yuko Ikegawa
- Laboratory of Molecular Cell Biology and Development, Kyoto University, Kobe, 650-0047, Japan
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
| | - Shivakshi Sulekh
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
- Division of Developmental Biology and Regenerative Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0047, Japan
| | - Ugurcan Sakizli
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
- Division of Developmental Biology and Regenerative Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0047, Japan
| | - Yasuhiro Minami
- Division of Cell Physiology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan
| | - Shigenobu Yonemura
- Laboratory for Ultrastructural Research, RIKEN BDR, Kobe, 650-0047, Japan
- Department of Cell Biology, Tokushima University Graduate School of Medicine, Tokushima, 770-8503, Japan
| | - Yu-Chiun Wang
- Laboratory for Epithelial Morphogenesis, RIKEN BDR, Kobe, 650-0047, Japan
| | - Sa Kan Yoo
- Physiological Genetics Laboratory, RIKEN CPR, Kobe, 650-0047, Japan
- Laboratory for Homeodynamics, RIKEN BDR, Kobe, 650-0047, Japan
- Division of Developmental Biology and Regenerative Medicine, Graduate School of Medicine, Kobe University, Kobe, 650-0047, Japan
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Dezfulian MH, Kula T, Pranzatelli T, Kamitaki N, Meng Q, Khatri B, Perez P, Xu Q, Chang A, Kohlgruber AC, Leng Y, Jupudi AA, Joachims ML, Chiorini JA, Lessard CJ, Farris AD, Muthuswamy SK, Warner BM, Elledge SJ. TScan-II: A genome-scale platform for the de novo identification of CD4 + T cell epitopes. Cell 2023; 186:5569-5586.e21. [PMID: 38016469 PMCID: PMC10841602 DOI: 10.1016/j.cell.2023.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/12/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023]
Abstract
CD4+ T cells play fundamental roles in orchestrating immune responses and tissue homeostasis. However, our inability to associate peptide human leukocyte antigen class-II (HLA-II) complexes with their cognate T cell receptors (TCRs) in an unbiased manner has hampered our understanding of CD4+ T cell function and role in pathologies. Here, we introduce TScan-II, a highly sensitive genome-scale CD4+ antigen discovery platform. This platform seamlessly integrates the endogenous HLA-II antigen-processing machinery in synthetic antigen-presenting cells and TCR signaling in T cells, enabling the simultaneous screening of multiple HLAs and TCRs. Leveraging genome-scale human, virome, and epitope mutagenesis libraries, TScan-II facilitates de novo antigen discovery and deep exploration of TCR specificity. We demonstrate TScan-II's potential for basic and translational research by identifying a non-canonical antigen for a cancer-reactive CD4+ T cell clone. Additionally, we identified two antigens for clonally expanded CD4+ T cells in Sjögren's disease, which bind distinct HLAs and are expressed in HLA-II-positive ductal cells within affected salivary glands.
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Affiliation(s)
- Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Tomasz Kula
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Thomas Pranzatelli
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Qingda Meng
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bhuwan Khatri
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Paola Perez
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Qikai Xu
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Aiquan Chang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ayano C Kohlgruber
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ananth Aditya Jupudi
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Departmentment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michelle L Joachims
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - John A Chiorini
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Christopher J Lessard
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - A Darise Farris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Departmentment of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Senthil K Muthuswamy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Blake M Warner
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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3
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To TL, Li X, Shu X. Spying on SARS-CoV-2 with Fluorescent Tags and Protease Reporters. Viruses 2023; 15:2005. [PMID: 37896782 PMCID: PMC10612051 DOI: 10.3390/v15102005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The SARS-CoV-2 coronavirus has caused worldwide disruption through the COVID-19 pandemic, providing a sobering reminder of the profound impact viruses can have on human well-being. Understanding virus life cycles and interactions with host cells lays the groundwork for exploring therapeutic strategies against virus-related diseases. Fluorescence microscopy plays a vital role in virus imaging, offering high spatiotemporal resolution, sensitivity, and spectroscopic versatility. In this opinion piece, we first highlight two recent techniques, SunTag and StayGold, for the in situ imaging of viral RNA translation and viral assembly. Next, we discuss a new class of genetically encoded fluorogenic protease reporters, such as FlipGFP, which can be customized to monitor SARS-CoV-2's main (Mpro) or papain-like (PLpro) protease activity. These assays have proven effective in identifying potential antivirals through high-throughput screening, making fluorogenic viral protease reporters a promising platform for viral disease diagnostics and therapeutics.
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Affiliation(s)
| | - Xiaoquan Li
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, UC San Francisco, San Francisco, CA 94158, USA
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4
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Zhou K, Litfin T, Solayman M, Zhao H, Zhou Y, Zhan J. High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing. Int J Biol Macromol 2022; 203:543-552. [PMID: 35120933 DOI: 10.1016/j.ijbiomac.2022.01.173] [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: 08/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Splitting a protein at a position may lead to self- or assisted-complementary fragments depending on whether two resulting fragments can reconstitute to maintain the native function spontaneously or require assistance from two interacting molecules. Assisted complementary fragments with high contrast are an important tool for probing biological interactions. However, only a small number of assisted-complementary split-variants have been identified due to manual, labour-intensive optimization of a candidate gene. Here, we introduce a technique for high-throughput split-protein profiling (HiTS) that allows fast identification of self- and assisted complementary positions by transposon mutagenesis, a rapamycin-regulated FRB-FKBP protein interaction pair, and deep sequencing. We test this technique by profiling three antibiotic-resistant genes (fosfomycin-resistant gene, fosA3, erythromycin-resistant gene, ermB, and chloramphenicol-resistant gene, catI). Self- and assisted complementary fragments discovered by the high-throughput technique were subsequently confirmed by low-throughput testing of individual split positions. Thus, the HiTS technique provides a quicker alternative for discovering the proteins with suitable self- and assisted-complementary split positions when combining with a readout such as fluorescence, bioluminescence, cell survival, gene transcription or genome editing.
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Affiliation(s)
- Kai Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Thomas Litfin
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Md Solayman
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
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5
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Gerber PP, Duncan LM, Greenwood EJD, Marelli S, Naamati A, Teixeira-Silva A, Crozier TWM, Gabaev I, Zhan JR, Mulroney TE, Horner EC, Doffinger R, Willis AE, Thaventhiran JED, Protasio AV, Matheson NJ. A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection. PLoS Pathog 2022; 18:e1010265. [PMID: 35143592 PMCID: PMC8865646 DOI: 10.1371/journal.ppat.1010265] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 02/23/2022] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Efforts to define serological correlates of protection against COVID-19 have been hampered by the lack of a simple, scalable, standardised assay for SARS-CoV-2 infection and antibody neutralisation. Plaque assays remain the gold standard, but are impractical for high-throughput screening. In this study, we show that expression of viral proteases may be used to quantitate infected cells. Our assays exploit the cleavage of specific oligopeptide linkers, leading to the activation of cell-based optical biosensors. First, we characterise these biosensors using recombinant SARS-CoV-2 proteases. Next, we confirm their ability to detect viral protease expression during replication of authentic virus. Finally, we generate reporter cells stably expressing an optimised luciferase-based biosensor, enabling viral infection to be measured within 24 h in a 96- or 384-well plate format, including variants of concern. We have therefore developed a luminescent SARS-CoV-2 reporter cell line, and demonstrated its utility for the relative quantitation of infectious virus and titration of neutralising antibodies.
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Affiliation(s)
- Pehuén Pereyra Gerber
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Lidia M. Duncan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Edward JD Greenwood
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sara Marelli
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Adi Naamati
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ana Teixeira-Silva
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Thomas WM Crozier
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ildar Gabaev
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jun R. Zhan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | | | - Emily C. Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Anne E. Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - James ED Thaventhiran
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- MRC Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Anna V. Protasio
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J. Matheson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
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6
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Asensio T, Dian C, Boyer JB, Rivière F, Meinnel T, Giglione C. A Continuous Assay Set to Screen and Characterize Novel Protein N-Acetyltransferases Unveils Rice General Control Non-repressible 5-Related N-Acetyltransferase2 Activity. FRONTIERS IN PLANT SCIENCE 2022; 13:832144. [PMID: 35273627 PMCID: PMC8902505 DOI: 10.3389/fpls.2022.832144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 05/19/2023]
Abstract
Protein N-acetyltransferases (NATs) belong to the general control non-repressible 5 (Gcn5)-related N-acetyltransferases (GNATs) superfamily. GNATs catalyze the transfer of acetyl from acetyl-CoA to the reactive amine moiety of a wide range of acceptors. NAT sequences are difficult to distinguish from other members of the GNAT superfamily and there are many uncharacterized GNATs. To facilitate the discovery and characterization of new GNATs, we have developed a new continuous, non-radioactive assay. This assay is virtually independent of the substrate and can be used to get substrate specificity hints. We validated first the assay with the well-characterized Schizosaccharomyces pombe NatA (SpNatA). The SpNatA kinetic parameters were determined with various peptides confirming the robustness of the new assay. We reveal that the longer the peptide substrate the more efficient the enzyme. As a proof of concept of the relevance of the new assay, we characterized a NAA90 member from rice (Oryza sativa), OsGNAT2. We took advantage of an in vivo medium-scale characterization of OsGNAT2 specificity to identify and then validate in vitro several specific peptide substrates. With this assay, we reveal long-range synergic effects of basic residues on OsGNAT2 activity. Overall, this new, high-throughput assay allows better understanding of the substrate specificity and activity of any GNAT.
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Pe KBA, Yatsuzuka K, Hakariya H, Kida T, Katsuda Y, Fukuda M, Sato SI. RNA-based cooperative protein labeling that permits direct monitoring of the intracellular concentration change of an endogenous protein. Nucleic Acids Res 2021; 49:e132. [PMID: 34581825 PMCID: PMC8682759 DOI: 10.1093/nar/gkab839] [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: 02/01/2021] [Revised: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Imaging the dynamics of proteins in living cells is a powerful means for understanding cellular functions at a deeper level. Here, we report a versatile method for spatiotemporal imaging of specific endogenous proteins in living mammalian cells. The method employs a bifunctional aptamer capable of selective protein recognition and fluorescent probe-binding, which is induced only when the aptamer specifically binds to its target protein. An aptamer for β-actin protein preferentially recognizes its monomer forms over filamentous forms, resulting in selective G-actin staining in both fixed and living cells. Through actin-drug treatment, the method permitted direct monitoring of the intracellular concentration change of endogenous G-actin. This protein-labeling method, which is highly selective and non-covalent, provides rich insights into the study of spatiotemporal protein dynamics in living cells.
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Affiliation(s)
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hayase Hakariya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masatora Fukuda
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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8
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Zhang JF, Mehta S, Zhang J. Signaling Microdomains in the Spotlight: Visualizing Compartmentalized Signaling Using Genetically Encoded Fluorescent Biosensors. Annu Rev Pharmacol Toxicol 2021; 61:587-608. [PMID: 33411579 DOI: 10.1146/annurev-pharmtox-010617-053137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
How cells muster a network of interlinking signaling pathways to faithfully convert diverse external cues to specific functional outcomes remains a central question in biology. Through their ability to convert dynamic biochemical activities to rapid and precise optical readouts, genetically encoded fluorescent biosensors have become instrumental in unraveling the molecular logic controlling the specificity of intracellular signaling. In this review, we discuss how the use of genetically encoded fluorescent biosensors to visualize dynamic signaling events within their native cellular context is elucidating the different strategies employed by cells to organize signaling activities into discrete compartments, or signaling microdomains, to ensure functional specificity.
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Affiliation(s)
- Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA; .,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA;
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA; .,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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9
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Rusu AD, Cornhill ZE, Coutiño BC, Uribe MC, Lourdusamy A, Markus Z, May ST, Rahman R, Georgiou M. CG7379 and ING1 suppress cancer cell invasion by maintaining cell-cell junction integrity. Open Biol 2021; 11:210077. [PMID: 34493070 PMCID: PMC8424350 DOI: 10.1098/rsob.210077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Approximately 90% of cancer-related deaths can be attributed to a tumour's ability to spread. We have identified CG7379, the fly orthologue of human ING1, as a potent invasion suppressor. ING1 is a type II tumour suppressor with well-established roles in the transcriptional regulation of genes that control cell proliferation, response to DNA damage, oncogene-induced senescence and apoptosis. Recent work suggests a possible role for ING1 in cancer cell invasion and metastasis, but the molecular mechanism underlying this observation is lacking. Our results show that reduced expression of CG7379 promotes invasion in vivo in Drosophila, reduces the junctional localization of several adherens and septate junction components, and severely disrupts cell-cell junction architecture. Similarly, ING1 knockdown significantly enhances invasion in vitro and disrupts E-cadherin distribution at cell-cell junctions. A transcriptome analysis reveals that loss of ING1 affects the expression of several junctional and cytoskeletal modulators, confirming ING1 as an invasion suppressor and a key regulator of cell-cell junction integrity.
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Affiliation(s)
- Alexandra D. Rusu
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Zoe E. Cornhill
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Brenda Canales Coutiño
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK,Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Anbarasu Lourdusamy
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zsuzsa Markus
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Sean T. May
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Ruman Rahman
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Marios Georgiou
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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10
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Habif M, Corbat AA, Silberberg M, Grecco HE. CASPAM: A Triple-Modality Biosensor for Multiplexed Imaging of Caspase Network Activity. ACS Sens 2021; 6:2642-2653. [PMID: 34191492 DOI: 10.1021/acssensors.1c00554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding signal propagation across biological networks requires to simultaneously monitor the dynamics of several nodes to uncover correlations masked by inherent intercellular variability. To monitor the enzymatic activity of more than two components over short time scales has proven challenging. Exploiting the narrow spectral width of homo-FRET-based biosensors, up to three activities can be imaged through fluorescence polarization anisotropy microscopy. We introduce Caspase Activity Sensor by Polarization Anisotropy Multiplexing (CASPAM) a single-plasmid triple-modality reporter of key nodes of the apoptotic network. Apoptosis provides an ideal molecular framework to study interactions between its three composing pathways (intrinsic, extrinsic, and effector). We characterized the biosensor performance and demonstrated the advantages that equimolar expression has in both simplifying experimental procedure and reducing observable variation, thus enabling robust data-driven modeling. Tools like CASPAM become essential to analyze molecular pathways where multiple nodes need to be simultaneously monitored.
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Affiliation(s)
- Martín Habif
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Agustín A. Corbat
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Mauro Silberberg
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Hernán E. Grecco
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
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11
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Abstract
Apoptosis is a process in which cells are genetically regulated to cause a series of changes in morphology and metabolic activity, which ultimately lead to cell death. Apoptosis plays a vital role in the entire life cycle of an organism. Too much or too little apoptosis can cause a variety of diseases. Therefore, efficient and convenient methods for detecting apoptosis are necessary for clinical treatment and drug development. Traditional methods for detecting apoptosis may cause damage to the body during sample collection, such as for flow cytometry analysis. So it is necessary to monitor apoptosis without invasion in vivo. Optical imaging technique provides a more sensitive and economical way for apoptosis visualization. A subset of engineered reporter genes based on fluorescent proteins or luciferases are currently developed to monitor the dynamic changes in apoptotic markers, such as activation of caspases and exposure of phosphatidylserine on the surface of dying cells. These reporters detect apoptosis when cells have not undergone significant morphological changes, providing conditions for early diagnosis of tumors. In addition, these reporters show considerable value in high-throughput screening of apoptosis-related drugs and evaluation of their efficacy in treating tumors. In this review, we will discuss the recent research progress in the optical imaging of apoptosis based on the genetically encoded reporter genes.
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12
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Davis ZH, Mediani L, Antoniani F, Vinet J, Li S, Alberti S, Lu B, Holehouse AS, Carra S, Brandman O. Protein products of nonstop mRNA disrupt nucleolar homeostasis. Cell Stress Chaperones 2021; 26:549-561. [PMID: 33619693 PMCID: PMC8065075 DOI: 10.1007/s12192-021-01200-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
Stalled mRNA translation results in the production of incompletely synthesized proteins that are targeted for degradation by ribosome-associated quality control (RQC). Here we investigated the fate of defective proteins translated from stall-inducing, nonstop mRNA that escape ubiquitylation by the RQC protein LTN1. We found that nonstop protein products accumulated in nucleoli and this localization was driven by polylysine tracts produced by translation of the poly(A) tails of nonstop mRNA. Nucleolar sequestration increased the solubility of invading proteins but disrupted nucleoli, altering their dynamics, morphology, and resistance to stress in cell culture and intact flies. Our work elucidates how stalled translation may affect distal cellular processes and may inform studies on the pathology of diseases caused by failures in RQC and characterized by nucleolar stress.
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Affiliation(s)
- Zoe H Davis
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Laura Mediani
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio, Emilia, Modena, Italy
| | - Francesco Antoniani
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio, Emilia, Modena, Italy
| | - Jonathan Vinet
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio, Emilia, Modena, Italy
| | - Shuangxi Li
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universitat Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - Bingwei Lu
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Serena Carra
- Centre for Neuroscience and Nanotechnology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio, Emilia, Modena, Italy.
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
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13
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Yoshikawa M, Yoshii T, Ikuta M, Tsukiji S. Synthetic Protein Condensates That Inducibly Recruit and Release Protein Activity in Living Cells. J Am Chem Soc 2021; 143:6434-6446. [PMID: 33890764 DOI: 10.1021/jacs.0c12375] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Compartmentation of proteins into biomolecular condensates or membraneless organelles formed by phase separation is an emerging principle for the regulation of cellular processes. Creating synthetic condensates that accommodate specific intracellular proteins on demand would have various applications in chemical biology, cell engineering, and synthetic biology. Here, we report the construction of synthetic protein condensates capable of recruiting and/or releasing proteins of interest in living mammalian cells in response to a small molecule or light. By a modular combination of a tandem fusion of two oligomeric proteins, which forms phase-separated synthetic protein condensates in cells, with a chemically induced dimerization tool, we first created a chemogenetic protein condensate system that can rapidly recruit target proteins from the cytoplasm to the condensates by addition of a small-molecule dimerizer. We next coupled the protein-recruiting condensate system with an engineered proximity-dependent protease, which gave a second protein condensate system wherein target proteins previously expressed inside the condensates are released into the cytoplasm by small-molecule-triggered protease recruitment. Furthermore, an optogenetic condensate system that allows reversible release and sequestration of protein activity in a repeatable manner using light was constructed successfully. These condensate systems were applicable to control protein activity and cellular processes such as membrane ruffling and ERK signaling in a time scale of minutes. This proof-of-principle work provides a new platform for chemogenetic and optogenetic control of protein activity in mammalian cells and represents a step toward tailor-made engineering of synthetic protein condensate-based soft materials with various functionalities for biological and biomedical applications.
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Affiliation(s)
- Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiro Ikuta
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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14
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Liu L, Downs M, Guidry J, Wojcik EJ. Inter-organelle interactions between the ER and mitotic spindle facilitates Zika protease cleavage of human Kinesin-5 and results in mitotic defects. iScience 2021; 24:102385. [PMID: 33997675 PMCID: PMC8100630 DOI: 10.1016/j.isci.2021.102385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/21/2021] [Accepted: 03/30/2021] [Indexed: 12/03/2022] Open
Abstract
Here we identify human Kinesin-5, Kif11/HsEg5, as a cellular target of Zika protease. We show that Zika NS2B-NS3 protease targets several sites within the motor domain of HsEg5 irrespective of motor binding to microtubules. The native integral ER-membrane protease triggers mitotic spindle positioning defects and a prolonged metaphase delay in cultured cells. Our data support a model whereby loss of function of HsEg5 is mediated by Zika protease and is spatially restricted to the ER-mitotic spindle interface during mitosis. The resulting phenotype is distinct from the monopolar phenotype that typically results from uniform inhibition of HsEg5 by RNAi or drugs. In addition, our data reveal novel inter-organelle interactions between the mitotic apparatus and the surrounding reticulate ER network. Given that Kif11 is haplo-insufficient in humans, and reduced dosage results in microcephaly, we propose that Zika protease targeting of HsEg5 may be a key event in the etiology of Zika syndrome microcephaly. Zika protease cleavage of Kinesin-5 impairs mitotic progression Inter-organelle interactions spatially control Zika proteolysis of Kinesin-5 Native Zika protease affects mitosis differently than soluble Zika protease Zika protease may elicit fetal microcephaly and blindness via Kif11/Kinesin-5
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Affiliation(s)
- Liqiong Liu
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, New Orleans, LA 70112, USA
| | - Micquel Downs
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, New Orleans, LA 70112, USA
| | - Jesse Guidry
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, New Orleans, LA 70112, USA
- The Proteomics Core Facility, LSU School of Medicine & Health Sciences Center, New Orleans, LA 70112, USA
| | - Edward J Wojcik
- Department of Biochemistry and Molecular Biology, LSU School of Medicine & Health Sciences Center, New Orleans, LA 70112, USA
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15
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Chin MY, Espinosa JA, Pohan G, Markossian S, Arkin MR. Reimagining dots and dashes: Visualizing structure and function of organelles for high-content imaging analysis. Cell Chem Biol 2021; 28:320-337. [PMID: 33600764 PMCID: PMC7995685 DOI: 10.1016/j.chembiol.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022]
Abstract
Organelles are responsible for biochemical and cellular processes that sustain life and their dysfunction causes diseases from cancer to neurodegeneration. While researchers are continuing to appreciate new roles of organelles in disease, the rapid development of specifically targeted fluorescent probes that report on the structure and function of organelles will be critical to accelerate drug discovery. Here, we highlight four organelles that collectively exemplify the progression of phenotypic discovery, starting with mitochondria, where many functional probes have been described, then continuing with lysosomes and Golgi and concluding with nascently described membraneless organelles. We introduce emerging probe designs to explore organelle-specific morphology and dynamics and highlight recent case studies using high-content analysis to stimulate further development of probes and approaches for organellar high-throughput screening.
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Affiliation(s)
- Marcus Y Chin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Jether Amos Espinosa
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Grace Pohan
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.
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16
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Abstract
Engineered biocircuits designed with biological components have the capacity to expand and augment living functions. Here we demonstrate that proteases can be integrated into digital or analog biocircuits to process biological information. We first construct peptide-caged liposomes that treat protease activity as two-valued (i.e., signal is 0 or 1) operations to construct the biological equivalent of Boolean logic gates, comparators and analog-to-digital converters. We use these modules to assemble a cell-free biocircuit that can combine with bacteria-containing blood, quantify bacteria burden, and then calculate and unlock a selective drug dose. By contrast, we treat protease activity as multi-valued (i.e., signal is between 0 and 1) by controlling the degree to which a pool of enzymes is shared between two target substrates. We perform operations on these analog values by manipulating substrate concentrations and combine these operations to solve the mathematical problem Learning Parity with Noise (LPN). These results show that protease activity can be used to process biological information by binary Boolean logic, or as multi-valued analog signals under conditions where substrate resources are shared.
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Affiliation(s)
- Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, 30332, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, GA, 30332, USA.
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA, 30332, USA.
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA, 30332, USA.
- Integrated Cancer Research Center, Georgia Tech, Atlanta, GA, 30332, USA.
- The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, 30332, USA.
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17
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Zhou X, Mehta S, Zhang J. Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks. Trends Biochem Sci 2020; 45:889-905. [PMID: 32660810 PMCID: PMC7502535 DOI: 10.1016/j.tibs.2020.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Cell signaling networks are intricately regulated in time and space to determine the responses and fates of cells to different cues. Genetically encodable fluorescent and bioluminescent biosensors enable the direct visualization of these spatiotemporal signaling dynamics within the native biological context, and have therefore become powerful molecular tools whose unique benefits are being used to address challenging biological questions. We first review the basis of biosensor design and remark on recent technologies that are accelerating biosensor development. We then discuss a few of the latest advances in the development and application of genetically encodable fluorescent and bioluminescent biosensors that have led to scientific or technological breakthroughs.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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18
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Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
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19
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Huey J, Keutler K, Schultz C. Chemical Biology Toolbox for Studying Pancreatic Islet Function - A Perspective. Cell Chem Biol 2020; 27:1015-1031. [PMID: 32822616 DOI: 10.1016/j.chembiol.2020.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/10/2020] [Accepted: 07/28/2020] [Indexed: 01/14/2023]
Abstract
The islets of Langerhans represent one of the many complex endocrine organs in mammals. Traditionally, islet function is studied by a mixture of physiological, cell biological, and molecular biological methods. Recently, novel techniques stemming from the ever-increasing toolbox provided by chemical laboratories have been added to the repertoire. Many emerging techniques will soon be available to manipulate and monitor islet function at the single-cell level and potentially in intact model animals, as well as in isolated human islets. Here, we review the most current small-molecule-based and genetically encoded molecular tool sets available to study islet function. We provide an outlook regarding future tool developments that will impact islet research, with a special focus on the interplay between different islet cell types.
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Affiliation(s)
- Julia Huey
- Program in Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97210, USA; Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97210, USA
| | - Kaya Keutler
- Program in Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97210, USA; Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97210, USA
| | - Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97210, USA.
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20
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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21
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Canales Coutiño B, Cornhill ZE, Couto A, Mack NA, Rusu AD, Nagarajan U, Fan YN, Hadjicharalambous MR, Castellanos Uribe M, Burrows A, Lourdusamy A, Rahman R, May ST, Georgiou M. A Genetic Analysis of Tumor Progression in Drosophila Identifies the Cohesin Complex as a Suppressor of Individual and Collective Cell Invasion. iScience 2020; 23:101237. [PMID: 32629605 PMCID: PMC7317029 DOI: 10.1016/j.isci.2020.101237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023] Open
Abstract
Metastasis is the leading cause of death for patients with cancer. Consequently it is imperative that we improve our understanding of the molecular mechanisms that underlie progression of tumor growth toward malignancy. Advances in genome characterization technologies have been very successful in identifying commonly mutated or misregulated genes in a variety of human cancers. However, the difficulty in evaluating whether these candidates drive tumor progression remains a major challenge. Using the genetic amenability of Drosophila melanogaster we generated tumors with specific genotypes in the living animal and carried out a detailed systematic loss-of-function analysis to identify conserved genes that enhance or suppress epithelial tumor progression. This enabled the discovery of functional cooperative regulators of invasion and the establishment of a network of conserved invasion suppressors. This includes constituents of the cohesin complex, whose loss of function either promotes individual or collective cell invasion, depending on the severity of effect on cohesin complex function. Screen identifies genes that affect tumor behavior in a wide variety of ways A functionally validated network of invasion-suppressor genes was generated Loss of cohesin complex function can promote individual or collective cell invasion The fly pupal notum is an excellent in vivo system to study tumor progression
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Affiliation(s)
| | - Zoe E Cornhill
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Africa Couto
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Natalie A Mack
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Alexandra D Rusu
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Usha Nagarajan
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Department of Biochemistry, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana, 123029, India
| | - Yuen Ngan Fan
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PL, UK
| | - Marina R Hadjicharalambous
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, UK
| | | | - Amy Burrows
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | | | - Ruman Rahman
- School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Sean T May
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Marios Georgiou
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
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22
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Kula T, Dezfulian MH, Wang CI, Abdelfattah NS, Hartman ZC, Wucherpfennig KW, Lyerly HK, Elledge SJ. T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes. Cell 2020; 178:1016-1028.e13. [PMID: 31398327 PMCID: PMC6939866 DOI: 10.1016/j.cell.2019.07.009] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/20/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
T cell recognition of specific antigens mediates protection from pathogens and controls neoplasias, but can also cause autoimmunity. Our knowledge of T cell antigens and their implications for human health is limited by the technical limitations of T cell profiling technologies. Here, we present T-Scan, a high-throughput platform for identification of antigens productively recognized by T cells. T-Scan uses lentiviral delivery of antigen libraries into cells for endogenous processing and presentation on major histocompatibility complex (MHC) molecules. Target cells functionally recognized by T cells are isolated using a reporter for granzyme B activity, and the antigens mediating recognition are identified by next-generation sequencing. We show T-Scan correctly identifies cognate antigens of T cell receptors (TCRs) from viral and human genome-wide libraries. We apply T-Scan to discover new viral antigens, perform high-resolution mapping of TCR specificity, and characterize the reactivity of a tumor-derived TCR. T-Scan is a powerful approach for studying T cell responses.
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Affiliation(s)
- Tomasz Kula
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Charlotte I Wang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Nouran S Abdelfattah
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Zachary C Hartman
- Departments of Surgery and Pathology, Duke University Medical Center, 571 Research Drive, Suite 433, Box 2606, Durham, NC 27710, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Herbert Kim Lyerly
- Departments of Surgery, Immunology, and Pathology, Duke University Medical Center, 571 Research Drive, Suite 433, Box 2606, Durham, NC 27710, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA.
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23
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Li J, Li B, Sun J, Ma C, Wan S, Li Y, Göstl R, Herrmann A, Liu K, Zhang H. Engineered Near-Infrared Fluorescent Protein Assemblies for Robust Bioimaging and Therapeutic Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2000964. [PMID: 32162422 DOI: 10.1002/adma.202000964] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 05/21/2023]
Abstract
Fluorescent proteins are investigated extensively as markers for the imaging of cells and tissues that are treated by gene transfection. However, limited transfection efficiency and lack of targeting restrict the clinical application of this method rooted in the challenging development of robust fluorescent proteins for in vivo bioimaging. To address this, a new type of near-infrared (NIR) fluorescent protein assemblies manufactured by genetic engineering is presented. Due to the formation of well-defined nanoparticles and spectral operation within the phototherapeutic window, the NIR protein aggregates allow stable and specific tumor imaging via simple exogenous injection. Importantly, in vivo tumor metastases are tracked and this overcomes the limitations of in vivo imaging that can only be implemented relying on the gene transfection of fluorescent proteins. Concomitantly, the efficient loading of hydrophobic drugs into the protein nanoparticles is demonstrated facilitating the therapy of tumors in a mouse model. It is believed that these theranostic NIR fluorescent protein assemblies, hence, show great potential for the in vivo detection and therapy of cancer.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Bo Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Jing Sun
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Chao Ma
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - Sikang Wan
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Yuanxin Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Robert Göstl
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, Aachen, 52056, Germany
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, Aachen, 52056, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
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24
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Lee H, Kim SJ, Shin H, Kim YP. Collagen-Immobilized Extracellular FRET Reporter for Visualizing Protease Activity Secreted by Living Cells. ACS Sens 2020; 5:655-664. [PMID: 32036648 DOI: 10.1021/acssensors.9b01456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the diverse roles of cell-secreted proteases in the extracellular matrix (ECM), classical methods to analyze protease activity have not been explored at the cell culture site. Here, we report a stable, matrix-sticky, and protease-sensitive extracellular reporter that comprises a collagen-binding protein and a Förster resonance energy transfer (FRET) coupler of an enhanced green fluorescent protein and a small dye molecule. The extracellular FRET reporter via split intein-mediated protein trans-splicing is able to adhere to collagen matrices, leading to fluorescence changes by matrix metalloproteinase-2 (MMP2) activity during living cell culture without impeding cell viability. When a proMMP2 mutant (Y581A) with altered protease secretion and activity was transfected into cancer cells, the reporter revealed a dramatic reduction in MMP2 activity in both two- and three-dimensional culture systems, compared with cells transfected with wild-type proMMP2. Our reporter is immediately amenable to monitor protease activity in diverse ECM-resident cells as well as to study protease-related extracellular signaling and tissue remodeling.
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Affiliation(s)
- Hawon Lee
- Department of Life Science, BK21 Plus Bio-Defense Research Team, Hanyang University, Seoul 04763, Republic of Korea
| | - Se-jeong Kim
- Department of Bioengineering, BK21 Plus Future Biopharmaceutical Human Resources Training and Research Team, Hanyang University, Seoul 04763, Republic of Korea
| | - Heungsoo Shin
- Department of Bioengineering, BK21 Plus Future Biopharmaceutical Human Resources Training and Research Team, Hanyang University, Seoul 04763, Republic of Korea
- Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea
| | - Young-Pil Kim
- Department of Life Science, BK21 Plus Bio-Defense Research Team, Hanyang University, Seoul 04763, Republic of Korea
- Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea
- Research Institute for Natural Sciences and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
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25
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Jia H, Song Y, Huang B, Ge W, Luo KQ. Engineered Sensor Zebrafish for Fast Detection and Real-Time Tracking of Apoptosis at Single-Cell Resolution in Live Animals. ACS Sens 2020; 5:823-830. [PMID: 32090557 DOI: 10.1021/acssensors.9b02489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Apoptosis plays crucial roles during development and in disease conditions. While there are some methods to detect apoptosis in vitro, most of them are end-point assays that cannot be used to detect apoptosis in the physiological context of live animals. In this study, transgenic sensor zebrafish were generated that specifically produce a fluorescence resonance energy transfer (FRET)-based biosensor in the zebrafish skin. Under normal conditions, the skin cells of the sensor zebrafish emit green fluorescence; when caspase-3 is activated during apoptosis, the skin cells of the sensor zebrafish switch to emitting blue fluorescence. Through time-lapse FRET imaging with the sensor zebrafish, we observed that caspase-3 can be activated within 5 min and apoptosis can be completed in around 30 min in live zebrafish, no matter the apoptosis occurs several hours after UV irradiation or during the normal development. Using the sensor zebrafish, we found that apoptosis can occur in different parts of the zebrafish skin including the skin covering the trunk, eye, yolk sac, and head during development. Interestingly, we observed that the yolk sac diameter of the zebrafish reduced from 723.8 ± 25.1 μm at 24 h postfertilization (hpf) to 346.1 ± 24.6 μm at 120 hpf. To accommodate this dramatic reduction of the yolk sac size, we found that some excess skin cells on the surface of the yolk sac were removed by apoptosis during this process. The sensor zebrafish provide a powerful and convenient tool for the noninvasive and real-time detection of apoptosis at the single-cell resolution in live zebrafish.
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Affiliation(s)
- Hao Jia
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Yanlong Song
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Bin Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Wei Ge
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Kathy Qian Luo
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
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26
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Timms RT, Zhang Z, Rhee DY, Harper JW, Koren I, Elledge SJ. A glycine-specific N-degron pathway mediates the quality control of protein N-myristoylation. Science 2020; 365:365/6448/eaaw4912. [PMID: 31273098 DOI: 10.1126/science.aaw4912] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/29/2019] [Accepted: 05/15/2019] [Indexed: 12/21/2022]
Abstract
The N-terminal residue influences protein stability through N-degron pathways. We used stability profiling of the human N-terminome to uncover multiple additional features of N-degron pathways. In addition to uncovering extended specificities of UBR E3 ligases, we characterized two related Cullin-RING E3 ligase complexes, Cul2ZYG11B and Cul2ZER1, that act redundantly to target N-terminal glycine. N-terminal glycine degrons are depleted at native N-termini but strongly enriched at caspase cleavage sites, suggesting roles for the substrate adaptors ZYG11B and ZER1 in protein degradation during apoptosis. Furthermore, ZYG11B and ZER1 were found to participate in the quality control of N-myristoylated proteins, in which N-terminal glycine degrons are conditionally exposed after a failure of N-myristoylation. Thus, an additional N-degron pathway specific for glycine regulates the stability of metazoan proteomes.
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Affiliation(s)
- Richard T Timms
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhiqian Zhang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David Y Rhee
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Itay Koren
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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27
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Eschliman K, Bossmann SH. Protease-Activated Sensors for In Vivo Imaging of Cell Populations. Methods Mol Biol 2020; 2126:117-126. [PMID: 32112384 DOI: 10.1007/978-1-0716-0364-2_11] [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: 06/10/2023]
Abstract
Biosensors are important devices that can be used to obtain information from within a living organism. They can be implanted within living tissues in order to continuously monitor for changes. This allows for personalized, noninvasive medicine, since a baseline can be more accurately established and any deviations, even slight, can be detected. These devices have applications in the treatment of diseases such as diabetes and cancer, as well as the study of pathways of interest and tailored drug dosing. Proteases within the tumor microenvironment can be studied in vivo in order to indicate the effectiveness of treatments received. This unprecedented real-time information is extremely valuable as it can be used to alter the course of treatment accordingly.
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Affiliation(s)
- Kayla Eschliman
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Stefan H Bossmann
- Department of Chemistry and Johnson Cancer Center, Kansas State University, Manhattan, KS, USA.
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28
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Péresse T, Gautier A. Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging. Int J Mol Sci 2019; 20:E6142. [PMID: 31817528 PMCID: PMC6940837 DOI: 10.3390/ijms20246142] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.
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Affiliation(s)
- Tiphaine Péresse
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
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29
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Shu X. Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters. Curr Opin Chem Biol 2019; 54:1-9. [PMID: 31678813 DOI: 10.1016/j.cbpa.2019.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/08/2019] [Accepted: 09/19/2019] [Indexed: 12/27/2022]
Abstract
Dynamical features of cell signaling are the essence of living organisms. To understand animal development, it is fundamental to investigate signaling dynamics in vivo. Robust reporters are required to visualize spatial and temporal dynamics of enzyme activities and protein-protein interactions involved in signaling pathways. In this review, we summarize recent development in the design of new classes of fluorescent reporters for imaging dynamic activities of proteases, kinases, and protein-protein interactions. These reporters operate on new physical and/or chemical principles; achieve large dynamic range, high brightness, and fast kinetics; and reveal spatiotemporal dynamics of signaling that is correlated with developmental events such as embryonic morphogenesis in live animals including Drosophila and zebrafish. Therefore, many of these reporters are great tools for biological discovery and mechanistic understanding of animal development and disease progression.
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Affiliation(s)
- Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA, United States; Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA, United States.
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30
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Zhuang Q, Holt BA, Kwong GA, Qiu P. Deconvolving multiplexed protease signatures with substrate reduction and activity clustering. PLoS Comput Biol 2019; 15:e1006909. [PMID: 31479443 PMCID: PMC6743790 DOI: 10.1371/journal.pcbi.1006909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 09/13/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
Proteases are multifunctional, promiscuous enzymes that degrade proteins as well as peptides and drive important processes in health and disease. Current technology has enabled the construction of libraries of peptide substrates that detect protease activity, which provides valuable biological information. An ideal library would be orthogonal, such that each protease only hydrolyzes one unique substrate, however this is impractical due to off-target promiscuity (i.e., one protease targets multiple different substrates). Therefore, when a library of probes is exposed to a cocktail of proteases, each protease activates multiple probes, producing a convoluted signature. Computational methods for parsing these signatures to estimate individual protease activities primarily use an extensive collection of all possible protease-substrate combinations, which require impractical amounts of training data when expanding to search for more candidate substrates. Here we provide a computational method for estimating protease activities efficiently by reducing the number of substrates and clustering proteases with similar cleavage activities into families. We envision that this method will be used to extract meaningful diagnostic information from biological samples. The activity of enzymatic proteins, which are called proteases, drives numerous important processes in health and disease: including cancer, immunity, and infectious disease. Many labs have developed useful diagnostics by designing sensors that measure the activity of these proteases. However, if we want to detect multiple proteases at the same time, it becomes impractical to design sensors that only detect one protease. This is due to a phenomenon called protease promiscuity, which means that proteases will activate multiple different sensors. Computational methods have been created to solve this problem, but the challenge is that these often require large amounts of training data. Further, completely different proteases may be detected by the same subset of sensors. In this work, we design a computational method to overcome this problem by clustering similar proteases into "subfamilies", which increases estimation accuracy. Further, our method tests multiple combinations of sensors to maintain accuracy while minimizing the number of sensors used. Together, we envision that this work will increase the amount of useful information we can extract from biological samples, which may lead to better clinical diagnostics.
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Affiliation(s)
- Qinwei Zhuang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia, United States of America
| | - Gabriel A. Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia, United States of America
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Integrated Cancer Research Center, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Georgia ImmunoEngineering Consortium, Georgia Tech and Emory University, Atlanta, Georgia, United States of America
- * E-mail: (GAK); (PQ)
| | - Peng Qiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, Atlanta, Georgia, United States of America
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (GAK); (PQ)
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31
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Karasev MM, Stepanenko OV, Rumyantsev KA, Turoverov KK, Verkhusha VV. Near-Infrared Fluorescent Proteins and Their Applications. BIOCHEMISTRY (MOSCOW) 2019; 84:S32-S50. [PMID: 31213194 DOI: 10.1134/s0006297919140037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
High transparency, low light-scattering, and low autofluorescence of mammalian tissues in the near-infrared (NIR) spectral range (~650-900 nm) open a possibility for in vivo imaging of biological processes at the micro- and macroscales to address basic and applied problems in biology and biomedicine. Recently, probes that absorb and fluoresce in the NIR optical range have been engineered using bacterial phytochromes - natural NIR light-absorbing photoreceptors that regulate metabolism in bacteria. Since the chromophore in all these proteins is biliverdin, a natural product of heme catabolism in mammalian cells, they can be used as genetically encoded fluorescent probes, similarly to GFP-like fluorescent proteins. In this review, we discuss photophysical and biochemical properties of NIR fluorescent proteins, reporters, and biosensors and analyze their characteristics required for expression of these molecules in mammalian cells. Structural features and molecular engineering of NIR fluorescent probes are discussed. Applications of NIR fluorescent proteins and biosensors for studies of molecular processes in cells, as well as for tissue and organ visualization in whole-body imaging in vivo, are described. We specifically focus on the use of NIR fluorescent probes in advanced imaging technologies that combine fluorescence and bioluminescence methods with photoacoustic tomography.
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Affiliation(s)
- M M Karasev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Medicum, University of Helsinki, Helsinki, 00290, Finland
| | - O V Stepanenko
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - K A Rumyantsev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - K K Turoverov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - V V Verkhusha
- Medicum, University of Helsinki, Helsinki, 00290, Finland. .,Albert Einstein College of Medicine, Bronx, NY 10461, USA
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32
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Fernández-Fernández ÁD, Van der Hoorn RAL, Gevaert K, Van Breusegem F, Stael S. Caught green-handed: methods for in vivo detection and visualization of protease activity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2125-2141. [PMID: 30805604 DOI: 10.1093/jxb/erz076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Proteases are enzymes that cleave peptide bonds of other proteins. Their omnipresence and diverse activities make them important players in protein homeostasis and turnover of the total cell proteome as well as in signal transduction in plant stress responses and development. To understand protease function, it is of paramount importance to assess when and where a specific protease is active. Here, we review the existing methods to detect in vivo protease activity by means of imaging chemical activity-based probes and genetically encoded sensors. We focus on the diverse fluorescent and luminescent sensors at the researcher's disposal and evaluate the potential of imaging techniques to deliver in vivo spatiotemporal detail of protease activity. We predict that in the coming years, revised techniques will help to elucidate plant protease activity and functions and hence expand the current status of the field.
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Affiliation(s)
- Álvaro Daniel Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
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33
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Zhang Q, Schepis A, Huang H, Yang J, Ma W, Torra J, Zhang SQ, Yang L, Wu H, Nonell S, Dong Z, Kornberg TB, Coughlin SR, Shu X. Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals. J Am Chem Soc 2019; 141:4526-4530. [PMID: 30821975 PMCID: PMC6486793 DOI: 10.1021/jacs.8b13042] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A family of proteases called caspases mediate apoptosis signaling in animals. We report a GFP-based fluorogenic protease reporter, dubbed "FlipGFP", by flipping a beta strand of the GFP. Upon protease activation and cleavage, the beta strand is restored, leading to reconstitution of the GFP and fluorescence. FlipGFP-based TEV protease reporter achieves 100-fold fluorescence change. A FlipGFP-based executioner caspase reporter visualized apoptosis in live zebrafish embryos with spatiotemporal resolution. FlipGFP also visualized apoptotic cells in the midgut of Drosophila. Thus, the FlipGFP-based caspase reporter will be useful for monitoring apoptosis during animal development and for designing reporters of proteases beyond caspases. The design strategy can be further applied to a red fluorescent protein for engineering a red fluorogenic protease reporter.
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Affiliation(s)
- Qiang Zhang
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94158, United States
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Antonino Schepis
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Hai Huang
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94158, United States
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Wen Ma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Joaquim Torra
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94158, United States
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
- institut Quimic de Sarria, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Shao-Qing Zhang
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - Lina Yang
- Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Haifan Wu
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94158, United States
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Santi Nonell
- institut Quimic de Sarria, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Zhiqiang Dong
- Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Thomas B. Kornberg
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Shaun R. Coughlin
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California 94158, United States
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, California 94158, United States
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Glial ensheathment of the somatodendritic compartment regulates sensory neuron structure and activity. Proc Natl Acad Sci U S A 2019; 116:5126-5134. [PMID: 30804200 DOI: 10.1073/pnas.1814456116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sensory neurons perceive environmental cues and are important of organismal survival. Peripheral sensory neurons interact intimately with glial cells. While the function of axonal ensheathment by glia is well studied, less is known about the functional significance of glial interaction with the somatodendritic compartment of neurons. Herein, we show that three distinct glia cell types differentially wrap around the axonal and somatodendritic surface of the polymodal dendritic arborization (da) neuron of the Drosophila peripheral nervous system for detection of thermal, mechanical, and light stimuli. We find that glial cell-specific loss of the chromatin modifier gene dATRX in the subperineurial glial layer leads to selective elimination of somatodendritic glial ensheathment, thus allowing us to investigate the function of such ensheathment. We find that somatodendritic glial ensheathment regulates the morphology of the dendritic arbor, as well as the activity of the sensory neuron, in response to sensory stimuli. Additionally, glial ensheathment of the neuronal soma influences dendritic regeneration after injury.
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35
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Zlobovskaya OA, Shirmanova MV, Kovaleva TF, Sarkisyan KS, Zagaynova EV, Lukyanov KA. Sensors for Caspase Activities. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162018060109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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37
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Baena-Lopez LA, Arthurton L, Bischoff M, Vincent JP, Alexandre C, McGregor R. Novel initiator caspase reporters uncover previously unknown features of caspase-activating cells. Development 2018; 145:dev170811. [PMID: 30413561 PMCID: PMC6288387 DOI: 10.1242/dev.170811] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
Abstract
The caspase-mediated regulation of many cellular processes, including apoptosis, justifies the substantial interest in understanding all of the biological features of these enzymes. To complement functional assays, it is crucial to identify caspase-activating cells in live tissues. Our work describes novel initiator caspase reporters that, for the first time, provide direct information concerning the initial steps of the caspase activation cascade in Drosophila tissues. One of our caspase sensors capitalises on the rapid subcellular localisation change of a fluorescent marker to uncover novel cellular apoptotic events relating to the actin-mediated positioning of the nucleus before cell delamination. The other construct benefits from caspase-induced nuclear translocation of a QF transcription factor. This feature enables the genetic manipulation of caspase-activating cells and reveals the spatiotemporal patterns of initiator caspase activity. Collectively, our sensors offer experimental opportunities not available by using previous reporters and have proven useful to illuminate previously unknown aspects of caspase-dependent processes in apoptotic and non-apoptotic cellular scenarios.
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Affiliation(s)
- Luis Alberto Baena-Lopez
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxfordshire, OX1 3RE, UK
| | - Lewis Arthurton
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxfordshire, OX1 3RE, UK
| | - Marcus Bischoff
- Biomolecular Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, Scotland, KY16 9ST, UK
| | | | | | - Reuben McGregor
- Faculty of Medical and Health Sciences, Molecular Medicine & Pathology, The University of Auckland, M&HS Building 502, 85 Park Road, Grafton, Auckland 1023, New Zealand
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38
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Gao XJ, Chong LS, Kim MS, Elowitz MB. Programmable protein circuits in living cells. Science 2018; 361:1252-1258. [PMID: 30237357 DOI: 10.1126/science.aat5062] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.
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Affiliation(s)
- Xiaojing J Gao
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lucy S Chong
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Kim
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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39
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Baena-Lopez LA, Arthurton L, Xu DC, Galasso A. Non-apoptotic Caspase regulation of stem cell properties. Semin Cell Dev Biol 2018; 82:118-126. [PMID: 29102718 PMCID: PMC6191935 DOI: 10.1016/j.semcdb.2017.10.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 12/13/2022]
Abstract
The evolutionarily conserved family of proteins called caspases are the main factors mediating the orchestrated programme of cell suicide known as apoptosis. Since this protein family was associated with this essential biological function, the majority of scientific efforts were focused towards understanding their molecular activation and function during cell death. However, an emerging body of evidence has highlighted a repertoire of non-lethal roles within a large variety of cell types, including stem cells. Here we intend to provide a comprehensive overview of the key role of caspases as regulators of stem cell properties. Finally, we briefly discuss the possible pathological consequences of caspase malfunction in stem cells, and the therapeutic potential of caspase regulation applied to this context.
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Affiliation(s)
| | - Lewis Arthurton
- University of Oxford, Sir William Dunn School of Pathology, Oxford, OX13RE, United Kingdom
| | - Derek Cui Xu
- University of Oxford, Sir William Dunn School of Pathology, Oxford, OX13RE, United Kingdom
| | - Alessia Galasso
- University of Oxford, Sir William Dunn School of Pathology, Oxford, OX13RE, United Kingdom
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40
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Gautier A, Tebo AG. Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing. Bioessays 2018; 40:e1800118. [DOI: 10.1002/bies.201800118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
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41
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Shcherbakova DM, Stepanenko OV, Turoverov KK, Verkhusha VV. Near-Infrared Fluorescent Proteins: Multiplexing and Optogenetics across Scales. Trends Biotechnol 2018; 36:1230-1243. [PMID: 30041828 DOI: 10.1016/j.tibtech.2018.06.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
Since mammalian tissue is relatively transparent to near-infrared (NIR) light, NIR fluorescent proteins (FPs) engineered from bacterial phytochromes have become widely used probes for non-invasive in vivo imaging. Recently, these genetically encoded NIR probes have been substantially improved, enabling imaging experiments that were not possible previously. Here, we discuss the use of monomeric NIR FPs and NIR biosensors for multiplexed imaging with common visible GFP-based probes and blue light-activatable optogenetic tools. These NIR probes are suitable for visualization of functional activities from molecular to organismal levels. In combination with advanced imaging techniques, such as two-photon microscopy with adaptive optics, photoacoustic tomography and its recent modification reversibly switchable photoacoustic computed tomography, NIR probes allow subcellular resolution at millimeter depths.
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Affiliation(s)
- Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation; Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland.
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42
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Xu DC, Arthurton L, Baena-Lopez LA. Learning on the Fly: The Interplay between Caspases and Cancer. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5473180. [PMID: 29854765 PMCID: PMC5949197 DOI: 10.1155/2018/5473180] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/14/2018] [Indexed: 02/07/2023]
Abstract
The ease of genetic manipulation, as well as the evolutionary conservation of gene function, has placed Drosophila melanogaster as one of the leading model organisms used to understand the implication of many proteins with disease development, including caspases and their relation to cancer. The family of proteases referred to as caspases have been studied over the years as the major regulators of apoptosis: the most common cellular mechanism involved in eliminating unwanted or defective cells, such as cancerous cells. Indeed, the evasion of the apoptotic programme resulting from caspase downregulation is considered one of the hallmarks of cancer. Recent investigations have also shown an instrumental role for caspases in non-lethal biological processes, such as cell proliferation, cell differentiation, intercellular communication, and cell migration. Importantly, malfunction of these essential biological tasks can deeply impact the initiation and progression of cancer. Here, we provide an extensive review of the literature surrounding caspase biology and its interplay with many aspects of cancer, emphasising some of the key findings obtained from Drosophila studies. We also briefly describe the therapeutic potential of caspase modulation in relation to cancer, highlighting shortcomings and hopeful promises.
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Affiliation(s)
- Derek Cui Xu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX13RE, UK
- Cell Biology Section, National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lewis Arthurton
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX13RE, UK
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43
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Tang HM, Fung MC, Tang HL. Detecting Anastasis In Vivo by CaspaseTracker Biosensor. J Vis Exp 2018. [PMID: 29443051 DOI: 10.3791/54107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Anastasis (Greek for "rising to life") is a recently discovered cell recovery phenomenon whereby dying cells can reverse late-stage cell death processes that are generally assumed to be intrinsically irreversible. Promoting anastasis could in principle rescue or preserve injured cells that are difficult to replace such as cardiomyocytes or neurons, thereby facilitating tissue recovery. Conversely, suppressing anastasis in cancer cells, undergoing apoptosis after anti-cancer therapies, may ensure cancer cell death and reduce the chances of recurrence. However, these studies have been hampered by the lack of tools for tracking the fate of cells that undergo anastasis in live animals. The challenge is to identify the cells that have reversed the cell death process despite their morphologically normal appearance after recovery. To overcome this difficulty, we have developed Drosophila and mammalian CaspaseTracker biosensor systems that can identify and permanently track the anastatic cells in vitro or in vivo. Here, we present in vivo protocols for the generation and use of the CaspaseTracker dual biosensor system to detect and track anastasis in Drosophila melanogaster after transient exposure to cell death stimuli. While conventional biosensors and protocols can label cells actively undergoing apoptotic cell death, the CaspaseTracker biosensor can permanently label cells that have recovered after caspase activation - a hallmark of late-stage apoptosis, and simultaneously identify active apoptotic processes. This biosensor can also track the recovery of the cells that attempted other forms of cell death that directly or indirectly involved caspase activity. Therefore, this protocol enables us to continuously track the fate of these cells and their progeny, facilitating future studies of the biological functions, molecular mechanisms, physiological and pathological consequences, and therapeutic implications of anastasis. We also discuss the appropriate controls to distinguish cells that undergo anastasis from those that display non-apoptotic caspase activity in vivo.
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Affiliation(s)
- Ho Man Tang
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine; School of Life Sciences, Chinese University of Hong Kong;
| | - Ming Chiu Fung
- School of Life Sciences, Chinese University of Hong Kong;
| | - Ho Lam Tang
- Department of Neurosurgery, Johns Hopkins University School of Medicine;
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44
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Sakamoto T, Hasegawa D, Fujimoto K. Disassembly-driven signal turn-on probes for bimodal detection of DNA with 19F NMR and fluorescence. Org Biomol Chem 2018; 16:7157-7162. [DOI: 10.1039/c8ob02218f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembling molecular probes that can detect DNA in a 19F NMR and fluorescence signal turn-on manner were successfully developed.
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Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| | - Daisaku Hasegawa
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
| | - Kenzo Fujimoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi
- Japan
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45
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Rational Design of a GFP-Based Fluorogenic Caspase Reporter for Imaging Apoptosis In Vivo. Cell Chem Biol 2017; 23:875-882. [PMID: 27447051 DOI: 10.1016/j.chembiol.2016.06.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 12/22/2022]
Abstract
Fluorescence resonance energy transfer-based executioner caspase reporters using GFP are important tools for imaging apoptosis. While these reporters are useful for imaging apoptosis in cultured cells, their in vivo application has been handicapped by poor signal to noise. Here, we report the design and characterization of a GFP-based fluorogenic protease reporter, dubbed ZipGFP. ZipGFP-based TEV protease reporter increased fluorescence 10-fold after activation by protease. A ZipGFP-based executioner caspase reporter visualized apoptosis in live zebrafish embryos with spatiotemporal resolution. Thus, the ZipGFP-based caspase reporter may be useful for monitoring apoptosis during animal development and for designing reporters of proteases beyond the executioner caspases.
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46
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To TL, Shu X. Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity. Biochemistry 2017; 56:5163-5164. [PMID: 28915023 DOI: 10.1021/acs.biochem.7b00788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Tsz-Leung To
- Broad Institute , Cambridge, Massachusetts 02139, United States
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California San Francisco , San Francisco, California 94158, United States
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47
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Schott S, Ambrosini A, Barbaste A, Benassayag C, Gracia M, Proag A, Rayer M, Monier B, Suzanne M. A fluorescent toolkit for spatiotemporal tracking of apoptotic cells in living Drosophila tissues. Development 2017; 144:3840-3846. [PMID: 28870988 DOI: 10.1242/dev.149807] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/29/2017] [Indexed: 02/01/2023]
Abstract
Far from being passive, apoptotic cells influence their environment. For example, they promote tissue folding, myoblast fusion and modulate tumor growth. Understanding the role of apoptotic cells necessitates their efficient tracking within living tissues, a task that is currently challenging. In order to easily spot apoptotic cells in developing Drosophila tissues, we generated a series of fly lines expressing different fluorescent sensors of caspase activity. We show that three of these reporters (GFP-, Cerulean- and Venus-derived molecules) are detected specifically in apoptotic cells and throughout the whole process of programmed cell death. These reporters allow the specific visualization of apoptotic cells directly within living tissues, without any post-acquisition processing. They overcome the limitations of other apoptosis detection methods developed so far and, notably, they can be combined with any kind of fluorophore.
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Affiliation(s)
- Sonia Schott
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Arnaud Ambrosini
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Audrey Barbaste
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Corinne Benassayag
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Mélanie Gracia
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Amsha Proag
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Mégane Rayer
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Bruno Monier
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Magali Suzanne
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 118 route de Narbonne, 31062 Toulouse, France
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48
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Improved split fluorescent proteins for endogenous protein labeling. Nat Commun 2017; 8:370. [PMID: 28851864 PMCID: PMC5575300 DOI: 10.1038/s41467-017-00494-8] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/30/2017] [Indexed: 12/22/2022] Open
Abstract
Self-complementing split fluorescent proteins (FPs) have been widely used for protein labeling, visualization of subcellular protein localization, and detection of cell–cell contact. To expand this toolset, we have developed a screening strategy for the direct engineering of self-complementing split FPs. Via this strategy, we have generated a yellow–green split-mNeonGreen21–10/11 that improves the ratio of complemented signal to the background of FP1–10-expressing cells compared to the commonly used split GFP1–10/11; as well as a 10-fold brighter red-colored split-sfCherry21–10/11. Based on split sfCherry2, we have engineered a photoactivatable variant that enables single-molecule localization-based super-resolution microscopy. We have demonstrated dual-color endogenous protein tagging with sfCherry211 and GFP11, revealing that endoplasmic reticulum translocon complex Sec61B has reduced abundance in certain peripheral tubules. These new split FPs not only offer multiple colors for imaging interaction networks of endogenous proteins, but also hold the potential to provide orthogonal handles for biochemical isolation of native protein complexes. Split fluorescent proteins (FPs) have been widely used to visualise proteins in cells. Here the authors develop a screen for engineering new split FPs, and report a yellow-green split-mNeonGreen2 with reduced background, a red split-sfCherry2 for multicolour labeling, and its photoactivatable variant for super-resolution use.
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49
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Oliinyk OS, Chernov KG, Verkhusha VV. Bacterial Phytochromes, Cyanobacteriochromes and Allophycocyanins as a Source of Near-Infrared Fluorescent Probes. Int J Mol Sci 2017; 18:E1691. [PMID: 28771184 PMCID: PMC5578081 DOI: 10.3390/ijms18081691] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial photoreceptors absorb light energy and transform it into intracellular signals that regulate metabolism. Bacterial phytochrome photoreceptors (BphPs), some cyanobacteriochromes (CBCRs) and allophycocyanins (APCs) possess the near-infrared (NIR) absorbance spectra that make them promising molecular templates to design NIR fluorescent proteins (FPs) and biosensors for studies in mammalian cells and whole animals. Here, we review structures, photochemical properties and molecular functions of several families of bacterial photoreceptors. We next analyze molecular evolution approaches to develop NIR FPs and biosensors. We then discuss phenotypes of current BphP-based NIR FPs and compare them with FPs derived from CBCRs and APCs. Lastly, we overview imaging applications of NIR FPs in live cells and in vivo. Our review provides guidelines for selection of existing NIR FPs, as well as engineering approaches to develop NIR FPs from the novel natural templates such as CBCRs.
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Affiliation(s)
- Olena S Oliinyk
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
| | - Konstantin G Chernov
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
| | - Vladislav V Verkhusha
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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50
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Ni Q, Mehta S, Zhang J. Live-cell imaging of cell signaling using genetically encoded fluorescent reporters. FEBS J 2017; 285:203-219. [PMID: 28613457 DOI: 10.1111/febs.14134] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/19/2017] [Accepted: 06/09/2017] [Indexed: 12/31/2022]
Abstract
Synergistic advances in fluorescent protein engineering and live-cell imaging techniques in recent years have fueled the concurrent development and application of genetically encoded fluorescent reporters that are tailored for tracking signaling dynamics in living systems over multiple length and time scales. These biosensors are uniquely suited for this challenging task, owing to their specificity, sensitivity, and versatility, as well as to the noninvasive and nondestructive nature of fluorescence and the power of genetic encoding. Over the past 10 years, a growing number of fluorescent reporters have been developed for tracking a wide range of biological signals in living cells and animals, including second messenger and metabolite dynamics, enzyme activation and activity, and cell cycle progression and neuronal activity. Many of these biosensors are gaining wide use and are proving to be indispensable for unraveling the complex biological functions of individual signaling molecules in their native environment, the living cell, shedding new light on the structural and molecular underpinnings of cell signaling. In this review, we highlight recent advances in protein engineering that are likely to help expand and improve the design and application of these valuable tools. We then turn our focus to specific examples of live-cell imaging using genetically encoded fluorescent reporters as an important platform for advancing our understanding of G protein-coupled receptor signaling and neuronal activity.
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Affiliation(s)
- Qiang Ni
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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