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Tsao KK, Imai S, Chang M, Hario S, Terai T, Campbell RE. The best of both worlds: Chemigenetic fluorescent sensors for biological imaging. Cell Chem Biol 2024:S2451-9456(24)00322-2. [PMID: 39236713 DOI: 10.1016/j.chembiol.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024]
Abstract
Synthetic-based fluorescent chemosensors and protein-based fluorescent biosensors are two well-established classes of tools for visualizing and monitoring biological processes in living tissues. Chemigenetic sensors, created using a combination of both synthetic parts and protein parts, are an emerging class of tools that aims to combine the strengths, and overcome the drawbacks, of traditional chemosensors and biosensors. This review will survey the landscape of strategies used for fluorescent chemigenetic sensor design. These strategies include: attachment of synthetic elements to proteins using in vitro protein conjugation; attachment of synthetic elements to proteins using autonomous protein labeling; and translational incorporation of unnatural amino acids.
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Affiliation(s)
- Kelvin K Tsao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shosei Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Michael Chang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Saaya Hario
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuya Terai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Robert E Campbell
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; CERVO, Brain Research Center and Department of Biochemistry, Microbiology, and Bioinformatics, Université Laval, Québec, QC G1J 2G3, Canada.
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2
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Ji J, Du S, Wang K, Qi Z, Zhang C, Wang R, Bruening G, Wang P, Duanmu D, Fan Q. Cowpea lipid transfer protein 1 regulates plant defense by inhibiting the cysteine protease of cowpea mosaic virus. Proc Natl Acad Sci U S A 2024; 121:e2403424121. [PMID: 39159367 PMCID: PMC11363299 DOI: 10.1073/pnas.2403424121] [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: 02/26/2024] [Accepted: 06/28/2024] [Indexed: 08/21/2024] Open
Abstract
Many virus genomes encode proteases that facilitate infection. The molecular mechanism of plant recognition of viral proteases is largely unexplored. Using the system of Vigna unguiculata and cowpea mosaic virus (CPMV), we identified a cowpea lipid transfer protein (LTP1) which interacts with CPMV-encoded 24KPro, a cysteine protease, but not with the enzymatically inactive mutant 24KPro(C166A). Biochemical assays showed that LTP1 inhibited 24KPro proteolytic cleavage of the coat protein precursor large coat protein-small coat protein. Transient overexpression of LTP1 in cowpea reduced CPMV infection, whereas RNA interference-mediated LTP1 silencing increased CPMV accumulation in cowpea. LTP1 is mainly localized in the apoplast of uninfected plant cells, and after CPMV infection, most of the LTP1 is relocated to intracellular compartments, including chloroplast. Moreover, in stable LTP1-transgenic Nicotiana benthamiana plants, LTP1 repressed soybean mosaic virus (SMV) nuclear inclusion a protease activity, and accumulation of SMV was significantly reduced. We propose that cowpea LTP1 suppresses CPMV and SMV accumulation by directly inhibiting viral cysteine protease activity.
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Affiliation(s)
- Jie Ji
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Shengli Du
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Kun Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Ziyan Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Chunyang Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Rui Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - George Bruening
- Department of Plant Pathology, University of California, Davis, CA95616
| | - Pengwei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Deqiang Duanmu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Qiuling Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan430070, China
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3
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Pedre B. A guide to genetically-encoded redox biosensors: State of the art and opportunities. Arch Biochem Biophys 2024; 758:110067. [PMID: 38908743 DOI: 10.1016/j.abb.2024.110067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Genetically-encoded redox biosensors have become invaluable tools for monitoring cellular redox processes with high spatiotemporal resolution, coupling the presence of the redox-active analyte with a change in fluorescence signal that can be easily recorded. This review summarizes the available fluorescence recording methods and presents an in-depth classification of the redox biosensors, organized by the analytes they respond to. In addition to the fluorescent protein-based architectures, this review also describes the recent advances on fluorescent, chemigenetic-based redox biosensors and other emerging chemigenetic strategies. This review examines how these biosensors are designed, the biosensors sensing mechanism, and their practical advantages and disadvantages.
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Affiliation(s)
- Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU Leuven, Belgium.
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4
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Sheng CQ, Wu SS, Cheng YK, Wu Y, Li YM. Comprehensive review of indicators and techniques for optical mapping of intracellular calcium ions. Cereb Cortex 2024; 34:bhae346. [PMID: 39191664 DOI: 10.1093/cercor/bhae346] [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: 05/01/2024] [Revised: 07/27/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Calcium ions (Ca2+) play crucial roles in almost every cellular process, making the detection of changes in intracellular Ca2+ essential to understanding cell function. The fluorescence indicator method has garnered widespread application due to its exceptional sensitivity, rapid analysis, cost-effectiveness, and user-friendly nature. It has successfully delineated the spatial and temporal dynamics of Ca2+ signaling across diverse cell types. However, it is vital to understand that different indicators have varying levels of accuracy, sensitivity, and stability, making choosing the right inspection method crucial. As optical detection technologies advance, they continually broaden the horizons of scientific inquiry. This primer offers a systematic synthesis of the current fluorescence indicators and optical imaging modalities utilized for the detection of intracellular Ca2+. It elucidates their practical applications and inherent limitations, serving as an essential reference for researchers seeking to identify the most suitable detection methodologies for their calcium-centric investigations.
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Affiliation(s)
- Chu-Qiao Sheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun, Jilin 130012, China
| | - Shuang-Shuang Wu
- Department of Pediatric Hematology, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yong-Kang Cheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yao Wu
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yu-Mei Li
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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5
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Berksoz M, Atilgan C. Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor. Proteins 2024; 92:923-932. [PMID: 38572606 DOI: 10.1002/prot.26688] [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: 12/18/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Genetically encoded fluorescent biosensors (GEFBs) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are revealed only in hindsight when the crystal structures of both ligand-bound and ligand-free forms are available. This makes the development of new biosensors for desired analytes a long trial-and-error process. In the current study, we conducted μs-long all atom molecular dynamics (MD) simulations of a maltose biosensor in both the apo (dark) and holo (bright) forms. We performed detailed hydrogen bond occupancy analyses to shed light on the mechanism of ligand induced conformational change in the sensor protein and its allosteric effect on the chromophore environment. We find that two strong indicators for distinguishing bright and dark states of biosensors are due to substantial changes in hydrogen bond dynamics in the system and solvent accessibility of the chromophore.
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Affiliation(s)
- Melike Berksoz
- Faculty of Engineering and Natural Sciences, Sabanci University, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Turkey
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6
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Das D, Ainavarapu SRK. Protein engineering using circular permutation - structure, function, stability, and applications. FEBS J 2024; 291:3581-3596. [PMID: 38676939 DOI: 10.1111/febs.17146] [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: 10/12/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Hu M, Feng X, Liu Q, Liu S, Huang F, Xu H. The ion channels of endomembranes. Physiol Rev 2024; 104:1335-1385. [PMID: 38451235 DOI: 10.1152/physrev.00025.2023] [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: 06/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The endomembrane system consists of organellar membranes in the biosynthetic pathway [endoplasmic reticulum (ER), Golgi apparatus, and secretory vesicles] as well as those in the degradative pathway (early endosomes, macropinosomes, phagosomes, autophagosomes, late endosomes, and lysosomes). These endomembrane organelles/vesicles work together to synthesize, modify, package, transport, and degrade proteins, carbohydrates, and lipids, regulating the balance between cellular anabolism and catabolism. Large ion concentration gradients exist across endomembranes: Ca2+ gradients for most endomembrane organelles and H+ gradients for the acidic compartments. Ion (Na+, K+, H+, Ca2+, and Cl-) channels on the organellar membranes control ion flux in response to cellular cues, allowing rapid informational exchange between the cytosol and organelle lumen. Recent advances in organelle proteomics, organellar electrophysiology, and luminal and juxtaorganellar ion imaging have led to molecular identification and functional characterization of about two dozen endomembrane ion channels. For example, whereas IP3R1-3 channels mediate Ca2+ release from the ER in response to neurotransmitter and hormone stimulation, TRPML1-3 and TMEM175 channels mediate lysosomal Ca2+ and H+ release, respectively, in response to nutritional and trafficking cues. This review aims to summarize the current understanding of these endomembrane channels, with a focus on their subcellular localizations, ion permeation properties, gating mechanisms, cell biological functions, and disease relevance.
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Affiliation(s)
- Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xinghua Feng
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiang Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Siyu Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Fangqian Huang
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States
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8
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Hara Y, Ichiraku A, Matsuda T, Sakane A, Sasaki T, Nagai T, Horikawa K. High-affinity tuning of single fluorescent protein-type indicators by flexible linker length optimization in topology mutant. Commun Biol 2024; 7:705. [PMID: 38851844 PMCID: PMC11162441 DOI: 10.1038/s42003-024-06394-0] [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: 05/17/2023] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
Genetically encoded Ca2+ indicators (GECIs) are versatile for live imaging of cellular activities. Besides the brightness and dynamic range of signal change of GECIs, Ca2+ affinity is another critical parameter for successful Ca2+ imaging, as the concentration range of Ca2+ dynamics differs from low nanomolar to sub-millimolar depending on the celltype and organism. However, ultrahigh-affinity GECIs, particularly the single fluorescent protein (1FP)-type, are lacking. Here, we report a simple strategy that increases Ca2+ affinity through the linker length optimization in topology mutants of existing 1FP-type GECIs. The resulting ultrahigh-affinity GECIs, CaMPARI-nano, BGECO-nano, and RCaMP-nano (Kd = 17-25 nM), enable unique biological applications, including the detection of low nanomolar Ca2+ dynamics, highlighting active signaling cells, and multi-functional imaging with other second messengers. The linker length optimization in topology mutants could be applied to other 1FP-type indicators of glutamate and potassium, rendering it a widely applicable technique for modulating indicator affinity.
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Affiliation(s)
- Yusuke Hara
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Aya Ichiraku
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Tomoki Matsuda
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Ayuko Sakane
- Department of Biochemistry, Tokushima University Graduate School of Medicine, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Takuya Sasaki
- Department of Biochemistry, Tokushima University Graduate School of Medicine, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Takeharu Nagai
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - Kazuki Horikawa
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan.
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Chen H, Wang S, Cao Y, Lei H. Molecular Force Sensors for Biological Application. Int J Mol Sci 2024; 25:6198. [PMID: 38892386 PMCID: PMC11173168 DOI: 10.3390/ijms25116198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The mechanical forces exerted by cells on their surrounding microenvironment are known as cellular traction forces. These forces play crucial roles in various biological processes, such as tissue development, wound healing and cell functions. However, it is hard for traditional techniques to measure cellular traction forces accurately because their magnitude (from pN to nN) and the length scales over which they occur (from nm to μm) are extremely small. In order to fully understand mechanotransduction, highly sensitive tools for measuring cellular forces are needed. Current powerful techniques for measuring traction forces include traction force microscopy (TFM) and fluorescent molecular force sensors (FMFS). In this review, we elucidate the force imaging principles of TFM and FMFS. Then we highlight the application of FMFS in a variety of biological processes and offer our perspectives and insights into the potential applications of FMFS.
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Affiliation(s)
- Huiyan Chen
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Shouhan Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Hai Lei
- School of Physics, Zhejiang University, Hangzhou 310027, China
- Institute for Advanced Study in Physics, Zhejiang University, Hangzhou 310027, China
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10
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Jiang S, Lin Y, Zheng S. Development of the IMP biosensor for rapid and stable analysis of IMP concentrations in fermentation broth. Biotechnol J 2024; 19:e2400040. [PMID: 38863123 DOI: 10.1002/biot.202400040] [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: 01/17/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
IMP (inosinic acid) is a crucial intermediate in the purine metabolic pathway and is continuously synthesized in all cells. Besides its role as a precursor for DNA and RNA, IMP also plays a critical or essential role in cell growth, energy storage, conversion, and metabolism. In our study, we utilized the circularly permuted fluorescent protein (cpFP) and IMP dehydrogenase to screen and develop the IMP biosensor, IMPCP1. By introducing a mutation in the catalytically active site of IMPCP1, from Cys to Ala, we disrupted its ability to catalyze IMP while retaining its capability to bind to IMP without affecting the IMP concentration in the sample. To immobilize IMPCP1, we employed the SpyCatcher/SpyTag system and securely attached it to Magarose-Epoxy, resulting in the development of the IMP rapid test kit, referred to as IMPTK. The biosensor integrated into IMPTK offers enhanced stability, resistance to degradation activity, and specific recognition of IMP. It is also resistant to peroxides and temperature changes. IMPTK serves as a rapid and stable assay for analyzing IMP concentrations in fermentation broth. Within the linear range of IMP concentrations, it can be utilized as a substitute for HPLC. The IMPTK biosensor provides a reliable and efficient alternative for monitoring IMP levels, offering advantages such as speed, stability, and resistance to environmental factors.
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Affiliation(s)
- Shibo Jiang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P.R. China
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11
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Gonzalez-Ramos A, Puigsasllosas-Pastor C, Arcas-Marquez A, Tornero D. Updated Toolbox for Assessing Neuronal Network Reconstruction after Cell Therapy. Bioengineering (Basel) 2024; 11:487. [PMID: 38790353 PMCID: PMC11118929 DOI: 10.3390/bioengineering11050487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Cell therapy has proven to be a promising treatment for a range of neurological disorders, including Parkinson Disease, drug-resistant epilepsy, and stroke, by restoring function after brain damage. Nevertheless, evaluating the true effectiveness of these therapeutic interventions requires a deep understanding of the functional integration of grafted cells into existing neural networks. This review explores a powerful arsenal of molecular techniques revolutionizing our ability to unveil functional integration of grafted cells within the host brain. From precise manipulation of neuronal activity to pinpoint the functional contribution of transplanted cells by using opto- and chemo-genetics, to real-time monitoring of neuronal dynamics shedding light on functional connectivity within the reconstructed circuits by using genetically encoded (calcium) indicators in vivo. Finally, structural reconstruction and mapping communication pathways between grafted and host neurons can be achieved by monosynaptic tracing with viral vectors. The cutting-edge toolbox presented here holds immense promise for elucidating the impact of cell therapy on neural circuitry and guiding the development of more effective treatments for neurological disorders.
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Affiliation(s)
- Ana Gonzalez-Ramos
- Stanley Center for Psychiatric Research at Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Puigsasllosas-Pastor
- Laboratory of Neural Stem Cells and Brain Damage, Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Ainhoa Arcas-Marquez
- Laboratory of Neural Stem Cells and Brain Damage, Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Daniel Tornero
- Laboratory of Neural Stem Cells and Brain Damage, Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
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12
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Kaczmarczyk A, van Vliet S, Jakob RP, Teixeira RD, Scheidat I, Reinders A, Klotz A, Maier T, Jenal U. A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution. Nat Commun 2024; 15:3920. [PMID: 38724508 PMCID: PMC11082216 DOI: 10.1038/s41467-024-48295-0] [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: 01/18/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Monitoring changes of signaling molecules and metabolites with high temporal resolution is key to understanding dynamic biological systems. Here, we use directed evolution to develop a genetically encoded ratiometric biosensor for c-di-GMP, a ubiquitous bacterial second messenger regulating important biological processes like motility, surface attachment, virulence and persistence. The resulting biosensor, cdGreen2, faithfully tracks c-di-GMP in single cells and with high temporal resolution over extended imaging times, making it possible to resolve regulatory networks driving bimodal developmental programs in different bacterial model organisms. We further adopt cdGreen2 as a simple tool for in vitro studies, facilitating high-throughput screens for compounds interfering with c-di-GMP signaling and biofilm formation. The sensitivity and versatility of cdGreen2 could help reveal c-di-GMP dynamics in a broad range of microorganisms with high temporal resolution. Its design principles could also serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites and antibiotics.
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Affiliation(s)
- Andreas Kaczmarczyk
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| | - Simon van Vliet
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Roman Peter Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | | | - Inga Scheidat
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alberto Reinders
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alexander Klotz
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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13
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Anderson NT, Xie JS, Chacko AN, Liu VL, Fan KC, Mukherjee A. Rational Design of a Circularly Permuted Flavin-Based Fluorescent Protein. Chembiochem 2024; 25:e202300814. [PMID: 38356332 PMCID: PMC11065581 DOI: 10.1002/cbic.202300814] [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: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
Flavin-based fluorescent proteins are oxygen-independent reporters that hold great promise for imaging anaerobic and hypoxic biological systems. In this study, we explored the feasibility of applying circular permutation, a valuable method for the creation of fluorescent sensors, to flavin-based fluorescent proteins. We used rational design and structural data to identify a suitable location for circular permutation in iLOV, a flavin-based reporter derived from A. thaliana. However, relocating the N- and C-termini to this position resulted in a significant reduction in fluorescence. This loss of fluorescence was reversible, however, by fusing dimerizing coiled coils at the new N- and C-termini to compensate for the increase in local chain entropy. Additionally, by inserting protease cleavage sites in circularly permuted iLOV, we developed two protease sensors and demonstrated their application in mammalian cells. In summary, our work establishes the first approach to engineer circularly permuted FbFPs optimized for high fluorescence and further showcases the utility of circularly permuted FbFPs to serve as a scaffold for sensor engineering.
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Affiliation(s)
| | - Jason S. Xie
- Department of Molecular, Cellular, and Developmental Biology
| | | | - Vannie L. Liu
- Department of Molecular, Cellular, and Developmental Biology
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14
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Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
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Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
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15
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Koveal D. Functional principles of genetically encoded fluorescent biosensors for metabolism and their quantitative use. J Neurochem 2024; 168:496-505. [PMID: 37314388 DOI: 10.1111/jnc.15878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
Genetically encoded fluorescent biosensors provide an attractive means of measuring chemical changes in single cells on fast timescales (milliseconds to seconds). While their most prominent application has been in tracking neural activity and neurotransmitter release, there has been growing interest in developing and deploying new versions of these tools to study brain metabolism. However, the careful use of these tools and the interpretation of the data they provide remain challenging. Many biosensors are subject to interferences that can alter sensor responses within a single cell or between cells, producing ambiguous results. This presents a challenge for quantitation and for our ability to accurately interpret sensor responses. This review describes current methods of sensor quantitation, with a focus on cellular interferences that commonly affect sensor performance, ways to avoid false inferences, and recent advances in sensor optimization to make them more robust.
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Affiliation(s)
- Dorothy Koveal
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia, USA
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16
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [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] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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17
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Ohara N, Kawakami N, Arai R, Adachi N, Ikeda A, Senda T, Miyamoto K. Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage. Chem Commun (Camb) 2024; 60:4605-4608. [PMID: 38586927 DOI: 10.1039/d4cc00115j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A split-protein system is a simple approach to introduce new termini which are useful as modification sites in protein engineering, but has been adapted mainly for monomeric proteins. Here we demonstrate the design of split subunits of the 60-mer artificial fusion-protein nanocage TIP60. The subunit fragments successfully reformed the cage structure in the same manner as prior to splitting. One of the newly introduced terminals at the interior surface can be modified using a tag peptide and green fluorescent protein. Therefore, the termini could serve as a versatile modification site for incorporating a wide variety of functional peptides and proteins.
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Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
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18
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Zhang Y, Looger LL. Fast and sensitive GCaMP calcium indicators for neuronal imaging. J Physiol 2024; 602:1595-1604. [PMID: 36811153 DOI: 10.1113/jp283832] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
We review the principles of development and deployment of genetically encoded calcium indicators (GECIs) for the detection of neural activity. Our focus is on the popular GCaMP family of green GECIs, culminating in the recent release of the jGCaMP8 sensors, with dramatically improved kinetics relative to previous generations. We summarize the properties of GECIs in multiple colour channels (blue, cyan, green, yellow, red, far-red) and highlight areas for further improvement. With their low-millisecond rise-times, the jGCaMP8 indicators allow new classes of experiments following neural activity in time frames approaching the underlying computations.
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Affiliation(s)
- Yan Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
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19
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Zhuo Y, Luo B, Yi X, Dong H, Miao X, Wan J, Williams JT, Campbell MG, Cai R, Qian T, Li F, Weber SJ, Wang L, Li B, Wei Y, Li G, Wang H, Zheng Y, Zhao Y, Wolf ME, Zhu Y, Watabe-Uchida M, Li Y. Improved green and red GRAB sensors for monitoring dopaminergic activity in vivo. Nat Methods 2024; 21:680-691. [PMID: 38036855 PMCID: PMC11009088 DOI: 10.1038/s41592-023-02100-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023]
Abstract
Dopamine (DA) plays multiple roles in a wide range of physiological and pathological processes via a large network of dopaminergic projections. To dissect the spatiotemporal dynamics of DA release in both dense and sparsely innervated brain regions, we developed a series of green and red fluorescent G-protein-coupled receptor activation-based DA (GRABDA) sensors using a variety of DA receptor subtypes. These sensors have high sensitivity, selectivity and signal-to-noise ratio with subsecond response kinetics and the ability to detect a wide range of DA concentrations. We then used these sensors in mice to measure both optogenetically evoked and behaviorally relevant DA release while measuring neurochemical signaling in the nucleus accumbens, amygdala and cortex. Using these sensors, we also detected spatially resolved heterogeneous cortical DA release in mice performing various behaviors. These next-generation GRABDA sensors provide a robust set of tools for imaging dopaminergic activity under a variety of physiological and pathological conditions.
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Affiliation(s)
- Yizhou Zhuo
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Bin Luo
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Beijing, China
| | - Xinyang Yi
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Hui Dong
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Beijing, China
| | - Xiaolei Miao
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Department of Anesthesiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jinxia Wan
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Beijing, China
| | - John T Williams
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Malcolm G Campbell
- Center for Brain Science, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Ruyi Cai
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Tongrui Qian
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Fengling Li
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sophia J Weber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Lei Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Peking University, Beijing, China
| | - Bozhi Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yu Wei
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Guochuan Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Yu Zheng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Yulin Zhao
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Marina E Wolf
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Yingjie Zhu
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mitsuko Watabe-Uchida
- Center for Brain Science, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Beijing, China.
- Chinese Institute for Brain Research, Beijing, China.
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
- National Biomedical Imaging Center, Peking University, Beijing, China.
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20
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Bremshey S, Groß J, Renken K, Masseck OA. The role of serotonin in depression-A historical roundup and future directions. J Neurochem 2024. [PMID: 38477031 DOI: 10.1111/jnc.16097] [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: 10/30/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Depression is one of the most common psychiatric disorders worldwide, affecting approximately 280 million people, with probably much higher unrecorded cases. Depression is associated with symptoms such as anhedonia, feelings of hopelessness, sleep disturbances, and even suicidal thoughts. Tragically, more than 700 000 people commit suicide each year. Although depression has been studied for many decades, the exact mechanisms that lead to depression are still unknown, and available treatments only help a fraction of patients. In the late 1960s, the serotonin hypothesis was published, suggesting that serotonin is the key player in depressive disorders. However, this hypothesis is being increasingly doubted as there is evidence for the influence of other neurotransmitters, such as noradrenaline, glutamate, and dopamine, as well as larger systemic causes such as altered activity in the limbic network or inflammatory processes. In this narrative review, we aim to contribute to the ongoing debate on the involvement of serotonin in depression. We will review the evolution of antidepressant treatments, systemic research on depression over the years, and future research applications that will help to bridge the gap between systemic research and neurotransmitter dynamics using biosensors. These new tools in combination with systemic applications, will in the future provide a deeper understanding of the serotonergic dynamics in depression.
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Affiliation(s)
- Svenja Bremshey
- Synthetic Biology, University of Bremen, Bremen, Germany
- Neuropharmacology, University of Bremen, Bremen, Germany
| | - Juliana Groß
- Synthetic Biology, University of Bremen, Bremen, Germany
| | - Kim Renken
- Synthetic Biology, University of Bremen, Bremen, Germany
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21
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Choi HJ, Lee H, Cheong DE, Yoo SK, Lee DE, Kim GJ. Construction and characterization of a functional variant hFGF7 with enhanced properties by circular permutation. Biotechnol J 2024; 19:e2300712. [PMID: 38528341 DOI: 10.1002/biot.202300712] [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: 12/16/2023] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Human fibroblast growth factor 7 (hFGF7) is a member of the paracrine-acting FGF family and mediates various reactions such as wound healing, tissue homeostasis, and liver regeneration. These activities make it a plausible candidate for pharmaceutical applications as a drug. However, the low expression level and stability of the recombinant hFGF7 were known to be major hurdles for further applications. Here, the expression level and stability of hFGF7 were attempted to improve by changing the order of amino acids through circular permutation (CP), thereby expecting an alternative fate according to the N-end rule. CP-hFGF7 variants were constructed systematically by using putative amino acid residues in the loop region that avoided the disruption of the structural integrity especially in the functional motif. Among them, cp-hFGF7115-114 revealed a relatively higher expression level in the soluble fraction than the wild-type hFGF7 and was efficiently purified (7 mg L-1) to apparent homogeneity. The activity and stability of the purified variant cp-hFGF7115-114 were comparable or superior to that of the wild-type hFGF7, thereby strongly suggesting that CP could be an alternative tool for the functional expression of hFGF7 in Escherichia coli.
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Affiliation(s)
- Hye-Ji Choi
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Hanui Lee
- Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Dae-Eun Cheong
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Su-Kyoung Yoo
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Dong-Eun Lee
- Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
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22
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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23
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Wait SJ, Expòsit M, Lin S, Rappleye M, Lee JD, Colby SA, Torp L, Asencio A, Smith A, Regnier M, Moussavi-Harami F, Baker D, Kim CK, Berndt A. Machine learning-guided engineering of genetically encoded fluorescent calcium indicators. NATURE COMPUTATIONAL SCIENCE 2024; 4:224-236. [PMID: 38532137 DOI: 10.1038/s43588-024-00611-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which outperforms the tested sixth-, seventh- and eighth-generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient engineering of proteins for desired biophysical characteristics.
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Affiliation(s)
- Sarah J Wait
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Marc Expòsit
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Davis, CA, USA
| | - Michael Rappleye
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Samuel A Colby
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Lily Torp
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Anthony Asencio
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Annette Smith
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Michael Regnier
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Farid Moussavi-Harami
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Cardiology, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Christina K Kim
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Davis, CA, USA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA, USA.
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24
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Rohner VL, Lamothe-Molina PJ, Patriarchi T. Engineering, applications, and future perspectives of GPCR-based genetically encoded fluorescent indicators for neuromodulators. J Neurochem 2024; 168:163-184. [PMID: 38288673 DOI: 10.1111/jnc.16045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 02/23/2024]
Abstract
This review explores the evolving landscape of G-protein-coupled receptor (GPCR)-based genetically encoded fluorescent indicators (GEFIs), with a focus on their development, structural components, engineering strategies, and applications. We highlight the unique features of this indicator class, emphasizing the importance of both the sensing domain (GPCR structure and activation mechanism) and the reporting domain (circularly permuted fluorescent protein (cpFP) structure and fluorescence modulation). Further, we discuss indicator engineering approaches, including the selection of suitable cpFPs and expression systems. Additionally, we showcase the diversity and flexibility of their application by presenting a summary of studies where such indicators were used. Along with all the advantages, we also focus on the current limitations as well as common misconceptions that arise when using these indicators. Finally, we discuss future directions in indicator engineering, including strategies for screening with increased throughput, optimization of the ligand-binding properties, structural insights, and spectral diversity.
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Affiliation(s)
- Valentin Lu Rohner
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | | | - Tommaso Patriarchi
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
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25
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 PMCID: PMC11324865 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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26
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Kubitschke M, Masseck OA. Illuminating the brain-genetically encoded single wavelength fluorescent biosensors to unravel neurotransmitter dynamics. Biol Chem 2024; 405:55-65. [PMID: 37246368 DOI: 10.1515/hsz-2023-0175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Understanding how neuronal networks generate complex behavior is one of the major goals of Neuroscience. Neurotransmitter and Neuromodulators are crucial for information flow between neurons and understanding their dynamics is the key to unravel their role in behavior. To understand how the brain transmits information and how brain states arise, it is essential to visualize the dynamics of neurotransmitters, neuromodulators and neurochemicals. In the last five years, an increasing number of single-wavelength biosensors either based on periplasmic binding proteins (PBPs) or on G-protein-coupled receptors (GPCR) have been published that are able to detect neurotransmitter release in vitro and in vivo with high spatial and temporal resolution. Here we review and discuss recent progress in the development of these sensors, their limitations and future directions.
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27
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Zhang H, Tian X, Zhang J, Ai HW. Engineering and Characterization of 3-Aminotyrosine-Derived Red Fluorescent Variants of Circularly Permutated Green Fluorescent Protein. BIOSENSORS 2024; 14:54. [PMID: 38275307 PMCID: PMC10813706 DOI: 10.3390/bios14010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Introducing 3-aminotyrosine (aY), a noncanonical amino acid (ncAA), into green fluorescent protein (GFP)-like chromophores shows promise for achieving red-shifted fluorescence. However, inconsistent results, including undesired green fluorescent species, hinder the effectiveness of this approach. In this study, we optimized expression conditions for an aY-derived cpGFP (aY-cpGFP). Key factors like rich culture media and oxygen restriction pre- and post-induction enabled high-yield, high-purity production of the red-shifted protein. We also engineered two variants of aY-cpGFP with enhanced brightness by mutating a few amino acid residues surrounding the chromophore. We further investigated the sensitivity of the aY-derived protein to metal ions, reactive oxygen species (ROS), and reactive nitrogen species (RNS). Incorporating aY into cpGFP had minimal impact on metal ion reactivity but increased the response to RNS. Expanding on these findings, we examined aY-cpGFP expression in mammalian cells and found that reductants in the culture media significantly increased the red-emitting product. Our study indicates that optimizing expression conditions to promote a reduced cellular state proved effective in producing the desired red-emitting product in both E. coli and mammalian cells, while targeted mutagenesis-based protein engineering can further enhance brightness and increase method robustness.
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Affiliation(s)
- Hao Zhang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Xiaodong Tian
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jing Zhang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA; (H.Z.); (X.T.); (J.Z.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- The UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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28
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Lee HN, Lee SE, Inn KS, Seong J. Optical sensing and control of T cell signaling pathways. Front Physiol 2024; 14:1321996. [PMID: 38269062 PMCID: PMC10806162 DOI: 10.3389/fphys.2023.1321996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
T cells regulate adaptive immune responses through complex signaling pathways mediated by T cell receptor (TCR). The functional domains of the TCR are combined with specific antibodies for the development of chimeric antigen receptor (CAR) T cell therapy. In this review, we first overview current understanding on the T cell signaling pathways as well as traditional methods that have been widely used for the T cell study. These methods, however, are still limited to investigating dynamic molecular events with spatiotemporal resolutions. Therefore, genetically encoded biosensors and optogenetic tools have been developed to study dynamic T cell signaling pathways in live cells. We review these cutting-edge technologies that revealed dynamic and complex molecular mechanisms at each stage of T cell signaling pathways. They have been primarily applied to the study of dynamic molecular events in TCR signaling, and they will further aid in understanding the mechanisms of CAR activation and function. Therefore, genetically encoded biosensors and optogenetic tools offer powerful tools for enhancing our understanding of signaling mechanisms in T cells and CAR-T cells.
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Affiliation(s)
- Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technoloy, Seoul, Republic of Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Soo Inn
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jihye Seong
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
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29
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Ejike JO, Sadoine M, Shen Y, Ishikawa Y, Sunal E, Hänsch S, Hamacher AB, Frommer WB, Wudick MM, Campbell RE, Kleist TJ. A Monochromatically Excitable Green-Red Dual-Fluorophore Fusion Incorporating a New Large Stokes Shift Fluorescent Protein. Biochemistry 2024; 63:171-180. [PMID: 38113455 PMCID: PMC10765376 DOI: 10.1021/acs.biochem.3c00451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Genetically encoded sensors enable quantitative imaging of analytes in live cells. Sensors are commonly constructed by combining ligand-binding domains with one or more sensitized fluorescent protein (FP) domains. Sensors based on a single FP can be susceptible to artifacts caused by changes in sensor levels or distribution in vivo. To develop intensiometric sensors with the capacity for ratiometric quantification, dual-FP Matryoshka sensors were generated by using a single cassette with a large Stokes shift (LSS) reference FP nested within the reporter FP (cpEGFP). Here, we present a genetically encoded calcium sensor that employs green apple (GA) Matryoshka technology by incorporating a newly designed red LSSmApple fluorophore. LSSmApple matures faster and provides an optimized excitation spectrum overlap with cpEGFP, allowing for monochromatic coexcitation with blue light. The LSS of LSSmApple results in improved emission spectrum separation from cpEGFP, thereby minimizing fluorophore bleed-through and facilitating imaging using standard dichroic and red FP (RFP) emission filters. We developed an image analysis pipeline for yeast (Saccharomyces cerevisiae) timelapse imaging that utilizes LSSmApple to segment and track cells for high-throughput quantitative analysis. In summary, we engineered a new FP, constructed a genetically encoded calcium indicator (GA-MatryoshCaMP6s), and performed calcium imaging in yeast as a demonstration.
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Affiliation(s)
- J. Obinna Ejike
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
- Cluster
of
Excellence on Plant Sciences, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Mayuri Sadoine
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
| | - Yi Shen
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Canada
| | - Yuuma Ishikawa
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
- Cluster
of
Excellence on Plant Sciences, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Erdem Sunal
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
| | - Sebastian Hänsch
- Heinrich
Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Centre for Advanced
Imaging, Düsseldorf 40225, Germany
| | - Anna B. Hamacher
- Heinrich
Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Centre for Advanced
Imaging, Düsseldorf 40225, Germany
| | - Wolf B. Frommer
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
- Institute
of Transformative Bio-Molecules (WPI-ITbM) Nagoya University, Nagoya 464-8601, Japan
- Cluster
of
Excellence on Plant Sciences, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Michael M. Wudick
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
- Cluster
of
Excellence on Plant Sciences, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Robert E. Campbell
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Canada
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Thomas J. Kleist
- Heinrich
Heine University Düsseldorf, Faculty
of Mathematics and Natural Sciences, Institute for Molecular Physiology, Düsseldorf 40225, Germany
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30
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McMillen A, Chew Y. Neural mechanisms of dopamine function in learning and memory in Caenorhabditis elegans. Neuronal Signal 2024; 8:NS20230057. [PMID: 38572143 PMCID: PMC10987485 DOI: 10.1042/ns20230057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 04/05/2024] Open
Abstract
Research into learning and memory over the past decades has revealed key neurotransmitters that regulate these processes, many of which are evolutionarily conserved across diverse species. The monoamine neurotransmitter dopamine is one example of this, with countless studies demonstrating its importance in regulating behavioural plasticity. However, dopaminergic neural networks in the mammalian brain consist of hundreds or thousands of neurons, and thus cannot be studied at the level of single neurons acting within defined neural circuits. The nematode Caenorhabditis elegans (C. elegans) has an experimentally tractable nervous system with a completely characterized synaptic connectome. This makes it an advantageous system to undertake mechanistic studies into how dopamine encodes lasting yet flexible behavioural plasticity in the nervous system. In this review, we synthesize the research to date exploring the importance of dopaminergic signalling in learning, memory formation, and forgetting, focusing on research in C. elegans. We also explore the potential for dopamine-specific fluorescent biosensors in C. elegans to visualize dopaminergic neural circuits during learning and memory formation in real-time. We propose that the use of these sensors in C. elegans, in combination with optogenetic and other light-based approaches, will further illuminate the detailed spatiotemporal requirements for encoding behavioural plasticity in an accessible experimental system. Understanding the key molecules and circuit mechanisms that regulate learning and forgetting in more compact invertebrate nervous systems may reveal new druggable targets for enhancing memory storage and delaying memory loss in bigger brains.
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Affiliation(s)
- Anna McMillen
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Yee Lian Chew
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, 5042, South Australia, Australia
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31
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Khramova YV, Katrukha VA, Chebanenko VV, Kostyuk AI, Gorbunov NP, Panasenko OM, Sokolov AV, Bilan DS. Reactive Halogen Species: Role in Living Systems and Current Research Approaches. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S90-S111. [PMID: 38621746 DOI: 10.1134/s0006297924140062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 10/04/2023] [Indexed: 04/17/2024]
Abstract
Reactive halogen species (RHS) are highly reactive compounds that are normally required for regulation of immune response, inflammatory reactions, enzyme function, etc. At the same time, hyperproduction of highly reactive compounds leads to the development of various socially significant diseases - asthma, pulmonary hypertension, oncological and neurodegenerative diseases, retinopathy, and many others. The main sources of (pseudo)hypohalous acids are enzymes from the family of heme peroxidases - myeloperoxidase, lactoperoxidase, eosinophil peroxidase, and thyroid peroxidase. Main targets of these compounds are proteins and peptides, primarily methionine and cysteine residues. Due to the short lifetime, detection of RHS can be difficult. The most common approach is detection of myeloperoxidase, which is thought to reflect the amount of RHS produced, but these methods are indirect, and the results are often contradictory. The most promising approaches seem to be those that provide direct registration of highly reactive compounds themselves or products of their interaction with components of living cells, such as fluorescent dyes. However, even such methods have a number of limitations and can often be applied mainly for in vitro studies with cell culture. Detection of reactive halogen species in living organisms in real time is a particularly acute issue. The present review is devoted to RHS, their characteristics, chemical properties, peculiarities of interaction with components of living cells, and methods of their detection in living systems. Special attention is paid to the genetically encoded tools, which have been introduced recently and allow avoiding a number of difficulties when working with living systems.
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Affiliation(s)
- Yuliya V Khramova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Veronika A Katrukha
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Victoria V Chebanenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander I Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | | | - Oleg M Panasenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alexey V Sokolov
- Institute of Experimental Medicine, Saint-Petersburg, 197022, Russia.
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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32
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Sekhon H, Ha JH, Presti MF, Procopio SB, Jarvis AR, Mirsky PO, John AM, Loh SN. Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells. Nat Methods 2023; 20:1920-1929. [PMID: 37945909 PMCID: PMC11080272 DOI: 10.1038/s41592-023-02065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
A grand challenge in biosensor design is to develop a single-molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Here, we created a family of adaptable, turn-on maturation (ATOM) biosensors consisting of a monobody (circularly permuted at one of two positions) or a nanobody (circularly permuted at one of three positions) inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells coexpressing cyan, yellow and red ATOM sensors detected biosensor targets that were specifically localized to various subcellular compartments. Fluorescence activation involved ligand-dependent chromophore maturation with turn-on ratios of up to 62-fold in cells and 100-fold in vitro. Endoplasmic reticulum- and mitochondria-localized ATOM sensors detected ligands that were targeted to those organelles. The ATOM design was validated with three monobodies and one nanobody inserted into distinct fluorescent proteins, suggesting that customized ATOM sensors can be generated quickly.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Spencer B Procopio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ava R Jarvis
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Paige O Mirsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anna M John
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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33
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Rappleye M, Wait SJ, Lee JD, Siebart JC, Torp L, Smith N, Muster J, Matreyek KA, Fowler DM, Berndt A. Optogenetic Microwell Array Screening System: A High-Throughput Engineering Platform for Genetically Encoded Fluorescent Indicators. ACS Sens 2023; 8:4233-4244. [PMID: 37956352 PMCID: PMC10683761 DOI: 10.1021/acssensors.3c01573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Genetically encoded fluorescent indicators (GEFIs) are protein-based optogenetic tools that change their fluorescence intensity when binding specific ligands in cells and tissues. GEFI encoding DNA can be expressed in cell subtypes while monitoring cellular physiological responses. However, engineering GEFIs with physiological sensitivity and pharmacological specificity often requires iterative optimization through trial-and-error mutagenesis while assessing their biophysical function in vitro one by one. Here, the vast mutational landscape of proteins constitutes a significant obstacle that slows GEFI development, particularly for sensors that rely on mammalian host systems for testing. To overcome these obstacles, we developed a multiplexed high-throughput engineering platform called the optogenetic microwell array screening system (Opto-MASS) that functionally tests thousands of GEFI variants in parallel in mammalian cells. Opto-MASS represents the next step for engineering optogenetic tools as it can screen large variant libraries orders of magnitude faster than current methods. We showcase this system by testing over 13,000 dopamine and 21,000 opioid sensor variants. We generated a new dopamine sensor, dMASS1, with a >6-fold signal increase to 100 nM dopamine exposure compared to its parent construct. Our new opioid sensor, μMASS1, has a ∼4.6-fold signal increase over its parent scaffold's response to 500 nM DAMGO. Thus, Opto-MASS can rapidly engineer new sensors while significantly shortening the optimization time for new sensors with distinct biophysical properties.
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Affiliation(s)
- Michael Rappleye
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Sarah J. Wait
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, 3946 W Stevens Way NE, Seattle, Washington 98195, United States
| | - Justin Daho Lee
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
- Molecular
Engineering and Sciences Institute, University
of Washington, 3946 W Stevens Way NE, Seattle, Washington 98195, United States
| | - Jamison C. Siebart
- The Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Dr NW, Atlanta, Georgia 30332, United States
| | - Lily Torp
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Netta Smith
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Jeanot Muster
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
| | - Kenneth A. Matreyek
- Department
of Pathology, Case Western Reserve University
School of Medicine, 2103 Cornell Road, Wolstein Research Building, Cleveland, Ohio 44106, United States
| | - Douglas M. Fowler
- Department
of Genome Sciences, Foege
Building S-250, 3720 15th Ave NE, Seattle, Washington 98195-5065, United States
| | - Andre Berndt
- Department
of Bioengineering, University of Washington, 850 Republican Street, Seattle, Washington 98105, United States
- Institute
of Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, Washington 98109, United States
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34
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Chen Y, Pang S, Li J, Lu Y, Gao C, Xiao Y, Chen M, Wang M, Ren X. Genetically encoded protein sensors for metal ion detection in biological systems: a review and bibliometric analysis. Analyst 2023; 148:5564-5581. [PMID: 37872814 DOI: 10.1039/d3an01412f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Metal ions are indispensable elements in living organisms and are associated with regulating various biological processes. An imbalance in metal ion content can lead to disorders in normal physiological functions of the human body and cause various diseases. Genetically encoded fluorescent protein sensors have the advantages of low biotoxicity, high specificity, and a long imaging time in vivo and have become a powerful tool to visualize or quantify the concentration level of biomolecules in vivo and in vitro, temporal and spatial distribution, and life activity process. This review analyzes the development status and current research hotspots in the field of genetically encoded fluorescent protein sensors by bibliometric analysis. Based on the results of bibliometric analysis, the research progress of genetically encoded fluorescent protein sensors for metal ion detection is reviewed, and the construction strategies, physicochemical properties, and applications of such sensors in biological imaging are summarized.
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Affiliation(s)
- Yuxueyuan Chen
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuChao Pang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Jingya Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yun Lu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chenxia Gao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanyu Xiao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Meiling Chen
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Meng Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin 301617, China
| | - Xiaoliang Ren
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
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Giuraniuc CV, Parkin C, Almeida MC, Fricker M, Shadmani P, Nye S, Wehmeier S, Chawla S, Bedekovic T, Lehtovirta-Morley L, Richards DM, Gow NA, Brand AC. Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans. mBio 2023; 14:e0115723. [PMID: 37750683 PMCID: PMC10653887 DOI: 10.1128/mbio.01157-23] [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: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Intracellular calcium signaling plays an important role in the resistance and adaptation to stresses encountered by fungal pathogens within the host. This study reports the optimization of the GCaMP fluorescent calcium reporter for live-cell imaging of dynamic calcium responses in single cells of the pathogen, Candida albicans, for the first time. Exposure to membrane, osmotic or oxidative stress generated both specific changes in single cell intracellular calcium spiking and longer calcium transients across the population. Repeated treatments showed that calcium dynamics become unaffected by some stresses but not others, consistent with known cell adaptation mechanisms. By expressing GCaMP in mutant strains and tracking the viability of individual cells over time, the relative contributions of key signaling pathways to calcium flux, stress adaptation, and cell death were demonstrated. This reporter, therefore, permits the study of calcium dynamics, homeostasis, and signaling in C. albicans at a previously unattainable level of detail.
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Affiliation(s)
- C. V. Giuraniuc
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - C. Parkin
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - M. C. Almeida
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - M. Fricker
- School of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - P. Shadmani
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - S. Nye
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - S. Wehmeier
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - S. Chawla
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - T. Bedekovic
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - L. Lehtovirta-Morley
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - D. M. Richards
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - N. A. Gow
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - A. C. Brand
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
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36
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Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023; 480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
Abstract
As cell signaling research has advanced, it has become clearer that signal transduction has complex spatiotemporal regulation that goes beyond foundational linear transduction models. Several technologies have enabled these discoveries, including fluorescent biosensors designed to report live biochemical signaling events. As genetically encoded and live-cell compatible tools, fluorescent biosensors are well suited to address diverse cell signaling questions across different spatial scales of regulation. In this review, methods of examining spatial signaling regulation and the design of fluorescent biosensors are introduced. Then, recent biosensor developments that illuminate the importance of spatial regulation in cell signaling are highlighted at several scales, including membranes and organelles, molecular assemblies, and cell/tissue heterogeneity. In closing, perspectives on how fluorescent biosensors will continue enhancing cell signaling research are discussed.
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Affiliation(s)
- Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, U.S.A
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37
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Marchetti M, Ronda L, Cozzi M, Bettati S, Bruno S. Genetically Encoded Biosensors for the Fluorescence Detection of O 2 and Reactive O 2 Species. SENSORS (BASEL, SWITZERLAND) 2023; 23:8517. [PMID: 37896609 PMCID: PMC10611200 DOI: 10.3390/s23208517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
The intracellular concentrations of oxygen and reactive oxygen species (ROS) in living cells represent critical information for investigating physiological and pathological conditions. Real-time measurement often relies on genetically encoded proteins that are responsive to fluctuations in either oxygen or ROS concentrations. The direct binding or chemical reactions that occur in their presence either directly alter the fluorescence properties of the binding protein or alter the fluorescence properties of fusion partners, mostly consisting of variants of the green fluorescent protein. Oxygen sensing takes advantage of several mechanisms, including (i) the oxygen-dependent hydroxylation of a domain of the hypoxia-inducible factor-1, which, in turn, promotes its cellular degradation along with fluorescent fusion partners; (ii) the naturally oxygen-dependent maturation of the fluorophore of green fluorescent protein variants; and (iii) direct oxygen binding by proteins, including heme proteins, expressed in fusion with fluorescent partners, resulting in changes in fluorescence due to conformational alterations or fluorescence resonance energy transfer. ROS encompass a group of highly reactive chemicals that can interconvert through various chemical reactions within biological systems, posing challenges for their selective detection through genetically encoded sensors. However, their general reactivity, and particularly that of the relatively stable oxygen peroxide, can be exploited for ROS sensing through different mechanisms, including (i) the ROS-induced formation of disulfide bonds in engineered fluorescent proteins or fusion partners of fluorescent proteins, ultimately leading to fluorescence changes; and (ii) conformational changes of naturally occurring ROS-sensing domains, affecting the fluorescence properties of fusion partners. In this review, we will offer an overview of these genetically encoded biosensors.
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Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Monica Cozzi
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
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38
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Valiente-Gabioud AA, Garteizgogeascoa Suñer I, Idziak A, Fabritius A, Basquin J, Angibaud J, Nägerl UV, Singh SP, Griesbeck O. Fluorescent sensors for imaging of interstitial calcium. Nat Commun 2023; 14:6220. [PMID: 37798285 PMCID: PMC10556026 DOI: 10.1038/s41467-023-41928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the scarcity of methods that allow monitoring in tight inter-cell spaces of living tissues. Here we present high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (Kds) ranging from 0.8 mM to 2.9 mM, making them tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafish in vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Inés Garteizgogeascoa Suñer
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Agata Idziak
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Arne Fabritius
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Julie Angibaud
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - U Valentin Nägerl
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Sumeet Pal Singh
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Oliver Griesbeck
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany.
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39
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Xu S, Momin M, Ahmed S, Hossain A, Veeramuthu L, Pandiyan A, Kuo CC, Zhou T. Illuminating the Brain: Advances and Perspectives in Optoelectronics for Neural Activity Monitoring and Modulation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303267. [PMID: 37726261 DOI: 10.1002/adma.202303267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/30/2023] [Indexed: 09/21/2023]
Abstract
Optogenetic modulation of brain neural activity that combines optical and electrical modes in a unitary neural system has recently gained robust momentum. Controlling illumination spatial coverage, designing light-activated modulators, and developing wireless light delivery and data transmission are crucial for maximizing the use of optical neuromodulation. To this end, biocompatible electrodes with enhanced optoelectrical performance, device integration for multiplexed addressing, wireless transmission, and multimodal operation in soft systems have been developed. This review provides an outlook for uniformly illuminating large brain areas while spatiotemporally imaging the neural responses upon optoelectrical stimulation with little artifacts. Representative concepts and important breakthroughs, such as head-mounted illumination, multiple implanted optical fibers, and micro-light-delivery devices, are discussed. Examples of techniques that incorporate electrophysiological monitoring and optoelectrical stimulation are presented. Challenges and perspectives are posed for further research efforts toward high-density optoelectrical neural interface modulation, with the potential for nonpharmacological neurological disease treatments and wireless optoelectrical stimulation.
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Affiliation(s)
- Shumao Xu
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Marzia Momin
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Salahuddin Ahmed
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Arafat Hossain
- Department of Electrical Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Loganathan Veeramuthu
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Archana Pandiyan
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Chi-Ching Kuo
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Tao Zhou
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
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40
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Valiente-Gabioud AA, Fabritius A, Griesbeck O. Probing the interstitial calcium compartment. J Physiol 2023; 601:4217-4226. [PMID: 36073135 DOI: 10.1113/jp279510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Calcium in interstitial fluids is a crucial ion pool for entry into cells through a plethora of calcium-permeable channels. It is also sensed actively by dedicated receptors. While the mechanisms of global calcium homeostasis and regulation in body fluids appear well understood, more efforts and new technology are needed to elucidate local calcium handling in the small and relatively isolated interstitial spaces between cells. Here we review current methodology for monitoring interstitial calcium and highlight the potential of new approaches for its study. In particular, new generations of high-performance low-affinity genetically encoded calcium indicators could allow imaging of calcium in relatively inaccessible intercellular structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
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41
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Dynes JL, Yeromin AV, Cahalan MD. Photoswitching alters fluorescence readout of jGCaMP8 Ca 2+ indicators tethered to Orai1 channels. Proc Natl Acad Sci U S A 2023; 120:e2309328120. [PMID: 37729200 PMCID: PMC10523504 DOI: 10.1073/pnas.2309328120] [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: 06/02/2023] [Accepted: 08/15/2023] [Indexed: 09/22/2023] Open
Abstract
We used electrophysiology and Ca2+ channel tethering to evaluate the performance of jGCaMP8 genetically encoded Ca2+ indicators (GECIs). Orai1 Ca2+ channel-jGCaMP8 fusions were transfected into HEK 293A cells and jGCaMP8 fluorescence responses recorded by simultaneous total internal reflection fluorescence microscopy and whole-cell patch clamp electrophysiology. Noninactivating currents from the Orai1 Y80E mutant provided a steady flux of Ca2+ controlled on a millisecond time scale by step changes in membrane potential. Test pulses to -100 mV produced Orai1 Y80E-jGCaMP8f fluorescence traces that unexpectedly declined by ~50% over 100 ms before reaching a stable plateau. Testing of Orai1-jGCaMP8f using unroofed cells further demonstrated that rapid and partial fluorescence inactivation is a property of the indicator itself, rather than channel function. Photoinactivation spontaneously recovered over 5 min in the dark, and recovery was accelerated in the absence of Ca2+. Mutational analysis of residues near the tripeptide fluorophore of jGCaMP8f pointed to a mechanism: Q69M/C70V greatly increased (~90%) photoinactivation, reminiscent of fluorescent protein fluorophore cis-trans photoswitching. Indeed, 405-nm illumination of jGCaMP8f or 8m/8s/6f led to immediate photorecovery, and simultaneous illumination with 405 and 488-nm light blocked photoinactivation. Subsequent mutagenesis produced a variant, V203Y, that lacks photoinactivation but largely preserves the desirable properties of jGCaMP8f. Our results point to caution in interpreting rapidly changing Ca2+ signals using jGCaMP8 and earlier series GECIs, suggest strategies to avoid photoswitching, and serve as a starting point to produce more photostable, and thus more accurate, GECI derivatives.
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Affiliation(s)
- Joseph L. Dynes
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - Andriy V. Yeromin
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - Michael D. Cahalan
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
- Institute for Immunology, University of California, Irvine, CA92697
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42
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Mann MM, Berger BW. A genetically-encoded biosensor for direct detection of perfluorooctanoic acid. Sci Rep 2023; 13:15186. [PMID: 37704644 PMCID: PMC10499884 DOI: 10.1038/s41598-023-41953-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
Determination of per- and polyfluoroalkyl substances (PFAS) in drinking water at the low levels set by regulatory officials has been a major focus for sensor developing researchers. However, it is becoming more apparent that detection of these contaminants in soils, foods and consumer products is relevant and necessary at part per billion and even part per million levels. Here, a fluorescent biosensor for the rapid detection of PFOA was engineered based on human liver fatty acid binding protein (hLFABP). By conjugating circularly permuted green fluorescent protein (cp.GFP) to a split hLFABP construct, the biosensor was able to detect perfluorooctanoic acid PFOA in PBS as well as environmental water samples with LODs of 236 and 330 ppb respectively. Furthermore, E. coli cells cytosolically expressing the protein-based sensor were demonstrated to quickly detect PFOA, demonstrating feasibility of whole-cell sensing. Overall, this work demonstrates a platform technology utilizing a circularly permuted GFP and split hLFABP conjugate as a label-free optical biosensor for PFOA.
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Affiliation(s)
- Madison M Mann
- Department of Chemical Engineering, University of Virginia, 102 Engineers Way, Charlottesville, VA, 22901, USA
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, 102 Engineers Way, Charlottesville, VA, 22901, USA.
- Department of Biomedical Engineering, University of Virginia, Charlottesville, USA.
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43
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Sadoine M, De Michele R, Župunski M, Grossmann G, Castro-Rodríguez V. Monitoring nutrients in plants with genetically encoded sensors: achievements and perspectives. PLANT PHYSIOLOGY 2023; 193:195-216. [PMID: 37307576 PMCID: PMC10469547 DOI: 10.1093/plphys/kiad337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023]
Abstract
Understanding mechanisms of nutrient allocation in organisms requires precise knowledge of the spatiotemporal dynamics of small molecules in vivo. Genetically encoded sensors are powerful tools for studying nutrient distribution and dynamics, as they enable minimally invasive monitoring of nutrient steady-state levels in situ. Numerous types of genetically encoded sensors for nutrients have been designed and applied in mammalian cells and fungi. However, to date, their application for visualizing changing nutrient levels in planta remains limited. Systematic sensor-based approaches could provide the quantitative, kinetic information on tissue-specific, cellular, and subcellular distributions and dynamics of nutrients in situ that is needed for the development of theoretical nutrient flux models that form the basis for future crop engineering. Here, we review various approaches that can be used to measure nutrients in planta with an overview over conventional techniques, as well as genetically encoded sensors currently available for nutrient monitoring, and discuss their strengths and limitations. We provide a list of currently available sensors and summarize approaches for their application at the level of cellular compartments and organelles. When used in combination with bioassays on intact organisms and precise, yet destructive analytical methods, the spatiotemporal resolution of sensors offers the prospect of a holistic understanding of nutrient flux in plants.
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Affiliation(s)
- Mayuri Sadoine
- Institute of Cell and Interaction Biology, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
| | - Roberto De Michele
- Institute of Biosciences and Bioresources, National Research Council of Italy, Palermo 90129, Italy
| | - Milan Župunski
- Institute of Cell and Interaction Biology, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
| | - Vanessa Castro-Rodríguez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga 29071, Spain
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44
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Chai F, Cheng D, Nasu Y, Terai T, Campbell RE. Maximizing the performance of protein-based fluorescent biosensors. Biochem Soc Trans 2023; 51:1585-1595. [PMID: 37431791 PMCID: PMC10586770 DOI: 10.1042/bst20221413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Fluorescent protein (FP)-based biosensors are genetically encoded tools that enable the imaging of biological processes in the context of cells, tissues, or live animals. Though widely used in biological research, practically all existing biosensors are far from ideal in terms of their performance, properties, and applicability for multiplexed imaging. These limitations have inspired researchers to explore an increasing number of innovative and creative ways to improve and maximize biosensor performance. Such strategies include new molecular biology methods to develop promising biosensor prototypes, high throughput microfluidics-based directed evolution screening strategies, and improved ways to perform multiplexed imaging. Yet another approach is to effectively replace components of biosensors with self-labeling proteins, such as HaloTag, that enable the biocompatible incorporation of synthetic fluorophores or other ligands in cells or tissues. This mini-review will summarize and highlight recent innovations and strategies for enhancing the performance of FP-based biosensors for multiplexed imaging to advance the frontiers of research.
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Affiliation(s)
- Fu Chai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Dazhou Cheng
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yusuke Nasu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Takuya Terai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Robert E. Campbell
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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45
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Zhuo Y, Luo B, Yi X, Dong H, Wan J, Cai R, Williams JT, Qian T, Campbell MG, Miao X, Li B, Wei Y, Li G, Wang H, Zheng Y, Watabe-Uchida M, Li Y. Improved dual-color GRAB sensors for monitoring dopaminergic activity in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554559. [PMID: 37662187 PMCID: PMC10473776 DOI: 10.1101/2023.08.24.554559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Dopamine (DA) plays multiple roles in a wide range of physiological and pathological processes via a vast network of dopaminergic projections. To fully dissect the spatiotemporal dynamics of DA release in both dense and sparsely innervated brain regions, we developed a series of green and red fluorescent GPCR activation-based DA (GRABDA) sensors using a variety of DA receptor subtypes. These sensors have high sensitivity, selectivity, and signal-to-noise properties with subsecond response kinetics and the ability to detect a wide range of DA concentrations. We then used these sensors in freely moving mice to measure both optogenetically evoked and behaviorally relevant DA release while measuring neurochemical signaling in the nucleus accumbens, amygdala, and cortex. Using these sensors, we also detected spatially resolved heterogeneous cortical DA release in mice performing various behaviors. These next-generation GRABDA sensors provide a robust set of tools for imaging dopaminergic activity under a variety of physiological and pathological conditions.
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Affiliation(s)
- Yizhou Zhuo
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- These authors contributed equally
| | - Bin Luo
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
- These authors contributed equally
| | - Xinyang Yi
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Hui Dong
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Jinxia Wan
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Ruyi Cai
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - John T. Williams
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Tongrui Qian
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Malcolm G. Campbell
- Center for Brain Science, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Xiaolei Miao
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- Department of Anesthesiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Bozhi Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Fuxing Road 28, Haidian District, Beijing 100853, China
| | - Yu Wei
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Guochuan Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Yu Zheng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Mitsuko Watabe-Uchida
- Center for Brain Science, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing 102206, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
- National Biomedical Imaging Center, Peking University, Beijing 100871, China
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46
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Wait SJ, Rappleye M, Lee JD, Goy ME, Smith N, Berndt A. Machine Learning Ensemble Directed Engineering of Genetically Encoded Fluorescent Calcium Indicators. RESEARCH SQUARE 2023:rs.3.rs-3146778. [PMID: 37609342 PMCID: PMC10441480 DOI: 10.21203/rs.3.rs-3146778/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
In this study, we focused on the transformative potential of machine learning in the engineering of genetically encoded fluorescent indicators (GEFIs), protein-based sensing tools that are critical for real-time monitoring of biological activity. GEFIs are complex proteins with multiple dynamic states, rendering optimization by trial-and-error mutagenesis a challenging problem. We applied an alternative approach using machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. We used the trained ensemble to perform an in silico functional screen on 1423 novel, uncharacterized GCaMP variants. As a result, we identified the novel ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, that achieve both faster kinetics and larger fluorescent responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, that outperforms the tested 6th, 7th, and 8th generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient pre-screening of mutants for functional characteristics. By leveraging the learning capabilities of our ensemble, we were able to accelerate the identification of promising mutations and reduce the experimental burden associated with trial-and-error mutagenesis. Overall, these findings have significant implications for optimizing GEFIs and other protein-based tools, demonstrating the utility of machine learning as a powerful asset in protein engineering.
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Affiliation(s)
- Sarah J. Wait
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Michael Rappleye
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
| | - Marc Exposit Goy
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
| | - Netta Smith
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA
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47
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Christensen EK, Konomi-Pilkati A, Rombach J, Comaposada-Baro R, Wang H, Li Y, Sørensen AT. Detection of endogenous NPY release determined by novel GRAB sensor in cultured cortical neurons. Front Cell Neurosci 2023; 17:1221147. [PMID: 37545877 PMCID: PMC10399118 DOI: 10.3389/fncel.2023.1221147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Neuropeptide Y (NPY) is an abundantly expressed peptide in the nervous system. Its widespread distribution along with its receptors, both centrally and peripherally, indicates its broad functions in numerous biological processes. However, the low endogenous concentration and diffuse distribution of NPY make it challenging to study its actions and dynamics directly and comprehensively. Studies on the role of NPY have primarily been limited to exogenous application, transgene expression, or knock-out in biological systems, which are often combined with pharmacological probes to delineate the involvement of specific NPY receptors. Therefore, to better understand the function of NPY in time and space, direct visualization of the real-time dynamics of endogenous NPY is a valuable and desired tool. Using the first-generation and newly developed intensiometric green fluorescent G-protein-coupled NPY sensor (GRAB NPY1.0), we, for the first time, demonstrate and characterize the direct detection of endogenously released NPY in cultured cortical neurons. A dose-dependent fluorescent signal was observed upon exogenous NPY application in nearly all recorded neurons. Pharmacologically evoked neuronal activity induced a significant increase in fluorescent signal in 32% of neurons, reflecting the release of NPY, despite only 3% of all neurons containing NPY. The remaining pool of neurons expressing the sensor were either non-responsive or displayed a notable decline in the fluorescent signal. Such decline in fluorescent signal was not rescued in cortical cultures transduced with an NPY overexpression vector, where 88% of the neurons were NPY-positive. Overexpression of NPY did, however, result in sensor signals that were more readily distinguishable. This may suggest that biological factors, such as subtle changes in intracellular pH, could interfere with the fluorescent signal, and thereby underestimate the release of endogenous NPY when using this new sensor in its present configuration. However, the development of next-generation NPY GRAB sensor technology is expected soon, and will eventually enable much-wanted studies on endogenous NPY release dynamics in both cultured and intact biological systems.
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Affiliation(s)
- Emma Kragelund Christensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ainoa Konomi-Pilkati
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joscha Rombach
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Comaposada-Baro
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Andreas Toft Sørensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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48
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Zheng Y, Li Y. Past, present, and future of tools for dopamine detection. Neuroscience 2023:S0306-4522(23)00295-6. [PMID: 37419404 DOI: 10.1016/j.neuroscience.2023.06.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023]
Abstract
Dopamine (DA) is a critical neuromodulator involved in various brain functions. To understand how DA regulates neural circuits and behaviors in the physiological and pathological conditions, it is essential to have tools that enable the direct detection of DA dynamics in vivo. Recently, genetically encoded DA sensors based on G protein-coupled receptors revolutionized this field, as it allows us to track in vivo DA dynamic with unprecedented spatial-temporal resolution, high molecular specificity, and sub-second kinetics. In this review, we first summarize traditional DA detection methods. Then we focus on the development of genetically encoded DA sensors and feature its significance to understanding dopaminergic neuromodulation across diverse behaviors and species. Finally, we present our perspectives about the future direction of the next-generation DA sensors and extend their potential applications. Overall, this review offers a comprehensive perspective on the past, present, and future of DA detection tools, with important implications for the study of DA functions in health and disease.
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Affiliation(s)
- Yu Zheng
- Peking-Tsinghua Center for Life Sciences, 100871 Beijing, China
| | - Yulong Li
- Peking-Tsinghua Center for Life Sciences, 100871 Beijing, China; State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, 100871 Beijing, China; PKU-IDG/McGovern Institute for Brain Research, 100871 Beijing, China; National Biomedical Imaging Center, Peking University, 100871 Beijing, China.
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49
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Yang EJN, Boldogh IR, Ji H, Pon L, Swayne TC. Imaging of mtHyPer7, a Ratiometric Biosensor for Mitochondrial Peroxide, in Living Yeast Cells. J Vis Exp 2023:10.3791/65428. [PMID: 37335116 PMCID: PMC11091793 DOI: 10.3791/65428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Mitochondrial dysfunction, or functional alteration, is found in many diseases and conditions, including neurodegenerative and musculoskeletal disorders, cancer, and normal aging. Here, an approach is described to assess mitochondrial function in living yeast cells at cellular and subcellular resolutions using a genetically encoded, minimally invasive, ratiometric biosensor. The biosensor, mitochondria-targeted HyPer7 (mtHyPer7), detects hydrogen peroxide (H2O2) in mitochondria. It consists of a mitochondrial signal sequence fused to a circularly permuted fluorescent protein and the H2O2-responsive domain of a bacterial OxyR protein. The biosensor is generated and integrated into the yeast genome using a CRISPR-Cas9 marker-free system, for more consistent expression compared to plasmid-borne constructs. mtHyPer7 is quantitatively targeted to mitochondria, has no detectable effect on yeast growth rate or mitochondrial morphology, and provides a quantitative readout for mitochondrial H2O2 under normal growth conditions and upon exposure to oxidative stress. This protocol explains how to optimize imaging conditions using a spinning-disk confocal microscope system and perform quantitative analysis using freely available software. These tools make it possible to collect rich spatiotemporal information on mitochondria both within cells and among cells in a population. Moreover, the workflow described here can be used to validate other biosensors.
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Affiliation(s)
- Emily Jie-Ning Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center; Confocal and Specialized Microscopy Shared Resource in the Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center
| | - Haojie Ji
- Confocal and Specialized Microscopy Shared Resource in the Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center
| | - Liza Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center; Confocal and Specialized Microscopy Shared Resource in the Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center
| | - Theresa C Swayne
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center; Confocal and Specialized Microscopy Shared Resource in the Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center;
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50
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Torres-Ocampo AP, Palmer AE. Genetically encoded fluorescent sensors for metals in biology. Curr Opin Chem Biol 2023; 74:102284. [PMID: 36917910 PMCID: PMC10573084 DOI: 10.1016/j.cbpa.2023.102284] [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: 11/01/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 03/14/2023]
Abstract
Metal ions intersect a wide range of biological processes. Some metal ions are essential and hence absolutely required for the growth and health of an organism, others are toxic and there is great interest in understanding mechanisms of toxicity. Genetically encoded fluorescent sensors are powerful tools that enable the visualization, quantification, and tracking of dynamics of metal ions in biological systems. Here, we review recent advances in the development of genetically encoded fluorescent sensors for metal ions. We broadly focus on 5 classes of sensors: single fluorescent protein, FRET-based, chemigenetic, DNAzymes, and RNA-based. We highlight recent developments in the past few years and where these developments stand concerning the rest of the field.
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Affiliation(s)
- Ana P Torres-Ocampo
- BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Ave, CO, 80303, Boulder, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado, Boulder, 3415 Colorado Ave, CO, 80303, Boulder, United States; BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Ave, CO, 80303, Boulder, United States.
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