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Yuan S, Bremmer A, Yang X, Li J, Hu Q. Splittable systems in biomedical applications. Biomater Sci 2024; 12:4103-4116. [PMID: 39012216 DOI: 10.1039/d4bm00709c] [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: 07/17/2024]
Abstract
Splittable systems have emerged as a powerful approach for the precise spatiotemporal control of biological processes. This concept relies on splitting a functional molecule into inactive fragments, which can be reassembled under specific conditions or stimuli to regain activity. Several binding pairs and orthogonal split fragments are introduced by fusing with other modalities to develop more complex and robust designs. One of the pillars of these splittable systems is modularity, which involves decoupling targeting, activation, and effector functions. Challenges, such as off-target effects and overactivation, can be addressed through precise control. This review provides an overview of the design principles, strategies, and applications of splittable systems across diverse fields including immunotherapy, gene editing, prodrug activation, biosensing, and synthetic biology.
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Affiliation(s)
- Sichen Yuan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
- Wisconsin Center for NanoBioSystems, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
| | - Alexa Bremmer
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Xicheng Yang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Jiayue Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA.
- Wisconsin Center for NanoBioSystems, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin 53705, USA
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Bae J, Kim J, Choi J, Lee H, Koh M. Split Proteins and Reassembly Modules for Biological Applications. Chembiochem 2024; 25:e202400123. [PMID: 38530024 DOI: 10.1002/cbic.202400123] [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: 02/08/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.
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Affiliation(s)
- Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
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3
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Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023; 51:557-569. [PMID: 36876879 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
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Rapid clonal identification of biallelic CRISPR/Cas9 knock-ins using SNEAK PEEC. Sci Rep 2023; 13:1719. [PMID: 36720908 PMCID: PMC9889345 DOI: 10.1038/s41598-023-28732-8] [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: 09/17/2021] [Accepted: 01/24/2023] [Indexed: 02/02/2023] Open
Abstract
One of the challenges faced by current CRISPR/Cas9 editing strategies is the difficulty in rapidly selecting clonal populations of biallelically edited cells. Here we present Surface engiNeered fluorEscence Assisted Kit with Protein Epitope Enhanced Capture (SNEAK PEEC), a platform that combines human genome editing with cell-surface display, which enables the direct identification of biallelically edited clones with minimal screening.
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Akhuli D, Dhar A, Viji AS, Bhojappa B, Palani S. ALIBY: ALFA Nanobody-Based Toolkit for Imaging and Biochemistry in Yeast. mSphere 2022; 7:e0033322. [PMID: 36190134 PMCID: PMC9599267 DOI: 10.1128/msphere.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Specialized epitope tags continue to be integral components of various biochemical and cell biological applications such as fluorescence microscopy, immunoblotting, immunoprecipitation, and protein purification. However, until recently, no single tag could offer this complete set of functionalities on its own. Here, we present a plasmid-based toolkit named ALIBY (ALFA toolkit for imaging and biochemistry in yeast) that provides a universal workflow to adopt the versatile ALFA tag/NbALFA system within the well-established model organism Saccharomyces cerevisiae. The kit comprises tagging plasmids for labeling a protein of interest with the ALFA tag and detection plasmids encoding fluorescent-protein-tagged NbALFA for live-cell imaging purposes. We demonstrate the suitability of ALIBY for visualizing the spatiotemporal localization of yeast proteins (i.e., the cytoskeleton, nucleus, centrosome, mitochondria, vacuole, endoplasmic reticulum, exocyst, and divisome) in live cells. Our approach has yielded an excellent signal-to-noise ratio without off-target effects or any effect on cell growth. In summary, our yeast-specific toolkit aims to simplify and further advance the live-cell imaging of differentially abundant yeast proteins while also being suitable for biochemical applications. IMPORTANCE In yeast research, conventional fluorescent protein tags and small epitope tags are widely used to study the spatiotemporal dynamics and activity of proteins. Although proven to be efficient, these tags lack the versatility for use across different cell biological and biochemical studies of a given protein of interest. Therefore, there is an urgent need for a unified platform for visualization and biochemical and functional analyses of proteins of interest in yeast. Here, we have engineered ALIBY, a plasmid-based toolkit that expands the benefits of the recently developed ALFA tag/NbALFA system to studies in the well-established model organism Saccharomyces cerevisiae. We demonstrate that ALIBY provides a simple and versatile strain construction workflow for long-duration live-cell imaging and biochemical applications in yeast.
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Affiliation(s)
- Dipayan Akhuli
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Anubhav Dhar
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Aileen Sara Viji
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Bindu Bhojappa
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Saravanan Palani
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
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Graham TGW, Ferrie JJ, Dailey GM, Tjian R, Darzacq X. Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA). eLife 2022; 11:e76870. [PMID: 35976226 PMCID: PMC9531946 DOI: 10.7554/elife.76870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here, we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the 'sender') can reactivate a second fluorophore (the 'receiver') from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a subpopulation of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.
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Affiliation(s)
- Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - John Joseph Ferrie
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Proc Natl Acad Sci U S A 2022; 119:e2207200119. [PMID: 35858375 PMCID: PMC9388094 DOI: 10.1073/pnas.2207200119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.
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Toulmay A, Whittle FB, Yang J, Bai X, Diarra J, Banerjee S, Levine TP, Golden A, Prinz WA. Vps13-like proteins provide phosphatidylethanolamine for GPI anchor synthesis in the ER. J Biophys Biochem Cytol 2022; 221:212952. [PMID: 35015055 PMCID: PMC8757616 DOI: 10.1083/jcb.202111095] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) is a glycolipid membrane anchor found on surface proteins in all eukaryotes. It is synthesized in the ER membrane. Each GPI anchor requires three molecules of ethanolamine phosphate (P-Etn), which are derived from phosphatidylethanolamine (PE). We found that efficient GPI anchor synthesis in Saccharomyces cerevisiae requires Csf1; cells lacking Csf1 accumulate GPI precursors lacking P-Etn. Structure predictions suggest Csf1 is a tube-forming lipid transport protein like Vps13. Csf1 is found at contact sites between the ER and other organelles. It interacts with the ER protein Mcd4, an enzyme that adds P-Etn to nascent GPI anchors, suggesting Csf1 channels PE to Mcd4 in the ER at contact sites to support GPI anchor biosynthesis. CSF1 has orthologues in Caenorhabditis elegans (lpd-3) and humans (KIAA1109/TWEEK); mutations in KIAA1109 cause the autosomal recessive neurodevelopmental disorder Alkuraya-Kučinskas syndrome. Knockout of lpd-3 and knockdown of KIAA1109 reduced GPI-anchored proteins on the surface of cells, suggesting Csf1 orthologues in human cells support GPI anchor biosynthesis.
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Affiliation(s)
- Alexandre Toulmay
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Fawn B Whittle
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Jerry Yang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Xiaofei Bai
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Jessica Diarra
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Subhrajit Banerjee
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Tim P Levine
- University College London, Institute of Ophthalmology, London, UK
| | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
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Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics 2021; 217:6156631. [PMID: 33713129 DOI: 10.1093/genetics/iyab019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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