1
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 DOI: 10.1007/s41061-024-00455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
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Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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3
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [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: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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4
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Eddins AJ, Bednar RM, Jana S, Pung AH, Mbengi L, Meyer K, Perona JJ, Cooley RB, Karplus PA, Mehl RA. Truncation-Free Genetic Code Expansion with Tetrazine Amino Acids for Quantitative Protein Ligations. Bioconjug Chem 2023; 34:2243-2254. [PMID: 38047550 DOI: 10.1021/acs.bioconjchem.3c00380] [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: 12/05/2023]
Abstract
Quantitative labeling of biomolecules is necessary to advance areas of antibody-drug conjugation, super-resolution microscopy imaging of molecules in live cells, and determination of the stoichiometry of protein complexes. Bio-orthogonal labeling to genetically encodable noncanonical amino acids (ncAAs) offers an elegant solution; however, their suboptimal reactivity and stability hinder the utility of this method. Previously, we showed that encoding stable 1,2,4,5-tetrazine (Tet)-containing ncAAs enables rapid, complete conjugation, yet some expression conditions greatly limited the quantitative reactivity of the Tet-protein. Here, we demonstrate that reduction of on-protein Tet ncAAs impacts their reactivity, while the leading cause of the unreactive protein is near-cognate suppression (NCS) of UAG codons by endogenous aminoacylated tRNAs. To overcome incomplete conjugation due to NCS, we developed a more catalytically efficient tRNA synthetase and developed a series of new machinery plasmids harboring the aminoacyl tRNA synthetase/tRNA pair (aaRS/tRNA pair). These plasmids enable robust production of homogeneously reactive Tet-protein in truncation-free cell lines, eliminating the contamination caused by NCS and protein truncation. Furthermore, these plasmid systems utilize orthogonal synthetic origins, which render these machinery vectors compatible with any common expression system. Through developing these new machinery plasmids, we established that the aaRS/tRNA pair plasmid copy-number greatly affects the yields and quality of the protein produced. We then produced quantitatively reactive soluble Tet-Fabs, demonstrating the utility of this system for rapid, homogeneous conjugations of biomedically relevant proteins.
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Affiliation(s)
- Alex J Eddins
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Abigail H Pung
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Lea Mbengi
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - Kyle Meyer
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- GCE4All Biomedical Technology Development and Dissemination Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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5
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Koehler C, Sauter PF, Klasen B, Waldmann C, Pektor S, Bausbacher N, Lemke EA, Miederer M. Genetic Code Expansion for Site-Specific Labeling of Antibodies with Radioisotopes. ACS Chem Biol 2023; 18:443-448. [PMID: 36889678 PMCID: PMC10029752 DOI: 10.1021/acschembio.2c00634] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Due to their target specificity, antibody-drug conjugates─monoclonal antibodies conjugated to a cytotoxic moiety─are efficient therapeutics that can kill malignant cells overexpressing a target gene. Linking an antibody with radioisotopes (radioimmunoconjugates) enables powerful diagnostics and/or closely related therapeutic applications, depending on the isotope. To generate site-specific radioimmunoconjugates, we utilized genetic code expansion and subsequent conjugation by inverse electron-demand Diels-Alder cycloaddition reactions. We show that, using this approach, site-specific labeling of trastuzumab with either zirconium-89 (89Zr) for diagnostics or lutetium-177 (177Lu) for therapeutics yields efficient radioimmunoconjugates. Positron emission tomography imaging revealed a high accumulation of site-specifically 89Zr-labeled trastuzumab in tumors after 24 h and low accumulation in other organs. The corresponding 177Lu-trastuzumab radioimmunoconjugates were comparably distributed in vivo.
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Affiliation(s)
- Christine Koehler
- VERAXA
Biotech GmbH, Carl-Friedrich
Gauß-Ring 5, 69124 Heidelberg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paul F. Sauter
- VERAXA
Biotech GmbH, Carl-Friedrich
Gauß-Ring 5, 69124 Heidelberg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Benedikt Klasen
- Department
of Chemistry, TRIGA site, Johannes Gutenberg
University, Fritz-Strassmann-Weg 2, 55128 Mainz, Germany
| | - Christopher Waldmann
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
| | - Stefanie Pektor
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
| | - Nicole Bausbacher
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
| | - Edward A. Lemke
- BIOCENTER, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
- IMB
Institute
of Molecular Biology, gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Matthias Miederer
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
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6
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Reinkemeier CD, Lemke EA. Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansions in Eukaryotes. Methods Mol Biol 2023; 2563:341-369. [PMID: 36227482 DOI: 10.1007/978-1-0716-2663-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Engineering new functionalities into living eukaryotic systems is one of the main goals of synthetic biology. To this end, often enzyme evolution or de novo protein design is employed, which each have their own advantages and disadvantages. As complimentary tools, we recently developed orthogonally translating and film-like synthetic organelles that allow to create new enzyme functionalities based on spatial separation. We applied this technology to genetic code expansion (GCE) and showed that it is possible to equip eukaryotic cells with multiple orthogonal genetic codes that enable the specific reprogramming of distinct translational machineries, each with single-residue precision.In this protocol, we describe how synthetic organelles can be used to perform mRNA selective GCE and how they can be further developed to allow the simultaneous incorporation of distinct noncanonical amino acids (ncAAs) into selected proteins and how this can be used to label proteins selectively with fluorescent dyes via bioorthogonal chemistry.
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Affiliation(s)
- Christopher D Reinkemeier
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Molecular Biology gGmbH, Mainz, Germany.
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7
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Ryan A, Shade O, Bardhan A, Bartnik A, Deiters A. Quantitative Analysis and Optimization of Site-Specific Protein Bioconjugation in Mammalian Cells. Bioconjug Chem 2022; 33:2361-2369. [PMID: 36459098 DOI: 10.1021/acs.bioconjchem.2c00451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Despite a range of covalent protein modifications, few techniques exist for quantification of protein bioconjugation in cells. Here, we describe a novel method for quantifying in cellulo protein bioconjugation through covalent bond formation with HaloTag. This approach utilizes unnatural amino acid (UAA) mutagenesis to selectively install a small and bioorthogonally reactive handle onto the surface of a protein. We utilized the fast kinetics and high selectivity of inverse electron-demand Diels-Alder cycloadditions to evaluate reactions of tetrazine phenylalanine (TetF) with strained trans-cyclooctene-chloroalkane (sTCO-CA) and trans-cyclooctene lysine (TCOK) with tetrazine-chloroalkane (Tet-CA). Following bioconjugation, the chloroalkane ligand is exposed for labeling by the HaloTag enzyme, allowing for straightforward quantification of bioconjugation via simple western blot analysis. We demonstrate the versatility of this tool for quickly and accurately determining the bioconjugation efficiency of different UAA/chloroalkane pairs and for different sites on different proteins of interest, including EGFP and the estrogen-related receptor ERRα.
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Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Olivia Shade
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Aleksander Bartnik
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Hild F, Werther P, Yserentant K, Wombacher R, Herten DP. A dark intermediate in the fluorogenic reaction between tetrazine fluorophores and trans-cyclooctene. BIOPHYSICAL REPORTS 2022; 2:100084. [PMID: 36570717 PMCID: PMC9782730 DOI: 10.1016/j.bpr.2022.100084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022]
Abstract
Fluorogenic labeling via bioorthogonal tetrazine chemistry has proven to be highly successful in fluorescence microscopy of living cells. To date, trans-cyclooctene (TCO) and bicyclonyne have been found to be the most useful substrates for live-cell labeling owing to their fast labeling kinetics, high biocompatibility, and bioorthogonality. Recent kinetic studies of fluorogenic click reactions with TCO derivatives showed a transient fluorogenic effect but could not explain the reaction sequence and the contributions of different intermediates. More recently, fluorescence quenching by potential intermediates has been investigated, suggesting their occurrence in the reaction sequence. However, in situ studies of the click reaction that directly relate these observations to the known reaction sequence are still missing. In this study, we developed a single-molecule fluorescence detection framework to investigate fluorogenic click reactions. In combination with data from ultra-performance liquid chromatography-tandem mass spectrometry, this explains the transient intensity increase by relating fluorescent intermediates to the known reaction sequence of TCO with fluorogenic tetrazine dyes. More specifically, we confirm that the reaction of TCO with tetrazine rapidly forms a fluorescent 4,5-dihydropyridazine species that slowly tautomerizes to a weakly fluorescent 1,4-dihydropyridazine, explaining the observed drop in fluorescence intensity. On a much slower timescale of hours/days, the fluorescence intensity may be recovered by oxidation of the intermediate to a pyridazine. Our findings are of importance for quantitative applications in fluorescence microscopy and spectroscopy as the achieved peak intensity with TCO depends on the specific experimental settings. They clearly indicate the requirement for more robust benchmarking of click reactions with tetrazine dyes and the need for alternative dienophiles with fast reaction kinetics and stable fluorescence emission to further applications in advanced fluorescence microscopy.
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Affiliation(s)
- Felix Hild
- Physikalisch-Chemisches Institut, Heidelberg University, Heidelberg, Germany
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Klaus Yserentant
- Physikalisch-Chemisches Institut, Heidelberg University, Heidelberg, Germany,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences and School of Chemistry, University of Birmingham, Birmingham, United Kingdom,Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, Birmingham, West Midlands, United Kingdom
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany,Max-Planck-Institut für Medizinische Forschung, Heidelberg, Germany
| | - Dirk-Peter Herten
- Physikalisch-Chemisches Institut, Heidelberg University, Heidelberg, Germany,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences and School of Chemistry, University of Birmingham, Birmingham, United Kingdom,Centre of Membrane Proteins and Receptors (COMPARE), The Universities of Birmingham and Nottingham, Birmingham, West Midlands, United Kingdom,Corresponding author
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9
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Li Y, Yu P, Gan Y, Wang R. Labeling of prenylated proteins via Ene-ligation using naturally-occurring citronellol. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Arsić A, Hagemann C, Stajković N, Schubert T, Nikić-Spiegel I. Minimal genetically encoded tags for fluorescent protein labeling in living neurons. Nat Commun 2022; 13:314. [PMID: 35031604 PMCID: PMC8760255 DOI: 10.1038/s41467-022-27956-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Modern light microscopy, including super-resolution techniques, has brought about a demand for small labeling tags that bring the fluorophore closer to the target. This challenge can be addressed by labeling unnatural amino acids (UAAs) with bioorthogonal click chemistry. The minimal size of the UAA and the possibility to couple the fluorophores directly to the protein of interest with single-residue precision in living cells make click labeling unique. Here, we establish click labeling in living primary neurons and use it for fixed-cell, live-cell, dual-color pulse-chase, and super-resolution microscopy of neurofilament light chain (NFL). We also show that click labeling can be combined with CRISPR/Cas9 genome engineering for tagging endogenous NFL. Due to its versatile nature and compatibility with advanced multicolor microscopy techniques, we anticipate that click labeling will contribute to novel discoveries in the neurobiology field.
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Affiliation(s)
- Aleksandra Arsić
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Cathleen Hagemann
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Nevena Stajković
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Timm Schubert
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Institute for Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Straße 7, 72076, Tübingen, Germany
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany.
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11
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Reinkemeier CD, Lemke EA. Condensed, microtubule-coating thin organelles for orthogonal translation in mammalian cells. J Mol Biol 2022; 434:167454. [PMID: 35033560 DOI: 10.1016/j.jmb.2022.167454] [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: 10/26/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 10/19/2022]
Abstract
Membraneless organelles are capable of selectively performing complex tasks in living cells despite dynamically exchanging with their surroundings. This is an exquisite example how self-organization of proteins and RNAs can lead to more complex functionalities in living systems. Importantly, the absence of a membrane boundary can enable easier access to larger macromolecular complexes that can be challenging to be transported across a membrane. We previously formed orthogonally translating designer membraneless organelles by combining phase separation with kinesin motor proteins to highly enrich engineered translational factors in large organelles. We also showed that even submicron thick designer organelles can be formed, by mounting them onto membranes, which, presumable assisted by 2D condensation, leads to thin film-like condensates. In this study we show that orthogonal translation can also be built with fiber-like appearing organelles. Here, the microtubule-end binding protein EB1 was used to form fiber-like OT organelles along the microtubule cytoskeleton that perform highly selective and efficient orthogonal translation. We also show an improved simplified design of OT organelles. Together this extends OT technology and demonstrates that the microtubule cytoskeleton is a powerful platform for advanced synthetic organelle engineering.
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Affiliation(s)
- Christopher D Reinkemeier
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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12
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Aphicho K, Kittipanukul N, Uttamapinant C. Visualizing the complexity of proteins in living cells with genetic code expansion. Curr Opin Chem Biol 2022; 66:102108. [PMID: 35026612 DOI: 10.1016/j.cbpa.2021.102108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Genetic code expansion has emerged as an enabling tool to provide insight into functions of understudied proteinogenic species, such as small proteins and peptides, and to probe protein biophysics in the cellular context. Here, we discuss recent technical advances and applications of genetic code expansion in cellular imaging of complex mammalian protein species, along with considerations and challenges on using the method.
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Affiliation(s)
- Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Narongyot Kittipanukul
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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13
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Reinkemeier CD, Lemke EA. Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation. Cell 2021; 184:4886-4903.e21. [PMID: 34433013 PMCID: PMC8480389 DOI: 10.1016/j.cell.2021.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 05/03/2021] [Accepted: 08/02/2021] [Indexed: 11/18/2022]
Abstract
Engineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. Cells do not rely exclusively on DNA-based evolution to generate new functionality but often utilize membrane encapsulation or formation of membraneless organelles to separate distinct molecular processes that execute complex operations. Applying this principle and the concept of two-dimensional phase separation, we develop film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes. These sub-resolution synthetic films provide a path to make functionally distinct enzymes within the same cell. We use these film-like organelles to equip eukaryotic cells with dual orthogonal expanded genetic codes that enable the specific reprogramming of distinct translational machineries with single-residue precision. The ability to spatially tune the output of translation within tens of nanometers is not only important for synthetic biology but has implications for understanding the function of membrane-associated protein condensation in cells. 2D phase separation was utilized to design orthogonal enzymes Film-like organelles maintained distinct suppressor tRNA microenvironments Dual film-like synthetic organelles enabled orthogonal translation in eukaryotes Cells were equipped with two expanded genetic codes in addition to the canonical one
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Affiliation(s)
- Christopher D Reinkemeier
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Reinkemeier CD, Koehler C, Sauter PF, Shymanska NV, Echalier C, Rutkowska A, Will DW, Schultz C, Lemke EA. Synthesis and Evaluation of Novel Ring-Strained Noncanonical Amino Acids for Residue-Specific Bioorthogonal Reactions in Living Cells. Chemistry 2021; 27:6094-6099. [PMID: 33577120 PMCID: PMC8049044 DOI: 10.1002/chem.202100322] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 12/13/2022]
Abstract
Bioorthogonal reactions are ideally suited to selectively modify proteins in complex environments, even in vivo. Kinetics and product stability of these reactions are crucial parameters to evaluate their usefulness for specific applications. Strain promoted inverse electron demand Diels-Alder cycloadditions (SPIEDAC) between tetrazines and strained alkenes or alkynes are particularly popular, as they allow ultrafast labeling inside cells. In combination with genetic code expansion (GCE)-a method that allows to incorporate noncanonical amino acids (ncAAs) site-specifically into proteins in vivo. These reactions enable residue-specific fluorophore attachment to proteins in living mammalian cells. Several SPIEDAC capable ncAAs have been presented and studied under diverse conditions, revealing different instabilities ranging from educt decomposition to product loss due to β-elimination. To identify which compounds yield the best labeling inside living mammalian cells has frequently been difficult. In this study we present a) the synthesis of four new SPIEDAC reactive ncAAs that cannot undergo β-elimination and b) a fluorescence flow cytometry based FRET-assay to measure reaction kinetics inside living cells. Our results, which at first sight can be seen conflicting with some other studies, capture GCE-specific experimental conditions, such as long-term exposure of the ring-strained ncAA to living cells, that are not taken into account in other assays.
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Affiliation(s)
- Christopher D. Reinkemeier
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
| | - Christine Koehler
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | - Paul F. Sauter
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | | | - Cecile Echalier
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
| | - Anna Rutkowska
- Cellzome GmbHGlaxoSmithKlineMeyerhofstrasse 169117HeidelbergGermany
| | - David W. Will
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health & Science University (OHSU)PortlandOregon97239-3098USA
| | - Edward A. Lemke
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
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