1
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 DOI: 10.1021/acs.chemrev.4c00031] [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: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G Koch
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- Chemical Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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2
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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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3
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Ding W, Yu W, Chen Y, Lao L, Fang Y, Fang C, Zhao H, Yang B, Lin S. Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells. Science 2024; 384:1134-1142. [PMID: 38843324 DOI: 10.1126/science.adm8143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or previously unknown properties. However, existing strategies in mammalian cells rely on the introduction of a blank codon to incorporate ncAAs, which is inefficient and limits their widespread applications. In this study, we developed a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data-model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to six-site ncAAs or four distinct ncAAs in mammalian cells for downstream applications.
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Affiliation(s)
- Wenlong Ding
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Wei Yu
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Yulin Chen
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Lihui Lao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Chengzhu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hongxia Zhao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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4
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Dunkelmann DL, Piedrafita C, Dickson A, Liu KC, Elliott TS, Fiedler M, Bellini D, Zhou A, Cervettini D, Chin JW. Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism. Nature 2024; 625:603-610. [PMID: 38200312 PMCID: PMC10794150 DOI: 10.1038/s41586-023-06897-6] [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: 04/29/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1-3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4-6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs-this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-L-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.
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Affiliation(s)
| | - Carlos Piedrafita
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alexandre Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dom Bellini
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew Zhou
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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5
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Lightle HE, Kafley P, Lewis TR, Wang RE. Site-specific protein conjugates incorporating Para-Azido-L-Phenylalanine for cellular and in vivo imaging. Methods 2023; 219:95-101. [PMID: 37804961 PMCID: PMC10841489 DOI: 10.1016/j.ymeth.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023] Open
Abstract
This work features the use of amber suppression-mediated unnatural amino acid (UAA) incorporation into proteins for various imaging purposes. The site-specific incorporation of the UAA, p-azido-L-phenylalanine (pAzF), provides an azide handle that can be used to complete the strain promoted azide-alkyne click cycloaddition (SPAAC) reaction to introduce an imaging modality such as a fluorophore or a positron emission tomography (PET) tracer on the protein of interest (POI). Such methodology can be pursued directly in mammalian cell lines or on proteins expressed in vitro, thereby conferring a homogeneous pool of protein conjugates. A general procedure for UAA incorporation to use with a site-specific protein labeling method is provided allowing for in vitro and in vivo imaging applications based on the representative proteins PTEN and PD-L1. This approach would help elucidate the cellular or in vivo biological activities of the POI.
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Affiliation(s)
- Hailey E Lightle
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Todd R Lewis
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA.
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6
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Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [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: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
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Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
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7
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Lahiri P, Martin MS, Lino BR, Scheck RA, Van Deventer JA. Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast. Biochemistry 2023; 62:2098-2114. [PMID: 37377426 PMCID: PMC11146674 DOI: 10.1021/acs.biochem.2c00711] [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: 06/29/2023]
Abstract
Incorporation of more than one noncanonical amino acid (ncAA) within a single protein endows the resulting construct with multiple useful features such as augmented molecular recognition or covalent cross-linking capabilities. Herein, for the first time, we demonstrate the incorporation of two chemically distinct ncAAs into proteins biosynthesized in Saccharomyces cerevisiae. To complement ncAA incorporation in response to the amber (TAG) stop codon in yeast, we evaluated opal (TGA) stop codon suppression using three distinct orthogonal translation systems. We observed selective TGA readthrough without detectable cross-reactivity from host translation components. Readthrough efficiency at TGA was modulated by factors including the local nucleotide environment, gene deletions related to the translation process, and the identity of the suppressor tRNA. These observations facilitated systematic investigation of dual ncAA incorporation in both intracellular and yeast-displayed protein constructs, where we observed efficiencies up to 6% of wild-type protein controls. The successful display of doubly substituted proteins enabled the exploration of two critical applications on the yeast surface─(A) antigen binding functionality and (B) chemoselective modification with two distinct chemical probes through sequential application of two bioorthogonal click chemistry reactions. Lastly, by utilizing a soluble form of a doubly substituted construct, we validated the dual incorporation system using mass spectrometry and demonstrated the feasibility of conducting selective labeling of the two ncAAs sequentially using a "single-pot" approach. Overall, our work facilitates the addition of a 22nd amino acid to the genetic code of yeast and expands the scope of applications of ncAAs for basic biological research and drug discovery.
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Affiliation(s)
- Priyanka Lahiri
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Meghan S. Martin
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Rebecca A. Scheck
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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8
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Xiong B, Li Q, Yao J, Zheng W, Ou Y, He Y, Liao L, Wang X, Deng H, Zhang M, Sun G, He S, He J, Zhang X, Wang Z. Transcriptome and UPLC-MS/MS reveal mechanisms of amino acid biosynthesis in sweet orange 'Newhall' after different rootstocks grafting. FRONTIERS IN PLANT SCIENCE 2023; 14:1216826. [PMID: 37496860 PMCID: PMC10366444 DOI: 10.3389/fpls.2023.1216826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Sweet orange 'Newhall' (C. sinensis) is a popular fruit in high demand all over the world. Its peel and pulp are rich in a variety of nutrients and are widely used in catering, medicine, food and other industries. Grafting is commonly practiced in citrus production. Different rootstock types directly affect the fruit quality and nutritional flavor of citrus. However, the studies on citrus metabolites by grafting with different rootstocks are very limited, especially for amino acids (AAs). The preliminary test showed that there were significant differences in total amino acid content of two rootstocks (Poncirus trifoliata (CT) and C. junos Siebold ex Tanaka (CJ)) after grafting, and total amino acid content in the peel was higher than flesh. However, the molecular mechanism affecting amino acid differential accumulation remains unclear. Therefore, this study selected peel as the experimental material to reveal the amino acid components and differential accumulation mechanism of sweet orange 'Newhall' grafted with different rootstocks through combined transcriptome and metabolome analysis. Metabolome analysis identified 110 amino acids (AAs) and their derivatives in sweet orange 'Newhall' peels, with L-valine being the most abundant. L-asparagine was observed to be affected by both developmental periods and rootstock grafting. Weighted gene co-expression network analysis (WGCNA) combined with Redundancy Analysis (RDA) revealed eight hub structural genes and 41 transcription factors (TFs) that significantly influenced amino acid biosynthesis in sweet orange 'Newhall' peels. Our findings further highlight the significance of rootstock selection in enhancing the nutritional value of citrus fruits and might contribute to the development of functional citrus foods and nutritional amino acid supplements.
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Affiliation(s)
- Bo Xiong
- *Correspondence: Bo Xiong, ; Zhihui Wang,
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9
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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10
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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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11
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Koch NG, Baumann T, Nickling JH, Dziegielewski A, Budisa N. Engineered bacterial host for genetic encoding of physiologically stable protein nitration. Front Mol Biosci 2022; 9:992748. [PMID: 36353730 PMCID: PMC9638147 DOI: 10.3389/fmolb.2022.992748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
Across scales, many biological phenomena, such as protein folding or bioadhesion and cohesion, rely on synergistic effects of different amino acid side chains at multiple positions in the protein sequence. These are often fine-tuned by post-translational modifications that introduce additional chemical properties. Several PTMs can now be genetically encoded and precisely installed at single and multiple sites by genetic code expansion. Protein nitration is a PTM of particular interest because it has been associated with several diseases. However, even when these nitro groups are directly incorporated into proteins, they are often physiologically reduced during or shortly after protein production. We have solved this problem by using an engineered Escherichia coli host strain. Six genes that are associated with nitroreductase activity were removed from the genome in a simple and robust manner. The result is a bacterial expression host that can stably produce proteins and peptides containing nitro groups, especially when these are amenable to modification. To demonstrate the applicability of this strain, we used this host for several applications. One of these was the multisite incorporation of a photocaged 3,4-dihydroxyphenylalanine derivative into Elastin-Like Polypeptides. For this non-canonical amino acid and several other photocaged ncAAs, the nitro group is critical for photocleavability. Accordingly, our approach also enhances the production of biomolecules containing photocaged tyrosine in the form of ortho-nitrobenzyl-tyrosine. We envision our engineered host as an efficient tool for the production of custom designed proteins, peptides or biomaterials for various applications ranging from research in cell biology to large-scale production in biotechnology.
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Affiliation(s)
- Nikolaj G. Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jessica H. Nickling
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Anna Dziegielewski
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Chemical Synthetic Biology Group, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Nediljko Budisa,
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12
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Tittle JM, Schwark DG, Biddle W, Schmitt MA, Fisk JD. Impact of queuosine modification of endogenous E. coli tRNAs on sense codon reassignment. Front Mol Biosci 2022; 9:938114. [PMID: 36120552 PMCID: PMC9471426 DOI: 10.3389/fmolb.2022.938114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
The extent to which alteration of endogenous tRNA modifications may be exploited to improve genetic code expansion efforts has not been broadly investigated. Modifications of tRNAs are strongly conserved evolutionarily, but the vast majority of E. coli tRNA modifications are not essential. We identified queuosine (Q), a non-essential, hypermodified guanosine nucleoside found in position 34 of the anticodons of four E. coli tRNAs as a modification that could potentially be utilized to improve sense codon reassignment. One suggested purpose of queuosine modification is to reduce the preference of tRNAs with guanosine (G) at position 34 of the anticodon for decoding cytosine (C) ending codons over uridine (U) ending codons. We hypothesized that introduced orthogonal translation machinery with adenine (A) at position 34 would reassign U-ending codons more effectively in queuosine-deficient E. coli. We evaluated the ability of introduced orthogonal tRNAs with AUN anticodons to reassign three of the four U-ending codons normally decoded by Q34 endogenous tRNAs: histidine CAU, asparagine AAU, and aspartic acid GAU in the presence and absence of queuosine modification. We found that sense codon reassignment efficiencies in queuosine-deficient strains are slightly improved at Asn AAU, equivalent at His CAU, and less efficient at Asp GAU codons. Utilization of orthogonal pair-directed sense codon reassignment to evaluate competition events that do not occur in the standard genetic code suggests that tRNAs with inosine (I, 6-deaminated A) at position 34 compete much more favorably against G34 tRNAs than Q34 tRNAs. Continued evaluation of sense codon reassignment following targeted alterations to endogenous tRNA modifications has the potential to shed new light on the web of interactions that combine to preserve the fidelity of the genetic code as well as identify opportunities for exploitation in systems with expanded genetic codes.
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13
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Lou H, Yang Y, Zheng S, Ma Z, Chen W, Yu C, Song L, Wu J. Identification of key genes contributing to amino acid biosynthesis in Torreya grandis using transcriptome and metabolome analysis. Food Chem 2022; 379:132078. [PMID: 35063846 DOI: 10.1016/j.foodchem.2022.132078] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/29/2022]
Abstract
Torreya grandis has high economic and nutritional value due to the high nutrients in its kernels. The kernels of different development stages vary enormously in their amino acids content. However, the molecular basis and the regulatory mechanism of amino acid biosynthesis remain unclear. Here, transcriptome and metabolome analysis were performed. Correlation analysis result showed that 4 unigenes were significantly and positively correlated with at least 10 amino acids. The full length CDS of 2 unigenes (TgDAHP2 and TgASA1) were successfully cloned from the 4 unigenes for DAHP, ASA and CITS. Subcelluar localization analysis showed that both TgDAHP2 and TgASA1 were localized to the chloroplast. Overexpression of TgDAHP2 and TgASA1 in Arabidopsis can greatly increase the content of most amino acids. Moreover, 3 transcription factors were found to positively regulate the expression of TgASA1. This research contributes to understand the molecular regulatory mechanisms of amino acid biosynthesis in T. grandis.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yi Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhenmin Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
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14
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Xiong Q, Zheng T, Shen X, Li B, Fu J, Zhao X, Wang C, Yu Z. Expanding the functionality of proteins with genetically encoded dibenzo[ b, f][1,4,5]thiadiazepine: a photo-transducer for photo-click decoration. Chem Sci 2022; 13:3571-3581. [PMID: 35432856 PMCID: PMC8943893 DOI: 10.1039/d1sc05710c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic incorporation of novel noncanonical amino acids (ncAAs) that are specialized for the photo-click reaction allows the precisely orthogonal and site-specific functionalization of proteins in living cells under photo-control. However, the development of a r̲ing-strain i̲n situ l̲oadable d̲ipolarophile (RILD) as a genetically encodable reporter for photo-click bioconjugation with spatiotemporal controllability is quite rare. Herein, we report the design and synthesis of a photo-switchable d̲ib̲enzo[b,f][1,4,5]t̲hiad̲iazepine-based a̲lanine (DBTDA) ncAA, together with the directed evolution of a pyrrolysyl-tRNA synthetase/tRNACUA pair (PylRS/tRNACUA), to encode the DBTDA into recombinant proteins as a RILD in living E. coli cells. The fast-responsive photo-isomerization of the DBTDA residue can be utilized as a converter of photon energy into ring-strain energy to oscillate the conformational changes of the parent proteins. Due to the photo-activation of RILD, the photo-switching of the DBTDA residue on sfGFP and OmpC is capable of promoting the photo-click ligation with diarylsydnone (DASyd) derived probes with high efficiency and selectivity. We demonstrate that the genetic code expansion (GCE) with DBTDA benefits the studies on the distribution of decorated OmpC-DBTD on specific E. coli cells under a spatiotemporal resolved photo-stimulation. The GCE for encoding DBTDA enables further functional diversity of artificial proteins in living systems.
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Affiliation(s)
- Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Chunxia Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
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15
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Koch NG, Baumann T, Budisa N. Efficient Unnatural Protein Production by Pyrrolysyl-tRNA Synthetase With Genetically Fused Solubility Tags. Front Bioeng Biotechnol 2022; 9:807438. [PMID: 35284428 PMCID: PMC8905625 DOI: 10.3389/fbioe.2021.807438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022] Open
Abstract
Introducing non-canonical amino acids (ncAAs) by engineered orthogonal pairs of aminoacyl-tRNA synthetases and tRNAs has proven to be a highly useful tool for the expansion of the genetic code. Pyrrolysyl-tRNA synthetase (PylRS) from methanogenic archaeal and bacterial species is particularly attractive due to its natural orthogonal reactivity in bacterial and eukaryotic cells. However, the scope of such a reprogrammed translation is often limited, due to low yields of chemically modified target protein. This can be the result of substrate specificity engineering, which decreases the aminoacyl-tRNA synthetase stability and reduces the abundance of active enzyme. We show that the solubility and folding of these engineered enzymes can become a bottleneck for the production of ncAA-containing proteins in vivo. Solubility tags derived from various species provide a strategy to remedy this issue. We find the N-terminal fusion of the small metal binding protein from Nitrosomonas europaea to the PylRS sequence to improve enzyme solubility and to boost orthogonal translation efficiency. Our strategy enhances the production of site-specifically labelled proteins with a variety of engineered PylRS variants by 200–540%, and further allows triple labeling. Even the wild-type enzyme gains up to 245% efficiency for established ncAA substrates.
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Affiliation(s)
- Nikolaj G Koch
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany.,Bioanalytik, Institut für Biotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany.,Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
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16
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Biddle W, Schwark DG, Schmitt MA, Fisk JD. Directed Evolution Pipeline for the Improvement of Orthogonal Translation Machinery for Genetic Code Expansion at Sense Codons. Front Chem 2022; 10:815788. [PMID: 35252113 PMCID: PMC8891652 DOI: 10.3389/fchem.2022.815788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
The expansion of the genetic code beyond a single type of noncanonical amino acid (ncAA) is hindered by inefficient machinery for reassigning the meaning of sense codons. A major obstacle to using directed evolution to improve the efficiency of sense codon reassignment is that fractional sense codon reassignments lead to heterogeneous mixtures of full-length proteins with either a ncAA or a natural amino acid incorporated in response to the targeted codon. In stop codon suppression systems, missed incorporations lead to truncated proteins; improvements in activity may be inferred from increased protein yields or the production of downstream reporters. In sense codon reassignment, the heterogeneous proteins produced greatly complicate the development of screens for variants of the orthogonal machinery with improved activity. We describe the use of a previously-reported fluorescence-based screen for sense codon reassignment as the first step in a directed evolution workflow to improve the incorporation of a ncAA in response to the Arg AGG sense codon. We first screened a library with diversity introduced into both the orthogonal Methanocaldococcus jannaschii tyrosyl tRNA anticodon loop and the cognate aminoacyl tRNA synthetase (aaRS) anticodon binding domain for variants that improved incorporation of tyrosine in response to the AGG codon. The most efficient variants produced fluorescent proteins at levels indistinguishable from the E. coli translation machinery decoding tyrosine codons. Mutations to the M. jannaschii aaRS that were found to improve tyrosine incorporation were transplanted onto a M. jannaschii aaRS evolved for the incorporation of para-azidophenylalanine. Improved ncAA incorporation was evident using fluorescence- and mass-based reporters. The described workflow is generalizable and should enable the rapid tailoring of orthogonal machinery capable of activating diverse ncAAs to any sense codon target. We evaluated the selection based improvements of the orthogonal pair in a host genomically engineered for reduced target codon competition. Using this particular system for evaluation of arginine AGG codon reassignment, however, E. coli strains with genomes engineered to remove competing tRNAs did not outperform a standard laboratory E. coli strain in sense codon reassignment.
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17
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Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nat Commun 2021; 12:7039. [PMID: 34857769 PMCID: PMC8639764 DOI: 10.1038/s41467-021-27399-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/16/2021] [Indexed: 01/24/2023] Open
Abstract
Site-specific incorporation of unnatural amino acids (UAAs) with similar incorporation efficiency to that of natural amino acids (NAAs) and low background activity is extremely valuable for efficient synthesis of proteins with diverse new chemical functions and design of various synthetic auxotrophs. However, such efficient translation systems remain largely unknown in the literature. Here, we describe engineered chimeric phenylalanine systems that dramatically increase the yield of proteins bearing UAAs, through systematic engineering of the aminoacyl-tRNA synthetase and its respective cognate tRNA. These engineered synthetase/tRNA pairs allow single-site and multi-site incorporation of UAAs with efficiencies similar to those of NAAs and high fidelity. In addition, using the evolved chimeric phenylalanine system, we construct a series of E. coli strains whose growth is strictly dependent on exogenously supplied of UAAs. We further show that synthetic auxotrophic cells can grow robustly in living mice when UAAs are supplemented.
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18
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Kim S, Yi H, Kim YT, Lee HS. Engineering Translation Components for Genetic Code Expansion. J Mol Biol 2021; 434:167302. [PMID: 34673113 DOI: 10.1016/j.jmb.2021.167302] [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: 07/29/2021] [Revised: 09/26/2021] [Accepted: 10/05/2021] [Indexed: 12/18/2022]
Abstract
The expansion of the genetic code consisting of four bases and 20 amino acids into diverse building blocks has been an exciting topic in synthetic biology. Many biochemical components are involved in gene expression; therefore, adding a new component to the genetic code requires engineering many other components that interact with it. Genetic code expansion has advanced significantly for the last two decades with the engineering of several components involved in protein synthesis. These components include tRNA/aminoacyl-tRNA synthetase, new codons, ribosomes, and elongation factor Tu. In addition, biosynthesis and enhanced uptake of non-canonical amino acids have been attempted and have made meaningful progress. This review discusses the efforts to engineer these translation components, to improve the genetic code expansion technology.
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Affiliation(s)
- Sooin Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Hanbin Yi
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Yurie T Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 04107, Republic of Korea.
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19
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Bartoschek MD, Ugur E, Nguyen TA, Rodschinka G, Wierer M, Lang K, Bultmann S. Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. Nucleic Acids Res 2021; 49:e62. [PMID: 33684219 PMCID: PMC8216290 DOI: 10.1093/nar/gkab132] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022] Open
Abstract
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
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Affiliation(s)
- Michael D Bartoschek
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Enes Ugur
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tuan-Anh Nguyen
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Geraldine Rodschinka
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kathrin Lang
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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20
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Manandhar M, Chun E, Romesberg FE. Genetic Code Expansion: Inception, Development, Commercialization. J Am Chem Soc 2021; 143:4859-4878. [DOI: 10.1021/jacs.0c11938] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Miglena Manandhar
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | - Eugene Chun
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
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21
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Islam M, Kehoe HP, Lissoos JB, Huang M, Ghadban CE, Sánchez GB, Lane HZ, Van Deventer JA. Chemical Diversification of Simple Synthetic Antibodies. ACS Chem Biol 2021; 16:344-359. [PMID: 33482061 PMCID: PMC8096149 DOI: 10.1021/acschembio.0c00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibodies possess properties that make them valuable as therapeutics, diagnostics, and basic research tools. However, antibody chemical reactivity and covalent antigen binding are constrained, or even prevented, by the narrow range of chemistries encoded in canonical amino acids. In this work, we investigate strategies for leveraging an expanded range of chemical functionality using yeast displayed antibodies containing noncanonical amino acids (ncAAs) in or near antibody complementarity determining regions (CDRs). To enable systematic characterization of the effects of ncAA incorporation on antibody function, we first investigated whether diversification of a single antibody loop would support the isolation of binding clones against immunoglobulins from three species. We constructed and screened a billion-member library containing canonical amino acid diversity and loop length diversity only within the third complementarity determining region of the heavy chain (CDR-H3). Isolated clones exhibited moderate affinities (double- to triple-digit nanomolar affinities) and, in several cases, single-species specificity, confirming that antibody specificity can be mediated by a single CDR. This constrained diversity enabled the utilization of additional CDRs for the installation of chemically reactive and photo-cross-linkable ncAAs. Binding studies of ncAA-substituted antibodies revealed that ncAA incorporation is reasonably well tolerated, with observed changes in affinity occurring as a function of ncAA side chain identity, substitution site, and the ncAA incorporation machinery used. Multiple azide-containing ncAAs supported copper-catalyzed azide-alkyne cycloaddition (CuAAC) and strain-promoted azide-alkyne cycloaddition (SPAAC) without the abrogation of binding function. Similarly, several alkyne substitutions facilitated CuAAC without the apparent disruption of binding. Finally, antibodies substituted with a photo-cross-linkable ncAA were evaluated for ultraviolet-mediated cross-linking on the yeast surface. Competition-based assays revealed position-dependent covalent linkages, strongly suggesting successful cross-linking. Key findings regarding CuAAC reactions and photo-cross-linking on the yeast surface were confirmed using soluble forms of ncAA-substituted clones. The consistency of findings on the yeast surface and in solution suggest that chemical diversification can be incorporated into yeast display screening approaches. Taken together, our results highlight the power of integrating the use of yeast display and ncAAs in search of proteins with "chemically augmented" binding functions. This includes strategies for systematically introducing small molecule functionality within binding protein structures and evaluating protein-based covalent target binding. The efficient preparation and chemical diversification of antibodies on the yeast surface open up new possibilities for discovering "drug-like" protein leads in high throughput.
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Affiliation(s)
- Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Jacob B. Lissoos
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Manjie Huang
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Christopher E. Ghadban
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Greg B. Sánchez
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Hanan Z. Lane
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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22
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Walsh SJ, Bargh JD, Dannheim FM, Hanby AR, Seki H, Counsell AJ, Ou X, Fowler E, Ashman N, Takada Y, Isidro-Llobet A, Parker JS, Carroll JS, Spring DR. Site-selective modification strategies in antibody-drug conjugates. Chem Soc Rev 2021; 50:1305-1353. [PMID: 33290462 DOI: 10.1039/d0cs00310g] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibody-drug conjugates (ADCs) harness the highly specific targeting capabilities of an antibody to deliver a cytotoxic payload to specific cell types. They have garnered widespread interest in drug discovery, particularly in oncology, as discrimination between healthy and malignant tissues or cells can be achieved. Nine ADCs have received approval from the US Food and Drug Administration and more than 80 others are currently undergoing clinical investigations for a range of solid tumours and haematological malignancies. Extensive research over the past decade has highlighted the critical nature of the linkage strategy adopted to attach the payload to the antibody. Whilst early generation ADCs were primarily synthesised as heterogeneous mixtures, these were found to have sub-optimal pharmacokinetics, stability, tolerability and/or efficacy. Efforts have now shifted towards generating homogeneous constructs with precise drug loading and predetermined, controlled sites of attachment. Homogeneous ADCs have repeatedly demonstrated superior overall pharmacological profiles compared to their heterogeneous counterparts. A wide range of methods have been developed in the pursuit of homogeneity, comprising chemical or enzymatic methods or a combination thereof to afford precise modification of specific amino acid or sugar residues. In this review, we discuss advances in chemical and enzymatic methods for site-specific antibody modification that result in the generation of homogeneous ADCs.
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Affiliation(s)
- Stephen J Walsh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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23
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Schwark DG, Schmitt MA, Fisk JD. Directed Evolution of the Methanosarcina barkeri Pyrrolysyl tRNA/aminoacyl tRNA Synthetase Pair for Rapid Evaluation of Sense Codon Reassignment Potential. Int J Mol Sci 2021; 22:E895. [PMID: 33477414 PMCID: PMC7830368 DOI: 10.3390/ijms22020895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic code expansion has largely focused on the reassignment of amber stop codons to insert single copies of non-canonical amino acids (ncAAs) into proteins. Increasing effort has been directed at employing the set of aminoacyl tRNA synthetase (aaRS) variants previously evolved for amber suppression to incorporate multiple copies of ncAAs in response to sense codons in Escherichia coli. Predicting which sense codons are most amenable to reassignment and which orthogonal translation machinery is best suited to each codon is challenging. This manuscript describes the directed evolution of a new, highly efficient variant of the Methanosarcina barkeri pyrrolysyl orthogonal tRNA/aaRS pair that activates and incorporates tyrosine. The evolved M. barkeri tRNA/aaRS pair reprograms the amber stop codon with 98.1 ± 3.6% efficiency in E. coli DH10B, rivaling the efficiency of the wild-type tyrosine-incorporating Methanocaldococcus jannaschii orthogonal pair. The new orthogonal pair is deployed for the rapid evaluation of sense codon reassignment potential using our previously developed fluorescence-based screen. Measurements of sense codon reassignment efficiencies with the evolved M. barkeri machinery are compared with related measurements employing the M. jannaschii orthogonal pair system. Importantly, we observe different patterns of sense codon reassignment efficiency for the M. jannaschii tyrosyl and M. barkeri pyrrolysyl systems, suggesting that particular codons will be better suited to reassignment by different orthogonal pairs. A broad evaluation of sense codon reassignment efficiencies to tyrosine with the M. barkeri system will highlight the most promising positions at which the M. barkeri orthogonal pair may infiltrate the E. coli genetic code.
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Affiliation(s)
| | | | - John D. Fisk
- Department of Chemistry, University of Colorado Denver, Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA; (D.G.S.); (M.A.S.)
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24
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Mekkattu Tharayil S, Mahawaththa M, Loh CT, Adekoya I, Otting G. Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:1-13. [PMID: 37904776 PMCID: PMC10539748 DOI: 10.5194/mr-2-1-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/12/2020] [Indexed: 11/01/2023]
Abstract
Pseudocontact shifts (PCSs) generated by paramagnetic lanthanide ions provide valuable long-range structural information in nuclear magnetic resonance (NMR) spectroscopic analyses of biological macromolecules such as proteins, but labelling proteins site-specifically with a single lanthanide ion remains an ongoing challenge, especially for proteins that are not suitable for ligation with cysteine-reactive lanthanide complexes. We show that a specific lanthanide-binding site can be installed on proteins by incorporation of phosphoserine in conjunction with other negatively charged residues, such as aspartate, glutamate or a second phosphoserine residue. The close proximity of the binding sites to the protein backbone leads to good immobilization of the lanthanide ion, as evidenced by the excellent quality of fits between experimental PCSs and PCSs calculated with a single magnetic susceptibility anisotropy (Δ χ ) tensor. An improved two-plasmid system was designed to enhance the yields of proteins with genetically encoded phosphoserine, and good lanthanide ion affinities were obtained when the side chains of the phosphoserine and aspartate residues are not engaged in salt bridges, although the presence of too many negatively charged residues in close proximity can also lead to unfolding of the protein. In view of the quality of the Δ χ tensors that can be obtained from lanthanide-binding sites generated by site-specific incorporation of phosphoserine, this method presents an attractive tool for generating PCSs in stable proteins, particularly as it is independent of cysteine residues.
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Affiliation(s)
- Sreelakshmi Mekkattu Tharayil
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Mithun Chamikara Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Choy-Theng Loh
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
- present address: Hangzhou Wayland Bioscience Co. Ltd, Hangzhou
310030, PR China
| | - Ibidolapo Adekoya
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
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25
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Abstract
The encoded biosynthesis of proteins provides the ultimate paradigm for high-fidelity synthesis of long polymers of defined sequence and composition, but it is limited to polymerizing the canonical amino acids. Recent advances have built on genetic code expansion - which commonly permits the cellular incorporation of one type of non-canonical amino acid into a protein - to enable the encoded incorporation of several distinct non-canonical amino acids. Developments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize completely recoded genomes and create orthogonal translational components with reprogrammed specificities. These advances may enable the genetically encoded synthesis of non-canonical biopolymers and provide a platform for transforming the discovery and evolution of new materials and therapeutics.
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Affiliation(s)
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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26
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Witte A, Muñoz-López Á, Metz M, Schweiger MR, Janning P, Summerer D. Encoded, click-reactive DNA-binding domains for programmable capture of specific chromatin segments. Chem Sci 2020; 11:12506-12511. [PMID: 34123231 PMCID: PMC8162481 DOI: 10.1039/d0sc02707c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/16/2020] [Indexed: 11/21/2022] Open
Abstract
Enrichment of chromatin segments from specific genomic loci of living cells is an important goal in chromatin biology, since it enables establishing local molecular compositions as the basis of locus function. A central enrichment strategy relies on the expression of DNA-binding domains that selectively interact with a local target sequence followed by fixation and isolation of the associated chromatin segment. The efficiency and selectivity of this approach critically depend on the employed enrichment tag and the strategy used for its introduction into the DNA-binding domain or close-by proteins. We here report chromatin enrichment by expressing programmable transcription-activator-like effectors (TALEs) bearing single strained alkynes or alkenes introduced via genetic code expansion. This enables in situ biotinylation at a defined TALE site via strain-promoted inverse electron demand Diels Alder cycloadditions for single-step, high affinity enrichment. By targeting human pericentromeric SATIII repeats, the origin of nuclear stress bodies, we demonstrate enrichment of SATIII DNA and SATIII-associated proteins, and identify factors enriched during heat stress.
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Affiliation(s)
- Anna Witte
- Faculty of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Álvaro Muñoz-López
- Faculty of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Malte Metz
- Max-Planck Institute for Molecular Physiology Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Michal R Schweiger
- Institute for Translational Epigenetics, Medical Faculty, University of Cologne Weyertal 115b 50931 Köln Germany
- Center for Molecular Medicine Cologne Robert-Koch-Str. 21 50931 Cologne Germany
| | - Petra Janning
- Max-Planck Institute for Molecular Physiology Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
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27
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Pérez-Mejías G, Velázquez-Cruz A, Guerra-Castellano A, Baños-Jaime B, Díaz-Quintana A, González-Arzola K, Ángel De la Rosa M, Díaz-Moreno I. Exploring protein phosphorylation by combining computational approaches and biochemical methods. Comput Struct Biotechnol J 2020; 18:1852-1863. [PMID: 32728408 PMCID: PMC7369424 DOI: 10.1016/j.csbj.2020.06.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications of proteins expand their functional diversity, regulating the response of cells to a variety of stimuli. Among these modifications, phosphorylation is the most ubiquitous and plays a prominent role in cell signaling. The addition of a phosphate often affects the function of a protein by altering its structure and dynamics. However, these alterations are often difficult to study and the functional and structural implications remain unresolved. New approaches are emerging to overcome common obstacles related to the production and manipulation of these samples. Here, we summarize the available methods for phosphoprotein purification and phosphomimetic engineering, highlighting the advantages and disadvantages of each. We propose a general workflow for protein phosphorylation analysis combining computational and biochemical approaches, building on recent advances that enable user-friendly and easy-to-access Molecular Dynamics simulations. We hope this innovative workflow will inform the best experimental approach to explore such post-translational modifications. We have applied this workflow to two different human protein models: the hemeprotein cytochrome c and the RNA binding protein HuR. Our results illustrate the usefulness of Molecular Dynamics as a decision-making tool to design the most appropriate phosphomimetic variant.
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Affiliation(s)
- Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Katiuska González-Arzola
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Miguel Ángel De la Rosa
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
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28
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Wang T, Liang C, Xu H, An Y, Xiao S, Zheng M, Liu L, Nie L. Incorporation of nonstandard amino acids into proteins: principles and applications. World J Microbiol Biotechnol 2020; 36:60. [PMID: 32266578 DOI: 10.1007/s11274-020-02837-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/04/2020] [Indexed: 01/01/2023]
Abstract
The cellular ribosome shows a naturally evolved strong preference for the synthesis of proteins with standard amino acids. An in-depth understanding of the translation process enables scientists to go beyond this natural limitation and engineer translating systems capable of synthesizing proteins with artificially designed and synthesized non-standard amino acids (nsAA) featuring more bulky sidechains. The sidechains can be functional groups, with chosen biophysical or chemical activities, that enable the direct application of these proteins. Alternatively, the sidechains can be designed to contain highly reactive groups: enabling the ready formation of conjugates via a covalent bond between the sidechain and other chemicals or biomolecules. This co-translational incorporation of nsAAs into proteins allows for a vast number of possible applications. In this paper, we first systematically summarized the advances in the engineering of the translation system. Subsequently, we reviewed the extensive applications of these nsAA-containing proteins (after chemical modification) by discussing representative reports on how they can be utilized for different purposes. Finally, we discussed the direction of further studies which could be undertaken to improve the current technology utilized in incorporating nsAAs in order to use them to their full potential and improve accessibility across disciplines.
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Affiliation(s)
- Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Chen Liang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Hongjv Xu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yafei An
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Sha Xiao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Mengyuan Zheng
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Lu Liu
- College of International Education, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Lei Nie
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China.
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29
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Scheidler CM, Vrabel M, Schneider S. Genetic Code Expansion, Protein Expression, and Protein Functionalization in Bacillus subtilis. ACS Synth Biol 2020; 9:486-493. [PMID: 32053368 DOI: 10.1021/acssynbio.9b00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The site-specific chemical modification of proteins through incorporation of noncanonical amino acids enables diverse applications, such as imaging, probing, and expanding protein functions, as well as to precisely engineer therapeutics. Here we report a general strategy that allows the incorporation of noncanonical amino acids into target proteins using the amber suppression method and their efficient secretion in the biotechnological relevant expression host Bacillus subtilis. This facilitates efficient purification of target proteins directly from the supernatant, followed by their functionalization using click chemistry. We used this strategy to site-specifically introduce norbornene lysine into a single chain antibody and functionalize it with fluorophores for the detection of human target proteins.
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Affiliation(s)
- Christopher M. Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstraße 5-13, Munich, 81377, Germany
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, Prague 6, CZ-166 10, Czech Republic
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstraße 5-13, Munich, 81377, Germany
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30
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Potts KA, Stieglitz JT, Lei M, Van Deventer JA. Reporter system architecture affects measurements of noncanonical amino acid incorporation efficiency and fidelity. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:573-588. [PMID: 33791108 PMCID: PMC8009230 DOI: 10.1039/c9me00107g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) within proteins supports a growing number of applications ranging from fundamental biological studies to enhancing the properties of biological therapeutics. Currently, our quantitative understanding of ncAA incorporation systems is confounded by the diverse set of characterization and analysis approaches used to quantify ncAA incorporation events. While several effective reporter systems support such measurements, it is not clear how quantitative results from different reporters relate to one another, or which details influence measurements most strongly. Here, we evaluate the quantitative performance of single-fluorescent protein reporters, dual-fluorescent protein reporters, and cell surface-displayed protein reporters of ncAA insertion in response to the TAG (amber) codon in yeast. While different reporters support varying levels of apparent readthrough efficiencies, flow cytometry-based evaluations with dual reporters yielded measurements exhibiting consistent quantitative trends and precision across all evaluated conditions. Further investigations of dual-fluorescent protein reporter architecture revealed that quantitative outputs are influenced by stop codon location and N- and C-terminal fluorescent protein identity. Both dual-fluorescent protein reporters and a "drop-in" version of yeast display support quantification of ncAA incorporation in several single-gene knockout strains, revealing strains that enhance ncAA incorporation efficiency without compromising fidelity. Our studies reveal critical details regarding reporter system performance in yeast and how to effectively deploy such reporters. These findings have substantial implications for how to engineer ncAA incorporation systems-and protein translation apparatuses-to better accommodate alternative genetic codes for expanding the chemical diversity of biosynthesized proteins.
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Affiliation(s)
- K A Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - J T Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - M Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - J A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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31
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Roy G, Reier J, Garcia A, Martin T, Rice M, Wang J, Prophet M, Christie R, Dall’Acqua W, Ahuja S, Bowen MA, Marelli M. Development of a high yielding expression platform for the introduction of non-natural amino acids in protein sequences. MAbs 2020; 12:1684749. [PMID: 31775561 PMCID: PMC6927762 DOI: 10.1080/19420862.2019.1684749] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
The ability to genetically encode non-natural amino acids (nnAAs) into proteins offers an expanded tool set for protein engineering. nnAAs containing unique functional moieties have enabled the study of post-translational modifications, protein interactions, and protein folding. In addition, nnAAs have been developed that enable a variety of biorthogonal conjugation chemistries that allow precise and efficient protein conjugations. These are being studied to create the next generation of antibody-drug conjugates with improved efficacy, potency, and stability for the treatment of cancer. However, the efficiency of nnAA incorporation, and the productive yields of cell-based expression systems, have limited the utility and widespread use of this technology. We developed a process to isolate stable cell lines expressing a pyrrolysyl-tRNA synthetase/tRNApyl pair capable of efficient nnAA incorporation. Two different platform cell lines generated by these methods were used to produce IgG-expressing cell lines with normalized antibody titers of 3 g/L using continuous perfusion. We show that the antibodies produced by these platform cells contain the nnAA functionality that enables facile conjugations. Characterization of these highly active and robust platform hosts identified key parameters that affect nnAA incorporation efficiency. These highly efficient host platforms may help overcome the expression challenges that have impeded the developability of this technology for manufacturing proteins with nnAAs and represents an important step in expanding its utility.
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Affiliation(s)
- Gargi Roy
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jason Reier
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Andrew Garcia
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Tom Martin
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Megan Rice
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jihong Wang
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Meagan Prophet
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Ronald Christie
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - William Dall’Acqua
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Sanjeev Ahuja
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
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32
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Budisa N, Schneider T. Expanding the DOPA Universe with Genetically Encoded, Mussel-Inspired Bioadhesives for Material Sciences and Medicine. Chembiochem 2019; 20:2163-2190. [PMID: 30830997 DOI: 10.1002/cbic.201900030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Catechols are a biologically relevant group of aromatic diols that have attracted much attention as mediators of adhesion of "bio-glue" proteins in mussels of the genus Mytilus. These organisms use catechols in the form of the noncanonical amino acid l-3,4-dihydroxyphenylalanine (DOPA) as a building block for adhesion proteins. The DOPA is generated post-translationally from tyrosine. Herein, we review the properties, natural occurrence, and reactivity of catechols in the design of bioinspired materials. We also provide a basic description of the mussel's attachment apparatus, the interplay between its different molecules that play a crucial role in adhesion, and the role of post-translational modifications (PTMs) of these proteins. Our focus is on the microbial production of mussel foot proteins with the aid of orthogonal translation systems (OTSs) and the use of genetic code engineering to solve some fundamental problems in the bioproduction of these bioadhesives and to expand their chemical space. The major limitation of bacterial expression systems is their intrinsic inability to introduce PTMs. OTSs have the potential to overcome these challenges by replacing canonical amino acids with noncanonical ones. In this way, PTM steps are circumvented while the genetically programmed precision of protein sequences is preserved. In addition, OTSs should enable spatiotemporal control over the complex adhesion process, because the catechol function can be masked by suitable chemical protection. Such caged residues can then be noninvasively unmasked by, for example, UV irradiation or thermal treatment. All of these features make OTSs based on genetic code engineering in reprogrammed microbial strains new and promising tools in bioinspired materials science.
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Affiliation(s)
- Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany.,Chair of Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2, Winnipeg, MB, Canada
| | - Tobias Schneider
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
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Widder P, Berner F, Summerer D, Drescher M. Double Nitroxide Labeling by Copper-Catalyzed Azide-Alkyne Cycloadditions with Noncanonical Amino Acids for Electron Paramagnetic Resonance Spectroscopy. ACS Chem Biol 2019; 14:839-844. [PMID: 30998314 PMCID: PMC6534342 DOI: 10.1021/acschembio.8b01111] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 01/17/2023]
Abstract
Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling (SDSL) is an important tool to obtain long-range distance restraints for protein structural research. We here study a variety of azide- and alkyne-bearing noncanonical amino acids (ncAA) in terms of protein single- and double-incorporation efficiency via nonsense suppression, metabolic stability, yields of nitroxide labeling via copper-catalyzed [3 + 2] azide-alkyne cycloadditions (CuAAC), and spectroscopic properties in continuous-wave and double electron-electron resonance measurements. We identify para-ethynyl-l-phenylalanine and para-propargyloxy-l-phenylalanine as suitable ncAA for CuAAC-based SDSL that will complement current SDSL approaches, particularly in cases in which essential cysteines of a target protein prevent the use of sulfhydryl-reactive spin labels.
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Affiliation(s)
- Pia Widder
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Frederic Berner
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Summerer
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund, Germany
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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34
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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35
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Müller TG, Sakin V, Müller B. A Spotlight on Viruses-Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules 2019; 24:molecules24030481. [PMID: 30700005 PMCID: PMC6385038 DOI: 10.3390/molecules24030481] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/03/2023] Open
Abstract
The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Volkan Sakin
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
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36
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Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair. Genes (Basel) 2018; 9:genes9110546. [PMID: 30424562 PMCID: PMC6266110 DOI: 10.3390/genes9110546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1.
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37
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Hostetler ZM, Ferrie JJ, Bornstein MR, Sungwienwong I, Petersson EJ, Kohli RM. Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability. ACS Chem Biol 2018; 13:2855-2861. [PMID: 30216041 PMCID: PMC6195468 DOI: 10.1021/acschembio.8b00696] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Improvements in genetic code expansion have made preparing proteins with diverse functional groups almost routine. Nonetheless, unnatural amino acids (Uaas) pose theoretical burdens on protein solubility, and determinants of position-specific tolerability to Uaas remain underexplored. To broadly examine associations, we systematically assessed the effect of substituting the fluorescent Uaa, acridonylalanine, at more than 50 chemically, evolutionarily, and structurally diverse residues in two bacterial proteins: LexA and RecA. Surprisingly, properties that ostensibly contribute to Uaa tolerability-such as conservation, hydrophobicity, or accessibility-demonstrated no consistent correlations with resulting protein solubility. Instead, solubility is closely dependent on the location of the substitution within the overall tertiary structure, suggesting that intrinsic properties of protein domains, and not individual positions, are stronger determinants of Uaa tolerability. Consequently, those who seek to install Uaas in new target proteins should consider broadening, rather than narrowing, the types of residues screened for Uaa incorporation.
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Affiliation(s)
- Zachary M. Hostetler
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - John J. Ferrie
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Marc R. Bornstein
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Itthipol Sungwienwong
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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38
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Site-Specific Labelling of Multidomain Proteins by Amber Codon Suppression. Sci Rep 2018; 8:14864. [PMID: 30291265 PMCID: PMC6173736 DOI: 10.1038/s41598-018-33115-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/18/2018] [Indexed: 01/30/2023] Open
Abstract
The access to information on the dynamic behaviour of large proteins is usually hindered as spectroscopic methods require the site-specific attachment of biophysical probes. A powerful emerging tool to tackle this issue is amber codon suppression. Till date, its application on large and complex multidomain proteins of MDa size has not been reported. Herein, we systematically investigate the feasibility to introduce different non-canonical amino acids into a 540 kDa homodimeric fatty acid synthase type I by genetic code expansion with subsequent fluorescent labelling. Our approach relies on a microplate-based reporter assay of low complexity using a GFP fusion protein to quickly screen for sufficient suppression conditions. Once identified, these findings were successfully utilized to upscale both the expression scale and the protein size to full-length constructs. These fluorescently labelled samples of fatty acid synthase were subjected to initial biophysical experiments, including HPLC analysis, activity assays and fluorescence spectroscopy. Successful introduction of such probes into a molecular machine such as fatty acid synthases may pave the way to understand the conformational variability, which is a primary intrinsic property required for efficient interplay of all catalytic functionalities, and to engineer them.
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39
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Schmidt A, Altincekic N, Gustmann H, Wachtveitl J, Hengesbach M. The Protein Microenvironment Governs the Suitability of Labeling Sites for Single-Molecule Spectroscopy of RNP Complexes. ACS Chem Biol 2018; 13:2472-2483. [PMID: 30060648 DOI: 10.1021/acschembio.8b00348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule techniques allow unique insights into biological systems as they provide unrivaled access to structural dynamics and conformational heterogeneity. One major bottleneck for reliable single-molecule Förster resonance energy transfer (smFRET) analysis is the identification of suitable fluorophore labeling sites that neither impair the function of the biological system nor cause photophysical artifacts of the fluorophore. To address this issue, we identified the contribution of virtually all individual parameters that affect Förster resonance energy transfer between two fluorophores attached to a ribonucleoprotein complex consisting of the RNA-binding protein L7Ae and a cognate kink turn containing RNA. A non-natural amino acid was incorporated at various positions of the protein using an amber suppression system (pEVOL) to label the protein via copper(I)-catalyzed alkyne-azide cycloaddition. On the basis of simulations followed by functional, structural, and multiparameter fluorescence analysis of five different smFRET RNPs, new insights into the design of smFRET RNPs were obtained. From this, a correlation between the photophysical properties of fluorophores attached to the protein and the predictability of the corresponding smFRET construct was established. Additionally, we identify a straightforward experimental method for characterizing selected labeling sites. Overall, this protocol allows fast generation and assessment of functional RNPs for accurate single-molecule experiments.
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Affiliation(s)
- Andreas Schmidt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Henrik Gustmann
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
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40
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Stieglitz JT, Kehoe HP, Lei M, Van Deventer JA. A Robust and Quantitative Reporter System To Evaluate Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2018; 7:2256-2269. [PMID: 30139255 PMCID: PMC6214617 DOI: 10.1021/acssynbio.8b00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Engineering protein translation machinery to incorporate noncanonical amino acids (ncAAs) into proteins has advanced applications ranging from proteomics to single-molecule studies. As applications of ncAAs emerge, efficient ncAA incorporation is crucial to exploiting unique chemistries. We have established a quantitative reporter platform to evaluate ncAA incorporation in response to the TAG (amber) codon in yeast. This yeast display-based reporter utilizes an antibody fragment containing an amber codon at which a ncAA is incorporated when the appropriate orthogonal translation system (OTS) is present. Epitope tags at both termini allow for flow cytometry-based end point readouts of OTS efficiency and fidelity. Using this reporter, we evaluated several factors that influence amber suppression, including the amber codon position and different aminoacyl-tRNA synthetase/tRNA (aaRS/tRNA) pairs. Interestingly, previously described aaRSs that evolved from different parent enzymes to incorporate O-methyl-l-tyrosine exhibit vastly different behavior. Escherichia coli leucyl-tRNA synthetase variants demonstrated efficient incorporation of a range of ncAAs, and we discovered unreported activities of several variants. Compared to a plate reader-based reporter, our assay yields more precise bulk-level measurements while also supporting single-cell readouts compatible with cell sorting. This platform is expected to allow quantitative elucidation of principles dictating efficient stop codon suppression and evolution of next-generation stop codon suppression systems to further enhance genetic code manipulation in eukaryotes. These efforts will improve our understanding of how the genetic code can be further evolved while expanding the range of chemical diversity available in proteins for applications ranging from fundamental epigenetics studies to engineering new classes of therapeutics.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Ming Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, United States
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41
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Nikić-Spiegel I. Genetic Code Expansion- and Click Chemistry-Based Site-Specific Protein Labeling for Intracellular DNA-PAINT Imaging. Methods Mol Biol 2018; 1728:279-295. [PMID: 29405005 DOI: 10.1007/978-1-4939-7574-7_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Super-resolution microscopy allows imaging of cellular structures at nanometer resolution. This comes with a demand for small labels which can be attached directly to the structures of interest. In the context of protein labeling, one way to achieve this is by using genetic code expansion (GCE) and click chemistry. With GCE, small labeling handles in the form of noncanonical amino acids (ncAAs) are site-specifically introduced into a target protein. In a subsequent step, these amino acids can be directly labeled with small organic dyes by click chemistry reactions. Click chemistry labeling can also be combined with other methods, such as DNA-PAINT in which a "clickable" oligonucleotide is first attached to the ncAA-bearing target protein and then labeled with complementary fluorescent oligonucleotides. This protocol will cover both aspects: I describe (1) how to encode ncAAs and perform intracellular click chemistry-based labeling with an improved GCE system for eukaryotic cells and (2) how to combine click chemistry-based labeling with DNA-PAINT super-resolution imaging. As an example, I show click-PAINT imaging of vimentin and low-abundance nuclear protein, nucleoporin 153.
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Affiliation(s)
- Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, The Eberhard Karls University of Tübingen, Tübingen, Germany.
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42
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Volkwein W, Maier C, Krafczyk R, Jung K, Lassak J. A Versatile Toolbox for the Control of Protein Levels Using N ε-Acetyl-l-lysine Dependent Amber Suppression. ACS Synth Biol 2017; 6:1892-1902. [PMID: 28594177 DOI: 10.1021/acssynbio.7b00048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The analysis of the function of essential genes in vivo depends on the ability to experimentally modulate levels of their protein products. Current methods to address this are based on transcriptional or post-transcriptional regulation of mRNAs, but approaches based on the exploitation of translation regulation have so far been neglected. Here we describe a toolbox, based on amber suppression in the presence of Nε-acetyl-l-lysine (AcK), for translational tuning of protein output. We chose the highly sensitive luminescence system LuxCDABE as a reporter and incorporated a UAG stop codon into the gene for the reductase subunit LuxC. The system was used to measure and compare the effects of AcK- and Nε-(tert-butoxycarbonyl)-l-lysine (BocK) dependent amber suppression in Escherichia coli. We also demonstrate here that, in combination with transcriptional regulation, the system allows protein production to be either totally repressed or gradually adjusted. To identify sequence motifs that provide improved translational regulation, we varied the sequence context of the amber codon and found that insertion of two preceding prolines drastically decreases luminescence. In addition, using LacZ as a reporter, we demonstrated that a strain encoding a variant with a Pro-Pro amber motif can only grow on lactose when AcK is supplied, thus confirming the tight translational regulation of protein output. In parallel, we constructed an E. coli strain that carries an isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible version of the AcK-tRNA synthetase (AcKRS) gene on the chromosome, thus preventing mischarging of noncognate substrates. Subsequently, a diaminopimelic acid auxotrophic mutant (ΔdapA) was generated demonstrating the potential of this strain in regulating essential gene products. Furthermore, we assembled a set of vectors based on the broad-host-range pBBR ori that enable the AcK-dependent amber suppression system to control protein output not only in E. coli, but also in Salmonella enterica and Vibrio cholerae.
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Affiliation(s)
- Wolfram Volkwein
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Christopher Maier
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Ralph Krafczyk
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Jürgen Lassak
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
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43
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Ramil CP, Dong M, An P, Lewandowski TM, Yu Z, Miller LJ, Lin Q. Spirohexene-Tetrazine Ligation Enables Bioorthogonal Labeling of Class B G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2017; 139:13376-13386. [PMID: 28876923 DOI: 10.1021/jacs.7b05674] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new bioorthogonal reactant pair, spiro[2.3]hex-1-ene (Sph) and 3,6-di(2-pyridyl)-s-tetrazine (DpTz), for the strain-promoted inverse electron-demand Diels-Alder cycloaddition, that is, tetrazine ligation, is reported. As compared to the previously reported strained alkenes such as trans-cyclooctene (TCO) and 1,3-disubstituted cyclopropene, Sph exhibits balanced reactivity and stability in tetrazine ligation with the protein substrates. A lysine derivative of Sph, SphK, was site-selectively incorporated into the extracellular loop regions (ECLs) of GCGR and GLP-1R, two members of class B G protein-coupled receptors (GPCRs) in mammalian cells with the incorporation efficiency dependent on the location. Subsequent bioorthogonal reactions with the fluorophore-conjugated DpTz reagents afforded the fluorescently labeled GCGR and GLP-1R ECL mutants with labeling yield as high as 68%. A multitude of functional assays were performed with these GPCR mutants, including ligand binding, ligand-induced receptor internalization, and ligand-stimulated intracellular cAMP accumulation. Several positions in the ECL3s of GCGR and GLP-1R were identified that tolerate SphK mutagenesis and subsequent bioorthogonal labeling. The generation of functional, fluorescently labeled ECL3 mutants of GCGR and GLP-1R should allow biophysical studies of conformation dynamics of this important class of GPCRs in their native environment in live cells.
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Affiliation(s)
- Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tracey M Lewandowski
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
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44
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Schvartz T, Aloush N, Goliand I, Segal I, Nachmias D, Arbely E, Elia N. Direct fluorescent-dye labeling of α-tubulin in mammalian cells for live cell and superresolution imaging. Mol Biol Cell 2017; 28:2747-2756. [PMID: 28835375 PMCID: PMC5638579 DOI: 10.1091/mbc.e17-03-0161] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/28/2022] Open
Abstract
This work describes an elegant approach for direct, site-specific labeling of proteins with fluorescent-dyes for live cell imaging. By integrating a noncanonical amino acid that is capable of binding a fluorescent dye into tubulin, we directly and specifically labeled tubulin with a fluorescent-dye and imaged microtubules in live mammlian cells. Genetic code expansion and bioorthogonal labeling provide for the first time a way for direct, site-specific labeling of proteins with fluorescent-dyes in live cells. Although the small size and superb photophysical parameters of fluorescent-dyes offer unique advantages for high-resolution microscopy, this approach has yet to be embraced as a tool in live cell imaging. Here we evaluated the feasibility of this approach by applying it for α-tubulin labeling. After a series of calibrations, we site-specifically labeled α-tubulin with silicon rhodamine (SiR) in live mammalian cells in an efficient and robust manner. SiR-labeled tubulin successfully incorporated into endogenous microtubules at high density, enabling video recording of microtubule dynamics in interphase and mitotic cells. Applying this labeling approach to structured illumination microscopy resulted in an increase in resolution, highlighting the advantages in using a smaller, brighter tag. Therefore, using our optimized assay, genetic code expansion provides an attractive tool for labeling proteins with a minimal, bright tag in quantitative high-resolution imaging.
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Affiliation(s)
- Tomer Schvartz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Noa Aloush
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Inna Goliand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Inbar Segal
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Eyal Arbely
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel .,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
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45
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Zhang Z, Xu H, Si L, Chen Y, Zhang B, Wang Y, Wu Y, Zhou X, Zhang L, Zhou D. Construction of an inducible stable cell line for efficient incorporation of unnatural amino acids in mammalian cells. Biochem Biophys Res Commun 2017; 489:490-496. [DOI: 10.1016/j.bbrc.2017.05.178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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46
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Owens AE, Grasso KT, Ziegler CA, Fasan R. Two-Tier Screening Platform for Directed Evolution of Aminoacyl-tRNA Synthetases with Enhanced Stop Codon Suppression Efficiency. Chembiochem 2017; 18:1109-1116. [PMID: 28383180 PMCID: PMC5586079 DOI: 10.1002/cbic.201700039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 01/06/2023]
Abstract
Genetic code expansion through amber stop codon suppression provides a powerful tool for introducing non-proteinogenic functionalities into proteins for a broad range of applications. However, ribosomal incorporation of noncanonical amino acids (ncAAs) by means of engineered aminoacyl-tRNA synthetases (aaRSs) often proceeds with significantly reduced efficiency compared to sense codon translation. Here, we report the implementation of a versatile platform for the development of engineered aaRSs with enhanced efficiency in mediating ncAA incorporation by amber stop codon suppression. This system integrates a white/blue colony screen with a plate-based colorimetric assay, thereby combining high-throughput capabilities with reliable and quantitative measurement of aaRS-dependent ncAA incorporation efficiency. This two-tier functional screening system was successfully applied to obtain a pyrrolysyl-tRNA synthetase (PylRS) variant (CrtK-RS(4.1)) with significantly improved efficiency (+250-370 %) for mediating the incorporation of Nϵ -crotonyl-lysine and other lysine analogues of relevance for the study of protein post-translational modifications into a target protein. Interestingly, the beneficial mutations accumulated by CrtK-RS(4.1) were found to localize within the noncatalytic N-terminal domain of the enzyme and could be transferred to another PylRS variant, improving the ability of the variant to incorporate its corresponding ncAA substrate. This work introduces an efficient platform for the improvement of aaRSs that could be readily extended to other members of this enzyme family and/or other target ncAAs.
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Affiliation(s)
- Andrew E Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
| | - Katherine T Grasso
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
| | - Christine A Ziegler
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, NY, 14627, USA
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47
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Cui Z, Mureev S, Polinkovsky ME, Tnimov Z, Guo Z, Durek T, Jones A, Alexandrov K. Combining Sense and Nonsense Codon Reassignment for Site-Selective Protein Modification with Unnatural Amino Acids. ACS Synth Biol 2017; 6:535-544. [PMID: 27966891 DOI: 10.1021/acssynbio.6b00245] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incorporation of unnatural amino acids (uAAs) via codon reassignment is a powerful approach for introducing novel chemical and biological properties to synthesized polypeptides. However, the site-selective incorporation of multiple uAAs into polypeptides is hampered by the limited number of reassignable nonsense codons. This challenge is addressed in the current work by developing Escherichia coli in vitro translation system depleted of specific endogenous tRNAs. The translational activity in this system is dependent on the addition of synthetic tRNAs for the chosen sense codon. This allows site-selective uAA incorporation via addition of tRNAs pre- or cotranslationally charged with uAA. We demonstrate the utility of this system by incorporating the BODIPY fluorophore into the unique AGG codon of the calmodulin(CaM) open reading frame using in vitro precharged BODIPY-tRNACysCCU. The deacylated tRNACysCCU is a poor substrate for Cysteinyl-tRNA synthetase, which ensures low background incorporation of Cys into the chosen codon. Simultaneously, p-azidophenylalanine mediated amber-codon suppression and its post-translational conjugation to tetramethylrhodamine dibenzocyclooctyne (TAMRA-DIBO) were performed on the same polypeptide. This simple and robust approach takes advantage of the compatibility of BODIPY fluorophore with the translational machinery and thus requires only one post-translational derivatization step to introduce two fluorescent labels. Using this approach, we obtained CaM nearly homogeneously labeled with two FRET-forming fluorophores. Single molecule FRET analysis revealed dramatic changes in the conformation of the CaM probe upon its exposure to Ca2+ or a chelating agent. The presented approach is applicable to other sense codons and can be directly transferred to eukaryotic cell-free systems.
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Affiliation(s)
- Zhenling Cui
- Institute
for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sergey Mureev
- Institute
for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mark E. Polinkovsky
- StemProtein, 6350 Nancy
Ridge Drive, San Diego, California 92121, United States
| | - Zakir Tnimov
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Zhong Guo
- Institute
for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Thomas Durek
- Institute
for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alun Jones
- Institute
for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kirill Alexandrov
- Institute
for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
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48
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Kipper K, Lundius EG, Ćurić V, Nikić I, Wiessler M, Lemke EA, Elf J. Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. ACS Synth Biol 2017; 6:233-255. [PMID: 27775882 DOI: 10.1021/acssynbio.6b00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells. We find that the noncanonical amino acid incorporation into the target protein is robust for diverse amino acids and that the usefulness of the recoded E. coli strain mainly derives from the absence of release factor RF1. However, the membrane permeable dyes display high nonspecific binding in intracellular environment and the electroporation of hydrophilic nonmembrane permeable dyes severely impairs growth of the recoded strain. In contrast, proteins exposed on the outer membrane of E. coli can be labeled with hydrophilic dyes with a high specificity as demonstrated by labeling of the osmoporin OmpC. Here, labeling can be made sufficiently specific to enable single molecule studies as exemplified by OmpC single particle tracking.
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Affiliation(s)
- Kalle Kipper
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Ebba G. Lundius
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Vladimir Ćurić
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Ivana Nikić
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Manfred Wiessler
- Biological
Chemistry, Deutsche Krebsforschungszentrum, Heidelberg, 69120, Germany
| | - Edward A. Lemke
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Johan Elf
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
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49
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Völler JS, Biava H, Hildebrandt P, Budisa N. An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy. Biochim Biophys Acta Gen Subj 2017; 1861:3053-3059. [PMID: 28229928 DOI: 10.1016/j.bbagen.2017.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics. GENERAL SIGNIFICANCE Mapping the electrostatics in proteins will improve our understanding of natural catalytic processes and, in beyond, will be helpful for biocatalyst engineering. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Jan-Stefan Völler
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany.
| | - Hernan Biava
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany; Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany.
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50
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