1
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Tian R, Rehm FBH, Czernecki D, Gu Y, Zürcher JF, Liu KC, Chin JW. Establishing a synthetic orthogonal replication system enables accelerated evolution in E. coli. Science 2024; 383:421-426. [PMID: 38271510 DOI: 10.1126/science.adk1281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024]
Abstract
The evolution of new function in living organisms is slow and fundamentally limited by their critical mutation rate. Here, we established a stable orthogonal replication system in Escherichia coli. The orthogonal replicon can carry diverse cargos of at least 16.5 kilobases and is not copied by host polymerases but is selectively copied by an orthogonal DNA polymerase (O-DNAP), which does not copy the genome. We designed mutant O-DNAPs that selectively increase the mutation rate of the orthogonal replicon by two to four orders of magnitude. We demonstrate the utility of our system for accelerated continuous evolution by evolving a 150-fold increase in resistance to tigecycline in 12 days. And, starting from a GFP variant, we evolved a 1000-fold increase in cellular fluorescence in 5 days.
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Affiliation(s)
- Rongzhen Tian
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dariusz Czernecki
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Yangqi Gu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- 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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Abstract
Mutually orthogonal aminoacyl transfer RNA synthetase/transfer RNA pairs provide a foundation for encoding non-canonical amino acids into proteins, and encoded non-canonical polymer and macrocycle synthesis. Here we discover quintuply orthogonal pyrrolysyl-tRNA synthetase (PylRS)/pyrrolysyl-tRNA (tRNAPyl) pairs. We discover empirical sequence identity thresholds for mutual orthogonality and use these for agglomerative clustering of PylRS and tRNAPyl sequences; this defines numerous sequence clusters, spanning five classes of PylRS/tRNAPyl pairs (the existing classes +N, A and B, and newly defined classes C and S). Most of the PylRS clusters belong to classes that were unexplored for orthogonal pair generation. By testing pairs from distinct clusters and classes, and pyrrolysyl-tRNAs with unusual structures, we resolve 80% of the pairwise specificities required to make quintuply orthogonal PylRS/tRNAPyl pairs; we control the remaining specificities by engineering and directed evolution. Overall, we create 924 mutually orthogonal PylRS/tRNAPyl pairs, 1,324 triply orthogonal pairs, 128 quadruply orthogonal pairs and 8 quintuply orthogonal pairs. These advances may provide a key foundation for encoded polymer synthesis.
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Affiliation(s)
- Adam T Beattie
- 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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4
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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- 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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Patton AP, Morris EL, McManus D, Wang H, Li Y, Chin JW, Hastings MH. Astrocytic control of extracellular GABA drives circadian timekeeping in the suprachiasmatic nucleus. Proc Natl Acad Sci U S A 2023; 120:e2301330120. [PMID: 37186824 PMCID: PMC10214171 DOI: 10.1073/pnas.2301330120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The hypothalamic suprachiasmatic nucleus (SCN) is the master mammalian circadian clock. Its cell-autonomous timing mechanism, a transcriptional/translational feedback loop (TTFL), drives daily peaks of neuronal electrical activity, which in turn control circadian behavior. Intercellular signals, mediated by neuropeptides, synchronize and amplify TTFL and electrical rhythms across the circuit. SCN neurons are GABAergic, but the role of GABA in circuit-level timekeeping is unclear. How can a GABAergic circuit sustain circadian cycles of electrical activity, when such increased neuronal firing should become inhibitory to the network? To explore this paradox, we show that SCN slices expressing the GABA sensor iGABASnFR demonstrate a circadian oscillation of extracellular GABA ([GABA]e) that, counterintuitively, runs in antiphase to neuronal activity, with a prolonged peak in circadian night and a pronounced trough in circadian day. Resolving this unexpected relationship, we found that [GABA]e is regulated by GABA transporters (GATs), with uptake peaking during circadian day, hence the daytime trough and nighttime peak. This uptake is mediated by the astrocytically expressed transporter GAT3 (Slc6a11), expression of which is circadian-regulated, being elevated in daytime. Clearance of [GABA]e in circadian day facilitates neuronal firing and is necessary for circadian release of the neuropeptide vasoactive intestinal peptide, a critical regulator of TTFL and circuit-level rhythmicity. Finally, we show that genetic complementation of the astrocytic TTFL alone, in otherwise clockless SCN, is sufficient to drive [GABA]e rhythms and control network timekeeping. Thus, astrocytic clocks maintain the SCN circadian clockwork by temporally controlling GABAergic inhibition of SCN neurons.
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Affiliation(s)
- Andrew P. Patton
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Emma L. Morris
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - David McManus
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University, School of Life Sciences, 100871Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University, School of Life Sciences, 100871Beijing, China
| | - Jason W. Chin
- PNAC Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Michael H. Hastings
- Neurobiology Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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6
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Kehrloesser S, Cast O, Elliott TS, Ernst RJ, Machel AC, Chen JX, Chin JW, Miller ML. Cell-of-origin-specific proteomics of extracellular vesicles. PNAS Nexus 2023; 2:pgad107. [PMID: 37091541 PMCID: PMC10119638 DOI: 10.1093/pnasnexus/pgad107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/21/2023] [Indexed: 04/25/2023]
Abstract
The ability to assign cellular origin to low-abundance secreted factors in extracellular vesicles (EVs) would greatly facilitate the analysis of paracrine-mediated signaling. Here, we report a method, named selective isolation of extracellular vesicles (SIEVE), which uses cell type-specific proteome labeling via stochastic orthogonal recoding of translation (SORT) to install bioorthogonal reactive groups into the proteins derived from the cells targeted for labeling. We establish the native purification of intact EVs from a target cell, via a bioorthogonal tetrazine ligation, leading to copurification of the largely unlabeled EV proteome from the same cell. SIEVE enables capture of EV proteins at levels comparable with those obtained by antibody-based methods, which capture all EVs regardless of cellular origin, and at levels 20× higher than direct capture of SORT-labeled proteins. Using proteomic analysis, we analyze nonlabeled cargo proteins of EVs and show that the enhanced sensitivity of SIEVE allows for unbiased and comprehensive analysis of EV proteins from subpopulations of cells as well as for cell-specific EV proteomics in complex coculture systems. SIEVE can be applied with high efficiency in a diverse range of existing model systems for cell-cell communication and has direct applications for cell-of-origin EV analysis and for protein biomarker discovery.
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Affiliation(s)
- Sebastian Kehrloesser
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Oliver Cast
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Anne C Machel
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Jia-Xuan Chen
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Oncology Data Science, Oncology R&D, AstraZeneca, 1 Francis Crick Ave, Cambridge CB2 0AA, UK
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7
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Spinck M, Piedrafita C, Robertson WE, Elliott TS, Cervettini D, de la Torre D, Chin JW. Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles. Nat Chem 2023; 15:61-69. [PMID: 36550233 PMCID: PMC9836938 DOI: 10.1038/s41557-022-01082-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022]
Abstract
The direct genetically encoded cell-based synthesis of non-natural peptide and depsipeptide macrocycles is an outstanding challenge. Here we programme the encoded synthesis of 25 diverse non-natural macrocyclic peptides, each containing two non-canonical amino acids, in Syn61Δ3-derived cells; these cells contain a synthetic Escherichia coli genome in which the annotated occurrences of two sense codons and a stop codon, and the cognate transfer RNAs (tRNAs) and release factor that normally decode these codons, have been removed. We further demonstrate that pyrrolysyl-tRNA synthetase/tRNA pairs from distinct classes can be engineered to direct the co-translational incorporation of diverse alpha hydroxy acids, with both aliphatic and aromatic side chains. We define 49 engineered mutually orthogonal pairs that recognize distinct non-canonical amino acids or alpha hydroxy acids and decode distinct codons. Finally, we combine our advances to programme Syn61Δ3-derived cells for the encoded synthesis of 12 diverse non-natural depsipeptide macrocycles, which contain two non-canonical side chains and either one or two ester bonds.
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Affiliation(s)
- Martin Spinck
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Carlos Piedrafita
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Wesley E. Robertson
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Thomas S. Elliott
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Daniele Cervettini
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Daniel de la Torre
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W. Chin
- grid.42475.300000 0004 0605 769XMedical Research Council Laboratory of Molecular Biology, Cambridge, UK
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8
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Zürcher JF, Robertson WE, Kappes T, Petris G, Elliott TS, Salmond GPC, Chin JW. Refactored genetic codes enable bidirectional genetic isolation. Science 2022; 378:516-523. [PMID: 36264827 PMCID: PMC7614150 DOI: 10.1126/science.add8943] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The near-universal genetic code defines the correspondence between codons in genes and amino acids in proteins. We refactored the structure of the genetic code in Escherichia coli and created orthogonal genetic codes that restrict the escape of synthetic genetic information into natural life. We developed orthogonal and mutually orthogonal horizontal gene transfer systems, which permit the transfer of genetic information between organisms that use the same genetic code but restrict the transfer of genetic information between organisms that use different genetic codes. Moreover, we showed that locking refactored codes into synthetic organisms completely blocks invasion by mobile genetic elements, including viruses, which carry their own translation factors and successfully invade organisms with canonical and compressed genetic codes.
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Affiliation(s)
- Jérôme F. Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Tomás Kappes
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Thomas S. Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK,Correspondence to:
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9
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Inside Cover: Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET (Angew. Chem. Int. Ed. 37/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202210188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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10
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022; 61:e202203061. [PMID: 35656865 PMCID: PMC7613822 DOI: 10.1002/anie.202203061] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/24/2022]
Abstract
We report a bioinformatic workflow and subsequent discovery of a new polyethylene terephthalate (PET) hydrolase, which we named MG8, from the human saliva metagenome. MG8 has robust PET plastic degradation activities under different temperature and salinity conditions, outperforming several naturally occurring and engineered hydrolases in degrading PET. Moreover, we genetically encoded 2,3-diaminopropionic acid (DAP) in place of the catalytic serine residue of MG8, thereby converting a PET hydrolase into a covalent binder for bio-functionalization of PET. We show that MG8(DAP), in conjunction with a split green fluorescent protein system, can be used to attach protein cargos to PET as well as other polyester plastics. The discovery of a highly active PET hydrolase from the human metagenome—currently an underexplored resource for industrial enzyme discovery—as well as the repurposing of such an enzyme into a plastic functionalization tool, should facilitate ongoing efforts to degrade and maximize reusability of PET.
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Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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11
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McManus D, Polidarova L, Smyllie NJ, Patton AP, Chesham JE, Maywood ES, Chin JW, Hastings MH. Cryptochrome 1 as a state variable of the circadian clockwork of the suprachiasmatic nucleus: Evidence from translational switching. Proc Natl Acad Sci U S A 2022; 119:e2203563119. [PMID: 35976881 PMCID: PMC9407638 DOI: 10.1073/pnas.2203563119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The suprachiasmatic nucleus (SCN) of the hypothalamus is the principal clock driving circadian rhythms of physiology and behavior that adapt mammals to environmental cycles. Disruption of SCN-dependent rhythms compromises health, and so understanding SCN time keeping will inform management of diseases associated with modern lifestyles. SCN time keeping is a self-sustaining transcriptional/translational delayed feedback loop (TTFL), whereby negative regulators inhibit their own transcription. Formally, the SCN clock is viewed as a limit-cycle oscillator, the simplest being a trajectory of successive phases that progresses through two-dimensional space defined by two state variables mapped along their respective axes. The TTFL motif is readily compatible with limit-cycle models, and in Neurospora and Drosophila the negative regulators Frequency (FRQ) and Period (Per) have been identified as state variables of their respective TTFLs. The identity of state variables of the SCN oscillator is, however, less clear. Experimental identification of state variables requires reversible and temporally specific control over their abundance. Translational switching (ts) provides this, the expression of a protein of interest relying on the provision of a noncanonical amino acid. We show that the negative regulator Cryptochrome 1 (CRY1) fulfills criteria defining a state variable: ts-CRY1 dose-dependently and reversibly suppresses the baseline, amplitude, and period of SCN rhythms, and its acute withdrawal releases the TTFL to oscillate from a defined phase. Its effect also depends on its temporal pattern of expression, although constitutive ts-CRY1 sustained (albeit less stable) oscillations. We conclude that CRY1 has properties of a state variable, but may operate among several state variables within a multidimensional limit cycle.
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Affiliation(s)
- David McManus
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Lenka Polidarova
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Nicola J. Smyllie
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Andrew P. Patton
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Johanna E. Chesham
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Elizabeth S. Maywood
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Jason W. Chin
- bPNAC Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom
| | - Michael H. Hastings
- aNeurobiology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- 1To whom correspondence may be addressed.
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12
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin‐Dezot N, Tang S, Suginta W, Paosawatyanyong B, Madan Babu M, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Jariya Jitdee
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | | | - M. Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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13
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Piyachat Meesawat
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Thanakrit Wongsatit
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Jariya Jitdee
- Chulalongkorn University Faculty of Science Chemistry THAILAND
| | | | - Maturada Patchsung
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Kanokpol Aphicho
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Surased Suraritdechachai
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - Shan Tang
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | - Wipa Suginta
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - M. Madan Babu
- St Jude Children's Research Hospital Department of Structural Biology Structural Biology UNITED STATES
| | - Jason W Chin
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | | | | | - Chayasith Uttamapinant
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering 555 Moo 1 PayupnaiWangchan Valley 21210 Rayong THAILAND
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14
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Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Mechanism-based traps enable protease and hydrolase substrate discovery. Nature 2022; 602:701-707. [PMID: 35173328 PMCID: PMC8866121 DOI: 10.1038/s41586-022-04414-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.
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Affiliation(s)
- Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Adam T Beattie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Lucie Kafkova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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15
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Bürmann F, Funke LFH, Chin JW, Löwe J. Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites. Mol Cell 2021; 81:4891-4906.e8. [PMID: 34739874 PMCID: PMC8669397 DOI: 10.1016/j.molcel.2021.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022]
Abstract
The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
| | - Louise F H Funke
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jason W Chin
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
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16
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Dunkelmann DL, Oehm SB, Beattie AT, Chin JW. A 68-codon genetic code to incorporate four distinct non-canonical amino acids enabled by automated orthogonal mRNA design. Nat Chem 2021; 13:1110-1117. [PMID: 34426682 DOI: 10.1038/s41557-021-00764-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
Orthogonal (O) ribosome-mediated translation of O-mRNAs enables the incorporation of up to three distinct non-canonical amino acids (ncAAs) into proteins in Escherichia coli (E. coli). However, the general and efficient incorporation of multiple distinct ncAAs by O-ribosomes requires scalable strategies for both creating efficiently and specifically translated O-mRNAs, and the compact expression of multiple O-aminoacyl-tRNA synthetase (O-aaRS)/O-tRNA pairs. We automate the discovery of O-mRNAs that lead to up to 40 times more protein, and are up to 50-fold more orthogonal, than previous O-mRNAs; protein yields from our O-mRNAs match or exceed those from wild-type mRNAs. These advances enable a 33-fold increase in yield for incorporating three distinct ncAAs. We automate the creation of operons for O-tRNA genes, and develop operons for O-aaRS genes. Combining our advances creates a 68-codon, 24-amino-acid genetic code to efficiently incorporate four distinct ncAAs into a single protein in response to four distinct quadruplet codons.
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Affiliation(s)
| | - Sebastian B Oehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Adam T Beattie
- 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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17
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Davis L, Radman I, Goutou A, Tynan A, Baxter K, Xi Z, O'Shea JM, Chin JW, Greiss S. Precise optical control of gene expression in C. elegans using improved genetic code expansion and Cre recombinase. eLife 2021; 10:67075. [PMID: 34350826 PMCID: PMC8448529 DOI: 10.7554/elife.67075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Synthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an improved genetic code expansion system in Caenorhabditis elegans and use it to create a photoactivatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP-controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to the C. elegans touch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted. Animal behaviour and movement emerges from the stimulation of nerve cells that are connected together like a circuit. Researchers use various tools to investigate these neural networks in model organisms such as roundworms, fruit flies and zebrafish. The trick is to activate some nerve cells, but not others, so as to isolate their specific role within the neural circuit. One way to do this is to switch genes on or off in individual cells as a way to control their neuronal activity. This can be achieved by building a photocaged version of the enzyme Cre recombinase which is designed to target specific genes. The modified Cre recombinase contains an amino acid (the building blocks of proteins) that inactivates the enzyme. When the cell is illuminated with UV light, a part of the amino acid gets removed allowing Cre recombinase to turn on its target gene. However, cells do not naturally produce these photocaged amino acids. To overcome this, researchers can use a technology called genetic code expansion which provides cells with the tools they need to build proteins containing these synthetic amino acids. Although this technique has been used in live animals, its application has been limited due to the small amount of proteins it produces. Davis et al. therefore set out to improve the efficiency of genetic code expansion so that it can be used to study single nerve cells in freely moving roundworms. In the new system, named LaserTAC, individual cells are targeted with UV light that ‘uncages’ the Cre recombinase enzyme so it can switch on a gene for a protein that controls neuronal activity. Davis et al. used this approach to stimulate a pair of neurons sensitive to touch to see how this impacted the roundworm’s behaviour. This revealed that individual neurons within this pair contribute to the touch response in different ways. However, input from both neurons is required to produce a robust reaction. These findings show that the LaserTAC system can be used to manipulate gene activity in single cells, such as neurons, using light. It allows researchers to precisely control in which cells and when a given gene is switched on or off. Also, with the improved efficiency of the genetic code expansion, this technology could be used to modify proteins other than Cre recombinase and be applied to other artificial amino acids that have been developed in recent years.
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Affiliation(s)
- Lloyd Davis
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Inja Radman
- Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Angeliki Goutou
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ailish Tynan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kieran Baxter
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Zhiyan Xi
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jack M O'Shea
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sebastian Greiss
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
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18
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Robertson WE, Funke LFH, de la Torre D, Fredens J, Elliott TS, Spinck M, Christova Y, Cervettini D, Böge FL, Liu KC, Buse S, Maslen S, Salmond GPC, Chin JW. Sense codon reassignment enables viral resistance and encoded polymer synthesis. Science 2021; 372:1057-1062. [PMID: 34083482 DOI: 10.1126/science.abg3029] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
It is widely hypothesized that removing cellular transfer RNAs (tRNAs)-making their cognate codons unreadable-might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.
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Affiliation(s)
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Yonka Christova
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Franz L Böge
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Salvador Buse
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sarah Maslen
- 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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19
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Abstract
![]()
Discovering molecules that regulate
closely related protein isoforms
is challenging, and in many cases the consequences of isoform-specific
pharmacological regulation remains unknown. RAF isoforms are commonly
mutated oncogenes that serve as effector kinases in MAP kinase signaling.
BRAF/CRAF heterodimers are believed to be the primary RAF signaling
species, and many RAF inhibitors lead to a “paradoxical activation”
of RAF kinase activity through transactivation of the CRAF protomer;
this leads to resistance mechanisms and secondary tumors. It has been
hypothesized that CRAF-selective inhibition might bypass paradoxical
activation, but no CRAF-selective inhibitor has been reported and
the consequences of pharmacologically inhibiting CRAF have remained
unknown. Here, we use bio-orthogonal ligand tethering (BOLT) to selectively
target inhibitors to CRAF. Our results suggest that selective CRAF
inhibition promotes paradoxical activation and exemplify how BOLT
may be used to triage potential targets for drug discovery before
any target-selective small molecules are known.
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Affiliation(s)
- Charles W Morgan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ian L Dale
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andrew P Thomas
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - James Hunt
- Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge CB21 6GH, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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20
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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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21
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Dunkelmann DL, Willis JCW, Beattie AT, Chin JW. Engineered triply orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. Nat Chem 2020; 12:535-544. [PMID: 32472101 DOI: 10.1038/s41557-020-0472-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 04/23/2020] [Indexed: 01/03/2023]
Abstract
Expanding and reprogramming the genetic code of cells for the incorporation of multiple distinct non-canonical amino acids (ncAAs), and the encoded biosynthesis of non-canonical biopolymers, requires the discovery of multiple orthogonal aminoacyl-transfer RNA synthetase/tRNA pairs. These pairs must be orthogonal to both the host synthetases and tRNAs and to each other. Pyrrolysyl-tRNA synthetase (PylRS)/PyltRNA pairs are the most widely used system for genetic code expansion. Here, we reveal that the sequences of ΔNPylRS/ΔNPyltRNA pairs (which lack N-terminal domains) form two distinct classes. We show that the measured specificities of the ΔNPylRSs and ΔNPyltRNAs correlate with sequence-based clustering, and most ΔNPylRSs preferentially function with ΔNPyltRNAs from their class. We then identify 18 mutually orthogonal pairs from the 88 ΔNPylRS/ΔNPyltRNA combinations tested. Moreover, we generate a set of 12 triply orthogonal pairs, each composed of three new PylRS/PyltRNA pairs. Finally, we diverge the ncAA specificity and decoding properties of each pair, within a triply orthogonal set, and direct the incorporation of three distinct non-canonical amino acids into a single polypeptide.
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Affiliation(s)
| | - Julian C W Willis
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Adam T Beattie
- 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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22
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Wang K, de la Torre D, Robertson WE, Chin JW. Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly. Science 2020; 365:922-926. [PMID: 31467221 DOI: 10.1126/science.aay0737] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/02/2019] [Indexed: 12/26/2022]
Abstract
The design and creation of synthetic genomes provide a powerful approach to understanding and engineering biology. However, it is often limited by the paucity of methods for precise genome manipulation. Here, we demonstrate the programmed fission of the Escherichia coli genome into diverse pairs of synthetic chromosomes and the programmed fusion of synthetic chromosomes to generate genomes with user-defined inversions and translocations. We further combine genome fission, chromosome transplant, and chromosome fusion to assemble genomic regions from different strains into a single genome. Thus, we program the scarless assembly of new genomes with nucleotide precision, a key step in the convergent synthesis of genomes from diverse progenitors. This work provides a set of precise, rapid, large-scale (megabase) genome-engineering operations for creating diverse synthetic genomes.
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Affiliation(s)
- Kaihang Wang
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Daniel de la Torre
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Wesley E Robertson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK.
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23
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Oller‐Salvia B, Chin JW. Efficient Phage Display with Multiple Distinct Non‐Canonical Amino Acids Using Orthogonal Ribosome‐Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benjamí Oller‐Salvia
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
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24
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Oller‐Salvia B, Chin JW. Frontispiz: Efficient Phage Display with Multiple Distinct Non‐Canonical Amino Acids Using Orthogonal Ribosome‐Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201983261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Benjamí Oller‐Salvia
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
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25
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Oller-Salvia B, Chin JW. Frontispiece: Efficient Phage Display with Multiple Distinct Non-Canonical Amino Acids Using Orthogonal Ribosome-Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/anie.201983261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benjamí Oller-Salvia
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
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26
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Oller-Salvia B, Chin JW. Efficient Phage Display with Multiple Distinct Non-Canonical Amino Acids Using Orthogonal Ribosome-Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019; 58:10844-10848. [PMID: 31157495 PMCID: PMC6771915 DOI: 10.1002/anie.201902658] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Indexed: 11/10/2022]
Abstract
Phage display is a powerful approach for evolving proteins and peptides with new functions, but the properties of the molecules that can be evolved are limited by the chemical diversity encoded. Herein, we report a system for incorporating non-canonical amino acids (ncAAs) into proteins displayed on phage using the pyrrolysyl-tRNA synthetase/tRNA pair. We improve the efficiency of ncAA incorporation using an evolved orthogonal ribosome (riboQ1), and encode a cyclopropene-containing ncAA (CypK) at diverse sites on a displayed single-chain antibody variable fragment (ScFv), in response to amber and quadruplet codons. CypK and an alkyne-containing ncAA are incorporated at distinct sites, enabling the double labeling of ScFv with distinct probes, through mutually orthogonal reactions, in a one-pot procedure. These advances expand the number of functionalities that can be encoded on phage-displayed proteins and provide a foundation to further expand the scope of phage display applications.
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Affiliation(s)
- Benjamí Oller-Salvia
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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27
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Fredens J, Wang K, de la Torre D, Funke LFH, Robertson WE, Christova Y, Chia T, Schmied WH, Dunkelmann DL, Beránek V, Uttamapinant C, Llamazares AG, Elliott TS, Chin JW. Total synthesis of Escherichia coli with a recoded genome. Nature 2019; 569:514-518. [PMID: 31092918 DOI: 10.1038/s41586-019-1192-5] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 11/09/2022]
Abstract
Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon-out of up to 6 synonyms-to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme-with simple corrections at just seven positions-to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.
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Affiliation(s)
- Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kaihang Wang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Yonka Christova
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Tiongsun Chia
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | | | - Thomas S Elliott
- 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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28
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Schmied WH, Tnimov Z, Uttamapinant C, Rae CD, Fried SD, Chin JW. Controlling orthogonal ribosome subunit interactions enables evolution of new function. Nature 2018; 564:444-448. [PMID: 30518861 PMCID: PMC6525102 DOI: 10.1038/s41586-018-0773-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/15/2018] [Indexed: 11/09/2022]
Abstract
Orthogonal ribosomes are unnatural ribosomes that are directed towards orthogonal messenger RNAs in Escherichia coli, through an altered version of the 16S ribosomal RNA of the small subunit1. Directed evolution of orthogonal ribosomes has provided access to new ribosomal function, and the evolved orthogonal ribosomes have enabled the encoding of multiple non-canonical amino acids into proteins2-4. The original orthogonal ribosomes shared the pool of 23S ribosomal RNAs, contained in the large subunit, with endogenous ribosomes. Selectively directing a new 23S rRNA to an orthogonal mRNA, by controlling the association between the orthogonal 16S rRNAs and 23S rRNAs, would enable the evolution of new function in the large subunit. Previous work covalently linked orthogonal 16S rRNA and a circularly permuted 23S rRNA to create orthogonal ribosomes with low activity5,6; however, the linked subunits in these ribosomes do not associate specifically with each other, and mediate translation by associating with endogenous subunits. Here we discover engineered orthogonal 'stapled' ribosomes (with subunits linked through an optimized RNA staple) with activities comparable to that of the parent orthogonal ribosome; they minimize association with endogenous subunits and mediate translation of orthogonal mRNAs through the association of stapled subunits. We evolve cells with genomically encoded stapled ribosomes as the sole ribosomes, which support cellular growth at similar rates to natural ribosomes. Moreover, we visualize the engineered stapled ribosome structure by cryo-electron microscopy at 3.0 Å, revealing how the staple links the subunits and controls their association. We demonstrate the utility of controlling subunit association by evolving orthogonal stapled ribosomes which efficiently polymerize a sequence of monomers that the natural ribosome is intrinsically unable to translate. Our work provides a foundation for evolving the rRNA of the entire orthogonal ribosome for the encoded cellular synthesis of non-canonical biological polymers7.
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MESH Headings
- Base Sequence
- Cross-Linking Reagents/chemistry
- Cryoelectron Microscopy
- Directed Molecular Evolution
- Escherichia coli/classification
- Escherichia coli/cytology
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Models, Molecular
- Peptides/genetics
- Peptides/metabolism
- Protein Biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/ultrastructure
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 23S/ultrastructure
- Ribosome Subunits/chemistry
- Ribosome Subunits/metabolism
- Ribosome Subunits/ultrastructure
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
| | - Zakir Tnimov
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Christopher D Rae
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Stephen D Fried
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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29
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Uttamapinant C, Howe JD, Lang K, Beránek V, Davis L, Mahesh M, Barry NP, Chin JW. Correction to "Genetic Code Expansion Enables Live-Cell and Super-Resolution Imaging of Site-Specifically Labeled Cellular Proteins". J Am Chem Soc 2018; 140:13986. [PMID: 30351131 PMCID: PMC8154428 DOI: 10.1021/jacs.8b10479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Beránek V, Willis JCW, Chin JW. An Evolved Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase/tRNA Pair Is Highly Active and Orthogonal in Mammalian Cells. Biochemistry 2018; 58:387-390. [PMID: 30260626 PMCID: PMC6365905 DOI: 10.1021/acs.biochem.8b00808] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We recently characterized a new class of pyrrolysyl-tRNA synthetase (PylRS)/PyltRNA pairs from Methanomassiliicocales that are active and orthogonal in Escherichia coli. The aminoacyl-tRNA synthetases (aaRSs) of these pairs lack the N-terminal domain that is essential for tRNA recognition and in vivo activity in the Methanosarcina mazei ( Mm) PylRS but share a homologous active site with MmPylRS; this facilitates the transplantation of mutations discovered with existing PylRS systems into the new PylRS systems to reprogram their substrate specificity for the incorporation of noncanonical amino acids (ncAAs). Several of the new PylRS/PyltRNA pairs, or their evolved variants [including Methanomethylophilus alvus ( Ma) PylRS/ MaPyltRNA(6)CUA], are mutually orthogonal to the MmPylRS/ MmPyltRNA pair, and the active sites of the Mm pair and Ma pair can be diverged to enable the incorporation of distinct ncAAs in response to distinct codons via orthogonal translation in E. coli. Here we demonstrate that MaPylRS/ MaPyltRNA(6)CUA is orthogonal to the aaRSs and tRNAs in mammalian cells and directs efficient incorporation of ncAAs into proteins. Moreover, we confirm that the MaPylRS/ MaPyltRNA(6) and MmPylRS/ MmPyltRNA pairs are mutually orthogonal in mammalian cells and demonstrates that these pairs can be used to encode distinct ncAAs into a protein in mammalian cells. Thus, the MaPylRS/ MaPyltRNA(6)CUA pair provides an additional pair that is orthogonal in both E. coli and mammalian systems and is mutually orthogonal to the most widely used system for genetic code expansion. Our results provide a foundation for expanding the scope of genetic code expansion and may also facilitate strategies for proteome-wide ncAA tagging with mutually orthogonal systems.
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Affiliation(s)
- Václav Beránek
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , England , U.K
| | - Julian C W Willis
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , England , U.K
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , England , U.K
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31
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Baumdick M, Gelléri M, Uttamapinant C, Beránek V, Chin JW, Bastiaens PIH. A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation. Nat Commun 2018; 9:3847. [PMID: 30242154 PMCID: PMC6155120 DOI: 10.1038/s41467-018-06299-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 12/26/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) activation by growth factors (GFs) relies on dimerization and allosteric activation of its intrinsic kinase activity, resulting in trans-phosphorylation of tyrosines on its C-terminal tail. While structural and biochemical studies identified this EGF-induced allosteric activation, imaging collective EGFR activation in cells and molecular dynamics simulations pointed at additional catalytic EGFR activation mechanisms. To gain more insight into EGFR activation mechanisms in living cells, we develop a Förster resonance energy transfer (FRET)-based conformational EGFR indicator (CONEGI) using genetic code expansion that reports on conformational transitions in the EGFR activation loop. Comparing conformational transitions, self-association and auto-phosphorylation of CONEGI and its Y845F mutant reveals that Y845 phosphorylation induces a catalytically active conformation in EGFR monomers. This conformational transition depends on EGFR kinase activity and auto-phosphorylation on its C-terminal tail, generating a looped causality that leads to autocatalytic amplification of EGFR phosphorylation at low EGF dose. Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers.
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Affiliation(s)
- Martin Baumdick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Márton Gelléri
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany.
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32
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Mukherjee M, Sabir S, O'Regan L, Sampson J, Richards MW, Huguenin-Dezot N, Ault JR, Chin JW, Zhuravleva A, Fry AM, Bayliss R. Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release. Sci Signal 2018; 11:11/543/eaao2464. [PMID: 30108182 DOI: 10.1126/scisignal.aao2464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hsp72 is a member of the 70-kDa heat shock family of molecular chaperones (Hsp70s) that comprise a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD) connected by a linker that couples the exchange of adenosine diphosphate (ADP) for adenosine triphosphate (ATP) with the release of the protein substrate. Mitotic phosphorylation of Hsp72 by the kinase NEK6 at Thr66 located in the NBD promotes the localization of Hsp72 to the mitotic spindle and is required for efficient spindle assembly and chromosome congression and segregation. We determined the crystal structure of the Hsp72 NBD containing a genetically encoded phosphoserine at position 66. This revealed structural changes that stabilized interactions between subdomains within the NBD. ATP binding to the NBD of unmodified Hsp72 resulted in the release of substrate from the SBD, but phosphorylated Hsp72 retained substrate in the presence of ATP. Mutations that prevented phosphorylation-dependent subdomain interactions restored the connection between ATP binding and substrate release. Thus, phosphorylation of Thr66 is a reversible mechanism that decouples the allosteric connection between nucleotide binding and substrate release, providing further insight into the regulation of the Hsp70 family. We propose that phosphorylation of Hsp72 on Thr66 by NEK6 during mitosis promotes its localization to the spindle by stabilizing its interactions with components of the mitotic spindle.
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Affiliation(s)
- Manjeet Mukherjee
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah Sabir
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Josephina Sampson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Mark W Richards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nicolas Huguenin-Dezot
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anastasia Zhuravleva
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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33
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Marmelstein AM, Morgan JAM, Penkert M, Rogerson DT, Chin JW, Krause E, Fiedler D. Pyrophosphorylation via selective phosphoprotein derivatization. Chem Sci 2018; 9:5929-5936. [PMID: 30079207 PMCID: PMC6050540 DOI: 10.1039/c8sc01233d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 01/13/2023] Open
Abstract
An important step in elucidating the function of protein post-translational modifications (PTMs) is gaining access to site-specifically modified, homogeneous samples for biochemical characterization. Protein pyrophosphorylation is a poorly characterized PTM, and here a chemical approach to obtain pyrophosphoproteins is reported. Photo-labile phosphorimidazolide reagents were developed for selective pyrophosphorylation, affinity-capture, and release of pyrophosphoproteins. Kinetic analysis of the reaction revealed rate constants between 9.2 × 10-3 to 0.58 M-1 s-1, as well as a striking proclivity of the phosphorimidazolides to preferentially react with phosphate monoesters over other nucleophilic side chains. Besides enabling the characterization of pyrophosphorylation on protein function, this work highlights the utility of phosphoryl groups as handles for selective protein modification for a variety of applications, such as phosphoprotein bioconjugation and enrichment.
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Affiliation(s)
- Alan M Marmelstein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Department of Chemistry , Princeton University , Washington Road , Princeton , New Jersey 08544 , USA
| | - Jeremy A M Morgan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
| | - Martin Penkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Institut für Chemie , Humboldt Universität zu Berlin , Brook-Taylor-Str. 2 , 12489 Berlin , Germany
| | - Daniel T Rogerson
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , UK
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Institut für Chemie , Humboldt Universität zu Berlin , Brook-Taylor-Str. 2 , 12489 Berlin , Germany
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34
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Abstract
Genetically encoding distinct non-canonical amino acids (ncAAs) into proteins synthesized in cells requires mutually orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs. The pyrrolysyl-tRNA synthetase/PyltRNA pair from Methanosarcina mazei (Mm) has been engineered to incorporate diverse ncAAs and is commonly considered an ideal pair for genetic code expansion. However, finding new aaRS/tRNA pairs that share the advantages of the MmPylRS/MmPyltRNA pair and are orthogonal to both endogenous aaRS/tRNA pairs and the MmPylRS/MmPyltRNA pair has proved challenging. Here we demonstrate that several ΔNPylRS/PyltRNACUA pairs, in which PylRS lacks an N-terminal domain, are active, orthogonal and efficiently incorporate ncAAs in Escherichia coli. We create new PylRS/PyltRNA pairs that are mutually orthogonal to the MmPylRS/MmPyltRNA pair and show that transplanting mutations that reprogram the ncAA specificity of MmPylRS into the new PylRS reprograms its substrate specificity. Finally, we show that distinct PylRS/PyltRNA-derived pairs can function in the same cell, decode distinct codons and incorporate distinct ncAAs.
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Affiliation(s)
- Julian C W Willis
- 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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35
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Dickson C, Fletcher AJ, Vaysburd M, Yang JC, Mallery DL, Zeng J, Johnson CM, McLaughlin SH, Skehel M, Maslen S, Cruickshank J, Huguenin-Dezot N, Chin JW, Neuhaus D, James LC. Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21. eLife 2018; 7:32660. [PMID: 29667579 PMCID: PMC5906095 DOI: 10.7554/elife.32660] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/16/2018] [Indexed: 12/18/2022] Open
Abstract
Cell surface Fc receptors activate inflammation and are tightly controlled to prevent autoimmunity. Antibodies also simulate potent immune signalling from inside the cell via the cytosolic antibody receptor TRIM21, but how this is regulated is unknown. Here we show that TRIM21 signalling is constitutively repressed by its B-Box domain and activated by phosphorylation. The B-Box occupies an E2 binding site on the catalytic RING domain by mimicking E2-E3 interactions, inhibiting TRIM21 ubiquitination and preventing immune activation. TRIM21 is derepressed by IKKβ and TBK1 phosphorylation of an LxxIS motif in the RING domain, at the interface with the B-Box. Incorporation of phosphoserine or a phosphomimetic within this motif relieves B-Box inhibition, promoting E2 binding, RING catalysis, NF-κB activation and cytokine transcription upon infection with DNA or RNA viruses. These data explain how intracellular antibody signalling is regulated and reveal that the B-Box is a critical regulator of RING E3 ligase activity. Antibodies are molecules made by the immune system that protect us from infections. They were discovered over 100 years ago, and for most of that time scientists thought they only worked in the bloodstream. Yet recent research showed that when a virus infects our cells it also carries antibodies in with it. Once inside the cell, a protein called TRIM21 recognises the antibody-covered virus and – together with other proteins called ubiquitin enzymes – targets it for destruction via the cell’s waste disposal system. At the same time TRIM21 sends a signal to the cell’s nucleus to activate certain genes that protect cells across the body from subsequent infection. The genes activated by TRIM21 have potent antiviral activity. Yet they can also damage the body’s own tissues if they are switched on at the wrong time, which may lead to autoimmune diseases like rheumatoid arthritis and multiple sclerosis. It is thus critical that TRIM21 is carefully regulated and only activated during an infection, but it was not clear how this is achieved. Dickson, Fletcher et al. now show that although TRIM21 is made all the time and is always ready to detect an incoming virus it is made in an inactive state. This is because part of TRIM21, called a B-Box, inhibits the protein’s own activity. This was an unexpected discovery because, although the B-Box domain is found in around 100 other human proteins, it was unclear what it did. Dickson, Fletcher et al. then combined structural biology and biochemical approaches to show that the B-Box mimics specific enzymes that work with TRIM21, and blocks them from binding to it. This keeps TRIM21 in an inactive state. Next, Dickson, Fletcher et al. discovered that TRIM21 becomes active when a chemical tag, specifically a phosphate group, is added to the protein. This modification displaces the B-Box, allowing ubiquitin enzymes to bind to TRIM21 and switch on its activity. Further experiments then showed that this process helps regulate TRIM21 during infections with different viruses, including rhinovirus – the virus behind the common cold – and adenovirus – a common cause of respiratory infection. Antibodies are now used to treat many medical conditions, but present technologies are based on our understanding of how antibodies work outside cells. By revealing the basis of antibody immunity inside cells, these new findings may lead to new treatments for a range of conditions. Future studies could also explore how failures in the TRIM21 system contribute to autoimmune diseases.
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Affiliation(s)
- Claire Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Adam J Fletcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Marina Vaysburd
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ji-Chun Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Donna L Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jingwei Zeng
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Stephen H McLaughlin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mark Skehel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sarah Maslen
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - James Cruickshank
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - David Neuhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Leo C James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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36
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Burgess SG, Mukherjee M, Sabir S, Joseph N, Gutiérrez-Caballero C, Richards MW, Huguenin-Dezot N, Chin JW, Kennedy EJ, Pfuhl M, Royle SJ, Gergely F, Bayliss R. Mitotic spindle association of TACC3 requires Aurora-A-dependent stabilization of a cryptic α-helix. EMBO J 2018; 37:e97902. [PMID: 29510984 PMCID: PMC5897774 DOI: 10.15252/embj.201797902] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 12/26/2022] Open
Abstract
Aurora-A regulates the recruitment of TACC3 to the mitotic spindle through a phospho-dependent interaction with clathrin heavy chain (CHC). Here, we describe the structural basis of these interactions, mediated by three motifs in a disordered region of TACC3. A hydrophobic docking motif binds to a previously uncharacterized pocket on Aurora-A that is blocked in most kinases. Abrogation of the docking motif causes a delay in late mitosis, consistent with the cellular distribution of Aurora-A complexes. Phosphorylation of Ser558 engages a conformational switch in a second motif from a disordered state, needed to bind the kinase active site, into a helical conformation. The helix extends into a third, adjacent motif that is recognized by a helical-repeat region of CHC, not a recognized phospho-reader domain. This potentially widespread mechanism of phospho-recognition provides greater flexibility to tune the molecular details of the interaction than canonical recognition motifs that are dominated by phosphate binding.
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Affiliation(s)
- Selena G Burgess
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Manjeet Mukherjee
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sarah Sabir
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Nimesh Joseph
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | - Mark W Richards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Mark Pfuhl
- Cardiovascular & Randall Division, Kings College London, London, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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37
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Oller‐Salvia B, Kym G, Chin JW. Rapid and Efficient Generation of Stable Antibody-Drug Conjugates via an Encoded Cyclopropene and an Inverse-Electron-Demand Diels-Alder Reaction. Angew Chem Int Ed Engl 2018; 57:2831-2834. [PMID: 29356244 PMCID: PMC5861662 DOI: 10.1002/anie.201712370] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Indexed: 01/16/2023]
Abstract
Homogeneous antibody-drug conjugates (ADCs), generated by site-specific toxin linkage, show improved therapeutic indices with respect to traditional ADCs. However, current methods to produce site-specific conjugates suffer from low protein expression, slow reaction kinetics, and low yields, or are limited to particular conjugation sites. Here we describe high yielding expression systems that efficiently incorporate a cyclopropene derivative of lysine (CypK) into antibodies through genetic-code expansion. We express trastuzumab bearing CypK and conjugate tetrazine derivatives to the antibody. We show that the dihydropyridazine linkage resulting from the conjugation reaction is stable in serum, and generate an ADC bearing monomethyl auristatin E that selectively kills cells expressing a high level of HER2. Our results demonstrate that CypK is a minimal bioorthogonal handle for the rapid production of stable therapeutic protein conjugates.
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Affiliation(s)
- Benjamí Oller‐Salvia
- Medical Research Council Laboratory of Molecular BiologyFrancis Crick AvenueCambridgeCB2 0QHUK
| | - Gene Kym
- Medical Research Council Laboratory of Molecular BiologyFrancis Crick AvenueCambridgeCB2 0QHUK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular BiologyFrancis Crick AvenueCambridgeCB2 0QHUK
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38
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Oller-Salvia B, Kym G, Chin JW. Rapid and Efficient Generation of Stable Antibody-Drug Conjugates via an Encoded Cyclopropene and an Inverse-Electron-Demand Diels-Alder Reaction. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712370] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benjamí Oller-Salvia
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
| | - Gene Kym
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH UK
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39
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Ranasinghe RT, Challand MR, Ganzinger KA, Lewis BW, Softley C, Schmied WH, Horrocks MH, Shivji N, Chin JW, Spencer J, Klenerman D. Detecting RNA base methylations in single cells by in situ hybridization. Nat Commun 2018; 9:655. [PMID: 29440632 PMCID: PMC5811446 DOI: 10.1038/s41467-017-02714-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 12/20/2017] [Indexed: 12/16/2022] Open
Abstract
Methylated bases in tRNA, rRNA and mRNA control a variety of cellular processes, including protein synthesis, antimicrobial resistance and gene expression. Currently, bulk methods that report the average methylation state of ~104-107 cells are used to detect these modifications, obscuring potentially important biological information. Here, we use in situ hybridization of Molecular Beacons for single-cell detection of three methylations (m62A, m1G and m3U) that destabilize Watson-Crick base pairs. Our method-methylation-sensitive RNA fluorescence in situ hybridization-detects single methylations of rRNA, quantifies antibiotic-resistant bacteria in mixtures of cells and simultaneously detects multiple methylations using multicolor fluorescence imaging.
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Affiliation(s)
- Rohan T Ranasinghe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Martin R Challand
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| | - Kristina A Ganzinger
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Max-Planck-Institut für Biochemie (MPI for Biochemistry), 82152, Martinsried, Germany
| | - Benjamin W Lewis
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Charlotte Softley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Wolfgang H Schmied
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Mathew H Horrocks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Nadia Shivji
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jason W Chin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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40
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Luo J, Arbely E, Zhang J, Chou C, Uprety R, Chin JW, Deiters A. Genetically encoded optical activation of DNA recombination in human cells. Chem Commun (Camb) 2018; 52:8529-32. [PMID: 27277957 PMCID: PMC5048445 DOI: 10.1039/c6cc03934k] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We developed two tightly regulated, light-activated Cre recombinase enzymes through site-specific incorporation of two genetically-encoded photocaged amino acids in human cells. Excellent optical off to on switching of DNA recombination was achieved. Furthermore, we demonstrated precise spatial control of Cre recombinase through patterned illumination.
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Affiliation(s)
- J Luo
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania 15260, USA.
| | - E Arbely
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB20QH, UK and Department of Chemistry and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - J Zhang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - C Chou
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - R Uprety
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB20QH, UK
| | - A Deiters
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania 15260, USA.
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41
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Lambert WD, Scinto SL, Dmitrenko O, Boyd SJ, Magboo R, Mehl RA, Chin JW, Fox JM, Wallace S. Computationally guided discovery of a reactive, hydrophilic trans-5-oxocene dienophile for bioorthogonal labeling. Org Biomol Chem 2018; 15:6640-6644. [PMID: 28752889 PMCID: PMC5708333 DOI: 10.1039/c7ob01707c] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The use of organic chemistry principles and prediction techniques has enabled the development of new bioorthogonal reactions. As this "toolbox" expands to include new reaction manifolds and orthogonal reaction pairings, the continued development of existing reactions remains an important objective. This is particularly important in cellular imaging, where non-specific background fluorescence has been linked to the hydrophobicity of the bioorthogonal moiety. Here we report that trans-5-oxocene (oxoTCO) displays enhanced reactivity and hydrophilicity compared to trans-cyclooctene (TCO) in the tetrazine ligation reaction. Aided by ab initio calculations we show that the insertion of a single oxygen atom into the trans-cyclooctene (TCO) ring system is sufficient to impart aqueous solubility and also results in significant rate acceleration by increasing angle strain. We demonstrate the rapid and quantitative cycloaddition of oxoTCO using a water-soluble tetrazine derivative and a protein substrate containing a site-specific genetically encoded tetrazine moiety both in vitro and in vivo. We anticipate that oxoTCO will find use in studies where hydrophilicity and fast bioconjugation kinetics are paramount.
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Affiliation(s)
- William D Lambert
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Samuel L Scinto
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Olga Dmitrenko
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Samantha J Boyd
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | | | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Joseph M Fox
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Stephen Wallace
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK and Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, UK
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42
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Abstract
The central dogma processes of DNA replication, transcription, and translation are responsible for the maintenance and expression of every gene in an organism. An orthogonal central dogma may insulate genetic programs from host regulation and allow expansion in the roles of these processes within the cell.
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Affiliation(s)
- Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, California, USA
- Department of Chemistry, University of California, Irvine, California, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Chemistry, Cambridge University, Cambridge, UK
| | - Chris A. Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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43
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Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW. Labeling and identifying cell-specific proteomes in the mouse brain. Nat Biotechnol 2017; 36:156-159. [PMID: 29251727 DOI: 10.1038/nbt.4056] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 12/08/2017] [Indexed: 11/09/2022]
Abstract
We develop an approach to tag proteomes synthesized by specific cell types in dissociated cortex, brain slices, and the brains of live mice. By viral-mediated expression of an orthogonal pyrrolysyl-tRNA synthetase-tRNAXXX pair in a cell type of interest and providing a non-canonical amino acid with a chemical handle, we selectively label neuronal or glial proteomes. The method enables the identification of proteins from spatially and genetically defined regions of the brain.
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Affiliation(s)
- Toke P Krogager
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Laura Calo
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, England, UK
| | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Ernesto Ciabatti
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | | | - Marco Tripodi
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Michael H Hastings
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
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44
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Elliott TS, Bianco A, Townsley FM, Fried SD, Chin JW. Tagging and Enriching Proteins Enables Cell-Specific Proteomics. Cell Chem Biol 2017; 23:805-815. [PMID: 27447048 PMCID: PMC4959846 DOI: 10.1016/j.chembiol.2016.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/23/2016] [Indexed: 01/01/2023]
Abstract
Cell-specific proteomics in multicellular systems and whole animals is a promising approach to understand the differentiated functions of cells and tissues. Here, we extend our stochastic orthogonal recoding of translation (SORT) approach for the co-translational tagging of proteomes with a cyclopropene-containing amino acid in response to diverse codons in genetically targeted cells, and create a tetrazine-biotin probe containing a cleavable linker that offers a way to enrich and identify tagged proteins. We demonstrate that SORT with enrichment, SORT-E, efficiently recovers and enriches SORT tagged proteins and enables specific identification of enriched proteins via mass spectrometry, including low-abundance proteins. We show that tagging at distinct codons enriches overlapping, but distinct sets of proteins, suggesting that tagging at more than one codon enhances proteome coverage. Using SORT-E, we accomplish cell-specific proteomics in the fly. These results suggest that SORT-E will enable the definition of cell-specific proteomes in animals during development, disease progression, and learning and memory. A tetrazine-biotin probe containing a cleavable linker was created Proteomes labeled with cyclopropene amino acids were enriched and identified Proteome coverage is increased by targeting the amino acids to multiple codons Cell-specific proteomics was accomplished in the fly
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Affiliation(s)
- Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ambra Bianco
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Fiona M Townsley
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen D Fried
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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45
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Liaunardy-Jopeace A, Murton BL, Mahesh M, Chin JW, James JR. Encoding optical control in LCK kinase to quantitatively investigate its activity in live cells. Nat Struct Mol Biol 2017; 24:1155-1163. [PMID: 29083415 PMCID: PMC5736103 DOI: 10.1038/nsmb.3492] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/25/2017] [Indexed: 11/16/2022]
Abstract
LCK is a tyrosine kinase essential for initiating T-cell antigen receptor (TCR) signaling. A complete understanding of LCK function is constrained by a paucity of methods to quantitatively study its function within live cells. To address this limitation, we generated LCK*, in which a key active site lysine is replaced by a photo-caged equivalent, using genetic code expansion. This enabled fine temporal and spatial control over kinase activity, allowing us to quantify phosphorylation kinetics in situ using biochemical and imaging approaches. We find that auto-phosphorylation of the LCK active site loop is indispensable for its catalytic activity and that LCK can stimulate its own activation by adopting a more open conformation, which can be modulated by point mutations. We then show that CD4 and CD8, the T cell coreceptors, can enhance LCK activity, helping to explain their effect in physiological TCR signaling. Our approach also provides general insights into SRC-family kinase dynamics.
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Affiliation(s)
| | - Ben L Murton
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC-LMB, Cambridge, UK
| | - Mohan Mahesh
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - John R James
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC-LMB, Cambridge, UK
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46
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Abstract
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK
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47
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Gramespacher JA, Stevens AJ, Nguyen DP, Chin JW, Muir TW. Intein Zymogens: Conditional Assembly and Splicing of Split Inteins via Targeted Proteolysis. J Am Chem Soc 2017; 139:8074-8077. [PMID: 28562027 PMCID: PMC5533455 DOI: 10.1021/jacs.7b02618] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Naturally split inteins have found widespread use in chemical biology due to their ability to drive the ligation of separately expressed polypeptides through a process termed protein trans-splicing (PTS). In this study, we harness PTS by rendering association of split intein fragments conditional upon the presence of a user-defined protease. We show that these intein "zymogens" can be used to create protein sensors and actuators that respond to the presence of various stimuli, including bacterial pathogens, viral infections, and light. We also show that this design strategy is compatible with several orthogonal split intein pairs, thereby opening the way to the creation of multiplexed sensor systems.
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Affiliation(s)
- Josef A Gramespacher
- Frick Laboratory, Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Adam J Stevens
- Frick Laboratory, Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Duy P Nguyen
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Tom W Muir
- Frick Laboratory, Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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48
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Zhang MS, Brunner SF, Huguenin-Dezot N, Liang AD, Schmied WH, Rogerson DT, Chin JW. Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing. Nat Methods 2017; 14:729-736. [PMID: 28553966 DOI: 10.1038/nmeth.4302] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The phosphorylation of threonine residues in proteins regulates diverse processes in eukaryotic cells, and thousands of threonine phosphorylations have been identified. An understanding of how threonine phosphorylation regulates biological function will be accelerated by general methods to biosynthesize defined phosphoproteins. Here we describe a rapid approach for directly discovering aminoacyl-tRNA synthetase-tRNA pairs that selectively incorporate non-natural amino acids into proteins; our method uses parallel positive selections combined with deep sequencing and statistical analysis and enables the direct, scalable discovery of aminoacyl-tRNA synthetase-tRNA pairs with mutually orthogonal substrate specificity. By combining a method to biosynthesize phosphothreonine in cells with this selection approach, we discover a phosphothreonyl-tRNA synthetase-tRNACUA pair and create an entirely biosynthetic route to incorporating phosphothreonine in proteins. We biosynthesize several phosphoproteins and demonstrate phosphoprotein structure determination and synthetic protein kinase activation.
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Affiliation(s)
- Michael Shaofei Zhang
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Simon F Brunner
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Nicolas Huguenin-Dezot
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Alexandria D Liang
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Wolfgang H Schmied
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Daniel T Rogerson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
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49
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Kwan TTL, Boutureira O, Frye EC, Walsh SJ, Gupta MK, Wallace S, Wu Y, Zhang F, Sore HF, Galloway WRJD, Chin JW, Welch M, Bernardes GJL, Spring DR. Protein modification via alkyne hydrosilylation using a substoichiometric amount of ruthenium(ii) catalyst. Chem Sci 2017; 8:3871-3878. [PMID: 28966779 PMCID: PMC5578368 DOI: 10.1039/c6sc05313k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/04/2017] [Indexed: 01/20/2023] Open
Abstract
Transition metal catalysis has emerged as a powerful strategy to expand synthetic flexibility of protein modification. Herein, we report a cationic Ru(ii) system that enables the first example of alkyne hydrosilylation between dimethylarylsilanes and O-propargyl-functionalized proteins using a substoichiometric amount or low-loading of Ru(ii) catalyst to achieve the first C-Si bond formation on full-length substrates. The reaction proceeds under physiological conditions at a rate comparable to other widely used bioorthogonal reactions. Moreover, the resultant gem-disubstituted vinylsilane linkage can be further elaborated through thiol-ene coupling or fluoride-induced protodesilylation, demonstrating its utility in further rounds of targeted modifications.
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Affiliation(s)
- Terence T-L Kwan
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Omar Boutureira
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Elizabeth C Frye
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Stephen J Walsh
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Moni K Gupta
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Stephen Wallace
- Medical Research Council , Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , UK
- School of Biological Sciences , University of Edinburgh , The King's Buildings , Edinburgh , EH9 3FF , UK
| | - Yuteng Wu
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Fengzhi Zhang
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Warren R J D Galloway
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
| | - Jason W Chin
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
- Medical Research Council , Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , UK
| | - Martin Welch
- Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge CB2 1QW , UK
| | - Gonçalo J L Bernardes
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
- Instituto de Medicina Molecular , Faculdade de Medicina , Universidade de Lisboa , Avenida Professor Egas Moniz , 1649-028 , Lisboa , Portugal
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Rd , Cambridge CB2 1EW , UK .
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50
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Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PMW, Chin JW, Gervasio FL, Tate EW, Katan M. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017; 7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
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Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Alan R. Lowe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- London Centre for Nanotechnology, 17-19 Gower St, London, WC1H 0AH, UK
- Division of Biosciences, Birkbeck College, Malet St, London, WC1E 7HX, UK
| | - Giorgio Saladino
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Yuriy Alexandrov
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M. W. French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Jason W. Chin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Luigi Gervasio
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
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