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Schipp CJ, Ma Y, Al‐Shameri A, D'Alessio F, Neubauer P, Contestabile R, Budisa N, di Salvo ML. An Engineered Escherichia coli Strain with Synthetic Metabolism for in-Cell Production of Translationally Active Methionine Derivatives. Chembiochem 2020; 21:3525-3538. [PMID: 32734669 PMCID: PMC7756864 DOI: 10.1002/cbic.202000257] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/28/2020] [Indexed: 01/26/2023]
Abstract
In the last decades, it has become clear that the canonical amino acid repertoire codified by the universal genetic code is not up to the needs of emerging biotechnologies. For this reason, extensive genetic code re-engineering is essential to expand the scope of ribosomal protein translation, leading to reprogrammed microbial cells equipped with an alternative biochemical alphabet to be exploited as potential factories for biotechnological purposes. The prerequisite for this to happen is a continuous intracellular supply of noncanonical amino acids through synthetic metabolism from simple and cheap precursors. We have engineered an Escherichia coli bacterial system that fulfills these requirements through reconfiguration of the methionine biosynthetic pathway and the introduction of an exogenous direct trans-sulfuration pathway. Our metabolic scheme operates in vivo, rescuing intermediates from core cell metabolism and combining them with small bio-orthogonal compounds. Our reprogrammed E. coli strain is capable of the in-cell production of l-azidohomoalanine, which is directly incorporated into proteins in response to methionine codons. We thereby constructed a prototype suitable for economic, versatile, green sustainable chemistry, pushing towards enzyme chemistry and biotechnology-based production.
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Affiliation(s)
- Christian Johannes Schipp
- Chair of Bioprocess Engineering, Institute of BiotechnologyTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Ying Ma
- Paraxel International GmbH, Berlin, Campus DRK Kliniken Berlin Westend Haus 18Spandauer Damm 13014050BerlinGermany
| | - Ammar Al‐Shameri
- Institut für ChemieTechnische Universität BerlinMüller-Breslau-Straße. 1010623BerlinGermany
| | - Federico D'Alessio
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaPiazzale Aldo Moro, 5 – Edificio CU2000185RomaItaly
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of BiotechnologyTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaPiazzale Aldo Moro, 5 – Edificio CU2000185RomaItaly
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität BerlinMüller-Breslau-Straße. 1010623BerlinGermany
- Department of ChemistryUniversity of ManitobaWinnipegMB, R3T 2N2Canada
| | - Martino Luigi di Salvo
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”Sapienza Università di RomaPiazzale Aldo Moro, 5 – Edificio CU2000185RomaItaly
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Budisa N, Schneider T. Expanding the DOPA Universe with Genetically Encoded, Mussel-Inspired Bioadhesives for Material Sciences and Medicine. Chembiochem 2019; 20:2163-2190. [PMID: 30830997 DOI: 10.1002/cbic.201900030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Catechols are a biologically relevant group of aromatic diols that have attracted much attention as mediators of adhesion of "bio-glue" proteins in mussels of the genus Mytilus. These organisms use catechols in the form of the noncanonical amino acid l-3,4-dihydroxyphenylalanine (DOPA) as a building block for adhesion proteins. The DOPA is generated post-translationally from tyrosine. Herein, we review the properties, natural occurrence, and reactivity of catechols in the design of bioinspired materials. We also provide a basic description of the mussel's attachment apparatus, the interplay between its different molecules that play a crucial role in adhesion, and the role of post-translational modifications (PTMs) of these proteins. Our focus is on the microbial production of mussel foot proteins with the aid of orthogonal translation systems (OTSs) and the use of genetic code engineering to solve some fundamental problems in the bioproduction of these bioadhesives and to expand their chemical space. The major limitation of bacterial expression systems is their intrinsic inability to introduce PTMs. OTSs have the potential to overcome these challenges by replacing canonical amino acids with noncanonical ones. In this way, PTM steps are circumvented while the genetically programmed precision of protein sequences is preserved. In addition, OTSs should enable spatiotemporal control over the complex adhesion process, because the catechol function can be masked by suitable chemical protection. Such caged residues can then be noninvasively unmasked by, for example, UV irradiation or thermal treatment. All of these features make OTSs based on genetic code engineering in reprogrammed microbial strains new and promising tools in bioinspired materials science.
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Affiliation(s)
- Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany.,Chair of Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2, Winnipeg, MB, Canada
| | - Tobias Schneider
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
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Nediljko (Ned) Budisa. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201711475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Nediljko (Ned) Budisa. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Agostini F, Völler J, Koksch B, Acevedo‐Rocha CG, Kubyshkin V, Budisa N. Biocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology. Angew Chem Int Ed Engl 2017; 56:9680-9703. [DOI: 10.1002/anie.201610129] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Federica Agostini
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Jan‐Stefan Völler
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | | | - Vladimir Kubyshkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
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Biokatalyse mit nicht‐natürlichen Aminosäuren: Enzymologie trifft Xenobiologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Liutkus M, Fraser SA, Caron K, Stigers DJ, Easton CJ. Peptide Synthesis through Cell-Free Expression of Fusion Proteins Incorporating Modified Amino Acids as Latent Cleavage Sites for Peptide Release. Chembiochem 2016; 17:908-12. [PMID: 26918308 DOI: 10.1002/cbic.201600091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Indexed: 01/03/2023]
Abstract
Chlorinated analogues of Leu and Ile are incorporated during cell-free expression of peptides fused to protein, by exploiting the promiscuity of the natural biosynthetic machinery. They then act as sites for clean and efficient release of the peptides simply by brief heat treatment. Dehydro analogues of Leu and Ile are similarly incorporated as latent sites for peptide release through treatment with iodine under cold conditions. These protocols complement enzyme-catalyzed methods and have been used to prepare calcitonin, gastrin-releasing peptide, cholecystokinin-7, and prolactin-releasing peptide prohormones, as well as analogues substituted with unusual amino acids, thus illustrating their practical utility as alternatives to more traditional chemical peptide synthesis.
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Affiliation(s)
- Mantas Liutkus
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Samuel A Fraser
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Karine Caron
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Dannon J Stigers
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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Deepankumar K, Nadarajan SP, Mathew S, Lee SG, Yoo TH, Hong EY, Kim BG, Yun H. Engineering Transaminase for Stability Enhancement and Site-Specific Immobilization through Multiple Noncanonical Amino Acids Incorporation. ChemCatChem 2014. [DOI: 10.1002/cctc.201402882] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Bröcker MJ, Ho JML, Church GM, Söll D, O'Donoghue P. Recoding the genetic code with selenocysteine. Angew Chem Int Ed Engl 2014; 53:319-23. [PMID: 24511637 DOI: 10.1002/anie.201308584] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selenocysteine (Sec) is naturally incorporated into proteins by recoding the stop codon UGA. Sec is not hardwired to UGA, as the Sec insertion machinery was found to be able to site-specifically incorporate Sec directed by 58 of the 64 codons. For 15 sense codons, complete conversion of the codon meaning from canonical amino acid (AA) to Sec was observed along with a tenfold increase in selenoprotein yield compared to Sec insertion at the three stop codons. This high-fidelity sense-codon recoding mechanism was demonstrated for Escherichia coli formate dehydrogenase and recombinant human thioredoxin reductase and confirmed by independent biochemical and biophysical methods. Although Sec insertion at UGA is known to compete against protein termination, it is surprising that the Sec machinery has the ability to outcompete abundant aminoacyl-tRNAs in decoding sense codons. The findings have implications for the process of translation and the information storage capacity of the biological cell.
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Abstract
Substantial efforts in the past decade have resulted in the systematic expansion of genetic codes, allowing for the direct ribosomal incorporation of ∼100 unnatural amino acids into bacteria, yeast, mammalian cells, and animals. Here, we illustrate the versatility of expanded genetic codes in biology and bioengineering, focusing on the application of expanded genetic codes to problems in protein, cell, synthetic, and experimental evolutionary biology. As the expanded genetic code field continues to develop, its place as a foundational technology in the whole of biological sciences will solidify.
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Affiliation(s)
- Xiang Li
- Department of Biomedical Engineering, University of California at Irvine, 3120 Natural Sciences II, Irvine, CA 92697 (USA)
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Quitterer F, Beck P, Bacher A, Groll M. Pyrrolysin-Synthase (PylD) katalysiert die Bildung von Pyrrolin- und Tetrahydropyridinringen in Aminosäuren. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Quitterer F, Beck P, Bacher A, Groll M. The formation of pyrroline and tetrahydropyridine rings in amino acids catalyzed by pyrrolysine synthase (PylD). Angew Chem Int Ed Engl 2014; 53:8150-3. [PMID: 24916332 DOI: 10.1002/anie.201402595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Indexed: 11/11/2022]
Abstract
The dehydrogenase PylD catalyzes the ultimate step of the pyrrolysine pathway by converting the isopeptide L-lysine-Nε-3R-methyl-D-ornithine to the 22nd proteinogenic amino acid. In this study, we demonstrate how PylD can be harnessed to oxidize various isopeptides to novel amino acids by combining chemical synthesis with enzyme kinetics and X-ray crystallography. The data enable a detailed description of the PylD reaction trajectory for the biosynthesis of pyrroline and tetrahydropyridine rings as constituents of pyrrolysine analogues.
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Affiliation(s)
- Felix Quitterer
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany)
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Deepankumar K, Shon M, Nadarajan SP, Shin G, Mathew S, Ayyadurai N, Kim BG, Choi SH, Lee SH, Yun H. Enhancing Thermostability and Organic Solvent Tolerance of ω-Transaminase through Global Incorporation of Fluorotyrosine. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300706] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Bröcker MJ, Ho JML, Church GM, Söll D, O'Donoghue P. Umkodierung des genetischen Codes mit Selenocystein. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Willems LI, Li N, Florea BI, Ruben M, van der Marel GA, Overkleeft HS. Triple Bioorthogonal Ligation Strategy for Simultaneous Labeling of Multiple Enzymatic Activities. Angew Chem Int Ed Engl 2012; 51:4431-4. [DOI: 10.1002/anie.201200923] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 12/26/2022]
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Willems LI, Li N, Florea BI, Ruben M, van der Marel GA, Overkleeft HS. Triple Bioorthogonal Ligation Strategy for Simultaneous Labeling of Multiple Enzymatic Activities. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200923] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Oldach F, Al Toma R, Kuthning A, Caetano T, Mendo S, Budisa N, Süssmuth RD. Lantibiotika-Kongenere mit nicht-kanonischen Aminosäuren durch ribosomale In-vivo-Peptidsynthese. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Oldach F, Al Toma R, Kuthning A, Caetano T, Mendo S, Budisa N, Süssmuth RD. Congeneric lantibiotics from ribosomal in vivo peptide synthesis with noncanonical amino acids. Angew Chem Int Ed Engl 2011; 51:415-8. [PMID: 22128014 DOI: 10.1002/anie.201106154] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/20/2011] [Indexed: 11/10/2022]
Abstract
Expanded repetoire: Synthetic amino acids translated into propeptides dramatically increase the chemical diversity of the two-component lantibiotic lichenicidin. This opens new routes towards novel and unique peptide antibiotic sequences, which could display features important for medical applications.
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Affiliation(s)
- Florian Oldach
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
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Ayyadurai N, Saravanan Prabhu N, Deepankumar K, Lee SG, Jeong HH, Lee CS, Yun H. Development of a Selective, Sensitive, and Reversible Biosensor by the Genetic Incorporation of a Metal-Binding Site into Green Fluorescent Protein. Angew Chem Int Ed Engl 2011; 50:6534-7. [DOI: 10.1002/anie.201008289] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 04/19/2011] [Indexed: 11/06/2022]
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Development of a Selective, Sensitive, and Reversible Biosensor by the Genetic Incorporation of a Metal-Binding Site into Green Fluorescent Protein. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008289] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hoesl MG, Budisa N. In Vivo Incorporation of Multiple Noncanonical Amino Acids into Proteins. Angew Chem Int Ed Engl 2011; 50:2896-902. [DOI: 10.1002/anie.201005680] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Indexed: 11/11/2022]
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Hoesl MG, Budisa N. Paralleler In-vivo-Einbau von mehreren nichtkanonischen Aminosäuren in Proteine. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005680] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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