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An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C. Engineered Living Materials For Sustainability. Chem Rev 2023; 123:2349-2419. [PMID: 36512650 DOI: 10.1021/acs.chemrev.2c00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.
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Affiliation(s)
- Bolin An
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanyi Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuzhu Liu
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongmin Xun
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - George M Church
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Zhuojun Dai
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiao Yi
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tzu-Chieh Tang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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2
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Nowak-Król A, Dydio P. The 55 th Bürgenstock Conference under the Banner of Sustainability. Angew Chem Int Ed Engl 2022; 61:e202214722. [PMID: 36477955 DOI: 10.1002/anie.202214722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Agnieszka Nowak-Król
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Paweł Dydio
- University of Strasbourg, CNRS, ISIS UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
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3
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Nowak‐Król A, Dydio P. The 55
th
Bürgenstock Conference under the Banner of Sustainability**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Agnieszka Nowak‐Król
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Paweł Dydio
- University of Strasbourg CNRS ISIS UMR 7006 8 allée Gaspard Monge 67000 Strasbourg France
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4
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Schmidt M, Kubyshkin V. How To Quantify a Genetic Firewall? A Polarity-Based Metric for Genetic Code Engineering. Chembiochem 2021; 22:1268-1284. [PMID: 33231343 PMCID: PMC8049029 DOI: 10.1002/cbic.202000758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Indexed: 12/14/2022]
Abstract
Genetic code engineering aims to produce organisms that translate genetic information in a different way from that prescribed by the standard genetic code. This endeavor could eventually lead to genetic isolation, where an organism that operates under a different genetic code will not be able to transfer functional genes with other living species, thereby standing behind a genetic firewall. It is not clear however, how distinct the code should be, or how to measure the distance. We have developed a metric (Δcode ) where we assigned polarity indices (clog D7 ) to amino acids to calculate the distances between pairs of genetic codes. We then calculated the distance between a set of 204 genetic codes, including the 24 known distinct natural codes, 11 extreme-distance codes created computationally, nine theoretical special purpose codes from literature and 160 codes in which canonical amino acids were replaced by noncanonical chemical analogues. The metric can be used for building strategies towards creating semantically alienated organisms, and testing the strength of genetic firewalls. This metric provides the basis for a map of the genetic codes that could guide future efforts towards novel biochemical worlds, biosafety and deep barcoding applications.
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Affiliation(s)
| | - Vladimir Kubyshkin
- Department of ChemistryUniversity of ManitobaDysart Road 144WinnipegR3T 2N2Canada
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5
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Yang H, Eremeeva E, Abramov M, Herdewijn P. The Network of Replication, Transcription, and Reverse Transcription of a Synthetic Genetic Cassette. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hui Yang
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Elena Eremeeva
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Mikhail Abramov
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
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6
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Yang H, Eremeeva E, Abramov M, Herdewijn P. The Network of Replication, Transcription, and Reverse Transcription of a Synthetic Genetic Cassette. Angew Chem Int Ed Engl 2020; 60:4175-4182. [PMID: 33142013 DOI: 10.1002/anie.202011887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Indexed: 11/07/2022]
Abstract
Synthetic nucleic acids, with four non-canonical nucleobases, can function as genetic materials. A comprehensive analysis of PCR amplification, transcription, reverse transcription, and cloning was done to screen for alternative genetic monomers. A small library of six modified nucleobases was selected: the modified 2'-deoxyribonucleoside (dZTPs) and ribonucleoside (rZTPs) triphosphates of 7-deaza-adenine, 5-chlorouracil, 7-deaza-guanine or inosine together with 5-fluorocytosine or 5-bromocytosine. The fragments composed of one to four modified nucleotides (denoted as DZA) have been successfully recognized and transcribed to natural or modified RNA (denoted as RZA) by T7 RNA polymerase. The fully modified RZA fragment could be reverse transcribed and then amplified in the presence of various dZTPs. Noticeably, modified fragments could function as genetic templates in vivo by encoding the 678 base pair gene of a fluorescent protein in bacteria. These results demonstrate the existence of a fully simulated genetic circuit that uses synthetic materials.
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Affiliation(s)
- Hui Yang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Elena Eremeeva
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
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7
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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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8
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Csibra E, Renders M, Pinheiro VB. Bacterial Cell Display as a Robust and Versatile Platform for Engineering Low-Affinity Ligands and Enzymes. Chembiochem 2020; 21:2844-2853. [PMID: 32413179 PMCID: PMC7586821 DOI: 10.1002/cbic.202000203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/11/2020] [Indexed: 12/31/2022]
Abstract
Directed evolution has been remarkably successful at expanding the chemical and functional boundaries of biology. That progress is heavily dependent on the robustness and flexibility of the available selection platforms, given the significant cost to (re)develop a given platform to target a new desired function. Bacterial cell display has a significant track record as a viable strategy for the engineering of mesophilic enzymes, as enzyme activity can be probed directly and free from interference from the cellular milieu, but its adoption has lagged behind other display-based methods. Herein, we report the development of SNAP as a quantitative reporter for bacterial cell display, which enables fast troubleshooting and the systematic development of the display-based selection platform, thus improving its robustness. In addition, we demonstrate that even weak interactions between displayed proteins and nucleic acids can be harnessed for the specific labelling of bacterial cells, allowing functional characterisation of DNA binding proteins and enzymes, thus making it a highly flexible platform for these biochemical functions. Together, this establishes bacterial display as a robust and flexible platform, ideally suited for the systematic engineering of ligands and enzymes needed for XNA molecular biology.
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Affiliation(s)
- Eszter Csibra
- University College LondonDepartment of Structural and Molecular BiologyGower StreetLondonWC1E 6BTUK
- Current address: Imperial College LondonExhibition RoadLondonSW7 2AZUK
| | - Marleen Renders
- Rega Institute for Medical ResearchKU LeuvenHerestraat, 49 box 10413000LeuvenBelgium
- Current address: Touchlight Genetics Ltd. Morelands & Riverdale BuildingsLower Sunbury RoadHamptonTW12 2ERUK
| | - Vitor B. Pinheiro
- University College LondonDepartment of Structural and Molecular BiologyGower StreetLondonWC1E 6BTUK
- Rega Institute for Medical ResearchKU LeuvenHerestraat, 49 box 10413000LeuvenBelgium
- Institute of Structural and Molecular BiologyBirkbeck CollegeUniversity of LondonMalet StreetLondonWC1E 7HXUK
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9
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Algar E, Al‐Ramahi Y, Lorenzo V, Martínez‐García E. Environmental Performance of
Pseudomonas putida
with a Uracylated Genome. Chembiochem 2020; 21:3255-3265. [DOI: 10.1002/cbic.202000330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/27/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Elena Algar
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
| | - Yamal Al‐Ramahi
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
| | - Víctor Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
| | - Esteban Martínez‐García
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC) Campus de Cantoblanco 28049 Madrid Spain
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10
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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11
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Budisa N, Kubyshkin V, Schmidt M. Xenobiology: A Journey towards Parallel Life Forms. Chembiochem 2020; 21:2228-2231. [PMID: 32323410 DOI: 10.1002/cbic.202000141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/29/2020] [Indexed: 12/11/2022]
Abstract
Xenobiology is the science of estranged life forms. More specifically, this is an emergent technoscience that combines advances in genetic engineering with the design of biological systems based on unusual biochemistries delivered by chemical compounds of mostly anthropogenic origin. Xenobiology enables us to create and study strange new life forms, "aliens", not in the way science fiction books do it, but in terms of enlightened science, design, and engineering.
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Affiliation(s)
- Nediljko Budisa
- Department of Chemistry, University of Manitoba, Dysart Road 144, Winnipeg, R2T 2N2, Canada.,Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
| | - Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, Dysart Road 144, Winnipeg, R2T 2N2, Canada
| | - Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, 1030, Vienna, Austria
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12
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Danchin A. Isobiology: A Variational Principle for Exploring Synthetic Life. Chembiochem 2020; 21:1781-1792. [DOI: 10.1002/cbic.202000060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Antoine Danchin
- Stellate TherapeuticsInstitut Cochin 24 rue du Faubourg Saint-Jacques 75014 Paris France
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13
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Gasse C, Zaarour M, Noppen S, Abramov M, Marlière P, Liekens S, De Strooper B, Herdewijn P. Modulation of BACE1 Activity by Chemically Modified Aptamers. Chembiochem 2018; 19:754-763. [PMID: 29327496 DOI: 10.1002/cbic.201700461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
A modified DNA aptamer that binds BACE1, a therapeutic target involved in Alzheimer's disease has been developed. This ssXNA not only tightly binds to BACE1 but also inhibits its protease activity in vitro in the same range as a previously described unmodified aptamer. We report the in vitro selection of functional oligonucleotides incorporating two nucleobase modifications: 5-chlorouracil and 7-deazaadenine. The nucleoside analogue 5-chloro-2'-deoxyuridine has already been explored as a replacement for thymidine in a chemically modified genome of a bacterium. Thus, 5-chlorouracil modification is a good candidate to support genetic transfer in vivo as well as functional activity.
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Affiliation(s)
- Cécile Gasse
- Univ Evry, CNRS-UMR8030-Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, 5 rue Henri Desbruères, Évry, 91030, France
| | - Marwa Zaarour
- Univ Evry, CNRS-UMR8030-Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, 5 rue Henri Desbruères, Évry, 91030, France
| | - Sam Noppen
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Postbus 1043, 3000, Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Philippe Marlière
- The European Syndicate of Synthetic Scientists and Industrialists (TESSI), 81 rue Réaumur, 75002, Paris, France
| | - Sandra Liekens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Postbus 1043, 3000, Leuven, Belgium
| | - Bart De Strooper
- VIB, Center for Brain & Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Department of Neurosciences, Leuven Institute for Neuroscience and Disease, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.,Dementia Research Institute (UK), University College London, Gower Street, WC1E 6BT, London, UK
| | - Piet Herdewijn
- Univ Evry, CNRS-UMR8030-Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, 5 rue Henri Desbruères, Évry, 91030, France.,Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
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14
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Gramelsberger G. Continuous culture techniques as simulators for standard cells: Jacques Monod's, Aron Novick's and Leo Szilard's quantitative approach to microbiology. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018; 40:23. [PMID: 29383456 DOI: 10.1007/s40656-017-0182-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Continuous culture techniques were developed in the early twentieth century to replace cumbersome studies of cell growth in batch cultures. In contrast to batch cultures, they constituted an open concept, as cells are forced to proliferate by adding new medium while cell suspension is constantly removed. During the 1940s and 1950s new devices have been designed-called "automatic syringe mechanism," "turbidostat," "chemostat," "bactogen," and "microbial auxanometer"-which allowed increasingly accurate quantitative measurements of bacterial growth. With these devices cell growth came under the external control of the experimenters and thus accessible for developing a mathematical theory of growth kinetics-developed mainly by Jacques Monod, Aron Novick and Leo Szilard in the early 1950s and still in use today. The paper explores the development of continuous culture devices and claims that these devices are simulators for standard cells following specific requirements, in particular involving mathematical constraints in the design and setting of the devices as well as experiments. These requirements have led to contemporary designs of continuous culture techniques realizing a specific event-based flow algorithm able to simulate directed evolution and produce artificial cells and microorganisms. This current development is seen as an alternative approach to today's synthetic biology.
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15
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Eremeeva E, Abramov M, Margamuljana L, Herdewijn P. Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology. Chemistry 2017; 23:9560-9576. [PMID: 28513881 DOI: 10.1002/chem.201700679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/10/2022]
Abstract
The ability of various nucleoside triphosphate analogues of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A1 ) and 5-chlorodeoxyuridine (T1 ) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set composed of A1 , T1 , and 7-deazadeoxyguanosine with either 5-methyldeoxycytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of a 1 kb PCR product was A1 , T1 , deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This approach can be used to regulate the endonuclease cleavage pattern.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Michail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium.,Université d'évry, CNRS-UMR8030/ Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, évry, 91000, Paris, France
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16
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Diafa S, Evéquoz D, Leumann CJ, Hollenstein M. Enzymatic Synthesis of 7',5'-Bicyclo-DNA Oligonucleotides. Chem Asian J 2017; 12:1347-1352. [PMID: 28371464 DOI: 10.1002/asia.201700374] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/30/2017] [Indexed: 01/06/2023]
Abstract
The selection of artificial genetic polymers with tailor-made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo-DNA triphosphate (i.e., 7',5'-bc-TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7',5'-bc-TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA-dependent DNA synthesis and potentially also XNA-dependent XNA synthesis. However, DNA-dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7',5'-bc-TTP.
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Affiliation(s)
- Stella Diafa
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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17
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Evéquoz D, Leumann CJ. Probing the Backbone Topology of DNA: Synthesis and Properties of 7',5'-Bicyclo-DNA. Chemistry 2017; 23:7953-7968. [PMID: 28262999 DOI: 10.1002/chem.201700435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Indexed: 01/18/2023]
Abstract
We describe the synthesis and pairing properties of the novel DNA analogue 7',5'-bicyclo(bc)-DNA. In this analogue, the point of attachment of the connecting phosphodiester group is switched from the 3' to the 7' position of the underlying bicyclic sugar unit and is thus in a topological position that is inaccessible in natural DNA. The corresponding phosphoramidite building blocks carrying all natural nucleobases were synthesized and incorporated into oligonucleotides. From Tm experiments of duplexes with complementary DNA and RNA we find that single modifications are generally well tolerated with some variability as to the nature of the nucleobase. Fully modified oligonucleotides show low affinity for RNA and DNA complements. However, they form antiparallel homo-duplexes with similar thermal stability as DNA. CD spectra of the homo-duplexes show distinct changes in the helix conformation compared to natural DNA. A conformational analysis at the ab initio level of the mononucleosides revealed two minimal energy structures which primarily deviate in the conformation of the cyclopentane ring. Molecular dynamics simulation of a 7',5'-bc-DNA homo-duplex revealed a right-handed structure with a smaller helical rise and a significantly wider minor groove compared to DNA. Interestingly, this duplex is characterized by an atypical, alternating 6'-endo/6'-exo conformational pattern of consecutive nucleotides which seems to be responsible for the poor binding to natural nucleic acids.
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Affiliation(s)
- Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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18
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Mair P, Gielen F, Hollfelder F. Exploring sequence space in search of functional enzymes using microfluidic droplets. Curr Opin Chem Biol 2017; 37:137-144. [PMID: 28390246 DOI: 10.1016/j.cbpa.2017.02.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/08/2017] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Abstract
Screening of enzyme mutants in monodisperse picoliter compartments, generated at kilohertz speed in microfluidic devices, is coming of age. After a decade of proof-of-principle experiments, workflows have emerged that combine existing microfluidic modules to assay reaction progress quantitatively and yield improved enzymes. Recent examples of the screening of libraries of randomised proteins and from metagenomic sources suggest that this approach is not only faster and cheaper, but solves problems beyond the feasibility scope of current methodologies. The establishment of new assays in this format - so far covering hydrolases, aldolases, polymerases and dehydrogenases - will enable the exploration of sequence space for new catalysts of natural and non-natural chemical transformations.
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Affiliation(s)
- Philip Mair
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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19
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016; 55:7515-9. [PMID: 27159019 DOI: 10.1002/anie.201601529] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/04/2023]
Abstract
The ability of alternative nucleic acids, in which all four nucleobases are substituted, to replicate in vitro and to serve as genetic templates in vivo was evaluated. A nucleotide triphosphate set of 5-chloro-2'-deoxyuridine, 7-deaza-2'-deoxyadenosine, 5-fluoro-2'-deoxycytidine, and 7-deaza-2'deoxyguanosine successfully underwent polymerase chain reaction (PCR) amplification using templates of different lengths (57 or 525mer) and Taq or Vent (exo-) DNA polymerases as catalysts. Furthermore, a fully morphed gene encoding a dihydrofolate reductase was generated by PCR using these fully substituted nucleotides and was shown to transform and confer trimethoprim resistance to E. coli. These results demonstrated that fully modified templates were accurately read by the bacterial replication machinery and provide the first example of a long fully modified DNA molecule being functional in vivo.
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Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Valerie Pezo
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Philippe Marlière
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium. .,ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France.
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20
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Valerie Pezo
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Philippe Marlière
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
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21
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Acevedo-Rocha CG, Schulze-Makuch D. How Many Biochemistries Are Available To Build a Cell? Chembiochem 2015; 16:2137-9. [DOI: 10.1002/cbic.201500379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Terrestrische Mikrobiologie; Small Prokaryotic RNA Biology Group; Karl-von-Frisch-Strasse 10 35043 Marburg Germany
- Landes-Offensive zur Entwicklung Wissenschafltich-Ökonomischer Exzellenz (LOEWE); Zentrum für Synthetische Mikrobiologie (SYNMIKRO); Philipps-Universität Marburg; Hans-Meerwein-Strasse 6 35042 Marburg Germany
| | - Dirk Schulze-Makuch
- School of the Environment; Washington State University; Webster Hall 1148 Pullman WA 99163 USA
- Beyond Center; Arizona State University; P. O. Box 871504 Tempe AZ 85827 USA
- Center for Astronomy and Astrophysics; Technical University Berlin; Hardenbergstrasse 36 10623 Berlin Germany
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22
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Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L, Aerni HR, Rappsilber J, Rinehart J, Leach D, Söll D, Budisa N. Chemical Evolution of a Bacterial Proteome. Angew Chem Int Ed Engl 2015; 54:10030-4. [PMID: 26136259 PMCID: PMC4782924 DOI: 10.1002/anie.201502868] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/09/2022]
Abstract
We have changed the amino acid set of the genetic code of Escherichia coli by evolving cultures capable of growing on the synthetic noncanonical amino acid L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) as a sole surrogate for the canonical amino acid L-tryptophan (Trp). A long-term cultivation experiment in defined synthetic media resulted in the evolution of cells capable of surviving Trp→[3,2]Tpa substitutions in their proteomes in response to the 20,899 TGG codons of the E. coli W3110 genome. These evolved bacteria with new-to-nature amino acid composition showed robust growth in the complete absence of Trp. Our experimental results illustrate an approach for the evolution of synthetic cells with alternative biochemical building blocks.
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Affiliation(s)
- Michael Georg Hoesl
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany)
| | - Stefan Oehm
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany)
| | - Patrick Durkin
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany)
| | - Elise Darmon
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh (UK)
| | - Lauri Peil
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, 4.17 Michael Swann Building, Edinburgh EH9 3BF (UK)
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516 (USA)
| | - Juri Rappsilber
- Institut für Biotechnolgie, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin (Germany)
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, 4.17 Michael Swann Building, Edinburgh EH9 3BF (UK)
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516 (USA)
| | - David Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh (UK)
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520 (USA)
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin (Germany).
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23
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Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L, Aerni HR, Rappsilber J, Rinehart J, Leach D, Söll D, Budisa N. Chemische Evolution eines bakteriellen Proteoms. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Bande O, Abu El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marlière P, Herdewijn P. Isoguanine and 5-methyl-isocytosine bases, in vitro and in vivo. Chemistry 2015; 21:5009-22. [PMID: 25684598 PMCID: PMC4531829 DOI: 10.1002/chem.201406392] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 11/10/2022]
Abstract
The synthesis, base-pairing properties and in vitro and in vivo characteristics of 5-methyl-isocytosine (isoCMe) and isoguanine (isoG) nucleosides, incorporated in an HNA(h) (hexitol nucleic acid)–DNA(d) mosaic backbone, are described. The required h-isoG phosphoramidite was prepared by a selective deamination as a key step. As demonstrated by Tm measurements the hexitol sugar showed slightly better mismatch discrimination against dT. The d-isoG base mispairing follows the order T>G>C while the h-isoG base mispairing follows the order G>C>T. The h- and d-isoCMe bases mainly mispair with G. Enzymatic incorporation experiments show that the hexitol backbone has a variable effect on selectivity. In the enzymatic assays, isoG misincorporates mainly with T, and isoCMe misincorporates mainly with A. Further analysis in vivo confirmed the patterns of base-pair interpretation for the deoxyribose and hexitol isoCMe/isoG bases in a cellular context, through incorporation of the bases into plasmidic DNA. Results in vivo demonstrated that mispairing and misincorporation was dependent on the backbone scaffold of the base, which indicates rational advances towards orthogonality.
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Affiliation(s)
- Omprakash Bande
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven (Belgium)
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25
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Mei H, Ingale SA, Seela F. Imidazolo-dC metal-mediated base pairs: purine nucleosides capture two Ag(+) ions and form a duplex with the stability of a covalent DNA cross-link. Chemistry 2014; 20:16248-57. [PMID: 25336305 DOI: 10.1002/chem.201404422] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 12/13/2022]
Abstract
8-Phenylimidazolo-dC ((ph) ImidC, 2) forms metal-mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent "purine" 2'-deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6. Owing to the ease of nucleobase deprotonation, the new Ag(+) -mediated base pair containing a "purine" skeleton is much stronger than that derived from the pyrrolo- [3,4-d]pyrimidine system ((ph) PyrdC, 1). The silver-mediated (ph) ImidC-(ph) ImidC base pair fits well into the DNA double helix and has the stability of a covalent cross-link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857; Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
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26
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Chaput JC. Replicating an expanded genetic alphabet in cells. Chembiochem 2014; 15:1869-71. [PMID: 25044483 DOI: 10.1002/cbic.201402289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 12/17/2022]
Abstract
Recent advances in synthetic biology have made it possible to replicate an unnatural base pair in living cells. This study highlights the technologies developed to create a semisynthetic organism with an expanded genetic alphabet and the potential challenges of moving forward.
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Affiliation(s)
- John C Chaput
- Center for Evolutionary Medicine and Bioinformatics, The Biodesign Institute, Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301 (USA).
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27
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Bohlke N, Budisa N. Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion. FEMS Microbiol Lett 2014; 351:133-44. [PMID: 24433543 PMCID: PMC4237120 DOI: 10.1111/1574-6968.12371] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function – a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering.
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Affiliation(s)
- Nina Bohlke
- Department of Chemistry, TU Berlin, Berlin, Germany
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28
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Event report: SynBio Workshop (Paris 2012) – Risk assessment challenges of Synthetic Biology. J Verbrauch Lebensm 2013. [DOI: 10.1007/s00003-013-0829-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Pezo V, Liu FW, Abramov M, Froeyen M, Herdewijn P, Marlière P. Binary Genetic Cassettes for Selecting XNA-Templated DNA Synthesis In Vivo. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303288] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Pezo V, Liu FW, Abramov M, Froeyen M, Herdewijn P, Marlière P. Binary genetic cassettes for selecting XNA-templated DNA synthesis in vivo. Angew Chem Int Ed Engl 2013; 52:8139-43. [PMID: 23804524 DOI: 10.1002/anie.201303288] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Valérie Pezo
- ISSB, Génopole, Genavenir6, Equipe Xénome, 5 rue Henri Desbruères, 91030 Evry Cedex, France
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