1
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Satanowski A, Marchal DG, Perret A, Petit JL, Bouzon M, Döring V, Dubois I, He H, Smith EN, Pellouin V, Petri HM, Rainaldi V, Nattermann M, Burgener S, Paczia N, Zarzycki J, Heinemann M, Bar-Even A, Erb TJ. Design and implementation of aerobic and ambient CO 2-reduction as an entry-point for enhanced carbon fixation. Nat Commun 2025; 16:3134. [PMID: 40169551 PMCID: PMC11961710 DOI: 10.1038/s41467-025-57549-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 02/25/2025] [Indexed: 04/03/2025] Open
Abstract
The direct reduction of CO2 into one-carbon molecules is key to highly efficient biological CO2-fixation. However, this strategy is currently restricted to anaerobic organisms and low redox potentials. In this study, we introduce the CORE cycle, a synthetic metabolic pathway that converts CO2 to formate at aerobic conditions and ambient CO2 levels, using only NADPH as a reductant. Combining theoretical pathway design and analysis, enzyme bioprospecting and high-throughput screening, modular assembly and adaptive laboratory evolution, we realize the CORE cycle in vivo and demonstrate that the cycle supports growth of E. coli by supplementing C1-metabolism and serine biosynthesis from CO2. We further analyze the theoretical potential of the CORE cycle as a new entry-point for carbon in photorespiration and autotrophy. Overall, our work expands the solution space for biological carbon reduction, offering a promising approach to enhance CO2 fixation processes such as photosynthesis, and opening avenues for synthetic autotrophy.
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Affiliation(s)
- Ari Satanowski
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, Germany.
| | - Daniel G Marchal
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry-Courcouronnes, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry-Courcouronnes, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry-Courcouronnes, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry-Courcouronnes, France
| | - Ivan Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry-Courcouronnes, France
| | - Hai He
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Edward N Smith
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen, Netherlands
| | - Virginie Pellouin
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry-Courcouronnes, France
| | - Henrik M Petri
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Vittorio Rainaldi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, Germany
| | - Maren Nattermann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Simon Burgener
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen, Netherlands
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 14, Marburg, Germany.
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2
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Paupelin-Vaucelle H, Boschiero C, Lazennec-Schurdevin C, Schmitt E, Mechulam Y, Marlière P, Pezo V. Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria. ACS OMEGA 2025; 10:4548-4560. [PMID: 39959092 PMCID: PMC11822699 DOI: 10.1021/acsomega.4c08326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 11/18/2024] [Accepted: 12/16/2024] [Indexed: 02/18/2025]
Abstract
We report the construction of an alternative protein priming system to recode genetic translation in Escherichia coli by designing, through trial and error, a chimeric initiator whose sequence identity points partly to elongator tRNACys and partly to initiator tRNAf Met. The elaboration of a selection based on the N-terminal cysteine imperative for the function of glucosamine-6-phosphate synthase, an essential enzyme in bacterial cell wall synthesis, was a crucial step to achieve the engineering of this Cys-tRNAj. Iterative improvement of successive versions of Cys-tRNAj was corroborated in vitro by using a biochemical luciferase assay and in vivo by selecting for translation priming of E. coli thymidylate synthase. Condensation assays using specific fluorescent reagent FITC-Gly-cyanobenzothiazole provided biochemical evidence of cysteine coding at the protein priming stage. We showed that translation can be initiated, by N-terminal incorporation of cysteine, at a codon other than UGC by expressing a tRNAj with the corresponding anticodon. The optimized tRNAj is now available to recode the priming of an arbitrary subset of proteins in the bacterial proteome with absolute control of their expression and to evolve the use of xenonucleotides and the emergence of a tXNAj in vivo.
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Affiliation(s)
- Humbeline Paupelin-Vaucelle
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Claire Boschiero
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christine Lazennec-Schurdevin
- Laboratoire
de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique,
CNRS, Institut Polytechnique de Paris, Bat 84, Route de Saclay, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire
de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique,
CNRS, Institut Polytechnique de Paris, Bat 84, Route de Saclay, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire
de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique,
CNRS, Institut Polytechnique de Paris, Bat 84, Route de Saclay, 91128 Palaiseau cedex, France
| | - Philippe Marlière
- TESSSI, 81 rue Réaumur, 75002 Paris, France
- Theraxen
SA, 296 route de Longwy, L-1940, Luxembourg, Luxembourg
| | - Valérie Pezo
- Génomique
Métabolique, Genoscope, Institut François Jacob, CEA,
CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
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3
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Edelmann M, Couperus S, Rodríguez-Robles E, Rivollier J, Roberts T, Panke S, Marlière P. Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code. Nucleic Acids Res 2024; 52:12650-12668. [PMID: 39315692 PMCID: PMC11551756 DOI: 10.1093/nar/gkae806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/08/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024] Open
Abstract
All known bacterial tRNAs adopt the canonical cloverleaf 2D and L-shaped 3D structures. We aimed to explore whether alternative tRNA structures could be introduced in bacterial translation. To this end, we crafted a vitamin-based genetic system to evolve Escherichia coli toward activity of structurally non-canonical tRNAs. The system reliably couples (escape frequency <10-12) growth with the activities of a novel orthogonal histidine suppressor tRNA (HisTUAC) and of the cognate ARS (HisS) via suppression of a GTA valine codon in the mRNA of an enzyme in thiamine biosynthesis (ThiN). Suppression results in the introduction of an essential histidine and thereby confers thiamine prototrophy. We then replaced HisTUAC in the system with non-canonical suppressor tRNAs and selected for growth. A strain evolved to utilize mini HisT, a tRNA lacking the D-arm, and we identified the responsible mutation in an RNase gene (pnp) involved in tRNA degradation. This indicated that HisS, the ribosome, and EF-Tu accept mini HisT ab initio, which we confirmed genetically and through in vitro translation experiments. Our results reveal a previously unknown flexibility of the bacterial translation machinery for the accepted fold of the adaptor of the genetic code and demonstrate the power of the vitamin-based suppression system.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genetic Code
- RNA, Transfer/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/chemistry
- Nucleic Acid Conformation
- Protein Biosynthesis
- Thiamine/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Bacterial/chemistry
- Mutation
- Histidine/metabolism
- Histidine/genetics
- RNA, Transfer, His/metabolism
- RNA, Transfer, His/genetics
- RNA, Transfer, His/chemistry
- Ribosomes/metabolism
- Ribosomes/genetics
- RNA Folding
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Peptide Elongation Factor Tu/genetics
- Peptide Elongation Factor Tu/metabolism
- Codon/genetics
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Affiliation(s)
- Martin P Edelmann
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Sietse Couperus
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Emilio Rodríguez-Robles
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Julie Rivollier
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 75002 Paris, France
| | - Tania M Roberts
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 75002 Paris, France
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4
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Pezo V, Jaziri F, Bourguignon PY, Louis D, Jacobs-Sera D, Rozenski J, Pochet S, Herdewijn P, Hatfull GF, Kaminski PA, Marliere P. Noncanonical DNA polymerization by aminoadenine-based siphoviruses. Science 2021; 372:520-524. [PMID: 33926956 DOI: 10.1126/science.abe6542] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/25/2021] [Indexed: 01/05/2023]
Abstract
Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.
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Affiliation(s)
- Valerie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Faten Jaziri
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Pierre-Yves Bourguignon
- Werkstatt fuer Potenzielle Genetik, Naunynstrasse 30, 10997 Berlin, Germany.,TESSSI, 81 Rue Réaumur, 75002 Paris, France
| | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Sylvie Pochet
- Organic Chemistry, CNRS UMR3523, Department of Chemistry and Biocatalysis, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Pierre-Alexandre Kaminski
- Biology of Gram-Positive Pathogens, CNRS URL3526, Department of Microbiology, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Philippe Marliere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France. .,TESSSI, 81 Rue Réaumur, 75002 Paris, France
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5
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Ros E, Torres AG, Ribas de Pouplana L. Learning from Nature to Expand the Genetic Code. Trends Biotechnol 2020; 39:460-473. [PMID: 32896440 DOI: 10.1016/j.tibtech.2020.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 01/14/2023]
Abstract
The genetic code is the manual that cells use to incorporate amino acids into proteins. It is possible to artificially expand this manual through cellular, molecular, and chemical manipulations to improve protein functionality. Strategies for in vivo genetic code expansion are under the same functional constraints as natural protein synthesis. Here, we review the approaches used to incorporate noncanonical amino acids (ncAAs) into designer proteins through the manipulation of the translation machinery and draw parallels between these methods and natural adaptations that improve translation in extant organisms. Following this logic, we propose new nature-inspired tactics to improve genetic code expansion (GCE) in synthetic organisms.
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Affiliation(s)
- Enric Ros
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, 08028, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, 08028, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, 08028, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, 08010, Spain.
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6
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Yao A, Reed SA, Koh M, Yu C, Luo X, Mehta AP, Schultz PG. Progress toward a reduced phage genetic code. Bioorg Med Chem 2018; 26:5247-5252. [PMID: 29609949 DOI: 10.1016/j.bmc.2018.03.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/14/2018] [Accepted: 03/23/2018] [Indexed: 12/23/2022]
Abstract
All known living organisms use at least 20 amino acids as the basic building blocks of life. Efforts to reduce the number of building blocks in a replicating system to below the 20 canonical amino acids have not been successful to date. In this work, we use filamentous phage as a model system to investigate the feasibility of removing methionine (Met) from the proteome. We show that all 24 elongation Met sites in the M13 phage genome can be replaced by other canonical amino acids. Most of these changes involve substitution of methionine by leucine (Leu), but in some cases additional compensatory mutations are required. Combining Met substituted sites in the proteome generally led to lower viability/infectivity of the mutant phages, which remains the major challenge in eliminating all methionines from the phage proteome. To date a total of 15 (out of all 24) elongation Mets have been simultaneously deleted from the M13 proteome, providing a useful foundation for future efforts to minimize the genetic code.
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Affiliation(s)
- Anzhi Yao
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Sean A Reed
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Minseob Koh
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Chenguang Yu
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Xiaozhou Luo
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Angad P Mehta
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Peter G Schultz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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7
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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: 16.4] [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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8
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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: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Martínez-García E, de Lorenzo V. The quest for the minimal bacterial genome. Curr Opin Biotechnol 2016; 42:216-224. [DOI: 10.1016/j.copbio.2016.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 01/09/2023]
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10
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Acevedo-Rocha CG, Budisa N. Xenomicrobiology: a roadmap for genetic code engineering. Microb Biotechnol 2016; 9:666-76. [PMID: 27489097 PMCID: PMC4993186 DOI: 10.1111/1751-7915.12398] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/27/2022] Open
Abstract
Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high‐throughput and low‐cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non‐natural building blocks in living cells. In this context, genetic code engineering respectively enables the re‐design of genes/genomes and proteins/proteomes with non‐canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new‐to‐nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a ‘genetic firewall’ will also allow to study and understand the relation between code evolution and horizontal gene transfer.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Biosyntia ApS, 2970, Hørsholm, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Nediljko Budisa
- Department of Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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11
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Nikel PI, Chavarría M, Danchin A, de Lorenzo V. From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 2016; 34:20-29. [PMID: 27239751 DOI: 10.1016/j.cbpa.2016.05.011] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/04/2016] [Accepted: 05/10/2016] [Indexed: 01/14/2023]
Abstract
The soil bacterium Pseudomonas putida is endowed with a central carbon metabolic network capable of fulfilling high demands of reducing power. This situation arises from a unique metabolic architecture that encompasses the partial recycling of triose phosphates to hexose phosphates-the so-called EDEMP cycle. In this article, the value of P. putida as a bacterial chassis of choice for contemporary, industrially-oriented metabolic engineering is addressed. The biochemical properties that make this bacterium adequate for hosting biotransformations involving redox reactions as well as toxic compounds and intermediates are discussed. Finally, novel developments and open questions in the continuous quest for an optimal microbial cell factory are presented at the light of current and future needs in the area of biocatalysis.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain.
| | - Max Chavarría
- Escuela de Química & CIPRONA, Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Antoine Danchin
- AMAbiotics SAS, Institut of Cardiometabolism and Nutrition (ICAN), Hôpital Universitaire de la Pitié-Salpêtrière, 75013 Paris, France
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain.
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12
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Lajoie MJ, Söll D, Church GM. Overcoming Challenges in Engineering the Genetic Code. J Mol Biol 2016; 428:1004-21. [PMID: 26348789 PMCID: PMC4779434 DOI: 10.1016/j.jmb.2015.09.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/19/2015] [Accepted: 09/01/2015] [Indexed: 11/24/2022]
Abstract
Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code.
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Affiliation(s)
- M J Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - D Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - G M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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13
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Kawahara-Kobayashi A, Hitotsuyanagi M, Amikura K, Kiga D. Experimental evolution of a green fluorescent protein composed of 19 unique amino acids without tryptophan. ORIGINS LIFE EVOL B 2014; 44:75-86. [PMID: 25399308 DOI: 10.1007/s11084-014-9371-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
Abstract
At some stage of evolution, genes of organisms may have encoded proteins that were synthesized using fewer than 20 unique amino acids. Similar to evolution of the natural 19-amino-acid proteins GroEL/ES, proteins composed of 19 unique amino acids would have been able to evolve by accumulating beneficial mutations within the 19-amino-acid repertoire encoded in an ancestral genetic code. Because Trp is thought to be the last amino acid included in the canonical 20-amino-acid repertoire, this late stage of protein evolution could be mimicked by experimental evolution of 19-amino-acid proteins without tryptophan (Trp). To further understand the evolution of proteins, we tried to mimic the evolution of a 19-amino-acid protein involving the accumulation of beneficial mutations using directed evolution by random mutagenesis on the whole targeted gene sequence. We created active 19-amino-acid green fluorescent proteins (GFPs) without Trp from a poorly fluorescent 19-amino-acid mutant, S1-W57F, by using directed evolution with two rounds of mutagenesis and selection. The N105I and S205T mutations showed beneficial effects on the S1-W57F mutant. When these two mutations were combined on S1-W57F, we observed an additive effect on the fluorescence intensity. In contrast, these mutations showed no clear improvement individually or in combination on GFPS1, which is the parental GFP mutant composed of 20 amino acids. Our results provide an additional example for the experimental evolution of 19-amino-acid proteins without Trp, and would help understand the mechanisms underlying the evolution of 19-amino-acid proteins. (236 words).
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Affiliation(s)
- Akio Kawahara-Kobayashi
- Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
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Okumus B, Yildiz S, Toprak E. Fluidic and microfluidic tools for quantitative systems biology. Curr Opin Biotechnol 2013; 25:30-8. [PMID: 24484878 DOI: 10.1016/j.copbio.2013.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/22/2013] [Indexed: 11/18/2022]
Abstract
Understanding genes and their functions is a daunting task due to the level of complexity in biological organisms. For discovering how genotype and phenotype are linked to each other, it is essential to carry out systematic studies with maximum sensitivity and high-throughput. Recent developments in fluid-handling technologies, both at the macro and micro scale, are now allowing us to apply engineering approaches to achieve this goal. With these newly developed tools, it is now possible to identify genetic factors that are responsible for particular phenotypes, perturb and monitor cells at the single-cell level, evaluate cell-to-cell variability, detect very rare phenotypes, and construct faithful in vitro disease models.
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Affiliation(s)
- Burak Okumus
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Sadik Yildiz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Erdal Toprak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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