1
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Wong TF. Triphasic Development of the Genetic Code. Chem Rev 2024; 124:9866-9872. [PMID: 39088192 PMCID: PMC11393795 DOI: 10.1021/acs.chemrev.3c00915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
The genetic code contains an alphabet of genetically encoded amino acids. The ten Phase 1 amino acids, including Gly, Ala, Ser, Asp, Glu, Val, Leu, Ile, Pro and Thr, were available from the prebiotic environment, whereas the ten Phase 2 amino acids, including Phe, Tyr, Arg, His, Trp, Asn, Gln, Lys, Cys, and Met, became available only later from amino acid biosyntheses. In the archaeon Methanopyrus kandleri, the oldest organism known, the standard alphabet of 20 amino acids was "frozen" and no additional amino acid was encoded in the subsequent 3 Gyrs. Four decades ago, it was discovered that the code was frozen because all the organisms were so well adapted to the standard amino acids that oligogenic barriers, consisting of genes that are thoroughly dependent on the standard code, would cause loss of viability upon the deletion of any one amino acid from the code. Once the reason for the freezing of the code was ascertained, procedures were devised by scientists worldwide to enable the encoding of novel noncanonical amino acids (ncAAs). These encoded Phase 3 ncAAs now surpass the 20 canonical Phase 2 amino acids in the code.
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Affiliation(s)
- Tze-Fei Wong
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology Hong Kong, China
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2
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Qianzhu H, Abdelkader EH, Otting G, Huber T. Genetic Encoding of Fluoro-l-tryptophans for Site-Specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. J Am Chem Soc 2024; 146:13641-13650. [PMID: 38687675 DOI: 10.1021/jacs.4c03743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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3
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Saalim M, Liu S, Bennett SD, Zaleta-Pinet DA, Poulin RX, Clark BR. Precursor-Directed Biosynthesis of Antialgal Fluorinated Bacillamide Derivatives in Bacillus atrophaeus. JOURNAL OF NATURAL PRODUCTS 2024; 87:388-395. [PMID: 38319739 DOI: 10.1021/acs.jnatprod.3c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The bacillamides are a class of indole alkaloids produced by the Bacillus genus that possess significant antialgal activity. Incorporation of fluorine into the bacillamides was carried out using a precursor-directed biosynthesis approach, with 4-, 5-, and 6-fluorotryptophan added to growing cultures of Bacillus atrophaeus IMG-11. This yielded the corresponding fluorinated analogues of bacillamides A and C, in addition to new derivatives of the related metabolite N-acetyltryptamine, thus demonstrating a degree of plasticity in the bacillamide biosynthetic pathway. The bacillamide derivatives were tested for activity against bloom-forming algae, which revealed that fluorination could improve the antialgal activity of these compounds in a site-specific manner, with fluorination at the 6-position consistently resulting in improved activity.
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Affiliation(s)
- Muhammad Saalim
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, People's Republic of China
| | - Sijing Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, People's Republic of China
| | - Sandra D Bennett
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Diana A Zaleta-Pinet
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, People's Republic of China
| | - Remington X Poulin
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Benjamin R Clark
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, People's Republic of China
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4
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Danchin A, Huang JD. SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience. Environ Microbiol 2023; 25:64-78. [PMID: 36045561 DOI: 10.1111/1462-2920.16140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Jian Dong Huang
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
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5
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Qianzhu H, Abdelkader EH, Herath ID, Otting G, Huber T. Site-Specific Incorporation of 7-Fluoro-L-tryptophan into Proteins by Genetic Encoding to Monitor Ligand Binding by 19F NMR Spectroscopy. ACS Sens 2022; 7:44-49. [PMID: 35005899 DOI: 10.1021/acssensors.1c02467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A mutant aminoacyl-tRNA synthetase identified by a library selection system affords site-specific incorporation of 7-fluoro-L-tryptophan in response to an amber stop codon. The enzyme allows the production of proteins with a single hydrogen atom replaced by a fluorine atom as a sensitive nuclear magnetic resonance (NMR) probe. The substitution of a single hydrogen atom by another element that is as closely similar in size and hydrophobicity as possible minimizes possible perturbations in the structure, stability, and solubility of the protein. The fluorine atom enables site-selective monitoring of the protein response to ligand binding by 19F NMR spectroscopy, as demonstrated with the Zika virus NS2B-NS3 protease.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H. Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Iresha D. Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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6
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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7
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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8
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Kubyshkin V. Experimental lipophilicity scale for coded and noncoded amino acid residues. Org Biomol Chem 2021; 19:7031-7040. [PMID: 34333582 DOI: 10.1039/d1ob01213d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Among other features, the polarity of amino acid residues is the key parameter for understanding their role in proteins. The wide occurrence of protein modifications in nature and the advent of genetic code engineering techniques created a need for an experimental polarity value integrating both coded (canonical) and noncoded (noncanonical) residues on one universal scale. To address this issue, this work reports on a polarity scale based on the experimental lipophilicity of methyl esters of N-acetylamino acids. The derivatization of amino acids was performed in two steps under mild conditions that allowed conversion of a wide array of amino acids into analytical derivatives. The partitioning/distribution between octan-1-ol and water/buffer was measured using the intensity of the NMR signal as a characteristic for the concentration. The reference set of twenty coded amino acids generated log P values spanning 5.1 units: from tryptophan being the most hydrophobic to aspartate being the most hydrophilic. Furthermore, lipophilicity was measured for a set of analogues of phenylalanine, tyrosine, tryptophan, methionine, proline, and lysine that are typical in nature and/or laboratory practice. The polarity scale reported here will aid the rationalization of amino acid replacements in proteins, and will guide further efforts in experimental genetic code engineering.
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Affiliation(s)
- Vladimir Kubyshkin
- Chemistry Department, University of Manitoba, 144 Dysart road, Winnipeg, Manitoba R3T 2N2, Canada.
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9
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Cation-π Interactions and their Functional Roles in Membrane Proteins. J Mol Biol 2021; 433:167035. [PMID: 33957146 PMCID: PMC8338773 DOI: 10.1016/j.jmb.2021.167035] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 01/25/2023]
Abstract
Cation-π interactions arise as a result of strong attractive forces between positively charged entities and the π-electron cloud of aromatic groups. The physicochemical characteristics of cation-π interactions are particularly well-suited to the dual hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins bring molecular features into increasingly sharper view, cation-π interactions are gaining traction as essential contributors to membrane protein chemistry, function, and pharmacology. Here we review the physicochemical properties of cation-π interactions and present several prominent examples which demonstrate significant roles for this specialized biological chemistry.
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10
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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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11
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Kubyshkin V, Davis R, Budisa N. Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement. Beilstein J Org Chem 2021; 17:439-460. [PMID: 33727970 PMCID: PMC7934785 DOI: 10.3762/bjoc.17.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.
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Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
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12
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Zhang F, Ellington AD. Hurdling and Hurtling Toward New Genetic Codes. ACS CENTRAL SCIENCE 2021; 7:7-10. [PMID: 33532562 PMCID: PMC7844845 DOI: 10.1021/acscentsci.0c01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Fan Zhang
- Center for Systems and Synthetic Biology University of Texas at Austin Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology University of Texas at Austin Austin, Texas 78712, United States
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13
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Agostini F, Sinn L, Petras D, Schipp CJ, Kubyshkin V, Berger AA, Dorrestein PC, Rappsilber J, Budisa N, Koksch B. Multiomics Analysis Provides Insight into the Laboratory Evolution of Escherichia coli toward the Metabolic Usage of Fluorinated Indoles. ACS CENTRAL SCIENCE 2021; 7:81-92. [PMID: 33532571 PMCID: PMC7844855 DOI: 10.1021/acscentsci.0c00679] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 05/23/2023]
Abstract
Organofluorine compounds are known to be toxic to a broad variety of living beings in different habitats, and chemical fluorination has been historically exploited by mankind for the development of therapeutic drugs or agricultural pesticides. On the other hand, several studies so far have demonstrated that, under appropriate conditions, living systems (in particular bacteria) can tolerate the presence of fluorinated molecules (e.g., amino acids analogues) within their metabolism and even repurpose them as alternative building blocks for the synthesis of cellular macromolecules such as proteins. Understanding the molecular mechanism behind these phenomena would greatly advance approaches to the biotechnological synthesis of recombinant proteins and peptide drugs. However, information about the metabolic effects of long-term exposure of living cells to fluorinated amino acids remains scarce. Hereby, we report the long-term propagation of Escherichia coli (E. coli) in an artificially fluorinated habitat that yielded two strains naturally adapted to live on fluorinated amino acids. In particular, we applied selective pressure to force a tryptophan (Trp)-auxotrophic strain to use either 4- or 5-fluoroindole as essential precursors for the in situ synthesis of Trp analogues, followed by their incorporation in the cellular proteome. We found that full adaptation to both fluorinated Trp analogues requires a low number of genetic mutations but is accompanied by large rearrangements in regulatory networks, membrane integrity, and quality control of protein folding. These findings highlight the cellular mechanisms behind the adaptation to unnatural amino acids and provide the molecular foundation for bioengineering of novel microbial strains for synthetic biology and biotechnology.
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Affiliation(s)
- Federica Agostini
- Institute
of Biochemistry—Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ludwig Sinn
- Institute
of Biotechnology—Bioanalytics, Technische
Universität Berlin, Berlin 10623, Germany
| | - Daniel Petras
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States
| | - Christian J. Schipp
- Institute
of Chemistry—Biocatalysis, Technische
Universität Berlin, Berlin 10623, Germany
| | - Vladimir Kubyshkin
- Institute
of Chemistry—Biocatalysis, Technische
Universität Berlin, Berlin 10623, Germany
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Allison Ann Berger
- Institute
of Chemistry and Biochemistry—Organic Chemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Pieter C. Dorrestein
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States
| | - Juri Rappsilber
- Institute
of Biotechnology—Bioanalytics, Technische
Universität Berlin, Berlin 10623, Germany
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Nediljko Budisa
- Institute
of Chemistry—Biocatalysis, Technische
Universität Berlin, Berlin 10623, Germany
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry—Organic Chemistry, Freie Universität Berlin, Berlin 14195, Germany
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14
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Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets. Sci Rep 2019; 9:12468. [PMID: 31462646 PMCID: PMC6713743 DOI: 10.1038/s41598-019-47574-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/08/2019] [Indexed: 01/11/2023] Open
Abstract
Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded amino acids could have comprised the earlier sets. We explore the hypothesis that the CAAs were selectively fixed due to their unique adaptive chemical properties, which facilitate folding, catalysis, and solubility of proteins, and gave adaptive value to organisms able to encode them. Specifically, we studied in silico hypothetical CAA sets of 3–19 amino acids comprised of 1913 structurally diverse α-amino acids, exploring the adaptive value of their combined physicochemical properties relative to those of the modern CAA set. We find that even hypothetical sets containing modern CAA members are especially adaptive; it is difficult to find sets even among a large choice of alternatives that cover the chemical property space more amply. These results suggest that each time a CAA was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.
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15
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Schmitt MA, Biddle W, Fisk JD. Mapping the Plasticity of the Escherichia coli Genetic Code with Orthogonal Pair-Directed Sense Codon Reassignment. Biochemistry 2018; 57:2762-2774. [PMID: 29668270 DOI: 10.1021/acs.biochem.8b00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incorporation of a single amino acid in response to individual sense and nonsense codons provides a suite of related data with which to examine the plasticity of the code. Each directed sense codon reassignment measurement is an in vivo competition experiment between the introduced orthogonal translation machinery and the natural machinery in Escherichia coli. This report discusses 20 new, related genetic codes, in which a targeted E. coli wobble codon is reassigned to tyrosine utilizing the orthogonal tyrosine tRNA/aminoacyl tRNA synthetase pair from Methanocaldococcus jannaschii. One at a time, reassignment of each targeted sense codon to tyrosine is quantified in cells by measuring the fluorescence of GFP variants in which the essential tyrosine residue is encoded by a non-tyrosine codon. Significantly, every wobble codon analyzed may be partially reassigned with efficiencies ranging from 0.8 to 41%. The accumulation of the suite of data enables a qualitative dissection of the relative importance of the factors affecting the fidelity of translation. While some correlation was observed between sense codon reassignment and either competing endogenous tRNA abundance or changes in aminoacylation efficiency of the altered orthogonal system, no single factor appears to predominately drive translational fidelity. Evaluation of relative cellular fitness in each of the 20 quantitatively characterized proteome-wide tyrosine substitution systems suggests that at a systems level, E. coli is robust to missense mutations.
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Affiliation(s)
- Margaret A Schmitt
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Wil Biddle
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - John D Fisk
- Department of Chemical and Biological Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,School of Biomedical Engineering , Colorado State University , Fort Collins , Colorado 80523 , United States
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16
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Baumann T, Schmitt FJ, Pelzer A, Spiering VJ, Freiherr von Sass GJ, Friedrich T, Budisa N. Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence. J Vis Exp 2018. [PMID: 29757279 PMCID: PMC6100899 DOI: 10.3791/57017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fluorescent proteins are fundamental tools for the life sciences, in particular for fluorescence microscopy of living cells. While wild-type and engineered variants of the green fluorescent protein from Aequorea victoria (avGFP) as well as homologs from other species already cover large parts of the optical spectrum, a spectral gap remains in the near-infrared region, for which avGFP-based fluorophores are not available. Red-shifted fluorescent protein (FP) variants would substantially expand the toolkit for spectral unmixing of multiple molecular species, but the naturally occurring red-shifted FPs derived from corals or sea anemones have lower fluorescence quantum yield and inferior photo-stability compared to the avGFP variants. Further manipulation and possible expansion of the chromophore's conjugated system towards the far-red spectral region is also limited by the repertoire of 20 canonical amino acids prescribed by the genetic code. To overcome these limitations, synthetic biology can achieve further spectral red-shifting via insertion of non-canonical amino acids into the chromophore triad. We describe the application of SPI to engineer avGFP variants with novel spectral properties. Protein expression is performed in a tryptophan-auxotrophic E. coli strain and by supplementing growth media with suitable indole precursors. Inside the cells, these precursors are converted to the corresponding tryptophan analogs and incorporated into proteins by the ribosomal machinery in response to UGG codons. The replacement of Trp-66 in the enhanced "cyan" variant of avGFP (ECFP) by an electron-donating 4-aminotryptophan results in GdFP featuring a 108 nm Stokes shift and a strongly red-shifted emission maximum (574 nm), while being thermodynamically more stable than its predecessor ECFP. Residue-specific incorporation of the non-canonical amino acid is analyzed by mass spectrometry. The spectroscopic properties of GdFP are characterized by time-resolved fluorescence spectroscopy as one of the valuable applications of genetically encoded FPs in life sciences.
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Affiliation(s)
- Tobias Baumann
- Institute of Chemistry L 1, Department of Biocatalysis, Technical University of Berlin
| | - Franz-Josef Schmitt
- Institute of Chemistry PC 14, Department of Bioenergetics, Technical University of Berlin
| | - Almut Pelzer
- Institute of Chemistry L 1, Department of Biocatalysis, Technical University of Berlin
| | - Vivian Jeanette Spiering
- Institute of Chemistry TC 7, Department of Physical Chemistry/Molecular Material Sciences, Technical University of Berlin
| | | | - Thomas Friedrich
- Institute of Chemistry PC 14, Department of Bioenergetics, Technical University of Berlin;
| | - Nediljko Budisa
- Institute of Chemistry L 1, Department of Biocatalysis, Technical University of Berlin
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17
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Tack DS, Cole AC, Shroff R, Morrow BR, Ellington AD. Evolving Bacterial Fitness with an Expanded Genetic Code. Sci Rep 2018; 8:3288. [PMID: 29459649 PMCID: PMC5818497 DOI: 10.1038/s41598-018-21549-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/06/2018] [Indexed: 11/21/2022] Open
Abstract
Since the fixation of the genetic code, evolution has largely been confined to 20 proteinogenic amino acids. The development of orthogonal translation systems that allow for the codon-specific incorporation of noncanonical amino acids may provide a means to expand the code, but these translation systems cannot be simply superimposed on cells that have spent billions of years optimizing their genomes with the canonical code. We have therefore carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21 amino acid code is enforced through the inclusion of an addicted, essential gene, a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000 generations of directed evolution, the fitness deficit of the original strain was largely repaired through mutations that limited the toxicity of the noncanonical. While the evolved lineages had not resolved the ambiguous coding of the amber codon, the improvements in fitness allowed new amber codons to populate protein coding sequences.
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Affiliation(s)
- Drew S Tack
- National Institute for Standards and Technology, Gaithersburg, Maryland, USA. .,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA.
| | - Austin C Cole
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Barrett R Morrow
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
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18
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Baril SA, Koenig AL, Krone MW, Albanese KI, Qixin He C, Lee GY, Houk KN, Waters ML, Brustad EM. Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis. J Am Chem Soc 2017; 139:17253-17256. [PMID: 29111699 PMCID: PMC6040664 DOI: 10.1021/jacs.7b09223] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.
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Affiliation(s)
- Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amber L. Koenig
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mackenzie W. Krone
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cyndi Qixin He
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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19
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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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20
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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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21
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Lin X, Yu ACS, Chan TF. Efforts and Challenges in Engineering the Genetic Code. Life (Basel) 2017; 7:life7010012. [PMID: 28335420 PMCID: PMC5370412 DOI: 10.3390/life7010012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 12/15/2022] Open
Abstract
This year marks the 48th anniversary of Francis Crick’s seminal work on the origin of the genetic code, in which he first proposed the “frozen accident” hypothesis to describe evolutionary selection against changes to the genetic code that cause devastating global proteome modification. However, numerous efforts have demonstrated the viability of both natural and artificial genetic code variations. Recent advances in genetic engineering allow the creation of synthetic organisms that incorporate noncanonical, or even unnatural, amino acids into the proteome. Currently, successful genetic code engineering is mainly achieved by creating orthogonal aminoacyl-tRNA/synthetase pairs to repurpose stop and rare codons or to induce quadruplet codons. In this review, we summarize the current progress in genetic code engineering and discuss the challenges, current understanding, and future perspectives regarding genetic code modification.
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Affiliation(s)
- Xiao Lin
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, NT, Hong Kong, China.
| | - Allen Chi Shing Yu
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, NT, Hong Kong, China.
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, NT, Hong Kong, China.
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22
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Future of the Genetic Code. Life (Basel) 2017; 7:life7010010. [PMID: 28264473 PMCID: PMC5370410 DOI: 10.3390/life7010010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/17/2022] Open
Abstract
The methods for establishing synthetic lifeforms with rewritten genetic codes comprising non-canonical amino acids (NCAA) in addition to canonical amino acids (CAA) include proteome-wide replacement of CAA, insertion through suppression of nonsense codon, and insertion via the pyrrolysine and selenocysteine pathways. Proteome-wide reassignments of nonsense codons and sense codons are also under development. These methods enable the application of NCAAs to enrich both fundamental and applied aspects of protein chemistry and biology. Sense codon reassignment to NCAA could incur problems arising from the usage of anticodons as identity elements on tRNA, and possible misreading of NNY codons by UNN anticodons. Evidence suggests that the problem of anticodons as identity elements can be diminished or resolved through removal from the tRNA of all identity elements besides the anticodon, and the problem of misreading of NNY codons by UNN anticodon can be resolved by the retirement of both the UNN anticodon and its complementary NNA codon from the proteome in the event that a restrictive post-transcriptional modification of the UNN anticodon by host enzymes to prevent the misreading cannot be obtained.
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23
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Biddle W, Schmitt MA, Fisk JD. Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. Nucleic Acids Res 2016; 44:10042-10050. [PMID: 27915288 PMCID: PMC5137457 DOI: 10.1093/nar/gkw948] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 12/25/2022] Open
Abstract
Breaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNAOpt. We suspected a modification of the tRNAOptAUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNAOptAUG is converted to inosine. We identified tRNAOptAUG anticodon loop variants that increase reassignment of the histidine CAU codon, decrease incorporation in response to the histidine CAC codon, and improve cell health and growth profiles. Recognizing tRNA modification as both a potential pitfall and avenue of directed alteration will be important as the field of genetic code engineering continues to infiltrate the genetic codes of diverse organisms.
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Affiliation(s)
- Wil Biddle
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Margaret A Schmitt
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - John D Fisk
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA .,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
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24
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Anderhuber N, Fladischer P, Gruber-Khadjawi M, Mairhofer J, Striedner G, Wiltschi B. High-level biosynthesis of norleucine in E. coli for the economic labeling of proteins. J Biotechnol 2016; 235:100-11. [PMID: 27107466 DOI: 10.1016/j.jbiotec.2016.04.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Abstract
The residue-specific labeling of proteins with non-canonical amino acids (ncAA) is well established in shake flask cultures. A key aspect for the transfer of the methodology to larger scales for biotechnological applications is the cost of the supplemented ncAAs. Therefore, we established a scalable bioprocess using an engineered host strain for the biosynthesis of the methionine analog norleucine at titers appropriate for the efficient and economic labeling of proteins. To enhance the biosynthesis of norleucine, which is a side-product of the branched chain amino acid pathway, we deleted all three acetolactate synthase isoforms of the methionine auxotrophic Escherichia coli expression strain B834(DE3). Additionally, we overexpressed leuABCD to boost the biosynthesis of norleucine. We systematically analyzed the production of norleucine under the conditions for its residue-specific incorporation in bioreactor cultures that had a 30-fold higher cell density than shake flask cultures. Under optimized conditions, 5g/L norleucine was biosynthesized. This titer is two times higher than the standard supplementation with norleucine of a culture with comparable cell density. We expect that our metabolically engineered strain for the improved biosynthesis of norleucine in combination with the proposed bioprocess will facilitate the efficient residue-specific labeling of proteins at a reasonable price in scales beyond the shake flask.
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Affiliation(s)
- Niklaus Anderhuber
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Patrik Fladischer
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Mandana Gruber-Khadjawi
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Department of Organic Chemistry, Graz University of Technology, Stremayrgasse 9/4, A-8010 Graz, Austria
| | - Juergen Mairhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, and Department of Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; enGenes Biotech GmbH, Mooslackengasse 17, A-1190 Vienna, Austria
| | - Gerald Striedner
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, and Department of Biotechnology, Muthgasse 18, A-1190 Vienna, Austria
| | - Birgit Wiltschi
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria.
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25
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Towards Biocontained Cell Factories: An Evolutionarily Adapted Escherichia coli Strain Produces a New-to-nature Bioactive Lantibiotic Containing Thienopyrrole-Alanine. Sci Rep 2016; 6:33447. [PMID: 27634138 PMCID: PMC5025777 DOI: 10.1038/srep33447] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/25/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic code engineering that enables reassignment of genetic codons to non-canonical amino acids (ncAAs) is a powerful strategy for enhancing ribosomally synthesized peptides and proteins with functions not commonly found in Nature. Here we report the expression of a ribosomally synthesized and post-translationally modified peptide (RiPP), the 32-mer lantibiotic lichenicidin with a canonical tryptophan (Trp) residue replaced by the ncAA L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) which does not sustain cell growth in the culture. We have demonstrated that cellular toxicity of [3,2]Tpa for the production of the new-to-nature bioactive congener of lichenicidin in the host Escherichia coli can be alleviated by using an evolutionarily adapted host strain MT21 which not only tolerates [3,2]Tpa but also uses it as a proteome-wide synthetic building block. This work underscores the feasibility of the biocontainment concept and establishes a general framework for design and large scale production of RiPPs with evolutionarily adapted host strains.
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26
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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: 5.1] [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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27
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Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life. Life (Basel) 2016; 6:life6010012. [PMID: 26999216 PMCID: PMC4810243 DOI: 10.3390/life6010012] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022] Open
Abstract
The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets.
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28
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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: 43] [Impact Index Per Article: 5.4] [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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29
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Addicting diverse bacteria to a noncanonical amino acid. Nat Chem Biol 2016; 12:138-40. [DOI: 10.1038/nchembio.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/13/2015] [Indexed: 12/15/2022]
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30
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Bezerra AR, Guimarães AR, Santos MAS. Non-Standard Genetic Codes Define New Concepts for Protein Engineering. Life (Basel) 2015; 5:1610-28. [PMID: 26569314 PMCID: PMC4695839 DOI: 10.3390/life5041610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/12/2015] [Accepted: 10/21/2015] [Indexed: 11/16/2022] Open
Abstract
The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.
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Affiliation(s)
- Ana R Bezerra
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Ana R Guimarães
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
| | - Manuel A S Santos
- Health Sciences Department, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal.
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31
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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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32
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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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33
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Weiss PS, Ermert J, Castillo Meleán J, Schäfer D, Coenen HH. Radiosynthesis of 4-[(18)F]fluoro-L-tryptophan by isotopic exchange on carbonyl-activated precursors. Bioorg Med Chem 2015; 23:5856-69. [PMID: 26193761 DOI: 10.1016/j.bmc.2015.06.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/27/2015] [Accepted: 06/29/2015] [Indexed: 12/18/2022]
Abstract
Several (18)F-labeled aromatic amino acids have been developed primarily for tumor imaging with positron-emission-tomography (PET). Also, (18)F-labeled tryptophan derivatives were synthesized by electrophilic (18)F-fluorination or by introducing a [(18)F]fluoroalkyl group. Here, a 3-step method for a nucleophilic radiosynthesis of 4-[(18)F]fluoro-L-tryptophan was developed. A carbonyl activated precursor containing a chiral amino acid building block was radiofluorinated by isotopic exchange, followed by removal of the activating formyl group by reductive decarbonylation and subsequent cleavage of the building block under acidic conditions. The title compound was obtained within 100 min with a radiochemical yield of about 13%, a molar activity of >70 MBq/mmol and an enantiomeric excess of >99%.
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Affiliation(s)
- Philipp S Weiss
- Institut für Neurowissenschaften und Medizin, INM-5: Nuklearchemie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Johannes Ermert
- Institut für Neurowissenschaften und Medizin, INM-5: Nuklearchemie, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Johnny Castillo Meleán
- Institut für Neurowissenschaften und Medizin, INM-5: Nuklearchemie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dominique Schäfer
- Institut für Neurowissenschaften und Medizin, INM-5: Nuklearchemie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Heinz H Coenen
- Institut für Neurowissenschaften und Medizin, INM-5: Nuklearchemie, Forschungszentrum Jülich, 52425 Jülich, Germany
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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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Concepción-Acevedo J, Weiss HN, Chaudhry WN, Levin BR. Malthusian Parameters as Estimators of the Fitness of Microbes: A Cautionary Tale about the Low Side of High Throughput. PLoS One 2015; 10:e0126915. [PMID: 26114477 PMCID: PMC4482697 DOI: 10.1371/journal.pone.0126915] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/09/2015] [Indexed: 01/29/2023] Open
Abstract
The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes. Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day. Here we compare estimates of the relative fitness of antibiotic susceptible and resistant strains of E. coli, Pseudomonas aeruginosa and Staphylococcus aureus based on MP data obtained with automated multi-well plate readers with the results from pairwise competition experiments. This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.
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Affiliation(s)
| | - Howard N. Weiss
- Department of Mathematics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Waqas Nasir Chaudhry
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- National University of Sciences and Technology, Islamabad, Pakistan
| | - Bruce R. Levin
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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36
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An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J Biotechnol 2014; 178:12-22. [DOI: 10.1016/j.jbiotec.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/08/2014] [Accepted: 02/14/2014] [Indexed: 11/19/2022]
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37
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Yu ACS, Yim AKY, Mat WK, Tong AHY, Lok S, Xue H, Tsui SKW, Wong JTF, Chan TF. Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code. Genome Biol Evol 2014; 6:629-41. [PMID: 24572018 PMCID: PMC3971595 DOI: 10.1093/gbe/evu044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2014] [Indexed: 12/26/2022] Open
Abstract
The 20 canonical amino acids of the genetic code have been invariant over 3 billion years of biological evolution. Although various aminoacyl-tRNA synthetases can charge their cognate tRNAs with amino acid analogs, there has been no known displacement of any canonical amino acid from the code. Experimental departure from this universal protein alphabet comprising the canonical amino acids was first achieved in the mutants of the Bacillus subtilis QB928 strain, which after serial selection and mutagenesis led to the HR23 strain that could use 4-fluorotryptophan (4FTrp) but not canonical tryptophan (Trp) for propagation. To gain insight into this displacement of Trp from the genetic code by 4FTrp, genome sequencing was performed on LC33 (a precursor strain of HR23), HR23, and TR7 (a revertant of HR23 that regained the capacity to propagate on Trp). Compared with QB928, the negative regulator mtrB of Trp transport was found to be knocked out in LC33, HR23, and TR7, and sigma factor sigB was mutated in HR23 and TR7. Moreover, rpoBC encoding RNA polymerase subunits were mutated in three independent isolates of TR7 relative to HR23. Increased expression of sigB was also observed in HR23 and in TR7 growing under 4FTrp. These findings indicated that stabilization of the genetic code can be provided by just a small number of analog-sensitive proteins, forming an oligogenic barrier that safeguards the canonical amino acids throughout biological evolution.
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Affiliation(s)
- Allen Chi-Shing Yu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Aldrin Kay-Yuen Yim
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai-Kin Mat
- Division of Life Science and Applied Genomics Center, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Amy Hin-Yan Tong
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Si Lok
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hong Xue
- Division of Life Science and Applied Genomics Center, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - J. Tze-Fei Wong
- Division of Life Science and Applied Genomics Center, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
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38
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Singh-Blom A, Hughes RA, Ellington AD. Residue-specific incorporation of unnatural amino acids into proteins in vitro and in vivo. Methods Mol Biol 2013; 978:93-114. [PMID: 23423891 DOI: 10.1007/978-1-62703-293-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The incorporation of noncanonical (unnatural) amino acids into proteins offers researchers the ability to augment the biochemical functionality of proteins for a myriad of applications including bioorthogonal conjugation, biophysical and structural studies, and the enhancement or de novo creation of novel enzymatic activities. The augmentation of a protein throughout its coding sequence by global residue-specific incorporation of unnatural amino acid analogs is an attractive technique for studying both the utility of individual chemistries available through unnatural amino acids and the general effects of unnatural amino acid substitution on protein structure and function. Herein we describe protocols to introduce unnatural amino acids into proteins using the Escherichia coli translation system either in vivo or in vitro. Special attention is paid to obtaining high levels of incorporation while maintaining high yields of protein expression.
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Affiliation(s)
- Amrita Singh-Blom
- Department of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX, USA
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39
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Kawahara-Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, Asami S, Matsuda T, Ishitani R, Dohmae N, Yokoyama S, Kigawa T, Nureki O, Kiga D. Simplification of the genetic code: restricted diversity of genetically encoded amino acids. Nucleic Acids Res 2012; 40:10576-84. [PMID: 22909996 PMCID: PMC3488234 DOI: 10.1093/nar/gks786] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered to be used. Although this notion is supported by a wide range of data, the actual existence and function of the genetic codes with a limited set of canonical amino acids have not been addressed experimentally, in contrast to the successful development of the expanded codes. Here, we constructed artificial genetic codes involving a reduced alphabet. In one of the codes, a tRNAAla variant with the Trp anticodon reassigns alanine to an unassigned UGG codon in the Escherichia coli S30 cell-free translation system lacking tryptophan. We confirmed that the efficiency and accuracy of protein synthesis by this Trp-lacking code were comparable to those by the universal genetic code, by an amino acid composition analysis, green fluorescent protein fluorescence measurements and the crystal structure determination. We also showed that another code, in which UGU/UGC codons are assigned to Ser, synthesizes an active enzyme. This method will provide not only new insights into primordial genetic codes, but also an essential protein engineering tool for the assessment of the early stages of protein evolution and for the improvement of pharmaceuticals.
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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, Midori-ku, Yokohama-shi, Kanagawa 226-8503, Japan
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40
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Merkel L, Budisa N. Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes. Org Biomol Chem 2012; 10:7241-61. [DOI: 10.1039/c2ob06922a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Brustad EM, Arnold FH. Optimizing non-natural protein function with directed evolution. Curr Opin Chem Biol 2010; 15:201-10. [PMID: 21185770 DOI: 10.1016/j.cbpa.2010.11.020] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/15/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
Abstract
Developing technologies such as unnatural amino acid mutagenesis, non-natural cofactor engineering, and computational design are generating proteins with novel functions; these proteins, however, often do not reach performance targets and would benefit from further optimization. Evolutionary methods can complement these approaches: recent work combining unnatural amino acid mutagenesis and phage selection has created useful proteins of novel composition. Weak initial activity in a computationally designed enzyme has been improved by iterative rounds of mutagenesis and screening. A marriage of ingenuity and evolution will expand the scope of protein function well beyond Mother Nature's designs.
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Affiliation(s)
- Eric M Brustad
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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42
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Mat WK, Xue H, Wong JTF. Genetic code mutations: the breaking of a three billion year invariance. PLoS One 2010; 5:e12206. [PMID: 20808824 PMCID: PMC2924881 DOI: 10.1371/journal.pone.0012206] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 07/10/2010] [Indexed: 11/19/2022] Open
Abstract
The genetic code has been unchanging for some three billion years in its canonical ensemble of encoded amino acids, as indicated by the universal adoption of this ensemble by all known organisms. Code mutations beginning with the encoding of 4-fluoro-Trp by Bacillus subtilis, initially replacing and eventually displacing Trp from the ensemble, first revealed the intrinsic mutability of the code. This has since been confirmed by a spectrum of other experimental code alterations in both prokaryotes and eukaryotes. To shed light on the experimental conversion of a rigidly invariant code to a mutating code, the present study examined code mutations determining the propagation of Bacillus subtilis on Trp and 4-, 5- and 6-fluoro-tryptophans. The results obtained with the mutants with respect to cross-inhibitions between the different indole amino acids, and the growth effects of individual nutrient withdrawals rendering essential their biosynthetic pathways, suggested that oligogenic barriers comprising sensitive proteins which malfunction with amino acid analogues provide effective mechanisms for preserving the invariance of the code through immemorial time, and mutations of these barriers open up the code to continuous change.
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Affiliation(s)
- Wai-Kin Mat
- Applied Genomics Center, Fok Ying Tung Graduate School and Department of Biochemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | - Hong Xue
- Applied Genomics Center, Fok Ying Tung Graduate School and Department of Biochemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | - J. Tze-Fei Wong
- Applied Genomics Center, Fok Ying Tung Graduate School and Department of Biochemistry, Hong Kong University of Science and Technology, Hong Kong, China
- * E-mail:
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43
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Hughes RA, Ellington AD. Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA. Nucleic Acids Res 2010; 38:6813-30. [PMID: 20571084 PMCID: PMC2965240 DOI: 10.1093/nar/gkq521] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
While a number of aminoacyl tRNA synthetase (aaRS):tRNA pairs have been engineered to alter or expand the genetic code, only the Methanococcus jannaschii tyrosyl tRNA synthetase and tRNA have been used extensively in bacteria, limiting the types and numbers of unnatural amino acids that can be utilized at any one time to expand the genetic code. In order to expand the number and type of aaRS/tRNA pairs available for engineering bacterial genetic codes, we have developed an orthogonal tryptophanyl tRNA synthetase and tRNA pair, derived from Saccharomyces cerevisiae. In the process of developing an amber suppressor tRNA, we discovered that the Escherichia coli lysyl tRNA synthetase was responsible for misacylating the initial amber suppressor version of the yeast tryptophanyl tRNA. It was discovered that modification of the G:C content of the anticodon stem and therefore reducing the structural flexibility of this stem eliminated misacylation by the E. coli lysyl tRNA synthetase, and led to the development of a functional, orthogonal suppressor pair that should prove useful for the incorporation of bulky, unnatural amino acids into the genetic code. Our results provide insight into the role of tRNA flexibility in molecular recognition and the engineering and evolution of tRNA specificity.
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Affiliation(s)
- Randall A Hughes
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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44
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Voloshchuk N, Montclare JK. Incorporation of unnatural amino acids for synthetic biology. ACTA ACUST UNITED AC 2010; 6:65-80. [DOI: 10.1039/b909200p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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45
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Marliere P. The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world. SYSTEMS AND SYNTHETIC BIOLOGY 2009; 3:77-84. [PMID: 19816802 PMCID: PMC2759432 DOI: 10.1007/s11693-009-9040-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 08/05/2009] [Accepted: 08/07/2009] [Indexed: 11/06/2022]
Abstract
Biotechnology has empirically established that it is easier to construct and evaluate variant genes and proteins than to account for the emergence and function of wild-type macromolecules. Systematizing this constructive approach, synthetic biology now promises to infer and assemble entirely novel genomes, cells and ecosystems. It is argued here that the theoretical and computational tools needed for this endeavor are missing altogether. However, such tools may not be required for diversifying organisms at the basic level of their chemical constitution by adding, substituting or removing elements and molecular components through directed evolution under selection. Most importantly, chemical diversification of life forms could be designed to block metabolic cross-feed and genetic cross-talk between synthetic and wild species and hence protect natural habitats and human health through novel types of containment.
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46
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Gomes AC, Miranda I, Silva RM, Moura GR, Thomas B, Akoulitchev A, Santos MAS. A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans. Genome Biol 2008; 8:R206. [PMID: 17916231 PMCID: PMC2246281 DOI: 10.1186/gb-2007-8-10-r206] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/31/2007] [Accepted: 10/04/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic code alterations have been reported in mitochondrial, prokaryotic, and eukaryotic cytoplasmic translation systems, but their evolution and how organisms cope and survive such dramatic genetic events are not understood. RESULTS Here we used an unusual decoding of leucine CUG codons as serine in the main human fungal pathogen Candida albicans to elucidate the global impact of genetic code alterations on the proteome. We show that C. albicans decodes CUG codons ambiguously and tolerates partial reversion of their identity from serine back to leucine on a genome-wide scale. CONCLUSION Such codon ambiguity expands the proteome of this human pathogen exponentially and is used to generate important phenotypic diversity. This study highlights novel features of C. albicans biology and unanticipated roles for codon ambiguity in the evolution of the genetic code.
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Affiliation(s)
- Ana C Gomes
- CESAM & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal.
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47
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Miranda I, Rocha R, Santos MC, Mateus DD, Moura GR, Carreto L, Santos MAS. A genetic code alteration is a phenotype diversity generator in the human pathogen Candida albicans. PLoS One 2007; 2:e996. [PMID: 17912373 PMCID: PMC1991585 DOI: 10.1371/journal.pone.0000996] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 09/18/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The discovery of genetic code alterations and expansions in both prokaryotes and eukaryotes abolished the hypothesis of a frozen and universal genetic code and exposed unanticipated flexibility in codon and amino acid assignments. It is now clear that codon identity alterations involve sense and non-sense codons and can occur in organisms with complex genomes and proteomes. However, the biological functions, the molecular mechanisms of evolution and the diversity of genetic code alterations remain largely unknown. In various species of the genus Candida, the leucine CUG codon is decoded as serine by a unique serine tRNA that contains a leucine 5'-CAG-3'anticodon (tRNA(CAG)(Ser)). We are using this codon identity redefinition as a model system to elucidate the evolution of genetic code alterations. METHODOLOGY/PRINCIPAL FINDINGS We have reconstructed the early stages of the Candida genetic code alteration by engineering tRNAs that partially reverted the identity of serine CUG codons back to their standard leucine meaning. Such genetic code manipulation had profound cellular consequences as it exposed important morphological variation, altered gene expression, re-arranged the karyotype, increased cell-cell adhesion and secretion of hydrolytic enzymes. CONCLUSION/SIGNIFICANCE Our study provides the first experimental evidence for an important role of genetic code alterations as generators of phenotypic diversity of high selective potential and supports the hypothesis that they speed up evolution of new phenotypes.
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Affiliation(s)
- Isabel Miranda
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Rita Rocha
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Maria C. Santos
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Denisa D. Mateus
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Gabriela R. Moura
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Laura Carreto
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
| | - Manuel A. S. Santos
- Department of Biology, Centro de Estudos do Ambiente e do Mar (CESAM), University of Aveiro, Aveiro, Portugal
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48
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Bacher JM, Waas WF, Metzgar D, de Crécy-Lagard V, Schimmel P. Genetic code ambiguity confers a selective advantage on Acinetobacter baylyi. J Bacteriol 2007; 189:6494-6. [PMID: 17616603 PMCID: PMC1951902 DOI: 10.1128/jb.00622-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A primitive genetic code, composed of a smaller set of amino acids, may have expanded via recursive periods of genetic code ambiguity that were followed by specificity. Here we model a step in this process by showing how genetic code ambiguity could result in an enhanced growth rate in Acinetobacter baylyi.
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Affiliation(s)
- Jamie M Bacher
- The Scripps Research Institute, 10550 N. Torrey Pines Rd., BCC-379, La Jolla, CA 92037, USA
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49
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Wiltschi B, Budisa N. Natural history and experimental evolution of the genetic code. Appl Microbiol Biotechnol 2007; 74:739-53. [PMID: 17268784 DOI: 10.1007/s00253-006-0823-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2006] [Revised: 12/19/2006] [Accepted: 12/20/2006] [Indexed: 10/23/2022]
Abstract
The standard genetic code is a set of rules that relates the 20 canonical amino acids in proteins to groups of three bases in the mRNA. It evolved from a more primitive form and the attempts to reconstruct its natural history are based on its present-day features. Genetic code engineering as a new research field was developed independently in a few laboratories during the last 15 years. The main intention is to re-program protein synthesis by expanding the coding capacities of the genetic code via re-assignment of specific codons to un-natural amino acids. This article focuses on the question as to which extent hypothetical scenarios that led to codon re-assignments during the evolution of the genetic code are relevant for its further evolution in the laboratory. Current attempts to engineer the genetic code are reviewed with reference to theoretical works on its natural history. Integration of the theoretical considerations into experimental concepts will bring us closer to designer cells with target-engineered genetic codes that should open not only tremendous possibilities for the biotechnology of the twenty-first century but will also provide a basis for the design of novel life forms.
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Affiliation(s)
- Birgit Wiltschi
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, Martinsried, Germany
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50
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Carlson JH, Wood H, Roshick C, Caldwell HD, McClarty G. In vivo and in vitro studies of Chlamydia trachomatis TrpR:DNA interactions. Mol Microbiol 2006; 59:1678-91. [PMID: 16553875 PMCID: PMC2808116 DOI: 10.1111/j.1365-2958.2006.05045.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We previously reported that Chlamydia trachomatis expresses the genes encoding tryptophan synthase (trpBA) and the tryptophan repressor (trpR). Here we employ primer extension analysis to identify the transcriptional origins of both trpR and trpBA, allowing for the identification of the putative operator sequences for both trpR and trpBA. Moreover we demonstrate that native recombinant chlamydial TrpR binds to the predicted operator sequence upstream of trpR. A restriction endonuclease protection assay was designed and used to demonstrate that 5-fluorotryptophan was the only tryptophan analogue capable of activating binding of native recombinant chlamydial TrpR to its operator. Additionally, 5-fluorotryptophan was the only analogue that repressed expression of trpBA at a level analogous to L-tryptophan itself. Based on these findings, a mutant selection protocol was designed and a C. trachomatis isolate containing a frameshift mutation in trpR was isolated. This chlamydial mutant synthesizes a truncated TrpR protein that cannot regulate expression of trpBA and trpR in response to changes in tryptophan levels. These findings provide the first genetic proof that TrpR acts as a negative regulator of transcription in C. trachomatis.
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Affiliation(s)
- John H Carlson
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, MT 59840, USA
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