1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Evans R, Krahn N, Weiss J, Vincent KA, Söll D, Armstrong FA. Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility. J Am Chem Soc 2024; 146:16971-16976. [PMID: 38747098 PMCID: PMC11212049 DOI: 10.1021/jacs.4c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/27/2024]
Abstract
Hydrogenases catalyze hydrogen/proton interconversion that is normally electrochemically reversible (having minimal overpotential requirement), a special property otherwise almost exclusive to platinum metals. The mechanism of [NiFe]-hydrogenases includes a long-range proton-coupled electron-transfer process involving a specific Ni-coordinated cysteine and the carboxylate of a nearby glutamate. A variant in which this cysteine has been exchanged for selenocysteine displays two distinct changes in electrocatalytic properties, as determined by protein film voltammetry. First, proton reduction, even in the presence of H2 (a strong product inhibitor), is greatly enhanced relative to H2 oxidation: this result parallels a characteristic of natural [NiFeSe]-hydrogenases which are superior H2 production catalysts. Second, an inflection (an S-shaped "twist" in the trace) appears around the formal potential, the small overpotentials introduced in each direction (oxidation and reduction) signaling a departure from electrocatalytic reversibility. Concerted proton-electron transfer offers a lower energy pathway compared to stepwise transfers. Given the much lower proton affinity of Se compared to that of S, the inflection provides compelling evidence that concerted proton-electron transfer is important in determining why [NiFe]-hydrogenases are reversible electrocatalysts.
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Affiliation(s)
- Rhiannon
M. Evans
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Natalie Krahn
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Joshua Weiss
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United
States
| | - Kylie A. Vincent
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Dieter Söll
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Fraser A. Armstrong
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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3
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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4
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Bennett ZD, Brunold TC. Non-standard amino acid incorporation into thiol dioxygenases. Methods Enzymol 2024; 703:121-145. [PMID: 39260993 PMCID: PMC11391102 DOI: 10.1016/bs.mie.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Thiol dioxygenases (TDOs) are non‑heme Fe(II)‑dependent enzymes that catalyze the O2-dependent oxidation of thiol substrates to their corresponding sulfinic acids. Six classes of TDOs have thus far been identified and two, cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO), are found in eukaryotes. All TDOs belong to the cupin superfamily of enzymes, which share a common β‑barrel fold and two cupin motifs: G(X)5HXH(X)3-6E(X)6G and G(X)5-7PXG(X)2H(X)3N. Crystal structures of TDOs revealed that these enzymes contain a relatively rare, neutral 3‑His iron‑binding facial triad. Despite this shared metal-binding site, TDOs vary greatly in their secondary coordination spheres. Site‑directed mutagenesis has been used extensively to explore the impact of changes in secondary sphere residues on substrate specificity and enzymatic efficiency. This chapter summarizes site-directed mutagenesis studies of eukaryotic TDOs, focusing on the tools and practicality of non‑standard amino acid incorporation.
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Affiliation(s)
- Zachary D Bennett
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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5
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Thaenert A, Sevostyanova A, Chung CZ, Vargas-Rodriguez O, Melnikov SV, Söll D. Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins. Proc Natl Acad Sci U S A 2024; 121:e2321700121. [PMID: 38442159 PMCID: PMC10945757 DOI: 10.1073/pnas.2321700121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA-ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins' active sites. Overall, our work demonstrates the feasibility of creating functional mRNA-rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.
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Affiliation(s)
- Anna Thaenert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT06511
| | | | - Christina Z. Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT06511
| | | | - Sergey V. Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- Biosciences Institute, Newcastle University Medical School, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT06511
- Department of Chemistry, Yale University, New Haven, CT06511
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6
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Kim Y, Cho S, Kim JC, Park HS. tRNA engineering strategies for genetic code expansion. Front Genet 2024; 15:1373250. [PMID: 38516376 PMCID: PMC10954879 DOI: 10.3389/fgene.2024.1373250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The advancement of genetic code expansion (GCE) technology is attributed to the establishment of specific aminoacyl-tRNA synthetase/tRNA pairs. While earlier improvements mainly focused on aminoacyl-tRNA synthetases, recent studies have highlighted the importance of optimizing tRNA sequences to enhance both unnatural amino acid incorporation efficiency and orthogonality. Given the crucial role of tRNAs in the translation process and their substantial impact on overall GCE efficiency, ongoing efforts are dedicated to the development of tRNA engineering techniques. This review explores diverse tRNA engineering approaches and provides illustrative examples in the context of GCE, offering insights into the user-friendly implementation of GCE technology.
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Affiliation(s)
| | | | | | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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7
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Wright DE, O’Donoghue P. Biosynthesis, Engineering, and Delivery of Selenoproteins. Int J Mol Sci 2023; 25:223. [PMID: 38203392 PMCID: PMC10778597 DOI: 10.3390/ijms25010223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Selenocysteine (Sec) was discovered as the 21st genetically encoded amino acid. In nature, site-directed incorporation of Sec into proteins requires specialized biosynthesis and recoding machinery that evolved distinctly in bacteria compared to archaea and eukaryotes. Many organisms, including higher plants and most fungi, lack the Sec-decoding trait. We review the discovery of Sec and its role in redox enzymes that are essential to human health and important targets in disease. We highlight recent genetic code expansion efforts to engineer site-directed incorporation of Sec in bacteria and yeast. We also review methods to produce selenoproteins with 21 or more amino acids and approaches to delivering recombinant selenoproteins to mammalian cells as new applications for selenoproteins in synthetic biology.
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Affiliation(s)
- David E. Wright
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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8
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Nunes LGA, Cain A, Comyns C, Hoffmann PR, Krahn N. Deciphering the Role of Selenoprotein M. Antioxidants (Basel) 2023; 12:1906. [PMID: 38001759 PMCID: PMC10668967 DOI: 10.3390/antiox12111906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
Selenocysteine (Sec), the 21st amino acid, is structurally similar to cysteine but with a sulfur to selenium replacement. This single change retains many of the chemical properties of cysteine but often with enhanced catalytic and redox activity. Incorporation of Sec into proteins is unique, requiring additional translation factors and multiple steps to insert Sec at stop (UGA) codons. These Sec-containing proteins (selenoproteins) are found in all three domains of life where they often are involved in cellular homeostasis (e.g., reducing reactive oxygen species). The essential role of selenoproteins in humans requires us to maintain appropriate levels of selenium, the precursor for Sec, in our diet. Too much selenium is also problematic due to its toxic effects. Deciphering the role of Sec in selenoproteins is challenging for many reasons, one of which is due to their complicated biosynthesis pathway. However, clever strategies are surfacing to overcome this and facilitate production of selenoproteins. Here, we focus on one of the 25 human selenoproteins, selenoprotein M (SELENOM), which has wide-spread expression throughout our tissues. Its thioredoxin motif suggests oxidoreductase function; however, its mechanism and functional role(s) are still being uncovered. Furthermore, the connection of both high and low expression levels of SELENOM to separate diseases emphasizes the medical application for studying the role of Sec in this protein. In this review, we aim to decipher the role of SELENOM through detailing and connecting current evidence. With multiple proposed functions in diverse tissues, continued research is still necessary to fully unveil the role of SELENOM.
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Affiliation(s)
- Lance G. A. Nunes
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813-5525, USA
| | - Antavius Cain
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA;
| | - Cody Comyns
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511-4902, USA
| | - Peter R. Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813-5525, USA
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA;
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511-4902, USA
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9
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Hoffman KS, Chung CZ, Mukai T, Krahn N, Jiang HK, Balasuriya N, O'Donoghue P, Söll D. Recoding UAG to selenocysteine in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2023; 29:1400-1410. [PMID: 37279998 PMCID: PMC10573291 DOI: 10.1261/rna.079658.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Unique chemical and physical properties are introduced by inserting selenocysteine (Sec) at specific sites within proteins. Recombinant and facile production of eukaryotic selenoproteins would benefit from a yeast expression system; however, the selenoprotein biosynthetic pathway was lost in the evolution of the kingdom Fungi as it diverged from its eukaryotic relatives. Based on our previous development of efficient selenoprotein production in bacteria, we designed a novel Sec biosynthesis pathway in Saccharomyces cerevisiae using Aeromonas salmonicida translation components. S. cerevisiae tRNASer was mutated to resemble A. salmonicida tRNASec to allow recognition by S. cerevisiae seryl-tRNA synthetase as well as A. salmonicida selenocysteine synthase (SelA) and selenophosphate synthetase (SelD). Expression of these Sec pathway components was then combined with metabolic engineering of yeast to enable the production of active methionine sulfate reductase enzyme containing genetically encoded Sec. Our report is the first demonstration that yeast is capable of selenoprotein production by site-specific incorporation of Sec.
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Affiliation(s)
- Kyle S Hoffman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Han-Kai Jiang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
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10
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Witkowska M, Jedrzejczak RP, Joachimiak A, Cavdar O, Malankowska A, Skowron PM, Zylicz-Stachula A. Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site. Microb Cell Fact 2023; 22:134. [PMID: 37479997 PMCID: PMC10362691 DOI: 10.1186/s12934-023-02127-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. RESULTS Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. CONCLUSION The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.
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Affiliation(s)
- Malgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Robert P Jedrzejczak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Onur Cavdar
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Anna Malankowska
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland.
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11
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Chaudière J. Biological and Catalytic Properties of Selenoproteins. Int J Mol Sci 2023; 24:10109. [PMID: 37373256 DOI: 10.3390/ijms241210109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Selenocysteine is a catalytic residue at the active site of all selenoenzymes in bacteria and mammals, and it is incorporated into the polypeptide backbone by a co-translational process that relies on the recoding of a UGA termination codon into a serine/selenocysteine codon. The best-characterized selenoproteins from mammalian species and bacteria are discussed with emphasis on their biological function and catalytic mechanisms. A total of 25 genes coding for selenoproteins have been identified in the genome of mammals. Unlike the selenoenzymes of anaerobic bacteria, most mammalian selenoenzymes work as antioxidants and as redox regulators of cell metabolism and functions. Selenoprotein P contains several selenocysteine residues and serves as a selenocysteine reservoir for other selenoproteins in mammals. Although extensively studied, glutathione peroxidases are incompletely understood in terms of local and time-dependent distribution, and regulatory functions. Selenoenzymes take advantage of the nucleophilic reactivity of the selenolate form of selenocysteine. It is used with peroxides and their by-products such as disulfides and sulfoxides, but also with iodine in iodinated phenolic substrates. This results in the formation of Se-X bonds (X = O, S, N, or I) from which a selenenylsulfide intermediate is invariably produced. The initial selenolate group is then recycled by thiol addition. In bacterial glycine reductase and D-proline reductase, an unusual catalytic rupture of selenium-carbon bonds is observed. The exchange of selenium for sulfur in selenoproteins, and information obtained from model reactions, suggest that a generic advantage of selenium compared with sulfur relies on faster kinetics and better reversibility of its oxidation reactions.
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Affiliation(s)
- Jean Chaudière
- CBMN (CNRS, UMR 5248), University of Bordeaux, 33600 Pessac, France
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12
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Morosky P, Comyns C, Nunes LGA, Chung CZ, Hoffmann PR, Söll D, Vargas-Rodriguez O, Krahn N. Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins. Front Mol Biosci 2023; 10:1096261. [PMID: 36762212 PMCID: PMC9902344 DOI: 10.3389/fmolb.2023.1096261] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Post-translational modifications (PTMs) can occur on almost all amino acids in eukaryotes as a key mechanism for regulating protein function. The ability to study the role of these modifications in various biological processes requires techniques to modify proteins site-specifically. One strategy for this is genetic code expansion (GCE) in bacteria. The low frequency of post-translational modifications in bacteria makes it a preferred host to study whether the presence of a post-translational modification influences a protein's function. Genetic code expansion employs orthogonal translation systems engineered to incorporate a modified amino acid at a designated protein position. Selenoproteins, proteins containing selenocysteine, are also known to be post-translationally modified. Selenoproteins have essential roles in oxidative stress, immune response, cell maintenance, and skeletal muscle regeneration. Their complicated biosynthesis mechanism has been a hurdle in our understanding of selenoprotein functions. As technologies for selenocysteine insertion have recently improved, we wanted to create a genetic system that would allow the study of post-translational modifications in selenoproteins. By combining genetic code expansion techniques and selenocysteine insertion technologies, we were able to recode stop codons for insertion of N ε-acetyl-l-lysine and selenocysteine, respectively, into multiple proteins. The specificity of these amino acids for their assigned position and the simplicity of reverting the modified amino acid via mutagenesis of the codon sequence demonstrates the capacity of this method to study selenoproteins and the role of their post-translational modifications. Moreover, the evidence that Sec insertion technology can be combined with genetic code expansion tools further expands the chemical biology applications.
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Affiliation(s)
- Pearl Morosky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Cody Comyns
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Lance G. A. Nunes
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Peter R. Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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13
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Chung CZ, Söll D, Krahn N. Creating Selenocysteine-Specific Reporters Using Inteins. Methods Mol Biol 2023; 2676:69-86. [PMID: 37277625 DOI: 10.1007/978-1-0716-3251-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The selenium moiety in selenocysteine (Sec) imparts enhanced chemical properties to this amino acid and ultimately the protein in which it is inserted. These characteristics are attractive for designing highly active enzymes or extremely stable proteins and studying protein folding or electron transfer, to name a few. There are also 25 human selenoproteins, of which many are essential for our survival. The ability to create or study these selenoproteins is significantly hindered by the inability to easily produce them. Engineering translation has yielded simpler systems to facilitate site-specific insertion of Sec; however, Ser misincorporation remains problematic. Therefore, we have designed two Sec-specific reporters which promote high-throughput screening of Sec translation systems to overcome this barrier. This protocol outlines the workflow to engineer these Sec-specific reporters, with the application to any gene of interest and the ability to transfer this strategy to any organism.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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14
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Chung CZ, Krahn N. The selenocysteine toolbox: A guide to studying the 21st amino acid. Arch Biochem Biophys 2022; 730:109421. [DOI: 10.1016/j.abb.2022.109421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
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15
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Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res 2022; 50:10201-10211. [PMID: 35882385 PMCID: PMC9561287 DOI: 10.1093/nar/gkac576] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNAUTu1, a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNAUTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.
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Affiliation(s)
| | | | | | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Miri Krupkin
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA
| | - Ziao Fu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Francisco J Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 24, Sweden
| | - Junhong Choi
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 24, Sweden
| | | | - Dieter Söll
- Correspondence may also be addressed to Dieter Söll.
| | - Joseph Puglisi
- To whom correspondence should be addressed. Tel: +1 650 498 4397;
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16
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Liao P, Liu H, He C. Chemical synthesis of human selenoprotein F and elucidation of its thiol-disulfide oxidoreductase activity. Chem Sci 2022; 13:6322-6327. [PMID: 35733894 PMCID: PMC9159075 DOI: 10.1039/d2sc00492e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/06/2022] [Indexed: 01/16/2023] Open
Abstract
Selenoprotein F (SelF) is an endoplasmic reticulum-residing eukaryotic protein that contains a selenocysteine (Sec) residue. It has been suggested to be involved in a number of physiological processes by acting as a thiol-disulfide oxidoreductase, but the exact role has remained unclear due to the lack of a reliable production method. We document herein a robust synthesis of the human SelF through a three-segment two-ligation semisynthesis strategy. Highlighted in this synthetic route are the use of a mild desulfurization process to protect the side-chain of the Sec residue from being affected and the simultaneous removal of acetamidomethyl and p-methoxybenzyl protection groups by PdCl2, thus facilitating the synthesis of multi-milligrams of homogenous SelF. The reduction potential of SelF was determined and the thiol-disulfide oxidoreductase activity was further supported by its ability to catalyze the reduction and isomerization of disulfide bonds.
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Affiliation(s)
- Peisi Liao
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
| | - Hongmei Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology Wuhan 430074 China
- Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen 518057 China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
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17
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Expressing recombinant selenoproteins using redefinition of a single UAG codon in an RF1-depleted E. coli host strain. Methods Enzymol 2022; 662:95-118. [PMID: 35101220 DOI: 10.1016/bs.mie.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selenoproteins containing the rare amino acid selenocysteine (Sec), typically being enzymes utilizing the selenium atom of Sec for promoted catalysis of redox reactions, are challenging to obtain at high amounts in pure form. The technical challenges limiting selenoprotein supply derive from intricacies in their translation, necessitating the recoding of a UGA stop codon to a sense codon for Sec. This, in turn, involves the interactions of a Sec-dedicated elongation factor, either directly or indirectly, with a structure in the selenoprotein-encoding mRNA called a SECIS element (Selenocysteine Insertion Sequence), a dedicated tRNA species for Sec with an anticodon for the UGA, and several accessory enzymes and proteins involved in the selenoprotein synthesis. Here, we describe an alternative method for recombinant selenoprotein production using UAG as the Sec codon in a specific strain of E. coli lacking other UAG codons and lacking the release factor RF1 that normally terminates translation at UAG. We also describe how such recombinant selenoproteins can be purified and further analyzed for final Sec contents. The methodology can be used for production of natural selenoproteins in recombinant form as well as for production of synthetic selenoproteins that may be designed to use the unique biophysical properties of Sec for diverse biotechnological applications.
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18
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Chung CZ, Söll D, Krahn N. Using selenocysteine-specific reporters to screen for efficient tRNA Sec variants. Methods Enzymol 2022; 662:63-93. [PMID: 35101219 DOI: 10.1016/bs.mie.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The unique properties of selenocysteine (Sec) have generated an interest in the scientific community to site-specifically incorporate Sec into a protein of choice. Current technologies have rewired the natural Sec-specific translation factor-dependent selenoprotein biosynthesis pathway by harnessing the canonical elongation factor (EF-Tu) to simplify the requirements for Sec incorporation in Escherichia coli. This strategy is versatile and can be applied to Sec incorporation at any position in a protein of interest. However, selenoprotein production is still limited by yield and serine misincorporation. This protocol outlines a method in E. coli to design and optimize tRNA libraries which can be selected and screened for by the use of Sec-specific intein-based reporters. This provides a fast and simple way to engineer tRNAs with enhanced Sec-incorporation ability.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States.
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
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19
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Tan Y, Wang M, Chen Y. Reprogramming the Biosynthesis of Precursor Peptide to Create a Selenazole-Containing Nosiheptide Analogue. ACS Synth Biol 2022; 11:85-91. [PMID: 35006674 DOI: 10.1021/acssynbio.1c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nosiheptide (NOS), a potent bactericidal thiopeptide, belongs to a class of natural products produced by ribosomal synthesis and post-translational modifications, and its biosynthetic pathway has largely been elucidated. However, the central trithiazolylpyridine structure of NOS remains inaccessible to structural changes. Here we report the creation of a NOS analogue containing a unique selenazole ring by the construction of an artificial system in Streptomyces actuosus ATCC25421, where the genes responsible for the biosynthesis of selenoprotein from Escherichia coli and the biosynthetic gene cluster of NOS were rationally integrated to produce a selenazole-containing analogue of NOS. The thiazole at the fifth position in NOS was specifically replaced by a selenazole to afford the first selenazole-containing "unnatural" natural product. The present strategy is useful for structural manipulation of various RiPP natural products.
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Affiliation(s)
- Yingzi Tan
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, P. R. China
| | - Miao Wang
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, P. R. China
| | - Yijun Chen
- State Key Laboratory of Natural Medicines and Laboratory of Chemical Biology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, P. R. China
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20
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Carducci F, Ardiccioni C, Fiorini R, Vignini A, Di Paolo A, Alia S, Barucca M, Biscotti MA. The ALA5/ALA6/ALA7 repeat polymorphisms of the glutathione peroxidase-1 (GPx1) gene and autism spectrum disorder. Autism Res 2022; 15:215-221. [PMID: 34997988 PMCID: PMC9304179 DOI: 10.1002/aur.2655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022]
Abstract
Autism is a severe neurodevelopmental disorder leading to deficits in social interaction, communication, and several activities. An increasing number of evidence suggests a role of oxidative stress in the etiology of autism spectrum disorder (ASD). Indeed, impaired antioxidant mechanisms may lead to the inadequate removal of H2O2 with a consequent increase in highly active hydroxyl radicals and other reactive oxygen species causing cellular damages. The GPx1 is one of the most important enzymes counteracting oxidative stress. In this work, we investigated a possible correlation between the GCG repeat polymorphism present in the first exon of GPx1 gene encoding a tract of five to seven alanine residues (ALA5, ALA6, and ALA7) and ASD. Our findings highlighted a high frequency of ALA5 allele in ASD subjects. Moreover, proteins corresponding to the three GPx1 variants were produced in vitro, and the evaluation of their activity showed a lower values for GPx1 having ALA5 polymorphism. The comparison of the secondary and tertiary structure predictions revealed an alpha‐helix in correspondence of alanine stretch only in the case of GPx1‐ALA7 variant. Finally, to better investigate protein structure, steady‐state fluorescence measurements of GPx1 intrinsic tryptophan were carried out and the three tested proteins exhibited a different stability under denaturing conditions. This work demonstrates the importance in adopting a multidisciplinary strategy to comprehend the role of GPx1 in ASD. Results here obtained suggest a possible role of ALA5 GPx1 variant in ASD. However, given the multifactorial nature of autism, this evidence might be a piece of a more complex puzzle being the GPx1 enzyme part of a complex pathway in which several proteins are involved.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Ancona, Italy
| | - Chiara Ardiccioni
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Università Politecnica Delle Marche, Ancona, Italy
| | - Rosamaria Fiorini
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Ancona, Italy
| | - Arianna Vignini
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche, Università Politecnica Delle Marche, Ancona, Italy
| | - Alice Di Paolo
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche, Università Politecnica Delle Marche, Ancona, Italy
| | - Sonila Alia
- Dipartimento di Scienze Cliniche Specialistiche ed Odontostomatologiche, Università Politecnica Delle Marche, Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Ancona, Italy
| | - Maria Assunta Biscotti
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Ancona, Italy
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21
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Patel A, Mulder DW, Söll D, Krahn N. Harnessing selenocysteine to enhance microbial cell factories for hydrogen production. FRONTIERS IN CATALYSIS 2022; 2. [PMID: 36844461 PMCID: PMC9961374 DOI: 10.3389/fctls.2022.1089176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.
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Affiliation(s)
- Armaan Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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22
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Cáceres JC, Bailey CA, Yokoyama K, Greene BL. Selenocysteine substitutions in thiyl radical enzymes. Methods Enzymol 2022; 662:119-141. [DOI: 10.1016/bs.mie.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Zhao Z, Shimon D, Metanis N. Chemoselective Copper-Mediated Modification of Selenocysteines in Peptides and Proteins. J Am Chem Soc 2021; 143:12817-12824. [PMID: 34346673 DOI: 10.1021/jacs.1c06101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Highly valuable bioconjugated molecules must be synthesized through efficient, chemoselective chemical modifications of peptides and proteins. Herein, we report the chemoselective modification of peptides and proteins via a reaction between selenocysteine residues and aryl/alkyl radicals. In situ radical generation from hydrazine substrates and copper ions proceeds rapidly in an aqueous buffer at near neutral pH (5-8), providing a variety of Se-modified linear and cyclic peptides and proteins conjugated to aryl and alkyl molecules, and to affinity label tag (biotin). This chemistry opens a new avenue for chemical protein modifications.
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Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem 91904, Israel
| | - Daphna Shimon
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem 91904, Israel
| | - Norman Metanis
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem 9190401, Israel
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24
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Chung CZ, Krahn N, Crnković A, Söll D. Intein-based Design Expands Diversity of Selenocysteine Reporters. J Mol Biol 2021; 434:167199. [PMID: 34411545 PMCID: PMC8847544 DOI: 10.1016/j.jmb.2021.167199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/27/2022]
Abstract
The presence of selenocysteine in a protein confers many unique properties that make the production of recombinant selenoproteins desirable. Targeted incorporation of Sec into a protein of choice is possible by exploiting elongation factor Tu-dependent reassignment of UAG codons, a strategy that has been continuously improved by a variety of means. Improving selenoprotein yield by directed evolution requires selection and screening markers that are titratable, have a high dynamic range, enable high-throughput screening, and can discriminate against nonspecific UAG decoding. Current screening techniques are limited to a handful of reporters where a cysteine (Cys) or Sec residue normally affords activity. Unfortunately, these existing Cys/Sec-dependent reporters lack the dynamic range of more ubiquitous reporters or suffer from other limitations. Here we present a versatile strategy to adapt established reporters for specific Sec incorporation. Inteins are intervening polypeptides that splice themselves from the precursor protein in an autocatalytic splicing reaction. Using an intein that relies exclusively on Sec for splicing, we show that this intein cassette can be placed in-frame within selection and screening markers, affording reporter activity only upon successful intein splicing. Furthermore, because functional splicing can only occur when a catalytic Sec is present, the amount of synthesized reporter directly measures UAG-directed Sec incorporation. Importantly, we show that results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry of isolated recombinant selenoproteins. This result validates the use of these intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA.
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25
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Chung CZ, Miller C, Söll D, Krahn N. Introducing Selenocysteine into Recombinant Proteins in Escherichia coli. Curr Protoc 2021; 1:e54. [PMID: 33566458 DOI: 10.1002/cpz1.54] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selenoproteins contain the 21st amino acid, selenocysteine. Selenocysteine is the only amino acid that is synthesized on its cognate tRNA, and it is inserted at specific recoded UGA stop codons via a complex translation system. Although highly similar to cysteine, selenocysteine has unique properties, including a stronger nucleophilic ability and lower reduction potential. Efforts to site-specifically incorporate selenocysteine to create recombinant selenoproteins involve a recoded UAG stop codon and expression of the necessary selenocysteine translation machinery. This article presents a protocol for expressing and purifying selenoproteins in Escherichia coli. © 2021 Wiley Periodicals LLC. Basic Protocol: Recombinant selenoprotein production in E. coli using a rewired translation system.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Corwin Miller
- Department of Biosciences, Rice University, Houston, Texas
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Department of Chemistry, Yale University, New Haven, Connecticut
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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26
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Wang Y, Liu P, Chang J, Xu Y, Wang J. Site-Specific Selenocysteine Incorporation into Proteins by Genetic Engineering. Chembiochem 2021; 22:2918-2924. [PMID: 33949764 DOI: 10.1002/cbic.202100124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/03/2021] [Indexed: 01/23/2023]
Abstract
Selenocysteine (Sec), a rare naturally proteinogenic amino acid, is the major form of essential trace element selenium in living organisms. Selenoproteins, with one or several Sec residues, are found in all three domains of life. Many selenoproteins play a role in critical cellular functions such as maintaining cell redox homeostasis. Sec is usually encoded by an in-frame stop codon UGA in the selenoprotein mRNA, and its incorporation in vivo is highly species-dependent and requires the reprogramming of translation. This mechanistic complexity of selenoprotein synthesis poses a big challenge to produce synthetic selenoproteins. To understand the functions of natural as well as engineered selenoproteins, many strategies have recently been developed to overcome the inherent barrier for recombinant selenoprotein production. In this review, we will describe the progress in selenoprotein production methodology.
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Affiliation(s)
- Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
| | - Pengcheng Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Jiao Chang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Yunping Xu
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China
| | - Jiangyun Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
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27
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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28
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Evans RM, Krahn N, Murphy BJ, Lee H, Armstrong FA, Söll D. Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance. Proc Natl Acad Sci U S A 2021; 118:e2100921118. [PMID: 33753519 PMCID: PMC8020662 DOI: 10.1073/pnas.2100921118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In [NiFe]-hydrogenases, the active-site Ni is coordinated by four cysteine-S ligands (Cys; C), two of which are bridging to the Fe(CO)(CN)2 fragment. Substitution of a single Cys residue by selenocysteine (Sec; U) occurs occasionally in nature. Using a recent method for site-specific Sec incorporation into proteins, each of the four Ni-coordinating cysteine residues in the oxygen-tolerant Escherichia coli [NiFe]-hydrogenase-1 (Hyd-1) has been replaced by U to identify its importance for enzyme function. Steady-state solution activity of each Sec-substituted enzyme (on a per-milligram basis) is lowered, although this may reflect the unquantified presence of recalcitrant inactive/immature/misfolded forms. Protein film electrochemistry, however, reveals detailed kinetic data that are independent of absolute activities. Like native Hyd-1, the variants have low apparent KMH2 values, do not produce H2 at pH 6, and display the same onset overpotential for H2 oxidation. Mechanistically important differences were identified for the C576U variant bearing the equivalent replacement found in native [NiFeSe]-hydrogenases, its extreme O2 tolerance (apparent KMH2 and Vmax [solution] values relative to native Hyd-1 of 0.13 and 0.04, respectively) implying the importance of a selenium atom in the position cis to the site where exogenous ligands (H-, H2, O2) bind. Observation of the same unusual electrocatalytic signature seen earlier for the proton transfer-defective E28Q variant highlights the direct role of the chalcogen atom (S/Se) at position 576 close to E28, with the caveat that Se is less effective than S in facilitating proton transfer away from the Ni during H2 oxidation by this enzyme.
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Affiliation(s)
- Rhiannon M Evans
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Bonnie J Murphy
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Harrison Lee
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, United Kingdom;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Chemistry, Yale University, New Haven, CT 06520
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29
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Welegedara AP, Maleckis A, Bandara R, Mahawaththa MC, Dilhani Herath I, Jiun Tan Y, Giannoulis A, Goldfarb D, Otting G, Huber T. Cell-Free Synthesis of Selenoproteins in High Yield and Purity for Selective Protein Tagging. Chembiochem 2021; 22:1480-1486. [PMID: 33319405 DOI: 10.1002/cbic.202000785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Indexed: 01/10/2023]
Abstract
The selenol group of selenocysteine is much more nucleophilic than the thiol group of cysteine. Selenocysteine residues in proteins thus offer reactive points for rapid post-translational modification. Herein, we show that selenoproteins can be expressed in high yield and purity by cell-free protein synthesis by global substitution of cysteine by selenocysteine. Complete alkylation of solvent-exposed selenocysteine residues was achieved in 10 minutes with 4-chloromethylene dipicolinic acid (4Cl-MDPA) under conditions that left cysteine residues unchanged even after overnight incubation. GdIII -GdIII distances measured by double electron-electron resonance (DEER) experiments of maltose binding protein (MBP) containing two selenocysteine residues tagged with 4Cl-MDPA-GdIII were indistinguishable from GdIII -GdIII distances measured of MBP containing cysteine reacted with 4Br-MDPA tags.
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Affiliation(s)
- Adarshi P Welegedara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.,Department of Chemistry, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, 1006, Riga, Latvia
| | - Ruchira Bandara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Iresha Dilhani Herath
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Yi Jiun Tan
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Angeliki Giannoulis
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
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30
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Takei T, Ando T, Takao T, Ohnishi Y, Kurisu G, Iwaoka M, Hojo H. Chemical synthesis of ferredoxin with 4 selenocysteine residues using a segment condensation method. Chem Commun (Camb) 2020; 56:14239-14242. [PMID: 33118552 DOI: 10.1039/d0cc06252a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferredoxin (Fd) is an electron carrier protein containing a [2Fe-2S] cluster. In this paper, we synthesized Se-Fd, in which four Cys residues coordinated to the cluster are substituted to selenocysteine. After the one-pot segment coupling by the thioester method, followed by deprotection and cluster loading, the desired Se-Fd was successfully obtained.
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Affiliation(s)
- Toshiki Takei
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
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31
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Mukai T. Rational Design of Aptamer-Tagged tRNAs. Int J Mol Sci 2020; 21:ijms21207793. [PMID: 33096801 PMCID: PMC7590224 DOI: 10.3390/ijms21207793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Reprogramming of the genetic code system is limited by the difficulty in creating new tRNA structures. Here, I developed translationally active tRNA variants tagged with a small hairpin RNA aptamer, using Escherichia coli reporter assay systems. As the tRNA chassis for engineering, I employed amber suppressor variants of allo-tRNAs having the 9/3 composition of the 12-base pair amino-acid acceptor branch as well as a long variable arm (V-arm). Although their V-arm is a strong binding site for seryl-tRNA synthetase (SerRS), insertion of a bulge nucleotide in the V-arm stem region prevented allo-tRNA molecules from being charged by SerRS with serine. The SerRS-rejecting allo-tRNA chassis were engineered to have another amino-acid identity of either alanine, tyrosine, or histidine. The tip of the V-arms was replaced with diverse hairpin RNA aptamers, which were recognized by their cognate proteins expressed in E. coli. A high-affinity interaction led to the sequestration of allo-tRNA molecules, while a moderate-affinity aptamer moiety recruited histidyl-tRNA synthetase variants fused with the cognate protein domain. The new design principle for tRNA-aptamer fusions will enhance radical and dynamic manipulation of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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32
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Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
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Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
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33
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Peeler JC, Falco JA, Kelemen RE, Abo M, Chartier BV, Edinger LC, Chen J, Chatterjee A, Weerapana E. Generation of Recombinant Mammalian Selenoproteins through Genetic Code Expansion with Photocaged Selenocysteine. ACS Chem Biol 2020; 15:1535-1540. [PMID: 32330002 DOI: 10.1021/acschembio.0c00147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Selenoproteins contain the amino acid selenocysteine (Sec) and are found in all domains of life. The functions of many selenoproteins are poorly understood, partly due to difficulties in producing recombinant selenoproteins for cell-biological evaluation. Endogenous mammalian selenoproteins are produced through a noncanonical translation mechanism requiring suppression of the UGA stop codon and a Sec insertion sequence (SECIS) element in the 3' untranslated region of the mRNA. Here, recombinant selenoproteins are generated in mammalian cells through genetic code expansion, circumventing the requirement for the SECIS element and selenium availability. An engineered orthogonal E. coli leucyl-tRNA synthetase/tRNA pair is used to incorporate a photocaged Sec (DMNB-Sec) at the UAG amber stop codon. DMNB-Sec is successfully incorporated into GFP and uncaged by irradiation of living cells. Furthermore, DMNB-Sec is used to generate the native selenoprotein methionine-R-sulfoxide reductase B1 (MsrB1). Importantly, MsrB1 is shown to be catalytically active after uncaging, constituting the first use of genetic code expansion to generate a functional selenoprotein in mammalian systems. The ability to site-specifically introduce Sec directly in mammalian cells, and temporally modulate selenoprotein activity, will aid in the characterization of mammalian selenoprotein function.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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34
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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35
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Greene BL, Stubbe J, Nocera DG. Selenocysteine Substitution in a Class I Ribonucleotide Reductase. Biochemistry 2019; 58:5074-5084. [PMID: 31774661 DOI: 10.1021/acs.biochem.9b00973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ribonucleotide reductases (RNRs) employ a complex radical-based mechanism during nucleotide reduction involving multiple active site cysteines that both activate the substrate and reduce it. Using an engineered allo-tRNA, we substituted two active site cysteines with distinct function in the class Ia RNR of Escherichia coli for selenocysteine (U) via amber codon suppression, with efficiency and selectivity enabling biochemical and biophysical studies. Examination of the interactions of the C439U α2 mutant protein with nucleotide substrates and the cognate β2 subunit demonstrates that the endogenous Y122• of β2 is reduced under turnover conditions, presumably through radical transfer to form a transient U439• species. This putative U439• species is formed in a kinetically competent fashion but is incapable of initiating nucleotide reduction via 3'-H abstraction. An analogous C225U α2 protein is also capable of radical transfer from Y122•, but the radical-based substrate chemistry partitions between turnover and stalled reduction akin to the reactivity of mechanism-based inhibitors of RNR. The results collectively demonstrate the essential role of cysteine redox chemistry in the class I RNRs and establish a new tool for investigating thiyl radical reactivity in biology.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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36
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Abstract
Selenoproteins are the family of proteins that contain the amino acid selenocysteine. Many selenoproteins, including glutathione peroxidases and thioredoxin reductases, play a role in maintaining cellular redox homeostasis. There are a number of examples of homologues of selenoproteins that utilize cysteine residues, raising the question of why selenocysteines are utilized. One hypothesis is that incorporation of selenocysteine protects against irreversible overoxidation, typical of cysteine-containing homologues under high oxidative stress. Studies of selenocysteine function are hampered by challenges both in detection and in recombinant expression of selenoproteins. In fact, about half of the 25 known human selenoproteins remain uncharacterized. Historically, selenoproteins were first detected via labeling with radioactive 75Se or by use of inductively coupled plasma-mass spectrometry to monitor nonradioactive selenium. More recently, tandem mass-spectrometry techniques have been developed to detect selenocysteine-containing peptides. For example, the isotopic distribution of selenium has been used as a unique signature to identify selenium-containing peptides from unenriched proteome samples. Additionally, selenocysteine-containing proteins and peptides were selectively enriched using thiol-reactive electrophiles by exploiting the increased reactivity of selenols relative to thiols, especially under low pH conditions. Importantly, the reactivity-based enrichment of selenoproteins can differentiate between oxidized and reduced selenoproteins, providing insight into the activity state. These mass spectrometry-based selenoprotein detection approaches have enabled (1) production of selenoproteome expression atlases, (2) identification of aging-associated changes in selenoprotein expression, (3) characterization of selenocysteine reactivity across the selenoprotein family, and (4) interrogation of selenoprotein targets of small-molecule drugs. Further investigations of selenoprotein function would benefit from recombinant expression of selenoproteins. However, the endogenous mechanism of selenoprotein production makes recombinant expression challenging. Primarily, selenocysteine is biosynthesized on its own tRNA, is dependent on multiple enzymatic steps, and is highly sensitive to selenium concentrations. Furthermore, selenocysteine is encoded by the stop codon UGA, and suppression of that stop codon requires a selenocysteine insertion sequence element in the selenoprotein mRNA. In order to circumvent the low efficiency of the endogenous machinery, selenoproteins have been produced in vitro through native chemical ligation and expressed protein ligation. Attempts have also been made to engineer the endogenous machinery for increased efficiency, including recoding the selenocysteine codon, and engineering the tRNA and the selenocysteine insertion sequence element. Alternatively, genetic code expansion can be used to generate selenoproteins. This approach allows for selenoprotein production directly within its native cellular environment, while bypassing the endogenous selenocysteine incorporation machinery. Furthermore, by incorporating a caged selenocysteine by genetic code expansion, selenoprotein activity can be spatially and temporally controlled. Genetic code expansion has allowed for the expression and uncaging of human selenoproteins in E. coli and more recently in mammalian cells. Together, advances in selenoprotein detection and expression should enable a better understanding of selenoprotein function and provide insight into the necessity for selenocysteine production.
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Affiliation(s)
- Jennifer C. Peeler
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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37
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Hoffman KS, Vargas-Rodriguez O, Bak DW, Mukai T, Woodward LK, Weerapana E, Söll D, Reynolds NM. A cysteinyl-tRNA synthetase variant confers resistance against selenite toxicity and decreases selenocysteine misincorporation. J Biol Chem 2019; 294:12855-12865. [PMID: 31296657 DOI: 10.1074/jbc.ra119.008219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/03/2019] [Indexed: 11/06/2022] Open
Abstract
Selenocysteine (Sec) is the 21st genetically encoded amino acid in organisms across all domains of life. Although structurally similar to cysteine (Cys), the Sec selenol group has unique properties that are attractive for protein engineering and biotechnology applications. Production of designer proteins with Sec (selenoproteins) at desired positions is now possible with engineered translation systems in Escherichia coli However, obtaining pure selenoproteins at high yields is limited by the accumulation of free Sec in cells, causing undesired incorporation of Sec at Cys codons due to the inability of cysteinyl-tRNA synthetase (CysRS) to discriminate against Sec. Sec misincorporation is toxic to cells and causes protein aggregation in yeast. To overcome this limitation, here we investigated a CysRS from the selenium accumulator plant Astragalus bisulcatus that is reported to reject Sec in vitro Sequence analysis revealed a rare His → Asn variation adjacent to the CysRS catalytic pocket. Introducing this variation into E. coli and Saccharomyces cerevisiae CysRS increased resistance to the toxic effects of selenite and selenomethionine (SeMet), respectively. Although the CysRS variant could still use Sec as a substrate in vitro, we observed a reduction in the frequency of Sec misincorporation at Cys codons in vivo We surmise that the His → Asn variation can be introduced into any CysRS to provide a fitness advantage for strains burdened by Sec misincorporation and selenium toxicity. Our results also support the notion that the CysRS variant provides higher specificity for Cys as a mechanism for plants to grow in selenium-rich soils.
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Affiliation(s)
- Kyle S Hoffman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Laura K Woodward
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.,Department of Chemistry, Yale University, New Haven, Connecticut 06511
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
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38
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Boknevitz K, Italia JS, Li B, Chatterjee A, Liu SY. Synthesis and characterization of an unnatural boron and nitrogen-containing tryptophan analogue and its incorporation into proteins. Chem Sci 2019; 10:4994-4998. [PMID: 31183048 PMCID: PMC6524624 DOI: 10.1039/c8sc05167d] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
A boron and nitrogen containing unnatural analogue of tryptophan is synthesized and incorporated into proteins.
A boron and nitrogen containing unnatural analogue of tryptophan is synthesized through the functionalization of BN-indole. The spectroscopic properties of BN-tryptophan are reported with respect to the natural tryptophan, and the incorporation of BN-tryptophan into proteins expressed in E. coli using selective pressure incorporation is described. This work shows that a cellular system can recognize the unnatural, BN-containing tryptophan. More importantly, it presents the first example of an azaborine containing amino acid being incorporated into proteins.
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Affiliation(s)
- Katherine Boknevitz
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - James S Italia
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - Bo Li
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - Abhishek Chatterjee
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
| | - Shih-Yuan Liu
- Department of Chemistry , Boston College , Chestnut Hill , MA 02467 , USA . ;
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39
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Crnković A, Vargas-Rodriguez O, Söll D. Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases. Int J Mol Sci 2019; 20:ijms20092294. [PMID: 31075874 PMCID: PMC6540133 DOI: 10.3390/ijms20092294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic incorporation of noncanonical amino acids (ncAAs) has become a powerful tool to enhance existing functions or introduce new ones into proteins through expanded chemistry. This technology relies on the process of nonsense suppression, which is made possible by directing aminoacyl-tRNA synthetases (aaRSs) to attach an ncAA onto a cognate suppressor tRNA. However, different mechanisms govern aaRS specificity toward its natural amino acid (AA) substrate and hinder the engineering of aaRSs for applications beyond the incorporation of a single l-α-AA. Directed evolution of aaRSs therefore faces two interlinked challenges: the removal of the affinity for cognate AA and improvement of ncAA acylation. Here we review aspects of AA recognition that directly influence the feasibility and success of aaRS engineering toward d- and β-AAs incorporation into proteins in vivo. Emerging directed evolution methods are described and evaluated on the basis of aaRS active site plasticity and its inherent constraints.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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40
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Aminoacyl-tRNA Synthetases and tRNAs for an Expanded Genetic Code: What Makes them Orthogonal? Int J Mol Sci 2019; 20:ijms20081929. [PMID: 31010123 PMCID: PMC6515474 DOI: 10.3390/ijms20081929] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022] Open
Abstract
In the past two decades, tRNA molecules and their corresponding aminoacyl-tRNA synthetases (aaRS) have been extensively used in synthetic biology to genetically encode post-translationally modified and unnatural amino acids. In this review, we briefly examine one fundamental requirement for the successful application of tRNA/aaRS pairs for expanding the genetic code. This requirement is known as “orthogonality”—the ability of a tRNA and its corresponding aaRS to interact exclusively with each other and avoid cross-reactions with additional types of tRNAs and aaRSs in a given organism.
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41
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Ohata J, Martin SC, Ball ZT. Metallvermittelte Funktionalisierung natürlicher Peptide und Proteine: Biokonjugation mit Übergangsmetallen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jun Ohata
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Samuel C. Martin
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Zachary T. Ball
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
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42
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Ohata J, Martin SC, Ball ZT. Metal‐Mediated Functionalization of Natural Peptides and Proteins: Panning for Bioconjugation Gold. Angew Chem Int Ed Engl 2019; 58:6176-6199. [DOI: 10.1002/anie.201807536] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jun Ohata
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Samuel C. Martin
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Zachary T. Ball
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
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43
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Fu X, Crnković A, Sevostyanova A, Söll D. Designing seryl-tRNA synthetase for improved serylation of selenocysteine tRNAs. FEBS Lett 2018; 592:3759-3768. [PMID: 30317559 PMCID: PMC6263840 DOI: 10.1002/1873-3468.13271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 12/28/2022]
Abstract
Selenocysteine (Sec) lacks a cognate aminoacyl-tRNA synthetase. Instead, seryl-tRNA synthetase (SerRS) produces Ser-tRNASec , which is subsequently converted by selenocysteine synthase to Sec-tRNASec . Escherichia coli SerRS serylates tRNASec poorly; this may hinder efficient production of designer selenoproteins in vivo. Guided by structural modelling and selection for chloramphenicol acetyltransferase activity, we evolved three SerRS variants capable of improved Ser-tRNASec synthesis. They display 10-, 8-, and 4-fold increased kcat /KM values compared to wild-type SerRS using synthetic tRNASec species as substrates. The enzyme variants also facilitate in vivo read-through of a UAG codon in the position of the critical serine146 of chloramphenicol acetyltransferase. These results indicate that the naturally evolved SerRS is capable of further evolution for increased recognition of a specific tRNA isoacceptor.
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MESH Headings
- Base Sequence
- Codon, Terminator/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Kinetics
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Protein Domains
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Selenoproteins/genetics
- Selenoproteins/metabolism
- Serine/genetics
- Serine/metabolism
- Serine-tRNA Ligase/chemistry
- Serine-tRNA Ligase/genetics
- Serine-tRNA Ligase/metabolism
- Substrate Specificity
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Affiliation(s)
- Xian Fu
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Ana Crnković
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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44
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Liu J, Zheng F, Cheng R, Li S, Rozovsky S, Wang Q, Wang L. Site-Specific Incorporation of Selenocysteine Using an Expanded Genetic Code and Palladium-Mediated Chemical Deprotection. J Am Chem Soc 2018; 140:8807-8816. [PMID: 29984990 PMCID: PMC6082430 DOI: 10.1021/jacs.8b04603] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Selenoproteins containing the 21st amino acid selenocysteine (Sec) exist in all three kingdoms of life and play essential roles in human health and development. The distinct low p Ka, high reactivity, and redox property of Sec also afford unique routes to protein modification and engineering. However, natural Sec incorporation requires idiosyncratic translational machineries that are dedicated to Sec and species-dependent, which makes it challenging to recombinantly prepare selenoproteins with high Sec specificity. As a consequence, the function of half of human selenoproteins remains unclear, and Sec-based protein manipulation has been greatly hampered. Here we report a new general method enabling the site-specific incorporation of Sec into proteins in E. coli. An orthogonal tRNAPyl-ASecRS was evolved to specifically incorporate Se-allyl selenocysteine (ASec) in response to the amber codon, and the incorporated ASec was converted to Sec in high efficiency through palladium-mediated cleavage under mild conditions compatible with proteins and cells. This approach completely obviates the natural Sec-dedicated factors, thus allowing various selenoproteins, regardless of Sec position and species source, to be prepared with high Sec specificity and enzyme activity, as shown by the preparation of human thioredoxin and glutathione peroxidase 1. Sec-selective labeling in the presence of Cys was also demonstrated on the surface of live E. coli cells. The tRNAPyl-ASecRS pair was further used in mammalian cells to incorporate ASec, which was converted into Sec by palladium catalyst in cellulo. This robust and versatile method should greatly facilitate the study of diverse natural selenoproteins and the engineering of proteins in general via site-specific introduction of Sec.
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Affiliation(s)
- Jun Liu
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA, 94158
| | - Feng Zheng
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, China, 310018
| | - Rujin Cheng
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Shanshan Li
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA, 94158
- Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sharon Rozovsky
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Qian Wang
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, China, 310018
| | - Lei Wang
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA, 94158
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45
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Welegedara AP, Adams LA, Huber T, Graham B, Otting G. Site-Specific Incorporation of Selenocysteine by Genetic Encoding as a Photocaged Unnatural Amino Acid. Bioconjug Chem 2018; 29:2257-2264. [DOI: 10.1021/acs.bioconjchem.8b00254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Adams
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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