151
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Zheng Y, Gilgenast MJ, Hauc S, Chatterjee A. Capturing Post-Translational Modification-Triggered Protein-Protein Interactions Using Dual Noncanonical Amino Acid Mutagenesis. ACS Chem Biol 2018; 13:1137-1141. [PMID: 29544052 DOI: 10.1021/acschembio.8b00021] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reversible post-translational modification (PTM) is a powerful and ubiquitous mechanism to regulate protein function. The mechanistic basis of the associated functional regulation by PTMs often involves the recruitment of interaction partners that selectively bind the modified protein. Identifying such functionally important protein-protein interactions that are uniquely triggered by PTMs remains difficult due to several technical challenges. To address this, here we develop technology to site-specifically incorporate two distinct noncanonical amino acids into recombinant proteins: one modeling a PTM of interest and the second harboring a photoaffinity probe. Using lysine-23 acetylation of histone 3 as a model system, we show that such dual-labeled "protein probes" can covalently capture its "reader" protein.
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Affiliation(s)
- Yunan Zheng
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Martin J. Gilgenast
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Sacha Hauc
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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152
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Balasuriya N, Kunkel MT, Liu X, Biggar KK, Li SSC, Newton AC, O'Donoghue P. Genetic code expansion and live cell imaging reveal that Thr-308 phosphorylation is irreplaceable and sufficient for Akt1 activity. J Biol Chem 2018; 293:10744-10756. [PMID: 29773654 DOI: 10.1074/jbc.ra118.002357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/08/2018] [Indexed: 01/05/2023] Open
Abstract
The proto-oncogene Akt/protein kinase B (PKB) is a pivotal signal transducer for growth and survival. Growth factor stimulation leads to Akt phosphorylation at two regulatory sites (Thr-308 and Ser-473), acutely activating Akt signaling. Delineating the exact role of each regulatory site is, however, technically challenging and has remained elusive. Here, we used genetic code expansion to produce site-specifically phosphorylated Akt1 to dissect the contribution of each regulatory site to Akt1 activity. We achieved recombinant production of full-length Akt1 containing site-specific pThr and pSer residues for the first time. Our analysis of Akt1 site-specifically phosphorylated at either or both sites revealed that phosphorylation at both sites increases the apparent catalytic rate 1500-fold relative to unphosphorylated Akt1, an increase attributable primarily to phosphorylation at Thr-308. Live imaging of COS-7 cells confirmed that phosphorylation of Thr-308, but not Ser-473, is required for cellular activation of Akt. We found in vitro and in the cell that pThr-308 function cannot be mimicked with acidic residues, nor could unphosphorylated Thr-308 be mimicked by an Ala mutation. An Akt1 variant with pSer-308 achieved only partial enzymatic and cellular signaling activity, revealing a critical interaction between the γ-methyl group of pThr-308 and Cys-310 in the Akt1 active site. Thus, pThr-308 is necessary and sufficient to stimulate Akt signaling in cells, and the common use of phosphomimetics is not appropriate for studying the biology of Akt signaling. Our data also indicate that pThr-308 should be regarded as the primary diagnostic marker of Akt activity.
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Affiliation(s)
| | - Maya T Kunkel
- the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | | | | | | | - Alexandra C Newton
- the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - Patrick O'Donoghue
- From the Departments of Biochemistry and .,Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada and
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153
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11th IUBMB Focused Meeting on the Aminoacyl-tRNA Synthetases: Sailing a New Sea of Complex Functions in Human Biology and Disease. Biomolecules 2018; 8:biom8020022. [PMID: 29723968 PMCID: PMC6023080 DOI: 10.3390/biom8020022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/18/2022] Open
Abstract
The 11th IUBMB Focused Meeting on Aminoacyl-tRNA Synthetases was held in Clearwater Beach, Florida from 29 October–2 November 2017, with the aim of presenting the latest research on these enzymes and promoting interchange among aminoacyl-tRNA synthetase (ARS) researchers. Topics covered in the meeting included many areas of investigation, including ARS evolution, mechanism, editing functions, biology in prokaryotic and eukaryotic cells and their organelles, their roles in human diseases, and their application to problems in emerging areas of synthetic biology. In this report, we provide a summary of the major themes of the meeting, citing contributions from the oral presentations in the meeting.
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154
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Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:7607463. [PMID: 29849913 PMCID: PMC5937447 DOI: 10.1155/2018/7607463] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/19/2018] [Indexed: 12/17/2022]
Abstract
Posttranslational modifications resulting from oxidation of proteins (Ox-PTMs) are present intracellularly under conditions of oxidative stress as well as basal conditions. In the past, these modifications were thought to be generic protein damage, but it has become increasingly clear that Ox-PTMs can have specific physiological effects. It is an arduous task to distinguish between the two cases, as multiple Ox-PTMs occur simultaneously on the same protein, convoluting analysis. Genetic code expansion (GCE) has emerged as a powerful tool to overcome this challenge as it allows for the site-specific incorporation of an Ox-PTM into translated protein. The resulting homogeneously modified protein products can then be rigorously characterized for the effects of individual Ox-PTMs. We outline the strengths and weaknesses of GCE as they relate to the field of oxidative stress and Ox-PTMs. An overview of the Ox-PTMs that have been genetically encoded and applications of GCE to the study of Ox-PTMs, including antibody validation and therapeutic development, is described.
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155
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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156
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Casiraghi M, Damian M, Lescop E, Banères JL, Catoire LJ. Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry 2018; 57:2297-2307. [PMID: 29607648 DOI: 10.1021/acs.biochem.8b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Conformational dynamics of GPCRs are central to their function but are difficult to explore at the atomic scale. Solution-state NMR has provided the major contribution in that area of study during the past decade, despite nonoptimized labeling schemes due to the use of insect cells and, to a lesser extent, yeast as the main expression hosts. Indeed, the most efficient isotope-labeling scheme ever to address energy landscape issues for large proteins or protein complexes relies on the use of 13CH3 probes immersed in a perdeuterated dipolar environment, which is essentially out of reach of eukaryotic expression systems. In contrast, although its contribution has been underestimated because of technical issues, Escherichia coli is by far the best-adapted host for such labeling. As it is now tightly controlled, we show in this review that bacterial expression can provide an NMR spectral resolution never achieved in the GPCR field.
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Affiliation(s)
- Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay , 1 av. de la Terrasse , 91198 Gif-sur-Yvette , France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
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157
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Abstract
Complex signaling cascades are difficult to study in vitro without phosphorylated proteins. Here, we describe a technique for the routine production of recombinant phosphoproteins by directly incorporating phosphoserine as a nonstandard amino acid. This protocol utilizes an optimized phosphoserine orthogonal translation system and an engineered strain of E. coli containing no genomic amber codons. This approach has been used to generate a variety of phosphorylated proteins to understand the role of protein phosphorylation in cell signaling.
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158
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Xie ZX, Liu D, Li BZ, Zhao M, Zeng BX, Wu Y, Shen Y, Lin T, Yang P, Dai J, Cai Y, Yang H, Yuan YJ. Design and chemical synthesis of eukaryotic chromosomes. Chem Soc Rev 2018; 46:7191-7207. [PMID: 29094136 DOI: 10.1039/c7cs00208d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Following the discovery of the DNA double helix structure and the advancement of genome sequencing, we have entered a promising stage with regard to genome writing. Recently, a milestone breakthrough was achieved in the chemical synthesis of designer yeast chromosomes. Here, we review the systematic approaches to the de novo synthesis of designer eukaryotic chromosomes, with an emphasis on technologies and methodologies that enable design, building, testing and debugging. The achievement of chemically synthesized genomes with customized genetic features offers an opportunity to rebuild genome organization, remold biological functions and promote life evolution, which will be of great benefit for application in medicine and industrial manufacturing.
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Affiliation(s)
- Ze-Xiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
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159
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Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids. Nat Commun 2018; 9:1203. [PMID: 29572528 PMCID: PMC5865108 DOI: 10.1038/s41467-018-03469-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/13/2018] [Indexed: 12/24/2022] Open
Abstract
Cell-free protein synthesis has emerged as a powerful approach for expanding the range of genetically encoded chemistry into proteins. Unfortunately, efforts to site-specifically incorporate multiple non-canonical amino acids into proteins using crude extract-based cell-free systems have been limited by release factor 1 competition. Here we address this limitation by establishing a bacterial cell-free protein synthesis platform based on genomically recoded Escherichia coli lacking release factor 1. This platform was developed by exploiting multiplex genome engineering to enhance extract performance by functionally inactivating negative effectors. Our most productive cell extracts enabled synthesis of 1,780 ± 30 mg/L superfolder green fluorescent protein. Using an optimized platform, we demonstrated the ability to introduce 40 identical p-acetyl-l-phenylalanine residues site specifically into an elastin-like polypeptide with high accuracy of incorporation ( ≥ 98%) and yield (96 ± 3 mg/L). We expect this cell-free platform to facilitate fundamental understanding and enable manufacturing paradigms for proteins with new and diverse chemistries. Cell-free protein synthesis allows for producing proteins without the need of a host organism, thus sparing the researcher experimental hassle. Here, the authors developed a cell-free synthesis method that enables incorporating non-standard amino acids in the product.
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160
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Venkat S, Sturges J, Stahman A, Gregory C, Gan Q, Fan C. Genetically Incorporating Two Distinct Post-translational Modifications into One Protein Simultaneously. ACS Synth Biol 2018; 7:689-695. [PMID: 29301074 DOI: 10.1021/acssynbio.7b00408] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational modifications (PTMs) play important roles in regulating a variety of biological processes. To facilitate PTM studies, the genetic code expansion strategy has been utilized to cotranslationally incorporate individual PTMs such as acetylation and phosphorylation into proteins at specific sites. However, recent studies have demonstrated that PTMs actually work together to regulate protein functions and structures. Thus, simultaneous incorporation of multiple distinct PTMs into one protein is highly desirable. In this study, we utilized the genetic incorporation systems of phosphoserine and acetyllysine to install both phosphorylation and acetylation into target proteins simultaneously in Escherichia coli. And we used this system to study the effect of coexisting acetylation and phosphorylation on malate dehydrogenase, demonstrating a practical application of this system in biochemical studies. Furthermore, we tested the mutual orthogonality of three widely used genetic incorporation systems, indicating the possibility of incorporating three distinct PTMs into one protein simultaneously.
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Affiliation(s)
- Sumana Venkat
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Jourdan Sturges
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Alleigh Stahman
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Caroline Gregory
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Qinglei Gan
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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161
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Crnković A, Vargas-Rodriguez O, Merkuryev A, Söll D. Effects of Heterologous tRNA Modifications on the Production of Proteins Containing Noncanonical Amino Acids. Bioengineering (Basel) 2018; 5:bioengineering5010011. [PMID: 29393901 PMCID: PMC5874877 DOI: 10.3390/bioengineering5010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/31/2018] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Synthesis of proteins with noncanonical amino acids (ncAAs) enables the creation of protein-based biomaterials with diverse new chemical properties that may be attractive for material science. Current methods for large-scale production of ncAA-containing proteins, frequently carried out in Escherichia coli, involve the use of orthogonal aminoacyl-tRNA synthetases (o-aaRSs) and tRNAs (o-tRNAs). Although o-tRNAs are designed to be orthogonal to endogenous aaRSs, their orthogonality to the components of the E. coli metabolism remains largely unexplored. We systematically investigated how the E. coli tRNA modification machinery affects the efficiency and orthogonality of o-tRNASep used for production of proteins with the ncAA O-phosphoserine (Sep). The incorporation of Sep into a green fluorescent protein (GFP) in 42 E. coli strains carrying deletions of single tRNA modification genes identified several genes that affect the o-tRNA activity. Deletion of cysteine desulfurase (iscS) increased the yield of Sep-containing GFP more than eightfold, while overexpression of dimethylallyltransferase MiaA and pseudouridine synthase TruB improved the specificity of Sep incorporation. These results highlight the importance of tRNA modifications for the biosynthesis of proteins containing ncAAs, and provide a novel framework for optimization of o-tRNAs.
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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.
| | - Anna Merkuryev
- Department of Chemistry, 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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162
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Wang L. Engineering the Genetic Code in Cells and Animals: Biological Considerations and Impacts. Acc Chem Res 2017; 50:2767-2775. [PMID: 28984438 DOI: 10.1021/acs.accounts.7b00376] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Expansion of the genetic code allows unnatural amino acids (Uaas) to be site-specifically incorporated into proteins in live biological systems, thus enabling novel properties selectively introduced into target proteins in vivo for basic biological studies and for engineering of novel biological functions. Orthogonal components including tRNA and aminoacyl-tRNA synthetase (aaRS) are expressed in live cells to decode a unique codon (often the amber stop codon UAG) as the desired Uaa. Initially developed in E. coli, this methodology has now been expanded in multiple eukaryotic cells and animals. In this Account, we focus on addressing various biological challenges for rewriting the genetic code, describing impacts of code expansion on cell physiology and discussing implications for fundamental studies of code evolution. Specifically, a general method using the type-3 polymerase III promoter was developed to efficiently express prokaryotic tRNAs as orthogonal tRNAs and a transfer strategy was devised to generate Uaa-specific aaRS for use in eukaryotic cells and animals. The aaRSs have been found to be highly amenable for engineering substrate specificity toward Uaas that are structurally far deviating from the native amino acid, dramatically increasing the stereochemical diversity of Uaas accessible. Preparation of the Uaa in ester or dipeptide format markedly increases the bioavailability of Uaas to cells and animals. Nonsense-mediated mRNA decay (NMD), an mRNA surveillance mechanism of eukaryotic cells, degrades mRNA containing a premature stop codon. Inhibition of NMD increases Uaa incorporation efficiency in yeast and Caenorhabditis elegans. In bacteria, release factor one (RF1) competes with the orthogonal tRNA for the amber stop codon to terminate protein translation, leading to low Uaa incorporation efficiency. Contradictory to the paradigm that RF1 is essential, it is discovered that RF1 is actually nonessential in E. coli. Knockout of RF1 dramatically increases Uaa incorporation efficiency and enables Uaa incorporation at multiple sites, making it feasible to use Uaa for directed evolution. Using these strategies, the genetic code has been effectively expanded in yeast, mammalian cells, stem cells, worms, fruit flies, zebrafish, and mice. It is also intriguing to find out that the legitimate UAG codons terminating endogenous genes are not efficiently suppressed by the orthogonal tRNA/aaRS in E. coli. Moreover, E. coli responds to amber suppression pressure promptly using transposon insertion to inactivate the introduced orthogonal aaRS. Persistent amber suppression evading transposon inactivation leads to global proteomic changes with a notable up-regulation of a previously uncharacterized protein YdiI, for which an unexpected function of expelling plasmids is discovered. Genome integration of the orthogonal tRNA/aaRS in mice results in minor changes in RNA transcripts but no significant physiological impairment. Lastly, the RF1 knockout E. coli strains afford a previously unavailable model organism for studying otherwise intractable questions on code evolution in real time in the laboratory. We expect that genetically encoding Uaas in live systems will continue to unfold new questions and directions for studying biology in vivo, investigating the code itself, and reprograming genomes for synthetic biology.
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Affiliation(s)
- Lei Wang
- Department of Pharmaceutical Chemistry
and the Cardiovascular Research Institute, University of California, San
Francisco, California 94158, United States
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163
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Structural basis for tRNA-dependent cysteine biosynthesis. Nat Commun 2017; 8:1521. [PMID: 29142195 PMCID: PMC5688128 DOI: 10.1038/s41467-017-01543-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022] Open
Abstract
Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNACys followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNACys, respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNACys between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNACys synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code. tRNA-dependent cysteine biosynthesis is catalyzed by the transsulfursome protein complex. Here, the authors use a multidisciplinary approach to structurally characterize the archaeal transsulfursome and propose a model for tRNA channeling in the complex.
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164
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Chin JW. Expanding and reprogramming the genetic code. Nature 2017; 550:53-60. [PMID: 28980641 DOI: 10.1038/nature24031] [Citation(s) in RCA: 504] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK
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165
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Chen S, Maini R, Bai X, Nangreave RC, Dedkova LM, Hecht SM. Incorporation of Phosphorylated Tyrosine into Proteins: In Vitro Translation and Study of Phosphorylated IκB-α and Its Interaction with NF-κB. J Am Chem Soc 2017; 139:14098-14108. [PMID: 28898075 PMCID: PMC5901656 DOI: 10.1021/jacs.7b05168] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphorylated proteins play important roles in the regulation of many different cell networks. However, unlike the preparation of proteins containing unmodified proteinogenic amino acids, which can be altered readily by site-directed mutagenesis and expressed in vitro and in vivo, the preparation of proteins phosphorylated at predetermined sites cannot be done easily and in acceptable yields. To enable the synthesis of phosphorylated proteins for in vitro studies, we have explored the use of phosphorylated amino acids in which the phosphate moiety bears a chemical protecting group, thus eliminating the negative charges that have been shown to have a negative effect on protein translation. Bis-o-nitrobenzyl protection of tyrosine phosphate enabled its incorporation into DHFR and IκB-α using wild-type ribosomes, and the elaborated proteins could subsequently be deprotected by photolysis. Also investigated in parallel was the re-engineering of the 23S rRNA of Escherichia coli, guided by the use of a phosphorylated puromycin, to identify modified ribosomes capable of incorporating unprotected phosphotyrosine into proteins from a phosphotyrosyl-tRNACUA by UAG codon suppression during in vitro translation. Selection of a library of modified ribosomal clones with phosphorylated puromycin identified six modified ribosome variants having mutations in nucleotides 2600-2605 of 23S rRNA; these had enhanced sensitivity to the phosphorylated puromycin. The six clones demonstrated some sequence homology in the region 2600-2605 and incorporated unprotected phosphotyrosine into IκB-α using a modified gene having a TAG codon in the position corresponding to amino acid 42 of the protein. The purified phosphorylated protein bound to a phosphotyrosine specific antibody and permitted NF-κB binding to a DNA duplex sequence corresponding to its binding site in the IL-2 gene promoter. Unexpectedly, phosphorylated IκB-α also mediated the exchange of exogenous DNA into an NF-κB-cellular DNA complex isolated from the nucleus of activated Jurkat cells.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C. Nangreave
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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166
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Yang A, Cho K, Park HS. Chemical biology approaches for studying posttranslational modifications. RNA Biol 2017; 15:427-440. [PMID: 28901832 DOI: 10.1080/15476286.2017.1360468] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Posttranslational modification (PTM) is a key mechanism for regulating diverse protein functions, and thus critically affects many essential biological processes. Critical for systematic study of the effects of PTMs is the ability to obtain recombinant proteins with defined and homogenous modifications. To this end, various synthetic and chemical biology approaches, including genetic code expansion and protein chemical modification methods, have been developed. These methods have proven effective for generating site-specific authentic modifications or structural mimics, and have demonstrated their value for in vitro and in vivo functional studies of diverse PTMs. This review will discuss recent advances in chemical biology strategies and their application to various PTM studies.
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Affiliation(s)
- Aerin Yang
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Kyukwang Cho
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Hee-Sung Park
- a Department of Chemistry , Korea Advanced Institute of Science and Technology , 291 Daehak-ro, Yuseong-gu , Daejeon , Republic of Korea
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167
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Pedersen SW, Albertsen L, Moran GE, Levesque B, Pedersen SB, Bartels L, Wapenaar H, Ye F, Zhang M, Bowen ME, Strømgaard K. Site-Specific Phosphorylation of PSD-95 PDZ Domains Reveals Fine-Tuned Regulation of Protein-Protein Interactions. ACS Chem Biol 2017; 12:2313-2323. [PMID: 28692247 DOI: 10.1021/acschembio.7b00361] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The postsynaptic density protein of 95 kDa (PSD-95) is a key scaffolding protein that controls signaling at synapses in the brain through interactions of its PDZ domains with the C-termini of receptors, ion channels, and enzymes. PSD-95 is highly regulated by phosphorylation. To explore the effect of phosphorylation on PSD-95, we used semisynthetic strategies to introduce phosphorylated amino acids at four positions within the PDZ domains and examined the effects on interactions with a large set of binding partners. We observed complex effects on affinity. Most notably, phosphorylation at Y397 induced a significant increase in affinity for stargazin, as confirmed by NMR and single molecule FRET. Additionally, we compared the effects of phosphorylation to phosphomimetic mutations, which revealed that phosphomimetics are ineffective substitutes for tyrosine phosphorylation. Our strategy to generate site-specifically phosphorylated PDZ domains provides a detailed understanding of the role of phosphorylation in the regulation of PSD-95 interactions.
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Affiliation(s)
- Søren W. Pedersen
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Louise Albertsen
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Griffin E. Moran
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Brié Levesque
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Stine B. Pedersen
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lina Bartels
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Hannah Wapenaar
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Fei Ye
- Division
of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Center of Systems Biology and Human Health, School of
Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Mingjie Zhang
- Division
of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Center of Systems Biology and Human Health, School of
Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Mark E. Bowen
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Kristian Strømgaard
- Center
for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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168
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Abstract
In ribosomal translation, only 20 kinds of proteinogenic amino acids (pAAs), namely 19 l-amino acids and glycine, are exclusively incorporated into polypeptide chain. To overcome this limitation, various methods to introduce non-proteinogenic amino acids (npAAs) other than the 20 pAAs have been developed to date. However, the repertoire of amino acids that can be simultaneously introduced is still limited. Moreover, the efficiency of npAA incorporation is not always sufficient depending on their structures. Fidelity of translation is sometimes low due to misincorporation of competing pAAs and/or undesired translation termination. Here, we provide an overview of efforts to solve these issues, focusing on the engineering of tRNAs.
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Affiliation(s)
- Takayuki Katoh
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo , Japan.,b JST, PRESTO , 7-3-1 Hongo, Bunkyo-ku , Tokyo , Japan
| | - Yoshihiko Iwane
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo , Japan
| | - Hiroaki Suga
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo , Japan.,c JST, CREST , 7-3-1 Hongo, Bunkyo-ku , Tokyo , Japan
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169
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Abstract
The genetic code-the language used by cells to translate their genomes into proteins that perform many cellular functions-is highly conserved throughout natural life. Rewriting the genetic code could lead to new biological functions such as expanding protein chemistries with noncanonical amino acids (ncAAs) and genetically isolating synthetic organisms from natural organisms and viruses. It has long been possible to transiently produce proteins bearing ncAAs, but stabilizing an expanded genetic code for sustained function in vivo requires an integrated approach: creating recoded genomes and introducing new translation machinery that function together without compromising viability or clashing with endogenous pathways. In this review, we discuss design considerations and technologies for expanding the genetic code. The knowledge obtained by rewriting the genetic code will deepen our understanding of how genomes are designed and how the canonical genetic code evolved.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511;
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; .,Department of Chemistry, Yale University, New Haven, Connecticut 06511
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170
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George S, Wang SM, Bi Y, Treidlinger M, Barber KR, Shaw GS, O'Donoghue P. Ubiquitin phosphorylated at Ser57 hyper-activates parkin. Biochim Biophys Acta Gen Subj 2017; 1861:3038-3046. [PMID: 28689991 DOI: 10.1016/j.bbagen.2017.06.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
Malfunction of the ubiquitin (Ub) E3 ligase, parkin, leads to defects in mitophagy and protein quality control linked to Parkinson's disease. Parkin activity is stimulated by phosphorylation of Ub at Ser65 (pUbS65). Since the upstream kinase is only known for Ser65 (PINK1), the biochemical function of other phosphorylation sites on Ub remain largely unknown. We used fluorescently labelled and site-specifically phosphorylated Ub substrates to quantitatively relate the position and stoichiometry of Ub phosphorylation to parkin activation. Fluorescence measurements show that pUbS65-stimulated parkin is 5-fold more active than auto-inhibited and un-stimulated parkin, which catalyzes a basal level of auto-ubiquitination. We consistently observed a low but detectable level of parkin activity with pUbS12. Strikingly, pUbS57 hyper-activates parkin, and our data demonstrate that parkin is able to selectively synthesize poly-pUbS57 chains, even when 90% of the Ub in the reaction is un-phosphorylated. We further found that parkin ubiquitinates its physiological substrate Miro-1 with chains solely composed of pUbS65 and more efficiently with pUbS57 chains. Parkin hyper-activation by pUbS57 demonstrates the first PINK1-independent route to active parkin, revealing the roles of multiple ubiquitin phosphorylation sites in governing parkin stimulation and catalytic activity. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Susanna George
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Sabrina M Wang
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Yumin Bi
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Margot Treidlinger
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Kathryn R Barber
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Gary S Shaw
- 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.
| | - 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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171
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Luo X, Fu G, Wang RE, Zhu X, Zambaldo C, Liu R, Liu T, Lyu X, Du J, Xuan W, Yao A, Reed SA, Kang M, Zhang Y, Guo H, Huang C, Yang PY, Wilson IA, Schultz PG, Wang F. Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria. Nat Chem Biol 2017; 13:845-849. [PMID: 28604693 PMCID: PMC5577365 DOI: 10.1038/nchembio.2405] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/14/2017] [Indexed: 01/14/2023]
Abstract
Tyrosine phosphorylation is a common protein posttranslational modification, which plays a critical role in signal transduction and the regulation of many cellular processes. Using a pro-peptide strategy to increase cellular uptake of O-phosphotyrosine (pTyr) and its nonhydrolyzable analog 4-phosphomethyl-L-phenylalanine (Pmp), we identified an orthogonal aminoacyl-tRNA synthetase/tRNA pair that allows the site-specific incorporation of both pTyr and Pmp into recombinant proteins in response to the amber stop codon in Escherichia coli in good yields. The X-ray crystal structure of the synthetase reveals a reconfigured substrate binding site formed by non-conservative mutations and substantial local structural perturbations. We demonstrate the utility of this method by introducing Pmp into a putative phosphorylation site whose corresponding kinase is unknown and determined the affinities of the individual variants for the substrate 3BP2. In summary, this work provides a useful recombinant tool to dissect the biological functions of tyrosine phosphorylation at specific sites in the proteome.
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Affiliation(s)
- Xiaozhou Luo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Guangsen Fu
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Rongsheng E Wang
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Renhe Liu
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Tao Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Xiaoxuan Lyu
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Jintang Du
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Weimin Xuan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Anzhi Yao
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Sean A Reed
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Mingchao Kang
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Yuhan Zhang
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Hui Guo
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Chunhui Huang
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Peng-Yu Yang
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ian A Wilson
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
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172
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Hoppmann C, Wong A, Yang B, Li S, Hunter T, Shokat KM, Wang L. Site-specific incorporation of phosphotyrosine using an expanded genetic code. Nat Chem Biol 2017; 13:842-844. [PMID: 28604697 PMCID: PMC5577362 DOI: 10.1038/nchembio.2406] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/15/2017] [Indexed: 02/03/2023]
Abstract
Access to phosphoproteins with stoichiometric and site-specific phosphorylation status is key to understanding the role of protein phosphorylation. Here we report an efficient method to generate pure, active phosphotyrosine-containing proteins by genetically encoding a stable phosphotyrosine analog that is convertible to native phosphotyrosine. We demonstrate its general compatibility with proteins of various sizes, phosphotyrosine sites and functions, and reveal a possible role of tyrosine phosphorylation in negative regulation of ubiquitination.
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Affiliation(s)
- Christian Hoppmann
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Allison Wong
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Bing Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, Maryland, USA
| | - Tony Hunter
- The Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, California, USA
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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173
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Zhang MS, Brunner SF, Huguenin-Dezot N, Liang AD, Schmied WH, Rogerson DT, Chin JW. Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing. Nat Methods 2017; 14:729-736. [PMID: 28553966 DOI: 10.1038/nmeth.4302] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The phosphorylation of threonine residues in proteins regulates diverse processes in eukaryotic cells, and thousands of threonine phosphorylations have been identified. An understanding of how threonine phosphorylation regulates biological function will be accelerated by general methods to biosynthesize defined phosphoproteins. Here we describe a rapid approach for directly discovering aminoacyl-tRNA synthetase-tRNA pairs that selectively incorporate non-natural amino acids into proteins; our method uses parallel positive selections combined with deep sequencing and statistical analysis and enables the direct, scalable discovery of aminoacyl-tRNA synthetase-tRNA pairs with mutually orthogonal substrate specificity. By combining a method to biosynthesize phosphothreonine in cells with this selection approach, we discover a phosphothreonyl-tRNA synthetase-tRNACUA pair and create an entirely biosynthetic route to incorporating phosphothreonine in proteins. We biosynthesize several phosphoproteins and demonstrate phosphoprotein structure determination and synthetic protein kinase activation.
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Affiliation(s)
- Michael Shaofei Zhang
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Simon F Brunner
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Nicolas Huguenin-Dezot
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Alexandria D Liang
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Wolfgang H Schmied
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Daniel T Rogerson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
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174
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Chen C, Nimlamool W, Miller CJ, Lou HJ, Turk BE. Rational Redesign of a Functional Protein Kinase-Substrate Interaction. ACS Chem Biol 2017; 12:1194-1198. [PMID: 28314095 PMCID: PMC5442603 DOI: 10.1021/acschembio.7b00089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Eukaryotic
protein kinases typically phosphorylate substrates in
the context of specific sequence motifs, contributing to specificity
essential for accurate signal transmission. Protein kinases recognize
their target sequences through complementary interactions within the
active site cleft. As a step toward the construction of orthogonal
kinase signaling systems, we have re-engineered the protein kinase
Pim1 to alter its phosphorylation consensus sequence. Residues in
the Pim1 catalytic domain interacting directly with a critical arginine
residue in the substrate were substituted to produce a kinase mutant
that instead accommodates a hydrophobic residue. We then introduced
a compensating mutation into a Pim1 substrate, the pro-apoptotic protein
BAD, to reconstitute phosphorylation both in vitro and in living cells. Coexpression of the redesigned kinase with
its substrate in cells protected them from apoptosis. Such orthogonal
kinase–substrate pairs provide tools to probe the functional
consequences of specific phosphorylation events in living cells and
to design synthetic signaling pathways.
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Affiliation(s)
- Catherine Chen
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Wutigri Nimlamool
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Chad J. Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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175
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Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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176
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Lin X, Yu ACS, Chan TF. Efforts and Challenges in Engineering the Genetic Code. Life (Basel) 2017; 7:life7010012. [PMID: 28335420 PMCID: PMC5370412 DOI: 10.3390/life7010012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 12/15/2022] Open
Abstract
This year marks the 48th anniversary of Francis Crick’s seminal work on the origin of the genetic code, in which he first proposed the “frozen accident” hypothesis to describe evolutionary selection against changes to the genetic code that cause devastating global proteome modification. However, numerous efforts have demonstrated the viability of both natural and artificial genetic code variations. Recent advances in genetic engineering allow the creation of synthetic organisms that incorporate noncanonical, or even unnatural, amino acids into the proteome. Currently, successful genetic code engineering is mainly achieved by creating orthogonal aminoacyl-tRNA/synthetase pairs to repurpose stop and rare codons or to induce quadruplet codons. In this review, we summarize the current progress in genetic code engineering and discuss the challenges, current understanding, and future perspectives regarding genetic code modification.
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Affiliation(s)
- Xiao Lin
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, NT, Hong Kong, China.
| | - Allen Chi Shing Yu
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, NT, Hong Kong, China.
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, NT, Hong Kong, China.
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177
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Han S, Yang A, Lee S, Lee HW, Park CB, Park HS. Expanding the genetic code of Mus musculus. Nat Commun 2017; 8:14568. [PMID: 28220771 PMCID: PMC5321798 DOI: 10.1038/ncomms14568] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/13/2017] [Indexed: 01/17/2023] Open
Abstract
Here we report the expansion of the genetic code of Mus musculus with various unnatural amino acids including Nɛ-acetyl-lysine. Stable integration of transgenes encoding an engineered Nɛ-acetyl-lysyl-tRNA synthetase (AcKRS)/tRNAPyl pair into the mouse genome enables site-specific incorporation of unnatural amino acids into a target protein in response to the amber codon. We demonstrate temporal and spatial control of protein acetylation in various organs of the transgenic mouse using a recombinant green fluorescent protein (GFPuv) as a model protein. This strategy will provide a powerful tool for systematic in vivo study of cellular proteins in the most commonly used mammalian model organism for human physiology and disease.
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Affiliation(s)
- Songmi Han
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Aerin Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Soonjang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Han-Woong Lee
- Department of Biochemistry, Yonsei Laboratory Animal Research Center, Yonsei University, Seoul 03722, Republic of Korea
| | - Chan Bae Park
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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178
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Lee BS, Kim S, Ko BJ, Yoo TH. An efficient system for incorporation of unnatural amino acids in response to the four-base codon AGGA in Escherichia coli. Biochim Biophys Acta Gen Subj 2017; 1861:3016-3023. [PMID: 28212794 DOI: 10.1016/j.bbagen.2017.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Adding new amino acids to the set of building blocks for protein synthesis expands the scope of protein engineering, and orthogonal pairs of tRNA and aminoacyl-tRNA synthetase have been developed for incorporating unnatural amino acids (UAAs) into proteins. While diverse systems have been developed to incorporate UAAs in response to the amber codon, less research has been focused on four-base codons despites their advantages. In this study, we report an efficient method to incorporate UAA in response to an AGGA codon in Escherichia coli. RESULTS The Methanococcus jannaschii tyrosyl-tRNA synthetase-tRNACUA(MjTyrRS-MjtRNACUA) orthogonal pair has been engineered to incorporate diverse UAAs in response to the amber codon. To apply the engineered MjTyrRS enzymes for UAAs to a four-base codon suppression, we developed an MjTyrRS-MjtRNAUCCU pair system that enabled incorporation of UAAs in response to the AGGA codon in E. coli. Using this system, we demonstrated that several UAAs could be incorporated quantitatively in the AGGA site. In addition, multiple AGGA codons were successfully suppressed in an E. coli strain when the endogenous tRNACCUArg gene was knocked out. CONCLUSION An efficient system was developed for the incorporation of UAAs in response to the AGGA four-base codon in E. coli, and the method was successfully demonstrated for several UAAs and for multiple AGGA sites. GENERAL SIGNIFICANCE The developed system can expand the repertoire of protein engineering tools based on amino acid analogues in combination with other UAA incorporation methods. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Suyeon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Byoung Joon Ko
- New Drug Development Center, Osong Medical Innovative Foundation, 123, Osongsaengmyeong-ro, Osong-eup, Cheongju 28160, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea.
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179
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Kim SW, Lee KJ, Kim S, Kim J, Cho K, Ro HS, Park HS. Genetic incorporation of N ε-acetyllysine reveals a novel acetylation-sumoylation switch in yeast. Biochim Biophys Acta Gen Subj 2017; 1861:3030-3037. [PMID: 28188860 DOI: 10.1016/j.bbagen.2017.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/02/2017] [Indexed: 10/20/2022]
Abstract
The lysine acetylation of proteins plays a key role in regulating protein functions, thereby controlling a wide range of cellular processes. Despite the prevalence and significance of lysine acetylation in eukaryotes, however, its systematic study has been challenged by the technical limitations of conventional approaches for selective lysine acetylation in vivo. Here, we report the in vivo study of lysine acetylation via the genetic incorporation of Nε-acetyllysine in yeast. We demonstrate that a newly discovered acetylation-sumoylation switch precisely controls the localization and cellular function of the yeast septin protein, Cdc11, during the cell cycle. This approach should facilitate the comprehensive in vivo study of lysine acetylation across a wide range of proteins in eukaryotic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Sang-Woo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyung Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sinil Kim
- Division of Applied Life Science and Research Institute for Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jihyo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyukwang Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute for Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea.
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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180
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Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnol Bioeng 2017; 114:1074-1086. [PMID: 27987323 DOI: 10.1002/bit.26239] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/28/2016] [Accepted: 12/13/2016] [Indexed: 01/15/2023]
Abstract
The ability to site-specifically incorporate non-canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p-azido-phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p-azido-phenylalanyl-tRNA synthetase anti-codon binding domain, (ii) evolving the elongation factor Tu amino acid-binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi-site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site-specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074-1086. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Ioanna Ntai
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, Connecticut.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-0001.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Simpson Querry Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
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181
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Mohler K, Aerni HR, Gassaway B, Ling J, Ibba M, Rinehart J. MS-READ: Quantitative measurement of amino acid incorporation. Biochim Biophys Acta Gen Subj 2017; 1861:3081-3088. [PMID: 28130155 DOI: 10.1016/j.bbagen.2017.01.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored. In particular, until recently technical challenges have limited the ability to detect and quantify comparatively rare amino acid misincorporation events, which occur orders of magnitude less frequently than canonical amino acid incorporation events. We now describe a technique for the quantitative analysis of amino acid incorporation that provides the sensitivity necessary to detect mistranslation events during translation of a single codon at frequencies as low as 1 in 10,000 for all 20 proteinogenic amino acids, as well as non-proteinogenic and modified amino acids. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Kyle Mohler
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Brandon Gassaway
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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182
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Rewiring protein synthesis: From natural to synthetic amino acids. Biochim Biophys Acta Gen Subj 2017; 1861:3024-3029. [PMID: 28095316 DOI: 10.1016/j.bbagen.2017.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. SCOPE OF REVIEW This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. MAJOR CONCLUSIONS The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. GENERAL SIGNIFICANCE Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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183
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Gan Q, Lehman BP, Bobik TA, Fan C. Expanding the genetic code of Salmonella with non-canonical amino acids. Sci Rep 2016; 6:39920. [PMID: 28008993 PMCID: PMC5180212 DOI: 10.1038/srep39920] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Brent P Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
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184
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Gan Q, Fan C. Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis. Biochim Biophys Acta Gen Subj 2016; 1861:3047-3052. [PMID: 27919800 DOI: 10.1016/j.bbagen.2016.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/04/2016] [Accepted: 12/01/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression. METHODS We performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation. By manipulating codon usage of target genes and tRNA species introduced into the cell-free protein synthesis system, we increased the fidelity of Sep incorporation at a specific position. RESULTS By removing three near cognate tRNA isoacceptors of the amber stop codon [tRNALys, tRNATyr, and tRNAGln(CUG)] from the total tRNA, the near cognate suppression decreased by 5-fold without impairing normal protein synthesis in the cell-free protein synthesis system. Mass spectrometry analyses indicated that the fidelity of ncAA incorporation was improved. CONCLUSIONS Removal of near cognate tRNA isoacceptors of the amber codon could increase ncAA incorporation fidelity towards the amber stop codon in release factor deficiency systems. GENERAL SIGNIFICANCE We provide a general strategy to improve fidelity of ncAA incorporation towards stop, quadruplet and sense codons in cell-free protein synthesis systems. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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185
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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186
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Goldberg AB, Cho E, Miller CJ, Lou HJ, Turk BE. Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor. J Biol Chem 2016; 292:814-825. [PMID: 27909054 DOI: 10.1074/jbc.m116.761734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/23/2016] [Indexed: 01/02/2023] Open
Abstract
The metalloproteinase anthrax lethal factor (LF) is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. LF is a highly specific protease, exclusively cleaving mitogen-activated protein kinase kinases (MKKs) and rodent NLRP1B (NACHT leucine-rich repeat and pyrin domain-containing protein 1B). How LF achieves such restricted substrate specificity is not understood. Previous studies have suggested the existence of an exosite interaction between LF and MKKs that promotes cleavage efficiency and specificity. Through a combination of in silico prediction and site-directed mutagenesis, we have mapped an exosite to a non-catalytic region of LF. Mutations within this site selectively impair proteolysis of full-length MKKs yet have no impact on cleavage of short peptide substrates. Although this region appears important for cleaving all LF protein substrates, we found that mutation of specific residues within the exosite differentially affects MKK and NLRP1B cleavage in vitro and in cultured cells. One residue in particular, Trp-271, is essential for cleavage of MKK3, MKK4, and MKK6 but dispensable for targeting of MEK1, MEK2, and NLRP1B. Analysis of chimeric substrates suggests that this residue interacts with the MKK catalytic domain. We found that LF-W271A blocked ERK phosphorylation and growth in a melanoma cell line, suggesting that it may provide a highly selective inhibitor of MEK1/2 for use as a cancer therapeutic. These findings provide insight into how a bacterial toxin functions to specifically impair host signaling pathways and suggest a general strategy for mapping protease exosite interactions.
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Affiliation(s)
- Allison B Goldberg
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eunice Cho
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Chad J Miller
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Hua Jane Lou
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Benjamin E Turk
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
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187
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Torres L, Krüger A, Csibra E, Gianni E, Pinheiro VB. Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem 2016; 60:393-410. [PMID: 27903826 PMCID: PMC5264511 DOI: 10.1042/ebc20160013] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022]
Abstract
Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs.
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Affiliation(s)
- Leticia Torres
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - Antje Krüger
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Eszter Csibra
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Edoardo Gianni
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Vitor B Pinheiro
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
- Birkbeck, Department of Biological Sciences, University of London, Malet Street, WC1E 7HX, U.K
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188
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Yang A, Ha S, Ahn J, Kim R, Kim S, Lee Y, Kim J, Söll D, Lee HY, Park HS. A chemical biology route to site-specific authentic protein modifications. Science 2016; 354:623-626. [PMID: 27708052 PMCID: PMC5135561 DOI: 10.1126/science.aah4428] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022]
Abstract
Many essential biological processes are controlled by posttranslational protein modifications. The inability to synthetically attain the diversity enabled by these modifications limits functional studies of many proteins. We designed a three-step approach for installing authentic posttranslational modifications in recombinant proteins. We first use the established O-phosphoserine (Sep) orthogonal translation system to create a Sep-containing recombinant protein. The Sep residue is then dephosphorylated to dehydroalanine (Dha). Last, conjugate addition of alkyl iodides to Dha, promoted by zinc and copper, enables chemoselective carbon-carbon bond formation. To validate our approach, we produced histone H3, ubiquitin, and green fluorescent protein variants with site-specific modifications, including different methylations of H3K79. The methylated histones stimulate transcription through histone acetylation. This approach offers a powerful tool to engineer diverse designer proteins.
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Affiliation(s)
- Aerin Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jihye Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Rira Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sungyoon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA
| | - Hee-Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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189
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Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
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Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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190
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Simonik EA, Cai Y, Kimmelshue KN, Brantley-Sieders DM, Loomans HA, Andl CD, Westlake GM, Youngblood VM, Chen J, Yarbrough WG, Brown BT, Nagarajan L, Brandt SJ. LIM-Only Protein 4 (LMO4) and LIM Domain Binding Protein 1 (LDB1) Promote Growth and Metastasis of Human Head and Neck Cancer (LMO4 and LDB1 in Head and Neck Cancer). PLoS One 2016; 11:e0164804. [PMID: 27780223 PMCID: PMC5079595 DOI: 10.1371/journal.pone.0164804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/01/2016] [Indexed: 12/18/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) accounts for more than 300,000 deaths worldwide per year as a consequence of tumor cell invasion of adjacent structures or metastasis. LIM-only protein 4 (LMO4) and LIM-domain binding protein 1 (LDB1), two directly interacting transcriptional adaptors that have important roles in normal epithelial cell differentiation, have been associated with increased metastasis, decreased differentiation, and shortened survival in carcinoma of the breast. Here, we implicate two LDB1-binding proteins, single-stranded binding protein 2 (SSBP2) and 3 (SSBP3), in controlling LMO4 and LDB1 protein abundance in HNSCC and in regulating specific tumor cell functions in this disease. First, we found that the relative abundance of LMO4, LDB1, and the two SSBPs correlated very significantly in a panel of human HNSCC cell lines. Second, expression of these proteins in tumor primaries and lymph nodes involved by metastasis were concordant in 3 of 3 sets of tissue. Third, using a Matrigel invasion and organotypic reconstruct assay, CRISPR/Cas9-mediated deletion of LDB1 in the VU-SCC-1729 cell line, which is highly invasive of basement membrane and cellular monolayers, reduced tumor cell invasiveness and migration, as well as proliferation on tissue culture plastic. Finally, inactivation of the LDB1 gene in these cells decreased growth and vascularization of xenografted human tumor cells in vivo. These data show that LMO4, LDB1, and SSBP2 and/or SSBP3 regulate metastasis, proliferation, and angiogenesis in HNSCC and provide the first evidence that SSBPs control LMO4 and LDB1 protein abundance in a cancer context.
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Affiliation(s)
- Elizabeth A. Simonik
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Ying Cai
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Katherine N. Kimmelshue
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Dana M. Brantley-Sieders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Holli A. Loomans
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Claudia D. Andl
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Grant M. Westlake
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Victoria M. Youngblood
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Jin Chen
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
| | - Wendell G. Yarbrough
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Brandee T. Brown
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Lalitha Nagarajan
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Stephen J. Brandt
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
- * E-mail:
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191
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Wandrey G, Wurzel J, Hoffmann K, Ladner T, Büchs J, Meinel L, Lühmann T. Probing unnatural amino acid integration into enhanced green fluorescent protein by genetic code expansion with a high-throughput screening platform. J Biol Eng 2016; 10:11. [PMID: 27733867 PMCID: PMC5045631 DOI: 10.1186/s13036-016-0031-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/14/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Genetic code expansion has developed into an elegant tool to incorporate unnatural amino acids (uAA) at predefined sites in the protein backbone in response to an amber codon. However, recombinant production and yield of uAA comprising proteins are challenged due to the additional translation machinery required for uAA incorporation. RESULTS We developed a microtiter plate-based high-throughput monitoring system (HTMS) to study and optimize uAA integration in the model protein enhanced green fluorescence protein (eGFP). Two uAA, propargyl-L-lysine (Plk) and (S)-2-amino-6-((2-azidoethoxy) carbonylamino) hexanoic acid (Alk), were incorporated at the same site into eGFP co-expressing the native PylRS/tRNAPylCUA pair originating from Methanosarcina barkeri in E. coli. The site-specific uAA functionalization was confirmed by LC-MS/MS analysis. uAA-eGFP production and biomass growth in parallelized E. coli cultivations was correlated to (i) uAA concentration and the (ii) time of uAA addition to the expression medium as well as to induction parameters including the (iii) time and (iv) amount of IPTG supplementation. The online measurements of the HTMS were consolidated by end point-detection using standard enzyme-linked immunosorbent procedures. CONCLUSION The developed HTMS is powerful tool for parallelized and rapid screening. In light of uAA integration, future applications may include parallelized screening of different PylRS/tRNAPylCUA pairs as well as further optimization of culture conditions.
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Affiliation(s)
- Georg Wandrey
- AVT, Biochemical Engineering, RWTH Aachen University, Aachen, 52074 Germany
| | - Joel Wurzel
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg, 97074 Germany
| | - Kyra Hoffmann
- AVT, Biochemical Engineering, RWTH Aachen University, Aachen, 52074 Germany
| | - Tobias Ladner
- AVT, Biochemical Engineering, RWTH Aachen University, Aachen, 52074 Germany
| | - Jochen Büchs
- AVT, Biochemical Engineering, RWTH Aachen University, Aachen, 52074 Germany
| | - Lorenz Meinel
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg, 97074 Germany
| | - Tessa Lühmann
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg, 97074 Germany
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192
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Fan C, Ip K, Söll D. Expanding the genetic code of Escherichia coli with phosphotyrosine. FEBS Lett 2016; 590:3040-7. [PMID: 27477338 DOI: 10.1002/1873-3468.12333] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 11/07/2022]
Abstract
Protein phosphorylation is one of the most important post-translational modifications in nature. However, the site-specific incorporation of O-phosphotyrosine into proteins in vivo has not yet been reported. Endogenous phosphatases present in cells can dephosphorylate phosphotyrosine as a free amino acid or as a protein residue. Therefore, we deleted the genes of five phosphatases from the genome of Escherichia coli with the aim of stabilizing phosphotyrosine. Together with an engineered aminoacyl-tRNA synthetase (derived from Methanocaldococcus jannaschii tyrosyl-tRNA synthetase) and an elongation factor Tu variant, we were able to cotranslationally incorporate O-phosphotyrosine into the superfolder green fluorescent protein at a desired position in vivo. This system will facilitate future studies of tyrosine phosphorylation.
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Affiliation(s)
- Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kevan Ip
- 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
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193
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Bag SS, Jana S, Pradhan MK. Synthesis, photophysical properties of triazolyl-donor/acceptor chromophores decorated unnatural amino acids: Incorporation of a pair into Leu-enkephalin peptide and application of triazolylperylene amino acid in sensing BSA. Bioorg Med Chem 2016; 24:3579-95. [DOI: 10.1016/j.bmc.2016.05.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/29/2016] [Accepted: 05/30/2016] [Indexed: 02/03/2023]
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194
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Regan L, Caballero D, Hinrichsen MR, Virrueta A, Williams DM, O'Hern CS. Protein design: Past, present, and future. Biopolymers 2016; 104:334-50. [PMID: 25784145 DOI: 10.1002/bip.22639] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 01/16/2023]
Abstract
Building on the pioneering work of Ho and DeGrado (J Am Chem Soc 1987, 109, 6751-6758) in the late 1980s, protein design approaches have revealed many fundamental features of protein structure and stability. We are now in the era that the early work presaged - the design of new proteins with practical applications and uses. Here we briefly survey some past milestones in protein design, in addition to highlighting recent progress and future aspirations.
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Affiliation(s)
- Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.,Department of Chemistry, Yale University, New Haven, CT.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT
| | - Diego Caballero
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT.,Department of Physics, Yale University, New Haven, CT
| | - Michael R Hinrichsen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Alejandro Virrueta
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT.,Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - Danielle M Williams
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Corey S O'Hern
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT.,Department of Physics, Yale University, New Haven, CT.,Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT.,Department of Applied Physics, Yale University, New Haven, CT
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195
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Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity. Cell Rep 2016; 16:1180-1193. [PMID: 27425610 PMCID: PMC4967478 DOI: 10.1016/j.celrep.2016.06.064] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/05/2016] [Accepted: 06/14/2016] [Indexed: 01/30/2023] Open
Abstract
Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages. Milligram quantities of ubiquitin phosphorylated at Ser 20, 57, or 65 are purified Twenty isomeric phosphoubiquitin dimers are assembled and purified UBE3C chain synthesis specificity is controlled by Ser 20 ubiquitin phosphorylation Phosphorylation of ubiquitin controls deubiquitinase activity and linkage specificity
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196
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Neumann-Staubitz P, Neumann H. The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol 2016; 38:119-28. [DOI: 10.1016/j.sbi.2016.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/21/2022]
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197
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Crnković A, Suzuki T, Söll D, Reynolds NM. Pyrrolysyl-tRNA synthetase, an aminoacyl-tRNA synthetase for genetic code expansion. CROAT CHEM ACTA 2016; 89:163-174. [PMID: 28239189 PMCID: PMC5321558 DOI: 10.5562/cca2825] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genetic code expansion (GCE) has become a central topic of synthetic biology. GCE relies on engineered aminoacyl-tRNA synthetases (aaRSs) and a cognate tRNA species to allow codon reassignment by co-translational insertion of non-canonical amino acids (ncAAs) into proteins. Introduction of such amino acids increases the chemical diversity of recombinant proteins endowing them with novel properties. Such proteins serve in sophisticated biochemical and biophysical studies both in vitro and in vivo, they may become unique biomaterials or therapeutic agents, and they afford metabolic dependence of genetically modified organisms for biocontainment purposes. In the Methanosarcinaceae the incorporation of the 22nd genetically encoded amino acid, pyrrolysine (Pyl), is facilitated by pyrrolysyl-tRNA synthetase (PylRS) and the cognate UAG-recognizing tRNAPyl. This unique aaRS•tRNA pair functions as an orthogonal translation system (OTS) in most model organisms. The facile directed evolution of the large PylRS active site to accommodate many ncAAs, and the enzyme's anticodon-blind specific recognition of the cognate tRNAPyl make this system highly amenable for GCE purposes. The remarkable polyspecificity of PylRS has been exploited to incorporate >100 different ncAAs into proteins. Here we review the Pyl-OT system and selected GCE applications to examine the properties of an effective OTS.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Tateki Suzuki
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Noah M. Reynolds
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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198
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Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A 2016; 113:E3461-7. [PMID: 27247408 DOI: 10.1073/pnas.1603799113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation.
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199
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George S, Aguirre JD, Spratt DE, Bi Y, Jeffery M, Shaw GS, O'Donoghue P. Generation of phospho-ubiquitin variants by orthogonal translation reveals codon skipping. FEBS Lett 2016; 590:1530-42. [DOI: 10.1002/1873-3468.12182] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/10/2016] [Accepted: 04/11/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Susanna George
- Department of Biochemistry; The University of Western Ontario; London Canada
| | - Jacob D. Aguirre
- Department of Biochemistry; The University of Western Ontario; London Canada
| | - Donald E. Spratt
- Department of Biochemistry; The University of Western Ontario; London Canada
| | - Yumin Bi
- Department of Biochemistry; The University of Western Ontario; London Canada
| | - Madeline Jeffery
- Department of Biochemistry; The University of Western Ontario; London Canada
| | - Gary S. Shaw
- Department of Biochemistry; The University of Western Ontario; London Canada
- Department of Chemistry; The University of Western Ontario; London Canada
| | - Patrick O'Donoghue
- Department of Biochemistry; The University of Western Ontario; London Canada
- Department of Chemistry; The University of Western Ontario; London Canada
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200
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Regan L, Hinrichsen MR, Oi C. Protein engineering strategies with potential applications for altering clinically relevant cellular pathways at the protein level. Expert Rev Proteomics 2016; 13:481-93. [PMID: 27031866 DOI: 10.1586/14789450.2016.1172966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
All diseases can be fundamentally viewed as the result of malfunctioning cellular pathways. Protein engineering offers the potential to develop new tools that will allow these dysfunctional pathways to be better understood, in addition to potentially providing new routes to restore proper function. Here we discuss different approaches that can be used to change the intracellular activity of a protein by intervening at the protein level: targeted protein sequestration, protein recruitment, protein degradation, and selective inhibition of binding interfaces. The potential of each of these tools to be developed into effective therapeutic treatments will also be discussed, along with any major barriers that currently block their translation into the clinic.
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Affiliation(s)
- Lynne Regan
- a Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA.,b Department of Chemistry , Yale University , New Haven , CT , USA.,c Integrated Graduate Program in Physical and Engineering Biology , Yale University , New Haven , CT , USA
| | - Michael R Hinrichsen
- a Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
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