51
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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: 37] [Impact Index Per Article: 6.2] [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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52
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Kubyshkin V, Acevedo-Rocha CG, Budisa N. On universal coding events in protein biogenesis. Biosystems 2018; 164:16-25. [DOI: 10.1016/j.biosystems.2017.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022]
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53
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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: 488] [Impact Index Per Article: 69.7] [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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54
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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: 13] [Impact Index Per Article: 1.9] [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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55
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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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56
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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: 70] [Impact Index Per Article: 10.0] [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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57
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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: 90] [Impact Index Per Article: 12.9] [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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58
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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: 43] [Impact Index Per Article: 6.1] [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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59
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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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