1
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Ishida S, Ngo PHT, Gundlach A, Ellington A. Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chem Rev 2024; 124:7712-7730. [PMID: 38829723 DOI: 10.1021/acs.chemrev.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The introduction of noncanonical amino acids into proteins has enabled researchers to modify fundamental physicochemical and functional properties of proteins. While the alteration of the genetic code, via the introduction of orthogonal aminoacyl-tRNA synthetase:tRNA pairs, has driven many of these efforts, the various components involved in the process of translation are important for the development of new genetic codes. In this review, we will focus on recent advances in engineering ribosomal machinery for noncanonical amino acid incorporation and genetic code modification. The engineering of the ribosome itself will be considered, as well as the many factors that interact closely with the ribosome, including both tRNAs and accessory factors, such as the all-important EF-Tu. Given the success of genome re-engineering efforts, future paths for radical alterations of the genetic code will require more expansive alterations in the translation machinery.
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Affiliation(s)
- Satoshi Ishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Phuoc H T Ngo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Arno Gundlach
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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2
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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3
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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4
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Reese A, de Moliner F, Mendive-Tapia L, Benson S, Kuru E, Bridge T, Richards J, Rittichier J, Kitamura T, Sachdeva A, McSorley HJ, Vendrell M. Inserting "OFF-to-ON" BODIPY Tags into Cytokines: A Fluorogenic Interleukin IL-33 for Real-Time Imaging of Immune Cells. ACS CENTRAL SCIENCE 2024; 10:143-154. [PMID: 38292608 PMCID: PMC10823590 DOI: 10.1021/acscentsci.3c01125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 02/01/2024]
Abstract
The essential functions that cytokine/immune cell interactions play in tissue homeostasis and during disease have prompted the molecular design of targeted fluorophores to monitor their activity in real time. Whereas activatable probes for imaging immune-related enzymes are common, many immunological functions are mediated by binding events between cytokines and their cognate receptors that are hard to monitor by live-cell imaging. A prime example is interleukin-33 (IL-33), a key cytokine in innate and adaptive immunity, whose interaction with the ST2 cell-surface receptor results in downstream signaling and activation of NF-κB and AP-1 pathways. In the present work, we have designed a chemical platform to site-specifically introduce OFF-to-ON BODIPY fluorophores into full cytokine proteins and generate the first nativelike fluorescent analogues of IL-33. Among different incorporation strategies, chemical aminoacylation followed by bioorthogonal derivatization led to the best labeling results. Importantly, the BODIPY-labeled IL-33 derivatives-unlike IL-33-GFP constructs-exhibited ST2-specific binding and downstream bioactivity profiles comparable to those of the wild-type interleukin. Real-time fluorescence microscopy assays under no wash conditions confirmed the internalization of IL-33 through ST2 receptors and its intracellular trafficking through the endosomal pathway. We envision that the modularity and versatility of our BODIPY labeling platform will facilitate the synthesis of minimally tagged fluorogenic cytokines as the next generation of imaging reagents for real-time visualization of signaling events in live immune cells.
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Affiliation(s)
- Abigail
E. Reese
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Fabio de Moliner
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Lorena Mendive-Tapia
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Sam Benson
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
| | - Erkin Kuru
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02215, United States
| | - Thomas Bridge
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Josh Richards
- Division
of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Jonathan Rittichier
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Takanori Kitamura
- Centre
for Reproductive Health, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
| | - Amit Sachdeva
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Henry J. McSorley
- Division
of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Marc Vendrell
- Centre
for Inflammation Research, The University
of Edinburgh, EH16 4UU Edinburgh, United Kingdom
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, EH16 4UU, Edinburgh, United Kingdom
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5
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Majumdar C, Walker JA, Francis MB, Schepartz A, Cate JHD. Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. ACS CENTRAL SCIENCE 2023; 9:1160-1169. [PMID: 37396857 PMCID: PMC10311655 DOI: 10.1021/acscentsci.3c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 07/04/2023]
Abstract
The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.
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Affiliation(s)
- Chandrima Majumdar
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Joshua A. Walker
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Jamie H. D. Cate
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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6
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Lee K, Willi JA, Cho N, Kim I, Jewett MC, Lee J. Cell-free Biosynthesis of Peptidomimetics. BIOTECHNOL BIOPROC E 2023; 28:1-17. [PMID: 36778039 PMCID: PMC9896473 DOI: 10.1007/s12257-022-0268-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/16/2022] [Accepted: 11/13/2022] [Indexed: 02/05/2023]
Abstract
A wide variety of peptidomimetics (peptide analogs) possessing innovative biological functions have been brought forth as therapeutic candidates through cell-free protein synthesis (CFPS) systems. A key feature of these peptidomimetic drugs is the use of non-canonical amino acid building blocks with diverse biochemical properties that expand functional diversity. Here, we summarize recent technologies leveraging CFPS platforms to expand the reach of peptidomimetics drugs. We also offer perspectives on engineering the translational machinery that may open new opportunities for expanding genetically encoded chemistry to transform drug discovery practice beyond traditional boundaries.
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Affiliation(s)
- Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Jessica A. Willi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Inseon Kim
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Joongoo Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
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7
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Chan AI, Sawant MS, Burdick DJ, Tom J, Song A, Cunningham CN. Evaluating Translational Efficiency of Noncanonical Amino Acids to Inform the Design of Druglike Peptide Libraries. ACS Chem Biol 2023; 18:81-90. [PMID: 36607609 PMCID: PMC9872084 DOI: 10.1021/acschembio.2c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Advances in genetic code reprogramming have allowed the site-specific incorporation of noncanonical functionalities into polypeptides and proteins, providing access to wide swaths of chemical space via in vitro translation techniques like mRNA display. Prior efforts have established that the translation machinery can tolerate amino acids with modifications to both the peptide backbone and side chains, greatly broadening the chemical space that can be interrogated in ligand discovery efforts. However, existing methods for confirming the translation yield of new amino acid building blocks for these technologies necessitate multistep workups and, more importantly, are not relevant for measuring translation within the context of a combinatorial library consisting of multiple noncanonical amino acids. In this study, we developed a luminescence-based assay to rapidly assess the relative translation yield of any noncanonical amino acid in real time. Among the 59 amino acids tested here, we found that many translate with high efficiency, but translational yield is not necessarily correlated to whether the amino acid is proteinogenic or has high tRNA acylation efficiency. Interestingly, we found that single-template translation data can inform the library-scale translation yield and that shorter peptide libraries are more tolerant of lower-efficiency amino acid monomers. Together our data show that the luminescence-based assay described herein is an essential tool in evaluating new building blocks and codon table designs within mRNA display toward the goal of developing druglike peptide-based libraries for drug discovery campaigns.
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Affiliation(s)
- Alix I Chan
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Manali S. Sawant
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Daniel J. Burdick
- Department
of Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Jeffrey Tom
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Aimin Song
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States,
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8
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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9
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Lee J, Coronado JN, Cho N, Lim J, Hosford BM, Seo S, Kim DS, Kofman C, Moore JS, Ellington AD, Anslyn EV, Jewett MC. Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Nat Commun 2022; 13:6322. [PMID: 36280685 PMCID: PMC9592601 DOI: 10.1038/s41467-022-33701-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/28/2022] [Indexed: 12/25/2022] Open
Abstract
The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the P-site and the α-amino groups in the A-site aligns the substrates for coupling. The plasticity of this catalytic mechanism has been observed in both remnants of the evolution of the genetic code and modern efforts to reprogram the genetic code (e.g., ribosomal incorporation of non-canonical amino acids, ribosomal ester formation). However, the limits of ribosome-mediated polymerization are underexplored. Here, rather than peptide bonds, we demonstrate ribosome-mediated polymerization of pyridazinone bonds via a cyclocondensation reaction between activated γ-keto and α-hydrazino ester monomers. In addition, we demonstrate the ribosome-catalyzed synthesis of peptide-hybrid oligomers composed of multiple sequence-defined alternating pyridazinone linkages. Our results highlight the plasticity of the ribosome's ancient bond-formation mechanism, expand the range of non-canonical polymeric backbones that can be synthesized by the ribosome, and open the door to new applications in synthetic biology.
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Affiliation(s)
- Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Jaime N Coronado
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jongdoo Lim
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Brandon M Hosford
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Sangwon Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Do Soon Kim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jeffrey S Moore
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Interdisplinary Biological Sciences Graduate Program, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Evanston, IL, 60208, USA.
- Robert H. Lurie Comprehensive Cancer Center, Evanston, IL, 60208, USA.
- Simpson Querrey Institute, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University and Biological Engineering, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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10
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Gowland S, Jewett MC. Mobile Translation Systems Generate Genomically Engineered Escherichia coli Cells with Improved Growth Phenotypes. ACS Synth Biol 2022; 11:2969-2978. [PMID: 35951371 PMCID: PMC9990117 DOI: 10.1021/acssynbio.2c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cellular translation is responsible for the synthesis of proteins, a highly diverse class of macromolecules that form the basis of biological function. In Escherichia coli, harnessing and engineering of the biomolecular components of translation, such as ribosomes, transfer RNAs (tRNAs), and aminoacyl-tRNA synthetases, has led to both biotechnology products and an expanded genetic code. However, the engineering potential of molecular translation is hampered by the limited capabilities for rapidly sampling the large genomic space necessary to evolve well-coordinated synthetic translation networks inside cells. To address this limitation, we developed a genome engineering method inspired by the action of mobile genetic elements termed mobilization. Mobilization utilizes the stochastic action of the recombinase flippase (FLP) to generate up to ∼400 million genomic insertions, deletions, or rearrangements at flippase recognition target sites per milliliter of culture per OD in living E. coli cells. As a model, we applied our approach to evolve faster-growing E. coli strains living exclusively off genomically expressed tethered ribosomes. In an iterative "pulse-passaging scheme," we generated genomic libraries of cells via induction of FLP recombinase (pulse) followed by passaging the population without induction of FLP to enrich the resulting population for cells with higher fitness. We observed large structural genomic diversity across these cells, with the fastest growing strains exhibiting a 71% increase in growth rate compared to the ancestral strain. We anticipate that both these strains and the mobilization method will be useful tools for synthetic biology efforts to engineer translation systems.
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Affiliation(s)
- Samuel Gowland
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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11
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Perez JG, Carlson ED, Weisser O, Kofman C, Seki K, Des Soye BJ, Karim AS, Jewett MC. Improving genomically recoded Escherichia coli to produce proteins containing non-canonical amino acids. Biotechnol J 2022; 17:e2100330. [PMID: 34894206 DOI: 10.1002/biot.202100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
Abstract
A genomically recoded Escherichia coli strain that lacks all amber codons and release factor 1 (C321.∆A) enables efficient genetic encoding of chemically diverse non-canonical amino acids (ncAAs) into proteins. While C321.∆A has opened new opportunities in chemical and synthetic biology, this strain has not been optimized for protein production, limiting its utility in widespread industrial and academic applications. To address this limitation, the construction of a series of genomically recoded organisms that are optimized for cellular protein production is described. It is demonstrated that the functional deactivation of nucleases (e.g., rne, endA) and proteases (e.g., lon) increases production of wild-type superfolder green fluorescent protein (sfGFP) and sfGFP containing two ncAAs up to ≈5-fold. Additionally, a genomic IPTG-inducible T7 RNA polymerase (T7RNAP) cassette into these strains is introduced. Using an optimized platform, the ability to introduce two identical N6 -(propargyloxycarbonyl)-L -Lysine residues site specifically into sfGFP with a 17-fold improvement in production relative to the parent strain is demonstrated. The authors envision that their library of organisms will provide the community with multiple options for increased expression of proteins with new and diverse chemistries.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Oliver Weisser
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Benjamin J Des Soye
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois, USA
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Wu Y, Bertran MT, Rowley J, Calder EDD, Joshi D, Walport LJ. Fluorescent Amino Acid Initiated de novo Cyclic Peptides for the Label-Free Assessment of Cell Permeability*. ChemMedChem 2021; 16:3185-3188. [PMID: 34236771 PMCID: PMC8597039 DOI: 10.1002/cmdc.202100315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 11/11/2022]
Abstract
The major obstacle in applying peptides to intracellular targets is their low inherent cell permeability. Standard approaches to attach a fluorophore (e. g. FITC, TAMRA) can change the physicochemical properties of the parent peptide and influence their ability to penetrate and localize in cells. We report a label-free strategy for evaluating the cell permeability of cyclic peptide leads. Fluorescent tryptophan analogues 4-cyanotryptophan (4CNW) and β-(1-azulenyl)-L-alanine (AzAla) were incorporated into in vitro translated macrocyclic peptides by initiator reprogramming. We then demonstrate these efficient blue fluorescent emitters are good tools for monitoring peptide penetration into cells.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
| | - M. Teresa Bertran
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
| | - James Rowley
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
| | - Ewen D. D. Calder
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
| | - Dhira Joshi
- Peptide ChemistryThe Francis Crick InstituteLondonNW1 1ATUK
| | - Louise J. Walport
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
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13
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Kofman C, Lee J, Jewett MC. Engineering molecular translation systems. Cell Syst 2021; 12:593-607. [PMID: 34139167 DOI: 10.1016/j.cels.2021.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/19/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Molecular translation systems provide a genetically encoded framework for protein synthesis, which is essential for all life. Engineering these systems to incorporate non-canonical amino acids (ncAAs) into peptides and proteins has opened many exciting opportunities in chemical and synthetic biology. Here, we review recent advances that are transforming our ability to engineer molecular translation systems. In cell-based systems, new processes to synthesize recoded genomes, tether ribosomal subunits, and engineer orthogonality with high-throughput workflows have emerged. In cell-free systems, adoption of flexizyme technology and cell-free ribosome synthesis and evolution platforms are expanding the limits of chemistry at the ribosome's RNA-based active site. Looking forward, innovations will deepen understanding of molecular translation and provide a path to polymers with previously unimaginable structures and functions.
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Affiliation(s)
- Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Interdisplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA; Simpson Querrey Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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