1
|
Pham Q, Glicksman J, Chatterjee A. Chemical approaches to probe and engineer AAV vectors. NANOSCALE 2024; 16:13820-13833. [PMID: 38978480 PMCID: PMC11271820 DOI: 10.1039/d4nr01300j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
Adeno-associated virus (AAV) has emerged as the most promising vector for in vivo human gene therapy, with several therapeutic approvals in the last few years and countless more under development. Underlying this remarkable success are several attractive features that AAV offers, including lack of pathogenicity, low immunogenicity, long-term gene expression without genomic integration, the ability to infect both dividing and non-dividing cells, etc. However, the commonly used wild-type AAV capsids in therapeutic development present significant challenges, including inadequate tissue specificity and the need for large doses to attain therapeutic effectiveness, raising safety concerns. Additionally, significant preexisting adaptive immunity against most natural capsids, and the development of such anti-capsid immunity after the first treatment, represent major challenges. Strategies to engineer the AAV capsid are critically needed to address these challenges and unlock the full promise of AAV gene therapy. Chemical modification of the AAV capsid has recently emerged as a powerful new approach to engineer its properties. Unlike genetic strategies, which can be more disruptive to the delicate capsid assembly and packaging processes, "late-stage" chemical modification of the assembled capsid-whether at natural amino acid residues or site-specifically installed noncanonical amino acid residues-often enables a versatile approach to introducing new properties to the capsid. This review summarizes the significant recent progress in AAV capsid engineering strategies, with a particular focus on chemical modifications in advancing the next generation of AAV-based gene therapies.
Collapse
Affiliation(s)
- Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Jake Glicksman
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| |
Collapse
|
2
|
Huang RL, Jewel D, Kelemen RE, Pham Q, Yared TJ, Wang S, Singha Roy SJ, Huang Z, Levinson SD, Sundaresh B, Miranda SE, van Opijnen T, Chatterjee A. Directed Evolution of a Bacterial Leucyl tRNA in Mammalian Cells for Enhanced Noncanonical Amino Acid Mutagenesis. ACS Synth Biol 2024; 13:2141-2149. [PMID: 38904157 DOI: 10.1021/acssynbio.4c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The Escherichia coli leucyl-tRNA synthetase (EcLeuRS)/tRNAEcLeu pair has been engineered to genetically encode a structurally diverse group of enabling noncanonical amino acids (ncAAs) in eukaryotes, including those with bioconjugation handles, environment-sensitive fluorophores, photocaged amino acids, and native post-translational modifications. However, the scope of this toolbox in mammalian cells is limited by the poor activity of tRNAEcLeu. Here, we overcome this limitation by evolving tRNAEcLeu directly in mammalian cells by using a virus-assisted selection scheme. This directed evolution platform was optimized for higher throughput such that the entire acceptor stem of tRNAEcLeu could be simultaneously engineered, which resulted in the identification of several variants with remarkably improved efficiency for incorporating a wide range of ncAAs. The advantage of the evolved leucyl tRNAs was demonstrated by expressing ncAA mutants in mammalian cells that were challenging to express before using the wild-type tRNAEcLeu, by creating viral vectors that facilitated ncAA mutagenesis at a significantly lower dose and by creating more efficient mammalian cell lines stably expressing the ncAA-incorporation machinery.
Collapse
Affiliation(s)
- Rachel L Huang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Delilah Jewel
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Rachel E Kelemen
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Quan Pham
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tarah J Yared
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Shu Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Zeyi Huang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Samantha D Levinson
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Bharathi Sundaresh
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
3
|
Ficaretta ED, Singha Roy SJ, Voss L, Chatterjee A. Native Aminoacyl-tRNA Synthetase/tRNA Pair Drives Highly Efficient Noncanonical Amino Acid Incorporation in Escherichia coli. ACS Chem Biol 2024; 19:1563-1569. [PMID: 38913984 DOI: 10.1021/acschembio.4c00221] [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] [Indexed: 06/26/2024]
Abstract
Site-specific noncanonical amino acid (ncAA) mutagenesis in living cells has traditionally relied on heterologous, nonsense-suppressing aminoacyl-tRNA synthetase (aaRS)/tRNA pairs that do not cross-react with their endogenous counterparts. Such heterologous pairs often perform suboptimally in a foreign host cell since they were not evolutionarily optimized to function in the foreign environment. This suboptimal performance restricts the number of ncAAs that can be simultaneously incorporated into a protein. Here, we show that the use of an endogenous aaRS/tRNA pair to drive ncAA incorporation can offer a potential solution to this limitation. To this end, we developed an engineered Escherichia coli strain (ATMY-C321), wherein the endogenous tyrosyl-tRNA synthetase (TyrRS)/tRNA pair has been functionally replaced with an archaeal counterpart, and the release factor 1 has been removed to eliminate competing termination at the UAG nonsense codons. The endogenous TyrRS/tRNACUATyr pair exhibits remarkably efficient nonsense suppression in the resulting cell, relative to established orthogonal ncAA-incorporation systems in E. coli, allowing the incorporation of an ncAA at up to 10 contiguous sites in a reporter protein. Our work highlights the limitations of orthogonal translation systems using heterologous aaRS/tRNA pairs and offers a potential alternative involving the use of endogenous pairs.
Collapse
Affiliation(s)
- Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Soumya Jyoti Singha Roy
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Lena Voss
- 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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Awawdeh A, Radecki AA, Vargas-Rodriguez O. Suppressor tRNAs at the interface of genetic code expansion and medicine. Front Genet 2024; 15:1420331. [PMID: 38798701 PMCID: PMC11116698 DOI: 10.3389/fgene.2024.1420331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Suppressor transfer RNAs (sup-tRNAs) are receiving renewed attention for their promising therapeutic properties in treating genetic diseases caused by nonsense mutations. Traditionally, sup-tRNAs have been created by replacing the anticodon sequence of native tRNAs with a suppressor sequence. However, due to their complex interactome, considering other structural and functional tRNA features for design and engineering can yield more effective sup-tRNA therapies. For over 2 decades, the field of genetic code expansion (GCE) has created a wealth of knowledge, resources, and tools to engineer sup-tRNAs. In this Mini Review, we aim to shed light on how existing knowledge and strategies to develop sup-tRNAs for GCE can be adopted to accelerate the discovery of efficient and specific sup-tRNAs for medical treatment options. We highlight methods and milestones and discuss how these approaches may enlighten the research and development of tRNA medicines.
Collapse
Affiliation(s)
| | | | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, Farmington, CT, United States
| |
Collapse
|
6
|
Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
Collapse
Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| |
Collapse
|
7
|
Osgood AO, Roy SJS, Koo D, Gu R, Chatterjee A. A Genetically Encoded Photocaged Cysteine for Facile Site-Specific Introduction of Conjugation-Ready Thiol Residues in Antibodies. Bioconjug Chem 2024; 35:457-464. [PMID: 38548654 DOI: 10.1021/acs.bioconjchem.3c00513] [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] [Indexed: 04/18/2024]
Abstract
Antibody-drug conjugates (ADCs) have emerged as a powerful class of anticancer therapeutics that enable the selective delivery of toxic payloads into target cells. There is increasing appreciation for the importance of synthesizing such ADCs in a defined manner where the payload is attached at specific permissive sites on the antibody with a defined drug to antibody ratio. Additionally, the ability to systematically alter the site of attachment is important to fine-tune the therapeutic properties of the ADC. Engineered cysteine residues have been used to achieve such site-specific programmable attachment of drug molecules onto antibodies. However, engineered cysteine residues on antibodies often get "disulfide-capped" during secretion and require reductive regeneration prior to conjugation. This reductive step also reduces structurally important disulfide bonds in the antibody itself, which must be regenerated through oxidation. This multistep, cumbersome process reduces the efficiency of conjugation and presents logistical challenges. Additionally, certain engineered cysteine sites are resistant to reductive regeneration, limiting their utility and the overall scope of this conjugation strategy. In this work, we utilize a genetically encoded photocaged cysteine residue that can be site-specifically installed into the antibody. This photocaged amino acid can be efficiently decaged using light, revealing a free cysteine residue available for conjugation without disrupting the antibody structure. We show that this ncAA can be incorporated at several positions within full-length recombinant trastuzumab and decaged efficiently. We further used this method to generate a functional ADC site-specifically modified with monomethyl auristatin F (MMAF).
Collapse
Affiliation(s)
- Arianna O Osgood
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Soumya Jyoti Singha Roy
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - David Koo
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Renpeng Gu
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
8
|
Loynd C, Singha Roy SJ, Ovalle VJ, Canarelli SE, Mondal A, Jewel D, Ficaretta ED, Weerapana E, Chatterjee A. Electrochemical labelling of hydroxyindoles with chemoselectivity for site-specific protein bioconjugation. Nat Chem 2024; 16:389-397. [PMID: 38082177 PMCID: PMC10932882 DOI: 10.1038/s41557-023-01375-y] [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: 05/23/2022] [Accepted: 10/18/2023] [Indexed: 02/06/2024]
Abstract
Electrochemistry has recently emerged as a powerful approach in small-molecule synthesis owing to its numerous attractive features, including precise control over the fundamental reaction parameters, mild reaction conditions and innate scalability. Even though these advantages also make it an attractive strategy for chemoselective modification of complex biomolecules such as proteins, such applications remain poorly developed. Here we report an electrochemically promoted coupling reaction between 5-hydroxytryptophan (5HTP) and simple aromatic amines-electrochemical labelling of hydroxyindoles with chemoselectivity (eCLIC)-that enables site-specific labelling of full-length proteins under mild conditions. Using genetic code expansion technology, the 5HTP residue can be incorporated into predefined sites of a recombinant protein expressed in either prokaryotic or eukaryotic hosts for subsequent eCLIC labelling. We used the eCLIC reaction to site-specifically label various recombinant proteins, including a full-length human antibody. Furthermore, we show that eCLIC is compatible with strain-promoted alkyne-azide and alkene-tetrazine click reactions, enabling site-specific modification of proteins at two different sites with distinct labels.
Collapse
Affiliation(s)
- Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | | | - Vincent J Ovalle
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Sarah E Canarelli
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Atanu Mondal
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA.
| |
Collapse
|
9
|
Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Malley K, Pham Q, Loynd C, Huang Z, van Opijnen T, Chatterjee A. Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis. Angew Chem Int Ed Engl 2024; 63:e202316428. [PMID: 38279536 PMCID: PMC10922736 DOI: 10.1002/anie.202316428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/28/2024]
Abstract
Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus-assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base-pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem of M. mazei pyrrolysyl tRNA (tRNAPyl ), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell-lines for ncAA mutagenesis.
Collapse
Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel L Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Kaitlin Malley
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| |
Collapse
|
10
|
Erickson SB, Pham Q, Cao X, Glicksman J, Kelemen RE, Shahraeini SS, Bodkin S, Kiyam Z, Chatterjee A. Precise Manipulation of the Site and Stoichiometry of Capsid Modification Enables Optimization of Functional Adeno-Associated Virus Conjugates. Bioconjug Chem 2024; 35:64-71. [PMID: 38103182 PMCID: PMC10924286 DOI: 10.1021/acs.bioconjchem.3c00411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The ability to engineer adeno-associated virus (AAV) vectors for targeted transduction of specific cell types is critically important to fully harness their potential for human gene therapy. A promising approach to achieve this objective involves chemically attaching retargeting ligands onto the virus capsid. Site-specific incorporation of a bioorthogonal noncanonical amino acid (ncAA) into the AAV capsid proteins provides a particularly attractive strategy to introduce such modifications with exquisite precision. In this study, we show that using ncAA mutagenesis, it is possible to systematically alter the attachment site of a retargeting ligand (cyclic-RGD) on the AAV capsid to create diverse conjugate architectures and that the site of attachment heavily impacts the retargeting efficiency. We further demonstrate that the performance of these AAV conjugates is highly sensitive to the stoichiometry of capsid labeling (labels per capsid), with an intermediate labeling density providing optimal activity for cRGD-mediated retargeting. Finally, we developed a technology to more precisely control the number of attachment sites per AAV capsid by selectively incorporating an ncAA into the minor capsid proteins with high fidelity and efficiency, such that AAV conjugates with varying stoichiometry can be synthesized. Together, this platform provides unparalleled control over the site and stoichiometry of capsid modification, which will enable the development of next-generation AAV vectors tailored with desirable attributes.
Collapse
Affiliation(s)
| | | | - Xiaofu Cao
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Jake Glicksman
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Rachel E. Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Seyed S. Shahraeini
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Sebastian Bodkin
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Zainab Kiyam
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
11
|
Feng Y, Lee J, Yang L, Hilton MB, Morris K, Seaman S, Edupuganti VVSR, Hsu KS, Dower C, Yu G, So D, Bajgain P, Zhu Z, Dimitrov DS, Patel NL, Robinson CM, Difilippantonio S, Dyba M, Corbel A, Basuli F, Swenson RE, Kalen JD, Suthe SR, Hussain M, Italia JS, Souders CA, Gao L, Schnermann MJ, St Croix B. Engineering CD276/B7-H3-targeted antibody-drug conjugates with enhanced cancer-eradicating capability. Cell Rep 2023; 42:113503. [PMID: 38019654 PMCID: PMC10872261 DOI: 10.1016/j.celrep.2023.113503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
CD276/B7-H3 represents a promising target for cancer therapy based on widespread overexpression in both cancer cells and tumor-associated stroma. In previous preclinical studies, CD276 antibody-drug conjugates (ADCs) exploiting a talirine-type pyrrolobenzodiazepine (PBD) payload showed potent activity against various solid tumors but with a narrow therapeutic index and dosing regimen higher than that tolerated in clinical trials using other antibody-talirine conjugates. Here, we describe the development of a modified talirine PBD-based fully human CD276 ADC, called m276-SL-PBD, that is cross-species (human/mouse) reactive and can eradicate large 500-1,000-mm3 triple-negative breast cancer xenografts at doses 10- to 40-fold lower than the maximum tolerated dose. By combining CD276 targeting with judicious genetic and chemical ADC engineering, improved ADC purification, and payload sensitivity screening, these studies demonstrate that the therapeutic index of ADCs can be substantially increased, providing an advanced ADC development platform for potent and selective targeting of multiple solid tumor types.
Collapse
Affiliation(s)
- Yang Feng
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Jaewon Lee
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Liping Yang
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Mary Beth Hilton
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA; Basic Research Program, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Karen Morris
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA; Basic Research Program, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Steven Seaman
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | | | - Kuo-Sheng Hsu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Christopher Dower
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Guojun Yu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Daeho So
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Pradip Bajgain
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Zhongyu Zhu
- Protein Interactions Section, Cancer and Inflammation Program, NCI, NIH, Frederick, MD 21702, USA
| | - Dimiter S Dimitrov
- Protein Interactions Section, Cancer and Inflammation Program, NCI, NIH, Frederick, MD 21702, USA
| | - Nimit L Patel
- Small Animal Imaging Program, FNLCR, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Christina M Robinson
- Animal Research Technical Support, FNLCR, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Simone Difilippantonio
- Animal Research Technical Support, FNLCR, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Marzena Dyba
- Biophysics Resource in the Center for Structural Biology, NCI, NIH, Frederick, MD, USA
| | - Amanda Corbel
- Invention Development Program, Technology Transfer Center, NCI, Frederick, MD 21701, USA
| | - Falguni Basuli
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, NIH, Rockville, MD 20850, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, NIH, Rockville, MD 20850, USA
| | - Joseph D Kalen
- Small Animal Imaging Program, FNLCR, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | | | | | | | | | - Ling Gao
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Martin J Schnermann
- Organic Synthesis Section, Chemical Biology Laboratory, CCR, NCI, Frederick, MD 21702, USA
| | - Brad St Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| |
Collapse
|
12
|
Singha Roy SJ, Loynd C, Jewel D, Canarelli SE, Ficaretta ED, Pham QA, Weerapana E, Chatterjee A. Photoredox-Catalyzed Labeling of Hydroxyindoles with Chemoselectivity (PhotoCLIC) for Site-Specific Protein Bioconjugation. Angew Chem Int Ed Engl 2023; 62:e202300961. [PMID: 37219923 PMCID: PMC10330600 DOI: 10.1002/anie.202300961] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Indexed: 05/24/2023]
Abstract
We have developed a novel visible-light-catalyzed bioconjugation reaction, PhotoCLIC, that enables chemoselective attachment of diverse aromatic amine reagents onto a site-specifically installed 5-hydroxytryptophan residue (5HTP) on full-length proteins of varied complexity. The reaction uses catalytic amounts of methylene blue and blue/red light-emitting diodes (455/650 nm) for rapid site-specific protein bioconjugation. Characterization of the PhotoCLIC product reveals a unique structure formed likely through a singlet oxygen-dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and its compatibility with strain-promoted azide-alkyne click reaction, enables site-specific dual-labeling of a target protein.
Collapse
Affiliation(s)
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Sarah E Canarelli
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Quan A Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| |
Collapse
|
13
|
Osgood AO, Zheng Y, Roy SJS, Biris N, Hussain M, Loynd C, Jewel D, Italia JS, Chatterjee A. An Efficient Opal-Suppressor Tryptophanyl Pair Creates New Routes for Simultaneously Incorporating up to Three Distinct Noncanonical Amino Acids into Proteins in Mammalian Cells. Angew Chem Int Ed Engl 2023; 62:e202219269. [PMID: 36905325 PMCID: PMC10133189 DOI: 10.1002/anie.202219269] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Site-specific incorporation of multiple distinct noncanonical amino acids (ncAAs) into proteins in mammalian cells is a promising technology, where each ncAA must be assigned to a different orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pair that reads a distinct nonsense codon. Available pairs suppress TGA or TAA codons at a considerably lower efficiency than TAG, limiting the scope of this technology. Here we show that the E. coli tryptophanyl (EcTrp) pair is an excellent TGA-suppressor in mammalian cells, which can be combined with the three other established pairs to develop three new routes for dual-ncAA incorporation. Using these platforms, we site-specifically incorporated two different bioconjugation handles into an antibody with excellent efficiency, and subsequently labeled it with two distinct cytotoxic payloads. Additionally, we combined the EcTrp pair with other pairs to site-specifically incorporate three distinct ncAAs into a reporter protein in mammalian cells.
Collapse
Affiliation(s)
- Arianna O Osgood
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Yunan Zheng
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | | | | | - Myer Hussain
- BrickBio, Inc., 600 Winter St, Waltham, MA, 02451, USA
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | | | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| |
Collapse
|
14
|
Puzzo F, Zhang C, Powell Gray B, Zhang F, Sullenger BA, Kay MA. Aptamer-programmable adeno-associated viral vectors as a novel platform for cell-specific gene transfer. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:383-397. [PMID: 36817723 PMCID: PMC9929486 DOI: 10.1016/j.omtn.2023.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Adeno-associated viruses (AAVs) are commonly used for in vivo gene therapy. Nevertheless, the wide tropism that characterizes these vectors limits specific targeting to a particular cell type or tissue. Here, we developed new chemically modified AAV vectors (Nε-AAVs) displaying a single site substitution on the capsid surface for post-production vector engineering through biorthogonal copper-free click chemistry. We were able to identify AAV vectors that would tolerate the unnatural amino acid substitution on the capsid without disrupting their packaging efficiency. We functionalized the Nε-AAVs through conjugation with DNA (AS1411) or RNA (E3) aptamers or with a folic acid moiety (FA). E3-, AS1411-, and FA-AAVs showed on average a 3- to 9-fold increase in transduction compared with their non-conjugated counterparts in different cancer cell lines. Using specific competitors, we established ligand-specific transduction. In vivo studies confirmed the selective uptake of FA-AAV and AS1411-AAV without off-target transduction in peripheral organs. Overall, the high versatility of these novel Nε-AAVs might pave the way to tailoring gene therapy vectors toward specific types of cells both for ex vivo and in vivo applications.
Collapse
Affiliation(s)
- Francesco Puzzo
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chuanling Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bethany Powell Gray
- Department of Surgery, Duke University School of Medicine, Durham, NC 27705, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Bruce A. Sullenger
- Department of Surgery, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mark A. Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
15
|
Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Cao X, Malley K, Huang Z, Pasha M, Anthony J, van Opijnen T, Chatterjee A. Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells. Nat Methods 2023; 20:95-103. [PMID: 36550276 PMCID: PMC9855281 DOI: 10.1038/s41592-022-01706-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Site-specific incorporation of unnatural amino acids (Uaas) in living cells relies on engineered aminoacyl-transfer RNA synthetase-tRNA pairs borrowed from a distant domain of life. Such heterologous suppressor tRNAs often have poor intrinsic activity, presumably due to suboptimal interaction with a non-native translation system. This limitation can be addressed in Escherichia coli using directed evolution. However, no suitable selection system is currently available to do the same in mammalian cells. Here we report virus-assisted directed evolution of tRNAs (VADER) in mammalian cells, which uses a double-sieve selection scheme to facilitate single-step enrichment of active yet orthogonal tRNA mutants from naive libraries. Using VADER we developed improved mutants of Methanosarcina mazei pyrrolysyl-tRNA, as well as a bacterial tyrosyl-tRNA. We also show that the higher activity of the most efficient mutant pyrrolysyl-tRNA is specific for mammalian cells, alluding to an improved interaction with the unique mammalian translation apparatus.
Collapse
Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | | | - Rachel L Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | | | - Xiaofu Cao
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Kaitlin Malley
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Muhammad Pasha
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | |
Collapse
|
16
|
Stieglitz JT, Van Deventer JA. High-Throughput Aminoacyl-tRNA Synthetase Engineering for Genetic Code Expansion in Yeast. ACS Synth Biol 2022; 11:2284-2299. [PMID: 35793554 PMCID: PMC10065163 DOI: 10.1021/acssynbio.1c00626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein expression with genetically encoded noncanonical amino acids (ncAAs) benefits a broad range of applications, from the discovery of biological therapeutics to fundamental biological studies. A major factor limiting the use of ncAAs is the lack of orthogonal translation systems (OTSs) that support efficient genetic code expansion at repurposed stop codons. Aminoacyl-tRNA synthetases (aaRSs) have been extensively evolved in Escherichia coli but are not always orthogonal in eukaryotes. In this work, we use a yeast display-based ncAA incorporation reporter platform with fluorescence-activated cell sorting to screen libraries of aaRSs in high throughput for (1) the incorporation of ncAAs not previously encoded in yeast; (2) the improvement of the performance of an existing aaRS; (3) highly selective OTSs capable of discriminating between closely related ncAA analogues; and (4) OTSs exhibiting enhanced polyspecificity to support translation with structurally diverse sets of ncAAs. The number of previously undiscovered aaRS variants we report in this work more than doubles the total number of translationally active aaRSs available for genetic code manipulation in yeast. The success of myriad screening strategies has important implications related to the fundamental properties and evolvability of aaRSs. Furthermore, access to OTSs with diverse activities and specific or polyspecific properties is invaluable for a range of applications within chemical biology, synthetic biology, and protein engineering.
Collapse
Affiliation(s)
- Jessica T Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| |
Collapse
|
17
|
Grasso K, Singha Roy SJ, Osgood AO, Yeo MJR, Soni C, Hillenbrand CM, Ficaretta ED, Chatterjee A. A Facile Platform to Engineer Escherichia coli Tyrosyl-tRNA Synthetase Adds New Chemistries to the Eukaryotic Genetic Code, Including a Phosphotyrosine Mimic. ACS CENTRAL SCIENCE 2022; 8:483-492. [PMID: 35559426 PMCID: PMC9088295 DOI: 10.1021/acscentsci.1c01465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Indexed: 06/03/2023]
Abstract
The Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNAEcTyr pair offers an attractive platform for genetically encoding new noncanonical amino acids (ncAA) in eukaryotes. However, challenges associated with a eukaryotic selection system, which is needed to engineer the platform, have impeded its success in the past. Recently, using a facile E. coli-based selection system, we showed that EcTyrRS could be engineered in a strain where the endogenous tyrosyl pair was substituted with an archaeal counterpart. However, significant cross-reactivity between the UAG-suppressing tRNACUA EcTyr and the bacterial glutaminyl-tRNA synthetase limited the scope of this strategy, preventing the selection of moderately active EcTyrRS mutants. Here we report an engineered tRNACUA EcTyr that overcomes this cross-reactivity. Optimized selection systems based on this tRNA enabled the efficient enrichment of both strongly and weakly active ncAA-selective EcTyrRS mutants. We also developed a wide dynamic range (WiDR) antibiotic selection to further enhance the activities of the weaker first-generation EcTyrRS mutants. We demonstrated the utility of our platform by developing several new EcTyrRS mutants that efficiently incorporated useful ncAAs in mammalian cells, including photoaffinity probes, bioconjugation handles, and a nonhydrolyzable mimic of phosphotyrosine.
Collapse
|
18
|
Incorporating, Quantifying, and Leveraging Noncanonical Amino Acids in Yeast. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:377-432. [PMID: 35094338 DOI: 10.1007/978-1-0716-1811-0_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetic code expansion has allowed for extraordinary advances in enhancing protein chemical diversity and functionality, but there remains a critical need for understanding and engineering genetic code expansion systems for improved efficiency. Incorporation of noncanonical amino acids (ncAAs) at stop codons provides a site-specific method for introducing unique chemistry into proteins, though often at reduced yields compared to wild-type proteins. A powerful platform for ncAA incorporation supports both the expression and evaluation of chemically diverse proteins for a broad range of applications. In yeast, ncAAs have been used to study dynamic cellular processes such as protein-protein interactions and also allow for exploration of eukaryotic-specific biology such as epigenetics. Furthermore, yeast display is an advantageous technology for engineering and screening the properties of proteins in high throughput. The protocols presented in this chapter describe detailed methods for the yeast-based genetic encoding of ncAAs in proteins intracellularly or on the yeast surface. In addition, methods are presented for modifying proteins on the yeast surface using bioorthogonal chemical reactions and evaluating reaction efficiency. Finally, protocols are included for the preparation of libraries that involve genetic code expansion. Libraries of proteins that contain ncAAs or libraries of the cellular machinery required to encode ncAAs can be constructed and screened in high throughput for many biological and chemical applications. Efficient incorporation of ncAAs facilitates elucidation of fundamental eukaryotic biology and advances tools for enzyme and genome engineering to evolve host cells that are better able to accommodate alternative genetic codes.
Collapse
|
19
|
Abstract
The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
Collapse
Affiliation(s)
- Christian S. Diercks
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - David A. Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - Peter G. Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Lead contact
| |
Collapse
|
20
|
Romesberg FE. Creation, Optimization, and Use of Semi-Synthetic Organisms that Store and Retrieve Increased Genetic Information. J Mol Biol 2021; 434:167331. [PMID: 34710400 DOI: 10.1016/j.jmb.2021.167331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/18/2022]
Abstract
With few exceptions, natural proteins are built from only 20 canonical (proteogenic) amino acids which limits the functionality and accordingly the properties they can possess. Genetic code expansion, i.e. the creation of codons and the machinery needed to assign them to non-canonical amino acids (ncAAs), promises to enable the discovery of proteins with novel properties that are otherwise difficult or impossible to obtain. One approach to expanding the genetic code is to expand the genetic alphabet via the development of unnatural nucleotides that pair to form an unnatural base pair (UBP). Semi-synthetic organisms (SSOs), i.e. organisms that stably maintain the UBP, transcribe its component nucleotides into RNA, and use it to translate proteins, would have available to them new codons and the anticodons needed to assign them to ncAAs. This review summarizes the development of a family of UBPs, their use to create SSOs, and the optimization and application of the SSOs to produce candidate therapeutic proteins with improved properties that are now undergoing evaluation in clinical trials.
Collapse
|
21
|
Ficaretta ED, Wrobel CJJ, Roy SJS, Erickson SB, Italia JS, Chatterjee A. A Robust Platform for Unnatural Amino Acid Mutagenesis in E. coli Using the Bacterial Tryptophanyl-tRNA synthetase/tRNA pair. J Mol Biol 2021; 434:167304. [PMID: 34655653 PMCID: PMC9005579 DOI: 10.1016/j.jmb.2021.167304] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/13/2023]
Abstract
We report the development of a robust user-friendly Escherichia coli (E. coli) expression system, derived from the BL21(DE3) strain, for site-specifically incorporating unnatural amino acids (UAAs) into proteins using engineered E. coli tryptophanyl-tRNA synthetase (EcTrpRS)-tRNATrp pairs. This was made possible by functionally replacing the endogenous EcTrpRS-tRNATrp pair in BL21(DE3) E. coli with an orthogonal counterpart from Saccharomyces cerevisiae, and reintroducing it into the resulting altered translational machinery tryptophanyl (ATMW-BL21) E. coli strain as an orthogonal nonsense suppressor. The resulting expression system benefits from the favorable characteristics of BL21(DE3) as an expression host, and is compatible with the broadly used T7-driven recombinant expression system. Furthermore, the vector expressing the nonsense-suppressing engineered EcTrpRS-tRNATrp pair was systematically optimized to significantly enhance the incorporation efficiency of various tryptophan analogs. Together, the improved strain and the optimized suppressor plasmids enable efficient UAA incorporation (up to 65% of wild-type levels) into several different proteins. This robust and user-friendly platform will significantly expand the scope of the genetically encoded tryptophan-derived UAAs.
Collapse
Affiliation(s)
- Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Chester J J Wrobel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Soumya J S Roy
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Sarah B Erickson
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| |
Collapse
|
22
|
Lyu Z, Genereux JC. Methodologies for Measuring Protein Trafficking across Cellular Membranes. Chempluschem 2021; 86:1397-1415. [PMID: 34636167 DOI: 10.1002/cplu.202100304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/19/2021] [Indexed: 12/11/2022]
Abstract
Nearly all proteins are synthesized in the cytosol. The majority of this proteome must be trafficked elsewhere, such as to membranes, to subcellular compartments, or outside of the cell. Proper trafficking of nascent protein is necessary for protein folding, maturation, quality control and cellular and organismal health. To better understand cellular biology, molecular and chemical technologies to properly characterize protein trafficking (and mistrafficking) have been developed and applied. Herein, we take a biochemical perspective to review technologies that enable spatial and temporal measurement of protein distribution, focusing on both the most widely adopted methodologies and exciting emerging approaches.
Collapse
Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
| |
Collapse
|
23
|
Yang Y, Luo S, Huang J, Xiao Y, Fu Y, Liu W, Yin H. Photoactivation of Innate Immunity Receptor TLR8 in Live Mammalian Cells by Genetic Encoding of Photocaged Tyrosine. Chembiochem 2021; 23:e202100344. [PMID: 34460982 DOI: 10.1002/cbic.202100344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Indexed: 11/10/2022]
Abstract
The effectiveness of innate immune responses relies on an intricate balance between activation and regulation. TLR8, a member of the Toll-like receptor (TLR) family, plays a fundamental role in host defense by sensing viral single-stranded RNAs (ssRNAs). However, the molecular recognition and regulatory mechanism of TLR8 is not fully understood, especially in a whole-cell environment. Here, we engineer the first light-controllable TLR8 model by genetically encoding a photocaged tyrosine, NBY, into specific sites of TLR8. In the caged forms, the activity of TLR8 is masked but can be restored upon decaging by exposure to UV light. To explain the mechanism clearly, we divide the sites with light responsiveness into three groups. They can separately block the ligands that bind to the pockets of TLR8, change the interaction modes between two TLR8 protomers, and interfere with the interactions between TLR8 cytosolic domains with its downstream adaptor. Specifically, we use this chemical caging strategy to probe and evaluate the function of several tyrosine sites located at the interface of TLR8 homodimers with a previously unknown regulatory mode, which may provide a new strategy for TLR8 modulator development. Effects on downstream signaling pathways are monitored at the transcriptional and translational levels in various cell lines. By photoactivating specific cells within a larger population, this powerful tool can provide novel mechanistic insights, with potential in biotechnological and pharmaceutical applications.
Collapse
Affiliation(s)
- Yi Yang
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China
| | - Shuchen Luo
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China
| | - Jian Huang
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China
| | - Yu Xiao
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China.,Zhujiang Hospital, Laboratory of Medicine Center, Southern Medical University, Guangzhou, 510282, P. R. China
| | - Yixuan Fu
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China
| | - Wei Liu
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China
| | - Hang Yin
- Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China
| |
Collapse
|
24
|
Hendel SJ, Shoulders MD. Directed evolution in mammalian cells. Nat Methods 2021; 18:346-357. [PMID: 33828274 DOI: 10.1038/s41592-021-01090-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Directed evolution experiments are typically carried out using in vitro systems, bacteria, or yeast-even when the goal is to probe or modulate mammalian biology. Performing directed evolution in systems that do not match the intended mammalian environment severely constrains the scope and functionality of the targets that can be evolved. We review new platforms that are now making it possible to use the mammalian cell itself as the setting for directed evolution and present an overview of frontier challenges and high-impact targets for this approach.
Collapse
Affiliation(s)
- Samuel J Hendel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
25
|
Reinkemeier CD, Koehler C, Sauter PF, Shymanska NV, Echalier C, Rutkowska A, Will DW, Schultz C, Lemke EA. Synthesis and Evaluation of Novel Ring-Strained Noncanonical Amino Acids for Residue-Specific Bioorthogonal Reactions in Living Cells. Chemistry 2021; 27:6094-6099. [PMID: 33577120 PMCID: PMC8049044 DOI: 10.1002/chem.202100322] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 12/13/2022]
Abstract
Bioorthogonal reactions are ideally suited to selectively modify proteins in complex environments, even in vivo. Kinetics and product stability of these reactions are crucial parameters to evaluate their usefulness for specific applications. Strain promoted inverse electron demand Diels–Alder cycloadditions (SPIEDAC) between tetrazines and strained alkenes or alkynes are particularly popular, as they allow ultrafast labeling inside cells. In combination with genetic code expansion (GCE)‐a method that allows to incorporate noncanonical amino acids (ncAAs) site‐specifically into proteins in vivo. These reactions enable residue‐specific fluorophore attachment to proteins in living mammalian cells. Several SPIEDAC capable ncAAs have been presented and studied under diverse conditions, revealing different instabilities ranging from educt decomposition to product loss due to β‐elimination. To identify which compounds yield the best labeling inside living mammalian cells has frequently been difficult. In this study we present a) the synthesis of four new SPIEDAC reactive ncAAs that cannot undergo β‐elimination and b) a fluorescence flow cytometry based FRET‐assay to measure reaction kinetics inside living cells. Our results, which at first sight can be seen conflicting with some other studies, capture GCE‐specific experimental conditions, such as long‐term exposure of the ring‐strained ncAA to living cells, that are not taken into account in other assays.
Collapse
Affiliation(s)
- Christopher D. Reinkemeier
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
| | - Christine Koehler
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | - Paul F. Sauter
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | | | - Cecile Echalier
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
| | - Anna Rutkowska
- Cellzome GmbHGlaxoSmithKlineMeyerhofstrasse 169117HeidelbergGermany
| | - David W. Will
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health & Science University (OHSU)PortlandOregon97239-3098USA
| | - Edward A. Lemke
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
| |
Collapse
|
26
|
Manandhar M, Chun E, Romesberg FE. Genetic Code Expansion: Inception, Development, Commercialization. J Am Chem Soc 2021; 143:4859-4878. [DOI: 10.1021/jacs.0c11938] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Miglena Manandhar
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | - Eugene Chun
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | | |
Collapse
|
27
|
Ozer E, Alfonta L. Genetic Code Expansion of Vibrio natriegens. Front Bioeng Biotechnol 2021; 9:594429. [PMID: 33718334 PMCID: PMC7953155 DOI: 10.3389/fbioe.2021.594429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has been considered as the most used model bacteria in the majority of studies for several decades. However, a new, faster chassis for synthetic biology is emerging in the form of the fast-growing gram-negative bacterium Vibrio natriegens. Different methodologies, well established in E. coli, are currently being adapted for V. natriegens in the hope to enable a much faster platform for general molecular biology studies. Amongst the vast technologies available for E. coli, genetic code expansion, the incorporation of unnatural amino acids into proteins, serves as a robust tool for protein engineering and biorthogonal modifications. Here we designed and adapted the genetic code expansion methodology for V. natriegens and demonstrate an unnatural amino acid incorporation into a protein for the first time in this organism.
Collapse
Affiliation(s)
- Eden Ozer
- Department of Life Sciences, Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lital Alfonta
- Department of Life Sciences, Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| |
Collapse
|
28
|
Grasso KT, Yeo MJR, Hillenbrand CM, Ficaretta ED, Italia JS, Huang RL, Chatterjee A. Structural Robustness Affects the Engineerability of Aminoacyl-tRNA Synthetases for Genetic Code Expansion. Biochemistry 2021; 60:489-493. [PMID: 33560840 DOI: 10.1021/acs.biochem.1c00056] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to engineer the substrate specificity of natural aminoacyl-tRNA synthetase/tRNA pairs facilitates the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins. The Methanocaldococcus jannaschii-derived tyrosyl-tRNA synthetase (MjTyrRS)/tRNA pair has been engineered to incorporate numerous ncAAs into protein expressed in bacteria. However, it cannot be used in eukaryotic cells due to cross-reactivity with its host counterparts. The Escherichia coli-derived tyrosyl-tRNA synthetase (EcTyrRS)/tRNA pair offers a suitable alternative to this end, but a much smaller subset of ncAAs have been genetically encoded using this pair. Here we report that this discrepancy, at least partly, stems from the structural robustness of EcTyrRS being lower than that of MjTyrRS. We show that the thermostability of engineered TyrRS mutants is generally significantly lower than those of their wild-type counterparts. Derived from a thermophilic archaeon, MjTyrRS is a remarkably sturdy protein and tolerates extensive active site engineering without a catastrophic loss of stability at physiological temperature. In contrast, EcTyrRS exhibits significantly lower thermostability, rendering some of its engineered mutants insufficiently stable at physiological temperature. Our observations identify the structural robustness of an aaRS as an important factor that significantly influences how extensively it can be engineered. To overcome this limitation, we have further developed chimeras between EcTyrRS and its homologue from a thermophilic bacterium, which offer an optimal balance between thermostability and activity. We show that the chimeric bacterial TyrRSs show enhanced tolerance for destabilizing active site mutations, providing a potentially more engineerable platform for genetic code expansion.
Collapse
Affiliation(s)
- Katherine T Grasso
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Megan J R Yeo
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Christen M Hillenbrand
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Rachel L Huang
- 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
| |
Collapse
|
29
|
Site-specific incorporation of citrulline into proteins in mammalian cells. Nat Commun 2021; 12:45. [PMID: 33398026 PMCID: PMC7782748 DOI: 10.1038/s41467-020-20279-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/20/2020] [Indexed: 12/02/2022] Open
Abstract
Citrullination is a post-translational modification (PTM) of arginine that is crucial for several physiological processes, including gene regulation and neutrophil extracellular trap formation. Despite recent advances, studies of protein citrullination remain challenging due to the difficulty of accessing proteins homogeneously citrullinated at a specific site. Herein, we report a technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterize the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and show that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme. This technology possesses the potential to decipher the biology of citrullination. Citrullination of arginine is crucial for several physiological processes. Here the authors report the site-specific incorporation of citrulline into proteins in mammalian cells using an engineered tRNA synthetase/tRNA pair and a photocaged-citrulline.
Collapse
|
30
|
Koehler C, Estrada Girona G, Reinkemeier CD, Lemke EA. Inducible Genetic Code Expansion in Eukaryotes. Chembiochem 2020; 21:3216-3219. [PMID: 32598534 PMCID: PMC7754456 DOI: 10.1002/cbic.202000338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/25/2020] [Indexed: 11/07/2022]
Abstract
Genetic code expansion (GCE) is a versatile tool to site-specifically incorporate a noncanonical amino acid (ncAA) into a protein, for example, to perform fluorescent labeling inside living cells. To this end, an orthogonal aminoacyl-tRNA-synthetase/tRNA (RS/tRNA) pair is used to insert the ncAA in response to an amber stop codon in the protein of interest. One of the drawbacks of this system is that, in order to achieve maximum efficiency, high levels of the orthogonal tRNA are required, and this could interfere with host cell functionality. To minimize the adverse effects on the host, we have developed an inducible GCE system that enables us to switch on tRNA or RS expression when needed. In particular, we tested different promotors in the context of the T-REx or Tet-On systems to control expression of the desired orthogonal tRNA and/or RS. We discuss our result with respect to the control of GCE components as well as efficiency. We found that only the T-REx system enables simultaneous control of tRNA and RS expression.
Collapse
Affiliation(s)
- Christine Koehler
- BiocentreJohannes-Gutenberg University Mainz55128MainzGermany
- Institute of Molecular Biology gGmbH55128MainzGermany
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| | - Christopher D. Reinkemeier
- BiocentreJohannes-Gutenberg University Mainz55128MainzGermany
- Institute of Molecular Biology gGmbH55128MainzGermany
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| | - Edward A. Lemke
- BiocentreJohannes-Gutenberg University Mainz55128MainzGermany
- Institute of Molecular Biology gGmbH55128MainzGermany
- Structural and Computational Biology Unit and Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryMeyerhofstraße 169117HeidelbergGermany
| |
Collapse
|
31
|
Peeler JC, Falco JA, Kelemen RE, Abo M, Chartier BV, Edinger LC, Chen J, Chatterjee A, Weerapana E. Generation of Recombinant Mammalian Selenoproteins through Genetic Code Expansion with Photocaged Selenocysteine. ACS Chem Biol 2020; 15:1535-1540. [PMID: 32330002 DOI: 10.1021/acschembio.0c00147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Selenoproteins contain the amino acid selenocysteine (Sec) and are found in all domains of life. The functions of many selenoproteins are poorly understood, partly due to difficulties in producing recombinant selenoproteins for cell-biological evaluation. Endogenous mammalian selenoproteins are produced through a noncanonical translation mechanism requiring suppression of the UGA stop codon and a Sec insertion sequence (SECIS) element in the 3' untranslated region of the mRNA. Here, recombinant selenoproteins are generated in mammalian cells through genetic code expansion, circumventing the requirement for the SECIS element and selenium availability. An engineered orthogonal E. coli leucyl-tRNA synthetase/tRNA pair is used to incorporate a photocaged Sec (DMNB-Sec) at the UAG amber stop codon. DMNB-Sec is successfully incorporated into GFP and uncaged by irradiation of living cells. Furthermore, DMNB-Sec is used to generate the native selenoprotein methionine-R-sulfoxide reductase B1 (MsrB1). Importantly, MsrB1 is shown to be catalytically active after uncaging, constituting the first use of genetic code expansion to generate a functional selenoprotein in mammalian systems. The ability to site-specifically introduce Sec directly in mammalian cells, and temporally modulate selenoprotein activity, will aid in the characterization of mammalian selenoprotein function.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
32
|
Italia JS, Peeler JC, Hillenbrand CM, Latour C, Weerapana E, Chatterjee A. Genetically encoded protein sulfation in mammalian cells. Nat Chem Biol 2020; 16:379-382. [PMID: 32198493 PMCID: PMC7564891 DOI: 10.1038/s41589-020-0493-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 12/11/2019] [Accepted: 01/17/2020] [Indexed: 11/14/2022]
Abstract
Tyrosine sulfation is an important post-translational modification found in higher eukaryotes. Here we report an engineered tyrosyl-tRNA synthetase/tRNA pair that co-translationally incorporates O-sulfotyrosine in response to UAG codons in E. coli and mammalian cells. This platform enables recombinant expression of eukaryotic proteins homogeneously sulfated at chosen sites, which was demonstrated by expressing human heparin cofactor II in mammalian cells in different states of sulfation.
Collapse
Affiliation(s)
- James S Italia
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | | | | | | | | | | |
Collapse
|
33
|
Segal I, Nachmias D, Konig A, Alon A, Arbely E, Elia N. A straightforward approach for bioorthogonal labeling of proteins and organelles in live mammalian cells, using a short peptide tag. BMC Biol 2020; 18:5. [PMID: 31937312 PMCID: PMC6961407 DOI: 10.1186/s12915-019-0708-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/15/2019] [Indexed: 11/29/2022] Open
Abstract
Background In the high-resolution microscopy era, genetic code expansion (GCE)-based bioorthogonal labeling offers an elegant way for direct labeling of proteins in live cells with fluorescent dyes. This labeling approach is currently not broadly used in live-cell applications, partly because it needs to be adjusted to the specific protein under study. Results We present a generic, 14-residue long, N-terminal tag for GCE-based labeling of proteins in live mammalian cells. Using this tag, we generated a library of GCE-based organelle markers, demonstrating the applicability of the tag for labeling a plethora of proteins and organelles. Finally, we show that the HA epitope, used as a backbone in our tag, may be substituted with other epitopes and, in some cases, can be completely removed, reducing the tag length to 5 residues. Conclusions The GCE-tag presented here offers a powerful, easy-to-implement tool for live-cell labeling of cellular proteins with small and bright probes.
Collapse
Affiliation(s)
- Inbar Segal
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Andres Konig
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Ariel Alon
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Eyal Arbely
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel. .,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
| |
Collapse
|
34
|
Swiecicki JM, Santana JT, Imperiali B. A Strategic Approach for Fluorescence Imaging of Membrane Proteins in a Native-like Environment. Cell Chem Biol 2019; 27:245-251.e3. [PMID: 31831268 DOI: 10.1016/j.chembiol.2019.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/22/2019] [Accepted: 11/14/2019] [Indexed: 01/06/2023]
Abstract
Biological membranes are complex barriers in which membrane proteins and thousands of lipidic species participate in structural and functional interactions. Developing a strategic approach that allows uniform labeling of membrane proteins while maintaining a lipidic environment that retains functional interactions is highly desirable for in vitro fluorescence studies. Herein, we focus on complementing current methods by integrating the powerful processes of unnatural amino acid mutagenesis, bioorthogonal labeling, and the detergent-free membrane protein solubilization based on the amphiphilic styrene-maleic acid (SMA) polymer. Importantly, the SMA polymer preserves a thermodynamically stable shell of phospholipids. The approach that we present is both rapid and generalizable providing a population of uniquely labeled membrane proteins in lipid nanoparticles for quantitative fluorescence-based studies.
Collapse
Affiliation(s)
- Jean-Marie Swiecicki
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jordan Tyler Santana
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| |
Collapse
|
35
|
Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
Collapse
Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| |
Collapse
|
36
|
Addy PS, Zheng Y, Italia JS, Chatterjee A. A "Quenchergenic" Chemoselective Protein Labeling Strategy. Chembiochem 2019; 20:1659-1663. [PMID: 30740850 PMCID: PMC6663590 DOI: 10.1002/cbic.201800817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Indexed: 12/21/2022]
Abstract
Dynamic changes in protein structure can be monitored by using a fluorescent probe and a dark quencher. This approach is contingent upon the ability to precisely introduce a fluorophore/quencher pair into two specific sites of a protein of interest. Despite recent advances, there is continued demand for new and convenient approaches to site-selectively label proteins with such optical probes. We have recently developed a chemoselectively rapid azo-coupling reaction (CRACR) for site-specific protein labeling; it relies on rapid coupling between a genetically encoded 5-hydroxytryptophan residue and various aromatic diazonium ions. Herein, it is reported that the product of this conjugation reaction, a highly chromophoric biarylazo group, is a potent fluorescence quencher. The absorption properties of this azo product can be tuned by systematically altering the structure of the aryldiazonium species. A particular "quenchergenic" aryldiazonium has been identified that, upon conjugation, efficiently quenches the fluorescence of green fluorescent protein, which is a widely used genetically encoded fluorescent probe that can be terminally attached to target proteins. This fluorophore/quencher pair was used to evaluate the protein-labeling kinetics of CRACR, as well as to monitor the proteolysis of a fusion protein.
Collapse
Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Yunan Zheng
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| |
Collapse
|
37
|
Porter JJ, Jang HS, Van Fossen EM, Nguyen DP, Willi TS, Cooley RB, Mehl RA. Genetically Encoded Protein Tyrosine Nitration in Mammalian Cells. ACS Chem Biol 2019; 14:1328-1336. [PMID: 31117397 DOI: 10.1021/acschembio.9b00371] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tyrosine nitration has served as a major biomarker for oxidative stress and is present in high abundance in over 50 disease pathologies in humans. While data mounts on specific disease pathways from specific sites of tyrosine nitration, the role of these modifications is still largely unclear. Strategies for installing site-specific tyrosine nitration in target proteins in eukaryotic cells, through routes not dependent on oxidative stress, would provide a powerful method to address the consequences of tyrosine nitration. Developed here is a Methanosarcina barkeri aminoacyl-tRNA synthetase/tRNA pair that efficiently incorporates nitrotyrosine site-specifically into proteins in mammalian cells. We demonstrate the utility of this approach to produce nitrated proteins identified in disease conditions by producing site-specific nitroTyr-containing manganese superoxide dismutase and 14-3-3 proteins in eukaryotic cells.
Collapse
Affiliation(s)
- Joseph J. Porter
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| | - Elise M. Van Fossen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| | - Duy P. Nguyen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| | - Taylor S. Willi
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, United States
| |
Collapse
|
38
|
Joiner CM, Breen ME, Mapp AK. Electron-deficient p-benzoyl-l-phenylalanine derivatives increase covalent chemical capture yields for protein-protein interactions. Protein Sci 2019; 28:1163-1170. [PMID: 30977234 DOI: 10.1002/pro.3621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/30/2022]
Abstract
The photoactivatable amino acid p-benzoyl-l-phenylalanine (pBpa) has been used for the covalent capture of protein-protein interactions (PPIs) in vitro and in living cells. However, this technique often suffers from poor photocrosslinking yields due to the low reactivity of the active species. Here we demonstrate that the incorporation of halogenated pBpa analogs into proteins leads to increased crosslinking yields for protein-protein interactions. The analogs can be incorporated into live yeast and upon irradiation capture endogenous PPIs. Halogenated pBpas will extend the scope of PPIs that can be captured and expand the toolbox for mapping PPIs in their native environment.
Collapse
Affiliation(s)
- Cassandra M Joiner
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Meghan E Breen
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
39
|
Italia JS, Addy PS, Erickson SB, Peeler JC, Weerapana E, Chatterjee A. Mutually Orthogonal Nonsense-Suppression Systems and Conjugation Chemistries for Precise Protein Labeling at up to Three Distinct Sites. J Am Chem Soc 2019; 141:6204-6212. [PMID: 30909694 DOI: 10.1021/jacs.8b12954] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Site-specific incorporation of multiple distinct noncanonical amino acids (ncAAs) into a protein is an emerging technology with tremendous potential. It relies on mutually orthogonal engineered aminoacyl-tRNA synthetase/tRNA pairs that suppress different nonsense/frameshift codons. So far, up to two distinct ncAAs have been incorporated into proteins expressed in E. coli, using archaea-derived tyrosyl and pyrrolysyl pairs. Here we report that the E. coli derived tryptophanyl pair can be combined with the archaeal tyrosyl or the pyrrolysyl pair in ATMW1 E. coli to incorporate two different ncAAs into one protein with high fidelity and efficiency. By combining all three orthogonal pairs, we further demonstrate simultaneous site-specific incorporation of three different ncAAs into one protein. To use this technology for chemoselectively labeling proteins with multiple distinct entities at predefined sites, we also sought to identify different bioconjugation handles that can be coincorporated into proteins as ncAA-side chains and subsequently functionalized through mutually compatible labeling chemistries. To this end, we show that the recently developed chemoselective rapid azo-coupling reaction (CRACR) directed to 5-hydroxytryptophan (5HTP) is compatible with strain-promoted azide-alkyne cycloaddition (SPAAC) targeted to p-azidophenylalanine (pAzF) and strain-promoted inverse electron-demand Diels-Alder cycloaddition (SPIEDAC) targeted to cyclopropene-lysine (CpK) for rapid, catalyst-free protein labeling at multiple sites. Combining these mutually orthogonal nonsense suppression systems and the mutually compatible bioconjugation handles they incorporate, we demonstrate site-specific labeling of recombinantly expressed proteins at up to three distinct sites.
Collapse
Affiliation(s)
- James S Italia
- Department of Chemistry , Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center , Chestnut Hill , Massachusetts 02467 , United States
| | - Partha Sarathi Addy
- Department of Chemistry , Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center , Chestnut Hill , Massachusetts 02467 , United States
| | - Sarah B Erickson
- Department of Chemistry , Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center , Chestnut Hill , Massachusetts 02467 , United States
| | - Jennifer C Peeler
- Department of Chemistry , Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center , Chestnut Hill , Massachusetts 02467 , United States
| | - Eranthie Weerapana
- Department of Chemistry , Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center , Chestnut Hill , Massachusetts 02467 , United States
| | - Abhishek Chatterjee
- Department of Chemistry , Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center , Chestnut Hill , Massachusetts 02467 , United States
| |
Collapse
|
40
|
Addy PS, Erickson SB, Italia JS, Chatterjee A. Labeling Proteins at Site-Specifically Incorporated 5-Hydroxytryptophan Residues Using a Chemoselective Rapid Azo-Coupling Reaction. Methods Mol Biol 2019; 2033:239-251. [PMID: 31332758 DOI: 10.1007/978-1-4939-9654-4_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chemoselective protein labeling is a valuable tool in the arsenal of modern chemical biology. The unnatural amino acid mutagenesis technology provides a powerful way to site-specifically introduce nonnatural chemical functionalities into recombinant proteins, which can be subsequently functionalized in a chemoselective manner. Even though several strategies currently exist to selectively label recombinant proteins in this manner, there is considerable interest for the development of additional chemoselective reactions that are fast, catalyst-free, use readily available reagents, and are compatible with existing conjugation chemistries. Here we describe a method to express recombinant proteins in E. coli site-specifically incorporating 5-hydroxytryptophan, followed by the chemoselective labeling of this residue using a chemoselective rapid azo-coupling reaction.
Collapse
Affiliation(s)
| | | | - James S Italia
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | | |
Collapse
|
41
|
Berman CM, Papa LJ, Hendel SJ, Moore CL, Suen PH, Weickhardt AF, Doan ND, Kumar CM, Uil TG, Butty VL, Hoeben RC, Shoulders MD. An Adaptable Platform for Directed Evolution in Human Cells. J Am Chem Soc 2018; 140:18093-18103. [PMID: 30427676 DOI: 10.1021/jacs.8b10937] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The discovery and optimization of biomolecules that reliably function in metazoan cells is imperative for both the study of basic biology and the treatment of disease. We describe the development, characterization, and proof-of-concept application of a platform for directed evolution of diverse biomolecules of interest (BOIs) directly in human cells. The platform relies on a custom-designed adenovirus variant lacking multiple genes, including the essential DNA polymerase and protease genes, features that allow us to evolve BOIs encoded by genes as large as 7 kb while attaining the mutation rates and enforcing the selection pressure required for successful directed evolution. High mutagenesis rates are continuously attained by trans-complementation of a newly engineered, highly error-prone form of the adenoviral polymerase. Selection pressure that couples desired BOI functions to adenoviral propagation is achieved by linking the functionality of the encoded BOI to the production of adenoviral protease activity by the human cell. The dynamic range for directed evolution can be enhanced to several orders of magnitude via application of a small-molecule adenoviral protease inhibitor to modulate selection pressure during directed evolution experiments. This platform makes it possible, in principle, to evolve any biomolecule activity that can be coupled to adenoviral protease expression or activation by simply serially passaging adenoviral populations carrying the BOI. As proof-of-concept, we use the platform to evolve, directly in the human cell environment, several transcription factor variants that maintain high levels of function while gaining resistance to a small-molecule inhibitor. We anticipate that this platform will substantially expand the repertoire of biomolecules that can be reliably and robustly engineered for both research and therapeutic applications in metazoan systems.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Taco G Uil
- Department of Cell and Chemical Biology , Leiden University Medical Center , 2300 RC Leiden , The Netherlands
| | | | - Robert C Hoeben
- Department of Cell and Chemical Biology , Leiden University Medical Center , 2300 RC Leiden , The Netherlands
| | | |
Collapse
|
42
|
Stieglitz JT, Kehoe HP, Lei M, Van Deventer JA. A Robust and Quantitative Reporter System To Evaluate Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2018; 7:2256-2269. [PMID: 30139255 PMCID: PMC6214617 DOI: 10.1021/acssynbio.8b00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Engineering protein translation machinery to incorporate noncanonical amino acids (ncAAs) into proteins has advanced applications ranging from proteomics to single-molecule studies. As applications of ncAAs emerge, efficient ncAA incorporation is crucial to exploiting unique chemistries. We have established a quantitative reporter platform to evaluate ncAA incorporation in response to the TAG (amber) codon in yeast. This yeast display-based reporter utilizes an antibody fragment containing an amber codon at which a ncAA is incorporated when the appropriate orthogonal translation system (OTS) is present. Epitope tags at both termini allow for flow cytometry-based end point readouts of OTS efficiency and fidelity. Using this reporter, we evaluated several factors that influence amber suppression, including the amber codon position and different aminoacyl-tRNA synthetase/tRNA (aaRS/tRNA) pairs. Interestingly, previously described aaRSs that evolved from different parent enzymes to incorporate O-methyl-l-tyrosine exhibit vastly different behavior. Escherichia coli leucyl-tRNA synthetase variants demonstrated efficient incorporation of a range of ncAAs, and we discovered unreported activities of several variants. Compared to a plate reader-based reporter, our assay yields more precise bulk-level measurements while also supporting single-cell readouts compatible with cell sorting. This platform is expected to allow quantitative elucidation of principles dictating efficient stop codon suppression and evolution of next-generation stop codon suppression systems to further enhance genetic code manipulation in eukaryotes. These efforts will improve our understanding of how the genetic code can be further evolved while expanding the range of chemical diversity available in proteins for applications ranging from fundamental epigenetics studies to engineering new classes of therapeutics.
Collapse
Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Ming Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, United States
| |
Collapse
|
43
|
Kelemen RE, Erickson SB, Chatterjee A. Synthesis at the interface of virology and genetic code expansion. Curr Opin Chem Biol 2018; 46:164-171. [PMID: 30086446 DOI: 10.1016/j.cbpa.2018.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/18/2018] [Accepted: 07/13/2018] [Indexed: 01/24/2023]
Abstract
How a virus efficiently invades its host cell and masterfully engineers its properties provides valuable lessons and resources for the emerging discipline of synthetic biology, which seeks to create engineered biological systems with novel functions. Recently, the toolbox of synthetic biology has also been enriched by the genetic code expansion technology, which has provided access to a large assortment of unnatural amino acids with novel chemical functionalities that can be site-specifically incorporated into proteins in living cells. The synergistic interplay of these two disciplines holds much promise to advance their individual progress, while creating new paradigms for synthetic biology. In this review we seek to provide an account of the recent advances at the interface of these two research areas.
Collapse
Affiliation(s)
- Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States
| | - Sarah B Erickson
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States.
| |
Collapse
|
44
|
Italia JS, Latour C, Wrobel CJJ, Chatterjee A. Resurrecting the Bacterial Tyrosyl-tRNA Synthetase/tRNA Pair for Expanding the Genetic Code of Both E. coli and Eukaryotes. Cell Chem Biol 2018; 25:1304-1312.e5. [PMID: 30078635 DOI: 10.1016/j.chembiol.2018.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/16/2018] [Accepted: 07/02/2018] [Indexed: 12/21/2022]
Abstract
The bacteria-derived tyrosyl-tRNA synthetase (TyrRS)/tRNA pair was first used for unnatural amino acid (Uaa) mutagenesis in eukaryotic cells over 15 years ago. It provides an ideal platform to genetically encode numerous useful Uaas in eukaryotes. However, this pair has been engineered to charge only a small collection of Uaas to date. Development of Uaa-selective variants of this pair has been limited by technical challenges associated with a yeast-based directed evolution platform, which is currently required to alter its substrate specificity. Here we overcome this limitation by enabling its directed evolution in an engineered strain of E. coli (ATMY), where the endogenous TyrRS/tRNA pair has been functionally replaced with an archaeal counterpart. The facile E. coli-based selection system enabled rapid engineering of this pair to develop variants that selectively incorporate various Uaas, including p-boronophenylalanine, into proteins expressed in mammalian cells as well as in the ATMY strain of E. coli.
Collapse
Affiliation(s)
- James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Christopher Latour
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Chester J J Wrobel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| |
Collapse
|
45
|
Sarathi Addy P, Italia JS, Chatterjee A. An Oxidative Bioconjugation Strategy Targeted to a Genetically Encoded 5-Hydroxytryptophan. Chembiochem 2018; 19:1375-1378. [PMID: 29644794 PMCID: PMC6392015 DOI: 10.1002/cbic.201800111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 12/11/2022]
Abstract
Approaches that enable the chemoselective, covalent modification of proteins in a site-specific manner have emerged as a powerful technology for a wide range of applications. The electron-rich unnatural amino acid 5-hydroxytryptophan was recently genetically encoded in both Escherichia coli and eukaryotes, thereby allowing its site-specific incorporation into virtually any recombinant protein. Herein, we report the chemoselective conjugation of various aromatic amines to full-length proteins under mild, oxidative conditions that target this site-specifically incorporated 5-hydroxytryptophan residue.
Collapse
Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| |
Collapse
|
46
|
Zheng Y, Mukherjee R, Chin MA, Igo P, Gilgenast MJ, Chatterjee A. Expanding the Scope of Single- and Double-Noncanonical Amino Acid Mutagenesis in Mammalian Cells Using Orthogonal Polyspecific Leucyl-tRNA Synthetases. Biochemistry 2017; 57:441-445. [PMID: 29106828 DOI: 10.1021/acs.biochem.7b00952] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineered aminoacyl-tRNA synthetase/tRNA pairs that enable site-specific incorporation of noncanonical amino acids (ncAAs) into proteins in living cells have emerged as powerful tools in chemical biology. The Escherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair is a promising candidate for ncAA mutagenesis in mammalian cells, but it has been engineered to charge only a limited set of ncAAs so far. Here we show that two highly polyspecific EcLeuRS mutants can efficiently charge a large array of useful ncAAs into proteins expressed in mammalian cells, while discriminating against the 20 canonical amino acids. When combined with an opal-suppressing pyrrolysyl pair, these EcLeuRS variants further enabled site-specific incorporation of different combinations of two distinct ncAAs into proteins expressed in mammalian cells.
Collapse
Affiliation(s)
- Yunan Zheng
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Raja Mukherjee
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Melissa A Chin
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Peter Igo
- 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
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
47
|
Addy PS, Erickson SB, Italia JS, Chatterjee A. A Chemoselective Rapid Azo-Coupling Reaction (CRACR) for Unclickable Bioconjugation. J Am Chem Soc 2017; 139:11670-11673. [PMID: 28787141 DOI: 10.1021/jacs.7b05125] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemoselective modification of complex biomolecules has become a cornerstone of chemical biology. Despite the exciting developments of the past two decades, the demand for new chemoselective reactions with unique abilities, and those compatible with existing chemistries for concurrent multisite-directed labeling, remains high. Here we show that 5-hydroxyindoles exhibit remarkably high reactivity toward aromatic diazonium ions and this reaction can be used to chemoselectively label proteins. We have previously genetically encoded the noncanonical amino acid 5-hydroxytryptophan in both E. coli and eukaryotes, enabling efficient site-specific incorporation of 5-hydroxyindole into virtually any protein. The 5-hydroxytryptophan residue was shown to allow rapid, chemoselective protein modification using the azo-coupling reaction, and the utility of this bioconjugation strategy was further illustrated by generating a functional antibody-fluorophore conjugate. Although the resulting azo-linkage is otherwise stable, we show that it can be efficiently cleaved upon treatment with dithionite. Our work establishes a unique chemoselective "unclickable" bioconjugation strategy to site-specifically modify proteins expressed in both bacteria and eukaryotes.
Collapse
Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Sarah B Erickson
- Department of Chemistry, Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - James S Italia
- Department of Chemistry, Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College , 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|