1
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Sushkin ME, Jung M, Lemke EA. Tuning the Functionality of Designer Translating Organelles with Orthogonal tRNA Synthetase/tRNA Pairs. J Mol Biol 2024:168728. [PMID: 39089364 DOI: 10.1016/j.jmb.2024.168728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024]
Abstract
Site-specific incorporation of noncanonical amino acids (ncAAs) can be realized by genetic code expansion (GCE) technology. Different orthogonal tRNA synthetase/tRNA (RS/tRNA) pairs have been developed to introduce a ncAA at the desired site, delivering a wide variety of functionalities that can be installed into selected proteins. Cytoplasmic expression of RS/tRNA pairs can cause a problem with background ncAA incorporation into host proteins. The application of orthogonally translating organelles (OTOs), inspired by the concept of phase separation, provides a solution for this issue in mammalian cells, allowing site-specific and protein-selective ncAA incorporation. So far, only Methanosarcina mazei (Mm) pyrrolysyl-tRNA synthetase (PylRS) has been used within OTOs, limiting the method's potential. Here, we explored the implementation of four other widely used orthogonal RS/tRNA pairs with OTOs, which, to our surprise, were unsuccessful in generating mRNA-selective GCE. Next, we tested several experimental solutions and developed a new chimeric phenylalanyl-RS/tRNA pair that enables ncAA incorporation in OTOs in a site-specific and protein-selective manner. Our work reveals unaccounted design constraints in the spatial engineering of enzyme functions using designer organelles and presents a strategy to overcome those in vivo. We then discuss current limitations and future directions of in-cell engineering in general and protein engineering using GCE specifically.
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Affiliation(s)
- Mikhail E Sushkin
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; International PhD Programme of the Institute of Molecular Biology (IMB) gGmbH, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Marius Jung
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Biocenter, IMPRS on Cellular Biophysics, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany.
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3
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [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
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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4
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Söllner J, Derler I. Genetic code expansion, an emerging tool in the Ca 2+ ion channel field. J Physiol 2024; 602:3297-3313. [PMID: 38695316 DOI: 10.1113/jp285840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 07/17/2024] Open
Abstract
Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.
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Affiliation(s)
- Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
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5
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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6
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Yang X, Su XC, Xuan W. Genetically Encoded Photocaged Proteinogenic and Non-Proteinogenic Amino Acids. Chembiochem 2024:e202400393. [PMID: 38831474 DOI: 10.1002/cbic.202400393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Photocaged amino acids could be genetically encoded into proteins via genetic code expansion (GCE) and constitute unique tools for innovative protein engineering. There are a number of photocaged proteinogenic amino acids that allow strategic conversion of proteins into their photocaged variants, thus enabling spatiotemporal and non-invasive regulation of protein functions using light. Meanwhile, there are a hand of photocaged non-proteinogenic amino acids that address the challenges in directly encoding certain non-canonical amino acids (ncAAs) that structurally resemble proteinogenic ones or possess highly reactive functional groups. Herein, we would like to summarize the efforts in encoding photocaged proteinogenic and non-proteinogenic amino acids, hoping to draw more attention to this fruitful and exciting scientific campaign.
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Affiliation(s)
- Xiaochen Yang
- Frontier Science Center for Synthetic Biology (Ministry of Education), School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Weimin Xuan
- Frontier Science Center for Synthetic Biology (Ministry of Education), School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
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7
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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.
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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
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8
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Fröhlich M, Söllner J, Derler I. Insights into the dynamics of the Ca2+ release-activated Ca2+ channel pore-forming complex Orai1. Biochem Soc Trans 2024; 52:747-760. [PMID: 38526208 DOI: 10.1042/bst20230815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024]
Abstract
An important calcium (Ca2+) entry pathway into the cell is the Ca2+ release-activated Ca2+ (CRAC) channel, which controls a series of downstream signaling events such as gene transcription, secretion and proliferation. It is composed of a Ca2+ sensor in the endoplasmic reticulum (ER), the stromal interaction molecule (STIM), and the Ca2+ ion channel Orai in the plasma membrane (PM). Their activation is initiated by receptor-ligand binding at the PM, which triggers a signaling cascade within the cell that ultimately causes store depletion. The decrease in ER-luminal Ca2+ is sensed by STIM1, which undergoes structural rearrangements that lead to coupling with Orai1 and its activation. In this review, we highlight the current understanding of the Orai1 pore opening mechanism. In this context, we also point out the questions that remain unanswered and how these can be addressed by the currently emerging genetic code expansion (GCE) technology. GCE enables the incorporation of non-canonical amino acids with novel properties, such as light-sensitivity, and has the potential to provide novel insights into the structure/function relationship of CRAC channels at a single amino acid level in the living cell.
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Affiliation(s)
- Maximilian Fröhlich
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
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9
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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).
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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
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10
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Bacsa B, Hopl V, Derler I. Synthetic Biology Meets Ca 2+ Release-Activated Ca 2+ Channel-Dependent Immunomodulation. Cells 2024; 13:468. [PMID: 38534312 DOI: 10.3390/cells13060468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Many essential biological processes are triggered by the proximity of molecules. Meanwhile, diverse approaches in synthetic biology, such as new biological parts or engineered cells, have opened up avenues to precisely control the proximity of molecules and eventually downstream signaling processes. This also applies to a main Ca2+ entry pathway into the cell, the so-called Ca2+ release-activated Ca2+ (CRAC) channel. CRAC channels are among other channels are essential in the immune response and are activated by receptor-ligand binding at the cell membrane. The latter initiates a signaling cascade within the cell, which finally triggers the coupling of the two key molecular components of the CRAC channel, namely the stromal interaction molecule, STIM, in the ER membrane and the plasma membrane Ca2+ ion channel, Orai. Ca2+ entry, established via STIM/Orai coupling, is essential for various immune cell functions, including cytokine release, proliferation, and cytotoxicity. In this review, we summarize the tools of synthetic biology that have been used so far to achieve precise control over the CRAC channel pathway and thus over downstream signaling events related to the immune response.
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Affiliation(s)
- Bernadett Bacsa
- Division of Medical Physics und Biophysics, Medical University of Graz, A-8010 Graz, Austria
| | - Valentina Hopl
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
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11
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Lin T, Engelhard L, Söldner B, Linser R, Summerer D. Light-Activatable MBD-Readers of 5-Methylcytosine Reveal Domain-Dependent Chromatin Association Kinetics In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307930. [PMID: 38164822 PMCID: PMC10953577 DOI: 10.1002/advs.202307930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/11/2023] [Indexed: 01/03/2024]
Abstract
5-Methylcytosine (5mC) is the central epigenetic mark of mammalian DNA, and plays fundamental roles in chromatin regulation. 5mC is dynamically read and translated into regulatory outputs by methyl-CpG-binding domain (MBD) proteins. These multidomain readers recognize 5mC via an MBD domain, and undergo additional domain-dependent interactions with multiple additional chromatin components. However, studying this dynamic process is limited by a lack of methods to conditionally control the 5mC affinity of MBD readers in cells. Light-control of MBD association to chromatin by genetically encoding a photocaged serine at the MBD-DNA interface is reported. The authors study the association of MBD1 to mouse pericentromeres, dependent on its CxxC3 and transcriptional repressor domains (TRD) which interact with unmethylated CpG and heterochromatin-associated complexes, respectively. Both domains significantly modulate association kinetics, arguing for a model in which the CxxC3 delays methylation responses of MBD1 by holding it at unmethylated loci, whereas the TRD promotes responses by aiding heterochromatin association is studied. Their approach offers otherwise inaccessible kinetic insights into the domain-specific regulation of a central MBD reader, and sets the basis for further unravelling how the integration of MBDs into complex heterochromatin interaction networks control the kinetics of 5mC reading and translation into altered chromatin states.
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Affiliation(s)
- Tzu‐Chen Lin
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn Str. 4a44227DortmundGermany
| | - Lena Engelhard
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn Str. 4a44227DortmundGermany
| | - Benedikt Söldner
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn Str. 4a44227DortmundGermany
| | - Rasmus Linser
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn Str. 4a44227DortmundGermany
| | - Daniel Summerer
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn Str. 4a44227DortmundGermany
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12
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [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] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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13
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Ornelas MY, Cournoyer JE, Bram S, Mehta AP. Evolution and synthetic biology. Curr Opin Microbiol 2023; 76:102394. [PMID: 37801925 PMCID: PMC10842511 DOI: 10.1016/j.mib.2023.102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Evolutionary observations have often served as an inspiration for biological design. Decoding of the central dogma of life at a molecular level and understanding of the cellular biochemistry have been elegantly used to engineer various synthetic biology applications, including building genetic circuits in vitro and in cells, building synthetic translational systems, and metabolic engineering in cells to biosynthesize and even bioproduce complex high-value molecules. Here, we review three broad areas of synthetic biology that are inspired by evolutionary observations: (i) combinatorial approaches toward cell-based biomolecular evolution, (ii) engineering interdependencies to establish microbial consortia, and (iii) synthetic immunology. In each of the areas, we will highlight the evolutionary premise that was central toward designing these platforms. These are only a subset of the examples where evolution and natural phenomena directly or indirectly serve as a powerful source of inspiration in shaping synthetic biology and biotechnology.
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Affiliation(s)
- Marya Y Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Jason E Cournoyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Stanley Bram
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana, Champaign, United States; Cancer Center at Illinois, University of Illinois at Urbana, Champaign, United States.
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14
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Yang X, Zhao L, Wang Y, Ji Y, Su XC, Ma JA, Xuan W. Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid. Angew Chem Int Ed Engl 2023; 62:e202308472. [PMID: 37587083 DOI: 10.1002/anie.202308472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/28/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Genetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.
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Affiliation(s)
- Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Lei Zhao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Ying Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Jun-An Ma
- Department of Chemistry, Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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15
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Beyond luciferase-luciferin system: Modification, improved imaging and biomedical application. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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16
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Maltan L, Weiß S, Najjar H, Leopold M, Lindinger S, Höglinger C, Höbarth L, Sallinger M, Grabmayr H, Berlansky S, Krivic D, Hopl V, Blaimschein A, Fahrner M, Frischauf I, Tiffner A, Derler I. Photocrosslinking-induced CRAC channel-like Orai1 activation independent of STIM1. Nat Commun 2023; 14:1286. [PMID: 36890174 PMCID: PMC9995687 DOI: 10.1038/s41467-023-36458-4] [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: 05/11/2022] [Accepted: 02/01/2023] [Indexed: 03/10/2023] Open
Abstract
Ca2+ release-activated Ca2+ (CRAC) channels, indispensable for the immune system and various other human body functions, consist of two transmembrane (TM) proteins, the Ca2+-sensor STIM1 in the ER membrane and the Ca2+ ion channel Orai1 in the plasma membrane. Here we employ genetic code expansion in mammalian cell lines to incorporate the photocrosslinking unnatural amino acids (UAA), p-benzoyl-L-phenylalanine (Bpa) and p-azido-L-phenylalanine (Azi), into the Orai1 TM domains at different sites. Characterization of the respective UAA-containing Orai1 mutants using Ca2+ imaging and electrophysiology reveal that exposure to UV light triggers a range of effects depending on the UAA and its site of incorporation. In particular, photoactivation at A137 using Bpa in Orai1 activates Ca2+ currents that best match the biophysical properties of CRAC channels and are capable of triggering downstream signaling pathways such as nuclear factor of activated T-cells (NFAT) translocation into the nucleus without the need for the physiological activator STIM1.
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Affiliation(s)
- Lena Maltan
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Sarah Weiß
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Hadil Najjar
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Melanie Leopold
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Sonja Lindinger
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Carmen Höglinger
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Lorenz Höbarth
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Matthias Sallinger
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Herwig Grabmayr
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Sascha Berlansky
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Denis Krivic
- Division of Medical Physics and Biophysics, Gottfried Schatz Research Center, Medical University of Graz, A-8010, Graz, Austria
| | - Valentina Hopl
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Anna Blaimschein
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Marc Fahrner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Irene Frischauf
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Adéla Tiffner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020, Linz, Austria.
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17
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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18
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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19
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Zhang Y, Han L, Tian X, Peng C, Chen Y. Ligand‐Directed Caging Enables the Control of Endogenous DNA Alkyltransferase Activity with Light inside Live Cells. Angew Chem Int Ed Engl 2022; 61:e202115472. [DOI: 10.1002/anie.202115472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 12/29/2022]
Affiliation(s)
- Yixin Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Lili Han
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and Technology ShanghaiTech University 100 Haike Road Shanghai 201210 China
| | - Xiaoxu Tian
- National Facility for Protein Science in Shanghai Zhangjiang Lab Shanghai Advanced Research Institute Chinese Academy of Science Shanghai 201210 China
| | - Chao Peng
- National Facility for Protein Science in Shanghai Zhangjiang Lab Shanghai Advanced Research Institute Chinese Academy of Science Shanghai 201210 China
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and Technology ShanghaiTech University 100 Haike Road Shanghai 201210 China
- School of Chemistry and Material Sciences Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 1 Sub-lane Xiangshan Hangzhou 310024 China
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20
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Häfner S, Sandoz G. Photopharmacological approaches for dissecting potassium channel physiology. Curr Opin Pharmacol 2022; 63:102178. [DOI: 10.1016/j.coph.2021.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 02/05/2023]
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21
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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22
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Xiong Q, Zheng T, Shen X, Li B, Fu J, Zhao X, Wang C, Yu Z. Expanding the functionality of proteins with genetically encoded dibenzo[ b, f][1,4,5]thiadiazepine: a photo-transducer for photo-click decoration. Chem Sci 2022; 13:3571-3581. [PMID: 35432856 PMCID: PMC8943893 DOI: 10.1039/d1sc05710c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic incorporation of novel noncanonical amino acids (ncAAs) that are specialized for the photo-click reaction allows the precisely orthogonal and site-specific functionalization of proteins in living cells under photo-control. However, the development of a r̲ing-strain i̲n situ l̲oadable d̲ipolarophile (RILD) as a genetically encodable reporter for photo-click bioconjugation with spatiotemporal controllability is quite rare. Herein, we report the design and synthesis of a photo-switchable d̲ib̲enzo[b,f][1,4,5]t̲hiad̲iazepine-based a̲lanine (DBTDA) ncAA, together with the directed evolution of a pyrrolysyl-tRNA synthetase/tRNACUA pair (PylRS/tRNACUA), to encode the DBTDA into recombinant proteins as a RILD in living E. coli cells. The fast-responsive photo-isomerization of the DBTDA residue can be utilized as a converter of photon energy into ring-strain energy to oscillate the conformational changes of the parent proteins. Due to the photo-activation of RILD, the photo-switching of the DBTDA residue on sfGFP and OmpC is capable of promoting the photo-click ligation with diarylsydnone (DASyd) derived probes with high efficiency and selectivity. We demonstrate that the genetic code expansion (GCE) with DBTDA benefits the studies on the distribution of decorated OmpC-DBTD on specific E. coli cells under a spatiotemporal resolved photo-stimulation. The GCE for encoding DBTDA enables further functional diversity of artificial proteins in living systems.
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Affiliation(s)
- Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Chunxia Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
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23
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Miura Y, Senoo A, Doura T, Kiyonaka S. Chemogenetics of cell surface receptors: beyond genetic and pharmacological approaches. RSC Chem Biol 2022; 3:269-287. [PMID: 35359495 PMCID: PMC8905536 DOI: 10.1039/d1cb00195g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Cell surface receptors transmit extracellular information into cells. Spatiotemporal regulation of receptor signaling is crucial for cellular functions, and dysregulation of signaling causes various diseases. Thus, it is highly desired to control receptor functions with high spatial and/or temporal resolution. Conventionally, genetic engineering or chemical ligands have been used to control receptor functions in cells. As the alternative, chemogenetics has been proposed, in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. The engineered receptor dissects the function of one receptor member among a highly homologous receptor family in a cell-specific manner. Notably, some chemogenetic strategies have been used to reveal the receptor signaling of target cells in living animals. In this review, we summarize the developing chemogenetic methods of transmembrane receptors for cell-specific regulation of receptor signaling. We also discuss the prospects of chemogenetics for clinical applications.
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Affiliation(s)
- Yuta Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Akinobu Senoo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
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24
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Zhang Y, Han L, Tian X, Peng C, Chen Y. Ligand‐Directed Caging Enables the Control of Endogenous DNA Alkyltransferase Activity with Light inside Live Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yixin Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Lili Han
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and Technology ShanghaiTech University 100 Haike Road Shanghai 201210 China
| | - Xiaoxu Tian
- National Facility for Protein Science in Shanghai Zhangjiang Lab Shanghai Advanced Research Institute Chinese Academy of Science Shanghai 201210 China
| | - Chao Peng
- National Facility for Protein Science in Shanghai Zhangjiang Lab Shanghai Advanced Research Institute Chinese Academy of Science Shanghai 201210 China
| | - Yiyun Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry Centre of Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and Technology ShanghaiTech University 100 Haike Road Shanghai 201210 China
- School of Chemistry and Material Sciences Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 1 Sub-lane Xiangshan Hangzhou 310024 China
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25
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Arsić A, Hagemann C, Stajković N, Schubert T, Nikić-Spiegel I. Minimal genetically encoded tags for fluorescent protein labeling in living neurons. Nat Commun 2022; 13:314. [PMID: 35031604 PMCID: PMC8760255 DOI: 10.1038/s41467-022-27956-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Modern light microscopy, including super-resolution techniques, has brought about a demand for small labeling tags that bring the fluorophore closer to the target. This challenge can be addressed by labeling unnatural amino acids (UAAs) with bioorthogonal click chemistry. The minimal size of the UAA and the possibility to couple the fluorophores directly to the protein of interest with single-residue precision in living cells make click labeling unique. Here, we establish click labeling in living primary neurons and use it for fixed-cell, live-cell, dual-color pulse-chase, and super-resolution microscopy of neurofilament light chain (NFL). We also show that click labeling can be combined with CRISPR/Cas9 genome engineering for tagging endogenous NFL. Due to its versatile nature and compatibility with advanced multicolor microscopy techniques, we anticipate that click labeling will contribute to novel discoveries in the neurobiology field.
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Affiliation(s)
- Aleksandra Arsić
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Cathleen Hagemann
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Nevena Stajković
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Timm Schubert
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Institute for Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Straße 7, 72076, Tübingen, Germany
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany.
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26
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Kleis P, Paschen E, Häussler U, Bernal Sierra YA, Haas CA. Long-term in vivo application of a potassium channel-based optogenetic silencer in the healthy and epileptic mouse hippocampus. BMC Biol 2022; 20:18. [PMID: 35031048 PMCID: PMC8760681 DOI: 10.1186/s12915-021-01210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Optogenetic tools allow precise manipulation of neuronal activity via genetically encoded light-sensitive proteins. Currently available optogenetic inhibitors are not suitable for prolonged use due to short-lasting photocurrents, tissue heating, and unintended changes in ion distributions, which may interfere with normal neuron physiology. To overcome these limitations, a novel potassium channel-based optogenetic silencer, named PACK, was recently developed. The PACK tool has two components: a photoactivated adenylyl cyclase from Beggiatoa (bPAC) and a cAMP-dependent potassium channel, SthK, which carries a large, long-lasting potassium current in mammalian cells. Previously, it has been shown that activating the PACK silencer with short light pulses led to a significant reduction of neuronal firing in various in vitro and acute in vivo settings. Here, we examined the viability of performing long-term studies in vivo by looking at the inhibitory action and side effects of PACK and its components in healthy and epileptic adult male mice. RESULTS We targeted hippocampal cornu ammonis (CA1) pyramidal cells using a viral vector and enabled illumination of these neurons via an implanted optic fiber. Local field potential (LFP) recordings from CA1 of freely moving mice revealed significantly reduced neuronal activity during 50-min intermittent (0.1 Hz) illumination, especially in the gamma frequency range. Adversely, PACK expression in healthy mice induced chronic astrogliosis, dispersion of pyramidal cells, and generalized seizures. These side effects were independent of the light application and were also present in mice expressing bPAC without the potassium channel. Light activation of bPAC alone increased neuronal activity, presumably via enhanced cAMP signaling. Furthermore, we applied bPAC and PACK in the contralateral hippocampus of chronically epileptic mice following a unilateral injection of intrahippocampal kainate. Unexpectedly, the expression of bPAC in the contralateral CA1 area was sufficient to prevent the spread of spontaneous epileptiform activity from the seizure focus to the contralateral hippocampus. CONCLUSION Our study highlights the PACK tool as a potent optogenetic inhibitor in vivo. However, further refinement of its light-sensitive domain is required to avoid unexpected physiological changes.
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Affiliation(s)
- P Kleis
- Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany
| | - E Paschen
- Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - U Häussler
- Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany.,BrainLinks-BrainTools, University of Freiburg, 79110, Freiburg, Germany
| | - Y A Bernal Sierra
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, 10115, Berlin, Germany
| | - C A Haas
- Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany. .,BrainLinks-BrainTools, University of Freiburg, 79110, Freiburg, Germany. .,Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany.
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27
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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28
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Kuhlemann A, Beliu G, Janzen D, Petrini EM, Taban D, Helmerich DA, Doose S, Bruno M, Barberis A, Villmann C, Sauer M, Werner C. Genetic Code Expansion and Click-Chemistry Labeling to Visualize GABA-A Receptors by Super-Resolution Microscopy. Front Synaptic Neurosci 2021; 13:727406. [PMID: 34899260 PMCID: PMC8664562 DOI: 10.3389/fnsyn.2021.727406] [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: 06/18/2021] [Accepted: 11/02/2021] [Indexed: 01/15/2023] Open
Abstract
Fluorescence labeling of difficult to access protein sites, e.g., in confined compartments, requires small fluorescent labels that can be covalently tethered at well-defined positions with high efficiency. Here, we report site-specific labeling of the extracellular domain of γ-aminobutyric acid type A (GABA-A) receptor subunits by genetic code expansion (GCE) with unnatural amino acids (ncAA) combined with bioorthogonal click-chemistry labeling with tetrazine dyes in HEK-293-T cells and primary cultured neurons. After optimization of GABA-A receptor expression and labeling efficiency, most effective variants were selected for super-resolution microscopy and functionality testing by whole-cell patch clamp. Our results show that GCE with ncAA and bioorthogonal click labeling with small tetrazine dyes represents a versatile method for highly efficient site-specific fluorescence labeling of proteins in a crowded environment, e.g., extracellular protein domains in confined compartments such as the synaptic cleft.
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Affiliation(s)
- Alexander Kuhlemann
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany.,Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Würzburg, Germany
| | - Dieter Janzen
- Institute of Clinical Neurobiology, University of Würzburg, Würzburg, Germany
| | - Enrica Maria Petrini
- Neuroscience and Brain Technologies Department, Istituto Italiano Di Tecnologia, Genova, Italy
| | - Danush Taban
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Dominic A Helmerich
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Martina Bruno
- Neuroscience and Brain Technologies Department, Istituto Italiano Di Tecnologia, Genova, Italy
| | - Andrea Barberis
- Neuroscience and Brain Technologies Department, Istituto Italiano Di Tecnologia, Genova, Italy
| | - Carmen Villmann
- Institute of Clinical Neurobiology, University of Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
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29
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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30
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Mangubat-Medina AE, Ball ZT. Triggering biological processes: methods and applications of photocaged peptides and proteins. Chem Soc Rev 2021; 50:10403-10421. [PMID: 34320043 DOI: 10.1039/d0cs01434f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There has been a significant push in recent years to deploy fundamental knowledge and methods of photochemistry toward biological ends. Photoreactive groups have enabled chemists to activate biological function using the concept of photocaging. By granting spatiotemporal control over protein activation, these photocaging methods are fundamental in understanding biological processes. Peptides and proteins are an important group of photocaging targets that present conceptual and technical challenges, requiring precise chemoselectivity in complex polyfunctional environments. This review focuses on recent advances in photocaging techniques and methodologies, as well as their use in living systems. Photocaging methods include genetic and chemical approaches that require a deep understanding of structure-function relationships based on subtle changes in primary structure. Successful implementation of these ideas can shed light on important spatiotemporal aspects of living systems.
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Affiliation(s)
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
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31
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van Husen LS, Katsori AM, Meineke B, Tjernberg LO, Schedin-Weiss S, Elsässer SJ. Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids. Chembiochem 2021; 22:3208-3213. [PMID: 34431592 PMCID: PMC9290828 DOI: 10.1002/cbic.202100399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/24/2021] [Indexed: 11/07/2022]
Abstract
Human induced pluripotent stem cell (hiPSC) technology has revolutionized studies on human biology. A wide range of cell types and tissue models can be derived from hiPSCs to study complex human diseases. Here, we use PiggyBac-mediated transgenesis to engineer hiPSCs with an expanded genetic code. We demonstrate that genomic integration of expression cassettes for a pyrrolysyl-tRNA synthetase (PylRS), pyrrolysyl-tRNA (PylT) and the target protein of interest enables site-specific incorporation of a non-canonical amino acid (ncAA) in response to an amber stop codon. Neural stem cells, neurons and brain organoids derived from the engineered hiPSCs continue to express the amber suppression machinery and produce ncAA-bearing reporter. The incorporated ncAA can serve as a minimal bioorthogonal handle for further modifications by labeling with fluorescent dyes. Site-directed ncAA mutagenesis will open a wide range of applications to probe and manipulate proteins in brain organoids and other hiPSC-derived cell types and complex tissue models.
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Affiliation(s)
- Lea S van Husen
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden.,Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Anna-Maria Katsori
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
| | - Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
| | - Lars O Tjernberg
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
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32
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Zhou W, Deiters A. Chemogenetic and optogenetic control of post-translational modifications through genetic code expansion. Curr Opin Chem Biol 2021; 63:123-131. [PMID: 33845403 PMCID: PMC8384655 DOI: 10.1016/j.cbpa.2021.02.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
Post-translational modifications (PTMs) of proteins extensively diversify the biological information flow from the genome to the proteome and thus have profound pathophysiological implications. Precise dissection of the regulatory networks of PTMs benefits from the ability to achieve conditional control through external optogenetic or chemogenetic triggers. Genetic code expansion provides a unique solution by allowing for site-specific installation of functionally masked unnatural amino acids (UAAs) into proteins, such as enzymes and enzyme substrates, rendering them inert until rapid activation through exposure to light or small molecules. Here, we summarize the most recent advances harnessing this methodology to study various forms of PTMs, as well as generalizable approaches to externally control nodes-of-interest in PTM networks.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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33
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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34
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Abstract
![]()
Since the establishment
of site-specific mutagenesis of single
amino acids to interrogate protein function in the 1970s, biochemists
have sought to tailor protein structure in the native cell environment.
Fine-tuning the chemical properties of proteins is an indispensable
way to address fundamental mechanistic questions. Unnatural amino
acids (UAAs) offer the possibility to expand beyond the 20 naturally
occurring amino acids in most species and install new and useful chemical
functions. Here, we review the literature about advances in UAA incorporation
technology from chemoenzymatic aminoacylation of modified tRNAs to in vitro translation systems to genetic encoding of UAAs
in the native cell environment and whole organisms. We discuss innovative
applications of the UAA technology to challenges in bioengineering
and medicine.
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Affiliation(s)
- Mia A Shandell
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, U.K
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, New York, New York 10027, United States.,Department of Systems Biology, Columbia University, New York, New York 10027, United States
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35
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Rakauskaitė R, Urbanavičiūtė G, Simanavičius M, Žvirblienė A, Klimašauskas S. Selective immunocapture and light-controlled traceless release of transiently caged proteins. STAR Protoc 2021; 2:100455. [PMID: 33937874 PMCID: PMC8076704 DOI: 10.1016/j.xpro.2021.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The 4,5-dimethoxy-2-nitrobenzyl (DMNB) photocaging group introduced into small biomolecules, peptides, oligonucleotides, and proteins is commonly used for spatiotemporal control of chemical and biological processes. Here, we describe the use of a DMNB-selective monoclonal antibody for non-covalent capture of chemically or biosynthetically produced proteins containing surface-exposed DMNB caging groups followed by light-controlled traceless decaging and release of the bound proteins into solution for a variety of downstream applications. For complete details on the use and execution of this protocol, please refer to Rakauskaitė et al. (2020).
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Affiliation(s)
- Rasa Rakauskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Giedrė Urbanavičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Martynas Simanavičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Aurelija Žvirblienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
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36
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Wolffgramm J, Buchmuller B, Palei S, Muñoz‐López Á, Kanne J, Janning P, Schweiger MR, Summerer D. Light-Activation of DNA-Methyltransferases. Angew Chem Int Ed Engl 2021; 60:13507-13512. [PMID: 33826797 PMCID: PMC8251764 DOI: 10.1002/anie.202103945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 12/27/2022]
Abstract
5-Methylcytosine (5mC), the central epigenetic mark of mammalian DNA, plays fundamental roles in chromatin regulation. 5mC is written onto genomes by DNA methyltransferases (DNMT), and perturbation of this process is an early event in carcinogenesis. However, studying 5mC functions is limited by the inability to control individual DNMTs with spatiotemporal resolution in vivo. We report light-control of DNMT catalysis by genetically encoding a photocaged cysteine as a catalytic residue. This enables translation of inactive DNMTs, their rapid activation by light-decaging, and subsequent monitoring of de novo DNA methylation. We provide insights into how cancer-related DNMT mutations alter de novo methylation in vivo, and demonstrate local and tuneable cytosine methylation by light-controlled DNMTs fused to a programmable transcription activator-like effector domain targeting pericentromeric satellite-3 DNA. We further study early events of transcriptome alterations upon DNMT-catalyzed cytosine methylation. Our study sets a basis to dissect the order and kinetics of diverse chromatin-associated events triggered by normal and aberrant DNA methylation.
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Affiliation(s)
- Jan Wolffgramm
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Shubhendu Palei
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Álvaro Muñoz‐López
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
| | - Julian Kanne
- Department of Epigenetics and Tumor Biology, Medical FacultyUniversity of CologneKerpener Str. 6250937KölnGermany
| | - Petra Janning
- Max-Planck-Institute for Molecular PhysiologyOtto-Hahn-Str. 1144227DortmundGermany
| | - Michal R. Schweiger
- Department of Epigenetics and Tumor Biology, Medical FacultyUniversity of CologneKerpener Str. 6250937KölnGermany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Str. 4a44227DortmundGermany
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37
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Wolffgramm J, Buchmuller B, Palei S, Muñoz‐López Á, Kanne J, Janning P, Schweiger MR, Summerer D. Light‐Activation of DNA‐Methyltransferases. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jan Wolffgramm
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Shubhendu Palei
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Álvaro Muñoz‐López
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Julian Kanne
- Department of Epigenetics and Tumor Biology, Medical Faculty University of Cologne Kerpener Str. 62 50937 Köln Germany
| | - Petra Janning
- Max-Planck-Institute for Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Michal R. Schweiger
- Department of Epigenetics and Tumor Biology, Medical Faculty University of Cologne Kerpener Str. 62 50937 Köln Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Str. 4a 44227 Dortmund Germany
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38
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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39
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Genetic code expansion in mammalian cells: A plasmid system comparison. Bioorg Med Chem 2020; 28:115772. [PMID: 33069552 DOI: 10.1016/j.bmc.2020.115772] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022]
Abstract
Genetic code expansion with unnatural amino acids (UAAs) has significantly broadened the chemical repertoire of proteins. Applications of this method in mammalian cells include probing of molecular interactions, conditional control of biological processes, and new strategies for therapeutics and vaccines. A number of methods have been developed for transient UAA mutagenesis in mammalian cells, each with unique features and advantages. All have in common a need to deliver genes encoding additional protein biosynthetic machinery (an orthogonal tRNA/tRNA synthetase pair) and a gene for the protein of interest. In this study, we present a comparative evaluation of select plasmid-based genetic code expansion systems and a detailed analysis of suppression efficiency with different UAAs and in different cell lines.
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40
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Braun N, Sheikh ZP, Pless SA. The current chemical biology tool box for studying ion channels. J Physiol 2020; 598:4455-4471. [DOI: 10.1113/jp276695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- N. Braun
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - Z. P. Sheikh
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - S. A. Pless
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
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41
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Wang N, Wang L. Acid-brightening fluorescent protein (abFP) for imaging acidic vesicles and organelles. Methods Enzymol 2020; 639:167-189. [PMID: 32475400 DOI: 10.1016/bs.mie.2020.04.013] [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] [Indexed: 01/06/2023]
Abstract
Acidic organelles and vesicles, such as endosomes, lysosomes, autophagosomes, trans-Golgi network, and synaptic vesicles, are known to play important roles in a broad range of cellular events. To facilitate studying these multifunctional systems, we describe here an acid-brightening fluorescent protein (abFP), which fluoresces strongly at acidic pH, but is almost nonfluorescent at or above physiological pH, making it well suited for imaging molecules residing in acidic microenvironment in live cells. Specifically, a quinoline-containing unnatural amino acid Qui is incorporated into the chromophore of EGFP via genetic code expansion to generate the abFP. When being exposed to acidic environment, protonation of Qui results in a cationic chromophore and fluorescence increase. Protocols are presented to express abFP in E. coli and mammalian cells, and to fluorescently image the endocytosis of δ opioid receptor-abFP fusion protein in mammalian cells. This strategy may be similarly applicable to other fluorescent proteins to enable acidic imaging.
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Affiliation(s)
- Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, United States.
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42
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Palei S, Buchmuller B, Wolffgramm J, Muñoz-Lopez Á, Jung S, Czodrowski P, Summerer D. Light-Activatable TET-Dioxygenases Reveal Dynamics of 5-Methylcytosine Oxidation and Transcriptome Reorganization. J Am Chem Soc 2020; 142:7289-7294. [DOI: 10.1021/jacs.0c01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shubhendu Palei
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Jan Wolffgramm
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Álvaro Muñoz-Lopez
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Sascha Jung
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Paul Czodrowski
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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43
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Paoletti P, Ellis-Davies GCR, Mourot A. Optical control of neuronal ion channels and receptors. Nat Rev Neurosci 2020; 20:514-532. [PMID: 31289380 DOI: 10.1038/s41583-019-0197-2] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Light-controllable tools provide powerful means to manipulate and interrogate brain function with relatively low invasiveness and high spatiotemporal precision. Although optogenetic approaches permit neuronal excitation or inhibition at the network level, other technologies, such as optopharmacology (also known as photopharmacology) have emerged that provide molecular-level control by endowing light sensitivity to endogenous biomolecules. In this Review, we discuss the challenges and opportunities of photocontrolling native neuronal signalling pathways, focusing on ion channels and neurotransmitter receptors. We describe existing strategies for rendering receptors and channels light sensitive and provide an overview of the neuroscientific insights gained from such approaches. At the crossroads of chemistry, protein engineering and neuroscience, optopharmacology offers great potential for understanding the molecular basis of brain function and behaviour, with promises for future therapeutics.
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Affiliation(s)
- Pierre Paoletti
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
| | | | - Alexandre Mourot
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS), CNRS, INSERM, Sorbonne Université, Paris, France.
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Mondoloni S, Durand-de Cuttoli R, Mourot A. Cell-Specific Neuropharmacology. Trends Pharmacol Sci 2019; 40:696-710. [PMID: 31400823 DOI: 10.1016/j.tips.2019.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/04/2019] [Accepted: 07/11/2019] [Indexed: 01/12/2023]
Abstract
Neuronal communication involves a multitude of neurotransmitters and an outstanding diversity of receptors and ion channels. Linking the activity of cell surface receptors and ion channels in defined neural circuits to brain states and behaviors has been a key challenge in neuroscience, since cell targeting is not possible with traditional neuropharmacology. We review here recent technologies that enable the effect of drugs to be restricted to specific cell types, thereby allowing acute manipulation of the brain's own proteins with circuit specificity. We highlight the importance of developing cell-specific neuropharmacology strategies for decoding the nervous system with molecular and circuit precision, and for developing future therapeutics with reduced side effects.
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Affiliation(s)
- Sarah Mondoloni
- Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), CNRS, INSERM, Sorbonne Université, Paris, France
| | - Romain Durand-de Cuttoli
- Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), CNRS, INSERM, Sorbonne Université, Paris, France; Nash Family Department of Neuroscience, Center for Affective Neuroscience, and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandre Mourot
- Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), CNRS, INSERM, Sorbonne Université, Paris, France.
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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.
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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
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Engineered Passive Potassium Conductance in the KR2 Sodium Pump. Biophys J 2019; 116:1941-1951. [PMID: 31036257 DOI: 10.1016/j.bpj.2019.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/31/2019] [Accepted: 04/03/2019] [Indexed: 11/23/2022] Open
Abstract
Light-driven sodium pumps (NaRs) are microbial rhodopsins that utilize light energy to actively transport sodium ions out of the cell. Here, we used targeted mutagenesis and electrophysiological methods in living cells to demonstrate that NaRs can be converted into light-activated cation channels by molecular engineering. Specifically, introduction of the R109Q mutation into the sodium ion pump of Dokdonia eikasta (KR2) results in passive ion conductance, with a high preference for potassium over sodium ions. However, in this mutant, residual active outward pumping of sodium ions competes with passive inward transport of potassium. Channel-like behavior could also be achieved by introduction of other mutations into the KR2 counterion complex, and further, these modifications were transferrable to other NaRs. Combining the R109Q replacement with modifications at position S70 removed the residual sodium pumping and greatly enhanced the channel-like activity. However, passive photocurrents were only observed in leak mutants if the KR2 counterions, D116 and D251, were deprotonated, which was only observed under alkaline conditions. Overall, our results reveal that interactions between R109 and the nearby residues, L75, S70, D116, and D251, prevent passive backflow during ion transport in NaRs.
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Light-triggered release of photocaged therapeutics - Where are we now? J Control Release 2019; 298:154-176. [PMID: 30742854 DOI: 10.1016/j.jconrel.2019.02.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/02/2023]
Abstract
The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.
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Genetically encoding photoswitchable click amino acids for general optical control of conformation and function of proteins. Methods Enzymol 2019; 624:249-264. [PMID: 31370932 PMCID: PMC6684330 DOI: 10.1016/bs.mie.2019.04.016] [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: 01/25/2023]
Abstract
Over the past decade, photoswitchable molecules have been emerging as attractive tools for investigating biological processes with spatiotemporal resolution in a minimally invasive fashion. Photoswitches built on light-sensitive proteins or domains have significantly advanced neuronal and cellular studies. To install photosensitivity to general proteins and to enable high specificity for modulation, photoswitchable click amino acids (PSCaas) based on azobenzene have been developed and recently genetically incorporated into proteins via the expansion of the genetic code. PSCaas allow targeting selected sites in a protein for high specificity and are generally applicable to various proteins. In addition, PSCaas contain a click functional group, which selectively reacts with an appropriately positioned cysteine forming a photocontrollable bridge on the protein in situ. The photocontrollable bridge enables reversible modulation of the secondary structure of the spanned region and thus the function of the protein. In this chapter we describe the design and genetic encoding of PSCaa. Protocols are presented for incorporating PSCaa into a model protein calmodulin to build the bridge followed by photocontrol of calmodulin's conformation and binding function.
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Genetically Encoding Unnatural Amino Acids in Neurons In Vitro and in the Embryonic Mouse Brain for Optical Control of Neuronal Proteins. Methods Mol Biol 2018; 1728:263-277. [PMID: 29405004 DOI: 10.1007/978-1-4939-7574-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Deciphering neuronal networks governing specific brain functions is a longstanding mission in neuroscience, yet global manipulation of protein functions pharmacologically or genetically lacks sufficient specificity to reveal a neuronal protein's function in a particular neuron or a circuitry. Photostimulation presents a great venue for researchers to control neuronal proteins with high temporal and spatial resolution. Recently, an approach to optically control the function of a neuronal protein directly in neurons has been demonstrated using genetically encoded light-sensitive Unnatural amino acids (Uaas). Here, we describe procedures for genetically incorporating Uaas into target neuronal proteins in neurons in vitro and in embryonic mouse brain. As an example, a photocaged Uaa was incorporated into an inwardly rectifying potassium channel Kir2.1 to render Kir2.1 photo-activatable. This method has the potential to be generally applied to many neuronal proteins to achieve optical regulation of different processes in brains. Uaas with other properties can be similarly incorporated into neuronal proteins in neurons for various applications.
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Abstract
Optogenetics enables manipulation of biological processes with light at high spatio-temporal resolution to control the behavior of cells, networks, or even whole animals. In contrast to the performance of excitatory rhodopsins, the effectiveness of inhibitory optogenetic tools is still insufficient. Here we report a two-component optical silencer system comprising photoactivated adenylyl cyclases (PACs) and the small cyclic nucleotide-gated potassium channel SthK. Activation of this ‘PAC-K’ silencer by brief pulses of low-intensity blue light causes robust and reversible silencing of cardiomyocyte excitation and neuronal firing. In vivo expression of PAC-K in mouse and zebrafish neurons is well tolerated, where blue light inhibits neuronal activity and blocks motor responses. In combination with red-light absorbing channelrhodopsins, the distinct action spectra of PACs allow independent bimodal control of neuronal activity. PAC-K represents a reliable optogenetic silencer with intrinsic amplification for sustained potassium-mediated hyperpolarization, conferring high operational light sensitivity to the cells of interest. Optogenetic tools enable precise experimental control of the behaviour of cells. Here, the authors introduce a genetically-encoded two-protein system that enables silencing of excitable cells such as neurons and cardiomyocytes using blue light, and demonstrate its utility both in vitro and In vivo.
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