101
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Fiore KE, Phan HAT, Robkis DM, Walters CR, Petersson EJ. Incorporating thioamides into proteins by native chemical ligation. Methods Enzymol 2021; 656:295-339. [PMID: 34325791 PMCID: PMC8617429 DOI: 10.1016/bs.mie.2021.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thioamide is a versatile replacement of the peptide backbone with altered hydrogen bonding and conformational preferences, as well the ability participate in energy and electron transfer processes. Semi-synthetic incorporation of a thioamide into a protein can be used to study protein folding or protein/protein interactions using these properties. Semi-synthesis also provides the opportunity to study the role of thioamides in natural proteins. Here we outline the semi-synthesis of a model protein, the B1 domain of protein G (GB1) with a thioamide at the N-terminus or the C-terminus. The thioamide is synthetically incorporated into a fragment by solid-phase peptide synthesis, whereas the remainder of the protein is recombinantly expressed. Then, the two fragments are joined by native chemical ligation. The explicit protocol for GB1 synthesis is accompanied by examples of applications with GB1 and other proteins in structural biology and protein misfolding studies.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher R Walters
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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102
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Ho TYH, Shao A, Lu Z, Savilahti H, Menolascina F, Wang L, Dalchau N, Wang B. A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction. Nat Commun 2021; 12:2200. [PMID: 33850130 PMCID: PMC8044194 DOI: 10.1038/s41467-021-22404-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.
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Affiliation(s)
- Trevor Y H Ho
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Hangzhou Innovation Centre, Zhejiang University, Hangzhou, China.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Alexander Shao
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Microsoft Research, Cambridge, UK
| | - Zeyu Lu
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Filippo Menolascina
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, UK
| | - Lei Wang
- School of Engineering, Westlake University, Hangzhou, China
| | | | - Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. .,Hangzhou Innovation Centre, Zhejiang University, Hangzhou, China. .,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China. .,ZJU-UoE Joint Research Centre for Engineering Biology, Zhejiang University, Haining, China.
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103
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Seath CP, Trowbridge AD, Muir TW, MacMillan DWC. Reactive intermediates for interactome mapping. Chem Soc Rev 2021; 50:2911-2926. [PMID: 33458734 DOI: 10.1039/d0cs01366h] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interactions of biomolecules underpin all cellular processes, and the understanding of their dynamic interplay can lead to significant advances in the treatment of disease through the identification of novel therapeutic strategies. Protein-protein interactions (PPIs) in particular play a vital role within this arena, providing the basis for the majority of cellular signalling pathways. Despite their great importance, the elucidation of weak or transient PPIs that cannot be identified by immunoprecipitation remains a significant challenge, particularly in a disease relevant cellular environment. Recent approaches towards this goal have utilized the in situ generation of high energy intermediates that cross-link with neighboring proteins, providing a snapshot of the biomolecular makeup of the local area or microenvironment, termed the interactome. In this tutorial review, we discuss these reactive intermediates, how they are generated, and the impact they have had on the discovery of new biology. Broadly, we believe this strategy has the potential to significantly accelerate our understanding of PPIs and how they affect cellular physiology.
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Affiliation(s)
- Ciaran P Seath
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA.
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104
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Podracky CJ, An C, DeSousa A, Dorr BM, Walsh DM, Liu DR. Laboratory evolution of a sortase enzyme that modifies amyloid-β protein. Nat Chem Biol 2021; 17:317-325. [PMID: 33432237 PMCID: PMC7904614 DOI: 10.1038/s41589-020-00706-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/06/2020] [Indexed: 01/28/2023]
Abstract
Epitope-specific enzymes are powerful tools for site-specific protein modification but generally require genetic manipulation of the target protein. Here, we describe the laboratory evolution of the bacterial transpeptidase sortase A to recognize the LMVGG sequence in endogenous amyloid-β (Aβ) protein. Using a yeast display selection for covalent bond formation, we evolved a sortase variant that prefers LMVGG substrates from a starting enzyme that prefers LPESG substrates, resulting in a >1,400-fold change in substrate preference. We used this evolved sortase to label endogenous Aβ in human cerebrospinal fluid, enabling the detection of Aβ with sensitivities rivaling those of commercial assays. The evolved sortase can conjugate a hydrophilic peptide to Aβ42, greatly impeding the ability of the resulting protein to aggregate into higher-order structures. These results demonstrate laboratory evolution of epitope-specific enzymes toward endogenous targets as a strategy for site-specific protein modification without target gene manipulation and enable potential future applications of sortase-mediated labeling of Aβ peptides.
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Affiliation(s)
- Christopher J. Podracky
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 021383
| | - Chihui An
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 021383
| | - Alexandra DeSousa
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115
| | - Brent M. Dorr
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 021383
| | - Dominic M. Walsh
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 021383,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
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105
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Chuang YF, Phipps AJ, Lin FL, Hecht V, Hewitt AW, Wang PY, Liu GS. Approach for in vivo delivery of CRISPR/Cas system: a recent update and future prospect. Cell Mol Life Sci 2021; 78:2683-2708. [PMID: 33388855 PMCID: PMC11072787 DOI: 10.1007/s00018-020-03725-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system provides a groundbreaking genetic technology that allows scientists to modify genes by targeting specific genomic sites. Due to the relative simplicity and versatility of the CRISPR/Cas system, it has been extensively applied in human genetic research as well as in agricultural applications, such as improving crops. Since the gene editing activity of the CRISPR/Cas system largely depends on the efficiency of introducing the system into cells or tissues, an efficient and specific delivery system is critical for applying CRISPR/Cas technology. However, there are still some hurdles remaining for the translatability of CRISPR/Cas system. In this review, we summarized the approaches used for the delivery of the CRISPR/Cas system in mammals, plants, and aquacultures. We further discussed the aspects of delivery that can be improved to elevate the potential for CRISPR/Cas translatability.
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Affiliation(s)
- Yu-Fan Chuang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Andrew J Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Fan-Li Lin
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Valerie Hecht
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Peng-Yuan Wang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China.
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, Australia.
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia.
- Aier Eye Institute, Changsha, Hunan, China.
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106
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Sarkar D, Harms H, Galleano I, Sheikh ZP, Pless SA. Ion channel engineering using protein trans-splicing. Methods Enzymol 2021; 654:19-48. [PMID: 34120713 DOI: 10.1016/bs.mie.2021.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Conventional site-directed mutagenesis and genetic code expansion approaches have been instrumental in providing detailed functional and pharmacological insight into membrane proteins such as ion channels. Recently, this has increasingly been complemented by semi-synthetic strategies, in which part of the protein is generated synthetically. This means a vast range of chemical modifications, including non-canonical amino acids (ncAA), backbone modifications, chemical handles, fluorescent or spectroscopic labels and any combination of these can be incorporated. Among these approaches, protein trans-splicing (PTS) is particularly promising for protein reconstitution in live cells. It relies on one or more split inteins, which can spontaneously and covalently link flanking peptide or protein sequences. Here, we describe the use of PTS and its variant tandem PTS (tPTS) in semi-synthesis of ion channels in Xenopus laevis oocytes to incorporate ncAAs, post-translational modifications or metabolically stable mimics thereof. This strategy has the potential to expand the type and number of modifications in ion channel research.
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Affiliation(s)
- Debayan Sarkar
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hendrik Harms
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Zeshan Pervez Sheikh
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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107
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Raducanu V, Raducanu D, Ouyang Y, Tehseen M, Takahashi M, Hamdan SM. TSGIT: An N- and C-terminal tandem tag system for purification of native and intein-mediated ligation-ready proteins. Protein Sci 2021; 30:497-512. [PMID: 33150985 PMCID: PMC7784762 DOI: 10.1002/pro.3989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 11/26/2022]
Abstract
A large variety of fusion tags have been developed to improve protein expression, solubilization, and purification. Nevertheless, these tags have been combined in a rather limited number of composite tags and usually these composite tags have been dictated by traditional commercially-available expression vectors. Moreover, most commercially-available expression vectors include either N- or C-terminal fusion tags but not both. Here, we introduce TSGIT, a fusion-tag system composed of both N- and a C-terminal composite fusion tags. The system includes two affinity tags, two solubilization tags and two cleavable tags distributed at both termini of the protein of interest. Therefore, the N- and the C-terminal composite fusion tags in TSGIT are fully orthogonal in terms of both affinity selection and cleavage. For using TSGIT, we streamlined the cloning, expression, and purification procedures. Each component tag is selected to maximize its benefits toward the final construct. By expressing and partially purifying the protein of interest between the components of the TSGIT fusion, the full-length protein is selected over truncated forms, which has been a long-standing problem in protein purification. Moreover, due to the nature of the cleavable tags in TSGIT, the protein of interest is obtained in its native form without any additional undesired N- or C-terminal amino acids. Finally, the resulting purified protein is ready for efficient ligation with other proteins or peptides for downstream applications. We demonstrate the use of this system by purifying a large amount of native fluorescent mRuby3 protein and bacteriophage T7 gp2.5 ssDNA-binding protein.
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Affiliation(s)
- Vlad‐Stefan Raducanu
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Daniela‐Violeta Raducanu
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Yujing Ouyang
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Muhammad Tehseen
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Samir M. Hamdan
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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108
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Barnes NG, Nyandoro K, Jin H, Macmillan D. Rapid access to Asp/Glu sidechain hydrazides as thioester precursors for peptide cyclization and glycosylation. Chem Commun (Camb) 2021; 57:1006-1009. [PMID: 33399597 DOI: 10.1039/d0cc07404g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Head-to-sidechain macrocylic peptides, and neoglycopeptides, were readily prepared by site-specific amidation of aspartic and glutamic acid sidechain hydrazides. Hydrazides, serving as latent thioesters, were introduced through regioselective opening of the corresponding Nα-Fmoc protected anhydride precursors.
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Affiliation(s)
- Natalie G Barnes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
| | - Kudakwashe Nyandoro
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
| | - Hanzhang Jin
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
| | - Derek Macmillan
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
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109
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Siau JW, Nonis S, Chee S, Koh LQ, Ferrer FJ, Brown CJ, Ghadessy FJ. Directed co-evolution of interacting protein-peptide pairs by compartmentalized two-hybrid replication (C2HR). Nucleic Acids Res 2021; 48:e128. [PMID: 33104786 PMCID: PMC7736784 DOI: 10.1093/nar/gkaa933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022] Open
Abstract
Directed evolution methodologies benefit from read-outs quantitatively linking genotype to phenotype. We therefore devised a method that couples protein–peptide interactions to the dynamic read-out provided by an engineered DNA polymerase. Fusion of a processivity clamp protein to a thermostable nucleic acid polymerase enables polymerase activity and DNA amplification in otherwise prohibitive high-salt buffers. Here, we recapitulate this phenotype by indirectly coupling the Sso7d processivity clamp to Taq DNA polymerase via respective fusion to a high affinity and thermostable interacting protein–peptide pair. Escherichia coli cells co-expressing protein–peptide pairs can directly be used in polymerase chain reactions to determine relative interaction strengths by the measurement of amplicon yields. Conditional polymerase activity is further used to link genotype to phenotype of interacting protein–peptide pairs co-expressed in E. coli using the compartmentalized self-replication directed evolution platform. We validate this approach, termed compartmentalized two-hybrid replication, by selecting for high-affinity peptides that bind two model protein partners: SpyCatcher and the large fragment of NanoLuc luciferase. We further demonstrate directed co-evolution by randomizing both protein and peptide components of the SpyCatcher–SpyTag pair and co-selecting for functionally interacting variants.
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Affiliation(s)
- Jia Wei Siau
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Samuel Nonis
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Sharon Chee
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Li Quan Koh
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Fernando J Ferrer
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Christopher J Brown
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Farid J Ghadessy
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
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110
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Chiarini V, Fiorillo A, Camerini S, Crescenzi M, Nakamura S, Battista T, Guidoni L, Colotti G, Ilari A. Structural basis of ubiquitination mediated by protein splicing in early Eukarya. Biochim Biophys Acta Gen Subj 2021; 1865:129844. [PMID: 33444728 DOI: 10.1016/j.bbagen.2021.129844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Inteins are intervening proteins, which are known to perform protein splicing. The reaction results in the production of an intein domain and an inteinless protein, which shows no trace of the insertion. BIL2 is part of the polyubiquitin locus of Tetrahymena thermophila (BUBL), where two bacterial-intein-like (BIL) domains lacking the C + 1 nucleophile, are flanked by two independent ubiquitin-like domains (ubl4/ubl5). METHODS We solved the X-ray structures of BIL2 in both the inactive and unprecedented, zinc-induced active, forms. Then, we characterized by mass spectrometry the BUBL splicing products in the absence and in the presence of T.thRas-GTPase. Finally, we investigated the effect of ubiquitination on T.thRas-GTPase by molecular dynamics simulations. RESULTS The structural analysis demonstrated that zinc-induced conformational change activates protein splicing. Moreover, mass spectrometry characterization of the splicing products shed light on the possible function of BIL2, which operates as a "single-ubiquitin-dispensing-platform", allowing the conjugation, via isopeptide bond formation (K(εNH2)-C-ter), of ubl4 to either ubl5 or T.thRas-GTPase. Lastly, we demonstrated that T.thRas-GTPase ubiquitination occurs in proximity of the nucleotide binding pocket and stabilizes the protein active state. CONCLUSIONS We demonstrated that BIL2 is activated by zinc and that protein splicing induced by this intein does not take place through classical or aminolysis mechanisms but via formation of a covalent isopeptide bond, causing the ubiquitination of endogenous substrates such as T.thRas-GTPase. GENERAL SIGNIFICANCE In this "enzyme-free" ubiquitination mechanism the isopeptide formation, which canonically requires E1-E2-E3 enzymatic cascade and constitutes the alphabet of ubiquitin biology, is achieved in a single, concerted step without energy consumption.
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Affiliation(s)
- Valerio Chiarini
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014 Helsinki, Finland
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Serena Camerini
- Core Facilities, Italian National Institute of Health, viale Regina Elena 299, 00161 Rome, Italy
| | - Marco Crescenzi
- Core Facilities, Italian National Institute of Health, viale Regina Elena 299, 00161 Rome, Italy
| | - Shin Nakamura
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Theo Battista
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Chimiche e Fisiche, Università degli Studi dell'Aquila, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology of The National Research Council of Italy (CNR), P.le A. Moro 5, 00185 Rome, Italy.
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of The National Research Council of Italy (CNR), P.le A. Moro 5, 00185 Rome, Italy.
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111
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Ji Y, Ren C, Miao H, Pang Z, Xiao R, Yang X, Xuan W. Genetically encoding ε-N-benzoyllysine in proteins. Chem Commun (Camb) 2021; 57:1798-1801. [DOI: 10.1039/d0cc07954e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetically encoding BzK can facilitate the biological investigation of the recently discovered protein PTM lysine ε-N-benzoylation.
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Affiliation(s)
- Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Conghui Ren
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Zhili Pang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Ruotong Xiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry
- College of Chemistry
- Nankai University
- Tianjin 300071
- China
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112
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Park J, Lee S, Kim Y, Yoo TH. Methods to generate site-specific conjugates of antibody and protein. Bioorg Med Chem 2021; 30:115946. [DOI: 10.1016/j.bmc.2020.115946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
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113
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Kim C, Park M, Yang J, Shin J, Park YC, Kim SK, Kweon DH. Inducible plasmid display system for high-throughput selection of proteins with improved solubility. J Biotechnol 2020; 329:143-150. [PMID: 33373627 DOI: 10.1016/j.jbiotec.2020.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022]
Abstract
Soluble expression of enzymes inside the cell is a prerequisite for the successful biotransformation of valuable products. Some key enzymes involved in biotransformation processes, however, are hardly expressed in their soluble forms. Here, we propose an inducible plasmid display, which is a molecular evolution strategy coupled with a high-throughput screening and/or selection method, as a simple and powerful tool for improving the solubility of target enzymes. Specifically, the Oct-1 DNA-binding domain and intein (i.e., auto-processing domain) were employed as anchoring and protein trans-splicing motifs to develop the system, in which the probability of protein trans-splicing is dependent on the soluble property of target proteins. The applicability of inducible plasmid display was investigated using an α-1,2-fucosyltransferase (FucT2) from Helicobacter pylori, a highly insoluble and unstable enzyme in the cytoplasmic space of Escherichia coli, as a model protein. One round of the overall inducible plasmid display process, which consists of in vivo production of FucT2 mutants and in vitro screening, enabled soluble expression of FucT2 and selection of plasmids containing the corresponding genetic information. The inducible plasmid display developed in this study will contribute to the rapid and efficient screening and/or selection of soluble proteins.
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Affiliation(s)
- Chakhee Kim
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Myungseo Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jinkyeong Yang
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jonghyeok Shin
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul, 02707, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea.
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi, 16419, Republic of Korea; Biomedical Institute for Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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114
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Inteins in Science: Evolution to Application. Microorganisms 2020; 8:microorganisms8122004. [PMID: 33339089 PMCID: PMC7765530 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.
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115
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Mivelaz M, Fierz B. Observing protein interaction dynamics to chemically defined chromatin fibers by colocalization single-molecule fluorescence microscopy. Methods 2020; 184:112-124. [PMID: 32004546 DOI: 10.1016/j.ymeth.2020.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/15/2020] [Accepted: 01/26/2020] [Indexed: 02/04/2023] Open
Abstract
In eukaryotic cells, the genome is packaged into chromatin and exists in different states, ranging from open euchromatic regions to highly condensed heterochromatic regions. Chromatin states are highly dynamic and are organized by an interplay of histone post-translational modifications and effector proteins, both of which are central in the regulation of gene expression. For this, chromatin effector proteins must first search the nucleus for their targets, before binding and performing their role. A key question is how chromatin effector proteins search, interact with and alter the different chromatin environments. Here we present a modular fluorescence based in vitro workflow to directly observe dynamic interactions of effector proteins with defined chromatin fibres, replicating different chromatin states. We discuss the design and creation of chromatin assemblies, the synthesis of modified histones, the fabrication of microchannels and the approach to data acquisition and analysis. All of this with the aim to better understand the complex in vivo relationship between chromatin structure and gene expression.
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Affiliation(s)
- Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne, SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne, SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland.
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116
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Martin V, Egelund PHG, Johansson H, Thordal Le Quement S, Wojcik F, Sejer Pedersen D. Greening the synthesis of peptide therapeutics: an industrial perspective. RSC Adv 2020; 10:42457-42492. [PMID: 35516773 PMCID: PMC9057961 DOI: 10.1039/d0ra07204d] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Solid-phase peptide synthesis (SPPS) is generally the method of choice for the chemical synthesis of peptides, allowing routine synthesis of virtually any type of peptide sequence, including complex or cyclic peptide products. Importantly, SPPS can be automated and is scalable, which has led to its widespread adoption in the pharmaceutical industry, and a variety of marketed peptide-based drugs are now manufactured using this approach. However, SPPS-based synthetic strategies suffer from a negative environmental footprint mainly due to extensive solvent use. Moreover, most of the solvents used in peptide chemistry are classified as problematic by environmental agencies around the world and will soon need to be replaced, which in recent years has spurred a movement in academia and industry to make peptide synthesis greener. These efforts have been centred around solvent substitution, recycling and reduction, as well as exploring alternative synthetic methods. In this review, we focus on methods pertaining to solvent substitution and reduction with large-scale industrial production in mind, and further outline emerging technologies for peptide synthesis. Specifically, the technical requirements for large-scale manufacturing of peptide therapeutics are addressed.
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Affiliation(s)
- Vincent Martin
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Peter H G Egelund
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Henrik Johansson
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | | | - Felix Wojcik
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
| | - Daniel Sejer Pedersen
- Novo Nordisk A/S, CMC API Development Smørmosevej 17-19 DK-2880 Bagsværd Denmark +45 4444 8888
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117
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Bhagawati M, Hoffmann S, Höffgen KS, Piehler J, Busch KB, Mootz HD. In Cellulo Protein Semi‐Synthesis from Endogenous and Exogenous Fragments Using the Ultra‐Fast Split Gp41‐1 Intein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maniraj Bhagawati
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Simon Hoffmann
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Katharina S. Höffgen
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics University of Osnabrück Barbarastrasse 11 49076 Osnabrück Germany
| | - Karin B. Busch
- Institute of Molecular Cell Biology University of Münster Schlossplatz 5 48149 Münster Germany
| | - Henning D. Mootz
- Department of Chemistry and Pharmacy Institute of Biochemistry, University of Münster Corrensstrasse 36 48149 Münster Germany
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118
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Bhagawati M, Hoffmann S, Höffgen KS, Piehler J, Busch KB, Mootz HD. In Cellulo Protein Semi-Synthesis from Endogenous and Exogenous Fragments Using the Ultra-Fast Split Gp41-1 Intein. Angew Chem Int Ed Engl 2020; 59:21007-21015. [PMID: 32777124 PMCID: PMC7693240 DOI: 10.1002/anie.202006822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/15/2020] [Indexed: 12/19/2022]
Abstract
Protein semi-synthesis inside live cells from exogenous and endogenous parts offers unique possibilities for studying proteins in their native context. Split-intein-mediated protein trans-splicing is predestined for such endeavors and has seen some successes, but a much larger variety of established split inteins and associated protocols is urgently needed. We characterized the association and splicing parameters of the Gp41-1 split intein, which favorably revealed a nanomolar affinity between the intein fragments combined with the exceptionally fast splicing rate. Following bead-loading of a chemically modified intein fragment precursor into live mammalian cells, we fluorescently labeled target proteins on their N- and C-termini with short peptide tags, thus ensuring minimal perturbation of their structure and function. In combination with a nuclear-entrapment strategy to minimize cytosolic fluorescence background, we applied our technique for super-resolution imaging and single-particle tracking of the outer mitochondrial protein Tom20 in HeLa cells.
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Affiliation(s)
- Maniraj Bhagawati
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Simon Hoffmann
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Katharina S. Höffgen
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
| | - Jacob Piehler
- Department of Biology and Center for Cellular NanoanalyticsUniversity of OsnabrückBarbarastrasse 1149076OsnabrückGermany
| | - Karin B. Busch
- Institute of Molecular Cell BiologyUniversity of MünsterSchlossplatz 548149MünsterGermany
| | - Henning D. Mootz
- Department of Chemistry and PharmacyInstitute of Biochemistry, University of MünsterCorrensstrasse 3648149MünsterGermany
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119
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Kawase M, Fujioka M, Takahashi T. Activation of Protease and Luciferase Using Engineered Nostoc punctiforme PCC73102 DnaE Intein with Altered Split Position. Chembiochem 2020; 22:577-584. [PMID: 32969142 DOI: 10.1002/cbic.202000609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/17/2020] [Indexed: 12/22/2022]
Abstract
Inteins, self-catalytic enzymes, have been widely used in the field of protein engineering and chemical biology. Here, Nostoc punctiforme PCC73102 (Npu) DnaE intein was engineered to have an altered split position. An 11-residue N-intein of DnaE in which Gly and Asp were substituted for Tyr4 and Glu5, respectively, was designed, and the active C-intein variants were acquired by a GFP fluorescence-based screening. The designed N-intein and the obtained active C-intein variants were used to construct a turn-on system for enzyme activities such as human immunodeficiency 1 protease and NanoLuc luciferase. Based on the NanoLuc-intein fusion, we developed two intein pairs, each of which is capable of reacting preferentially, by interchanging the charged amino acids on N- and C-inteins. The specific splicing reactions were easily monitored and discriminated by bioluminescence resonance energy transfer (BRET).
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Affiliation(s)
- Misaki Kawase
- Faculty of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Meiko Fujioka
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Tsuyoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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120
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Xia HF, Zhou TJ, Du YX, Wang YJ, Shi CH, Wood DW. Improved protein purification system based on C-terminal cleavage of Npu DnaE split intein. Bioprocess Biosyst Eng 2020; 43:1931-1941. [PMID: 32447513 DOI: 10.1007/s00449-020-02382-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/17/2020] [Indexed: 10/24/2022]
Abstract
A purification system was constructed with the N-segment of the Npu DnaE split intein as an affinity ligand immobilized onto an epoxy-activated medium and the C-segment used as the cleavable tag fusing target protein. The affinity properties of C-tagged proteins adsorbed on IN affinity chromatography medium were studied with GFP as a model target protein. The saturated adsorption capacity and dynamic adsorption capacity reached 51.9-21.0 mg mL-1, respectively. With this system, two model proteins, GFP and alcohol dehydrogenase (ADH), has been successfully taglessly purified with regulation of Zn2+ and DTT. The yield, purification factor and purity of purified tagless GFP reached 39, 11.7 and 97%, respectively; while these values for purified tagless ADH were 38.2, 6.8 and 91%, respectively. These results showed that the system for Npu DnaE split intein-mediated affinity adsorption and in situ cleavage is a potential platform for recombinant protein production.
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Affiliation(s)
- Hai-Feng Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
| | - Ting-Jun Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Ye-Xing Du
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yu-Jun Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chang-Hua Shi
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
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121
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Wang D, Zhang F, Gao G. CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors. Cell 2020; 181:136-150. [PMID: 32243786 DOI: 10.1016/j.cell.2020.03.023] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022]
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-based biotechnologies has revolutionized the life sciences and introduced new therapeutic modalities with the potential to treat a wide range of diseases. Here, we describe CRISPR-based strategies to improve human health, with an emphasis on the delivery of CRISPR therapeutics directly into the human body using adeno-associated virus (AAV) vectors. We also discuss challenges facing broad deployment of CRISPR-based therapeutics and highlight areas where continued discovery and technological development can further advance these revolutionary new treatments.
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Affiliation(s)
- Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Brain and Cognitive Sciences, Department of Biological Engineering, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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122
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Wang R, Sun F. The Spy that links: Creation of nonlinear protein architectures and materials using SpyTag/SpyCatcher chemistry. Methods Enzymol 2020; 647:283-301. [PMID: 33482993 DOI: 10.1016/bs.mie.2020.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The peptide/protein pair, SpyTag/SpyCatcher, which is derived from split immunoglobulin-like collagen adhesin domain (CnaB2) from Streptococcus pyogenes, can spontaneously form a stable Lys-Asp isopeptide bond under physiological conditions. This enabling technology- also known as genetically encoded click chemistry owing to its marked efficiency and specificity-has led to a variety of applications in protein engineering, materials science and synthetic biology in recent years. In this chapter, we discuss the use of SpyTag/SpyCatcher chemistry to create nonlinear protein architectures and materials, with emphasis on its role in shaping up topology engineering as an emerging branch of protein engineering. The synthesis of entirely protein-based molecular networks, Spy networks, is highlighted. The protocols for preparing Spy networks and applications thereof are also illustrated.
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Affiliation(s)
- Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China.
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123
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Chan JC, Maze I. Nothing Is Yet Set in (Hi)stone: Novel Post-Translational Modifications Regulating Chromatin Function. Trends Biochem Sci 2020; 45:829-844. [PMID: 32498971 PMCID: PMC7502514 DOI: 10.1016/j.tibs.2020.05.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/28/2020] [Accepted: 05/14/2020] [Indexed: 01/04/2023]
Abstract
Histone post-translational modifications (PTMs) have emerged as exciting mechanisms of biological regulation, impacting pathways related to cancer, immunity, brain function, and more. Over the past decade alone, several histone PTMs have been discovered, including acylation, lipidation, monoaminylation, and glycation, many of which appear to have crucial roles in nucleosome stability and transcriptional regulation. In this review, we discuss novel histone PTMs identified within the past 10 years, with an extended focus on enzymatic versus nonenzymatic mechanisms underlying modification and adduction. Furthermore, we consider how these novel histone PTMs might fit within the framework of a so-called 'histone code', emphasizing the physiological relevance of these PTMs in metabolism, development, and disease states.
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Affiliation(s)
- Jennifer C Chan
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ian Maze
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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124
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Raghavan AR, Salim K, Yadav VG. Optogenetic Control of Heterologous Metabolism in E. coli. ACS Synth Biol 2020; 9:2291-2300. [PMID: 32786352 DOI: 10.1021/acssynbio.9b00454] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multiobjective optimization of microbial chassis for the production of xenobiotic compounds requires the implementation of metabolic control strategies that permit dynamic distribution of cellular resources between biomass and product formation. We addressed this need in a previous study by engineering the T7 RNA polymerase to be thermally responsive. The modified polymerase is activated only after the temperature of the host cell falls below 18 °C, and Escherichia coli cells that employ the protein to transcribe the heterologous lycopene biosynthetic pathway exhibit impressive improvements in productivity. We have expanded our toolbox of metabolic switches in the current study by engineering a version of the T7 RNA polymerase that drives the transition between biomass and product formation upon stimulation with red light. The engineered polymerase is expressed as two distinct polypeptide chains. Each chain comprises one of two photoactive components from Arabidopsis thaliana, phytochrome B (PhyB) and phytochrome-integrating factor 3 (PIF3), as well as the N- or C-terminus domains of both, the vacuolar ATPase subunit (VMA) intein of Saccharomyces cerevisiae and the polymerase. Red light drives photodimerization of PhyB and PIF3, which then brings together the N- and C-terminus domains of the VMA intein. Trans-splicing of the intein follows suit and produces an active form of the polymerase that subsequently transcribes any sequence that is under the control of a T7 promoter. The photodimerization also involves a third element, the cyanobacterial chromophore phycocyanobilin (PCB), which too is expressed heterologously by E. coli. We deployed this version of the T7 RNA polymerase to control the production of lycopene in E. coli and observed tight control of pathway expression. We tested a variety of expression configurations to identify one that imposes the lowest metabolic burden on the strain, and we subsequently optimized key parameters such as the source, moment, and duration of photostimulation. We also identified targets for future refinement of the circuit. In summary, our work is a significant advance for the field and greatly expands on previous work by other groups that have used optogenetic circuits to control heterologous metabolism in prokaryotic hosts.
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Affiliation(s)
- Adhithi R. Raghavan
- Department of Chemical and Biological Engineering & School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Kevin Salim
- Department of Chemical and Biological Engineering & School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Vikramaditya G. Yadav
- Department of Chemical and Biological Engineering & School of Biomedical Engineering, The University of British Columbia, Vancouver, V6T 1Z3, Canada
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125
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Lysine acylation using conjugating enzymes for site-specific modification and ubiquitination of recombinant proteins. Nat Chem 2020; 12:1008-1015. [DOI: 10.1038/s41557-020-0528-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 07/22/2020] [Indexed: 12/31/2022]
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126
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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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127
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Khoo ATT, Kim PJ, Kim HM, Je HS. Neural circuit analysis using a novel intersectional split intein-mediated split-Cre recombinase system. Mol Brain 2020; 13:101. [PMID: 32616061 PMCID: PMC7331137 DOI: 10.1186/s13041-020-00640-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/23/2020] [Indexed: 11/10/2022] Open
Abstract
The defining features of a neuron are its functional and anatomical connections with thousands of other neurons in the brain. Together, these neurons form functional networks that direct animal behavior. Current approaches that allow the interrogation of specific populations of neurons and neural circuits rely heavily on targeting their gene expression profiles or connectivity. However, these approaches are often unable to delineate specific neuronal populations. Here, we developed a novel intersectional split intein-mediated split-Cre recombinase system that can selectively label specific types of neurons based on their gene expression profiles and structural connectivity. We developed this system by splitting Cre recombinase into two fragments with evolved split inteins and subsequently expressed one fragment under the influence of a cell type-specific promoter in a transgenic animal, and delivered the other fragment via retrograde viral gene transfer. This approach results in the reconstitution of Cre recombinase in only specific population of neurons projecting from a specific brain region or in those of a specific neuronal type. Taken together, our split intein-based split-Cre system will be useful for sophisticated characterization of mammalian brain circuits.
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Affiliation(s)
- Audrey Tze Ting Khoo
- Neuroscience and Behavioural Disorders Programme, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Paul Jong Kim
- Neuroscience and Behavioural Disorders Programme, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - H Shawn Je
- Neuroscience and Behavioural Disorders Programme, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore.
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128
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Tornabene P, Trapani I, Minopoli R, Centrulo M, Lupo M, de Simone S, Tiberi P, Dell'Aquila F, Marrocco E, Iodice C, Iuliano A, Gesualdo C, Rossi S, Giaquinto L, Albert S, Hoyng CB, Polishchuk E, Cremers FPM, Surace EM, Simonelli F, De Matteis MA, Polishchuk R, Auricchio A. Intein-mediated protein trans-splicing expands adeno-associated virus transfer capacity in the retina. Sci Transl Med 2020; 11:11/492/eaav4523. [PMID: 31092694 DOI: 10.1126/scitranslmed.aav4523] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/21/2018] [Accepted: 04/04/2019] [Indexed: 12/26/2022]
Abstract
Retinal gene therapy with adeno-associated viral (AAV) vectors holds promises for treating inherited and noninherited diseases of the eye. Although clinical data suggest that retinal gene therapy is safe and effective, delivery of large genes is hindered by the limited AAV cargo capacity. Protein trans-splicing mediated by split inteins is used by single-cell organisms to reconstitute proteins. Here, we show that delivery of multiple AAV vectors each encoding one of the fragments of target proteins flanked by short split inteins results in protein trans-splicing and full-length protein reconstitution in the retina of mice and pigs and in human retinal organoids. The reconstitution of large therapeutic proteins using this approach improved the phenotype of two mouse models of inherited retinal diseases. Our data support the use of split intein-mediated protein trans-splicing in combination with AAV subretinal delivery for gene therapy of inherited blindness due to mutations in large genes.
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Affiliation(s)
- Patrizia Tornabene
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Ivana Trapani
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Renato Minopoli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Miriam Centrulo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Mariangela Lupo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Sonia de Simone
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Paola Tiberi
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Fabio Dell'Aquila
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Elena Marrocco
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Carolina Iodice
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Antonella Iuliano
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Carlo Gesualdo
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania L. Vanvitelli, 80131 Naples, Italy
| | - Settimio Rossi
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania L. Vanvitelli, 80131 Naples, Italy
| | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Silvia Albert
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, Netherlands
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Frans P M Cremers
- Department of Ophthalmology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, Netherlands
| | - Enrico M Surace
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania L. Vanvitelli, 80131 Naples, Italy
| | - Maria A De Matteis
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University, 80131 Naples, Italy
| | - Roman Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy. .,Department of Advanced Biomedicine, Federico II University, 80131 Naples, Italy
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129
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Tang TMS, Cardella D, Lander AJ, Li X, Escudero JS, Tsai YH, Luk LYP. Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling. Chem Sci 2020; 11:5881-5888. [PMID: 32874509 PMCID: PMC7441500 DOI: 10.1039/d0sc02023k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are ideal for peptide and protein labeling. However, because of the reaction reversibility, a large excess of labels or backbone modified substrates are needed. In turn, simple and cheap reagents can be used to label N-terminal cysteine, but its availability inherently limits the potential applications. Aiming to address these issues, we have created a chemo-enzymatic labeling system that exploits the substrate promiscuity of AEP with the facile chemical reaction between N-terminal cysteine and 2-formyl phenylboronic acid (FPBA). In this approach, AEP is used to ligate polypeptides with a Asn-Cys-Leu recognition sequence with counterparts possessing an N-terminal Gly-Leu. Instead of being a labeling reagent, the commercially available FPBA serves as a scavenger converting the byproduct Cys-Leu into an inert thiazolidine derivative. This consequently drives the AEP labeling reaction forward to product formation with a lower ratio of label to protein substrate. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP-ligation/FPBA-coupling system was further demonstrated by site-specifically labeling the N- or C-termini of various proteins.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Davide Cardella
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Alexander J Lander
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Xuefei Li
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Jorge S Escudero
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Yu-Hsuan Tsai
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
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130
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Zhang Y, Kutateladze TG. Exploring epigenetics with chemical tools. Nat Chem 2020; 12:506-508. [PMID: 32472102 DOI: 10.1038/s41557-020-0471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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131
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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132
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Dual roles of the sterol recognition region in Hedgehog protein modification. Commun Biol 2020; 3:250. [PMID: 32440000 PMCID: PMC7242414 DOI: 10.1038/s42003-020-0977-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/28/2020] [Indexed: 11/08/2022] Open
Abstract
Nature provides a number of mechanisms to encode dynamic information in biomolecules. In metazoans, there exist rare chemical modifications that occur in entirely unique regimes. One such example occurs in the Hedgehog (Hh) morphogens, proteins singular across all domains of life for the nature of their covalent ligation to cholesterol. The isoform- and context-specific efficiency of this ligation profoundly impacts the activity of Hh morphogens and represents an unexplored facet of Hh ligand-dependent cancers. To elucidate the chemical mechanism of this modification, we have defined roles of the uncharacterized sterol recognition region (SRR) in Hh proteins. We use a combination of sequence conservation, directed mutagenesis, and biochemical assays to specify residues of the SRR participate in cellular and biochemical aspects of Hh cholesterolysis. Our investigations offer a functional portrait of this region, providing opportunities to identify parallel reactivity in nature and a template to design tools in chemical biology.
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133
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Abstract
Split inteins are privileged molecular scaffolds for the chemical modification of proteins. Though efficient for in vitro applications, these polypeptide ligases have not been utilized for the semisynthesis of proteins in live cells. Here, we biochemically and structurally characterize the naturally split intein VidaL. We show that this split intein, which features the shortest known N-terminal fragment, supports rapid and efficient protein trans-splicing under a range of conditions, enabling semisynthesis of modified proteins both in vitro and in mammalian cells. The utility of this protein engineering system is illustrated through the traceless assembly of multidomain proteins whose biophysical properties render them incompatible with a single expression system, as well as by the semisynthesis of dual posttranslationally modified histone proteins in live cells. We also exploit the domain swapping function of VidaL to effect simultaneous modification and translocation of the nuclear protein HP1α in live cells. Collectively, our studies highlight the VidaL system as a tool for the precise chemical modification of cellular proteins with spatial and temporal control.
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134
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Yao Z, Aboualizadeh F, Kroll J, Akula I, Snider J, Lyakisheva A, Tang P, Kotlyar M, Jurisica I, Boxem M, Stagljar I. Split Intein-Mediated Protein Ligation for detecting protein-protein interactions and their inhibition. Nat Commun 2020; 11:2440. [PMID: 32415080 PMCID: PMC7229206 DOI: 10.1038/s41467-020-16299-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Here, to overcome many limitations accompanying current available methods to detect protein-protein interactions (PPIs), we develop a live cell method called Split Intein-Mediated Protein Ligation (SIMPL). In this approach, bait and prey proteins are respectively fused to an intein N-terminal fragment (IN) and C-terminal fragment (IC) derived from a re-engineered split intein GP41-1. The bait/prey binding reconstitutes the intein, which splices the bait and prey peptides into a single intact protein that can be detected by regular protein detection methods such as Western blot analysis and ELISA, serving as readouts of PPIs. The method is robust and can be applied not only in mammalian cell lines but in animal models such as C. elegans. SIMPL demonstrates high sensitivity and specificity, and enables exploration of PPIs in different cellular compartments and tracking of kinetic interactions. Additionally, we establish a SIMPL ELISA platform that enables high-throughput screening of PPIs and their inhibitors. Protein-protein interactions are fundamental to the regulation of protein activity and cellular phyisology. Here the authors present Split Intein-Mediated Protein Ligation, which uses bait and prey proteins fused to intein fragments to generate single intact proteins upon interaction.
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Affiliation(s)
- Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Jason Kroll
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Indira Akula
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Priscilla Tang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Mike Boxem
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000, Split, Croatia.
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135
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Luan H, Kuzin A, Odenwald WF, White BH. Cre-assisted fine-mapping of neural circuits using orthogonal split inteins. eLife 2020; 9:e53041. [PMID: 32286225 PMCID: PMC7217698 DOI: 10.7554/elife.53041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/11/2020] [Indexed: 01/18/2023] Open
Abstract
Existing genetic methods of neuronal targeting do not routinely achieve the resolution required for mapping brain circuits. New approaches are thus necessary. Here, we introduce a method for refined neuronal targeting that can be applied iteratively. Restriction achieved at the first step can be further refined in a second step, if necessary. The method relies on first isolating neurons within a targeted group (i.e. Gal4 pattern) according to their developmental lineages, and then intersectionally limiting the number of lineages by selecting only those in which two distinct neuroblast enhancers are active. The neuroblast enhancers drive expression of split Cre recombinase fragments. These are fused to non-interacting pairs of split inteins, which ensure reconstitution of active Cre when all fragments are expressed in the same neuroblast. Active Cre renders all neuroblast-derived cells in a lineage permissive for Gal4 activity. We demonstrate how this system can facilitate neural circuit-mapping in Drosophila.
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Affiliation(s)
- Haojiang Luan
- Laboratory of Molecular Biology, National Institute of Mental Health, NIHBethesdaUnited States
| | - Alexander Kuzin
- Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, NIHBethesdaUnited States
| | - Ward F Odenwald
- Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, NIHBethesdaUnited States
| | - Benjamin H White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIHBethesdaUnited States
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136
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Luo Y, Jiang C, Yu L, Yang A. Chemical Biology of Autophagy-Related Proteins With Posttranslational Modifications: From Chemical Synthesis to Biological Applications. Front Chem 2020; 8:233. [PMID: 32309274 PMCID: PMC7145982 DOI: 10.3389/fchem.2020.00233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/11/2020] [Indexed: 02/03/2023] Open
Abstract
Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved lysosomal degradation pathway in all eukaryotic cells, which is critical for maintaining cell homeostasis. A series of autophagy-related (ATG) proteins are involved in the regulation of autophagy. The activities of ATG proteins are mainly modulated by posttranslational modifications (PTMs), such as phosphorylation, lipidation, acetylation, ubiquitination, and sumoylation. To tackle molecular mechanisms of autophagy, more and more researches are focusing on the roles of PTMs in regulation of the activity of ATG proteins and autophagy process. The protein ligation techniques have emerged as powerful tools for the chemical engineering of proteins with PTMs, and provided effective methods to elucidate the molecular mechanism and physiological significance of PTMs. Recently, several ATG proteins with PTM were prepared by protein ligation techniques such as native chemical ligation (NCL), expressed protein ligation (EPL), peptide hydrazide-based NCL, and Sortase A-mediated ligation (SML). More importantly, the synthesized ATG proteins are successfully used to probe the mechanism of autophagy. In this review, we summarize protein ligation techniques for the preparation of ATG proteins with PTMs. In addition, we highlight the biological applications of synthetic ATG proteins to probe the autophagy mechanism.
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Affiliation(s)
- Yu Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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137
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Seo HN, Bang D. Promiscuous Trans-splicing Activities Revealed by Next Generation Sequencing-based Analysis of 298 Split Inteins. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0394-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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138
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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139
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Pinto F, Thornton EL, Wang B. An expanded library of orthogonal split inteins enables modular multi-peptide assemblies. Nat Commun 2020; 11:1529. [PMID: 32251274 PMCID: PMC7090010 DOI: 10.1038/s41467-020-15272-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
Inteins are protein segments capable of joining adjacent residues via a peptide bond. In this process known as protein splicing, the intein itself is not present in the final sequence, thus achieving scarless peptide ligation. Here, we assess the splicing activity of 34 inteins (both uncharacterized and known) using a rapid split fluorescent reporter characterization platform, and establish a library of 15 mutually orthogonal split inteins for in vivo applications, 10 of which can be simultaneously used in vitro. We show that orthogonal split inteins can be coupled to multiple split transcription factors to implement complex logic circuits in living organisms, and that they can also be used for the in vitro seamless assembly of large repetitive proteins with biotechnological relevance. Our work demonstrates the versatility and vast potential of an expanded library of orthogonal split inteins for their use in the fields of synthetic biology and protein engineering.
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Affiliation(s)
- Filipe Pinto
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Ella Lucille Thornton
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
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140
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Marmelstein AM, Lobba MJ, Mogilevsky CS, Maza JC, Brauer DD, Francis MB. Tyrosinase-Mediated Oxidative Coupling of Tyrosine Tags on Peptides and Proteins. J Am Chem Soc 2020; 142:5078-5086. [PMID: 32093466 DOI: 10.1021/jacs.9b12002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidative coupling (OC) through o-quinone intermediates has been established as an efficient and site-selective way to modify protein N-termini and the unnatural amino acid p-aminophenylalanine (paF). Recently, we reported that the tyrosinase-mediated oxidation of phenol-tagged cargo molecules is a particularly convenient method of generating o-quinones in situ. The coupling partners can be easily prepared and stored, the reaction takes place under mild conditions (phosphate buffer, pH 6.5, 4 to 23 °C), and dissolved oxygen is the only oxidant required. Here, we show an important extension of this chemistry for the activation of tyrosine residues that project into solution from the N or C-termini of peptide and protein substrates. Generating the o-quinone electrophiles from tyrosine allows greater flexibility in choosing the nucleophilic coupling partner and expands the scope of the reaction to include C-terminal positions. We also introduce a new bacterial tyrosinase enzyme that shows improved activation for some tyrosine substrates. The efficacy of several secondary amines and aniline derivatives was evaluated in the coupling reactions, providing important information for coupling partner design. This strategy was used to modify the C-termini of an antibody scFv construct and of Protein L, a human IgG kappa light chain binding protein. The use of the modified proteins as immunolabeling agents was also demonstrated.
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Affiliation(s)
- Alan M Marmelstein
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Marco J Lobba
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Casey S Mogilevsky
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Daniel D Brauer
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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141
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Berckman EA, Hartzell EJ, Mitkas AA, Sun Q, Chen W. Biological Assembly of Modular Protein Building Blocks as Sensing, Delivery, and Therapeutic Agents. Annu Rev Chem Biomol Eng 2020; 11:35-62. [PMID: 32155350 DOI: 10.1146/annurev-chembioeng-101519-121526] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nature has evolved a wide range of strategies to create self-assembled protein nanostructures with structurally defined architectures that serve a myriad of highly specialized biological functions. With the advent of biological tools for site-specific protein modifications and de novo protein design, a wide range of customized protein nanocarriers have been created using both natural and synthetic biological building blocks to mimic these native designs for targeted biomedical applications. In this review, different design frameworks and synthetic decoration strategies for achieving these functional protein nanostructures are summarized. Key attributes of these designer protein nanostructures, their unique functions, and their impact on biosensing and therapeutic applications are discussed.
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Affiliation(s)
- Emily A Berckman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA; .,Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA;
| | - Alexander A Mitkas
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA;
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA;
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142
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Liu J, Ekanayake O, Santoleri D, Walker K, Rozovsky S. Efficient Generation of Hydrazides in Proteins by RadA Split Intein. Chembiochem 2020; 21:346-352. [PMID: 31265209 DOI: 10.1002/cbic.201900160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/30/2019] [Indexed: 12/27/2022]
Abstract
Protein C-terminal hydrazides are useful for bioconjugation and construction of proteins from multiple fragments through native chemical ligation. To generate C-terminal hydrazides in proteins, an efficient intein-based preparation method has been developed by using thiols and hydrazine to accelerate the formation of the transient thioester intermediate and subsequent hydrazinolysis. This approach not only increases the yield, but also improves biocompatibility. The scope of the method has been expanded by employing Pyrococcus horikoshii RadA split intein, which can accommodate a broad range of extein residues before the site of cleavage. The use of split RadA minimizes premature intein N cleavage in vivo and offers control over the initiation of the intein N cleavage reaction. It is expected that this versatile preparation method will expand the utilization of protein C-terminal hydrazides in protein preparation and modification.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA, 94158, USA
| | - Oshini Ekanayake
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Dominic Santoleri
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kelsi Walker
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
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143
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Abstract
In recent years, split inteins have seen widespread use as molecular platforms for the design of a variety of peptide and protein chemistry technologies, most notably protein ligation. The development of these approaches is dependent on the identification and/or design of split inteins with robust activity, stability, and solubility. Here, we describe two approaches to characterize and compare the activities of newly identified or engineered split inteins. The first assay employs an E. coli-based selection system to rapidly screen the activities of many inteins and can be repurposed for directed evolution. The second assay utilizes reverse-phase high-performance liquid chromatography (RP-HPLC) to provide insights into individual chemical steps in the protein splicing reaction, information that can guide further engineering efforts. These techniques provide useful alternatives to common assays that utilize SDS-PAGE to analyze splicing reaction progress.
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144
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Romero-Casañas A, Gordo V, Castro J, Ribó M. Protein Splicing: From the Foundations to the Development of Biotechnological Applications. Methods Mol Biol 2020; 2133:15-29. [PMID: 32144661 DOI: 10.1007/978-1-0716-0434-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Expressed protein ligation is a simple and powerful method in protein engineering to introduce sequences of unnatural amino acids, posttranslational modifications, and biophysical probes into proteins of any size. This methodology has been developed based on the knowledge obtained from protein splicing. Protein splicing is a multistep biochemical reaction that includes the concomitant cleavage and formation of peptide bonds carried out by self-processing domains named inteins. The natural substrates of protein splicing are essential proteins found in intein-containing organisms; inteins are also functional in nonnative frameworks and can be used to alter nearly any protein's primary amino acid sequence. Accordingly, different reactivity features of inteins have been largely exploited to manipulate proteins in countless methods encompassing fields from biochemical research to the development of biotechnological applications including the study of disease progression and validation of potential drug candidates. Here, we review almost three decades of research to uncover the chemical and biochemical enigmas of protein splicing and the development of inteins as potent protein engineering tools.
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Affiliation(s)
- Alejandro Romero-Casañas
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
| | - Verónica Gordo
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
| | - Jessica Castro
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain.
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145
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Abstract
The split inteins from the DnaE cyanobacterial family are efficient and versatile tools for protein engineering and chemical biology applications. Their ultrafast splicing kinetics allow for the efficient production of native proteins from two separate polypeptides both in vitro and in cells. They can also be used to generate proteins with C-terminal thioesters for downstream applications. In this chapter, we describe a method based on a genetically fused version of the DnaE intein Npu for the preparation of doubly modified proteins through recombinant expression. In particular, we provide protocols for the recombinant production of modified ubiquitin through amber suppression where fused Npu is used (1) as a traceless purification tag or (2) as a protein engineering tool to introduce C-terminal modifications for subsequent attachment to other proteins of interest. Our purification protocol allows for quick and facile separation of truncated products and eliminates the need for engineering protease cleavage sites. Our approach can be easily adapted to different proteins and applications where the simultaneous presence of internal and C-terminal modifications is desirable.
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146
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Abstract
The development of expressed protein ligation (EPL) widened the scope of questions that could be addressed by mechanistic biochemistry. Protein trans-splicing (PTS) relies on the same basic chemical principles, but utilizes split inteins to tracelessly ligate distinct peptide or polypeptide fragments together with native peptide bonds. Here we present a method to adapt PTS methodologies for their use in live cells, in order to deliver synthetic or native histone modifications. As an example, we provide a protocol to incorporate a small molecule fluorophore into chromatinized histones. The protocol should be easily adaptable to incorporate other modifications to chromatin in vivo.
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147
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Forte N, Benni I, Karu K, Chudasama V, Baker JR. Cysteine-to-lysine transfer antibody fragment conjugation. Chem Sci 2019; 10:10919-10924. [PMID: 32190247 PMCID: PMC7066670 DOI: 10.1039/c9sc03825f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
The modification of lysine residues with acylating agents has represented a ubiquitous approach to the construction of antibody conjugates, with the resulting amide bonds being robustly stable and clinically validated. However, the conjugates are highly heterogeneous, due to the presence of numerous lysines on the surface of the protein, and greater control of the sites of conjugation are keenly sought. Here we present a novel approach to achieve the targeted modification of lysines distal to an antibody fragment's binding site, using a disulfide bond as a temporary 'hook' to deliver the acylating agent. This cysteine-to-lysine transfer (CLT) methodology offers greatly improved homogeneity of lysine conjugates, whilst retaining the advantages offered by the formation of amide linkages.
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Affiliation(s)
- Nafsika Forte
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
| | - Irene Benni
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
| | - Kersti Karu
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
| | - Vijay Chudasama
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
- Research Institute for Medicines (iMed.ULisboa) , Faculty of Pharmacy , Universidade de Lisboa , Lisbon , Portugal
| | - James R Baker
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H 0AJ , UK . ;
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148
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Bowen CH, Reed TJ, Sargent CJ, Mpamo B, Galazka JM, Zhang F. Seeded Chain-Growth Polymerization of Proteins in Living Bacterial Cells. ACS Synth Biol 2019; 8:2651-2658. [PMID: 31742389 DOI: 10.1021/acssynbio.9b00362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Microbially produced protein-based materials (PBMs) are appealing due to use of renewable feedstock, low energy requirements, tunable side-chain chemistry, and biodegradability. However, high-strength PBMs typically have high molecular weights (HMW) and repetitive sequences that are difficult to microbially produce due to genetic instability and metabolic burden. We report the development of a biosynthetic strategy termed seeded chain-growth polymerization (SCP) for synthesis of HMW PBMs in living bacterial cells. SCP uses split intein (SI) chemistry to cotranslationally polymerize relatively small, genetically stable material protein subunits, effectively preventing intramolecular cyclization. We apply SCP to bioproduction of spider silk in Escherichia coli, generating HMW spider silk proteins (spidroins) up to 300 kDa, resulting in spidroin fibers of high strength, modulus, and toughness. SCP provides a modular strategy to synthesize HMW, repetitive material proteins, and may facilitate bioproduction of a variety of high-performance PBMs for broad applications.
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Affiliation(s)
| | | | | | | | - Jonathan M. Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, California 94035, United States
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149
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Moon SP, Balana AT, Galesic A, Rakshit A, Pratt MR. Ubiquitination Can Change the Structure of the α-Synuclein Amyloid Fiber in a Site Selective Fashion. J Org Chem 2019; 85:1548-1555. [PMID: 31809571 DOI: 10.1021/acs.joc.9b02641] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxic amyloid aggregates are a feature of many neurodegenerative diseases. A number of biochemical and structural studies have demonstrated that not all amyloids of a given protein are equivalent but rather that an aggregating protein can form different amyloid structures or polymorphisms. Different polymorphisms can also induce different amounts of pathology and toxicity in cells and in mice, suggesting that the structural differences may play important roles in disease. However, the features that cause the formation of polymorphisms in vivo are still being uncovered. Posttranslational modifications on several amyloid forming proteins, including the Parkinson's disease causing protein α-synuclein, may be one such cause. Here, we explore whether ubiquitination can induce structural changes in α-synuclein aggregates in vitro. We used protein chemistry to first synthesize ubiquitinated analogues at three different positions using disulfide linkages. After aggregation, these linkages can be reversed, allowing us to make relative comparisons between the structures using a proteinase K assay. We find that, while ubiquitination at residue 6, 23, or 96 inhibits α-synuclein aggregation, only modification at residue 96 causes an alteration in the aggregate structure, providing further evidence that posttranslational modifications may be an important feature in amyloid polymorphism formation.
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150
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Olorunniji FJ, Lawson-Williams M, McPherson AL, Paget JE, Stark WM, Rosser SJ. Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing. Nucleic Acids Res 2019; 47:11452-11460. [PMID: 31667500 PMCID: PMC6868429 DOI: 10.1093/nar/gkz936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Abstract
Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split into two extein domains, and intein sequences (Npu DnaEN and Ssp DnaEC) were attached to the two termini to be fused. Expression of these two components followed by post-translational protein trans-splicing in Escherichia coli generated a fully functional ϕC31 integrase. We showed that protein splicing is necessary for recombination activity; deletion of intein domains or mutation of key intein residues inactivated recombination. We used an invertible promoter reporter system to demonstrate a potential application of the split intein-regulated site-specific recombination system in building reversible genetic switches. We used the same split inteins to control the reconstitution of a split Integrase-Recombination Directionality Factor fusion (Integrase-RDF) that efficiently catalysed the reverse attR x attL recombination. This demonstrates the potential for split-intein regulation of the forward and reverse reactions using the integrase and the integrase-RDF fusion, respectively. The split-intein integrase is a potentially versatile, regulatable component for building synthetic genetic circuits and devices.
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Affiliation(s)
- Femi J Olorunniji
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK
| | - Makeba Lawson-Williams
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, UK
| | - Arlene L McPherson
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Jane E Paget
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK.,Institute for Bioengineering, University of Edinburgh, Faraday Building, The King's Buildings, Edinburgh, 2 EH9 3DW, UK
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Susan J Rosser
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK.,Institute for Bioengineering, University of Edinburgh, Faraday Building, The King's Buildings, Edinburgh, 2 EH9 3DW, UK
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