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Ai H, Pan M, Liu L. Chemical Synthesis of Human Proteoforms and Application in Biomedicine. ACS CENTRAL SCIENCE 2024; 10:1442-1459. [PMID: 39220697 PMCID: PMC11363345 DOI: 10.1021/acscentsci.4c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.
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Affiliation(s)
- Huasong Ai
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Man Pan
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
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2
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Romero‐Casañas A, García‐Lizarribar A, Castro J, Vilanova M, Benito A, Ribó M. Ligation of multiple protein domains using orthogonal inteins with non-native splice junctions. Protein Sci 2024; 33:e5070. [PMID: 38864750 PMCID: PMC11168065 DOI: 10.1002/pro.5070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
Protein splicing is a self-catalyzed process in which an internal protein domain (the intein) is excised from its flanking sequences, linking them together with a canonical peptide bond. Trans-inteins are separated in two different precursor polypeptide chains that must assemble to catalytically self-excise and ligate the corresponding flanking exteins to join even when expressed separately either in vitro or in vivo. They are very interesting to construct full proteins from separate domains because their common small size favors chemical synthesis approaches. Therefore, trans-inteins have multiple applications such as protein modification and purification, structural characterization of protein domains or production of intein-based biosensors, among others. For many of these applications, when using more than one trans-intein, orthogonality between them is a critical issue to ensure the proper ligation of the exteins. Here, we confirm the orthogonality (lack of cross-reactivity) of four different trans- or split inteins, gp41-1, gp41-8, IMPDH-1 and NrdJ-1 both in vivo and in vitro, and built different constructs that allow for the sequential fusion of up to four protein fragments into one final spliced product. We have characterized the splicing efficiency of these constructs. All harbor non-native extein residues at the splice junction between the trans-intein and the neighboring exteins, except for the essential Ser + 1. Our results show that it is possible to ligate four different protein domains using inteins gp41-1, IMPDH-1 and NrdJ-1 with non-native extein residues to obtain a final four-domain spliced product with a not negligible yield that keeps its native sequence.
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Affiliation(s)
| | | | - Jessica Castro
- Laboratori d'Enginyeria de Proteïnes, Departament de BiologiaUniversitat de GironaGironaSpain
- Institut d'Investigació Biomèdica de Girona Josep Trueta (IdIBGi)SaltSpain
| | - Maria Vilanova
- Laboratori d'Enginyeria de Proteïnes, Departament de BiologiaUniversitat de GironaGironaSpain
- Institut d'Investigació Biomèdica de Girona Josep Trueta (IdIBGi)SaltSpain
| | - Antoni Benito
- Laboratori d'Enginyeria de Proteïnes, Departament de BiologiaUniversitat de GironaGironaSpain
- Institut d'Investigació Biomèdica de Girona Josep Trueta (IdIBGi)SaltSpain
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de BiologiaUniversitat de GironaGironaSpain
- Institut d'Investigació Biomèdica de Girona Josep Trueta (IdIBGi)SaltSpain
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3
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Daniilidis M, Sperl LE, Müller BS, Babl A, Hagn F. Efficient Segmental Isotope Labeling of Integral Membrane Proteins for High-Resolution NMR Studies. J Am Chem Soc 2024; 146:15403-15410. [PMID: 38787792 PMCID: PMC11157531 DOI: 10.1021/jacs.4c03294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
High-resolution structural NMR analyses of membrane proteins are challenging due to their large size, resulting in broad resonances and strong signal overlap. Among the isotope labeling methods that can remedy this situation, segmental isotope labeling is a suitable strategy to simplify NMR spectra and retain high-resolution structural information. However, protein ligation within integral membrane proteins is complicated since the hydrophobic protein fragments are insoluble, and the removal of ligation side-products is elaborate. Here, we show that a stabilized split-intein system can be used for rapid and high-yield protein trans-splicing of integral membrane proteins under denaturing conditions. This setup enables segmental isotope labeling experiments within folded protein domains for NMR studies. We show that high-quality NMR spectra of markedly reduced complexity can be obtained in detergent micelles and lipid nanodiscs. Of note, the nanodisc insertion step specifically selects for the ligated and correctly folded membrane protein and simultaneously removes ligation byproducts. Using this tailored workflow, we show that high-resolution NMR structure determination is strongly facilitated with just two segmentally isotope-labeled membrane protein samples. The presented method will be broadly applicable to structural and dynamical investigations of (membrane-) proteins and their complexes by solution and solid-state NMR but also other structural methods where segmental labeling is beneficial.
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Affiliation(s)
- Melina Daniilidis
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Laura E. Sperl
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Benedikt S. Müller
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Antonia Babl
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian
NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85748 Garching, Germany
- Institute
of Structural Biology, Helmholtz Munich, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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4
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Hua Y, Tay NES, Ye X, Owen JA, Liu H, Thompson RE, Muir TW. Protein Editing using a Concerted Transposition Reaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597171. [PMID: 38895383 PMCID: PMC11185735 DOI: 10.1101/2024.06.03.597171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Protein engineering through the chemical or enzymatic ligation of polypeptide fragments has proven enormously powerful for studying countless biochemical processes in vitro. In general, this strategy necessitates a protein folding step following ligation of the unstructured fragments, a requirement that constrains the types of systems amenable to the approach. Here, we report an in vitro strategy that allows internal regions of target proteins to be replaced in a single operation. Conceptually, our system is analogous to a DNA transposition reaction, but employs orthogonal pairs of split inteins to swap out a designated region of a host protein with an exogenous molecular cassette. We show using isotopic labeling experiments that this 'protein transposition' reaction is concerted when the kinetics for the embedded intein pairs are suitably matched. Critically, this feature allows for efficient manipulation of protein primary structure in the context of a native fold. The utility of this method is illustrated using several protein systems including the multisubunit chromatin remodeling complex, ACF, where we also show protein transposition can occur in situ within the cell nucleus. By carrying out a molecular 'cut and paste' on a protein or protein complex under native folding conditions, our approach dramatically expands the scope of protein semisynthesis.
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Affiliation(s)
| | | | - Xuanjia Ye
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Jeremy A. Owen
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Hengyuan Liu
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA
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5
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Schmitz M, Ballestin JB, Liang J, Tomas F, Freist L, Voigt K, Di Ventura B, Öztürk MA. Int&in: A machine learning-based web server for active split site identification in inteins. Protein Sci 2024; 33:e4985. [PMID: 38717278 PMCID: PMC11078102 DOI: 10.1002/pro.4985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/06/2024] [Accepted: 03/24/2024] [Indexed: 05/12/2024]
Abstract
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragments must first form a complex for the splicing to occur. Contiguous inteins have previously been artificially split in two fragments because split inteins allow for distinct applications than contiguous ones. Even naturally split inteins have been split at unnatural split sites to obtain fragments with reduced affinity for one another, which are useful to create conditional inteins or to study protein-protein interactions. So far, split sites in inteins have been heuristically identified. We developed Int&in, a web server freely available for academic research (https://intein.biologie.uni-freiburg.de) that runs a machine learning model using logistic regression to predict active and inactive split sites in inteins with high accuracy. The model was trained on a dataset of 126 split sites generated using the gp41-1, Npu DnaE and CL inteins and validated using 97 split sites extracted from the literature. Despite the limited data size, the model, which uses various protein structural features, as well as sequence conservation information, achieves an accuracy of 0.79 and 0.78 for the training and testing sets, respectively. We envision Int&in will facilitate the engineering of novel split inteins for applications in synthetic and cell biology.
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Affiliation(s)
- Mirko Schmitz
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- 4HF Biotec GmbHFreiburgGermany
| | - Jara Ballestin Ballestin
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Bioprocess Innovation Unit, ViraTherapeutics GmbHRumAustria
| | - Junsheng Liang
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Franziska Tomas
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Leon Freist
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Karsten Voigt
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Barbara Di Ventura
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Mehmet Ali Öztürk
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
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6
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Diao F, Vasudevan D, Heckscher ES, White BH. Hox gene-specific cellular targeting using split intein Trojan exons. Proc Natl Acad Sci U S A 2024; 121:e2317083121. [PMID: 38602904 PMCID: PMC11047080 DOI: 10.1073/pnas.2317083121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
The Trojan exon method, which makes use of intronically inserted T2A-Gal4 cassettes, has been widely used in Drosophila to create thousands of gene-specific Gal4 driver lines. These dual-purpose lines provide genetic access to specific cell types based on their expression of a native gene while simultaneously mutating one allele of the gene to enable loss-of-function analysis in homozygous animals. While this dual use is often an advantage, the truncation mutations produced by Trojan exons are sometimes deleterious in heterozygotes, perhaps by creating translation products with dominant negative effects. Such mutagenic effects can cause developmental lethality as has been observed with genes encoding essential transcription factors. Given the importance of transcription factors in specifying cell type, alternative techniques for generating specific Gal4 lines that target them are required. Here, we introduce a modified Trojan exon method that retains the targeting fidelity and plug-and-play modularity of the original method but mitigates its mutagenic effects by exploiting the self-splicing capabilities of split inteins. "Split Intein Trojan exons" (siTrojans) ensure that the two truncation products generated from the interrupted allele of the native gene are trans-spliced to create a full-length native protein. We demonstrate the efficacy of siTrojans by generating a comprehensive toolkit of Gal4 and Split Gal4 lines for the segmentally expressed Hox transcription factors and illustrate their use in neural circuit mapping by targeting neurons according to their position along the anterior-posterior axis. Both the method and the Hox gene-specific toolkit introduced here should be broadly useful.
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Affiliation(s)
- Fengqiu Diao
- Laboratory of Molecular Biology, Section on Neural Function, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Deeptha Vasudevan
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Ellie S. Heckscher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Benjamin H. White
- Laboratory of Molecular Biology, Section on Neural Function, National Institute of Mental Health, NIH, Bethesda, MD20892
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7
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Lin T, Ge Y, Gao Q, Zhang D, Chen X, Hu Y, Fan J. Backbone Cyclization of Flavin Mononucleotide-Based Fluorescent Protein Increases Fluorescence and Stability. J Microbiol Biotechnol 2023; 33:1681-1691. [PMID: 37789714 PMCID: PMC10772547 DOI: 10.4014/jmb.2305.05011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 10/05/2023]
Abstract
Flavin mononucleotide-binding proteins or domains emit cyan-green fluorescence under aerobic and anaerobic conditions, but relatively low fluorescence and less thermostability limit their application as reporters. In this work, we incorporated the codon-optimized fluorescent protein from Chlamydomonas reinhardtii with two different linkers independently into the redox-responsive split intein construct, overexpressed the precursors in hyperoxic Escherichia coli SHuffle T7 strain, and cyclized the target proteins in vitro in the presence of the reducing agent. Compared with the purified linear protein, the cyclic protein with the short linker displayed enhanced fluorescence. In contrast, cyclized protein with incorporation of the long linker including the myc-tag and human rhinovirus 3C protease cleavable sequence emitted slightly increased fluorescence compared with the protein linearized with the protease cleavage. The cyclic protein with the short linker also exhibited increased thermal stability and exopeptidase resistance. Moreover, induction of the target proteins in an oxygen-deficient culture rendered fluorescent E. coli BL21 (DE3) cells brighter than those overexpressing the linear construct. Thus, the cyclic reporter can hopefully be used in certain thermophilic anaerobes.
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Affiliation(s)
- Tingting Lin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yuanyuan Ge
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Qing Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Di Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Xiaofeng Chen
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
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8
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Alexander MS, Velinov M. DOCK3-Associated Neurodevelopmental Disorder-Clinical Features and Molecular Basis. Genes (Basel) 2023; 14:1940. [PMID: 37895289 PMCID: PMC10606569 DOI: 10.3390/genes14101940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The protein product of DOCK3 is highly expressed in neurons and has a role in cell adhesion and neuronal outgrowth through its interaction with the actin cytoskeleton and key cell signaling molecules. The DOCK3 protein is essential for normal cell growth and migration. Biallelic variants in DOCK3 associated with complete or partial loss of function of the gene were recently reported in six patients with intellectual disability and muscle hypotonia. Only one of the reported patients had congenital malformations outside of the CNS. Further studies are necessary to better determine the prevalence of DOCK3-associated neurodevelopmental disorders and the frequency of non-CNS clinical manifestations in these patients. Since deficiency of the DOCK3 protein product is now an established pathway of this neurodevelopmental condition, supplementing the deficient gene product using a gene therapy approach may be an efficient treatment strategy.
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Affiliation(s)
- Matthew S. Alexander
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA;
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- UAB Civitan International Research Center (CIRC), University of Alabama at Birmingham, Birmingham, AL 35233, USA
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Milen Velinov
- Department of Pediatrics, Division of Genetics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
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9
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Ebberink E, Fernandes S, Hatzopoulos G, Agashe N, Chang PH, Guidotti N, Reichart TM, Reymond L, Velluz MC, Schneider F, Pourroy C, Janke C, Gönczy P, Fierz B, Aumeier C. Tubulin engineering by semi-synthesis reveals that polyglutamylation directs detyrosination. Nat Chem 2023:10.1038/s41557-023-01228-8. [PMID: 37386282 DOI: 10.1038/s41557-023-01228-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/28/2023] [Indexed: 07/01/2023]
Abstract
Microtubules, a critical component of the cytoskeleton, carry post-translational modifications (PTMs) that are important for the regulation of key cellular processes. Long-lived microtubules, in neurons particularly, exhibit both detyrosination of α-tubulin and polyglutamylation. Dysregulation of these PTMs can result in developmental defects and neurodegeneration. Owing to a lack of tools to study the regulation and function of these PTMs, the mechanisms that govern such PTM patterns are not well understood. Here we produce fully functional tubulin carrying precisely defined PTMs within its C-terminal tail. We ligate synthetic α-tubulin tails-which are site-specifically glutamylated-to recombinant human tubulin heterodimers by applying a sortase- and intein-mediated tandem transamidation strategy. Using microtubules reconstituted with these designer tubulins, we find that α-tubulin polyglutamylation promotes its detyrosination by enhancing the activity of the tubulin tyrosine carboxypeptidase vasohibin/small vasohibin-binding protein in a manner dependent on the length of polyglutamyl chains. We also find that modulating polyglutamylation levels in cells results in corresponding changes in detyrosination, corroborating the link between the detyrosination cycle to polyglutamylation.
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Affiliation(s)
- Eduard Ebberink
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Simon Fernandes
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Georgios Hatzopoulos
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Ninad Agashe
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Po-Han Chang
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Timothy M Reichart
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Luc Reymond
- Biomolecular Screening Facility, EPFL, Lausanne, Switzerland
| | | | - Fabian Schneider
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Cédric Pourroy
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland.
| | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.
- National Center for Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.
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10
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Ferreira MV, Fernandes S, Almeida AI, Neto S, Mendes JP, Silva RJS, Peixoto C, Coroadinha AS. Extending AAV Packaging Cargo through Dual Co-Transduction: Efficient Protein Trans-Splicing at Low Vector Doses. Int J Mol Sci 2023; 24:10524. [PMID: 37445701 DOI: 10.3390/ijms241310524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Adeno-associated viral (AAV) vectors represent one of the leading platforms for gene delivery. Nevertheless, their small packaging capacity restricts their use for diseases requiring large-gene delivery. To overcome this, dual-AAV vector systems that rely on protein trans-splicing were developed, with the split-intein Npu DnaE among the most-used. However, the reconstitution efficiency of Npu DnaE is still insufficient, requiring higher vector doses. In this work, two split-inteins, Cfa and Gp41-1, with reportedly superior trans-splicing were evaluated in comparison with Npu DnaE by transient transfections and dual-AAV in vitro co-transductions. Both Cfa and Gp41-1 split-inteins enabled reconstitution rates that were over two-fold higher than Npu DnaE and 100% of protein reconstitution. The impact of different vector preparation qualities in split-intein performances was also evaluated in co-transduction assays. Higher-quality preparations increased split-inteins' performances by three-fold when compared to low-quality preparations (60-75% vs. 20-30% full particles, respectively). Low-quality vector preparations were observed to limit split-gene reconstitutions by inhibiting co-transduction. We show that combining superior split-inteins with higher-quality vector preparations allowed vector doses to be decreased while maintaining high trans-splicing rates. These results show the potential of more-efficient protein-trans-splicing strategies in dual-AAV vector co-transduction, allowing the extension of its use to the delivery of larger therapeutic genes.
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Affiliation(s)
- Mariana V Ferreira
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sofia Fernandes
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Isabel Almeida
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Salomé Neto
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - João P Mendes
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ricardo J S Silva
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cristina Peixoto
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Sofia Coroadinha
- iBET-Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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11
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Yuan G, Lu H, De K, Hassan MM, Liu Y, Islam MT, Muchero W, Tuskan GA, Yang X. Split selectable marker systems utilizing inteins facilitate gene stacking in plants. Commun Biol 2023; 6:567. [PMID: 37237044 DOI: 10.1038/s42003-023-04950-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
The ability to stack multiple genes in plants is of great importance in the development of crops with desirable traits but can be challenging due to limited selectable marker options. Here we establish split selectable marker systems using protein splicing elements called "inteins" for Agrobacterium-mediated co-transformation in plants. First, we show that such a split selectable marker system can be used effectively in plants to reconstitute a visible marker, RUBY, from two non-functional fragments through tobacco leaf infiltration. Next, to determine the general applicability of our split selectable marker systems, we demonstrate the utility of these systems in the model plants Arabidopsis and poplar by successfully stacking two reporters eYGFPuv and RUBY, using split Kanamycin or Hygromycin resistance markers. In conclusion, this method enables robust plant co-transformation, providing a valuable tool for the simultaneous insertion of multiple genes into both herbaceous and woody plants efficiently.
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Affiliation(s)
- Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Academic Education, Central Community College-Hastings, Hastings, NE, 68902, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Md Torikul Islam
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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12
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Lin T, Zhang S, Zhang D, Chen X, Ge Y, Hu Y, Fan J. Use of the redox-dependent intein system for enhancing production of the cyclic green fluorescent protein. Protein Expr Purif 2023; 207:106272. [PMID: 37062513 DOI: 10.1016/j.pep.2023.106272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023]
Abstract
To expand the reported redox-dependent intein system application, in this work, we used the split intein variant with highly trans-splicing efficiency and minimal extein dependence to cyclize the green fluorescent protein variant reporter in vitro. The CPG residues were introduced adjacent to the intein's catalytic cysteine for reversible formation of a disulfide bond to retard the trans-splicing reaction under the oxidative environment. The cyclized reporter protein in Escherichia coli cells was easily prepared by organic extraction and identified by the exopeptidase digestion. The amounts of extracted cyclized protein reporter in BL21 (DE3) cells were higher than those in hyperoxic SHuffle T7 coexpression system for facilitating the disulfide bond formation. The double His6-tagged precursor was purified for in vitro cyclization of the protein for 3 h. Compared with the purified linear counterpart, the cyclic reporter showed about twofold increase in fluorescence intensity, exhibited thermal and hydrolytic stability, and displayed better folding efficiency in BL21 (DE3) cells at the elevated temperature. Taken together, the developed redox-dependent intein system will be used for producing other cyclic disulfide-free proteins. The cyclic reporter is a potential candidate applied in certain thermophilic aerobes.
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Affiliation(s)
- Tingting Lin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Shuncheng Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Di Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Xiaofeng Chen
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Yuanyuan Ge
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China.
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13
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Seath CP, Burton AJ, Sun X, Lee G, Kleiner RE, MacMillan DWC, Muir TW. Tracking chromatin state changes using nanoscale photo-proximity labelling. Nature 2023; 616:574-580. [PMID: 37020029 PMCID: PMC10408239 DOI: 10.1038/s41586-023-05914-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/02/2023] [Indexed: 04/07/2023]
Abstract
Interactions between biomolecules underlie all cellular processes and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects1,2. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health1. However, in the complex environment of the nucleus, it is challenging to determine protein-protein interactions owing to low abundance, transient or multivalent binding and a lack of technologies that are able to interrogate these interactions without disrupting the protein-binding surface under study3. Here, we describe a method for the traceless incorporation of iridium-photosensitizers into the nuclear micro-environment using engineered split inteins. These Ir-catalysts can activate diazirine warheads through Dexter energy transfer to form reactive carbenes within an approximately 10 nm radius, cross-linking with proteins in the immediate micro-environment (a process termed µMap) for analysis using quantitative chemoproteomics4. We show that this nanoscale proximity-labelling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. µMap improves our fundamental understanding of nuclear protein-protein interactions and, in doing so, is expected to have a significant effect on the field of epigenetic drug discovery in both academia and industry.
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Affiliation(s)
- Ciaran P Seath
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Scripps-UF, Jupiter, FL, USA
| | - Antony J Burton
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Discovery Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Xuemeng Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Gihoon Lee
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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14
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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15
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Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, White BH, Perrimon N. split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534001. [PMID: 36993523 PMCID: PMC10055387 DOI: 10.1101/2023.03.24.534001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues in Drosophila . However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a new split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is fully repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell-type specific genetic drivers based on in silico predictions generated by single cell RNAseq (scRNAseq) datasets, and we describe a new algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible. Significance statement The split-Gal4 system allows Drosophila researchers to drive transgene expression with extraordinary cell type specificity. However, the existing split-Gal4 system cannot be controlled temporally, and therefore cannot be applied to many important areas of research. Here, we present a new split-Gal4 system based on a self-excising split-intein, which is fully controllable by Gal80, as well as a related drug-inducible split GeneSwitch system. This approach can both leverage and inform single-cell RNAseq datasets, and we introduce an algorithm to identify pairs of genes that precisely and narrowly mark a desired cell cluster. Our split-intein Gal4 system will be of value to the Drosophila research community, and allow for the creation of highly specific genetic drivers that are also inducible/repressible.
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Affiliation(s)
- Ben Ewen-Campen
- These authors contributed equally
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Haojiang Luan
- These authors contributed equally
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Jun Xu
- These authors contributed equally
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, China
| | - Rohit Singh
- These authors contributed equally
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Neha Joshi
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tanuj Thakkar
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge MA 02143
| | - Benjamin H White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- HHMI, Boston, MA 02115, USA
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16
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Free K, Nakanishi H, Itaka K. Development of Synthetic mRNAs Encoding Split Cytotoxic Proteins for Selective Cell Elimination Based on Specific Protein Detection. Pharmaceutics 2023; 15:pharmaceutics15010213. [PMID: 36678842 PMCID: PMC9867180 DOI: 10.3390/pharmaceutics15010213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/25/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
For the selective elimination of deleterious cells (e.g., cancer cells and virus-infected cells), the use of a cytotoxic gene is a promising approach. DNA-based systems have achieved selective cell elimination but risk insertional mutagenesis. Here, we developed a synthetic mRNA-based system to selectively eliminate cells expressing a specific target protein. The synthetic mRNAs used in the system are designed to express an engineered protein pair that are based on a cytotoxic protein, Barnase. Each engineered protein is composed of an N- or C-terminal fragment of Barnase, a target protein binding domain, and an intein that aids in reconstituting full-length Barnase from the two fragments. When the mRNAs are transfected to cells expressing the target protein, both N- and C-terminal Barnase fragments bind to the target protein, causing the intein to excise itself and reconstitute cytotoxic full-length Barnase. In contrast, when the target protein is not present, the reconstitution of full-length Barnase is not induced. Four candidate constructs containing split Barnase were evaluated for the ability to selectively eliminate target protein-expressing cells. One of the candidate sets demonstrated highly selective cell death. This system will be a useful therapeutic tool to selectively eliminate deleterious cells.
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Affiliation(s)
| | - Hideyuki Nakanishi
- Correspondence: (H.N.); (K.I.); Tel.: +81-3-5280-8087 (H.N. & K.I.); Fax: +81-3-5280-8088 (H.N. & K.I.)
| | - Keiji Itaka
- Correspondence: (H.N.); (K.I.); Tel.: +81-3-5280-8087 (H.N. & K.I.); Fax: +81-3-5280-8088 (H.N. & K.I.)
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17
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Chung CZ, Söll D, Krahn N. Creating Selenocysteine-Specific Reporters Using Inteins. Methods Mol Biol 2023; 2676:69-86. [PMID: 37277625 DOI: 10.1007/978-1-0716-3251-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The selenium moiety in selenocysteine (Sec) imparts enhanced chemical properties to this amino acid and ultimately the protein in which it is inserted. These characteristics are attractive for designing highly active enzymes or extremely stable proteins and studying protein folding or electron transfer, to name a few. There are also 25 human selenoproteins, of which many are essential for our survival. The ability to create or study these selenoproteins is significantly hindered by the inability to easily produce them. Engineering translation has yielded simpler systems to facilitate site-specific insertion of Sec; however, Ser misincorporation remains problematic. Therefore, we have designed two Sec-specific reporters which promote high-throughput screening of Sec translation systems to overcome this barrier. This protocol outlines the workflow to engineer these Sec-specific reporters, with the application to any gene of interest and the ability to transfer this strategy to any organism.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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18
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Ohishi H, Shimada S, Uchino S, Li J, Sato Y, Shintani M, Owada H, Ohkawa Y, Pertsinidis A, Yamamoto T, Kimura H, Ochiai H. STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity. Nat Commun 2022; 13:7672. [PMID: 36539402 PMCID: PMC9768169 DOI: 10.1038/s41467-022-35286-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Transcription is a dynamic process. To detect the dynamic relationship among protein clusters of RNA polymerase II and coactivators, gene loci, and transcriptional activity, we insert an MS2 repeat, a TetO repeat, and inteins with a selection marker just downstream of the transcription start site. By optimizing the individual elements, we develop the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system. Clusters of RNA polymerase II and BRD4 are observed proximal to the transcription start site of Nanog when the gene is transcribed in mouse embryonic stem cells. In contrast, clusters of MED19 and MED22 tend to be located near the transcription start site, even without transcription activity. Thus, the STREAMING-tag system reveals the spatiotemporal relationships between transcriptional activity and protein clusters near the gene. This powerful tool is useful for quantitatively understanding transcriptional regulation in living cells.
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Affiliation(s)
- Hiroaki Ohishi
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Seiru Shimada
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Satoshi Uchino
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Jieru Li
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Yuko Sato
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Manabu Shintani
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Hitoshi Owada
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Yasuyuki Ohkawa
- grid.177174.30000 0001 2242 4849Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan
| | - Alexandros Pertsinidis
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Takashi Yamamoto
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
| | - Hiroshi Kimura
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Hiroshi Ochiai
- grid.257022.00000 0000 8711 3200Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-0046 Japan
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19
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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20
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Visual function restoration in a mouse model of Leber congenital amaurosis via therapeutic base editing. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:16-27. [PMID: 36589710 PMCID: PMC9792702 DOI: 10.1016/j.omtn.2022.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Leber congenital amaurosis (LCA), an inherited retinal degeneration, causes severe visual dysfunction in children and adolescents. In patients with LCA, pathogenic variants, such as RPE65, are evident in specific genes, related to the functions of retinal pigment epithelium and photoreceptors. In contrast to the original Cas9, base editing tools can correct pathogenic substitutions without generation of DNA double-stranded breaks (DSBs). In this study, dual adeno-associated virus (AAV) vectors containing split adenine base editors (ABEs) with trans-splicing intein were prepared for in vivo base editing in retinal degeneration of 12 (rd12) mice, an animal model of LCA, possessing a nonsense mutation of C to T transition in the Rpe65 gene (p.R44X). Subretinal injection of AAV-ABE in retinal pigment epithelial cells of rd12 mice resulted in an A to G transition. The on-target editing was sufficient for recovery of wild-type mRNA, RPE65 protein, and light-induced electrical responses from the retina. Compared with our previous therapeutic editing strategies using Cas9 and prime editing, or with the gene transfer strategy shown in the current study, our results suggest that, considering the editing efficacy and functional recovery, ABEs could be a strong, reliable method for correction of pathogenic variants in the treatment of LCA.
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21
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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22
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Lee CH, Lee JH, Lee JY, Cui CH, Cho BK, Kim SC. Novel Split Intein-Mediated Enzymatic Channeling Accelerates the Multimeric Bioconversion Pathway of Ginsenoside. ACS Synth Biol 2022; 11:3296-3304. [PMID: 36150110 DOI: 10.1021/acssynbio.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cascade reaction systems, such as protein fusion and synthetic protein scaffold systems, can both spatially control the metabolic flux and boost the productivity of multistep enzymatic reactions. Despite many efforts to generate fusion proteins, this task remains challenging due to the limited expression of complex enzymes. Therefore, we developed a novel fusion system that bypasses the limited expression of complex enzymes via a post-translational linkage. Here, we report a split intein-mediated cascade system wherein orthogonal split inteins serve as adapters for protein ligation. A genetically programmable, self-assembled, and traceless split intein was utilized to generate a biocatalytic cascade to produce the ginsenoside compound K (CK) with various pharmacological activities, including anticarcinogenic, anti-inflammatory, and antidiabetic effects. We used two types of split inteins, consensus atypical (Cat) and Rma DnaB, to form a covalent scaffold with the three enzymes involved in the CK conversion pathway. The multienzymatic complex with a size greater than 240 kDa was successfully assembled in a soluble form and exhibited specific activity toward ginsenoside conversion. Furthermore, our split intein cascade system significantly increased the CK conversion rate and reduced the production time by more than 2-fold. Our multienzymatic cascade system that uses split inteins can be utilized as a platform for regulating multimeric bioconversion pathways and boosting the production of various high-value substances.
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Affiliation(s)
- Cho-Heun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jun-Hyoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Ju Young Lee
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Korea
| | - Chang-Hao Cui
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sun-Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea.,Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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23
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Sekar G, Stevens AJ, Mostafavi AZ, Sashi P, Muir TW, Cowburn D. A Conserved Histidine Residue Drives Extein Dependence in an Enhanced Atypically Split Intein. J Am Chem Soc 2022; 144:19196-19203. [PMID: 36194550 PMCID: PMC10241006 DOI: 10.1021/jacs.2c08985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Split intein-mediated protein trans-splicing (PTS) is widely applied in chemical biology and biotechnology to carry out traceless and specific protein ligation. However, the external residues immediately flanking the intein (exteins) can reduce the splicing rate, thereby limiting certain applications of PTS. Splicing by a recently developed intein with atypical split architecture ("Cat") exhibits a stark dependence on the sequence of its N-terminal extein residues. Here, we further developed Cat using error-prone polymerase chain reaction (PCR) and a cell-based selection assay to produce Cat*, which exhibits greatly enhanced PTS activity in the presence of unfavorable N-extein residues. We then applied solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations to explore how the dynamics of a conserved B-block histidine residue (His78) contribute to this extein dependence. The enhanced extein tolerance of Cat* reported here should expand the applicability of atypically split inteins, and the mechanism highlights common principles that contribute to extein dependence.
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Affiliation(s)
- Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Anahita Z. Mostafavi
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Pulikallu Sashi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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24
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Padula A, Petruzzelli R, Philbert SA, Church SJ, Esposito F, Campione S, Monti M, Capolongo F, Perna C, Nusco E, Schmidt HH, Auricchio A, Cooper GJ, Polishchuk R, Piccolo P. Full-length ATP7B reconstituted through protein trans-splicing corrects Wilson disease in mice. Mol Ther Methods Clin Dev 2022; 26:495-504. [PMID: 36092366 PMCID: PMC9436707 DOI: 10.1016/j.omtm.2022.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/09/2022] [Indexed: 12/19/2022]
Abstract
Wilson disease (WD) is a genetic disorder of copper homeostasis, caused by deficiency of the copper transporter ATP7B. Gene therapy with recombinant adeno-associated vectors (AAV) holds promises for WD treatment. However, the full-length human ATP7B gene exceeds the limited AAV cargo capacity, hampering the applicability of AAV in this disease context. To overcome this limitation, we designed a dual AAV vector approach using split intein technology. Split inteins catalyze seamless ligation of two separate polypeptides in a highly specific manner. We selected a DnaE intein from Nostoc punctiforme (Npu) that recognizes a specific tripeptide in the human ATP7B coding sequence. We generated two AAVs expressing either the 5′-half of a codon-optimized human ATP7B cDNA followed by the N-terminal Npu DnaE intein or the C-terminal Npu DnaE intein followed by the 3′-half of ATP7B cDNA, under the control of a liver-specific promoter. Intravenous co-injection of the two vectors in wild-type and Atp7b−/− mice resulted in efficient reconstitution of full-length ATP7B protein in the liver. Moreover, Atp7b−/− mice treated with intein-ATP7B vectors were protected from liver damage and showed improvements in copper homeostasis. Taken together, these data demonstrate the efficacy of split intein technology to drive the reconstitution of full-length human ATP7B and to rescue copper-mediated liver damage in Atp7b−/− mice, paving the way to the development of a new gene therapy approach for WD.
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Affiliation(s)
- Agnese Padula
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Raffaella Petruzzelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Scuola Superiore Meridionale, University of Naples Federico II, Naples, Italy
| | - Sasha A. Philbert
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Manchester Academic Health Sciences Centre, Manchester, UK
| | - Stephanie J. Church
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Manchester Academic Health Sciences Centre, Manchester, UK
| | | | | | - Marcello Monti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Claudia Perna
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Hartmut H. Schmidt
- Department of Gastroenterology and Hepatology, University Hospital Duisburg-Essen, Essen, Germany
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Garth J.S. Cooper
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Manchester Academic Health Sciences Centre, Manchester, UK
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | | | - Pasquale Piccolo
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Corresponding author Pasquale Piccolo, PhD, Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy.
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25
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Clark ET, Sievers EE, Debelouchina GT. A Chemical Biology Primer for NMR Spectroscopists. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100044. [PMID: 35494416 PMCID: PMC9053072 DOI: 10.1016/j.jmro.2022.100044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Among structural biology techniques, NMR spectroscopy offers unique capabilities that enable the atomic resolution studies of dynamic and heterogeneous biological systems under physiological and native conditions. Complex biological systems, however, often challenge NMR spectroscopists with their low sensitivity, crowded spectra or large linewidths that reflect their intricate interaction patterns and dynamics. While some of these challenges can be overcome with the development of new spectroscopic approaches, chemical biology can also offer elegant and efficient solutions at the sample preparation stage. In this tutorial, we aim to present several chemical biology tools that enable the preparation of selectively and segmentally labeled protein samples, as well as the introduction of site-specific spectroscopic probes and post-translational modifications. The four tools covered here, namely cysteine chemistry, inteins, native chemical ligation, and unnatural amino acid incorporation, have been developed and optimized in recent years to be more efficient and applicable to a wider range of proteins than ever before. We briefly introduce each tool, describe its advantages and disadvantages in the context of NMR experiments, and offer practical advice for sample preparation and analysis. We hope that this tutorial will introduce beginning researchers in the field to the possibilities chemical biology can offer to NMR spectroscopists, and that it will inspire new and exciting applications in the quest to understand protein function in health and disease.
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Affiliation(s)
- Evan T. Clark
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Elanor E. Sievers
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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26
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Podolsky KA, Masubuchi T, Debelouchina GT, Hui E, Devaraj NK. In Situ Assembly of Transmembrane Proteins from Expressed and Synthetic Components in Giant Unilamellar Vesicles. ACS Chem Biol 2022; 17:1015-1021. [PMID: 35482050 PMCID: PMC9255206 DOI: 10.1021/acschembio.2c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstituting functional transmembrane (TM) proteins into model membranes is challenging due to the difficulty of expressing hydrophobic TM domains, which often require stabilizing detergents that can perturb protein structure and function. Recent model systems solve this problem by linking the soluble domains of membrane proteins to lipids, using noncovalent conjugation. Herein, we test an alternative solution involving the in vitro assembly of TM proteins from synthetic TM domains and expressed soluble domains using chemoselective peptide ligation. We developed an intein mediated ligation strategy to semisynthesize single-pass TM proteins in synthetic giant unilamellar vesicle (GUV) membranes by covalently attaching soluble protein domains to a synthetic TM polypeptide, avoiding the requirement for detergent. We show that the extracellular domain of programmed cell death protein 1, a mammalian immune checkpoint receptor, retains its ligand-binding function at a membrane interface after ligation to a synthetic TM peptide in GUVs, facilitating the study of receptor-ligand interactions.
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Affiliation(s)
- K. A. Podolsky
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, U.S.A
| | - T. Masubuchi
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, CA, U.S.A
| | - G. T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, U.S.A
| | - E. Hui
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, CA, U.S.A
| | - N. K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, U.S.A.,Corresponding Author: Neal K. Devaraj,
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27
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Riedmayr LM, Hinrichsmeyer KS, Karguth N, Böhm S, Splith V, Michalakis S, Becirovic E. dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy. Nat Protoc 2022; 17:781-818. [PMID: 35132255 DOI: 10.1038/s41596-021-00666-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Many disease-causing genes possess functionally equivalent counterparts, which are often expressed in distinct cell types. An attractive gene therapy approach for inherited disorders caused by mutations in such genes is to transcriptionally activate the appropriate counterpart(s) to compensate for the missing gene function. This approach offers key advantages over conventional gene therapies because it is mutation- and gene size-independent. Here, we describe a protocol for the design, execution and evaluation of such gene therapies using dCas9-VPR. We offer guidelines on how to identify functionally equivalent genes, design and clone single guide RNAs and evaluate transcriptional activation in vitro. Moreover, focusing on inherited retinal diseases, we provide a detailed protocol on how to apply this strategy in mice using dual recombinant adeno-associated virus vectors and how to evaluate its functionality and off-target effects in the target tissue. This strategy is in principle applicable to all organisms that possess functionally equivalent genes suitable for transcriptional activation and addresses pivotal unmet needs in gene therapy with high translational potential. The protocol can be completed in 15-20 weeks.
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Affiliation(s)
- Lisa M Riedmayr
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klara S Hinrichsmeyer
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nina Karguth
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sybille Böhm
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victoria Splith
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stylianos Michalakis
- Department of Ophthalmology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elvir Becirovic
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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28
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Wang H, Wang L, Zhong B, Dai Z. Protein Splicing of Inteins: A Powerful Tool in Synthetic Biology. Front Bioeng Biotechnol 2022; 10:810180. [PMID: 35265596 PMCID: PMC8899391 DOI: 10.3389/fbioe.2022.810180] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Inteins are protein segments that are capable of enabling the ligation of flanking extein into a new protein, a process known as protein splicing. Since its discovery, inteins have become powerful biotechnological tools for applications such as protein engineering. In the last 10 years, the development in synthetic biology has further endowed inteins with enhanced functions and diverse utilizations. Here we review these efforts and discuss the future directions.
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Affiliation(s)
- Hao Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lin Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Baihua Zhong
- Materials Interfaces Center, Institute of Advanced Materials Science and Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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29
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Yu G, Qiao Y, Blankenship LR, Liu WR. Protein Synthesis via Activated Cysteine-Directed Protein Ligation. Methods Mol Biol 2022; 2530:159-167. [PMID: 35761048 DOI: 10.1007/978-1-0716-2489-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteins with a functionalized C-terminus are critical to synthesizing large proteins via expressed protein ligation. To overcome the limitations of currently available C-terminus functionalization strategies, we established an approach based on a small molecule cyanylating reagent that chemically activates a cysteine in a recombinant protein at its N-side amide for undergoing nucleophilic acyl substitution with amines. We demonstrated the versatility of this approach by successfully synthesizing RNAse H with its RNA hydrolyzing activity restored and in vitro nucleosome build with a C-terminal posttranslational modified histone H2A. This technique will expand the landscape of protein chemical synthesis and its application in new research fields significantly.
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Affiliation(s)
- Ge Yu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Lauren R Blankenship
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, USA.
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30
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Horikawa M, Sabe H, Onodera Y. Strategies for all-at-once and stepwise selection of cells with multiple genetic manipulations. Biochem Biophys Res Commun 2021; 582:93-99. [PMID: 34695756 DOI: 10.1016/j.bbrc.2021.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/23/2022]
Abstract
The genetic manipulation of cells followed by their selection is indispensable for cell biological research. Although antibiotics-resistant genes are commonly used as selection markers, optimization of the condition for each selective agent is required. Here we utilized split-inteins and the drug-selectable marker puromycin N-acetyltransferase (PAC) to develop a system that enables the selection of cells simultaneously or sequentially transfected with multiple genetic constructs, using only puromycin. The active PAC enzyme was reconstituted by intein-mediated trans-splicing at several inherent or engineered serine/cysteine residues. Multiple splitting and reconstitution of active PAC was readily achieved by selecting optimum division sites based on the cellular tolerance to various puromycin concentrations. To achieve the stepwise selection method, PAC-intein fragments were transduced into cells using a virus-like particle (VLP) composed of HIV-1 gag-pol and VSV-G. The PAC-intein-VLP successfully conferred sufficient PAC activity for puromycin selection, which was quickly diminished in the absence of the VLP. Our findings demonstrate a versatile strategy for establishing markers for all-at-once or stepwise selection of multiple genetic manipulations, which will be useful in many fields of biology.
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Affiliation(s)
- Mei Horikawa
- Department of Molecular Biology, Faculty of Mecidine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Hisataka Sabe
- Department of Molecular Biology, Faculty of Mecidine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Yasuhito Onodera
- Department of Molecular Biology, Faculty of Mecidine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan; Global Center for Biomedical Science and Engineering, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan.
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31
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Ai H, Peng S, Li JB. Chemical methods for studying the crosstalk between histone H2B ubiquitylation and H3 methylation. J Pept Sci 2021; 28:e3381. [PMID: 34811838 DOI: 10.1002/psc.3381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 11/06/2022]
Abstract
The reversible and dynamic post-translational modifications (PTMs) of histones in eukaryotic chromatin are intimately connected to cell development and gene function, and abnormal regulation of PTMs can result in cancer and neurodegenerative diseases. Specific combinations of these modifications are mediated by a series of chromatin proteins that write, erase, and read the "histone codes," but mechanistic studies of the precise biochemical and structural relationships between different sets of modifications and their effects on chromatin function constitute a unique challenge to canonical biochemical approaches. In the past decade, the development and application of chemical methods for investigating histone PTM crosstalks has received considerable attention in the field of chemical biology. In this review, taking the functional crosstalk between H2B ubiquitylation at Lys120 (H2BK120ub) and H3 methylation at Lys79 (H3K79me) as a typical example, we survey recent developments of different chemical methods, in particular, protein synthetic chemistry and protein-based chemical probes, for studying the mechanism of the functional crosstalks of histone PTMs.
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Affiliation(s)
- Huasong Ai
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Shuai Peng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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32
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Yu Y, Ju X, Ding Q. A Nucleocapsid-based Transcomplementation Cell Culture System of SARS-CoV-2 to Recapitulate the Complete Viral Life Cycle. Bio Protoc 2021; 11:e4257. [PMID: 34859136 DOI: 10.21769/bioprotoc.4257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 11/02/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As this virus is classified as a biosafety level-3 (BSL-3) agent, the development of countermeasures and basic research methods is logistically difficult. Recently, using reverse genetics, we developed a BSL-2 cell culture system for production of transcription- and replication-component virus-like-particles (trVLPs) by genetic transcomplementation. The system consists of two parts: SARS-CoV-2 GFP/ΔN genomic RNA, in which the nucleocapsid (N) gene, a critical gene for virion packaging, is replaced by a GFP reporter gene; and a packaging cell line for ectopic expression of N (Caco-2-N). The complete viral life cycle can be recapitulated and confined to Caco-2-N cells, with GFP positivity serving as a surrogate readout for viral infection. In addition, we utilized an intein-mediated protein splicing technique to split the N gene into two independent vectors and generated the Caco-2-Nintein cells as a packaging cell line to further enhance the security of this cell culture model. Altogether, this system provides for a safe and convenient method to produce trVLPs in BSL-2 laboratories. These trVLPs can be modified to incorporate desired mutations, permitting high-throughput screening of antiviral compounds and evaluation of neutralizing antibodies. This protocol describes the details of the trVLP cell culture model to make SARS-CoV-2 research more readily accessible.
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Affiliation(s)
- Yanying Yu
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing 100084, China
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33
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Cheong DE, Choi HJ, Yoo SK, Lee HD, Kim GJ. A designed fusion tag for soluble expression and selective separation of extracellular domains of fibroblast growth factor receptors. Sci Rep 2021; 11:21453. [PMID: 34728710 PMCID: PMC8563715 DOI: 10.1038/s41598-021-01029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) generate various transduction signals by interaction with fibroblast growth factors (FGFs) and are involved in various biological functions such as cell proliferation, migration, and differentiation. Malfunction of these proteins may lead to the development of various diseases, including cancer. Accordingly, FGFRs are considered an alternative therapeutic target for protein and/or gene therapy. However, the screening of antagonists or agonists of FGFRs is challenging due to their complex structural features associated with protein expression. Herein, we conducted the development of a protease-free cleavable tag (PFCT) for enhancing the solubility of difficult-to express protein by combining maltose-binding protein (MBP) and the C-terminal region of Npu intein. To validate the availability of the resulting tag for the functional production of extracellular domains of FGFRs (Ec_FGFRs), we performed fusion of PFCT with the N-terminus of Ec_FGFRs and analyzed the expression patterns. Almost all PFCT-Ec_FGFR fusion proteins were mainly detected in the soluble fraction except for Ec_FGFR4. Upon addition of the N-terminal region of Npu intein, approximately 85% of the PFCT-Ec_FGFRs was separated into PFCT and Ec_FGFR via intein-mediated cleavage. Additionally, the structural integrity of Ec_FGFR was confirmed by affinity purification using heparin column. Taken together, our study demonstrated that the PFCT could be used for soluble expression and selective separation of Ec_FGFRs.
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Affiliation(s)
- Dae-Eun Cheong
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Hye-Ji Choi
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Su-Kyoung Yoo
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Hun-Dong Lee
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea.
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34
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Wall DA, Tarrant SP, Wang C, Mills KV, Lennon CW. Intein Inhibitors as Novel Antimicrobials: Protein Splicing in Human Pathogens, Screening Methods, and Off-Target Considerations. Front Mol Biosci 2021; 8:752824. [PMID: 34692773 PMCID: PMC8529194 DOI: 10.3389/fmolb.2021.752824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 01/20/2023] Open
Abstract
Protein splicing is a post-translational process by which an intervening polypeptide, or intein, catalyzes its own removal from the flanking polypeptides, or exteins, concomitant with extein ligation. Although inteins are highly abundant in the microbial world, including within several human pathogens, they are absent in the genomes of metazoans. As protein splicing is required to permit function of essential proteins within pathogens, inteins represent attractive antimicrobial targets. Here we review key proteins interrupted by inteins in pathogenic mycobacteria and fungi, exciting discoveries that provide proof of concept that intein activity can be inhibited and that this inhibition has an effect on the host organism's fitness, and bioanalytical methods that have been used to screen for intein activity. We also consider potential off-target inhibition of hedgehog signaling, given the similarity in structure and function of inteins and hedgehog autoprocessing domains.
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Affiliation(s)
- Diana A Wall
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Seanan P Tarrant
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States.,Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Christopher W Lennon
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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35
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Production of IgG1-based bispecific antibody without extra cysteine residue via intein-mediated protein trans-splicing. Sci Rep 2021; 11:19411. [PMID: 34593913 PMCID: PMC8484483 DOI: 10.1038/s41598-021-98855-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/09/2021] [Indexed: 11/09/2022] Open
Abstract
A major class of bispecific antibodies (BsAbs) utilizes heterodimeric Fc to produce the native immunoglobulin G (IgG) structure. Because appropriate pairing of heavy and light chains is required, the design of BsAbs produced through recombination or reassembly of two separately-expressed antigen-binding fragments is advantageous. One such method uses intein-mediated protein trans-splicing (IMPTS) to produce an IgG1-based structure. An extra Cys residue is incorporated as a consensus sequence for IMPTS in successful examples, but this may lead to potential destabilization or disturbance of the assay system. In this study, we designed a BsAb linked by IMPTS, without the extra Cys residue. A BsAb binding to both TNFR2 and CD30 was successfully produced. Cleaved side product formation was inevitable, but it was minimized under the optimized conditions. The fine-tuned design is suitable for the production of IgG-like BsAb with high symmetry between the two antigen-binding fragments that is advantageous for screening BsAbs.
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36
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Song H, Burton AJ, Shirran SL, Fahrig-Kamarauskaitė J, Kaspar H, Muir TW, Künzler M, Naismith JH. Engineering of a Peptide α-N-Methyltransferase to Methylate Non-Proteinogenic Amino Acids. Angew Chem Int Ed Engl 2021; 60:14319-14323. [PMID: 33856715 PMCID: PMC8251615 DOI: 10.1002/anie.202100818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Indexed: 12/24/2022]
Abstract
Introduction of α‐N‐methylated non‐proteinogenic amino acids into peptides can improve their biological activities, membrane permeability and proteolytic stability. This is commonly achieved, in nature and in the lab, by assembling pre‐methylated amino acids. The more appealing route of methylating amide bonds is challenging. Biology has evolved an α‐N‐automethylating enzyme, OphMA, which acts on the amide bonds of peptides fused to its C‐terminus. Due to the ribosomal biosynthesis of its substrate, the activity of this enzyme towards peptides with non‐proteinogenic amino acids has not been addressed. An engineered OphMA, intein‐mediated protein ligation and solid‐phase peptide synthesis have allowed us to demonstrate the methylation of amide bonds in the context of non‐natural amides. This approach may have application in the biotechnological production of therapeutic peptides.
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Affiliation(s)
- Haigang Song
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.,The Research Complex at Harwell, Harwell Campus, Oxford, OX11 0FA, UK.,The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - Antony J Burton
- Department of Chemistry, Frick Chemistry Laboratory, Princeton University, Princeton, NJ, USA
| | - Sally L Shirran
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife, KY16 9ST, UK
| | - Jūratė Fahrig-Kamarauskaitė
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hannelore Kaspar
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tom W Muir
- Department of Chemistry, Frick Chemistry Laboratory, Princeton University, Princeton, NJ, USA
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - James H Naismith
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.,The Research Complex at Harwell, Harwell Campus, Oxford, OX11 0FA, UK.,The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
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37
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Song H, Burton AJ, Shirran SL, Fahrig‐Kamarauskaitė J, Kaspar H, Muir TW, Künzler M, Naismith JH. Engineering of a Peptide α-N-Methyltransferase to Methylate Non-Proteinogenic Amino Acids. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:14440-14444. [PMID: 38505374 PMCID: PMC10947093 DOI: 10.1002/ange.202100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Indexed: 11/07/2022]
Abstract
Introduction of α-N-methylated non-proteinogenic amino acids into peptides can improve their biological activities, membrane permeability and proteolytic stability. This is commonly achieved, in nature and in the lab, by assembling pre-methylated amino acids. The more appealing route of methylating amide bonds is challenging. Biology has evolved an α-N-automethylating enzyme, OphMA, which acts on the amide bonds of peptides fused to its C-terminus. Due to the ribosomal biosynthesis of its substrate, the activity of this enzyme towards peptides with non-proteinogenic amino acids has not been addressed. An engineered OphMA, intein-mediated protein ligation and solid-phase peptide synthesis have allowed us to demonstrate the methylation of amide bonds in the context of non-natural amides. This approach may have application in the biotechnological production of therapeutic peptides.
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Affiliation(s)
- Haigang Song
- Division of Structural BiologyWellcome Centre for Human GeneticsRoosevelt DriveOxfordOX3 7BNUK
- The Research Complex at HarwellHarwell CampusOxfordOX11 0FAUK
- The Rosalind Franklin InstituteHarwell CampusOxfordOX11 0FAUK
| | - Antony J. Burton
- Department of ChemistryFrick Chemistry LaboratoryPrinceton UniversityPrincetonNJUSA
| | - Sally L. Shirran
- Biomedical Sciences Research Complex, North HaughUniversity of St. AndrewsFifeKY16 9STUK
| | - Jūratė Fahrig‐Kamarauskaitė
- Department of BiologyInstitute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZürichZürichSwitzerland
| | - Hannelore Kaspar
- Department of BiologyInstitute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZürichZürichSwitzerland
| | - Tom W. Muir
- Department of ChemistryFrick Chemistry LaboratoryPrinceton UniversityPrincetonNJUSA
| | - Markus Künzler
- Department of BiologyInstitute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZürichZürichSwitzerland
| | - James H. Naismith
- Division of Structural BiologyWellcome Centre for Human GeneticsRoosevelt DriveOxfordOX3 7BNUK
- The Research Complex at HarwellHarwell CampusOxfordOX11 0FAUK
- The Rosalind Franklin InstituteHarwell CampusOxfordOX11 0FAUK
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38
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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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39
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Niederacher G, Urwin D, Dijkwel Y, Tremethick DJ, Rosengren KJ, Becker CFW, Conibear AC. Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications. RSC Chem Biol 2021; 2:537-550. [PMID: 34458797 PMCID: PMC8341956 DOI: 10.1039/d0cb00175a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/16/2020] [Indexed: 01/03/2023] Open
Abstract
Interactions between histones, which package DNA in eukaryotes, and nuclear proteins such as the high mobility group nucleosome-binding protein HMGN1 are important for regulating access to DNA. HMGN1 is a highly charged and intrinsically disordered protein (IDP) that is modified at several sites by posttranslational modifications (PTMs) - acetylation, phosphorylation and ADP-ribosylation. These PTMs are thought to affect cellular localisation of HMGN1 and its ability to bind nucleosomes; however, little is known about how these PTMs regulate the structure and function of HMGN1 at a molecular level. Here, we combine the chemical biology tools of protein semi-synthesis and site-specific modification to generate a series of unique HMGN1 variants bearing precise PTMs at their N- or C-termini with segmental isotope labelling for NMR spectroscopy. With access to these precisely-defined variants, we show that PTMs in both the N- and C-termini cause changes in the chemical shifts and conformational populations in regions distant from the PTM sites; up to 50-60 residues upstream of the PTM site. The PTMs investigated had only minor effects on binding of HMGN1 to nucleosome core particles, suggesting that they have other regulatory roles. This study demonstrates the power of combining protein semi-synthesis for introduction of site-specific PTMs with segmental isotope labelling for structural biology, allowing us to understand the role of PTMs with atomic precision, from both structural and functional perspectives.
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Affiliation(s)
- Gerhard Niederacher
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 1090 Vienna Austria
| | - Debra Urwin
- John Curtin School of Medical Research, Department of Genome Sciences, The Australian National University ACT 2601 Australia
| | - Yasmin Dijkwel
- John Curtin School of Medical Research, Department of Genome Sciences, The Australian National University ACT 2601 Australia
| | - David J Tremethick
- John Curtin School of Medical Research, Department of Genome Sciences, The Australian National University ACT 2601 Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland Brisbane QLD 4072 Australia +61-7-3365-1738
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 1090 Vienna Austria
| | - Anne C Conibear
- School of Biomedical Sciences, The University of Queensland Brisbane QLD 4072 Australia +61-7-3365-1738
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40
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Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Transcription factor competition at the γ-globin promoters controls hemoglobin switching. Nat Genet 2021; 53:511-520. [PMID: 33649594 PMCID: PMC8038971 DOI: 10.1038/s41588-021-00798-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023]
Abstract
BCL11A, the major regulator of fetal hemoglobin (HbF, α2γ2) level, represses γ-globin expression through direct promoter binding in adult erythroid cells in a switch to adult hemoglobin (HbA, α2β2). To uncover how BCL11A initiates repression, we used CRISPR-Cas9, dCas9, dCas9-KRAB and dCas9-VP64 screens to dissect the γ-globin promoters and identified an activator element near the BCL11A-binding site. Using CUT&RUN and base editing, we demonstrate that a proximal CCAAT box is occupied by the activator NF-Y. BCL11A competes with NF-Y binding through steric hindrance to initiate repression. Occupancy of NF-Y is rapidly established following BCL11A depletion, and precedes γ-globin derepression and locus control region (LCR)-globin loop formation. Our findings reveal that the switch from fetal to adult globin gene expression within the >50-kb β-globin gene cluster is initiated by competition between a stage-selective repressor and a ubiquitous activating factor within a remarkably discrete region of the γ-globin promoters.
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Affiliation(s)
- Nan Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shuqian Xu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qiuming Yao
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Qian Zhu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Yan Kai
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jonathan Y Hsu
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Phraew Sakon
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit & Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Genetics and Genomic Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel E Bauer
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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41
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Cruz-Samperio R, Jordan M, Perriman A. Cell augmentation strategies for cardiac stem cell therapies. Stem Cells Transl Med 2021; 10:855-866. [PMID: 33660953 PMCID: PMC8133336 DOI: 10.1002/sctm.20-0489] [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: 10/30/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Myocardial infarction (MI) has been the primary cause of death in developed countries, resulting in a major psychological and financial burden for society. Current treatments for acute MI are directed toward rapid restoration of perfusion to limit damage to the myocardium, rather than promoting tissue regeneration and subsequent contractile function recovery. Regenerative cell therapies (CTs), in particular those using multipotent stem cells (SCs), are in the spotlight for treatment post‐MI. Unfortunately, the efficacy of CTs is somewhat limited by their poor long‐term viability, homing, and engraftment to the myocardium. In response, a range of novel SC‐based technologies are in development to provide additional cellular modalities, bringing CTs a step closer to the clinic. In this review, the current landscape of emerging CTs and their augmentation strategies for the treatment post‐MI are discussed. In doing so, we highlight recent advances in cell membrane reengineering via genetic modifications, recombinant protein immobilization, and the utilization of soft biomimetic scaffold interfaces.
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Affiliation(s)
| | - Millie Jordan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Adam Perriman
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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42
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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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43
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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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44
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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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45
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Conibear AC. Deciphering protein post-translational modifications using chemical biology tools. Nat Rev Chem 2020; 4:674-695. [PMID: 37127974 DOI: 10.1038/s41570-020-00223-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Proteins carry out a wide variety of catalytic, regulatory, signalling and structural functions in living systems. Following their assembly on ribosomes and throughout their lifetimes, most eukaryotic proteins are modified by post-translational modifications; small functional groups and complex biomolecules are conjugated to amino acid side chains or termini, and the protein backbone is cleaved, spliced or cyclized, to name just a few examples. These modifications modulate protein activity, structure, location and interactions, and, thereby, control many core biological processes. Aberrant post-translational modifications are markers of cellular stress or malfunction and are implicated in several diseases. Therefore, gaining an understanding of which proteins are modified, at which sites and the resulting biological consequences is an important but complex challenge requiring interdisciplinary approaches. One of the key challenges is accessing precisely modified proteins to assign functional consequences to specific modifications. Chemical biologists have developed a versatile set of tools for accessing specifically modified proteins by applying robust chemistries to biological molecules and developing strategies for synthesizing and ligating proteins. This Review provides an overview of these tools, with selected recent examples of how they have been applied to decipher the roles of a variety of protein post-translational modifications. Relative advantages and disadvantages of each of the techniques are discussed, highlighting examples where they are used in combination and have the potential to address new frontiers in understanding complex biological processes.
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46
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Oeemig JS, Beyer HM, Aranko AS, Mutanen J, Iwaï H. Substrate specificities of inteins investigated by QuickDrop-cassette mutagenesis. FEBS Lett 2020; 594:3338-3355. [PMID: 32805768 DOI: 10.1002/1873-3468.13909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 01/21/2023]
Abstract
Inteins catalyze self-excision from host precursor proteins while concomitantly ligating the flanking substrates (exteins) with a peptide bond. Noncatalytic extein residues near the splice junctions, such as the residues at the -1 and +2 positions, often strongly influence the protein-splicing efficiency. The substrate specificities of inteins have not been studied for many inteins. We developed a convenient mutagenesis platform termed "QuickDrop"-cassette mutagenesis for investigating the influences of 20 amino acid types at the -1 and +2 positions of different inteins. We elucidated 17 different profiles of the 20 amino acid dependencies across different inteins. The substrate specificities will accelerate our understanding of the structure-function relationship at the splicing junctions for broader applications of inteins in biotechnology and molecular biosciences.
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Affiliation(s)
- Jesper S Oeemig
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - A Sesilja Aranko
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Justus Mutanen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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47
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Dynamic structural order of a low-complexity domain facilitates assembly of intermediate filaments. Proc Natl Acad Sci U S A 2020; 117:23510-23518. [PMID: 32907935 PMCID: PMC7519307 DOI: 10.1073/pnas.2010000117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The main point of our manuscript is focused on the structure of the low-complexity (LC) domain of the Tm1-I/C intermediate filament protein in the context of assembled intermediate filaments. We found that the LC tail domain of Tm1-I/C exists in precisely the same cross-β conformation within its proper biologic assembly as it does in labile, amyloid-like polymers made from the tail domain alone. This science represents a conceptually distinct advance that may form the cornerstone understanding of how the thousands of LC domains expressed in eukaryotic cells operate in a mechanistic sense, and stands in conflict with previous research claiming that LC domains function in the absence of molecular structure. The coiled-coil domains of intermediate filament (IF) proteins are flanked by regions of low sequence complexity. Whereas IF coiled-coil domains assume dimeric and tetrameric conformations on their own, maturation of eight tetramers into cylindrical IFs is dependent on either “head” or “tail” domains of low sequence complexity. Here we confirm that the tail domain required for assembly of Drosophila Tm1-I/C IFs functions by forming labile cross-β interactions. These interactions are seen in polymers made from the tail domain alone, as well as in assembled IFs formed by the intact Tm1-I/C protein. The ability to visualize such interactions in situ within the context of a discrete cellular assembly lends support to the concept that equivalent interactions may be used in organizing other dynamic aspects of cell morphology.
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48
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Directed evolution of enzymes. Emerg Top Life Sci 2020; 4:119-127. [PMID: 32893862 DOI: 10.1042/etls20200047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
There are near-to-infinite combinations of possibilities for evolution to happen within nature, making it yet impossible to predict how it occurs. However, science is now able to understand the mechanisms underpinning the evolution of biological systems and can use this knowledge to experimentally mimic nature. The fundamentals of evolution have been used in vitro to improve enzymes as suitable biocatalysts for applications in a process called 'Directed Evolution of Enzymes' (DEE). It replicates nature's evolutionary steps of introducing genetic variability into enzymes, selecting the fittest variants and transmitting the genetic information for the next generation. DEE has tailored biocatalysts for applications, expanding the repertoire of enzymatic activities, besides providing experimental evidences to support mechanistic hypotheses of molecular evolution and deepen our understanding about nature. In this mini review, I discuss the basic concepts of DEE, the most used methodologies and current technical advancements, providing examples of applications and perspectives.
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Vu A, McCray PB. New Directions in Pulmonary Gene Therapy. Hum Gene Ther 2020; 31:921-939. [PMID: 32814451 PMCID: PMC7495918 DOI: 10.1089/hum.2020.166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
The lung has long been a target for gene therapy, yet efficient delivery and phenotypic disease correction has remained challenging. Although there have been significant advancements in gene therapies of other organs, including the development of several ex vivo therapies, in vivo therapeutics of the lung have been slower to transition to the clinic. Within the past few years, the field has witnessed an explosion in the development of new gene addition and gene editing strategies for the treatment of monogenic disorders. In this review, we will summarize current developments in gene therapy for cystic fibrosis, alpha-1 antitrypsin deficiency, and surfactant protein deficiencies. We will explore the different gene addition and gene editing strategies under investigation and review the challenges of delivery to the lung.
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Affiliation(s)
- Amber Vu
- Stead Family Department of Pediatrics, Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
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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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