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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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2
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Lee Y, Kim KM, Nguyen DL, Jannah F, Seong HJ, Kim JM, Kim YP. Cyclized proteins with tags as permeable and stable cargos for delivery into cells and liposomes. Int J Biol Macromol 2023; 252:126520. [PMID: 37625744 DOI: 10.1016/j.ijbiomac.2023.126520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023]
Abstract
Despite the therapeutic potential of recombinant proteins, their cell permeabilities and stabilities remain significant challenges. Here we demonstrate that cyclized recombinant proteins can be used as universal cargos for permeable and stable delivery into cells and polydiacetylene liposomes. Utilizing a split intein-mediated process, cyclized model fluorescent proteins containing short tetraarginine (R4) and hexahistidine (H6) tags were generated without compromising their native protein functions. Strikingly, as compared to linear R4/H6-tagged proteins, the cyclized counterparts have substantially increased permeabilities in both cancer cells and synthetic liposomes, as well as higher resistances to enzymatic degradation in cancer cells. These properties are likely a consequence of structural constraints imposed on the proteins in the presence of short functional peptides. Additionally, photodynamic therapy by cyclized photoprotein-loaded liposomes in cancer cells was significantly improved in comparison to that by their non-cyclized counterparts. These findings suggest that our strategy will be universally applicable to intercellular delivery of proteins and therapeutics.
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Affiliation(s)
- Yeonju Lee
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Kyung-Min Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Duc Long Nguyen
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Fadilatul Jannah
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyun-Jung Seong
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Jong-Man Kim
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; Department of HY-KIST Bio-Convergence, Hanyang University, Seoul 04763, Republic of Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Republic of Korea.
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3
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Xu M, Wang S, Zhan Q, Lin Y. Conditional protein splicing triggered by SUMO protease. Biochem Biophys Res Commun 2023; 655:44-49. [PMID: 36924678 DOI: 10.1016/j.bbrc.2023.03.023] [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: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Conditional protein splicing is a powerful biotechnological tool that can be used to post-translationally control the activity of target proteins. Here we demonstrated a novel conditional protein splicing approach in which the small ubiquitin-like modifier (SUMO) protease induced the splicing of an atypical split intein. The engineered Ter DnaE-3 S11 split intein which has a small C-intein segment with only 6 amino acids was used in this study. A SUMO tag was fused to the N-terminus of the C-intein to inhibit the protein trans-splicing in vitro. The splicing products could be detected in 15 min with the addition of SUMO protease by western blotting and the splicing efficiency was ∼4-fold higher than the control without SUMO protease for overnight reaction. This engineered Ter DnaE-3 S11 split intein-mediated protein trans-splicing had been further shown to be triggered by SUMO protease in different exteins in vitro. Our study provides new insights into the regulation of protein splicing and is a promising tool for the control of protein structure and function in vitro.
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Affiliation(s)
- Minghui Xu
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Suyang Wang
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Qin Zhan
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China
| | - Ying Lin
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, 201620, PR China.
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4
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Fan R, Hakanpää J, Elfving K, Taberman H, Linder MB, Aranko AS. Biomolecular Click Reactions Using a Minimal pH-Activated Catcher/Tag Pair for Producing Native-Sized Spider-Silk Proteins. Angew Chem Int Ed Engl 2023; 62:e202216371. [PMID: 36695475 DOI: 10.1002/anie.202216371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/26/2023]
Abstract
A type of protein/peptide pair known as Catcher/Tag pair spontaneously forms an intermolecular isopeptide bond which can be applied for biomolecular click reactions. Covalent protein conjugation using Catcher/Tag pairs has turned out to be a valuable tool in biotechnology and biomedicines, but it is essential to increase the current toolbox of orthogonal Catcher/Tag pairs to expand the range of applications further, for example, for controlled multiple-fragment ligation. We report here the engineering of novel Catcher/Tag pairs for protein ligation, aided by a crystal structure of a minimal CnaB domain from Lactobacillus plantarum. We show that a newly engineered pair, called SilkCatcher/Tag enables efficient pH-inducible protein ligation in addition to being compatible with the widely used SpyCatcher/Tag pair. Finally, we demonstrate the use of the SilkCatcher/Tag pair in the production of native-sized highly repetitive spider-silk-like proteins with >90 % purity, which is not possible by traditional recombinant production methods.
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Affiliation(s)
- Ruxia Fan
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - Johanna Hakanpää
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany.,Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603, Hamburg, Germany
| | - Karoliina Elfving
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - Helena Taberman
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
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5
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Kim YE, Kim S, Kim IH. Neural circuit-specific gene manipulation in mouse brain in vivo using split-intein-mediated split-Cre system. STAR Protoc 2022; 3:101807. [PMID: 36386891 PMCID: PMC9641071 DOI: 10.1016/j.xpro.2022.101807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neural network studies require efficient genetic tools to analyze individual neural circuit functions in vivo. Thus, we developed an advanced circuit-selective gene manipulating tool utilizing anterograde and retrograde adeno-associated viruses (AAVs) encoding split-intein-mediated split-Cre. This strategy can be applied to visualize a specific neural circuit as well as manipulate multiple genes in the circuit neurons. Here, we describe the production and purification of the AAVs, viral injection to the mouse brain, and imaging analysis for a specific neural circuit. For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).
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Affiliation(s)
- Yong-Eun Kim
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sunwhi Kim
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Il Hwan Kim
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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6
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Hou HW, Bishop CA, Huckauf J, Broer I, Klaus S, Nausch H, Buyel JF. Seed- and leaf-based expression of FGF21-transferrin fusion proteins for oral delivery and treatment of non-alcoholic steatohepatitis. FRONTIERS IN PLANT SCIENCE 2022; 13:998596. [PMID: 36247628 PMCID: PMC9557105 DOI: 10.3389/fpls.2022.998596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Non-alcoholic steatohepatitis (NASH) is a global disease with no effective medication. The fibroblast growth factor 21 (FGF21) can reverse this liver dysfunction, but requires targeted delivery to the liver, which can be achieved via oral administration. Therefore, we fused FGF21 to transferrin (Tf) via a furin cleavage site (F), to promote uptake from the intestine into the portal vein, yielding FGF21-F-Tf, and established its production in both seeds and leaves of commercial Nicotiana tabacum cultivars, compared their expression profile and tested the bioavailability and bioactivity in feeding studies. Since biopharmaceuticals need to be produced in a contained environment, e.g., greenhouses in case of plants, the seed production was increased in this setting from 239 to 380 g m-2 a-1 seed mass with costs of 1.64 € g-1 by side branch induction, whereas leaves yielded 8,193 g m-2 a-1 leave mass at 0.19 € g-1. FGF21-F-Tf expression in transgenic seeds and leaves yielded 6.7 and 5.6 mg kg-1 intact fusion protein, but also 4.5 and 2.3 mg kg-1 additional Tf degradation products. Removing the furin site and introducing the liver-targeting peptide PLUS doubled accumulation of intact FGF21-transferrin fusion protein when transiently expressed in Nicotiana benthamiana from 0.8 to 1.6 mg kg-1, whereas truncation of transferrin (nTf338) and reversing the order of FGF21 and nTf338 increased the accumulation to 2.1 mg kg-1 and decreased the degradation products to 7% for nTf338-FGF21-PLUS. Application of partially purified nTf338-FGF21-PLUS to FGF21-/- mice by oral gavage proved its transfer from the intestine into the blood circulation and acutely affected hepatic mRNA expression. Hence, the medication of NASH via oral delivery of nTf338-FGF21-PLUS containing plants seems possible.
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Affiliation(s)
- Hsuan-Wu Hou
- Department Bioprocess Engineering, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Chair for Agrobiotechnology, University of Rostock, Rostock, Germany
| | - Christopher A. Bishop
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Jana Huckauf
- Chair for Agrobiotechnology, University of Rostock, Rostock, Germany
| | - Inge Broer
- Chair for Agrobiotechnology, University of Rostock, Rostock, Germany
| | - Susanne Klaus
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Henrik Nausch
- Department Bioprocess Engineering, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Johannes F. Buyel
- Department Bioprocess Engineering, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
- Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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7
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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: 4] [Impact Index Per Article: 2.0] [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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8
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Noda N, Ozawa T. Castanospermine suppresses CD44 ectodomain cleavage as revealed by transmembrane bioluminescent sensors. J Cell Sci 2022; 135:274740. [PMID: 35194645 DOI: 10.1242/jcs.259314] [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: 08/24/2021] [Accepted: 02/12/2022] [Indexed: 11/20/2022] Open
Abstract
Cluster of differentiation 44 (CD44) is a single-pass transmembrane glycoprotein that is a widely distributed cell-surface adhesion molecule. CD44 undergoes ectodomain cleavage by membrane-associated metalloproteinases in breast cancer cells. Cleavage plays a critical role in cancer cell migration by mediating the interaction between CD44 and the extracellular matrix. To explore inhibitors of CD44 ectodomain cleavage, we developed two bioluminescent sensors for the detection of CD44 ectodomain cleavage. The sensors were designed as two-transmembrane proteins with split-luciferase fragments, one of which was cyclized by protein trans-splicing of a DnaE intein. These two sensors emit light by the cyclization or the spontaneous complementation of the luciferase fragments. The luminescence intensities decreased by cleavage of the ectodomain in breast cancer cells. The sensors revealed that castanospermine, an α-glucosidase inhibitor, suppressed the ectodomain cleavage of endogenous CD44 in breast cancer cells. Castanospermine also inhibited breast cancer cell invasion. Thus, the sensors are beneficial tools for evaluating the effects of different inhibitors.
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Affiliation(s)
- Natsumi Noda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Fok HKF, Yang Z, Jiang B, Sun F. From 4-arm star proteins to diverse stimuli-responsive molecular networks enabled by orthogonal genetically encoded click chemistries. Polym Chem 2022. [DOI: 10.1039/d2py00036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integrated use of genetically encoded click chemistries and protein topology engineering enabled the creation of various smart protein hydrogels.
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Affiliation(s)
- Hong Kiu Francis Fok
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zhongguang Yang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Bojing Jiang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
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10
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Haim A, Neubacher S, Grossmann TN. Protein Macrocyclization for Tertiary Structure Stabilization. Chembiochem 2021; 22:2672-2679. [PMID: 34060202 PMCID: PMC8453710 DOI: 10.1002/cbic.202100111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Proteins possess unique molecular recognition capabilities and enzymatic activities, features that are usually tied to a particular tertiary structure. To make use of proteins for biotechnological and biomedical purposes, it is often required to enforce their tertiary structure in order to ensure sufficient stability under the conditions inherent to the application of interest. The introduction of intramolecular crosslinks has proven efficient in stabilizing native protein folds. Herein, we give an overview of methods that allow the macrocyclization of expressed proteins, discussing involved reaction mechanisms and structural implications.
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Affiliation(s)
- Anissa Haim
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Incircular B.V.De Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Amsterdam Institute of Molecular and Life SciencesVU University AmsterdamAmsterdamThe Netherlands
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11
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Matsumoto D, Nomura W. Molecular Switch Engineering for Precise Genome Editing. Bioconjug Chem 2021; 32:639-648. [PMID: 33825445 DOI: 10.1021/acs.bioconjchem.1c00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genome editing technology commenced in 1996 with the discovery of the first zinc-finger nuclease. Application of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) associated protein 9 (Cas9) technology to genome editing of mammalian cells allowed researchers to use genome editing more easily and cost-effectively. However, one of the technological problems that remains to be solved is "off-target effects", which are unexpected mutations in nontarget DNA. One significant improvement in genome editing technology has been achieved with molecular/protein engineering. The key to this engineering is a "switch" to control function. In this review, we discuss recent efforts to design novel "switching" systems for precise editing using genome editing tools.
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Affiliation(s)
- Daisuke Matsumoto
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, 734-8553, Japan
| | - Wataru Nomura
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, 734-8553, Japan
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12
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Shi J, Hu J, Yuan Y, Zhang B, Guo W, Wu Y, Jiang L. Genetic Fusion of Transacting Activator of Transcription Peptide to Cyclized Green Fluorescence Protein Improves Stability, Intracellular Delivery, and Tumor Retention. ACS OMEGA 2021; 6:7931-7940. [PMID: 33778304 PMCID: PMC7992142 DOI: 10.1021/acsomega.1c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Therapeutic proteins such as enzymes, hormones, and cytokines suffer from poor stability, inefficient cellular penetration, and rapid clearance from circulation. Conjugation with polymers (such as poly(ethylene glycol)) and fusion with long-acting proteins (such as albumin and Fc fragments) have been utilized to partially address the delivery issues, but these strategies require the introduction of new macromolecular substances, resulting in potential immunogenicity and toxicity. Herein, we report an easy strategy to increase the intracellular delivery efficiency and stability of proteins by combining of sortase-mediated protein cyclization and cell-penetrating peptide (CPP)-mediated intracellular delivery. We, for the first time, genetically constructed a green fluorescence protein (GFP) fused with a CPP, a transacting activator of transcription (TAT) peptide, at its C-terminus for intracellular internalization, and two sortase recognition sequences, pentaglycine and LPETG, at its N- and C-termini for cyclization. Notably, the cyclized GFP-TAT (cGFP-TAT) not only highly retained the photophysical properties of the protein but also significantly improved the in vitro stability compared with the native linear GFP (lGFP) and linear TAT peptide-fused GFP (lGFP-TAT).Moreover, cGFP-TAT showed better cellular internalization ability compared with lGFP. In C26 tumor-inoculated mice, cGFP-TAT exhibited enhanced in vivo tumor retention, with increases of 7.79- and 6.52-fold relative to lGFP and lGFP-TAT in tumor retention 3 h after intratumor administration. This proof-of-concept study has provided an easy strategy to increase the in vitro stability, intracellular delivery efficiency, and in vivo tumor retention of GFP, which would be applicable to numerous therapeutic proteins and peptides for clinical practice.
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Affiliation(s)
- Jianquan Shi
- Department
of Intensive Care Unit, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor
Research Institute, Beijing 101149, China
| | - Jin Hu
- Department
of Medical Research Center, State Key Laboratory of Complex Severe
and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing 100730, China
| | - Yeshuang Yuan
- Department
of Medical Research Center, State Key Laboratory of Complex Severe
and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing 100730, China
- Department
of Microbiology and Immunology, North Sichuan
Medical College, Nanchong 637100, China
| | - Bo Zhang
- Department
of Medical Research Center, State Key Laboratory of Complex Severe
and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing 100730, China
| | - Wenting Guo
- Department
of Medical Research Center, State Key Laboratory of Complex Severe
and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing 100730, China
| | - Yuanhao Wu
- Department
of Medical Research Center, State Key Laboratory of Complex Severe
and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing 100730, China
| | - Lingjuan Jiang
- Department
of Medical Research Center, State Key Laboratory of Complex Severe
and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing 100730, China
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13
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Kagiya G, Sato A, Ogawa R, Hatashita M, Kato M, Kubo M, Kojima F, Kawakami F, Nishimura Y, Abe N, Hyodo F. Real-time visualization of intratumoral necrosis using split-luciferase reconstitution by protein trans-splicing. MOLECULAR THERAPY-ONCOLYTICS 2020; 20:48-58. [PMID: 33575470 PMCID: PMC7851486 DOI: 10.1016/j.omto.2020.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/05/2020] [Indexed: 11/07/2022]
Abstract
Necrosis, a form of cell death, occurs not only with the development of various diseases but also with a tumor tissue response to cancer treatment. Therefore, pursuing progress for cancer therapy through induction of necrosis may be one of the most effective approaches for cancer eradication. We herein describe the development of a real-time imaging system to visualize intratumoral necrosis. The system is composed of two types of cells expressing either one of two necrosis imaging reporters that consist of a DnaE intein sequence linking to one of two split-luciferase fragments. When necrosis occurs in a tumor composed of both of the cells, the two types of leaked reporters can reconstitute the enzymatic activity as a result of protein trans-splicing and thereby emit bioluminescence in the presence of the substrate. This system, which was constructed with shrimp-derived luciferase, allowed in vitro imaging of necrosis. We further confirmed real-time imaging of intratumoral necrosis caused by physical or chemical tissue disruption, validating its application in in vivo necrosis imaging. Thus, the constructed imaging system could be a powerful tool for the optimization of the therapeutic condition for cancer therapy and for the evaluation of novel anticancer drugs targeting necrosis.
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Affiliation(s)
- Go Kagiya
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan.,Regenerative Medicine and Cell Design Research Facility, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Ayaka Sato
- Department of Radiology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, Kanagawa 216-8511, Japan
| | - Ryohei Ogawa
- Department of Radiological Sciences, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Masanori Hatashita
- Biotechnology Division, The Wakasa Wan Energy Research Center, 64-52-1 Nagatani, Tsuruga, Fukui 914-0192, Japan
| | - Mana Kato
- Department of Radiological Services, Tokyo Women's Medical University Hospital, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Makoto Kubo
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan.,Regenerative Medicine and Cell Design Research Facility, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Fumiaki Kojima
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan.,Regenerative Medicine and Cell Design Research Facility, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Fumitaka Kawakami
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan.,Regenerative Medicine and Cell Design Research Facility, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yukari Nishimura
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoya Abe
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Fuminori Hyodo
- Department of Radiology Frontier Science for Imaging, School of Medicine, Gifu University, 1-1 Yanagida, Gifu 501-1194, Japan
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14
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Robinzon S, Cawood AR, Ruiz MA, Gophna U, Altman-Price N, Mills KV. Protein Splicing Activity of the Haloferax volcanii PolB-c Intein Is Sensitive to Homing Endonuclease Domain Mutations. Biochemistry 2020; 59:3359-3367. [PMID: 32822531 DOI: 10.1021/acs.biochem.0c00512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inteins are selfish genetic elements residing in open reading frames that can splice post-translationally, resulting in the ligation of an uninterrupted, functional protein. Like other inteins, the DNA polymerase B (PolB) intein of the halophilic archaeon Haloferax volcanii has an active homing endonuclease (HEN) domain, facilitating its horizontal transmission. Previous work has shown that the presence of the PolB intein exerts a significant fitness cost on the organism compared to an intein-free isogenic H. volcanii. Here, we show that mutation of a conserved residue in the HEN domain not only reduces intein homing but also slows growth. Surprisingly, although this mutation is far from the protein splicing active site, it also significantly reduces in vitro protein splicing. Moreover, two additional HEN domain mutations, which could not be introduced to H. volcanii, presumably due to lethality, also eliminate protein splicing activity in vitro. These results suggest an interplay between HEN residues and the protein splicing domain, despite an over 35 Å separation in a PolB intein homology model. The combination of in vivo and in vitro evidence strongly supports a model of codependence between the self-splicing domain and the HEN domain that has been alluded to by previous in vitro studies of protein splicing with HEN domain-containing inteins.
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Affiliation(s)
- Shachar Robinzon
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alexandra R Cawood
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610, United States
| | - Mercedes A Ruiz
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610, United States
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.,The Open University, Raanana 43107, Israel
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610, United States
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15
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Abstract
In recent years, split inteins have seen widespread use as molecular platforms for the design of a variety of peptide and protein chemistry technologies, most notably protein ligation. The development of these approaches is dependent on the identification and/or design of split inteins with robust activity, stability, and solubility. Here, we describe two approaches to characterize and compare the activities of newly identified or engineered split inteins. The first assay employs an E. coli-based selection system to rapidly screen the activities of many inteins and can be repurposed for directed evolution. The second assay utilizes reverse-phase high-performance liquid chromatography (RP-HPLC) to provide insights into individual chemical steps in the protein splicing reaction, information that can guide further engineering efforts. These techniques provide useful alternatives to common assays that utilize SDS-PAGE to analyze splicing reaction progress.
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16
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17
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Windsor IW, Graff CJ, Raines RT. Circular zymogens of human ribonuclease 1. Protein Sci 2019; 28:1713-1719. [PMID: 31306518 PMCID: PMC6699097 DOI: 10.1002/pro.3686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
The endogenous production of enzymes as zymogens provides a means to control catalytic activities. Here, we describe the heterologous production of ribonuclease 1 (RNase 1), which is the most prevalent secretory ribonuclease in humans, as a zymogen. In folded RNase 1, the N and C termini flank the enzymic active site. By using intein-mediated cis-splicing, we created circular proteins in which access to the active site of RNase 1 is obstructed by an amino-acid sequence that is recognized by the HIV-1 protease. Installing a sequence that does not perturb the RNase 1 fold led to only modest inactivation. In contrast, the ancillary truncation of residues from each terminus led to a substantial decrease in the catalytic activity of the zymogen with the maintenance of thermostability. For optimized zymogens, activation by HIV-1 protease led to a > 104 -fold increase in ribonucleolytic activity at a rate comparable to that for the cleavage of endogenous viral substrates. Molecular modeling indicated that these zymogens are inactivated by conformational distortion in addition to substrate occlusion. Because protease levels are elevated in many disease states and ribonucleolytic activity can be cytotoxic, RNase 1 zymogens have potential as generalizable prodrugs.
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Affiliation(s)
- Ian W. Windsor
- Department of BiochemistryUniversity of Wisconsin−MadisonMadisonWisconsin
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Crystal J. Graff
- Department of BiochemistryUniversity of Wisconsin−MadisonMadisonWisconsin
| | - Ronald T. Raines
- Department of BiochemistryUniversity of Wisconsin−MadisonMadisonWisconsin
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of ChemistryUniversity of Wisconsin−MadisonMadisonWisconsin
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18
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Salwig I, Spitznagel B, Vazquez-Armendariz AI, Khalooghi K, Guenther S, Herold S, Szibor M, Braun T. Bronchioalveolar stem cells are a main source for regeneration of distal lung epithelia in vivo. EMBO J 2019; 38:embj.2019102099. [PMID: 31028085 DOI: 10.15252/embj.2019102099] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/22/2022] Open
Abstract
Bronchioalveolar stem cells (BASCs) are a potential source for lung regeneration, but direct in vivo evidence for a multipotential lineage contribution during homeostasis and disease is critically missing, since specific genetic labeling of BASCs has not been possible. We developed a novel cell tracing approach based on intein-mediated assembly of newly engineered split-effectors, allowing selective targeting of dual-marker expressing BASCs in the mouse lung. RNA sequencing of isolated BASCs demonstrates that BASCs show a distinct transcriptional profile, characterized by co-expression of bronchiolar and alveolar epithelial genes. We found that BASCs generate the majority of distal lung airway cells after bronchiolar damage but only moderately contribute to cellular turnover under homeostatic conditions. Importantly, DTA-mediated ablation of BASCs compromised proper regeneration of distal airways. The study defines BASCs as crucial components of the lung repair machinery and provides a paradigmatic example for the detection and manipulation of stem cells that cannot be recognized by a single marker alone.
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Affiliation(s)
- Isabelle Salwig
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Birgit Spitznagel
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Ana Ivonne Vazquez-Armendariz
- Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Keynoosh Khalooghi
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Stefan Guenther
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Susanne Herold
- Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Marten Szibor
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
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19
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Wang XW, Zhang WB. Chemical Topology and Complexity of Protein Architectures. Trends Biochem Sci 2018; 43:806-817. [DOI: 10.1016/j.tibs.2018.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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20
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Li X, Zhang XL, Cai YM, Zhang L, Lin Y, Meng Q. Site specific labeling of two proteins in one system by atypical split inteins. Int J Biol Macromol 2018; 109:921-931. [DOI: 10.1016/j.ijbiomac.2017.11.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/06/2017] [Accepted: 11/12/2017] [Indexed: 01/25/2023]
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21
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Pavankumar TL. Inteins: Localized Distribution, Gene Regulation, and Protein Engineering for Biological Applications. Microorganisms 2018; 6:E19. [PMID: 29495613 PMCID: PMC5874633 DOI: 10.3390/microorganisms6010019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/24/2018] [Accepted: 02/25/2018] [Indexed: 11/25/2022] Open
Abstract
Inteins are self-splicing polypeptides with an ability to excise themselves from flanking host protein regions with remarkable precision; in the process, they ligate flanked host protein fragments. Inteins are distributed sporadically across all three domains of life (bacteria, archaea, and unicellular eukaryotes). However, their apparent localized distribution in DNA replication, repair, and recombination proteins (the 3Rs), particularly in bacteria and archaea, is enigmatic. Our understanding of the localized distribution of inteins in the 3Rs, and their possible regulatory role in such distribution, is still only partial. Nevertheless, understanding the chemistry of post-translational self-splicing of inteins has opened up opportunities for protein chemists to modify, manipulate, and bioengineer proteins. Protein-splicing technology is adapted to a wide range of applications, starting with untagged protein purification, site-specific protein labeling, protein biotinylation, isotope incorporation, peptide cyclization, as an antimicrobial target, and so on. This review is focused on the chemistry of splicing; the localized distribution of inteins, particularly in the 3Rs and their possible role in regulating host protein function; and finally, the use of protein-splicing technology in various protein engineering applications.
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Affiliation(s)
- Theetha L Pavankumar
- Department of Microbiology and Molecular Genetics, Briggs Hall, One Shields Ave, University of California, Davis, CA 95616, USA.
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22
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Engineered Ssp DnaX inteins for protein splicing with flanking proline residues. Saudi J Biol Sci 2017; 26:854-859. [PMID: 31049014 PMCID: PMC6486613 DOI: 10.1016/j.sjbs.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 07/19/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022] Open
Abstract
Inteins are internal protein sequences capable of catalyzing a protein splicing reaction by self-excising from a precursor protein and simultaneously joining the flanking sequences with a peptide bond. Split inteins have separate pieces (N-intein and C-intein) that reassemble non-covalently to catalyze a protein trans-splicing reaction joining two polypeptides. Protein splicing has become increasingly useful tools in many fields of biological research and biotechnology. However, natural and engineered inteins have failed previously to function when being flanked by proline residue at the -1 or +2 positions, which limits general uses of inteins. In this study, different engineered inteins were tested. We found that engineered Ssp DnaX mini-intein and split inteins could carry out protein splicing with proline at the +2 positions or at both -1 and +2 positions. Under in vivo conditions in E. coli cells, the mini-intein, S1 split intein, and S11 split intein spliced efficiently, whereas the S0 split intein did not splice with proline at both -1 and +2 positions. The S1 and S11 split inteins also trans-spliced efficiently in vitro with proline at the +2 positions or at both -1 and +2 positions, but the S0 split intein trans-spliced inefficiently with proline at the +2 position and did not trans-splice with proline at both -1 and +2 positions. These findings contribute significantly to the toolbox of intein-based technologies by allowing the use of inteins in proteins having proline at the splicing point.
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23
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Qi X, Xiong S. Intein-mediated backbone cyclization of VP1 protein enhanced protection of CVB3-induced viral myocarditis. Sci Rep 2017; 7:41485. [PMID: 28148910 PMCID: PMC5288654 DOI: 10.1038/srep41485] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/21/2016] [Indexed: 01/27/2023] Open
Abstract
CVB3 is a common human pathogen to be highly lethal to newborns and causes viral myocarditis and pancreatitis in adults. However, there is no vaccine available for clinical use. CVB3 capsid protein VP1 is an immunodominant structural protein, containing several B- and T-cell epitopes. However, immunization of mice with VP1 protein is ineffective. Cyclization of peptide is commonly used to improve their in vivo stability and biological activity. Here, we designed and synthesizd cyclic VP1 protein by using engineered split Rma DnaB intein and the cyclization efficiency was 100% in E. coli. As a result, the cyclic VP1 was significantly more stable against irreversible aggregation upon heating and against carboxypeptidase in vitro and the degradation rate was more slowly in vivo. Compared with linear VP1, immunization mice with circular VP1 significantly increased CVB3-specific serum IgG level and augmented CVB3-specific cellular immune responses, consequently afforded better protection against CVB3-induced viral myocarditis. The cyclic VP1 may be a novel candidate protein vaccine for preventing CVB3 infection and similar approaches could be employed to a variety of protein vaccines to enhance their protection effect.
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Affiliation(s)
- Xingmei Qi
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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24
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Ge J, Wang L, Yang C, Ran L, Wen M, Fu X, Fan D, Luo K. Intein-mediated Cre protein assembly for transgene excision in hybrid progeny of transgenic Arabidopsis. PLANT CELL REPORTS 2016; 35:2045-2053. [PMID: 27324752 DOI: 10.1007/s00299-016-2015-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
An approach for restoring recombination activity of complementation split-Cre was developed to excise the transgene in hybrid progeny of GM crops. Growing concerns about the biosafety of genetically modified (GM) crops has currently become a limited factor affecting the public acceptance. Several approaches have been developed to generate selectable-marker-gene-free GM crops. However, no strategy was reported to be broadly applicable to hybrid crops. Previous studies have demonstrated that complementation split-Cre recombinase restored recombination activity in transgenic plants. In this study, we found that split-Cre mediated by split-intein Synechocystis sp. DnaE had high recombination efficiency when Cre recombinase was split at Asp232/Asp233 (866 bp). Furthermore, we constructed two plant expression vectors, pCA-NCre-In and pCA-Ic-CCre, containing NCre866-In and Ic-CCre866 fragments, respectively. After transformation, parent lines of transgenic Arabidopsis with one single copy were generated and used for hybridization. The results of GUS staining demonstrated that the recombination activity of split-Cre could be reassembled in these hybrid progeny of transgenic plants through hybridization and the foreign genes flanked by two loxP sites were efficiently excised. Our strategy may provide an effective approach for generating the next generation of GM hybrid crops without biosafety concerns.
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Affiliation(s)
- Jia Ge
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lijun Wang
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chen Yang
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lingyu Ran
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Mengling Wen
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xianan Fu
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Di Fan
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Keming Luo
- Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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25
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Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci 2016; 17:ijms17081305. [PMID: 27517921 PMCID: PMC5000702 DOI: 10.3390/ijms17081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/13/2023] Open
Abstract
Spider aciniform (wrapping) silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units). In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR) spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1) and the two unit concatemer (W2). Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.
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26
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Freidel C, Kaloyanova S, Peneva K. Chemical tags for site-specific fluorescent labeling of biomolecules. Amino Acids 2016; 48:1357-72. [DOI: 10.1007/s00726-016-2204-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/18/2016] [Indexed: 01/24/2023]
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27
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An Engineered Rare Codon Device for Optimization of Metabolic Pathways. Sci Rep 2016; 6:20608. [PMID: 26852704 PMCID: PMC4745014 DOI: 10.1038/srep20608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/08/2016] [Indexed: 11/21/2022] Open
Abstract
Rare codons generally arrest translation due to rarity of their cognate tRNAs. This property of rare codons can be utilized to regulate protein expression. In this study, a linear relationship was found between expression levels of genes and copy numbers of rare codons inserted within them. Based on this discovery, we constructed a molecular device in Escherichia coli using the rare codon AGG, its cognate tRNA (tRNAArg (CCU)), modified tRNAAsp (GUC → CCU), and truncated aspartyl-tRNA synthetase (TDRS) to switch the expression of reporter genes on or off as well as to precisely regulate their expression to various intermediate levels. To underscore the applicability of our work, we used the rare codon device to alter the expression levels of four genes of the fatty acid synthesis II (FASII) pathway (i.e. fabZ, fabG, fabI, and tesA’) in E. coli to optimize steady-state kinetics, which produced nearly two-fold increase in fatty acid yield. Thus, the proposed method has potential applications in regulating target protein expression at desired levels and optimizing metabolic pathways by precisely tuning in vivo molar ratio of relevant enzymes.
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28
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Weichert N, Hauptmann V, Helmold C, Conrad U. Seed-Specific Expression of Spider Silk Protein Multimers Causes Long-Term Stability. FRONTIERS IN PLANT SCIENCE 2016; 7:6. [PMID: 26858734 PMCID: PMC4729946 DOI: 10.3389/fpls.2016.00006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/06/2016] [Indexed: 05/26/2023]
Abstract
Seeds enable plants to germinate and to grow in situations of limited availability of nutrients. The stable storage of different seed proteins is a remarkable presumption for successful germination and growth. These strategies have been adapted and used in several molecular farming projects. In this study, we explore the benefits of seed-based expression to produce the high molecular weight spider silk protein FLAG using intein-based trans-splicing. Multimers larger than 460 kDa in size are routinely produced, which is above the native size of the FLAG protein. The storage of seeds for 8 weeks and 1 year at an ambient temperature of 15°C does not influence the accumulation level. Even the extended storage time does not influence the typical pattern of multimerized bands. These results show that seeds are the method of choice for stable accumulation of products of complex transgenes and have the capability for long-term storage at moderate conditions, an important feature for the development of suitable downstream processes.
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29
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Lonzarić J, Lebar T, Majerle A, Manček-Keber M, Jerala R. Locked and proteolysis-based transcription activator-like effector (TALE) regulation. Nucleic Acids Res 2016; 44:1471-81. [PMID: 26748097 PMCID: PMC4756844 DOI: 10.1093/nar/gkv1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/26/2015] [Indexed: 11/13/2022] Open
Abstract
Development of orthogonal, designable and adjustable transcriptional regulators is an important goal of synthetic biology. Their activity has been typically modulated through stimulus-induced oligomerization or interaction between the DNA-binding and activation/repression domain. We exploited a feature of the designable Transcription activator-like effector (TALE) DNA-binding domain that it winds around the DNA which allows to topologically prevent it from binding by intramolecular cyclization. This new approach was investigated through noncovalent ligand-induced cyclization or through a covalent split intein cyclization strategy, where the topological inhibition of DNA binding by cyclization and its restoration by a proteolytic release of the topologic constraint was expected. We show that locked TALEs indeed have diminished DNA binding and regain full transcriptional activity by stimulation with the rapamycin ligand or site-specific proteolysis of the peptide linker, with much higher level of activation than rapamycin-induced heterodimerization. Additionally, we demonstrated reversibility, activation of genomic targets and implemented logic gates based on combinations of protein cyclization, proteolytic cleavage and ligand-induced dimerization, where the strongest fold induction was achieved by the proteolytic cleavage of a repression domain from a linear TALE.
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Affiliation(s)
- Jan Lonzarić
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Tina Lebar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Andreja Majerle
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Mateja Manček-Keber
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia EN-FIST Centre of Excellence, Ljubljana 1000, Slovenia
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30
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Dai X, Xun Q, Liu XQ, Meng Q. Cysteine-free non-canonical C-intein for versatile protein C-terminal labeling through trans-splicing. Appl Microbiol Biotechnol 2015; 99:8151-61. [DOI: 10.1007/s00253-015-6796-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/17/2015] [Accepted: 06/23/2015] [Indexed: 11/21/2022]
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31
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Li Y. Split-inteins and their bioapplications. Biotechnol Lett 2015; 37:2121-37. [DOI: 10.1007/s10529-015-1905-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023]
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32
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Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015; 3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022] Open
Abstract
Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
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Affiliation(s)
- Frank H Schumann
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Ranjani Varadan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Praveen P Tayakuniyil
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Jennifer H Grossman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, University of Southern California Los Angeles, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
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Miraula M, Enculescu C, Schenk G, Mitić N. Inteins—A Focus on the Biotechnological Applications of Splicing-Promoting Proteins. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajmb.2015.52005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Aranko AS, Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwaï H. Structure-based engineering and comparison of novel split inteins for protein ligation. MOLECULAR BIOSYSTEMS 2014; 10:1023-34. [PMID: 24574026 PMCID: PMC7709711 DOI: 10.1039/c4mb00021h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein splicing is an autocatalytic process involving self-excision of an internal protein domain, the intein, and concomitant ligation of the two flanking sequences, the exteins, with a peptide bond. Protein splicing can also take place in trans by naturally split inteins or artificially split inteins, ligating the exteins on two different polypeptide chains into one polypeptide chain. Protein trans-splicing could work in foreign contexts by replacing the native extein sequences with other protein sequences. Protein ligation using protein trans-splicing increasingly becomes a useful tool for biotechnological applications such as semi-synthesis of proteins, segmental isotopic labeling, and in vivo protein engineering. However, only a few split inteins have been successfully applied for protein ligation. Naturally split inteins have been widely used, but they are cross-reactive to each other, limiting their applications to multiple-fragment ligation. Based on the three-dimensional structures including two newly determined intein structures, we derived 21 new split inteins from four highly efficient cis-splicing inteins, in order to develop novel split inteins suitable for protein ligation. We systematically compared trans-splicing of 24 split inteins and tested the cross-activities among them to identify orthogonal split intein fragments that could be used in chemical biology and biotechnological applications.
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Affiliation(s)
- A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FIN-00014, Finland.
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Wood DW, Camarero JA. Intein applications: from protein purification and labeling to metabolic control methods. J Biol Chem 2014; 289:14512-9. [PMID: 24700459 DOI: 10.1074/jbc.r114.552653] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The discovery of inteins in the early 1990s opened the door to a wide variety of new technologies. Early engineered inteins from various sources allowed the development of self-cleaving affinity tags and new methods for joining protein segments through expressed protein ligation. Some applications were developed around native and engineered split inteins, which allow protein segments expressed separately to be spliced together in vitro. More recently, these early applications have been expanded and optimized through the discovery of highly efficient trans-splicing and trans-cleaving inteins. These new inteins have enabled a wide variety of applications in metabolic engineering, protein labeling, biomaterials construction, protein cyclization, and protein purification.
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Affiliation(s)
- David W Wood
- From the Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210 and
| | - Julio A Camarero
- the Departments of Pharmacology and Pharmaceutical Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90033
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36
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Topilina NI, Mills KV. Recent advances in in vivo applications of intein-mediated protein splicing. Mob DNA 2014; 5:5. [PMID: 24490831 PMCID: PMC3922620 DOI: 10.1186/1759-8753-5-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/07/2014] [Indexed: 01/27/2023] Open
Abstract
Intein-mediated protein splicing has become an essential tool in modern biotechnology. Fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. Recent work has extended these in vitro applications to the cell or to whole organisms. We review recent advances in intein-mediated protein expression and modification, post-translational processing and labeling, protein regulation by conditional protein splicing, biosensors, and expression of trans-genes.
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Affiliation(s)
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, 1 College Street, Worcester, MA 01610, USA.
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Alford SC, O'Sullivan C, Obst J, Christie J, Howard PL. Conditional protein splicing of α-sarcin in live cells. MOLECULAR BIOSYSTEMS 2014; 10:831-7. [DOI: 10.1039/c3mb70387h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Zhulenkovs D, Jaudzems K, Zajakina A, Leonchiks A. Enzymatic activity of circular sortase A under denaturing conditions: An advanced tool for protein ligation. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Kjelstrup S, Hansen PMP, Thomsen LE, Hansen PR, Løbner-Olesen A. Cyclic peptide inhibitors of the β-sliding clamp in Staphylococcus aureus. PLoS One 2013; 8:e72273. [PMID: 24023733 PMCID: PMC3762901 DOI: 10.1371/journal.pone.0072273] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/12/2013] [Indexed: 12/01/2022] Open
Abstract
Interaction between pairs of Staphylococcus aureus replication proteins was detected in an Escherichia coli based two-hybrid analysis. A reverse two-hybrid system was constructed for selection of compounds that hindered interaction between interacting protein pairs. A number of cyclic peptides, from a library generated by the split intein-mediated circular ligation of peptides and proteins technology, were found to interfere with dimerization of the β-sliding clamp of the replisome. Two 8-mer peptides were analyzed in more detail. Both inhibited DNA replication, led to SOS induction, altered cell morphology and cell death. The peptides were active when added to bacterial cultures indicating that they could traverse the bacterial membrane to find their intracellular target. Peptide specificity was confirmed by overproduction of the putative target (DnaN) which resulted in resistance. The minimum inhibitory concentration was ∼50 μg/ml for S. aureus cells. These compounds may serve as lead candidates for future development into novel classes of antibiotics as well as provide information on the function of the S. aureus replication process.
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Affiliation(s)
- Susanne Kjelstrup
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Line E. Thomsen
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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40
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Wasmuth A, Ludwig C, Mootz HD. Structure-activity studies on the upstream splice junction of a semisynthetic intein. Bioorg Med Chem 2013; 21:3495-503. [PMID: 23618706 DOI: 10.1016/j.bmc.2013.03.065] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/24/2013] [Accepted: 03/26/2013] [Indexed: 01/30/2023]
Abstract
Protein trans-splicing by split inteins holds great potential for the chemical modification and semisynthesis of proteins. However, the structural requirements of the extein sequences immediately flanking the intein are only poorly understood. This knowledge is of particular importance for protein labeling, when synthetic moieties are to be attached to the protein of interest as seamlessly as possible. Using the semisynthetic Ssp DnaB intein both in form of its wild-type sequence and its evolved M86 mutant, we systematically varied the sequence upstream of the short synthetic Int(N) fragment using both proteinogenic amino acids and unnatural building blocks. We could show for the wild-type variant that the native N-extein sequence could be reduced to the glycine residue at the (-1) position directly flanking the intein without significant loss of activity. The glycine at this position is strongly preferred over building blocks containing a phenyl group or extended alkyl chain adjacent to the scissile amide bond of the N-terminal splice junction. Despite their negative effects on the splicing yields, these unnatural substrates were well processed in the N-S acyl shift to form the respective thioesters and did not result in an increased decoupling of the asparagine cyclization step at the C-terminal splicing junction. Therefore, the transesterification step appeared to be the bottleneck of the protein splicing pathway. The fluorophore 7-hydroxycoumarinyl-4-acetic acid as a minimal N-extein was efficiently ligated to the model protein, in particular with the M86 mutant, probably because of its higher resemblance to glycine with an aliphatic c-α carbon atom at the (-1) position. This finding indicates a way for the virtually traceless labeling of proteins without inserting extra flanking residues. Due to its overall higher activity, the M86 mutant appears most promising for many protein labeling and chemical modification schemes using the split intein approach.
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Affiliation(s)
- Alexandra Wasmuth
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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41
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Volkmann G, Mootz HD. Recent progress in intein research: from mechanism to directed evolution and applications. Cell Mol Life Sci 2013; 70:1185-206. [PMID: 22926412 PMCID: PMC11113529 DOI: 10.1007/s00018-012-1120-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 07/23/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
Abstract
Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.
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Affiliation(s)
- Gerrit Volkmann
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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42
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Stoltzfus A. Constructive neutral evolution: exploring evolutionary theory's curious disconnect. Biol Direct 2012; 7:35. [PMID: 23062217 PMCID: PMC3534586 DOI: 10.1186/1745-6150-7-35] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/11/2012] [Indexed: 11/20/2022] Open
Abstract
Abstract Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the “mutational landscape” model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. Reviewers Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article.
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Affiliation(s)
- Arlin Stoltzfus
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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43
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Song H, Meng Q, Liu XQ. Protein trans-splicing of an atypical split intein showing structural flexibility and cross-reactivity. PLoS One 2012; 7:e45355. [PMID: 23024818 PMCID: PMC3443213 DOI: 10.1371/journal.pone.0045355] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/20/2012] [Indexed: 11/18/2022] Open
Abstract
Inteins catalyze a protein splicing reaction to excise the intein from a precursor protein and join the flanking sequences (exteins) with a peptide bond. In a split intein, the intein fragments (IN and IC) can reassemble non-covalently to catalyze a trans-splicing reaction that joins the exteins from separate polypeptides. An atypical split intein having a very small IN and a large IC is particularly useful for joining synthetic peptides with recombinant proteins, which can be a generally useful method of introducing site-specific chemical labeling or modifications into proteins. However, a large IC derived from an Ssp DnaX intein was found recently to undergo spontaneous C-cleavage, which raised questions regarding its structure-function and ability to trans-splice. Here, we show that this IC could undergo trans-splicing in the presence of IN, and the trans-splicing activity completely suppressed the C-cleavage activity. We also found that this IC could trans-splice with small IN sequences derived from two other inteins, showing a cross-reactivity of this atypical split intein. Furthermore, we found that this IC could trans-splice even when the IN sequence was embedded in a nearly complete intein sequence, suggesting that the small IN could project out of the central pocket of the intein to become accessible to the IC. Overall, these findings uncovered a new atypical split intein that can be valuable for peptide-protein trans-splicing, and they also revealed an interesting structural flexibility and cross-reactivity at the active site of this intein.
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Affiliation(s)
- Huiling Song
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People’s Republic of China
- * E-mail: (QM); (XQL)
| | - Xiang-Qin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail: (QM); (XQL)
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44
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Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwaï H. NMR and crystal structures of the Pyrococcus horikoshii RadA intein guide a strategy for engineering a highly efficient and promiscuous intein. J Mol Biol 2012; 421:85-99. [PMID: 22560994 PMCID: PMC3392434 DOI: 10.1016/j.jmb.2012.04.029] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 04/25/2012] [Accepted: 04/27/2012] [Indexed: 11/16/2022]
Abstract
In protein splicing, an intervening protein sequence (intein) in the host protein excises itself out and ligates two split host protein sequences (exteins) to produce a mature host protein. Inteins require the involvement for the splicing of the first residue of the extein that follows the intein (which is Cys, Ser, or Thr). Other extein residues near the splicing junctions could modulate splicing efficiency even when they are not directly involved in catalysis. Mutual interdependence between this molecular parasite (intein) and its host protein (exteins) is not beneficial for intein spread but could be advantageous for intein survival during evolution. Elucidating extein-intein dependency has increasingly become important since inteins are recognized as useful biotechnological tools for protein ligation. We determined the structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidated the structural basis for its high efficiency and directed our efforts of engineering that led to rational design of a functional minimized RadA intein. The crystal structure of the minimized RadA intein also revealed the precise interactions between N-extein and the intein. We systematically analyzed the effects at the -1 position of N-extein and were able to significantly improve the splicing efficiency of a less robust splicing variant by eliminating the unfavorable extein-intein interactions observed in the structure. This work provides an example of how unveiling structure-function relationships of inteins offer a promising way of improving their properties as better tools for protein engineering.
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Affiliation(s)
- Jesper S. Oeemig
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki. P.O. Box 65, Helsinki, FIN-00014, Finland
| | - Dongwen Zhou
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Tommi Kajander
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki. P.O. Box 65, Helsinki, FIN-00014, Finland
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki. P.O. Box 65, Helsinki, FIN-00014, Finland
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van Lieshout JFT, Gutiérrez ONP, Vroom W, Planas A, de Vos WM, van der Oost J, Koutsopoulos S. Thermal stabilization of an endoglucanase by cyclization. Appl Biochem Biotechnol 2012; 167:2039-53. [PMID: 22653681 PMCID: PMC3416981 DOI: 10.1007/s12010-012-9674-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
An intein-driven protein splicing approach allowed for the covalent linkage between the N- and C-termini of a polypeptide chain to create circular variants of the endo-β-1,3-1,4-glucanase, LicA, from Bacillus licheniformis. Two circular variants, LicA-C1 and LicA-C2, which have connecting loops of 20 and 14 amino acids, respectively, showed catalytic activities that are approximately two and three times higher, respectively, compared to that of the linear LicA (LicA-L1). The thermal stability of the circular variants was significantly increased compared to the linear form. Whereas the linear glucanase lost half of its activity after 3 min at 65 °C, the two circular variants have 6-fold (LicA-C1) and 16-fold (LicA-C2) increased half-life time of inactivation. In agreement with this, fluorescence spectroscopy and differential scanning calorimetry studies revealed that circular enzymes undergo structural changes at higher temperatures compared to that of the linear form. The effect of calcium on the conformational stability and function of the circular LicAs was also investigated, and we observed that the presence of calcium ions results in increased thermal stability. The impact of the length of the designed loops on thermal stability of the circular proteins is discussed, and it is suggested that cyclization may be an efficient strategy for the increased stability of proteins.
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Affiliation(s)
- Johan F. T. van Lieshout
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Odette N. Pérez Gutiérrez
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Wietse Vroom
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Sotirios Koutsopoulos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
- Center for Biomedical Engineering, NE47-307, Massachusetts Institute of Technology, Cambridge, MA 02139-4307 USA
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46
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Wang P, Chen T, Sakurai K, Han BX, He Z, Feng G, Wang F. Intersectional Cre driver lines generated using split-intein mediated split-Cre reconstitution. Sci Rep 2012; 2:497. [PMID: 22773946 PMCID: PMC3390602 DOI: 10.1038/srep00497] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/15/2012] [Indexed: 11/09/2022] Open
Abstract
Tissue and cell type highly specific Cre drivers are very rare due to the fact that most genes or promoters used to direct Cre expressions are generally expressed in more than one tissues and/or in multiple cell types. We developed a split-intein based split-Cre system for highly efficient Cre-reconstitution through protein splicing. This split-intein-split-Cre system can be used to intersect the expression patterns of two genes or promoters to restrict full-length Cre reconstitution in their overlapping domains. To test this system in vivo, we selected several conserved human enhancers to drive the expression of either Cre-N-intein-N, or intein-C-Cre-C transgene in different brain regions. In all paired CreN/CreC transgenic mice, Cre-dependent reporter was efficiently induced specifically in the intersectional expression domains of two enhancers. This split-intein based method is simpler to implement compared with other strategies for generating highly-restricted intersectional Cre drivers to study complex tissues such as the nervous system.
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Affiliation(s)
- Ping Wang
- Department of Cell Biology, Box 3709, Duke University Medical Center, Durham, NC, USA
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47
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Borra R, Dong D, Elnagar AY, Woldemariam GA, Camarero JA. In-cell fluorescence activation and labeling of proteins mediated by FRET-quenched split inteins. J Am Chem Soc 2012; 134:6344-53. [PMID: 22404648 DOI: 10.1021/ja300209u] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Methods to visualize, track, and modify proteins in living cells are central for understanding the spatial and temporal underpinnings of life inside cells. Although fluorescent proteins have proven to be extremely useful for in vivo studies of protein function, their utility is inherently limited because their spectral and structural characteristics are interdependent. These limitations have spurred the creation of alternative approaches for the chemical labeling of proteins. We report in this work the use of fluorescence resonance emission transfer (FRET)-quenched DnaE split inteins for the site-specific labeling and concomitant fluorescence activation of proteins in living cells. We have successfully employed this approach for the site-specific in-cell labeling of the DNA binding domain (DBD) of the transcription factor YY1 using several human cell lines. Moreover, we have shown that this approach can be also used for modifying proteins to control their cellular localization and potentially alter their biological activity.
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Affiliation(s)
- Radhika Borra
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90033, USA
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48
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Abstract
The establishment of traits that result from the concerted expression of complementing transgene fragments is a feasible tool for trait control or gene flow control in plants. This chapter describes the methodology for producing herbicide-resistant and pollen-sterile wheat plants by the intein-mediated assembly of inactive precursor protein fragments (protein trans-splicing). We suggest the design of intein-containing vectors for split-transgene expression. We describe transient plant assays that can be used to analyse the functionality of the system and describe the transformation of wheat plants using a split selection marker.We hope that this chapter will be a helpful guideline for researchers who are interested in applying similar split-gene approaches in wheat or other monocotyledonous crops.
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Affiliation(s)
- Mario Gils
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Gatersleben, Germany.
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49
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Abstract
Bacterial replicases are complex, tripartite replicative machines. They contain a polymerase, polymerase III (Pol III), a β₂ processivity factor, and a DnaX complex ATPase that loads β₂ onto DNA and chaperones Pol III onto the newly loaded β₂. Bacterial replicases are highly processive, yet cycle rapidly during Okazaki fragment synthesis in a regulated way. Many bacteria encode both a full-length τ and a shorter γ form of DnaX by a variety of mechanisms. γ appears to be uniquely placed in a single position relative to two τ protomers in a pentameric ring. The polymerase catalytic subunit of Pol III, α, contains a PHP domain that not only binds to a prototypical ε Mg²⁺-dependent exonuclease, but also contains a second Zn²⁺-dependent proofreading exonuclease, at least in some bacteria. This review focuses on a critical evaluation of recent literature and concepts pertaining to the above issues and suggests specific areas that require further investigation.
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Affiliation(s)
- Charles S McHenry
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.
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50
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Charalambous A, Antoniades I, Christodoulou N, Skourides PA. Split-inteins for simultaneous, site-specific conjugation of quantum dots to multiple protein targets in vivo. J Nanobiotechnology 2011; 9:37. [PMID: 21920033 PMCID: PMC3196691 DOI: 10.1186/1477-3155-9-37] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/15/2011] [Indexed: 02/05/2023] Open
Abstract
Background Proteins labelled with Quantum Dots (QDs) can be imaged over long periods of time with ultrahigh spatial and temporal resolution, yielding important information on the spatiotemporal dynamics of proteins within live cells or in vivo. However one of the major problems regarding the use of QDs for biological imaging is the difficulty of targeting QDs onto proteins. We have recently developed a DnaE split intein-based method to conjugate Quantum Dots (QDs) to the C-terminus of target proteins in vivo. In this study, we expand this approach to achieve site-specific conjugation of QDs to two or more proteins simultaneously with spectrally distinguishable QDs for multiparameter imaging of cellular functions. Results Using the DnaE split intein we target QDs to the C-terminus of paxillin and show that paxillin-QD conjugates become localized at focal adhesions allowing imaging of the formation and dissolution of these complexes. We go on to utilize a different split intein, namely Ssp DnaB mini-intein, to demonstrate N-terminal protein tagging with QDs. Combination of these two intein systems allowed us to simultaneously target two distinct proteins with spectrally distinguishable QDs, in vivo, without any cross talk between the two intein systems. Conclusions Multiple target labeling is a unique feature of the intein based methodology which sets it apart from existing tagging methodologies in that, given the large number of characterized split inteins, the number of individual targets that can be simultaneously tagged is only limited by the number of QDs that can be spectrally distinguished within the cell. Therefore, the intein-mediated approach for simultaneous, in vivo, site-specific (N- and C-terminus) conjugation of Quantum Dots to multiple protein targets opens up new possibilities for bioimaging applications and offers an effective system to target QDs and other nanostructures to intracellular compartments as well as specific molecular complexes.
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Affiliation(s)
- Anna Charalambous
- Department of Biological Sciences, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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