1
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Ramanujam V, Crawford T, Cristofori‐Armstrong B, Deuis JR, Jia X, Maxwell MJ, Jami S, Ma L, Vetter I, Mobli M. Structural Basis of the Bivalency of the TRPV1 Agonist DkTx. Angew Chem Int Ed Engl 2024; 63:e202314621. [PMID: 37953402 PMCID: PMC10952689 DOI: 10.1002/anie.202314621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023]
Abstract
Bivalency is a prevalent natural mechanism to enhance receptor avidity. Various two-domain disulfide-rich peptides exhibiting bivalent action have been identified from animal venoms. A unique characteristic of these peptides is that they induce a pharmacological response different from that provoked by any of the constituent domains. The enhanced potency and avidity of such peptides is therefore a consequence of their domain fusion by a peptide linker. The role of the linker itself, beyond conjugation, remains unclear. Here, we investigate how the linker affects the bivalency of the capsaicin receptor (TRPV1) agonist DkTx. We recombinantly produced isotope labelled DkTx using a protein splicing approach, to solve the high-resolution solution structure of DkTx, revealing residual linker order stabilised by linker-domain interactions leading to biased domain orientations. The significance of this was studied using a combination of mutagenesis, spin relaxation studies and electrophysiology measurements. Our results reveal that disrupting the pre-organisation of the domains of DkTx is accompanied by reductions in potency and onset of avidity. Our findings support a model of pre-configured two-domain binding, in favour of the previously suggested sequential binding model. This highlights the significance of ordered elements in linker design and the natural evolution of these in bivalent toxins.
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Affiliation(s)
- Venkatraman Ramanujam
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Theo Crawford
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Ben Cristofori‐Armstrong
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Jennifer R. Deuis
- Institute for Molecular BiosciencesSchool of PharmacyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Xinying Jia
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Michael J. Maxwell
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Sina Jami
- Institute for Molecular BiosciencesSchool of PharmacyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Linlin Ma
- Griffith Institute for Drug DiscoverySchool of Environment and ScienceGriffith UniversityNathan4111QueenslandAustralia
| | - Irina Vetter
- Institute for Molecular BiosciencesSchool of PharmacyThe University of QueenslandSt Lucia4072QueenslandAustralia
| | - Mehdi Mobli
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt Lucia4072QueenslandAustralia
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2
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Zhan Q, Shi C, Jiang Y, Gao X, Lin Y. Efficient splicing of the CPE intein derived from directed evolution of the Cryptococcus neoformans PRP8 intein. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1310-1318. [PMID: 37489009 PMCID: PMC10448054 DOI: 10.3724/abbs.2023135] [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: 01/09/2023] [Accepted: 03/19/2023] [Indexed: 07/26/2023] Open
Abstract
Intein-mediated protein splicing has been widely used in protein engineering; however, the splicing efficiency and extein specificity usually limit its further application. Thus, there is a demand for more general inteins that can overcome these limitations. Here, we study the trans-splicing of CPE intein obtained from the directed evolution of Cne PRP8, which shows that its splicing rate is ~29- fold higher than that of the wild-type. When the +1 residue of C-extein is changed to cysteine, CPE also shows high splicing activity. Faster association and higher affinity may contribute to the high splicing rate compared with wild-type intein. These findings have important implications for the future engineering of inteins and provide clues for fundamental studies of protein structure and folding.
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Affiliation(s)
- Qin Zhan
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Changhua Shi
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Yu Jiang
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
| | - Xianling Gao
- Shandong Guoli Biotechnology Co.Ltd.Jinan250101China
| | - Ying Lin
- College of Biological Science and Medical EngineeringDonghua UniversityShanghai201620China
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3
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Esposito F, Lyubenova H, Tornabene P, Auricchio S, Iuliano A, Nusco E, Merlin S, Olgasi C, Manni G, Gargaro M, Fallarino F, Follenzi A, Auricchio A. Liver gene therapy with intein-mediated F8 trans-splicing corrects mouse haemophilia A. EMBO Mol Med 2022; 14:e15199. [PMID: 35491676 PMCID: PMC9174883 DOI: 10.15252/emmm.202115199] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Liver gene therapy with adeno‐associated viral (AAV) vectors is under clinical investigation for haemophilia A (HemA), the most common inherited X‐linked bleeding disorder. Major limitations are the large size of the F8 transgene, which makes packaging in a single AAV vector a challenge, as well as the development of circulating anti‐F8 antibodies which neutralise F8 activity. Taking advantage of split‐intein‐mediated protein trans‐splicing, we divided the coding sequence of the large and highly secreted F8‐N6 variant in two separate AAV‐intein vectors whose co‐administration to HemA mice results in the expression of therapeutic levels of F8 over time. This occurred without eliciting circulating anti‐F8 antibodies unlike animals treated with the single oversized AAV‐F8 vector under clinical development. Therefore, liver gene therapy with AAV‐F8‐N6 intein should be considered as a potential therapeutic strategy for HemA.
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Affiliation(s)
- Federica Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | | | - Stefano Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Antonella Iuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Simone Merlin
- Department of Health Sciences, University of Piemonte Orientale "Amedeo Avogadro", Novara, Italy
| | - Cristina Olgasi
- Department of Health Sciences, University of Piemonte Orientale "Amedeo Avogadro", Novara, Italy
| | - Giorgia Manni
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Marco Gargaro
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Antonia Follenzi
- Department of Health Sciences, University of Piemonte Orientale "Amedeo Avogadro", Novara, Italy
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics, Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
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4
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SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines. Biosci Rep 2022; 42:230724. [PMID: 35234249 PMCID: PMC8891592 DOI: 10.1042/bsr20212207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
Inteins are auto-processing domains that implement a multistep biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe–S] cluster assembly protein SufB from Mycobacterium tuberculosis (Mtu). Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wildtype (WT) precursor protein. Structural analysis and molecular dynamics (MD) simulations suggested that Mtu SufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N–S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen-specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.
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5
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Nakanishi H, Saito H, Itaka K. Versatile Design of Intracellular Protein-Responsive Translational Regulation System for Synthetic mRNA. ACS Synth Biol 2022; 11:1077-1085. [PMID: 35188747 DOI: 10.1021/acssynbio.1c00567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Synthetic mRNA (mRNA) enables transgene expression without the necessity of nuclear import and the risk of insertional mutagenesis, which makes it an attractive tool for medical applications such as vaccination and protein replacement therapy. For further improvement of mRNA therapeutics, cell-selective translation is desirable, because transgene expression in nontarget cells sometimes causes adverse effects. In this study, we developed an intracellular protein-responsive translational regulation system based on Caliciviral VPg-based translational activator (CaVT) combined with inteins and target protein-binding nanobodies. This system enabled both translational activation and repression in a target protein-dependent manner. Importantly, the target protein can be altered by simply exchanging the nanobodies. The versatile design for target protein-responsive translational regulation holds promise for producing mRNA therapeutics with high safety.
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Affiliation(s)
- Hideyuki Nakanishi
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keiji Itaka
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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6
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Oeemig JS, Beyer HM, Aranko AS, Mutanen J, Iwaï H. Substrate specificities of inteins investigated by QuickDrop-cassette mutagenesis. FEBS Lett 2020; 594:3338-3355. [PMID: 32805768 DOI: 10.1002/1873-3468.13909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 01/21/2023]
Abstract
Inteins catalyze self-excision from host precursor proteins while concomitantly ligating the flanking substrates (exteins) with a peptide bond. Noncatalytic extein residues near the splice junctions, such as the residues at the -1 and +2 positions, often strongly influence the protein-splicing efficiency. The substrate specificities of inteins have not been studied for many inteins. We developed a convenient mutagenesis platform termed "QuickDrop"-cassette mutagenesis for investigating the influences of 20 amino acid types at the -1 and +2 positions of different inteins. We elucidated 17 different profiles of the 20 amino acid dependencies across different inteins. The substrate specificities will accelerate our understanding of the structure-function relationship at the splicing junctions for broader applications of inteins in biotechnology and molecular biosciences.
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Affiliation(s)
- Jesper S Oeemig
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - A Sesilja Aranko
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Justus Mutanen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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7
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Tornabene P, Trapani I, Minopoli R, Centrulo M, Lupo M, de Simone S, Tiberi P, Dell'Aquila F, Marrocco E, Iodice C, Iuliano A, Gesualdo C, Rossi S, Giaquinto L, Albert S, Hoyng CB, Polishchuk E, Cremers FPM, Surace EM, Simonelli F, De Matteis MA, Polishchuk R, Auricchio A. Intein-mediated protein trans-splicing expands adeno-associated virus transfer capacity in the retina. Sci Transl Med 2020; 11:11/492/eaav4523. [PMID: 31092694 DOI: 10.1126/scitranslmed.aav4523] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/21/2018] [Accepted: 04/04/2019] [Indexed: 12/26/2022]
Abstract
Retinal gene therapy with adeno-associated viral (AAV) vectors holds promises for treating inherited and noninherited diseases of the eye. Although clinical data suggest that retinal gene therapy is safe and effective, delivery of large genes is hindered by the limited AAV cargo capacity. Protein trans-splicing mediated by split inteins is used by single-cell organisms to reconstitute proteins. Here, we show that delivery of multiple AAV vectors each encoding one of the fragments of target proteins flanked by short split inteins results in protein trans-splicing and full-length protein reconstitution in the retina of mice and pigs and in human retinal organoids. The reconstitution of large therapeutic proteins using this approach improved the phenotype of two mouse models of inherited retinal diseases. Our data support the use of split intein-mediated protein trans-splicing in combination with AAV subretinal delivery for gene therapy of inherited blindness due to mutations in large genes.
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Affiliation(s)
- Patrizia Tornabene
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Ivana Trapani
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Renato Minopoli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Miriam Centrulo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Mariangela Lupo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Sonia de Simone
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Paola Tiberi
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Fabio Dell'Aquila
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Elena Marrocco
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Carolina Iodice
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Antonella Iuliano
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Carlo Gesualdo
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania L. Vanvitelli, 80131 Naples, Italy
| | - Settimio Rossi
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania L. Vanvitelli, 80131 Naples, Italy
| | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Silvia Albert
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, Netherlands
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Frans P M Cremers
- Department of Ophthalmology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, Netherlands
| | - Enrico M Surace
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania L. Vanvitelli, 80131 Naples, Italy
| | - Maria A De Matteis
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University, 80131 Naples, Italy
| | - Roman Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy. .,Department of Advanced Biomedicine, Federico II University, 80131 Naples, Italy
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8
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Seo HN, Bang D. Promiscuous Trans-splicing Activities Revealed by Next Generation Sequencing-based Analysis of 298 Split Inteins. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0394-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Beyer HM, Iwaï H. Off-Pathway-Sensitive Protein-Splicing Screening Based on a Toxin/Antitoxin System. Chembiochem 2019; 20:1933-1938. [PMID: 30963690 PMCID: PMC6771659 DOI: 10.1002/cbic.201900139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Indexed: 02/04/2023]
Abstract
Protein‐splicing domains are frequently used engineering tools that find application in the in vivo and in vitro ligation of protein domains. Directed evolution is among the most promising technologies used to advance this technology. However, the available screening systems for protein‐splicing activity are associated with bottlenecks such as the selection of pseudo‐positive clones arising from off‐pathway reaction products or fragment complementation. Herein, we report a stringent screening method for protein‐splicing activity in cis and trans, that exclusively selects productively splicing domains. By fusing splicing domains to an intrinsically disordered region of the antidote from the Escherichia coli CcdA/CcdB type II toxin/antitoxin system, we linked protein splicing to cell survival. The screen allows selecting novel cis‐ and trans‐splicing inteins catalyzing productive highly efficient protein splicing, for example, from directed‐evolution approaches or the natural intein sequence space.
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Affiliation(s)
- Hannes M Beyer
- Research Program in Structural Biology and Biophysics, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
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10
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Abd Elhameed HAH, Hajdu B, Balogh RK, Hermann E, Hunyadi-Gulyás É, Gyurcsik B. Purification of proteins with native terminal sequences using a Ni(II)-cleavable C-terminal hexahistidine affinity tag. Protein Expr Purif 2019; 159:53-59. [PMID: 30905870 DOI: 10.1016/j.pep.2019.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 11/26/2022]
Abstract
The role of the termini of protein sequences is often perturbed by remnant amino acids after the specific protease cleavage of the affinity tags and/or by the amino acids encoded by the plasmid at/around the restriction enzyme sites used to insert the genes. Here we describe a method for affinity purification of a metallonuclease with its precisely determined native termini. First, the gene encoding the target protein is inserted into a newly designed cloning site, which contains two self-eliminating BsmBI restriction enzyme sites. As a consequence, the engineered DNA code of Ni(II)-sensitive Ser-X-His-X motif is fused to the 3'-end of the inserted gene followed by the gene of an affinity tag for protein purification purpose. The C-terminal segment starting from Ser mentioned above is cleaved off from purified protein by a Ni(II)-induced protease-like action. The success of the purification and cleavage was confirmed by gel electrophoresis and mass spectrometry, while structural integrity of the purified protein was checked by circular dichroism spectroscopy. Our new protein expression DNA construct is an advantageous tool for protein purification, when the complete removal of affinity or other tags, without any remaining amino acid residue is essential. The described procedure can easily be generalized and combined with various affinity tags at the C-terminus for chromatographic applications.
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Affiliation(s)
- Heba A H Abd Elhameed
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Enikő Hermann
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary.
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11
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Friedel K, Popp MA, Matern JCJ, Gazdag EM, Thiel IV, Volkmann G, Blankenfeldt W, Mootz HD. A functional interplay between intein and extein sequences in protein splicing compensates for the essential block B histidine. Chem Sci 2018; 10:239-251. [PMID: 30713635 PMCID: PMC6333167 DOI: 10.1039/c8sc01074a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/03/2018] [Indexed: 01/28/2023] Open
Abstract
Steric bulk can compensate for a catalytically critical histidine in an intein's active site and promote the N–S acyl shift.
Inteins remove themselves from a precursor protein by protein splicing. Due to the concomitant structural changes of the host protein, this self-processing reaction has enabled many applications in protein biotechnology and chemical biology. We show that the evolved M86 mutant of the Ssp DnaB intein displays a significantly improved tolerance towards non-native amino acids at the N-terminally flanking (–1) extein position compared to the parent intein, in the form of both an artificially trans-splicing split intein and the cis-splicing mini-intein. Surprisingly, side chains with increased steric bulk compared to the native Gly(–1) residue, including d-amino acids, were found to compensate for the essential block B histidine in His73Ala mutants in the initial N–S acyl shift of the protein splicing pathway. In the case of the M86 intein, large (–1) side chains can even rescue protein splicing activity as a whole. With the comparison of three crystal structures, namely of the M86 intein as well as of its Gly(–1)Phe and Gly(–1)Phe/His73Ala mutants, our data supports a model in which the intein's active site can exert a strain by varying mechanisms on the different angles of the scissile bond at the extein–intein junction to effect a ground-state destabilization. The compensatory mechanism of the block B histidine is the first example for the direct functional role of an extein residue in protein splicing. It sheds new light on the extein–intein interplay and on possible consequences of their co-evolution as well as on the laboratory engineering of improved inteins.
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Affiliation(s)
- Kristina Friedel
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Monika A Popp
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany
| | - Julian C J Matern
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Emerich M Gazdag
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany
| | - Ilka V Thiel
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Gerrit Volkmann
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Wulf Blankenfeldt
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics , Technische Universität Braunschweig , Spielmannstraße 7 , 38106 Braunschweig , Germany
| | - Henning D Mootz
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
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12
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Muik A, Reul J, Friedel T, Muth A, Hartmann KP, Schneider IC, Münch RC, Buchholz CJ. Covalent coupling of high-affinity ligands to the surface of viral vector particles by protein trans-splicing mediates cell type-specific gene transfer. Biomaterials 2017; 144:84-94. [PMID: 28825979 DOI: 10.1016/j.biomaterials.2017.07.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/18/2017] [Accepted: 07/22/2017] [Indexed: 02/04/2023]
Abstract
We have established a novel approach for the covalent coupling of large polypeptides to the surface of fully assembled adeno-associated viral gene transfer vector (AAV) particles via split-intein mediated protein-trans-splicing (PTS). This way, we achieved selective gene transfer to distinct cell types. Single-chain variable fragments (scFvs) or designed ankyrin repeat proteins (DARPins), exhibiting high-affinity binding to cell surface receptors selectively expressed on the surface of target cells, were coupled to AAV particles harboring mutations in the capsid proteins which ablate natural receptor usage. Both, the AAV capsid protein VP2 and multiple separately produced targeting ligands recognizing Her2/neu, EpCAM, CD133 or CD30 were genetically fused with complementary split-intein domains. Optimized coupling conditions led to an effective conjugation of each targeting ligand to the universal AAV capsid and translated into specific gene transfer into target receptor-positive cell types in vitro and in vivo. Interestingly, PTS-based AAVs exhibited significantly less gene transfer into target receptor-negative cells than AAVs displaying the same targeting ligand but coupled genetically. Another important consequence of the PTS technology is the possibility to now display scFvs or other antibody-derived domain formats harboring disulfide-bonds in a functionally active form on the surface of AAV particles. Hence, the custom combination of a universal AAV vector particle and targeting ligands of various formats allows for an unprecedented flexibility in the generation of gene transfer vectors targeted to distinct cell types.
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Affiliation(s)
- Alexander Muik
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | - Johanna Reul
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | - Thorsten Friedel
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | - Anke Muth
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | | | - Irene C Schneider
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | - Robert C Münch
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany
| | - Christian J Buchholz
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225, Langen, Germany.
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Tori K, Perler F. Sequential formation of two branched intermediates during protein splicing of class three inteins. Extremophiles 2016; 21:41-49. [PMID: 27704298 PMCID: PMC5222942 DOI: 10.1007/s00792-016-0876-0] [Citation(s) in RCA: 6] [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: 07/15/2016] [Accepted: 09/24/2016] [Indexed: 11/25/2022]
Abstract
Inteins are the protein equivalent of introns. They are seamlessly removed during post-translational maturation of their host protein (extein). Inteins from extremophiles played a key role in understanding intein-mediated protein splicing. There are currently three classes of inteins defined by catalytic mechanism and sequence signatures. This study demonstrates splicing of three class 3 mini-inteins: Burkholderia vietnamiensis G4 Bvi IcmO intein, Mycobacterium smegmatis MC2 155 Msm DnaB-1 intein and Mycobacterium leprae strain TN Mle DnaB intein. B. vietnamiensis has a broad ecological range and remediates trichloroethene. M. smegmatis is a biofilm forming soil bacteria. Although other intein classes have only a single branched intermediate at the C-terminal splice junction, the class 3 intein reaction pathway includes two branched intermediates. The class 3 specific branched intermediate is formed by an internal cysteine, while the C-terminal branch intermediate is at a serine or threonine in all class 3 inteins except the Bvi IcmO intein, where it is a cysteine. This latter cysteine was unable to compensate for mutation of the class 3-specific internal catalytic cysteine despite the Bvi IcmO intein having an N-terminal splice junction naturally tuned for a cysteine nucleophile, demonstrating the mandatory order of branch intermediates in class 3 inteins.
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Affiliation(s)
- Kazuo Tori
- New England Biolabs, Inc., Ipswich, MA 01938 USA
- Takara Bio USA, Inc., 1290 Terra Bella Ave., Mountain View, CA 94043 USA
| | - Francine Perler
- New England Biolabs, Inc., Ipswich, MA 01938 USA
- Perls of Wisdom Biotech Consulting, Brookline, MA 02446 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA
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von der Heyde A, Lockhauserbäumer J, Uetrecht C, Elleuche S. A hydrolase-based reporter system to uncover the protein splicing performance of an archaeal intein. Appl Microbiol Biotechnol 2015; 99:7613-24. [PMID: 26026939 DOI: 10.1007/s00253-015-6689-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/06/2015] [Accepted: 05/17/2015] [Indexed: 11/30/2022]
Abstract
Extein amino acid residues around the splice site junctions affect the functionality of inteins. To identify an optimal sequence context for efficient protein splicing of an intein from the thermoacidophilic archaeon Picrophilus torridus, single extein amino acid residues at the splice site junctions were continuously deleted. The construction of a set of different truncated extein variants showed that this intein tolerates multiple amino acid variations near the excision sites and exhibits full activity when -1 and +1 extein amino acid residues are conserved in an artificial GST-intein-HIS fusion construct. Moreover, splicing of the recombinant intein took place at temperatures between 4 and 42 °C with high efficiency, when produced in Escherichia coli. Therefore, structural model predictions were used to identify optimal insertion sites for the intein to be embedded within a hemicellulase from the psychrophilic bacterium Pseudoalteromonas arctica. The P. torridus intein inserted before amino acid residue Thr75 of the reporter enzyme retained catalytic activity. Moreover, the catalytic activity of the xylan-degrading hydrolase could be easily monitored in routine plate assays and in liquid test measurements at room temperature when produced in recombinant form in E. coli. This tool allows the indirect detection of the intein's catalytic activity to be used in screenings.
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Affiliation(s)
- Amélie von der Heyde
- Hamburg University of Technology (TUHH), Institute of Technical Microbiology, Kasernenstr. 12, 21073, Hamburg, Germany
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