1
|
Wei M, Chen W, Dong Y, Gu Y, Wei D, Zhang J, Ren Y. Hypoxia-Inducible Factor-1α-Activated Protein Switch Based on Allosteric Self-Splicing Reduces Nonspecific Cytotoxicity of Pharmaceutical Drugs. Mol Pharm 2024; 21:5335-5347. [PMID: 39213620 DOI: 10.1021/acs.molpharmaceut.4c00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Protein-based therapeutic agents currently used for targeted tumor therapy exhibit limited penetrability, nonspecific toxicity, and a short circulation half-life. Although targeting cell surface receptors improves cancer selectivity, the receptors are also slightly expressed in normal cells; consequently, the nonspecific toxicity of recombinant protein-based therapeutic agents has not been eliminated. In this study, an allosteric-regulated protein switch was designed that achieved cytoplasmic reorganization of engineered immunotoxins in tumor cells via interactions between allosteric self-splicing elements and cancer markers. It can target the accumulated HIF-1α in hypoxic cancer cells and undergo allosteric activation, and the splicing products were present in hypoxic cancer cells but were absent in normoxic cells, selectively killing tumor cells and reducing nonspecific toxicity to normal cells. The engineered pro-protein provides a platform for targeted therapy of tumors while offering a novel universal strategy for combining the activation of therapeutic functions with specific cancer markers. The allosteric self-splicing element is a powerful tool that significantly reduces the nonspecific cytotoxicity of therapeutic proteins.
Collapse
Affiliation(s)
- Min Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Wenxin Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuguo Dong
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yiyang Gu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian Zhang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuhong Ren
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
2
|
Costello A, Peterson AA, Lanster DL, Li Z, Carver GD, Badran AH. Efficient genetic code expansion without host genome modifications. Nat Biotechnol 2024:10.1038/s41587-024-02385-y. [PMID: 39261591 DOI: 10.1038/s41587-024-02385-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 08/13/2024] [Indexed: 09/13/2024]
Abstract
Supplementing translation with noncanonical amino acids (ncAAs) can yield protein sequences with new-to-nature functions but existing ncAA incorporation strategies suffer from low efficiency and context dependence. We uncover codon usage as a previously unrecognized contributor to efficient genetic code expansion using non-native codons. Relying only on conventional Escherichia coli strains with native ribosomes, we develop a plasmid-based codon compression strategy that minimizes context dependence and improves ncAA incorporation at quadruplet codons. We confirm that this strategy is compatible with all known genetic code expansion resources, which allowed us to identify 12 mutually orthogonal transfer RNA (tRNA)-synthetase pairs. Enabled by these findings, we evolved and optimized five tRNA-synthetase pairs to incorporate a broad repertoire of ncAAs at orthogonal quadruplet codons. Lastly, we extend these resources to an in vivo biosynthesis platform that can readily create >100 new-to-nature peptide macrocycles bearing up to three unique ncAAs. Our approach will accelerate innovations in multiplexed genetic code expansion and the discovery of chemically diverse biomolecules.
Collapse
Affiliation(s)
- Alan Costello
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alexander A Peterson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - David L Lanster
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Doctoral Program in Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Zhiyi Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Doctoral Program in Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Gavriela D Carver
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Diao F, Vasudevan D, Heckscher ES, White BH. Hox gene-specific cellular targeting using split intein Trojan exons. Proc Natl Acad Sci U S A 2024; 121:e2317083121. [PMID: 38602904 PMCID: PMC11047080 DOI: 10.1073/pnas.2317083121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
The Trojan exon method, which makes use of intronically inserted T2A-Gal4 cassettes, has been widely used in Drosophila to create thousands of gene-specific Gal4 driver lines. These dual-purpose lines provide genetic access to specific cell types based on their expression of a native gene while simultaneously mutating one allele of the gene to enable loss-of-function analysis in homozygous animals. While this dual use is often an advantage, the truncation mutations produced by Trojan exons are sometimes deleterious in heterozygotes, perhaps by creating translation products with dominant negative effects. Such mutagenic effects can cause developmental lethality as has been observed with genes encoding essential transcription factors. Given the importance of transcription factors in specifying cell type, alternative techniques for generating specific Gal4 lines that target them are required. Here, we introduce a modified Trojan exon method that retains the targeting fidelity and plug-and-play modularity of the original method but mitigates its mutagenic effects by exploiting the self-splicing capabilities of split inteins. "Split Intein Trojan exons" (siTrojans) ensure that the two truncation products generated from the interrupted allele of the native gene are trans-spliced to create a full-length native protein. We demonstrate the efficacy of siTrojans by generating a comprehensive toolkit of Gal4 and Split Gal4 lines for the segmentally expressed Hox transcription factors and illustrate their use in neural circuit mapping by targeting neurons according to their position along the anterior-posterior axis. Both the method and the Hox gene-specific toolkit introduced here should be broadly useful.
Collapse
Affiliation(s)
- Fengqiu Diao
- Laboratory of Molecular Biology, Section on Neural Function, National Institute of Mental Health, NIH, Bethesda, MD20892
| | - Deeptha Vasudevan
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Ellie S. Heckscher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Benjamin H. White
- Laboratory of Molecular Biology, Section on Neural Function, National Institute of Mental Health, NIH, Bethesda, MD20892
| |
Collapse
|
5
|
Mich JK, Ryu J, Wei AD, Gore BB, Guo R, Bard AM, Martinez RA, Bishaw Y, Luber E, Oliveira Santos LM, Miranda N, Ramirez JM, Ting JT, Lein ES, Levi BP, Kalume FK. AAV-mediated interneuron-specific gene replacement for Dravet syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571820. [PMID: 38168178 PMCID: PMC10760176 DOI: 10.1101/2023.12.15.571820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Dravet syndrome (DS) is a devastating developmental epileptic encephalopathy marked by treatment-resistant seizures, developmental delay, intellectual disability, motor deficits, and a 10-20% rate of premature death. Most DS patients harbor loss-of-function mutations in one copy of SCN1A , which has been associated with inhibitory neuron dysfunction. Here we developed an interneuron-targeting AAV human SCN1A gene replacement therapy using cell class-specific enhancers. We generated a split-intein fusion form of SCN1A to circumvent AAV packaging limitations and deliver SCN1A via a dual vector approach using cell class-specific enhancers. These constructs produced full-length Na V 1.1 protein and functional sodium channels in HEK293 cells and in brain cells in vivo . After packaging these vectors into enhancer-AAVs and administering to mice, immunohistochemical analyses showed telencephalic GABAergic interneuron-specific and dose-dependent transgene biodistribution. These vectors conferred strong dose-dependent protection against postnatal mortality and seizures in two DS mouse models carrying independent loss-of-function alleles of Scn1a, at two independent research sites, supporting the robustness of this approach. No mortality or toxicity was observed in wild-type mice injected with single vectors expressing either the N-terminal or C-terminal halves of SCN1A , or the dual vector system targeting interneurons. In contrast, nonselective neuronal targeting of SCN1A conferred less rescue against mortality and presented substantial preweaning lethality. These findings demonstrate proof-of-concept that interneuron-specific AAV-mediated SCN1A gene replacement is sufficient for significant rescue in DS mouse models and suggest it could be an effective therapeutic approach for patients with DS.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Boral S, Sen S, Kushwaha T, Inampudi KK, De S. Extein residues regulate the catalytic function of Spl DnaX intein enzyme by restricting the near-attack conformations of the active-site residues. Protein Sci 2023; 32:e4699. [PMID: 37313648 PMCID: PMC10288555 DOI: 10.1002/pro.4699] [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: 03/23/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Intein enzymes catalyze the splicing of their flanking polypeptide chains and have found tremendous biotechnological applications. Their terminal residues form the catalytic core and participate in the splicing reaction. Hence, the neighboring N- and C-terminal extein residues influence the catalytic rate. As these extein residues vary depending on the substrate identity, we tested the influence of 20 amino acids at these sites in the Spl DnaX intein and observed significant variation of spliced product as well as N- and C-terminus cleavage product formation. We investigated the dependence of these reactions on the extein residues by molecular dynamics (MD) simulations on eight extein variants, and found that the conformational sampling of the active-site residues of the intein enzyme differed among these extein variants. We found that the extein variants that sample higher population of near-attack conformers (NACs) of the active-site residues undergo higher product formation in our activity assays. Ground state conformers that closely resemble the transition state are referred to as NACs. Very good correlation was observed between the NAC populations from the MD simulations of eight extein variants and the corresponding product formation from our activity assays. Furthermore, this molecular detail enabled us to elucidate the mechanistic roles of several conserved active-site residues in the splicing reaction. Overall, this study shows that the catalytic power of Spl DnaX intein enzyme, and most likely other inteins, depends on the efficiency of formation of NACs in the ground state, which is further modulated by the extein residues.
Collapse
Affiliation(s)
- Soumendu Boral
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Srijon Sen
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Tushar Kushwaha
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Krishna K. Inampudi
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Soumya De
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| |
Collapse
|
8
|
Liu Q, Chen Y, Hu S, Liu W, Xie D, Yang X, Huang W, Liu S, Chen X, Liu H, Huang J. Screening an effective dual-AAV split-CBE system for C-to-T conversion in vivo. Hum Gene Ther 2023. [PMID: 37279283 DOI: 10.1089/hum.2023.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
The cytosine base editor (CBE) has shown promise as a gene editing tool for gene therapy, as it can convert cytidine to thymidine. Adeno-associated virus (AAV) has been widely used for in vivo gene therapy, but its limited 4.7 kb packing capacity presents challenges in delivering CBE by a single AAV. To address this, one feasible solution is to split CBE into two sections for dual-AAV delivery. Here, we utilized BE3 as an example and constructed 22 potential split-BE3 pairs with the combination of 11 splitting sites and two split-inteins (Npu and Rma). These split-BE3 pairs were initially screened in the GFP reporter system, with 6 split-BE3 pairs selected for further evaluation. The subsequent screening of split-BE3 pairs was performed at two endogenous sites in 293T and HeLa cells, revealing that the split-BE3-Rma674, split-BE3-Rma713, and split-BE3-Rma1005 displayed effective C-to-T conversion after transfection. The effectiveness of dual-AAV split-BE3 was further validated in culture cells and adult mouse eyes. Of note, the split-BE3-Rma674 demonstrated the most efficient C-to-T editing after AAV infection, with a maximal editing efficiency of 23.29% ± 10.98% in the mouse RPE cells in vivo. Overall, our study presents a novel split-BE3 system with effective C-to-T conversion, which could be applied to CBE-based in vivo gene therapy.
Collapse
Affiliation(s)
- Qianyi Liu
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, Guangzhou, Guangdong, China;
| | - Yuxi Chen
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province,, Guangzhou, Guangdong, China;
| | - Sihui Hu
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province,, Guangzhou, Guangdong, China;
| | - Weiliang Liu
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| | - Dongchun Xie
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| | - Xin Yang
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| | - Wenyan Huang
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, , Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| | - Simiao Liu
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, , Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| | - Xiaolin Chen
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province,, Guangzhou, Guangdong, China;
| | - Haiying Liu
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol,, Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| | - Junjiu Huang
- Sun Yat-sen University School of Life Science, 98443, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, , Guangzhou, China
- Sun Yat-Sen University, 26469, School of Life Sciences and the First Affiliated Hospital, Key Laboratory of Reproductive Medicine of Guangdong Province, , Guangzhou, Guangdong, China;
| |
Collapse
|
9
|
Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
Collapse
Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
10
|
Peña N, Bland MJ, Sevillano E, Muñoz-Atienza E, Lafuente I, Bakkoury ME, Cintas LM, Hernández PE, Gabant P, Borrero J. In vitro and in vivo production and split-intein mediated ligation (SIML) of circular bacteriocins. Front Microbiol 2022; 13:1052686. [PMID: 36452926 PMCID: PMC9703936 DOI: 10.3389/fmicb.2022.1052686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/26/2022] [Indexed: 07/17/2024] Open
Abstract
Circular bacteriocins are antimicrobial peptides produced by bacteria that after synthesis undergo a head-to-tail circularization. Compared to their linear counterparts, circular bacteriocins are, in general, very stable to temperature and pH changes and more resistant to proteolytic enzymes, being considered as one of the most promising groups of antimicrobial peptides for their potential biotechnological applications. Up to now, only a reduced number of circular bacteriocins have been identified and fully characterized, although many operons potentially coding for new circular bacteriocins have been recently found in the genomes of different bacterial species. The production of these peptides is very complex and depends on the expression of different genes involved in their synthesis, circularization, and secretion. This complexity has greatly limited the identification and characterization of these bacteriocins, as well as their production in heterologous microbial hosts. In this work, we have evaluated a synthetic biology approach for the in vitro and in vivo production combined with a split-intein mediated ligation (SIML) of the circular bacteriocin garvicin ML (GarML). The expression of one single gene is enough to produce a protein that after intein splicing, circularizes in an active peptide with the exact molecular mass and amino acid sequence as native GarML. In vitro production coupled with SIML has been validated with other, well described and not yet characterized, circular bacteriocins. The results obtained suggest that this synthetic biology tool holds great potential for production, engineering, improving and testing the antimicrobial activity of circular bacteriocins.
Collapse
Affiliation(s)
- Nuria Peña
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | | | - Ester Sevillano
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Estefanía Muñoz-Atienza
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Irene Lafuente
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | | | - Luis M. Cintas
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Pablo E. Hernández
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | | | - Juan Borrero
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Madrid, Spain
| |
Collapse
|
11
|
Sekar G, Stevens AJ, Mostafavi AZ, Sashi P, Muir TW, Cowburn D. A Conserved Histidine Residue Drives Extein Dependence in an Enhanced Atypically Split Intein. J Am Chem Soc 2022; 144:19196-19203. [PMID: 36194550 PMCID: PMC10241006 DOI: 10.1021/jacs.2c08985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Split intein-mediated protein trans-splicing (PTS) is widely applied in chemical biology and biotechnology to carry out traceless and specific protein ligation. However, the external residues immediately flanking the intein (exteins) can reduce the splicing rate, thereby limiting certain applications of PTS. Splicing by a recently developed intein with atypical split architecture ("Cat") exhibits a stark dependence on the sequence of its N-terminal extein residues. Here, we further developed Cat using error-prone polymerase chain reaction (PCR) and a cell-based selection assay to produce Cat*, which exhibits greatly enhanced PTS activity in the presence of unfavorable N-extein residues. We then applied solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations to explore how the dynamics of a conserved B-block histidine residue (His78) contribute to this extein dependence. The enhanced extein tolerance of Cat* reported here should expand the applicability of atypically split inteins, and the mechanism highlights common principles that contribute to extein dependence.
Collapse
Affiliation(s)
- Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Anahita Z. Mostafavi
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - Pulikallu Sashi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| |
Collapse
|
12
|
Padula A, Petruzzelli R, Philbert SA, Church SJ, Esposito F, Campione S, Monti M, Capolongo F, Perna C, Nusco E, Schmidt HH, Auricchio A, Cooper GJ, Polishchuk R, Piccolo P. Full-length ATP7B reconstituted through protein trans-splicing corrects Wilson disease in mice. Mol Ther Methods Clin Dev 2022; 26:495-504. [PMID: 36092366 PMCID: PMC9436707 DOI: 10.1016/j.omtm.2022.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/09/2022] [Indexed: 12/19/2022]
Abstract
Wilson disease (WD) is a genetic disorder of copper homeostasis, caused by deficiency of the copper transporter ATP7B. Gene therapy with recombinant adeno-associated vectors (AAV) holds promises for WD treatment. However, the full-length human ATP7B gene exceeds the limited AAV cargo capacity, hampering the applicability of AAV in this disease context. To overcome this limitation, we designed a dual AAV vector approach using split intein technology. Split inteins catalyze seamless ligation of two separate polypeptides in a highly specific manner. We selected a DnaE intein from Nostoc punctiforme (Npu) that recognizes a specific tripeptide in the human ATP7B coding sequence. We generated two AAVs expressing either the 5′-half of a codon-optimized human ATP7B cDNA followed by the N-terminal Npu DnaE intein or the C-terminal Npu DnaE intein followed by the 3′-half of ATP7B cDNA, under the control of a liver-specific promoter. Intravenous co-injection of the two vectors in wild-type and Atp7b−/− mice resulted in efficient reconstitution of full-length ATP7B protein in the liver. Moreover, Atp7b−/− mice treated with intein-ATP7B vectors were protected from liver damage and showed improvements in copper homeostasis. Taken together, these data demonstrate the efficacy of split intein technology to drive the reconstitution of full-length human ATP7B and to rescue copper-mediated liver damage in Atp7b−/− mice, paving the way to the development of a new gene therapy approach for WD.
Collapse
Affiliation(s)
- Agnese Padula
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Raffaella Petruzzelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Scuola Superiore Meridionale, University of Naples Federico II, Naples, Italy
| | - Sasha A. Philbert
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Manchester Academic Health Sciences Centre, Manchester, UK
| | - Stephanie J. Church
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Manchester Academic Health Sciences Centre, Manchester, UK
| | | | | | - Marcello Monti
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Claudia Perna
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Hartmut H. Schmidt
- Department of Gastroenterology and Hepatology, University Hospital Duisburg-Essen, Essen, Germany
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Garth J.S. Cooper
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Manchester Academic Health Sciences Centre, Manchester, UK
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | | | - Pasquale Piccolo
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Corresponding author Pasquale Piccolo, PhD, Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy.
| |
Collapse
|
13
|
Allemann RK, Samperio R, Mart R, Luk L, Tsai YH, Jones A, Cruz-Samperio R. Spatio-temporal control of cell death by selective delivery of photo-activatable proteins. Chembiochem 2022; 23:e202200115. [PMID: 35420232 PMCID: PMC9321962 DOI: 10.1002/cbic.202200115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/10/2022] [Indexed: 11/24/2022]
Abstract
Protein therapeutics offer exquisite selectivity in targeting cellular processes and behaviors, but are rarely used against non‐cell surface targets due to their poor cellular uptake. While cell‐penetrating peptides can be used to deliver recombinant proteins to the cytosol, it is generally difficult to selectively deliver active proteins to target cells. Here, we report a recombinantly produced, intracellular protein delivery and targeting platform that uses a photocaged intein to regulate the spatio‐temporal activation of protein activity in selected cells upon irradiation with light. The platform was successfully demonstrated for two cytotoxic proteins to selectively kill cancer cells after photoactivation of intein splicing. This platform can generically be applied to any protein whose activity can be disrupted by a fused intein, allowing it to underpin a wide variety of future protein therapeutics.
Collapse
Affiliation(s)
- Rudolf K Allemann
- Cardiff University, School of Chemistry, Main Building, Park Place, CF10 3AT, Cardiff, UNITED KINGDOM
| | - Raquel Samperio
- Cardiff University, Chemistry, SchooCardiff University, Main Building, Park Place, CF10 3AT, Cardiff, UNITED KINGDOM
| | - Robert Mart
- Cardiff University, Chemistry, UNITED KINGDOM
| | - Louis Luk
- Cardiff University, Chemistry, UNITED KINGDOM
| | | | - Arwyn Jones
- Cardiff University, School of Pharmacy and Pharmaceutical Sciences, UNITED KINGDOM
| | - Raquel Cruz-Samperio
- University of Bristol School of Cellular and Molecular Medicine, School of Cellular and Molecular Medicine, UNITED KINGDOM
| |
Collapse
|
14
|
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.
Collapse
|
15
|
Ziegler T, Bozoglu T, Kupatt C. AAV-Mediated Somatic Gene Editing for Cardiac and Skeletal Muscle in a Large Animal Model. Methods Mol Biol 2022; 2573:63-74. [PMID: 36040587 DOI: 10.1007/978-1-0716-2707-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here we describe a protocol to produce a recombinant adeno-associated viral vector (rAAV)-based system to deliver the CRISPR-Cas9 complex into porcine skeletal muscle and myocardial cells. We initially describe the genomic composition of the rAAV-CRISPR vectors used in our lab. Furthermore, we give a step-by-step instruction into the production of recombinant viral vectors with high yields and purity. Lastly we describe the minimally invasive injection regimes to target the myocardium in a pig.
Collapse
Affiliation(s)
- Tilman Ziegler
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar der Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Tarik Bozoglu
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar der Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Christian Kupatt
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar der Technical University Munich, Munich, Germany.
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany.
| |
Collapse
|
16
|
Zong H, Han L, Chen J, Pan Z, Wang L, Sun R, Ding K, Xie Y, Jiang H, Lu H, Gilly J, Zhang B, Zhu J. Kinetics study of the natural split Npu DnaE intein in the generation of bispecific IgG antibodies. Appl Microbiol Biotechnol 2021; 106:161-171. [PMID: 34882254 DOI: 10.1007/s00253-021-11707-y] [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: 10/22/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 10/19/2022]
Abstract
Rapid and efficient bispecific antibody (BsAb) production for industrial applications is still facing many challenges. We reported a technology platform for generating bispecific IgG antibodies, "Bispecific Antibody by Protein Trans-splicing (BAPTS)." While the "BAPTS" method has shown potential in high-throughput screening of BsAbs, further understanding and optimizing the methodology is desirable. A large number of BsAbs were selected to illustrate the conversion efficiency and kinetics parameters. The temperature of reaction makes no significant influence in conversion efficiency, which can reach more than 70% within 2 h, and CD3 × HER2 BsAb can reach 90%. By fitting trans-splicing reaction to single-component exponential decay curves, the apparent first-order rate constants at a series of temperatures were determined. The rate constant ranges from 0.02 to 0.11 min-1 at 37 °C, which is a high rate reported for the protein trans-splicing reaction (PTS). The reaction process is activated rapidly with activation energy of 8.9 kcal·mol-1 (CD3 × HER2) and 5.2 kcal·mol-1 (CD3 × EGFR). The BsAbs generated by "BAPTS" technology not only had the similar post-translation modifications to the parental antibodies, but also demonstrated excellent in vitro and in vivo bioactivity. The kinetics parameters and activation energy of the reaction illustrate feasible for high-throughput screening and industrial applications using the "BAPTS" approach. KEY POINTS: • The trans-splicing reaction of Npu DnaE intein in "BAPTS" platform is a rapid process with low reaction activation and high rate. • The BsAb generated by "BAPTS" remained effective in tumor cell killing. • The kinetics parameters and activation energy of the reaction illustrate feasible for high-throughput screening and industrial applications using the "BAPTS" approach.
Collapse
Affiliation(s)
- Huifang Zong
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Han
- Jecho Biopharmaceuticals Co., Ltd., Tianjin, China
| | - Jie Chen
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Zhidi Pan
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Sun
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Ding
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yueqing Xie
- Jecho Laboratories, Inc., Frederick, MD, USA
| | - Hua Jiang
- Jecho Biopharmaceuticals Co., Ltd., Tianjin, China.,Jecho Laboratories, Inc., Frederick, MD, USA
| | - Huili Lu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - John Gilly
- Jecho Biopharmaceuticals Co., Ltd., Tianjin, China
| | - Baohong Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianwei Zhu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China. .,Jecho Biopharmaceuticals Co., Ltd., Tianjin, China. .,Jecho Laboratories, Inc., Frederick, MD, USA.
| |
Collapse
|
17
|
Development of ULYSSIS, a Tool for the Biosynthesis of Cyclotides and Cyclic Knottins. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10336-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Cheong DE, Choi HJ, Yoo SK, Lee HD, Kim GJ. A designed fusion tag for soluble expression and selective separation of extracellular domains of fibroblast growth factor receptors. Sci Rep 2021; 11:21453. [PMID: 34728710 PMCID: PMC8563715 DOI: 10.1038/s41598-021-01029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) generate various transduction signals by interaction with fibroblast growth factors (FGFs) and are involved in various biological functions such as cell proliferation, migration, and differentiation. Malfunction of these proteins may lead to the development of various diseases, including cancer. Accordingly, FGFRs are considered an alternative therapeutic target for protein and/or gene therapy. However, the screening of antagonists or agonists of FGFRs is challenging due to their complex structural features associated with protein expression. Herein, we conducted the development of a protease-free cleavable tag (PFCT) for enhancing the solubility of difficult-to express protein by combining maltose-binding protein (MBP) and the C-terminal region of Npu intein. To validate the availability of the resulting tag for the functional production of extracellular domains of FGFRs (Ec_FGFRs), we performed fusion of PFCT with the N-terminus of Ec_FGFRs and analyzed the expression patterns. Almost all PFCT-Ec_FGFR fusion proteins were mainly detected in the soluble fraction except for Ec_FGFR4. Upon addition of the N-terminal region of Npu intein, approximately 85% of the PFCT-Ec_FGFRs was separated into PFCT and Ec_FGFR via intein-mediated cleavage. Additionally, the structural integrity of Ec_FGFR was confirmed by affinity purification using heparin column. Taken together, our study demonstrated that the PFCT could be used for soluble expression and selective separation of Ec_FGFRs.
Collapse
Affiliation(s)
- Dae-Eun Cheong
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Hye-Ji Choi
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Su-Kyoung Yoo
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Hun-Dong Lee
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Korea.
| |
Collapse
|
19
|
Production of IgG1-based bispecific antibody without extra cysteine residue via intein-mediated protein trans-splicing. Sci Rep 2021; 11:19411. [PMID: 34593913 PMCID: PMC8484483 DOI: 10.1038/s41598-021-98855-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/09/2021] [Indexed: 11/09/2022] Open
Abstract
A major class of bispecific antibodies (BsAbs) utilizes heterodimeric Fc to produce the native immunoglobulin G (IgG) structure. Because appropriate pairing of heavy and light chains is required, the design of BsAbs produced through recombination or reassembly of two separately-expressed antigen-binding fragments is advantageous. One such method uses intein-mediated protein trans-splicing (IMPTS) to produce an IgG1-based structure. An extra Cys residue is incorporated as a consensus sequence for IMPTS in successful examples, but this may lead to potential destabilization or disturbance of the assay system. In this study, we designed a BsAb linked by IMPTS, without the extra Cys residue. A BsAb binding to both TNFR2 and CD30 was successfully produced. Cleaved side product formation was inevitable, but it was minimized under the optimized conditions. The fine-tuned design is suitable for the production of IgG-like BsAb with high symmetry between the two antigen-binding fragments that is advantageous for screening BsAbs.
Collapse
|
20
|
Mangubat-Medina AE, Ball ZT. Triggering biological processes: methods and applications of photocaged peptides and proteins. Chem Soc Rev 2021; 50:10403-10421. [PMID: 34320043 DOI: 10.1039/d0cs01434f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There has been a significant push in recent years to deploy fundamental knowledge and methods of photochemistry toward biological ends. Photoreactive groups have enabled chemists to activate biological function using the concept of photocaging. By granting spatiotemporal control over protein activation, these photocaging methods are fundamental in understanding biological processes. Peptides and proteins are an important group of photocaging targets that present conceptual and technical challenges, requiring precise chemoselectivity in complex polyfunctional environments. This review focuses on recent advances in photocaging techniques and methodologies, as well as their use in living systems. Photocaging methods include genetic and chemical approaches that require a deep understanding of structure-function relationships based on subtle changes in primary structure. Successful implementation of these ideas can shed light on important spatiotemporal aspects of living systems.
Collapse
Affiliation(s)
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
| |
Collapse
|
21
|
Amaranto M, Vaccarello P, Correa EME, Barra JL, Godino A. Novel intein-based self-cleaving affinity tag for recombinant protein production in Escherichia coli. J Biotechnol 2021; 332:126-134. [PMID: 33878389 DOI: 10.1016/j.jbiotec.2021.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/28/2022]
Abstract
We evaluated several intein-based self-cleaving affinity tags for expression and single-step affinity chromatography purification of recombinant proteins produced in Escherichia coli. We used human growth hormone (hGH) as target protein that contains two internal disulfide bridges and an N-terminal phenylalanine. Use of N-terminal thiol-induced Sce VMA1 intein affinity tag resulted in purified hGH deficient in disulfide bonds. Inteins with self-cleavage inducible by pH and/or temperature shift were analyzed. N-terminal Ssp DnaX intein affinity tag resulted in a completely cleaved cytosolic protein, whereas N-terminal Ssp DnaB intein affinity tag resulted in a cytosolic fusion protein incapable of releasing hGH. Periplasmic expression of target protein was analyzed using an N-terminal signal peptide and C-terminal Ssp DnaX pH-inducible self-cleaving affinity tag. The fusion protein was properly expressed in pH 8 buffered culture medium. Fusion of a periplasmic signal peptide to the N-terminus of the POI allowed secretion to the periplasmic region and presence of the natural N-terminal amino acid of the POI following cleavage. Periplasmic expression of hGH fused to this novel C-terminal DnaX intein-based self-cleaving affinity tag made possible expression and purification of hGH protein containing disulfide bonds and free of extra amino acids.
Collapse
Affiliation(s)
- Marilla Amaranto
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Paula Vaccarello
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Elisa M E Correa
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - José L Barra
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Agustina Godino
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| |
Collapse
|
22
|
Kupatt C, Windisch A, Moretti A, Wolf E, Wurst W, Walter MC. Genome editing for Duchenne muscular dystrophy: a glimpse of the future? Gene Ther 2021; 28:542-548. [PMID: 33531685 PMCID: PMC8455335 DOI: 10.1038/s41434-021-00222-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/01/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022]
Abstract
Mutations in Dystrophin, one of the largest proteins in the mammalian body, are causative for a severe form of muscle disease, Duchenne Muscular Dystrophy (DMD), affecting not only skeletal muscle, but also the heart. In particular, exons 45–52 constitute a hotspot for DMD mutations. A variety of molecular therapies have been developed, comprising vectors encoding micro- and minidystrophins as well as utrophin, a protein with partially overlapping functions. With the advent of the CRISPR-Cas9-nuclease, genome editing offers a novel option of correction of the disease-cuasing mutations. Full restoration of the healthy gene by homology directed repair is a rare event. However, non-homologous end-joining (NHEJ) may restore the reading frame by causing exon excision. This approach has first been demonstrated in mice and then translated to large animals (dogs, pigs). This review discusses the potential opportunities and limitations of genome editing in DMD, including the generation of appropriate animal models as well as new developments in genome editing tools.
Collapse
Affiliation(s)
- Christian Kupatt
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich, Germany. .,DZHK (German Center for Cardiovascular Research), Munich Heart Alliance, Munich, Germany.
| | - Alina Windisch
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,DZHK (German Center for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Alessandra Moretti
- Klinik und Poliklinik für Innere Medizin I, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,DZHK (German Center for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, and Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Wolfgang Wurst
- Institute of Development Genetics, Helmholtz-Centre Munich, Munich, Germany.,German Center for Neurodegenerative Diseases, Munich, Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Maggie C Walter
- Friedrich Baur Institute, Department of Neurology, LMU Munich, Munich, Germany
| |
Collapse
|
23
|
Chiarini V, Fiorillo A, Camerini S, Crescenzi M, Nakamura S, Battista T, Guidoni L, Colotti G, Ilari A. Structural basis of ubiquitination mediated by protein splicing in early Eukarya. Biochim Biophys Acta Gen Subj 2021; 1865:129844. [PMID: 33444728 DOI: 10.1016/j.bbagen.2021.129844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Inteins are intervening proteins, which are known to perform protein splicing. The reaction results in the production of an intein domain and an inteinless protein, which shows no trace of the insertion. BIL2 is part of the polyubiquitin locus of Tetrahymena thermophila (BUBL), where two bacterial-intein-like (BIL) domains lacking the C + 1 nucleophile, are flanked by two independent ubiquitin-like domains (ubl4/ubl5). METHODS We solved the X-ray structures of BIL2 in both the inactive and unprecedented, zinc-induced active, forms. Then, we characterized by mass spectrometry the BUBL splicing products in the absence and in the presence of T.thRas-GTPase. Finally, we investigated the effect of ubiquitination on T.thRas-GTPase by molecular dynamics simulations. RESULTS The structural analysis demonstrated that zinc-induced conformational change activates protein splicing. Moreover, mass spectrometry characterization of the splicing products shed light on the possible function of BIL2, which operates as a "single-ubiquitin-dispensing-platform", allowing the conjugation, via isopeptide bond formation (K(εNH2)-C-ter), of ubl4 to either ubl5 or T.thRas-GTPase. Lastly, we demonstrated that T.thRas-GTPase ubiquitination occurs in proximity of the nucleotide binding pocket and stabilizes the protein active state. CONCLUSIONS We demonstrated that BIL2 is activated by zinc and that protein splicing induced by this intein does not take place through classical or aminolysis mechanisms but via formation of a covalent isopeptide bond, causing the ubiquitination of endogenous substrates such as T.thRas-GTPase. GENERAL SIGNIFICANCE In this "enzyme-free" ubiquitination mechanism the isopeptide formation, which canonically requires E1-E2-E3 enzymatic cascade and constitutes the alphabet of ubiquitin biology, is achieved in a single, concerted step without energy consumption.
Collapse
Affiliation(s)
- Valerio Chiarini
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014 Helsinki, Finland
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Serena Camerini
- Core Facilities, Italian National Institute of Health, viale Regina Elena 299, 00161 Rome, Italy
| | - Marco Crescenzi
- Core Facilities, Italian National Institute of Health, viale Regina Elena 299, 00161 Rome, Italy
| | - Shin Nakamura
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Theo Battista
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Chimiche e Fisiche, Università degli Studi dell'Aquila, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology of The National Research Council of Italy (CNR), P.le A. Moro 5, 00185 Rome, Italy.
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of The National Research Council of Italy (CNR), P.le A. Moro 5, 00185 Rome, Italy.
| |
Collapse
|
24
|
Inteins in Science: Evolution to Application. Microorganisms 2020; 8:microorganisms8122004. [PMID: 33339089 PMCID: PMC7765530 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.
Collapse
|
25
|
Kawase M, Fujioka M, Takahashi T. Activation of Protease and Luciferase Using Engineered Nostoc punctiforme PCC73102 DnaE Intein with Altered Split Position. Chembiochem 2020; 22:577-584. [PMID: 32969142 DOI: 10.1002/cbic.202000609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/17/2020] [Indexed: 12/22/2022]
Abstract
Inteins, self-catalytic enzymes, have been widely used in the field of protein engineering and chemical biology. Here, Nostoc punctiforme PCC73102 (Npu) DnaE intein was engineered to have an altered split position. An 11-residue N-intein of DnaE in which Gly and Asp were substituted for Tyr4 and Glu5, respectively, was designed, and the active C-intein variants were acquired by a GFP fluorescence-based screening. The designed N-intein and the obtained active C-intein variants were used to construct a turn-on system for enzyme activities such as human immunodeficiency 1 protease and NanoLuc luciferase. Based on the NanoLuc-intein fusion, we developed two intein pairs, each of which is capable of reacting preferentially, by interchanging the charged amino acids on N- and C-inteins. The specific splicing reactions were easily monitored and discriminated by bioluminescence resonance energy transfer (BRET).
Collapse
Affiliation(s)
- Misaki Kawase
- Faculty of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Meiko Fujioka
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Tsuyoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Purde V, Kudryashova E, Heisler DB, Shakya R, Kudryashov DS. Intein-mediated cytoplasmic reconstitution of a split toxin enables selective cell ablation in mixed populations and tumor xenografts. Proc Natl Acad Sci U S A 2020; 117:22090-22100. [PMID: 32839344 PMCID: PMC7486740 DOI: 10.1073/pnas.2006603117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The application of proteinaceous toxins for cell ablation is limited by their high on- and off-target toxicity, severe side effects, and a narrow therapeutic window. The selectivity of targeting can be improved by intein-based toxin reconstitution from two dysfunctional fragments provided their cytoplasmic delivery via independent, selective pathways. While the reconstitution of proteins from genetically encoded elements has been explored, exploiting cell-surface receptors for boosting selectivity has not been attained. We designed a robust splitting algorithm and achieved reliable cytoplasmic reconstitution of functional diphtheria toxin from engineered intein-flanked fragments upon receptor-mediated delivery of one of them to the cells expressing the counterpart. Retargeting the delivery machinery toward different receptors overexpressed in cancer cells enables selective ablation of specific subpopulations in mixed cell cultures. In a mouse model, the transmembrane delivery of a split-toxin construct potently inhibits the growth of xenograft tumors expressing the split counterpart. Receptor-mediated delivery of engineered split proteins provides a platform for precise therapeutic and experimental ablation of tumors or desired cell populations while also greatly expanding the applicability of the intein-based protein transsplicing.
Collapse
Affiliation(s)
- Vedud Purde
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210;
| | - David B Heisler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
| | - Reena Shakya
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
| | - Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210;
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
28
|
Beyer HM, Mikula KM, Li M, Wlodawer A, Iwaï H. The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from cis-splicing inteins. FEBS J 2020; 287:1886-1898. [PMID: 31665813 PMCID: PMC7190452 DOI: 10.1111/febs.15113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/01/2019] [Accepted: 10/29/2019] [Indexed: 01/09/2023]
Abstract
Protein trans-splicing catalyzed by split inteins has increasingly become useful as a protein engineering tool. We solved the 1.0 Å-resolution crystal structure of a fused variant from the naturally split gp41-1 intein, previously identified from environmental metagenomic sequence data. The structure of the 125-residue gp41-1 intein revealed a compact pseudo-C2-symmetry commonly found in the Hedgehog/Intein superfamily with extensive charge-charge interactions between the split N- and C-terminal intein fragments that are common among naturally occurring split inteins. We successfully created orthogonal split inteins by engineering a similar charge network into the same region of a cis-splicing intein. This strategy could be applicable for creating novel natural-like split inteins from other, more prevalent cis-splicing inteins. DATABASE: Structural data are available in the RCSB Protein Data Bank under the accession number 6QAZ.
Collapse
Affiliation(s)
- Hannes Michael Beyer
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Kornelia Malgorzata Mikula
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Mi Li
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
29
|
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]
|
30
|
Ciragan A, Backlund SM, Mikula KM, Beyer HM, Samuli Ollila OH, Iwaï H. NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein. Front Chem 2020; 8:136. [PMID: 32266203 PMCID: PMC7098700 DOI: 10.3389/fchem.2020.00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 11/22/2022] Open
Abstract
The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.
Collapse
Affiliation(s)
- Annika Ciragan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
31
|
Abstract
While the model bacteria Escherichia coli and Bacillus subtilis harbor single chromosomes, which is known as monoploidy, some freshwater cyanobacteria contain multiple chromosome copies per cell throughout their cell cycle, which is known as polyploidy. In the model cyanobacteria Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, chromosome copy number (ploidy) is regulated in response to growth phase and environmental factors. In S. elongatus 7942, chromosome replication is asynchronous both among cells and chromosomes. Comparative analysis of S. elongatus 7942 and S. sp. 6803 revealed a variety of DNA replication mechanisms. In this review, the current knowledge of ploidy and DNA replication mechanisms in cyanobacteria is summarized together with information on the features common with plant chloroplasts. It is worth noting that the occurrence of polyploidy and its regulation are correlated with certain cyanobacterial lifestyles and are shared between some cyanobacteria and chloroplasts. ABBREVIATIONS NGS: next-generation sequencing; Repli-seq: replication sequencing; BrdU: 5-bromo-2'-deoxyuridine; TK: thymidine kinase; GCSI: GC skew index; PET: photosynthetic electron transport; RET: respiration electron transport; Cyt b6f complex: cytochrome b6f complex; PQ: plastoquinone; PC: plastocyanin.
Collapse
Affiliation(s)
- Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture , Tokyo, Japan
| |
Collapse
|
32
|
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.
Collapse
|
33
|
Split intein-mediated selection of cells containing two plasmids using a single antibiotic. Nat Commun 2019; 10:4967. [PMID: 31672972 PMCID: PMC6823396 DOI: 10.1038/s41467-019-12911-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/07/2019] [Indexed: 11/08/2022] Open
Abstract
To build or dissect complex pathways in bacteria and mammalian cells, it is often necessary to recur to at least two plasmids, for instance harboring orthogonal inducible promoters. Here we present SiMPl, a method based on rationally designed split enzymes and intein-mediated protein trans-splicing, allowing the selection of cells carrying two plasmids with a single antibiotic. We show that, compared to the traditional method based on two antibiotics, SiMPl increases the production of the antimicrobial non-ribosomal peptide indigoidine and the non-proteinogenic aromatic amino acid para-amino-L-phenylalanine from bacteria. Using a human T cell line, we employ SiMPl to obtain a highly pure population of cells double positive for the two chains of the T cell receptor, TCRα and TCRβ, using a single antibiotic. SiMPl has profound implications for metabolic engineering and for constructing complex synthetic circuits in bacteria and mammalian cells.
Collapse
|
34
|
Abstract
Selectable markers are widely used in transgenesis and genome editing for selecting engineered cells with a desired genotype but the variety of markers is limited. Here we present split selectable markers that each allow for selection of multiple “unlinked” transgenes in the context of lentivirus-mediated transgenesis as well as CRISPR-Cas-mediated knock-ins. Split marker gene segments fused to protein splicing elements called “inteins” can be separately co-segregated with different transgenic vectors, and rejoin via protein trans-splicing to reconstitute a full-length marker protein in host cells receiving all intended vectors. Using a lentiviral system, we create and validate 2-split Hygromycin, Puromycin, Neomycin and Blasticidin resistance genes as well as mScarlet fluorescent proteins. By combining split points, we create 3- and 6-split Hygromycin resistance genes, demonstrating that higher-degree split markers can be generated by a “chaining” design. We adapt the split marker system for selecting biallelically engineered cells after CRISPR gene editing. Future engineering of split markers may allow selection of a higher number of genetic modifications in target cells. Selectable markers are widely used in cell engineering but there is only a limited variety to choose from. Here the authors split markers using inteins, allowing up to six transgene integration events to be selected for with one marker.
Collapse
|
35
|
Gao Y, Hisey E, Bradshaw TWA, Erata E, Brown WE, Courtland JL, Uezu A, Xiang Y, Diao Y, Soderling SH. Plug-and-Play Protein Modification Using Homology-Independent Universal Genome Engineering. Neuron 2019; 103:583-597.e8. [PMID: 31272828 PMCID: PMC7200071 DOI: 10.1016/j.neuron.2019.05.047] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/13/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
Analysis of endogenous protein localization, function, and dynamics is fundamental to the study of all cells, including the diversity of cell types in the brain. However, current approaches are often low throughput and resource intensive. Here, we describe a CRISPR-Cas9-based homology-independent universal genome engineering (HiUGE) method for endogenous protein manipulation that is straightforward, scalable, and highly flexible in terms of genomic target and application. HiUGE employs adeno-associated virus (AAV) vectors of autonomous insertional sequences (payloads) encoding diverse functional modifications that can integrate into virtually any genomic target loci specified by easily assembled gene-specific guide-RNA (GS-gRNA) vectors. We demonstrate that universal HiUGE donors enable rapid alterations of proteins in vitro or in vivo for protein labeling and dynamic visualization, neural-circuit-specific protein modification, subcellular rerouting and sequestration, and truncation-based structure-function analysis. Thus, the "plug-and-play" nature of HiUGE enables high-throughput and modular analysis of mechanisms driving protein functions in cellular neurobiology.
Collapse
Affiliation(s)
- Yudong Gao
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Erin Hisey
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Tyler W A Bradshaw
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical School, Durham, NC 27710, USA
| | - Eda Erata
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Walter E Brown
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Jamie L Courtland
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical School, Durham, NC 27710, USA
| | - Akiyoshi Uezu
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical School, Durham, NC 27710, USA.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
A novel protein purification strategy mediated by the combination of CipA and Ssp DnaB intein. J Biotechnol 2019; 301:97-104. [PMID: 31181238 DOI: 10.1016/j.jbiotec.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
Protein purification is an indispensable step in diverse fields of biological research or production process. Conventional purification methods including the affinity purification or the usage of self-aggregating tags suffered from many drawbacks such as the complicated steps, high cost and low efficiency. Moreover, the fusion tag usually had negative effects on the activity of the target protein. To address the above issues, here we propose a novel protein purification method which needs simple operation steps, and this method is mediated by the combination of CipA protein and a mini-intein (Synechocystis sp. PCC6803 DnaB, Ssp DnaB), depending on the assembly function of CipA and the self-cleavage function of Ssp DnaB. To realize the purification, CipA-DnaB-eGFP protein was expressed and assembled into protein crystalline inclusions (PCIs) in E. coli. Then, only cell lysis, cleavage and centrifugation steps were required to purify eGFP. Purified eGFP was in the supernatant with a purity of over 90%. The cleavage efficiency and the yield of eGFP reached 51.96% and 13.99 ± 0.88 mg/L fermentation broth, respectively. Furthermore, to broaden the application of this approach, three other proteins which were maltose binding protein (MBP), ketoisovalerate decarboxylase (Kivd) and alcohol dehydrogenase (AdhP) were purified with high cleavage efficiency. The purified Kivd and AdhP remained high specific activities. This work demonstrated an effective and convenient protein purification method.
Collapse
|
38
|
Reduction of non-specific toxicity of immunotoxin by intein mediated reconstitution on target cells. Int Immunopharmacol 2019; 66:288-295. [DOI: 10.1016/j.intimp.2018.11.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/13/2022]
|
39
|
Abstract
With the increasing utilization of high-throughput screening for lead identification in drug discovery, the need for easily constructed and diverse libraries which cover significant chemical space is greater than ever. Cyclic peptides address this need; they combine the advantageous properties of peptides (ease of production, high diversity, high potential specificity) with increased resistance to proteolysis and often increased biological activity (due to conformational locking). There are a number of techniques for the generation and screening of cyclic peptide libraries. As drug discovery moves toward tackling challenging targets, such as protein-protein interactions, cyclic peptide libraries are expected to continue producing hits where small molecule libraries may be stymied. However, it is important to design robust systems for the generation and screening of these large libraries, and to be able to make sense of structure-activity relationships in these highly variable scaffolds. There are a plethora of possible modifications that can be made to cyclic peptides, which is both a weakness and a strength of these scaffolds; high variability will allow more precise tuning of leads to targets, but exploring the whole range of modifications may become an overwhelming challenge.
Collapse
|
40
|
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.
Collapse
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 .
| |
Collapse
|
41
|
Lee E, Min K, Chang YT, Kwon Y. Efficient and wash-free labeling of membrane proteins using engineered Npu DnaE split-inteins. Protein Sci 2018; 27:1568-1574. [PMID: 30151847 DOI: 10.1002/pro.3455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
An efficient and wash-free method to conjugate a fluorescent tag to a target membrane protein is developed, using engineered Npu DnaE split-inteins. This approach allowed fast labeling while avoiding the strenuous synthesis of a long polypeptide. Two different modes of labeling, namely specific binding and covalent conjugation, are observed. The covalent labeling was monitored within 5 min, without background staining.
Collapse
Affiliation(s)
- Euiyeon Lee
- Department of Biomedical Engineering, Dongguk University, Seoul, 04620, South Korea
| | - Kyoungmi Min
- Department of Biomedical Engineering, Dongguk University, Seoul, 04620, South Korea
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, South Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Youngeun Kwon
- Department of Biomedical Engineering, Dongguk University, Seoul, 04620, South Korea
| |
Collapse
|
42
|
Stevens AJ, Sekar G, Gramespacher JA, Cowburn D, Muir TW. An Atypical Mechanism of Split Intein Molecular Recognition and Folding. J Am Chem Soc 2018; 140:11791-11799. [PMID: 30156841 PMCID: PMC7232844 DOI: 10.1021/jacs.8b07334] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Split inteins associate to trigger protein splicing in trans, a post-translational modification in which protein sequences fused to the intein pair are ligated together in a traceless manner. Recently, a family of naturally split inteins has been identified that is split at a noncanonical location in the primary sequence. These atypically split inteins show considerable promise in protein engineering applications; however, the mechanism by which they associate is unclear and must be different from that of previously characterized canonically split inteins due to unique topological restrictions. Here, we use a consensus design strategy to generate an atypical split intein pair (Cat) that has greatly improved activity and is amenable to detailed biochemical and biophysical analysis. Guided by the solution structure of Cat, we show that the association of the fragments involves a disorder-to-order structural transition driven by hydrophobic interactions. This molecular recognition mechanism satisfies the topological constraints of the intein fold and, importantly, ensures that premature chemistry does not occur prior to fragment complementation. Our data lead a common blueprint for split intein complementation in which localized structural rearrangements are used to drive folding and regulate protein-splicing activity.
Collapse
Affiliation(s)
- Adam J. Stevens
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Giridhar Sekar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Josef A. Gramespacher
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
43
|
Matern JCJ, Friedel K, Binschik J, Becher KS, Yilmaz Z, Mootz HD. Altered Coordination of Individual Catalytic Steps in Different and Evolved Inteins Reveals Kinetic Plasticity of the Protein Splicing Pathway. J Am Chem Soc 2018; 140:11267-11275. [PMID: 30111090 DOI: 10.1021/jacs.8b04794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein splicing performed by inteins provides powerful opportunities to manipulate protein structure and function, however, detailed mechanistic knowledge of the multistep pathway to help engineering optimized inteins remains scarce. A typical intein has to coordinate three steps to maximize the product yield of ligated exteins. We have revealed a new type of coordination in the Ssp DnaB intein, in which the initial N- S acyl shift appears rate-limiting and acts as an up-regulation switch to dramatically accelerate the last step of succinimide formation, which is thus coupled to the first step. The structure-activity relationship at the N-terminal scissile bond was studied with atomic precision using a semisynthetic split intein. We show that the removal of the extein acyl group from the α-amino moiety of the intein's first residue is strictly required and sufficient for the up-regulation switch. Even an acetyl group as the smallest possible extein moiety completely blocked the switch. Furthermore, we investigated the M86 intein, a mutant with faster splicing kinetics previously obtained by laboratory evolution of the Ssp DnaB intein, and the individual impact of its eight mutations. The succinimide formation was decoupled from the first step in the M86 intein, but the acquired H143R mutation acts as a brake to prevent premature C-terminal cleavage and thereby maximizes splicing yields. Together, these results revealed a high degree of plasticity in the kinetic coordination of the splicing pathway. Furthermore, our study led to the rational design of improved M86 mutants with the highest yielding trans-splicing and fastest trans-cleavage activities.
Collapse
Affiliation(s)
- Julian C J Matern
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Kristina Friedel
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Jens Binschik
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Kira-Sophie Becher
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Zahide Yilmaz
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| | - Henning D Mootz
- Institute of Biochemistry, Department of Chemistry and Pharmacy , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany
| |
Collapse
|
44
|
Ye B, Shen W, Shi M, Zhang Y, Xu C, Zhao Z. Intein-mediated backbone cyclization of entolimod confers enhanced radioprotective activity in mouse models. PeerJ 2018; 6:e5043. [PMID: 29938138 PMCID: PMC6011820 DOI: 10.7717/peerj.5043] [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: 03/28/2018] [Accepted: 05/31/2018] [Indexed: 12/03/2022] Open
Abstract
Background Entolimod is a Salmonella enterica flagellin derivate. Previous work has demonstrated that entolimod effectively protects mice and non-human primates from ionizing radiation. However, it caused a “flu-like” syndrome after radioprotective and anticancer clinical application, indicating some type of immunogenicity and toxicity. Cyclization is commonly used to improve the in vivo stability and activity of peptides and proteins. Methods We designed and constructed cyclic entolimod using split Nostoc punctiforme DnaE intein with almost 100% cyclization efficiency. We adopted different strategies to purify the linear and circular entolimod due to their different topologies. Both of linear and circular entolimod were first purified by Ni-chelating affinity chromatography, and then the linear and circular entolimod were purified by size-exclusion and ion-exchange chromatography, respectively. Results The circular entolimod showed significantly increased both the in vitro NF-κB signaling and in vivo radioprotective activity in mice. Conclusion Our data indicates that circular entolimod might be a good candidate for further clinical investigation.
Collapse
Affiliation(s)
- Bingyu Ye
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.,Beijing Institute of Biotechnology, Beijing, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Minglei Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Cunshuan Xu
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
| |
Collapse
|
45
|
Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
Collapse
|
46
|
Schmelas C, Grimm D. Split Cas9, Not Hairs - Advancing the Therapeutic Index of CRISPR Technology. Biotechnol J 2018; 13:e1700432. [PMID: 29316283 DOI: 10.1002/biot.201700432] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/28/2017] [Indexed: 02/06/2023]
Abstract
The discovery that the bacterial CRISPR/Cas9 system can be translated into mammalian cells continues to have an unprecedented impact on the biomedical research community, as it largely facilitates efforts to experimentally interrogate or therapeutically modify the cellular genome. In particular, CRISPR promises the ability to correct disease-associated genetic defects, or to target and destroy invading foreign DNA, in a simple, efficient, and selective manner directly in affected human cells or tissues. Here, we highlight a set of exciting new strategies that aim at further increasing the therapeutic index of CRISPR technologies, by reducing the size of Cas9 expression cassettes and thus enhancing their compatibility with viral gene delivery vectors. Specifically, we discuss the concept of splitCas9 whereby the Cas9 holo-protein is segregated into two parts that are expressed individually and reunited in the cell by various means, including use of 1) the gRNA as a scaffold for Cas9 assembly; 2) the rapamycin-controlled FKBP/FRB system; 3) the light-regulated Magnet system; or 4) inteins. We describe how these avenues, despite pursuing the identical aim, differ in critical features comprising the extent of spatio-temporal control of CRISPR activity, and discuss additional improvements to their efficiency or specificity that should foster their clinical translation.
Collapse
Affiliation(s)
- Carolin Schmelas
- Heidelberg University Hospital, Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
| | - Dirk Grimm
- Heidelberg University Hospital, Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner site Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
| |
Collapse
|
47
|
Schubeis T, Nagaraj M, Ritter C. Segmental Isotope Labeling of Insoluble Proteins for Solid-State NMR by Protein Trans-Splicing. Methods Mol Biol 2018; 1495:147-160. [PMID: 27714615 DOI: 10.1007/978-1-4939-6451-2_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Solid-state NMR spectroscopy (ssNMR) is uniquely suited for atomic-resolution structural investigations of large protein assemblies, which are notoriously difficult to study due to their insoluble and non-crystalline nature. However, assignment ambiguities because of limited resolution and spectral crowding are currently major hurdles that quickly increase with the length of the polypeptide chain. The line widths of ssNMR signals are independent of proteins size, making segmental isotope labeling a powerful approach to overcome this limitation. It allows a scalable reduction of signal overlap, aids the assignment of repetitive amino acid sequences, and can be easily combined with other selective isotope labeling strategies. Here we present a detailed protocol for segmental isotope labeling of insoluble proteins using protein trans-splicing. Our protocol exploits the ability of many insoluble proteins, such as amyloid fibrils, to fold correctly under in vitro conditions. In combination with the robust trans-splicing efficiency of the intein DnaE from Nostoc punctiforme, this allows for high yields of segmentally labeled protein required for ssNMR analysis.
Collapse
Affiliation(s)
- Tobias Schubeis
- Macromolecular Interactions, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon/UCBL, University of Lyon, 69100, Villeurbanne, France
| | - Madhu Nagaraj
- Macromolecular Interactions, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, D-13125, Berlin, Germany
| | - Christiane Ritter
- Macromolecular Interactions, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany. .,SeNostic GmbH, Feodor-Lynen-Strasse 21, 30625, Hannover, Germany.
| |
Collapse
|
48
|
Techniques and strategies employing engineered transcription factors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
49
|
Kick LM, Harteis S, Koch MF, Schneider S. Mechanistic Insights into Cyclic Peptide Generation by DnaE Split-Inteins through Quantitative and Structural Investigation. Chembiochem 2017; 18:2242-2246. [DOI: 10.1002/cbic.201700503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Leonhard M. Kick
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Sabrina Harteis
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Maximilian F. Koch
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Sabine Schneider
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| |
Collapse
|
50
|
Efficient generation of bispecific IgG antibodies by split intein mediated protein trans-splicing system. Sci Rep 2017; 7:8360. [PMID: 28827777 PMCID: PMC5567192 DOI: 10.1038/s41598-017-08641-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/03/2017] [Indexed: 12/19/2022] Open
Abstract
Many methods have been developed to produce bispecific antibodies (BsAbs) for industrial application. However, huge challenges still remain in synthesizing whole length BsAbs, including their assembly, stability, immunogenicity, and pharmacodynamics. Here we present for first time a generic technology platform of generating bispecific IgG antibodies, “Bispecific Antibody by Protein Trans-splicing (BAPTS)”. Different from published methods, we assembled two parental antibody fragments in the hinge region by the protein trans-splicing reaction of a split intein to generate BsAbs without heavy/heavy and light/heavy chain mispairing. Utilizing this simple and efficient approach, there have been several BsAbs (CD3×HER2, CD3×EGFR, EGFR×HER2) synthesized to demonstrate its broad applicability. Correctly paired mAb arms were assembled to form BsAbs that were purified through protein A affinity chromatography to demonstrate industrial applicability at large scale. Further, the products were characterized through physical-biochemistry properties and biological activities to confirm expected quality of the products from “BAPTS”. More importantly, correct pairing was confirmed by mass spectrum. Proof-of-concept studies with CD3×HER2 BsAb (T-cell recruitment) demonstrated superior bioactivity compared with trastuzumab. The results of undetectable mispairing and high biological activity have indicated that this method has the potential to be utilized to manufacture BsAbs with high efficiency at industrial scale.
Collapse
|