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Foster MP, Benedek MJ, Billings TD, Montgomery JS. Dynamics in Cre-loxP site-specific recombination. Curr Opin Struct Biol 2024; 88:102878. [PMID: 39029281 DOI: 10.1016/j.sbi.2024.102878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/21/2024]
Abstract
Cre recombinase is a phage-derived enzyme that has found utility for precise manipulation of DNA sequences. Cre recognizes and recombines pairs of loxP sequences characterized by an inverted repeat and asymmetric spacer. Cre cleaves and religates its DNA targets such that error-prone repair pathways are not required to generate intact DNA products. Major obstacles to broader applications are lack of knowledge of how Cre recognizes its targets, and how its activity is controlled. The picture emerging from high resolution methods is that the dynamic properties of both the enzyme and its DNA target are important determinants of its activity in both sequence recognition and DNA cleavage. Improved understanding of the role of dynamics in the key steps along the pathway of Cre-loxP recombination should significantly advance our ability to both redirect Cre to new sequences and to control its DNA cleavage activity in the test tube and in cells.
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Affiliation(s)
- Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
| | - Matthew J Benedek
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tyler D Billings
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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2
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Tonetto E, Cucci A, Follenzi A, Bernardi F, Pinotti M, Balestra D. DNA base editing corrects common hemophilia A mutations and restores factor VIII expression in in vitro and ex vivo models. J Thromb Haemost 2024; 22:2171-2183. [PMID: 38718928 DOI: 10.1016/j.jtha.2024.04.020] [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: 01/22/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Replacement and nonreplacement therapies effectively control bleeding in hemophilia A (HA) but imply lifelong interventions. Authorized gene addition therapy could provide a cure but still poses questions on durability. FVIIIgene correction would definitively restore factor (F)VIII production, as shown in animal models through nuclease-mediated homologous recombination (HR). However, low efficiency and potential off-target double-strand break still limit HR translatability. OBJECTIVES To correct common model single point mutations leading to severe HA through the recently developed double-strand break/HR-independent base editing (BE) and prime editing (PE) approaches. METHODS Screening for efficacy of BE/PE systems in HEK293T cells transiently expressing FVIII variants and validation at DNA (sequencing) and protein (enzyme-linked immunosorbent assay; activated partial thromboplastin time) level in stable clones. Evaluation of rescue in engineered blood outgrowth endothelial cells by lentiviral-mediated delivery of BE. RESULTS Transient assays identified the best-performing BE/PE systems for each variant, with the highest rescue of FVIII expression (up to 25% of wild-type recombinant FVIII) for the p.R2166∗ and p.R2228Q mutations. In stable clones, we demonstrated that the mutation reversion on DNA (∼24%) was consistent with the rescue of FVIII secretion and activity of 20% to 30%. The lentiviral-mediated delivery of the selected BE systems was attempted in engineered blood outgrowth endothelial cells harboring the p.R2166∗ and p.R2228Q variants, which led to an appreciable and dose-dependent rescue of secreted functional FVIII. CONCLUSION Overall data provide the first proof-of-concept for effective BE/PE-mediated correction of HA-causing mutations, which encourage studies in mouse models to develop a personalized cure for large cohorts of patients through a single intervention.
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Affiliation(s)
- Elena Tonetto
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Alessia Cucci
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
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3
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Hoersten J, Ruiz-Gómez G, Paszkowski-Rogacz M, Gilioli G, Guillem-Gloria P, Lansing F, Pisabarro MT, Buchholz F. Engineering spacer specificity of the Cre/loxP system. Nucleic Acids Res 2024; 52:8017-8031. [PMID: 38869070 PMCID: PMC11260471 DOI: 10.1093/nar/gkae481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/16/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024] Open
Abstract
Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing Cre discrimination between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking. To fill this gap, we investigated target site variations of identical pairs of the loxP 8 bp spacer region, screening 6000 unique loxP-like sequences. Approximately 84% of these sites exhibited efficient recombination, affirming the plasticity of spacer sequences for catalysis. However, certain spacers negatively impacted recombination, emphasizing sequence dependence. Directed evolution of Cre on inefficiently recombined spacers not only yielded recombinases with enhanced activity but also mutants with reprogrammed selective activity. Mutations altering spacer specificity were identified, and molecular modelling and dynamics simulations were used to investigate the possible mechanisms behind the specificity switch. Our findings highlight the potential to fine-tune site-specific recombinases for spacer sequence specificity, offering a novel concept to enhance the applied properties of designer-recombinases for genome engineering applications.
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Affiliation(s)
- Jenna Hoersten
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Gloria Ruiz-Gómez
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Giorgio Gilioli
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | | | - Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - M Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
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4
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Sundaram SS, Kannan A, Chintaluri PG, Sreekala AGV, Nathan VK. Thermostable bacterial L-asparaginase for polyacrylamide inhibition and in silico mutational analysis. Int Microbiol 2024:10.1007/s10123-024-00493-y. [PMID: 38519776 DOI: 10.1007/s10123-024-00493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
The L-asparaginase (ASPN) enzyme has received recognition in various applications including acrylamide degradation in the food industry. The synthesis and application of thermostable ASPN enzymes is required for its use in the food sector, where thermostable enzymes can withstand high temperatures. To achieve this goal, the bacterium Bacillus subtilis was isolated from the hot springs of Tapovan for screening the production of thermostable ASPN enzyme. Thus, ASPN with a maximal specific enzymatic activity of 0.896 U/mg and a molecular weight of 66 kDa was produced from the isolated bacteria. The kinetic study of the enzyme yielded a Km value of 1.579 mM and a Vmax of 5.009 µM/min with thermostability up to 100 min at 75 °C. This may have had a positive indication for employing the enzyme to stop polyacrylamide from being produced. The current study has also been extended to investigate the interaction of native and mutated ASPN enzymes with acrylamide. This concluded that the M10 (with 10 mutations) has the highest protein and thermal stability compared to the wild-type ASPN protein sequence. Therefore, in comparison to a normal ASPN and all other mutant ASPNs, M10 is the most favorable mutation. This research has also demonstrated the usage of ASPN in food industrial applications.
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Affiliation(s)
| | - Aravind Kannan
- School of Chemical and Biotechnology, SASTRA Deemed to Be University, Thanjavur, Tamil Nadu, India
| | - Pratham Gour Chintaluri
- School of Chemical and Biotechnology, SASTRA Deemed to Be University, Thanjavur, Tamil Nadu, India
| | | | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, SASTRA Deemed to Be University, Thanjavur, Tamil Nadu, India.
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5
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Cautereels C, Smets J, De Saeger J, Cool L, Zhu Y, Zimmermann A, Steensels J, Gorkovskiy A, Jacobs TB, Verstrepen KJ. Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts. Nat Commun 2024; 15:1113. [PMID: 38326330 PMCID: PMC10850332 DOI: 10.1038/s41467-024-44996-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Lloyd Cool
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Yanmei Zhu
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium.
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6
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A conditional, zinc-finger-dependent recombinase system for DNA editing. Nat Biotechnol 2024:10.1038/s41587-023-02122-x. [PMID: 38302754 DOI: 10.1038/s41587-023-02122-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
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7
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Mukhametzyanova L, Schmitt LT, Torres-Rivera J, Rojo-Romanos T, Lansing F, Paszkowski-Rogacz M, Hollak H, Brux M, Augsburg M, Schneider PM, Buchholz F. Activation of recombinases at specific DNA loci by zinc-finger domain insertions. Nat Biotechnol 2024:10.1038/s41587-023-02121-y. [PMID: 38297187 DOI: 10.1038/s41587-023-02121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024]
Abstract
Recombinases have several potential advantages as genome editing tools compared to nucleases and other editing enzymes, but the process of engineering them to efficiently recombine predetermined DNA targets demands considerable investment of time and labor. Here we sought to harness zinc-finger DNA-binding domains (ZFDs) to program recombinase binding by developing fusions, in which ZFDs are inserted into recombinase coding sequences. By screening libraries of hybrid proteins, we optimized the insertion site, linker length, spacing and ZFD orientation and generated Cre-type recombinases that remain dormant unless the insertionally fused ZFD binds its target site placed in the vicinity of the recombinase binding site. The developed fusion improved targeted editing efficiencies of recombinases by four-fold and abolished measurable off-target activity in mammalian cells. The ZFD-dependent activity is transferable to a recombinase with relaxed specificity, providing the means for developing fully programmable recombinases. Our engineered recombinases provide improved genome editing tools with increased precision and efficiency.
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Affiliation(s)
- Liliya Mukhametzyanova
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Julia Torres-Rivera
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Teresa Rojo-Romanos
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Felix Lansing
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | | | - Heike Hollak
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Melanie Brux
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Martina Augsburg
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
| | - Paul Martin Schneider
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany
- Seamless Therapeutics GmbH, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty, Technical University Dresden, Dresden, Germany.
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8
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Tou CJ, Kleinstiver BP. Recent Advances in Double-Strand Break-Free Kilobase-Scale Genome Editing Technologies. Biochemistry 2023; 62:3493-3499. [PMID: 36049184 PMCID: PMC10239562 DOI: 10.1021/acs.biochem.2c00311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genome editing approaches have transformed the ability to make user-defined changes to genomes in both ex vivo and in vivo contexts. Despite the abundant development of technologies that permit the installation of nucleotide-level changes, until recently, larger-scale sequence edits via technologies independent of DNA double-strand breaks (DSBs) had remained less explored. Here, we review recent advances toward DSB-free technologies that enable kilobase-scale modifications including insertions, deletions, inversions, replacements, and others. These technologies provide new capabilities for users, while offering hope for the simplification of putative therapeutic strategies by moving away from small mutation-specific edits and toward more generalizable kilobase-scale approaches.
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Affiliation(s)
- Connor J. Tou
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
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9
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Schmitt LT, Schneider A, Posorski J, Lansing F, Jelicic M, Jain M, Sayed S, Buchholz F, Sürün D. Quantification of evolved DNA-editing enzymes at scale with DEQSeq. Genome Biol 2023; 24:254. [PMID: 37932818 PMCID: PMC10626641 DOI: 10.1186/s13059-023-03097-3] [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: 04/06/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length sequences, editing efficiencies, and specificities from thousands of evolved enzymes simultaneously, DEQSeq streamlines the process of identifying the most valuable variants for further study and application. We apply DEQSeq to evolved libraries of Cas12f-ABEs and designer-recombinases, identifying variants with improved properties for future applications. Our results demonstrate that DEQSeq is a powerful tool for accelerating enzyme discovery and advancing genome editing research.
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Affiliation(s)
- Lukas Theo Schmitt
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
- Present Address: Seamless Therapeutics GmbH, Tatzberg 47/49, 01307, Dresden, Germany
| | - Aksana Schneider
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
- Present Address: Seamless Therapeutics GmbH, Tatzberg 47/49, 01307, Dresden, Germany
| | - Jonas Posorski
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
- Present Address: Seamless Therapeutics GmbH, Tatzberg 47/49, 01307, Dresden, Germany
| | - Milica Jelicic
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Manavi Jain
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Shady Sayed
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany.
| | - Duran Sürün
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, Dresden, TU Dresden, 01307, Germany.
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10
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Rojo-Romanos T, Karpinski J, Millen S, Beschorner N, Simon F, Paszkowski-Rogacz M, Lansing F, Schneider PM, Sonntag J, Hauber J, Thoma-Kress AK, Buchholz F. Precise excision of HTLV-1 provirus with a designer-recombinase. Mol Ther 2023; 31:2266-2285. [PMID: 36934299 PMCID: PMC10362392 DOI: 10.1016/j.ymthe.2023.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 02/06/2023] [Accepted: 03/12/2023] [Indexed: 03/19/2023] Open
Abstract
The human T cell leukemia virus type 1 (HTLV-1) is a pathogenic retrovirus that persists as a provirus in the genome of infected cells and can lead to adult T cell leukemia (ATL). Worldwide, more than 10 million people are infected and approximately 5% of these individuals will develop ATL, a highly aggressive cancer that is currently incurable. In the last years, genome editing tools have emerged as promising antiviral agents. In this proof-of-concept study, we use substrate-linked directed evolution (SLiDE) to engineer Cre-derived site-specific recombinases to excise the HTLV-1 proviral genome from infected cells. We identified a conserved loxP-like sequence (loxHTLV) present in the long terminal repeats of the majority of virus isolates. After 181 cycles of SLiDE, we isolated a designer-recombinase (designated RecHTLV), which efficiently recombines the loxHTLV sequence in bacteria and human cells with high specificity. Expression of RecHTLV in human Jurkat T cells resulted in antiviral activity when challenged with an HTLV-1 infection. Moreover, expression of RecHTLV in chronically infected SP cells led to the excision of HTLV-1 proviral DNA. Our data suggest that recombinase-mediated excision of the HTLV-1 provirus represents a promising approach to reduce proviral load in HTLV-1-infected individuals, potentially preventing the development of HTLV-1-associated diseases.
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Affiliation(s)
- Teresa Rojo-Romanos
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Janet Karpinski
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Sebastian Millen
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Niklas Beschorner
- PROVIREX Genome Editing Therapies GmbH, Luruper Hauptstrasse 1, 22547 Hamburg, Germany
| | - Florian Simon
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Felix Lansing
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Paul Martin Schneider
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Jan Sonntag
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany
| | - Joachim Hauber
- PROVIREX Genome Editing Therapies GmbH, Luruper Hauptstrasse 1, 22547 Hamburg, Germany
| | - Andrea K Thoma-Kress
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Frank Buchholz
- Medical Systems Biology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, 01307 Dresden, Germany.
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11
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Chi H, Zhu X, Shen J, Lu Z, Lu F, Lyu Y, Zhu P. Thermostability enhancement and insight of L-asparaginase from Mycobacterium sp. via consensus-guided engineering. Appl Microbiol Biotechnol 2023; 107:2321-2333. [PMID: 36843197 DOI: 10.1007/s00253-023-12443-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Acrylamide alleviation in food has represented as a critical issue due to its neurotoxic effect on human health. L-Asparaginase (ASNase, EC 3.5.1.1) is considered a potential additive for acrylamide alleviation in food. However, low thermal stability hinders the application of ASNase in thermal food processing. To obtain highly thermal stable ASNase for its industrial application, a consensus-guided approach combined with site-directed saturation mutation (SSM) was firstly reported to engineer the thermostability of Mycobacterium gordonae L-asparaginase (GmASNase). The key residues Gly97, Asn159, and Glu249 were identified for improving thermostability. The combinatorial triple mutant G97T/N159Y/E249Q (TYQ) displayed significantly superior thermostability with half-life values of 61.65 ± 8.69 min at 50 °C and 5.12 ± 1.66 min at 55 °C, whereas the wild-type was completely inactive at these conditions. Moreover, its Tm value increased by 8.59 °C from parent wild-type. Interestingly, TYQ still maintained excellent catalytic efficiency and specific activity. Further molecular dynamics and structure analysis revealed that the additional hydrogen bonds, increased hydrophobic interactions, and favorable electrostatic potential were essential for TYQ being in a more rigid state for thermostability enhancement. These results suggested that our strategy was an efficient engineering approach for improving fundamental properties of GmASNase and offering GmASNase as a potential agent for efficient acrylamide mitigation in food industry. KEY POINTS: • The thermostability of GmASNase was firstly improved by consensus-guided engineering. • The half-life and Tm value of triple mutant TYQ were significantly increased. • Insight on improved thermostability of TYQ was revealed by MD and structure analysis.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Schmitt LT, Paszkowski-Rogacz M, Jug F, Buchholz F. Prediction of designer-recombinases for DNA editing with generative deep learning. Nat Commun 2022; 13:7966. [PMID: 36575171 PMCID: PMC9794738 DOI: 10.1038/s41467-022-35614-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designer-recombinases. We gather the sequence information of over one million Cre-like recombinase sequences evolved for 89 different target sites with which we train Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrates that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases.
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Affiliation(s)
- Lukas Theo Schmitt
- Medical Systems Biology, Medical Faculty, TU Dresden, 01307, Dresden, Germany
| | | | - Florian Jug
- Fondazione Human Technopole, Milano, Italy
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Medical Faculty, TU Dresden, 01307, Dresden, Germany.
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Williams JD, Voziyanova E, Voziyanov Y. The bacteriophage lambda integrase catalytic domain can be modified to act with the regulatory domain as a recombination-competent binary recombinase. J Biol Chem 2022; 299:102721. [PMID: 36410432 PMCID: PMC9791396 DOI: 10.1016/j.jbc.2022.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Site-specific recombinase Int mediates integration of the bacteriophage λ genome into the Escherichia coli chromosome. Integration occurs once the Int tetramer, assisted by the integration host factor IHF, forms the intasome, a higher order structure, within which Int, a heterobivalent protein, interacts with two nonhomologous DNA sequences: the core recombination sites and the accessory arm sites. The binding to these sites is mediated by the catalytic C-terminal domain (CTD) and the regulatory N-terminal domain (NTD) of Int, respectively. Within Int, the NTD can activate or inhibit the recombination activity of the CTD depending on whether the NTD is bound to the arm sites. The CTD alone cannot mediate recombination, and even when the NTD and the CTD are mixed together as individual polypeptides, the NTD cannot trigger recombination in the CTD. In this work, we set to determine what modifications can unlock the recombination activity in the CTD alone and how the CTD can be modified to respond to recombination-triggering signals from the NTD. For this, we performed a series of genetic analyses, which showed that a single mutation that stabilizes the CTD on DNA, E174K, allows the CTD to recombine the core DNA sequences. When the NTD is paired with the CTD (E174K) that also bears a short polypeptide from the C terminus of the NTD, the resulting binary Int can recombine arm-bearing substrates. Our results provide insights into the molecular basis of the regulation of the Int activity and suggest how binary recombinases of the integrase type can be engineered.
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Affiliation(s)
- Joe D Williams
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Eugenia Voziyanova
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Yuri Voziyanov
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA.
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