1
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Stark GF, Truchon AR, Wilhelm SW. Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype. BMC Genomics 2024; 25:922. [PMID: 39363260 PMCID: PMC11448079 DOI: 10.1186/s12864-024-10839-5] [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: 05/21/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024] Open
Abstract
The Microcystis mobilome is a well-known but understudied component of this bloom-forming cyanobacterium. Through genomic and transcriptomic comparisons, we found five families of transposases that altered the expression of genes in the well-studied toxigenic type-strain, Microcystis aeruginosa PCC 7086, and a non-toxigenic genetic mutant, Microcystis aeruginosa PCC 7806 ΔmcyB. Since its creation in 1997, the ΔmcyB strain has been used in comparative physiology studies against the wildtype strain by research labs throughout the world. Some differences in gene expression between what were thought to be otherwise genetically identical strains have appeared due to insertion events in both intra- and intergenic regions. In our ΔmcyB isolate, a sulfate transporter gene cluster (sbp-cysTWA) showed differential expression from the wildtype, which may have been caused by the insertion of a miniature inverted repeat transposable element (MITE) in the sulfate-binding protein gene (sbp). Differences in growth in sulfate-limited media also were also observed between the two isolates. This paper highlights how Microcystis strains continue to "evolve" in lab conditions and illustrates the importance of insertion sequences / transposable elements in shaping genomic and physiological differences between Microcystis strains thought otherwise identical. This study forces the necessity of knowing the complete genetic background of isolates in comparative physiological experiments, to facilitate the correct conclusions (and caveats) from experiments.
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Affiliation(s)
- Gwendolyn F Stark
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Alexander R Truchon
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA.
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2
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Zeh N, Schmidt M, Schulz P, Fischer S. The new frontier in CHO cell line development: From random to targeted transgene integration technologies. Biotechnol Adv 2024; 75:108402. [PMID: 38950872 DOI: 10.1016/j.biotechadv.2024.108402] [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: 02/24/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/03/2024]
Abstract
Cell line development represents a crucial step in the development process of a therapeutic glycoprotein. Chinese hamster ovary (CHO) cells are the most frequently employed mammalian host cell system for the industrial manufacturing of biologics. The predominant application of CHO cells for heterologous recombinant protein expression lies in the relative simplicity of stably introducing ectopic DNA into the CHO host cell genome. Since CHO cells were first used as expression host for the industrial production of biologics in the late 1980s, stable genomic transgene integration has been achieved almost exclusively by random integration. Since then, random transgene integration had become the gold standard for generating stable CHO production cell lines due to a lack of viable alternatives. However, it was eventually demonstrated that this approach poses significant challenges on the cell line development process such as an increased risk of inducing cell line instability. In recent years, significant discoveries of new and highly potent (semi)-targeted transgene integration systems have paved the way for a technological revolution in the cell line development sector. These advanced methodologies comprise the application of transposase-, recombinase- or Cas9 nuclease-mediated site-specific genomic integration techniques, which enable a scarless transfer of the transgene expression cassette into transcriptionally active loci within the host cell genome. This review summarizes recent advancements in the field of transgene integration technologies for CHO cell line development and compare them to the established random integration approach. Moreover, advantages and limitations of (semi)-targeted integration techniques are discussed, and benefits and opportunities for the biopharmaceutical industry are outlined.
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Affiliation(s)
- Nikolas Zeh
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH and Co.KG, Biberach an der Riss, Germany
| | - Moritz Schmidt
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH and Co.KG, Biberach an der Riss, Germany
| | - Patrick Schulz
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH and Co.KG, Biberach an der Riss, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH and Co.KG, Biberach an der Riss, Germany.
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3
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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] [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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4
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Anderson AC, Schultz BJ, Snow ED, Brott AS, Stangherlin S, Malloch T, London JR, Walker S, Clarke AJ. The mechanism of peptidoglycan O-acetylation in Gram-negative bacteria typifies bacterial MBOAT-SGNH acyltransferases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613324. [PMID: 39345430 PMCID: PMC11429678 DOI: 10.1101/2024.09.17.613324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Bacterial cell envelope polymers are commonly modified with acyl groups that provide fitness advantages. Many polymer acylation pathways involve pairs of membrane-bound O -acyltransferase (MBOAT) and SGNH family proteins. As an example, the MBOAT protein PatA and the SGNH protein PatB are required in Gram-negative bacteria for peptidoglycan O-acetylation. The mechanism for how MBOAT-SGNH transferases move acyl groups from acyl-CoA donors made in the cytoplasm to extracellular polymers is unclear. Using the peptidoglycan O -acetyltransferase proteins PatAB, we explore the mechanism of MBOAT-SGNH pairs. We find that the MBOAT protein PatA catalyzes auto-acetylation of an invariant Tyr residue in its conserved C-terminal hexapeptide motif. We also show that PatB can use a synthetic hexapeptide containing an acetylated tyrosine to donate an acetyl group to a peptidoglycan mimetic. Finally, we report the structure of PatB, finding that it has structural features that shape its activity as an O -acetyltransferase and distinguish it from other SGNH esterases and hydrolases. Taken together, our results support a model for peptidoglycan acylation in which a tyrosine-containing peptide at the MBOAT's C-terminus shuttles an acyl group from the MBOAT active site to the SGNH active site, where it is transferred to peptidoglycan. This model likely applies to other systems containing MBOAT-SGNH pairs, such as those that O-acetylate alginate, cellulose, and secondary cell wall polysaccharides. The use of an acyl-tyrosine intermediate for MBOAT-SGNH acyl transfer is also shared with AT3-SGNH proteins, a second major group of acyltransferases that modify cell envelope polymers.
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5
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Ren Y, Zeng L, Tang Y, Liao J, Jiang M, Cao X, Fan H, Chen J. Enhancing spleen-targeted mRNA delivery with branched biodegradable tails in lipid nanoparticles. J Mater Chem B 2024; 12:8062-8066. [PMID: 39099464 DOI: 10.1039/d4tb00960f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
The application of mRNA therapy is constrained by the current lipid nanoparticles' (LNPs) inability to target non-liver tissues. In this study, we demonstrate that ionizable lipids equipped with branched and biodegradable tails enhance the selective delivery of mRNA to the spleen, particularly to antigen-presenting cells. This approach offers novel insights into how the chemical structure of LNPs influences their organ-specific targeting capabilities.
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Affiliation(s)
- Yupeng Ren
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion, School of Materials Science and Engineering, Hunan University of Science and Technology, 2 Taoyuan Street, Xiangtan 411201, P. R. China.
| | - Ling Zeng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Yingsen Tang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jing Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Meng Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Xinxiu Cao
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion, School of Materials Science and Engineering, Hunan University of Science and Technology, 2 Taoyuan Street, Xiangtan 411201, P. R. China.
| | - Hui Fan
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion, School of Materials Science and Engineering, Hunan University of Science and Technology, 2 Taoyuan Street, Xiangtan 411201, P. R. China.
| | - Jinjin Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
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6
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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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7
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Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H. Structural mechanism of bridge RNA-guided recombination. Nature 2024; 630:994-1002. [PMID: 38926616 PMCID: PMC11208158 DOI: 10.1038/s41586-024-07570-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/15/2024] [Indexed: 06/28/2024]
Abstract
Insertion sequence (IS) elements are the simplest autonomous transposable elements found in prokaryotic genomes1. We recently discovered that IS110 family elements encode a recombinase and a non-coding bridge RNA (bRNA) that confers modular specificity for target DNA and donor DNA through two programmable loops2. Here we report the cryo-electron microscopy structures of the IS110 recombinase in complex with its bRNA, target DNA and donor DNA in three different stages of the recombination reaction cycle. The IS110 synaptic complex comprises two recombinase dimers, one of which houses the target-binding loop of the bRNA and binds to target DNA, whereas the other coordinates the bRNA donor-binding loop and donor DNA. We uncovered the formation of a composite RuvC-Tnp active site that spans the two dimers, positioning the catalytic serine residues adjacent to the recombination sites in both target and donor DNA. A comparison of the three structures revealed that (1) the top strands of target and donor DNA are cleaved at the composite active sites to form covalent 5'-phosphoserine intermediates, (2) the cleaved DNA strands are exchanged and religated to create a Holliday junction intermediate, and (3) this intermediate is subsequently resolved by cleavage of the bottom strands. Overall, this study reveals the mechanism by which a bispecific RNA confers target and donor DNA specificity to IS110 recombinases for programmable DNA recombination.
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Affiliation(s)
- Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Nicholas T Perry
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Teppei Soma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Naoto Nagahata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Sae Okazaki
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | | | - Yukari Isayama
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | | | | | - Silvana Konermann
- Arc Institute, Palo Alto, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Keitaro Yamashita
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
- Inamori Research Institute for Science, Kyoto, Japan.
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8
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de Oliveira MA, Florentino LH, Sales TT, Lima RN, Barros LRC, Limia CG, Almeida MSM, Robledo ML, Barros LMG, Melo EO, Bittencourt DM, Rehen SK, Bonamino MH, Rech E. Protocol for the establishment of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells. PLoS One 2024; 19:e0303999. [PMID: 38781126 PMCID: PMC11115199 DOI: 10.1371/journal.pone.0303999] [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: 09/06/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Serine integrases (Ints) are a family of site-specific recombinases (SSRs) encoded by some bacteriophages to integrate their genetic material into the genome of a host. Their ability to rearrange DNA sequences in different ways including inversion, excision, or insertion with no help from endogenous molecular machinery, confers important biotechnological value as genetic editing tools with high host plasticity. Despite advances in their use in prokaryotic cells, only a few Ints are currently used as gene editors in eukaryotes, partly due to the functional loss and cytotoxicity presented by some candidates in more complex organisms. To help expand the number of Ints available for the assembly of more complex multifunctional circuits in eukaryotic cells, this protocol describes a platform for the assembly and functional screening of serine-integrase-based genetic switches designed to control gene expression by directional inversions of DNA sequence orientation. The system consists of two sets of plasmids, an effector module and a reporter module, both sets assembled with regulatory components (as promoter and terminator regions) appropriate for expression in mammals, including humans, and plants. The complete method involves plasmid design, DNA delivery, testing and both molecular and phenotypical assessment of results. This platform presents a suitable workflow for the identification and functional validation of new tools for the genetic regulation and reprogramming of organisms with importance in different fields, from medical applications to crop enhancement, as shown by the initial results obtained. This protocol can be completed in 4 weeks for mammalian cells or up to 8 weeks for plant cells, considering cell culture or plant growth time.
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Affiliation(s)
- Marco A. de Oliveira
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
| | - Lilian H. Florentino
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Thais T. Sales
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Rayane N. Lima
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Luciana R. C. Barros
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Universidade de São Paulo, São Paulo, Brazil
| | - Cintia G. Limia
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Mariana S. M. Almeida
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Maria L. Robledo
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Leila M. G. Barros
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Eduardo O. Melo
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Daniela M. Bittencourt
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Stevens K. Rehen
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martín H. Bonamino
- Cell and Gene Therapy Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
- Vice-Presidency of Research and Biological Collections (VPPCB), FIOCRUZ – Oswaldo Cruz Foundation Institute, Rio de Janeiro, Brazil
| | - Elibio Rech
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
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9
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Beschorner N, Künzle P, Voges M, Hauber I, Indenbirken D, Nakel J, Virdi S, Bradtke P, Lory NC, Rothe M, Paszkowski-Rogacz M, Buchholz F, Grundhoff A, Schambach A, Thirion C, Mittrücker HW, Schulze zur Wiesch J, Hauber J, Chemnitz J. Preclinical toxicity analyses of lentiviral vectors expressing the HIV-1 LTR-specific designer-recombinase Brec1. PLoS One 2024; 19:e0298542. [PMID: 38457474 PMCID: PMC10923487 DOI: 10.1371/journal.pone.0298542] [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: 08/29/2023] [Accepted: 01/25/2024] [Indexed: 03/10/2024] Open
Abstract
Drug-based antiretroviral therapies (ART) efficiently suppress HIV replication in humans, but the virus persists as integrated proviral reservoirs in small numbers of cells. Importantly, ART cannot eliminate HIV from an infected individual, since it does not target the integrated provirus. Therefore, genome editing-based strategies that can inactivate or excise HIV genomes would provide the technology for novel curative therapies. In fact, the HIV-1 LTR-specific designer-recombinase Brec1 has been shown to remove integrated proviruses from infected cells and is highly efficacious on clinical HIV-1 isolates in vitro and in vivo, suggesting that Brec1 has the potential for clinical development of advanced HIV-1 eradication strategies in people living with HIV. In line with the preparation of a first-in-human advanced therapy medicinal product gene therapy trial, we here present an extensive preclinical evaluation of Brec1 and lentiviral vectors expressing the Brec1 transgene. This included detailed functional analysis of potential genomic off-target sites, assessing vector safety by investigating vector copy number (VCN) and the risk for potential vector-related insertional mutagenesis, as well as analyzing the potential of Brec1 to trigger an undesired strong T cell immune response. In conclusion, the antiviral designer-recombinase Brec1 is shown to lack any detectable cytopathic, genotoxic or T cell-related immunogenic effects, thereby meeting an important precondition for clinical application of the therapeutic lentiviral vector LV-Brec1 in novel HIV-1 curative strategies.
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Affiliation(s)
- Niklas Beschorner
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Paul Künzle
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Maike Voges
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Ilona Hauber
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Daniela Indenbirken
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Jacqueline Nakel
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Sanamjeet Virdi
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Peter Bradtke
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Niels Christian Lory
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Frank Buchholz
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Adam Grundhoff
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Hans-Willi Mittrücker
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Schulze zur Wiesch
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim Hauber
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
| | - Jan Chemnitz
- Leibniz-Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg–Lübeck–Borstel–Riems, Germany
- PROVIREX Genome Editing Therapies GmbH, Hamburg, Germany
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10
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [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: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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11
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Cautereels C, Smets J, Bircham P, De Ruysscher D, Zimmermann A, De Rijk P, Steensels J, Gorkovskiy A, Masschelein J, Verstrepen KJ. Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast. Nat Commun 2024; 15:1112. [PMID: 38326309 PMCID: PMC10850122 DOI: 10.1038/s41467-024-44997-7] [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: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter Bircham
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Dries De Ruysscher
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, 2610, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Joleen Masschelein
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium.
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12
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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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13
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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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14
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Sun C, Lei Y, Li B, Gao Q, Li Y, Cao W, Yang C, Li H, Wang Z, Li Y, Wang Y, Liu J, Zhao KT, Gao C. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat Biotechnol 2024; 42:316-327. [PMID: 37095350 DOI: 10.1038/s41587-023-01769-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023]
Abstract
A technique for chromosomal insertion of large DNA segments is much needed in plant breeding and synthetic biology to facilitate the introduction of desired agronomic traits and signaling and metabolic pathways. Here we describe PrimeRoot, a genome editing approach to generate targeted precise large DNA insertions in plants. Third-generation PrimeRoot editors employ optimized prime editing guide RNA designs, an enhanced plant prime editor and superior recombinases to enable precise large DNA insertions of up to 11.1 kilobases into plant genomes. We demonstrate the use of PrimeRoot to accurately introduce gene regulatory elements in rice. In this study, we also integrated a gene cassette comprising PigmR, which confers rice blast resistance driven by an Act1 promoter, into a predicted genomic safe harbor site of Kitaake rice and obtain edited plants harboring the expected insertion with an efficiency of 6.3%. We found that these rice plants have increased blast resistance. These results establish PrimeRoot as a promising approach to precisely insert large segments of DNA in plants.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Lei
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yunjia Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Cao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | - Chao Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | - Hongchao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Wang
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yan Li
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | | | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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15
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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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16
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Pasupuleti V, Vora L, Prasad R, Nandakumar DN, Khatri DK. Glioblastoma preclinical models: Strengths and weaknesses. Biochim Biophys Acta Rev Cancer 2024; 1879:189059. [PMID: 38109948 DOI: 10.1016/j.bbcan.2023.189059] [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: 08/26/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Glioblastoma multiforme is a highly malignant brain tumor with significant intra- and intertumoral heterogeneity known for its aggressive nature and poor prognosis. The complex signaling cascade that regulates this heterogeneity makes targeted drug therapy ineffective. The development of an optimal preclinical model is crucial for the comprehension of molecular heterogeneity and enhancing therapeutic efficacy. The ideal model should establish a relationship between various oncogenes and their corresponding responses. This review presents an analysis of preclinical in vivo and in vitro models that have contributed to the advancement of knowledge in model development. The experimental designs utilized in vivo models consisting of both immunodeficient and immunocompetent mice induced with intracranial glioma. The transgenic model was generated using various techniques, like the viral vector delivery system, transposon system, Cre-LoxP model, and CRISPR-Cas9 approaches. The utilization of the patient-derived xenograft model in glioma research is valuable because it closely replicates the human glioma microenvironment, providing evidence of tumor heterogeneity. The utilization of in vitro techniques in the initial stages of research facilitated the comprehension of molecular interactions. However, these techniques are inadequate in reproducing the interactions between cells and extracellular matrix (ECM). As a result, bioengineered 3D-in vitro models, including spheroids, scaffolds, and brain organoids, were developed to cultivate glioma cells in a three-dimensional environment. These models have enabled researchers to understand the influence of ECM on the invasive nature of tumors. Collectively, these preclinical models effectively depict the molecular pathways and facilitate the evaluation of multiple molecules while tailoring drug therapy.
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Affiliation(s)
- Vasavi Pasupuleti
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Lalitkumar Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, BT9 7BL, UK.
| | - Renuka Prasad
- Department of Anatomy, Korea University College of Medicine, Moonsuk Medical Research Building, 516, 5th floor, 73 Inchon-ro, Seongbuk-gu, Seoul 12841, Republic of Korea
| | - D N Nandakumar
- Department of Neurochemistry National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560029, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India.
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17
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Tague N, Andreani V, Fan Y, Timp W, Dunlop MJ. Comprehensive Screening of a Light-Inducible Split Cre Recombinase with Domain Insertion Profiling. ACS Synth Biol 2023; 12:2834-2842. [PMID: 37788288 DOI: 10.1021/acssynbio.3c00328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Splitting proteins with light- or chemically inducible dimers provides a mechanism for post-translational control of protein function. However, current methods for engineering stimulus-responsive split proteins often require significant protein engineering expertise and the laborious screening of individual constructs. To address this challenge, we use a pooled library approach that enables rapid generation and screening of nearly all possible split protein constructs in parallel, where results can be read out by using sequencing. We perform our method on Cre recombinase with optogenetic dimers as a proof of concept, resulting in comprehensive data on the split sites throughout the protein. To improve the accuracy in predicting split protein behavior, we develop a Bayesian computational approach to contextualize errors inherent to experimental procedures. Overall, our method provides a streamlined approach for achieving inducible post-translational control of a protein of interest.
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Affiliation(s)
- Nathan Tague
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Virgile Andreani
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Yunfan Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
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18
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Kohm K, Jalomo-Khayrova E, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau FM, Czech L. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ. Nucleic Acids Res 2023; 51:9452-9474. [PMID: 37602373 PMCID: PMC10516654 DOI: 10.1093/nar/gkad675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
Prophages control their lifestyle to either be maintained within the host genome or enter the lytic cycle. Bacillus subtilis contains the SPβ prophage whose lysogenic state depends on the MrpR (YopR) protein, a key component of the lysis-lysogeny decision system. Using a historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we demonstrate that the lytic cycle of SPβ c2 can be induced by heat due to a single nucleotide exchange in the mrpR gene, rendering the encoded MrpRG136E protein temperature-sensitive. Structural characterization revealed that MrpR is a DNA-binding protein resembling the overall fold of tyrosine recombinases. MrpR has lost its recombinase function and the G136E exchange impairs its higher-order structure and DNA binding activity. Genome-wide profiling of MrpR binding revealed its association with the previously identified SPbeta repeated element (SPBRE) in the SPβ genome. MrpR functions as a master repressor of SPβ that binds to this conserved element to maintain lysogeny. The heat-inducible excision of the SPβ c2 mutant remains reliant on the serine recombinase SprA. A suppressor mutant analysis identified a previously unknown component of the lysis-lysogeny management system that is crucial for the induction of the lytic cycle of SPβ.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Ekaterina Jalomo-Khayrova
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Aileen Krüger
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Syamantak Basu
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
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19
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Luo X, Liu Z, Xu R. Adult tissue-specific stem cell interaction: novel technologies and research advances. Front Cell Dev Biol 2023; 11:1220694. [PMID: 37808078 PMCID: PMC10551553 DOI: 10.3389/fcell.2023.1220694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Adult tissue-specific stem cells play a dominant role in tissue homeostasis and regeneration. Various in vivo markers of adult tissue-specific stem cells have been increasingly reported by lineage tracing in genetic mouse models, indicating that marked cells differentiation is crucial during homeostasis and regeneration. How adult tissue-specific stem cells with indicated markers contact the adjacent lineage with indicated markers is of significance to be studied. Novel methods bring future findings. Recent advances in lineage tracing, synthetic receptor systems, proximity labeling, and transcriptomics have enabled easier and more accurate cell behavior visualization and qualitative and quantitative analysis of cell-cell interactions than ever before. These technological innovations have prompted researchers to re-evaluate previous experimental results, providing increasingly compelling experimental results for understanding the mechanisms of cell-cell interactions. This review aimed to describe the recent methodological advances of dual enzyme lineage tracing system, the synthetic receptor system, proximity labeling, single-cell RNA sequencing and spatial transcriptomics in the study of adult tissue-specific stem cells interactions. An enhanced understanding of the mechanisms of adult tissue-specific stem cells interaction is important for tissue regeneration and maintenance of homeostasis in organisms.
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Affiliation(s)
| | | | - Ruoshi Xu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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20
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Loder S, Patel N, Morgani S, Sambon M, Leucht P, Levi B. Genetic models for lineage tracing in musculoskeletal development, injury, and healing. Bone 2023; 173:116777. [PMID: 37156345 PMCID: PMC10860167 DOI: 10.1016/j.bone.2023.116777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
Musculoskeletal development and later post-natal homeostasis are highly dynamic processes, marked by rapid structural and functional changes across very short periods of time. Adult anatomy and physiology are derived from pre-existing cellular and biochemical states. Consequently, these early developmental states guide and predict the future of the system as a whole. Tools have been developed to mark, trace, and follow specific cells and their progeny either from one developmental state to the next or between circumstances of health and disease. There are now many such technologies alongside a library of molecular markers which may be utilized in conjunction to allow for precise development of unique cell 'lineages'. In this review, we first describe the development of the musculoskeletal system beginning as an embryonic germ layer and at each of the key developmental stages that follow. We then discuss these structures in the context of adult tissues during homeostasis, injury, and repair. Special focus is given in each of these sections to the key genes involved which may serve as markers of lineage or later in post-natal tissues. We then finish with a technical assessment of lineage tracing and the techniques and technologies currently used to mark cells, tissues, and structures within the musculoskeletal system.
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Affiliation(s)
- Shawn Loder
- Department of Plastic Surgery, University of Pittsburgh, Scaife Hall, Suite 6B, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Nicole Patel
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | - Benjamin Levi
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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21
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Wang Y, Zhang K, Zhao Y, Li Y, Su W, Li S. Construction and Applications of Mammalian Cell-Based DNA-Encoded Peptide/Protein Libraries. ACS Synth Biol 2023; 12:1874-1888. [PMID: 37315219 DOI: 10.1021/acssynbio.3c00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA-encoded peptide/protein libraries are the starting point for protein evolutionary modification and functional peptide/antibody selection. Different display technologies, protein directed evolution, and deep mutational scanning (DMS) experiments employ DNA-encoded libraries to provide sequence variations for downstream affinity- or function-based selections. Mammalian cells promise the inherent post-translational modification and near-to-natural conformation of exogenously expressed mammalian proteins and thus are the best platform for studying transmembrane proteins or human disease-related proteins. However, due to the current technical bottlenecks of constructing mammalian cell-based large size DNA-encoded libraries, the advantages of mammalian cells as screening platforms have not been fully exploited. In this review, we summarize the current efforts in constructing DNA-encoded libraries in mammalian cells and the existing applications of these libraries in different fields.
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Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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22
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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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23
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Tague N, Andreani V, Fan Y, Timp W, Dunlop MJ. Comprehensive screening of a light-inducible split Cre recombinase with domain insertion profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542511. [PMID: 37293111 PMCID: PMC10245967 DOI: 10.1101/2023.05.26.542511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Splitting proteins with light- or chemically-inducible dimers provides a mechanism for post-translational control of protein function. However, current methods for engineering stimulus-responsive split proteins often require significant protein engineering expertise and laborious screening of individual constructs. To address this challenge, we use a pooled library approach that enables rapid generation and screening of nearly all possible split protein constructs in parallel, where results can be read out using sequencing. We perform our method on Cre recombinase with optogenetic dimers as a proof of concept, resulting in comprehensive data on split sites throughout the protein. To improve accuracy in predicting split protein behavior, we develop a Bayesian computational approach to contextualize errors inherent to experimental procedures. Overall, our method provides a streamlined approach for achieving inducible post-translational control of a protein of interest.
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24
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Systematic Discovery of a New Catalogue of Tyrosine-Type Integrases in Bacterial Genomic Islands. Appl Environ Microbiol 2023; 89:e0173822. [PMID: 36719242 PMCID: PMC9972944 DOI: 10.1128/aem.01738-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Site-specific recombinases (integrases) can mediate the horizontal transfer of genomic islands. The ability to integrate large DNA sequences into target sites is very important for genetic engineering in prokaryotic and eukaryotic cells. Here, we characterized an unprecedented catalogue of 530 tyrosine-type integrases by examining genes potentially encoding tyrosine integrases in bacterial genomic islands. The phylogeny of putative tyrosine integrases revealed that these integrases form an evolutionary clade that is distinct from those already known and are affiliated with novel integrase groups. We systematically searched for candidate integrase genes, and their integration activities were validated in a bacterial model. We verified the integration functions of six representative novel integrases by using a two-plasmid integration system consisting of a donor plasmid carrying the integrase gene and attP site and a recipient plasmid harboring an attB site in recA-deficient Escherichia coli. Further quantitative reverse transcription-PCR (qRT-PCR) assays validated that the six selected integrases can be expressed with their native promoters in E. coli. The attP region reductions showed that the extent of attP sites of integrases is approximately 200 bp for integration capacity. In addition, mutational analysis showed that the conserved tyrosine at the C terminus is essential for catalysis, confirming that these candidate proteins belong to the tyrosine-type recombinase superfamily, i.e., tyrosine integrases. This study revealed that the novel integrases from bacterial genomic islands have site-specific recombination functions, which is of physiological significance for their genomic islands in bacterial chromosomes. More importantly, our discovery expands the toolbox for genetic engineering, especially for efficient integration activity. IMPORTANCE Site-specific recombinases or integrases have high specificity for DNA large fragment integration, which is urgently needed for gene editing. However, known integrases are not sufficient for meeting multiple integrations. In this work, we discovered an array of integrases through bioinformatics analysis in bacterial genomes. Phylogeny and functional assays revealed that these new integrases belong to tyrosine-type integrases and have the ability to conduct site-specific recombination. Moreover, attP region extent and catalysis site analysis were characterized. Our study provides the methodology for discovery of novel integrases and increases the capacity of weapon pool for genetic engineering in bacteria.
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25
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Rodrigues AF, Rebelo C, Simões S, Paulo C, Pinho S, Francisco V, Ferreira L. A Polymeric Nanoparticle Formulation for Targeted mRNA Delivery to Fibroblasts. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205475. [PMID: 36529964 PMCID: PMC9929262 DOI: 10.1002/advs.202205475] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/18/2022] [Indexed: 05/10/2023]
Abstract
Messenger RNA (mRNA)-based therapies offer enhanced control over the production of therapeutic proteins for many diseases. Their clinical implementation warrants formulations capable of delivering them safely and effectively to target sites. Owing to their chemical versatility, polymeric nanoparticles can be designed by combinatorial synthesis of different ionizable, cationic, and aromatic moieties to modulate cell targeting, using inexpensive formulation steps. Herein, 152 formulations are evaluated by high-throughput screening using a reporter fibroblast model sensitive to functional delivery of mRNA encoding Cre recombinase. Using in vitro and in vivo models, a polymeric nanoformulation based on the combination of 3 specific monomers is identified to transfect fibroblasts much more effectively than other cell types populating the skin, with superior performance than lipid-based transfection agents in the delivery of Cas9 mRNA and guide RNA. This tropism can be explained by receptor-mediated endocytosis, involving CD26 and FAP, which are overexpressed in profibrotic fibroblasts. Structure-activity analysis reveals that efficient mRNA delivery required the combination of high buffering capacity and low mRNA binding affinity for rapid release upon endosomal escape. These results highlight the use of high-throughput screening to rapidly identify chemical features towards the design of highly efficient mRNA delivery systems targeting fibrotic diseases.
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Affiliation(s)
- Artur Filipe Rodrigues
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
| | - Catarina Rebelo
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
- Faculty of MedicinePólo das Ciências da SaúdeUnidade CentralUniversity of CoimbraCoimbra3000‐354Portugal
| | - Susana Simões
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
| | - Cristiana Paulo
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
| | - Sónia Pinho
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
| | - Vítor Francisco
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
| | - Lino Ferreira
- CNC–Center for Neurosciences and Cell BiologyUniversity of CoimbraCoimbra3000‐517Portugal
- Faculty of MedicinePólo das Ciências da SaúdeUnidade CentralUniversity of CoimbraCoimbra3000‐354Portugal
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26
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Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) genome editing, coupled with advances in computing and imaging capabilities, has initiated a new era in which genetic diseases and individual disease susceptibilities are both predictable and actionable. Likewise, genes responsible for plant traits can be identified and altered quickly, transforming the pace of agricultural research and plant breeding. In this Review, we discuss the current state of CRISPR-mediated genetic manipulation in human cells, animals, and plants along with relevant successes and challenges and present a roadmap for the future of this technology.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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27
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Wei Z, Hao C, Chen JK, Gan L, Fan X. A tamoxifen-inducible Cre knock-in mouse for lens-specific gene manipulation. Exp Eye Res 2023; 226:109306. [PMID: 36372215 PMCID: PMC9839650 DOI: 10.1016/j.exer.2022.109306] [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: 08/27/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
Mouse models are valuable tools in studying lens biology and biochemistry, and the Cre-loxP system is the most used technology for gene targeting in the lens. However, numerous genes are indispensable in lens development. The conventional knockout method either prevents lens formation or causes simultaneous cataract formation, hindering the studies of their roles in lens structure, growth, metabolism, and cataractogenesis during lens aging. An inducible Cre-loxP mouse line is an excellent way to achieve such a purpose. We established a lens-specific Cre ERT2 knock-in mouse (LCEK), an inducible mouse model for lens-specific gene targeting in a spatiotemporal manner. LCEK mice were created by in-frame infusion of a P2A-CreERT2 at the C-terminus of the last coding exon of the gene alpha A crystallin (Cryaa). LCEK mice express tamoxifen-inducible Cre recombinase uniquely in the lens. Through ROSAmT/mG and two endogenous genes (Gclc and Rbpj) targeting, we found no Cre recombinase leakage in the lens epithelium, but 50-80% leakage was observed in the lens cortex and nucleus. Administration of tamoxifen almost completely abolished target gene expression in both lens epithelium and cortex but only mildly enhanced gene deletion in the lens nucleus. Notably, no overt leakage of Cre activity was detected in developing LCEK lens when bred with mice carrying loxP floxed genes that are essential for lens development. This newly generated LCEK line will be a powerful tool to target genes in the lens for gene functions study in lens aging, posterior capsule opacification (PCO), and other areas requiring precision gene targeting.
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Affiliation(s)
- Zongbo Wei
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Caili Hao
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Jian-Kang Chen
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Lin Gan
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Xingjun Fan
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA.
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28
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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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29
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Li H, Wu Y, Qiu Y, Li X, Guan Y, Cao X, Liu M, Zhang D, Huang S, Lin L, Hui L, Ma X, Liu M, Zhang X, Wang L, Li D. Stable Transgenic Mouse Strain with Enhanced Photoactivatable Cre Recombinase for Spatiotemporal Genome Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201352. [PMID: 36266974 PMCID: PMC9731692 DOI: 10.1002/advs.202201352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Optogenetic genome engineering is a powerful technology for high-resolution spatiotemporal genetic manipulation, especially for in vivo studies. It is difficult to generate stable transgenic animals carrying a tightly regulated optogenetic system, as its long-term expression induces high background activity. Here, the generation of an enhanced photoactivatable Cre recombinase (ePA-Cre) transgenic mouse strain with stringent light responsiveness and high recombination efficiency is reported. Through serial optimization, ePA-Cre is developed to generate a transgenic mouse line that exhibits 175-fold induction upon illumination. Efficient light-dependent recombination is detected in embryos and various adult tissues of ePA-Cre mice crossed with the Ai14 tdTomato reporter. Importantly, no significant background Cre activity is detected in the tested tissues except the skin. Moreover, efficient light-inducible cell ablation is achieved in ePA-Cre mice crossed with Rosa26-LSL-DTA mice. In conclusion, ePA-Cre mice offer a tightly inducible, highly efficient, and spatiotemporal-specific genome engineering tool for multiple applications.
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Affiliation(s)
- Huiying Li
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
- Southern Medical University Affiliated Fengxian HospitalShanghai201499China
| | - Yingyin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Yuhao Qiu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Xinru Li
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Yuting Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Xiya Cao
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Meizhen Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Dan Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Sijie Huang
- Key Laboratory of Brain Functional Genomics (Ministry of Education)Institute of Brain Functional GenomicsEast China Normal UniversityShanghai200062China
| | - Longnian Lin
- Key Laboratory of Brain Functional Genomics (Ministry of Education)Institute of Brain Functional GenomicsEast China Normal UniversityShanghai200062China
| | - Lijian Hui
- State Key Laboratory of Cell BiologyCAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Xueyun Ma
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Xueli Zhang
- Southern Medical University Affiliated Fengxian HospitalShanghai201499China
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
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30
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Characterization of a New Temperate Escherichia coli Phage vB_EcoP_ZX5 and Its Regulatory Protein. Pathogens 2022; 11:pathogens11121445. [PMID: 36558779 PMCID: PMC9782041 DOI: 10.3390/pathogens11121445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The study of the interaction between temperate phages and bacteria is vital to understand their role in the development of human diseases. In this study, a novel temperate Escherichia coli phage, vB_EcoP_ZX5, with a genome size of 39,565 bp, was isolated from human fecal samples. It has a short tail and belongs to the genus Uetakevirus and the family Podoviridae. Phage vB_EcoP_ZX5 encodes three lysogeny-related proteins (ORF12, ORF21, and ORF4) and can be integrated into the 3'-end of guaA of its host E. coli YO1 for stable transmission to offspring bacteria. Phage vB_EcoP_ZX5 in lysogenized E. coli YO1+ was induced spontaneously, with a free phage titer of 107 PFU/mL. The integration of vB_EcoP_ZX5 had no significant effect on growth, biofilm, environmental stress response, antibiotic sensitivity, adherence to HeLa cells, and virulence of E. coli YO1. The ORF4 anti-repressor, ORF12 integrase, and ORF21 repressors that affect the lytic-lysogenic cycle of vB_EcoP_ZX5 were verified by protein overexpression. We could tell from changes of the number of total phages and the transcription level of phage genes that repressor protein is the key determinant of lytic-to-lysogenic conversion, and anti-repressor protein promotes the conversion from lysogenic cycle to lytic cycle.
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31
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Landau J, Cuba Samaniego C, Giordano G, Franco E. Computational characterization of recombinase circuits for periodic behaviors. iScience 2022; 26:105624. [PMID: 36619981 PMCID: PMC9812718 DOI: 10.1016/j.isci.2022.105624] [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: 11/02/2021] [Revised: 06/17/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Recombinases are site-specific proteins found in nature that are capable of rearranging DNA. This function has made them promising gene editing tools in synthetic biology, as well as key elements in complex artificial gene circuits implementing Boolean logic. However, since DNA rearrangement is irreversible, it is still unclear how to use recombinases to build dynamic circuits like oscillators. In addition, this goal is challenging because a few molecules of recombinase are enough for promoter inversion, generating inherent stochasticity at low copy number. Here, we propose six different circuit designs for recombinase-based oscillators operating at a single copy number. We model them in a stochastic setting, leveraging the Gillespie algorithm for extensive simulations, and show that they can yield coherent periodic behaviors. Our results support the experimental realization of recombinase-based oscillators and, more generally, the use of recombinases to generate dynamic behaviors in synthetic biology.
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Affiliation(s)
- Judith Landau
- California State University, Los Angeles, Los Angeles, CA, USA
| | | | - Giulia Giordano
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Elisa Franco
- University of California, Los Angeles, Los Angeles, CA, USA
- Corresponding author
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32
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A red light-responsive photoswitch for deep tissue optogenetics. Nat Biotechnol 2022; 40:1672-1679. [PMID: 35697806 DOI: 10.1038/s41587-022-01351-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Red light penetrates deep into mammalian tissues and has low phototoxicity, but few optogenetic tools that use red light have been developed. Here we present MagRed, a red light-activatable photoswitch that consists of a red light-absorbing bacterial phytochrome incorporating a mammalian endogenous chromophore, biliverdin and a photo-state-specific binder that we developed using Affibody library selection. Red light illumination triggers the binding of the two components of MagRed and the assembly of split-proteins fused to them. Using MagRed, we developed a red light-activatable Cre recombinase, which enables light-activatable DNA recombination deep in mammalian tissues. We also created red light-inducible transcriptional regulators based on CRISPR-Cas9 that enable an up to 378-fold activation (average, 135-fold induction) of multiple endogenous target genes. MagRed will facilitate optogenetic applications deep in mammalian organisms in a variety of biological research areas.
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Warthi G, Faulkner JL, Doja J, Ghanam AR, Gao P, Yang AC, Slivano OJ, Barris CT, Kress TC, Zawieja SD, Griffin SH, Xie X, Ashworth A, Christie CK, Bryant WB, Kumar A, Davis MJ, Long X, Gan L, de Chantemèle EJB, Lyu Q, Miano JM. Generation and Comparative Analysis of an Itga8-CreER T2 Mouse with Preferential Activity in Vascular Smooth Muscle Cells. NATURE CARDIOVASCULAR RESEARCH 2022; 1:1084-1100. [PMID: 36424917 PMCID: PMC9681021 DOI: 10.1038/s44161-022-00162-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022]
Abstract
All current smooth muscle cell (SMC) Cre mice similarly recombine floxed alleles in vascular and visceral SMCs. Here, we present an Itga8-CreER T2 knock-in mouse and compare its activity with a Myh11-CreER T2 mouse. Both Cre drivers demonstrate equivalent recombination in vascular SMCs. However, Myh11-CreER T2 mice, but not Itga8-CreER T2 mice, display high activity in visceral SMC-containing tissues such as intestine, show early tamoxifen-independent activity, and produce high levels of CreERT2 protein. Whereas Myh11-CreER T2 -mediated knockout of serum response factor (Srf) causes a lethal intestinal phenotype precluding analysis of the vasculature, loss of Srf with Itga8-CreER T2 (Srf Itga8 ) yields viable mice with no evidence of intestinal pathology. Male and female Srf Itga8 mice exhibit vascular contractile incompetence, and angiotensin II causes elevated blood pressure in wild type, but not Srf Itga8 , male mice. These findings establish the Itga8-CreER T2 mouse as an alternative to existing SMC Cre mice for unfettered phenotyping of vascular SMCs following selective gene loss.
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Affiliation(s)
- Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Jessica L. Faulkner
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Jaser Doja
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Amr R. Ghanam
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Pan Gao
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Allison C. Yang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Orazio J. Slivano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Candee T. Barris
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Taylor C. Kress
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Scott D. Zawieja
- Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Susan H. Griffin
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Xiaoling Xie
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158
| | - Christine K. Christie
- Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - William B. Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Ajay Kumar
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Michael J. Davis
- Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Lin Gan
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | | | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
- Biomedical and Health Institute, Chongqing Institute of Green and Intelligence Technology, Chongqing, China 400714
- Chongqing General Hospital, Chongqing, China 401147
| | - Joseph M. Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
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Yamauchi Y, Matsukura H, Motone K, Ueda M, Aoki W. Evaluation of a library of loxP variants with a wide range of recombination efficiencies by Cre. PLoS One 2022; 17:e0276657. [PMID: 36269789 PMCID: PMC9586403 DOI: 10.1371/journal.pone.0276657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022] Open
Abstract
Sparse labeling of individual cells is an important approach in neuroscience and many other fields of research. Various methods have been developed to sparsely label only a small population of cells; however, there is no simple and reproducible strategy for managing the probability of sparse labeling at desired levels. Here, we aimed to develop a novel methodology based on the Cre-lox system to regulate sparseness at desired levels, and we purely analyzed cleavage efficiencies of loxP mutants by Cre. We hypothesized that mutations in the loxP sequence reduce the recognition efficiency by Cre, which enables the regulation of the sparseness level of gene expression. In this research, we mutagenized the loxP sequence and analyzed a library of loxP variants. We evaluated more than 1000 mutant loxP sequences, including mutants with reduced excision efficiencies by Cre ranging from 0.51% to 59%. This result suggests that these mutant loxP sequences can be useful in regulating the sparseness of genetic labeling at desired levels.
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Affiliation(s)
- Yuji Yamauchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Hidenori Matsukura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Keisuke Motone
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail:
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35
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West PT, Chanin RB, Bhatt AS. From genome structure to function: insights into structural variation in microbiology. Curr Opin Microbiol 2022; 69:102192. [PMID: 36030622 PMCID: PMC9783807 DOI: 10.1016/j.mib.2022.102192] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 12/27/2022]
Abstract
Structural variation in bacterial genomes is an important evolutionary driver. Genomic rearrangements, such as inversions, duplications, and insertions, can regulate gene expression and promote niche adaptation. Importantly, many of these variations are reversible and preprogrammed to generate heterogeneity. While many tools have been developed to detect structural variation in eukaryotic genomes, variation in bacterial genomes and metagenomes remains understudied. However, recent advances in genome sequencing technology and the development of new bioinformatic pipelines hold promise in further understanding microbial genomics.
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Affiliation(s)
- Patrick T West
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA
| | - Rachael B Chanin
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA.
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36
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Swanson JL, Chin PS, Romero JM, Srivastava S, Ortiz-Guzman J, Hunt PJ, Arenkiel BR. Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry. Front Neural Circuits 2022; 16:886302. [PMID: 35719420 PMCID: PMC9204427 DOI: 10.3389/fncir.2022.886302] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 01/27/2023] Open
Abstract
Neural circuits and the cells that comprise them represent the functional units of the brain. Circuits relay and process sensory information, maintain homeostasis, drive behaviors, and facilitate cognitive functions such as learning and memory. Creating a functionally-precise map of the mammalian brain requires anatomically tracing neural circuits, monitoring their activity patterns, and manipulating their activity to infer function. Advancements in cell-type-specific genetic tools allow interrogation of neural circuits with increased precision. This review provides a broad overview of recombination-based and activity-driven genetic targeting approaches, contemporary viral tracing strategies, electrophysiological recording methods, newly developed calcium, and voltage indicators, and neurotransmitter/neuropeptide biosensors currently being used to investigate circuit architecture and function. Finally, it discusses methods for acute or chronic manipulation of neural activity, including genetically-targeted cellular ablation, optogenetics, chemogenetics, and over-expression of ion channels. With this ever-evolving genetic toolbox, scientists are continuing to probe neural circuits with increasing resolution, elucidating the structure and function of the incredibly complex mammalian brain.
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Affiliation(s)
- Jessica L. Swanson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Pey-Shyuan Chin
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Snigdha Srivastava
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Joshua Ortiz-Guzman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Patrick J. Hunt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
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37
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Chawda C, McMorrow R, Gaspar N, Zambito G, Mezzanotte L. Monitoring Immune Cell Function Through Optical Imaging: a Review Highlighting Transgenic Mouse Models. Mol Imaging Biol 2022; 24:250-263. [PMID: 34735680 PMCID: PMC8983637 DOI: 10.1007/s11307-021-01662-5] [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: 06/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022]
Abstract
Transgenic mouse models have facilitated research of human diseases and validation of therapeutic approaches. Inclusion of optical reporter genes (fluorescent or bioluminescent genes) in the targeting vectors used to develop such models makes in vivo imaging of cellular and molecular events possible, from the microscale to the macroscale. In particular, transgenic mouse models expressing optical reporter genes allowed accurately distinguishing immune cell types from trafficking in vivo using intravital microscopy or whole-body optical imaging. Besides lineage tracing and trafficking of different subsets of immune cells, the ability to monitor the function of immune cells is of pivotal importance for investigating the effects of immunotherapies against cancer. Here, we introduce the reader to state-of-the-art approaches to develop transgenics, optical imaging techniques, and several notable examples of transgenic mouse models developed for immunology research by critically highlighting the models that allow the following of immune cell function.
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Affiliation(s)
- Chintan Chawda
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Roisin McMorrow
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
- Percuros B.V, Leiden, The Netherlands
| | - Natasa Gaspar
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
- Percuros B.V, Leiden, The Netherlands
| | - Giorgia Zambito
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Mezzanotte
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands.
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38
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Stachowski K, Norris A, Potter D, Wysocki V, Foster M. Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM. Nucleic Acids Res 2022; 50:1753-1769. [PMID: 35104890 PMCID: PMC8860596 DOI: 10.1093/nar/gkac032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022] Open
Abstract
Cre recombinase selectively recognizes DNA and prevents non-specific DNA cleavage through an orchestrated series of assembly intermediates. Cre recombines two loxP DNA sequences featuring a pair of palindromic recombinase binding elements and an asymmetric spacer region, by assembly of a tetrameric synaptic complex, cleavage of an opposing pair of strands, and formation of a Holliday junction intermediate. We used Cre and loxP variants to isolate the monomeric Cre-loxP (54 kDa), dimeric Cre2-loxP (110 kDa), and tetrameric Cre4-loxP2 assembly intermediates, and determined their structures using cryo-EM to resolutions of 3.9, 4.5 and 3.2 Å, respectively. Progressive and asymmetric bending of the spacer region along the assembly pathway enables formation of increasingly intimate interfaces between Cre protomers and illuminates the structural bases of biased loxP strand cleavage order and half-the-sites activity. Application of 3D variability analysis to the tetramer data reveals constrained conformational sampling along the pathway between protomer activation and Holliday junction isomerization. These findings underscore the importance of protein and DNA flexibility in Cre-mediated site selection, controlled activation of alternating protomers, the basis for biased strand cleavage order, and recombination efficiency. Such considerations may advance development of site-specific recombinases for use in gene editing applications.
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Affiliation(s)
- Kye Stachowski
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew S Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Devante Potter
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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Park GS, Maeng JS. A novel isothermal method for amplification of long specific amplicon from linear template. Sci Rep 2022; 12:2756. [PMID: 35177762 PMCID: PMC8854607 DOI: 10.1038/s41598-022-06785-5] [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: 12/24/2021] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Isothermal nucleic acid amplification methods have been successfully developed and applied for diagnostic purpose, especially for detection of pathogens. However, amplicon size of such methods is relatively short (< 500 bp) to limit their application for long amplicon production that can be used for various downstream applications including genomic surveillance of pathogens. To fill the gap, we developed a method for specific amplification of kilobases-long target sequence from RNA templates. This method, named CREA, utilizes sequence specific recombination of Cre recombinase to generate circular intermediate template for subsequent RCA reaction. CREA with SARS-CoV-2 spike template could amplify ~ 2.9 kb target and up to ~ 1.9 kb amplicon was able to produce in sufficient amount for general cloning. Each step of CREA procedure was thoroughly analyzed to provide directions for further optimizations. Furthermore, we evaluated a variation of CREA which utilized DNA ligase.
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Affiliation(s)
- Gun-Soo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Division of Food Convergence, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
| | - Jin-Soo Maeng
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Division of Food Convergence, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
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40
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Hoersten J, Ruiz-Gómez G, Lansing F, Rojo-Romanos T, Schmitt L, Sonntag J, Pisabarro M, Buchholz F. Pairing of single mutations yields obligate Cre-type site-specific recombinases. Nucleic Acids Res 2022; 50:1174-1186. [PMID: 34951450 PMCID: PMC8789052 DOI: 10.1093/nar/gkab1240] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
Tyrosine site-specific recombinases (SSRs) represent a versatile genome editing tool with considerable therapeutic potential. Recent developments to engineer and evolve SSRs into heterotetramers to improve target site flexibility signified a critical step towards their broad utility in genome editing. However, SSR monomers can form combinations of different homo- and heterotetramers in cells, increasing their off-target potential. Here, we discover that two paired mutations targeting residues implicated in catalysis lead to simple obligate tyrosine SSR systems, where the presence of all distinct subunits to bind as a heterotetramer is obligatory for catalysis. Therefore, only when the paired mutations are applied as single mutations on each recombinase subunit, the engineered SSRs can efficiently recombine the intended target sequence, while the subunits carrying the point mutations expressed in isolation are inactive. We demonstrate the utility of the obligate SSR system to improve recombination specificity of a designer-recombinase for a therapeutic target in human cells. Furthermore, we show that the mutations render the naturally occurring SSRs, Cre and Vika, obligately heteromeric for catalytic proficiency, providing a straight-forward approach to improve their applied properties. These results facilitate the development of safe and effective therapeutic designer-recombinases and advance our mechanistic understanding of SSR catalysis.
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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 47-51, 01307 Dresden, Germany
| | - Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Teresa Rojo-Romanos
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Jan Sonntag
- 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 47-51, 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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Artificial nondirectional site-specific recombination systems. iScience 2022; 25:103716. [PMID: 35072008 PMCID: PMC8762395 DOI: 10.1016/j.isci.2021.103716] [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: 06/03/2021] [Revised: 10/23/2021] [Accepted: 12/29/2021] [Indexed: 11/22/2022] Open
Abstract
Site-specific recombination systems (SRSs) are widely used in studies on synthetic biology and related disciplines. Nondirectional SRSs can randomly trigger excision, integration, reversal, and translocation, which are effective tools to achieve large-scale genome recombination. In this study, we designed 6 new nondirectional SRSs named Vika/voxsym1-4 and Dre/roxsym1-2. All 6 artificial nondirectional SRSs were able to generate random deletion and inversion in Saccharomyces cerevisiae. Moreover, all six SRSs were orthogonal to Cre/loxPsym. The pairwise orthogonal nondirected SRSs can simultaneously initiate large-scale and independent gene recombination in two different regions of the genome, which could not be accomplished using previous orthogonal systems. These SRSs were found to be robust while working in the cells at different growth stages, as well as in the different spatial structure of the chromosome. These artificial pairwise orthogonal nondirected SRSs offer newfound potential for site-specific recombination in synthetic biology. Designed six new artificial nondirectional site-specific recombination systems Pairwise orthogonal nondirected recombination systems in yeast The deletion efficiency of systems is far greater than the inversion efficiency These nondirectional recombination systems were found to be robust
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Lansing F, Mukhametzyanova L, Rojo-Romanos T, Iwasawa K, Kimura M, Paszkowski-Rogacz M, Karpinski J, Grass T, Sonntag J, Schneider PM, Günes C, Hoersten J, Schmitt LT, Rodriguez-Muela N, Knöfler R, Takebe T, Buchholz F. Correction of a Factor VIII genomic inversion with designer-recombinases. Nat Commun 2022; 13:422. [PMID: 35058465 PMCID: PMC8776779 DOI: 10.1038/s41467-022-28080-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023] Open
Abstract
Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct the 140 kb inversion of the F8 gene frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we develop a coupled heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient-derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, results in 12% correction of the inversion and restores Factor VIII mRNA expression. In this work, we present designer-recombinases as an efficient and specific means towards treatment of monogenic diseases caused by large gene inversions. Correction of disease-causing large genomic inversions remains challenging. Here, the authors developed a dual designer-recombinase system (RecF8) that efficiently corrects a 140 kb inversion frequently found in patients with severe Hemophilia A.
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Wagner N, Foster MP. Nearest-Neighbor Effects Modulate loxP Spacer DNA Chemical Shifts and Guide Oligonucleotide Design for Nuclear Magnetic Resonance Studies. Biochemistry 2022; 61:67-76. [PMID: 34985267 DOI: 10.1021/acs.biochem.1c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Cre-loxP gene editing tool enables site-specific editing of DNA without leaving lesions that must be repaired by error-prone cellular processes. Cre recombines two 34-bp loxP DNA sites that feature a pair of palindromic recombinase-binding elements flanking an asymmetric 8-bp spacer region, via assembly of a tetrameric intasome complex and formation of a Holliday junction intermediate. Recombination proceeds by coordinated nucleophilic attack by pairs of catalytic tyrosine residues on specific phosphodiester bonds in the spacer regions of opposing strands. Despite not making base-specific contacts with the asymmetric spacer region of the DNA, Cre exhibits a preference for initial cleavage on one of the strands, suggesting that intrinsic properties of the uncontacted 8-bp spacer region give rise to this preference. Furthermore, little is known about the structural and dynamic features of the loxP spacer that make it a suitable target for Cre. To enable NMR spectroscopic studies of the spacer, we have aimed to identify a fragment of the 34-bp loxP site that retains the structural features of the spacer while minimizing the spectral crowding and line-broadening seen in longer oligonucleotides. Sequence-specific chemical shift differences between spacer oligos of different lengths, and of a mutant that inverts strand cleavage order, reveal how both nearest-neighbor and next-nearest-neighbor effects dominate the chemical environment experienced by the spacer. We have identified a 16-bp oligonucleotide that preserves the structural environment of the spacer, setting the stage for NMR-based structure determination and dynamics investigations.
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Affiliation(s)
- Nicole Wagner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
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Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases. Comput Struct Biotechnol J 2022; 20:989-1001. [PMID: 35242289 PMCID: PMC8860914 DOI: 10.1016/j.csbj.2022.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
New functional regions emerging in evolution of DNA site-specific recombinase tails. Transient structural nucleation promotes function-dispensable regions to essential. Molecular dynamics reveals conformational diversity and its functional implications. Evolved disordered molecular mechanisms of N-term tails for protein stability. Structural disorder-based link between protein evolution, stability and function.
Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structural disorder-to-function relationships need to be deciphered. The DNA site-specific recombinase system Cre/loxP represents an attractive model to investigate functional molecular mechanisms of IDRs. Cre contains a functionally dispensable disordered N-terminal tail, which becomes indispensable in the evolved Tre/loxLTR recombinase system. The difficulty to experimentally obtain structural information about this tail has so far precluded any mechanistic study on its involvement in DNA recombination. Here, we use in vitro and in silico evolution data, conformational dynamics, AI-based folding simulations, thermodynamic stability calculations, mutagenesis and DNA recombination assays to investigate how evolution and the dynamic behavior of this IDR may determine distinct functional properties. Our studies suggest that partial conformational order in the N-terminal tail of Tre recombinase and its packing to a conserved hydrophobic surface on the protein provide thermodynamic stability. Based on our results, we propose a link between protein stability and function, offering new plausible atom-detailed mechanistic insights into disorder-function relationships. Our work highlights the potential of N-terminal tails to be exploited for regulation of the activity of Cre-like tyrosine-type SSRs, which merits future investigations and could be of relevance in future rational engineering for their use in biotechnology and genomic medicine.
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Hamann MV, Beschorner N, Vu XK, Hauber I, Lange UC, Traenkle B, Kaiser PD, Foth D, Schneider C, Büning H, Rothbauer U, Hauber J. Improved targeting of human CD4+ T cells by nanobody-modified AAV2 gene therapy vectors. PLoS One 2021; 16:e0261269. [PMID: 34928979 PMCID: PMC8687595 DOI: 10.1371/journal.pone.0261269] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated viruses (AAV) are considered non-pathogenic in humans, and thus have been developed into powerful vector platforms for in vivo gene therapy. Although the various AAV serotypes display broad tropism, frequently infecting multiple tissues and cell types, vectors for specific and efficient targeting of human CD4+ T lymphocytes are largely missing. In fact, a substantial translational bottleneck exists in the field of therapeutic gene transfer that would require in vivo delivery into peripheral disease-related lymphocytes for subsequent genome editing. To solve this issue, capsid modification for retargeting AAV tropism, and in turn improving vector potency, is considered a promising strategy. Here, we genetically modified the minor AAV2 capsid proteins, VP1 and VP2, with a set of novel nanobodies with high-affinity for the human CD4 receptor. These novel vector variants demonstrated improved targeting of human CD4+ cells, including primary human peripheral blood mononuclear cells (PBMC) and purified human CD4+ T lymphocytes. Thus, the technical approach presented here provides a promising strategy for developing specific gene therapy vectors, particularly targeting disease-related peripheral blood CD4+ leukocytes.
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Affiliation(s)
- Martin V. Hamann
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
| | - Niklas Beschorner
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
| | - Xuan-Khang Vu
- Institute of Experimental Haematology, Hannover Medical School, Hannover, Germany
| | - Ilona Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Ulrike C. Lange
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
- Department of Anaesthesiology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Bjoern Traenkle
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
| | - Philipp D. Kaiser
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
| | - Daniel Foth
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Carola Schneider
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Hildegard Büning
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
- Institute of Experimental Haematology, Hannover Medical School, Hannover, Germany
| | - Ulrich Rothbauer
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Reutlingen, Germany
| | - Joachim Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
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Jones CM, Parrish S, Nielsen DR. Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria. ACS Synth Biol 2021; 10:2371-2382. [PMID: 34530614 DOI: 10.1021/acssynbio.1c00269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we describe a universal approach for plasmid-free genome engineering in cyanobacteria that exploits the polyploidy of their chromosomes as a natural counterselection system. Rather than being delivered via replicating plasmids, genes encoding for DNA modifying enzymes are instead integrated into essential genes on the chromosome by allelic exchange, as facilitated by antibiotic selection, a process that occurs readily and with only minor fitness defects. By virtue of the essentiality of these integration sites, full segregation is never achieved, with the strain instead remaining as a merodiploid so long as antibiotic selection is maintained. As a result, once the desired genome modification is complete, removal of antibiotic selection results in the gene encoding for the DNA modifying enzyme to then be promptly eliminated from the population. Proof of concept of this new and generalizable strategy is provided using two different site-specific recombination systems, CRE-lox and DRE-rox, in the fast-growing cyanobacterium Synechococcus sp. PCC 7002, as well as CRE-lox in the model cyanobacterium Synechocystis sp. PCC 6803. Reusability of the method, meanwhile, is demonstrated by constructing a high-CO2 requiring and markerless Δndh3 Δndh4 ΔbicA ΔsbtA mutant of Synechococcus sp. PCC 7002. Overall, this method enables the simple and efficient construction of stable and unmarked mutants in cyanobacteria without the need to develop additional shuttle vectors nor counterselection systems.
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Affiliation(s)
- Christopher M. Jones
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Sydney Parrish
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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Badel C, Da Cunha V, Oberto J. Archaeal tyrosine recombinases. FEMS Microbiol Rev 2021; 45:fuab004. [PMID: 33524101 PMCID: PMC8371274 DOI: 10.1093/femsre/fuab004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022] Open
Abstract
The integration of mobile genetic elements into their host chromosome influences the immediate fate of cellular organisms and gradually shapes their evolution. Site-specific recombinases catalyzing this integration have been extensively characterized both in bacteria and eukarya. More recently, a number of reports provided the in-depth characterization of archaeal tyrosine recombinases and highlighted new particular features not observed in the other two domains. In addition to being active in extreme environments, archaeal integrases catalyze reactions beyond site-specific recombination. Some of these integrases can catalyze low-sequence specificity recombination reactions with the same outcome as homologous recombination events generating deep rearrangements of their host genome. A large proportion of archaeal integrases are termed suicidal due to the presence of a specific recombination target within their own gene. The paradoxical maintenance of integrases that disrupt their gene upon integration implies novel mechanisms for their evolution. In this review, we assess the diversity of the archaeal tyrosine recombinases using a phylogenomic analysis based on an exhaustive similarity network. We outline the biochemical, ecological and evolutionary properties of these enzymes in the context of the families we identified and emphasize similarities and differences between archaeal recombinases and their bacterial and eukaryal counterparts.
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Affiliation(s)
- Catherine Badel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jacques Oberto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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Van Hoeck J, Van de Vyver T, Harizaj A, Goetgeluk G, Merckx P, Liu J, Wels M, Sauvage F, De Keersmaecker H, Vanhove C, de Jong OG, Vader P, Dewitte H, Vandekerckhove B, Braeckmans K, De Smedt SC, Raemdonck K. Hydrogel-Induced Cell Membrane Disruptions Enable Direct Cytosolic Delivery of Membrane-Impermeable Cargo. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2008054. [PMID: 34106486 DOI: 10.1002/adma.202008054] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Intracellular delivery of membrane-impermeable cargo offers unique opportunities for biological research and the development of cell-based therapies. Despite the breadth of available intracellular delivery tools, existing protocols are often suboptimal and alternative approaches that merge delivery efficiency with both biocompatibility, as well as applicability, remain highly sought after. Here, a comprehensive platform is presented that exploits the unique property of cationic hydrogel nanoparticles to transiently disrupt the plasma membrane of cells, allowing direct cytosolic delivery of uncomplexed membrane-impermeable cargo. Using this platform, which is termed Hydrogel-enabled nanoPoration or HyPore, the delivery of fluorescein isothiocyanate (FITC)-dextran macromolecules in various cancer cell lines and primary bovine corneal epithelial cells is convincingly demonstrated. Of note, HyPore demonstrates efficient FITC-dextran delivery in primary human T cells, outperforming state-of-the-art electroporation-mediated delivery. Moreover, the HyPore platform enables cytosolic delivery of functional proteins, including a histone-binding nanobody as well as the enzymes granzyme A and Cre-recombinase. Finally, HyPore-mediated delivery of the MRI contrast agent gadobutrol in primary human T cells significantly improves their T1 -weighted MRI signal intensities compared to electroporation. Taken together, HyPore is proposed as a straightforward, highly versatile, and cost-effective technique for high-throughput, ex vivo manipulation of primary cells and cell lines.
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Affiliation(s)
- Jelter Van Hoeck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Aranit Harizaj
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Glenn Goetgeluk
- Department of Diagnostic Sciences, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Pieterjan Merckx
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Jing Liu
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Mike Wels
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Félix Sauvage
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Herlinde De Keersmaecker
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Christian Vanhove
- Infinity Lab, Medical Imaging and Signal Processing Group-IBiTech, Faculty of Engineering and Architecture, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Olivier G de Jong
- CDL Research, Division LAB, UMC Utrecht, Faculty of Medicine, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Universiteitsweg 99, Utrecht, 3584 CG, The Netherlands
| | - Pieter Vader
- CDL Research, Division LAB, UMC Utrecht, Faculty of Medicine, Utrecht University, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Heleen Dewitte
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Kevin Braeckmans
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium
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Liu R, Long Q, Zou X, Wang Y, Pei Y. DNA methylation occurring in Cre-expressing cells inhibits loxP recombination and silences loxP-sandwiched genes. THE NEW PHYTOLOGIST 2021; 231:210-224. [PMID: 33742463 DOI: 10.1111/nph.17353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
The low DNA recombination efficiency of site-specific recombinase systems in plants limits their application; however, the underlying mechanism is unknown. We evaluate the gene deletion performance of four recombinase systems (Cre/loxP, Flp/FRT, KD/KDRT and B3/B3RT) in tobacco where the recombinases are under the control of germline-specific promoters. We find that the expression of these recombinases results mostly in gene silencing rather than gene deletion. Using the Cre/loxP system as a model, we reveal that the region flanked by loxP sites (floxed) is hypermethylated, which prevents floxed genes from deletion while silencing the expression of the genes. We further show CG methylation alone in the recombinase binding element of the loxP site is unable to impede gene deletion; instead, CHH methylation in the crossover region is required to inhibit loxP recombination. Our study illustrates the important role of recombinase-induced DNA methylation in the inhibition of site-specific DNA recombination and uncovers the mechanism underlying recombinase-associated gene silence in plants.
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Affiliation(s)
- Ruochen Liu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Qin Long
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xiuping Zou
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - You Wang
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yan Pei
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
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