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Zhang Q, Azarin SM, Sarkar CA. Model-guided engineering of DNA sequences with predictable site-specific recombination rates. Nat Commun 2022; 13:4152. [PMID: 35858965 PMCID: PMC9300676 DOI: 10.1038/s41467-022-31538-3] [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: 08/02/2021] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Site-specific recombination (SSR) is an important tool in synthetic biology, but its applications are limited by the inability to predictably tune SSR reaction rates. Facile rate manipulation could be achieved by modifying the DNA substrate sequence; however, this approach lacks rational design principles. Here, we develop an integrated experimental and computational method to engineer the DNA attachment sequence attP for predictably modulating the inversion reaction mediated by the recombinase Bxb1. After developing a qPCR method to measure SSR reaction rate, we design, select, and sequence attP libraries to inform a machine-learning model that computes Bxb1 inversion rate as a function of attP sequence. We use this model to predict reaction rates of attP variants in vitro and demonstrate their utility in gene circuit design in Escherichia coli. Our high-throughput, model-guided approach for rationally tuning SSR reaction rates enhances our understanding of recombinase function and expands the synthetic biology toolbox.
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Affiliation(s)
- Qiuge Zhang
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Samira M. Azarin
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Casim A. Sarkar
- grid.17635.360000000419368657Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
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Ata-Abadi NS, Forouzanfar M, Dormiani K, Varnosfaderani SR, Pirjamali L, Nasr-Esfahani MH, Hajidavaloo RM. Site-specific integration as an efficient method for production of recombinant human hyaluronidase PH20 in semi-adherent cells. Appl Microbiol Biotechnol 2022; 106:1459-1473. [PMID: 35107633 DOI: 10.1007/s00253-022-11794-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 11/02/2022]
Abstract
PH20 is a hyaluronidase enzyme that can hydrolyze the glycosidic bond in hyaluronic acid as the major proteoglycan found in extracellular matrices. In the present study, we constructed and characterized two donor plasmids, one of them with one and the second with two PH20 expression cassettes. The expression vectors were site specifically integrated into the genome of HEK293T cells using PhiC31 integrase system to develop HEK293T stable cell lines secreting His-tagged recombinant human PH20 (rhPH20) in the culture supernatant. The produced rhPH20 was quantified using ELISA and turbidimetric assay tests, and its catalytic activity was also assessed by treating the mouse cumulus-oocyte complexes. Our results showed that the secreted rhPH20 in the culture supernatant had the specific activity of 16,660 IU/mg and the recombinant enzyme was able to remove the cumulus cells from oocytes. The results also indicated that phiC31 enzyme inserted the PH20-expressing donor vectors into the specific pseudo attP sites including 10q21.2 and 20q11.22 in the genome of the target cells with different copy numbers. Taken together, our findings demonstrate that PhiC31 integrase system is able to be applied as a robust tool for efficient production and secretion of soluble and active rhPH20 by HEK293T cells as a semi-adherent human cell line. KEY POINTS: • Efficient production of human recombinant PH20 in a semi-adherent human cell line • Successful application of PhiC31 integrase system for generation of stable recombinant clones • Use of a human cell line for expression of a recombinant human protein due to complex and efficient post-translational modifications and protein folding.
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Affiliation(s)
- Nafiseh Sanei Ata-Abadi
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mahboobeh Forouzanfar
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kianoush Dormiani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Shiva Rouhollahi Varnosfaderani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Leila Pirjamali
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Reza Moradi Hajidavaloo
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
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Qu L, Wang L, Zhu X, Zhang Y, Ou Q, Ma A, Sheng F, Wei X, Dai Y, Li G, Xie S. Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq. Hereditas 2019; 156:3. [PMID: 30675136 PMCID: PMC6332687 DOI: 10.1186/s41065-018-0079-z] [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: 10/15/2018] [Accepted: 12/25/2018] [Indexed: 11/22/2022] Open
Abstract
Background ΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31 integrase. The present study was aimed to uncover the global map of ΦC31 integrase binding sites in bovine cells and analysis the features of these binding sites by comprehensive bioinformatics methods. Results In this study, we constructed a ChIP-seq method that can be used to uncover the global binding sites by phiC31 integrase. 6740 potential ΦC31 integrase binding sites were identified. A sequence motif was found that contains inverted repeats and has similarities to wild-type attP site. Using REPEATMASKER, we identified a total of 20,183 repeat-regions distributed in 50 repeat types for the 6740 binding sites. These sites enriched in “regulation of GTPase activity” of in the GO category of biological process and KEGG pathway of signal transmembrane transporter activity. Conclusion This study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals. Electronic supplementary material The online version of this article (10.1186/s41065-018-0079-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lijuan Qu
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Lei Wang
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Xueyuan Zhu
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Yan Zhang
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Qiang Ou
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Aying Ma
- Department of Respiratory Medicine, Shanghai First People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201620 China
| | - Fengying Sheng
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Xiaoqing Wei
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Yue Dai
- Department of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China
| | - Guoting Li
- Lab of Reproductive Pharmacology, NHC Key Lab of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, 200032 China
| | - Shuwu Xie
- Lab of Reproductive Pharmacology, NHC Key Lab of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, 200032 China
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Chaikind B, Bessen JL, Thompson DB, Hu JH, Liu DR. A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucleic Acids Res 2016; 44:9758-9770. [PMID: 27515511 PMCID: PMC5175349 DOI: 10.1093/nar/gkw707] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 02/07/2023] Open
Abstract
We describe the development of ‘recCas9’, an RNA-programmed small serine recombinase that functions in mammalian cells. We fused a catalytically inactive dCas9 to the catalytic domain of Gin recombinase using an optimized fusion architecture. The resulting recCas9 system recombines DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. We show that these recombinases can operate on DNA sites in mammalian cells identical to genomic loci naturally found in the human genome in a manner that is dependent on the guide RNA sequences. DNA sequencing reveals that recCas9 catalyzes guide RNA-dependent recombination in human cells with an efficiency as high as 32% on plasmid substrates. Finally, we demonstrate that recCas9 expressed in human cells can catalyze in situ deletion between two genomic sites. Because recCas9 directly catalyzes recombination, it generates virtually no detectable indels or other stochastic DNA modification products. This work represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state. Current and future generations of recCas9 may facilitate targeted agricultural breeding, or the study and treatment of human genetic diseases.
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Affiliation(s)
- Brian Chaikind
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
| | - Jeffrey L Bessen
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
| | - David B Thompson
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Johnny H Hu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - David R Liu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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In vitro gene manipulation of spinal muscular atrophy fibroblast cell line using gene-targeting fragment for restoration of SMN protein expression. Gene Ther 2015; 23:10-7. [DOI: 10.1038/gt.2015.92] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 06/17/2015] [Accepted: 08/05/2015] [Indexed: 11/08/2022]
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