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Levesque S, Cosentino A, Verma A, Genovese P, Bauer DE. Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism. Nat Biotechnol 2024:10.1038/s41587-024-02266-4. [PMID: 38806736 DOI: 10.1038/s41587-024-02266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024]
Abstract
Therapeutic prime editing of hematopoietic stem and progenitor cells (HSPCs) holds great potential to remedy blood disorders. Quiescent cells have low nucleotide levels and resist retroviral infection, and it is possible that nucleotide metabolism could limit reverse transcription-mediated prime editing in HSPCs. We demonstrate that deoxynucleoside supplementation and Vpx-mediated degradation of SAMHD1 improve prime editing efficiency in HSPCs, especially when coupled with editing approaches that evade mismatch repair.
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Affiliation(s)
- Sébastien Levesque
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Andrea Cosentino
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Milano-Bicocca University, Milan, Italy
| | - Archana Verma
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Pietro Genovese
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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Ponnienselvan K, Liu P, Nyalile T, Oikemus S, Joynt AT, Kelly K, Guo D, Chen Z, Lee JM, Schiffer CA, Emerson CP, Lawson ND, Watts JK, Sontheimer EJ, Luban J, Wolfe SA. Addressing the dNTP bottleneck restricting prime editing activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.21.563443. [PMID: 37904991 PMCID: PMC10614944 DOI: 10.1101/2023.10.21.563443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Prime editing efficiency is modest in cells that are quiescent or slowly proliferating where intracellular dNTP levels are tightly regulated. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. We report that prime editing efficiency in primary cells and in vivo is increased by mutations that enhance the enzymatic properties of MMLV-reverse transcriptase and can be further complemented by targeting SAMHD1 for degradation.
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3
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Ni P, Zhao Y, Zhou X, Liu Z, Huang Z, Ni Z, Sun Q, Zong Y. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biol 2023; 24:156. [PMID: 37386475 PMCID: PMC10308706 DOI: 10.1186/s13059-023-02990-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Prime editing is limited by low efficiency in plants. Here, we develop an upgraded engineered plant prime editor in hexaploid wheat, ePPEplus, by introducing a V223A substitution into reverse transcriptase in the ePPEmax* architecture. ePPEplus enhances the efficiency by an average 33.0-fold and 6.4-fold compared to the original PPE and ePPE, respectively. Importantly, a robust multiplex prime editing platform is established for simultaneous editing of four to ten genes in protoplasts and up to eight genes in regenerated wheat plants at frequencies up to 74.5%, thus expanding the applicability of prime editors for stacking of multiple agronomic traits.
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Affiliation(s)
- Pei Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ximeng Zhou
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zehua Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhengwei Huang
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yuan Zong
- Frontiers Science Center for Molecular Design Breeding (MOE), Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Dyudeeva ES, Pyshnaya IA. Phosphoryl guanidine oligonucleotides as primers for RNA-dependent DNA synthesis using murine leukemia virus reverse transcriptase. Vavilovskii Zhurnal Genet Selektsii 2022; 26:5-13. [PMID: 35342851 PMCID: PMC8892174 DOI: 10.18699/vjgb-22-02] [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: 09/01/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
Modern approaches to the detection and analysis of low-copy-number RNAs are often based on the use of RNA-dependent DNA polymerases, for example, in reverse-transcription PCR. The accuracy and eff iciency of cDNA synthesis in the reverse-transcription reaction catalyzed by reverse transcriptase (RNA-dependent DNA polymerase) signif icantly affect the correctness of the results of PCR diagnostic assays and/or RNA sequencing. In this regard, many studies are focused on the optimization of the reverse-transcription reaction, including the search for more perfect primers necessary to obtain a full-length DNA copy of RNA under study. The best-known completely uncharged analogs of oligonucleotides – morpholine oligonucleotides and peptide nucleic acids – cannot be substrates for enzymes that process nucleic acids. The aim of this work was to conduct a pilot study of uncharged phosphoryl guanidine oligodeoxyribonucleotides (PGOs) as primers for mouse leukemia virus reverse transcriptase (MMLV H-). Specif ic features of elongation of partially and completely uncharged PGO primers were investigated. It was demonstrated that PGOs can be elongated eff iciently, e. g., in the presence of a fragment of human ribosomal RNA having complex spatial structure. It was shown that the proportion (%) of abortive elongation products of a PGO primer depends on buffer ionic strength, nucleotide sequence of the primer, and the presence and location of phosphoryl guanidine groups in the primer. The results indicate the
suitability of PGOs, including completely electroneutral ones, as primers for reverse-transcription PCR, thereby
opening up new prospects for the creation of experimental models for the analysis of highly structured RNA.
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Affiliation(s)
- E. S. Dyudeeva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - I. A. Pyshnaya
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
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Oscorbin IP, Filipenko ML. M-MuLV reverse transcriptase: Selected properties and improved mutants. Comput Struct Biotechnol J 2021; 19:6315-6327. [PMID: 34900141 PMCID: PMC8640165 DOI: 10.1016/j.csbj.2021.11.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 11/06/2022] Open
Abstract
Reverse transcriptases (RTs) are enzymes synthesizing DNA using RNA as the template and serving as the standard tools in modern biotechnology and molecular diagnostics. To date, the most commonly used reverse transcriptase is the enzyme from Moloney murine leukemia virus, M-MuLV RT. Since its discovery, M-MuLV RT has become indispensable for modern RNA studies; the range of M-MuLV RT applications is vast, from scientific tasks to clinical testing of human pathogens. This review will give a brief description of the structure, thermal stability, processivity, and fidelity, focusing on improving M-MuLV RT for practical usage.
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Affiliation(s)
- Igor P Oscorbin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Maxim L Filipenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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Zhao W, Wu S, Du L, Li T, Cheng Z, Zhou Y, Ji Y. Development of a reverse-transcription loop-mediated isothermal amplification assay for the detection of Tobacco mild green mosaic virus (TMGMV). J Virol Methods 2021; 298:114277. [PMID: 34492235 DOI: 10.1016/j.jviromet.2021.114277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 08/02/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV), a member species of the genus Tobamovirus, infects pepper (Capsicum annuum) and a number of other economically important species in the Solanaceae family. TMGMV infections had seriously impacted pepper production worldwide, including China. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect TMGMV in pepper field samples and seed. This assay was based on four primers that matched to six sequences in the C-terminal region of the TMGMV genome. RT-LAMP assay could detect the presence of the virus in 3.0 × 10-7 µg of total RNA extract from pepper leaves, which was ten times more sensitive than the corresponding reverse-transcription polymerase chain reaction (RT-PCR) assay. This method specifically detected TMGMV but not the closely related species of the same genus Pepper mild mottle virus, Cucumber green mottle mosaic virus and Tomato mosaic virus. In addition, the use of SYBR Green I facilitated the detection of the TMGMV RT-LAMP products by the naked eye. These results indicated that the RT-LAMP assay was a simple, sensitive, specific and affordable diagnostic tool that has the potential to detect and monitor TMGMV infection in field samples.
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Affiliation(s)
- Wenhao Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Shuhua Wu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Tingfang Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Zhaobang Cheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yinghua Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China.
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Rejali NA, Zuiter AM, Quackenbush JF, Wittwer CT. Reverse transcriptase kinetics for one-step RT-PCR. Anal Biochem 2020; 601:113768. [PMID: 32416095 DOI: 10.1016/j.ab.2020.113768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023]
Abstract
Understanding reverse transcriptase (RT) activity is critical for designing fast one-step RT-PCRs. We report a stopped-flow assay that monitors SYBR Green I fluorescence to investigate RT activity in PCR conditions. We studied the influence of PCR conditions on RT activity and assessed the accuracy of cDNA synthesis predictions for one-step RT-PCR. Nucleotide incorporation increased from 26 to 89 s-1 between 1.5 and 6 mM MgCl2 but was largely unaffected by changes in KCl. Conversely, increasing KCl from 15 to 75 mM increased apparent rate constants for RT-oligonucleotide binding (0.010-0.026 nM-1 s-1) and unbinding (0.2-1.5 s-1). All rate constants increased between 22 and 42 °C. When evaluated by PCR quantification cycle, cDNA predictions differed from experiments using RNase H+ RT (average 1.7 cycles) and RNase H- (average 4.5 cycles). Decreasing H+ RT concentrations 10 to 104-fold from manufacturer recommendations improved cDNA predictions (average 0.8 cycles) and increased RT-PCR assay efficiency. RT activity assays and models can be used to aid assay design and improve the speed of RT-PCRs. RT type and concentration must be selected to promote rapid cDNA synthesis but minimize nonspecific amplification. We demonstrate 2-min one-step RT-PCR of a Zika virus target using reduced RT concentrations and extreme PCR.
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Affiliation(s)
- Nick A Rejali
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - Aisha M Zuiter
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - John F Quackenbush
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA
| | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84132, USA.
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