1
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Kalb MJ, Grenfell AW, Jain A, Fenske-Newbart J, Gralnick JA. Comparison of phage-derived recombinases for genetic manipulation of Pseudomonas species. Microbiol Spectr 2023; 11:e0317623. [PMID: 37882574 PMCID: PMC10714826 DOI: 10.1128/spectrum.03176-23] [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: 08/29/2023] [Accepted: 09/09/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The Pseudomonas genus contains many members currently being investigated for applications in biodegradation, biopesticides, biocontrol, and synthetic biology. Though several strains have been identified with beneficial properties, chromosomal manipulations to further improve these strains for commercial applications have been limited due to the lack of efficient genetic tools that have been tested across this genus. Here, we test the recombineering efficiencies of five phage-derived recombinases across three biotechnologically relevant Pseudomonas strains: P. putida KT2440, P. protegens Pf-5, and P. protegens CHA0. These results demonstrate a method to generate targeted mutations quickly and efficiently across these strains, ideally introducing a method that can be implemented across the Pseudomonas genus and a strategy that may be applied to develop analogous systems in other nonmodel bacteria.
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Affiliation(s)
- Madison J. Kalb
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Andrew W. Grenfell
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Abhiney Jain
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Jane Fenske-Newbart
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
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2
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Xue F, Ma X, Luo C, Li D, Shi G, Li Y. Construction of a bacteriophage-derived recombinase system in Bacillus licheniformis for gene deletion. AMB Express 2023; 13:89. [PMID: 37633871 PMCID: PMC10460339 DOI: 10.1186/s13568-023-01589-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/29/2023] [Indexed: 08/28/2023] Open
Abstract
Bacillus licheniformis and its related strains have found extensive applications in diverse industries, agriculture, and medicine. However, the current breeding methods for this strain primarily rely on natural screening and traditional mutagenesis. The limited availability of efficient genetic engineering tools, particularly recombination techniques, has hindered further advancements in its applications. In this study, we conducted a comprehensive investigation to identify and characterize a recombinase, RecT, derived from a Bacillus phage. Remarkably, the recombinase exhibited a 105-fold enhancement in the recombination efficiency of the strain. To facilitate genome editing, we developed a system based on the conditional expression of RecT using a rhamnose-inducible promoter (Prha). The efficacy of this system was evaluated by deleting the amyL gene, which encodes an α-amylase. Our findings revealed that the induction time and concentration of rhamnose, along with the generation time of the strain, significantly influenced the editing efficiency. Optimal conditions for genome editing were determined as follows: the wild-type strain was initially transformed with the genome editing plasmid, followed by cultivation and induction with 1.5% rhamnose for 8 h. Subsequently, the strain was further cultured for an additional 24 h, equivalent to approximately three generations. Consequently, the recombination efficiency reached an impressive 16.67%. This study represents a significant advancement in enhancing the recombination efficiency of B. licheniformis through the utilization of a RecT-based recombination system. Moreover, it provides a highly effective genome editing tool for genetic engineering applications in this strain.
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Affiliation(s)
- Fang Xue
- Key Laboratory of Chinese Cigar Fermentation, Cigar Technology Innovation Center of China Tobacco, Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, P. R. China
| | - Xufan Ma
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
| | - Cheng Luo
- Key Laboratory of Chinese Cigar Fermentation, Cigar Technology Innovation Center of China Tobacco, Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, P. R. China
| | - Dongliang Li
- Key Laboratory of Chinese Cigar Fermentation, Cigar Technology Innovation Center of China Tobacco, Tobacco Sichuan Industrial Co., Ltd, Chengdu, 610000, P. R. China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China
| | - Youran Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P. R. China.
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3
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Jiang K, Bai R, Gao T, Lu P, Zhang J, Zhang S, Xu F, Wang S, Zhao H. Optimization of hydrogen production in Enterobacter aerogenes by Complex I peripheral fragments destruction and maeA overexpression. Microb Cell Fact 2023; 22:137. [PMID: 37496040 PMCID: PMC10373349 DOI: 10.1186/s12934-023-02155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
As a concentrated energy source with high added value, hydrogen has great development prospects, with special emphasis on sustainable microbial production as a replacement for traditional fossil fuels. In this study, λ-Red recombination was used to alter the activity of Complex I by single and combined knockout of nuoE, nuoF and nuoG. In addition, the conversion of malic to pyruvic acid was promoted by overexpressing the maeA gene, which could increase the content of NADH and formic acid in the bacterial cells. Compared to the original strain, hydrogen production was 65% higher in the optimized strain IAM1183-EFG/M, in which the flux of the formic acid pathway was increased by 257%, the flux of the NADH pathway was increased by 13%, and the content of metabolites also changed significantly. In further bioreactor, the total hydrogen production of the scale-up IAM1183-EFG/M after 44 h of fermentation was 4.76 L, which increased by 18% compared with the starting strain. This study provides a new direction for future exploration of microbial hydrogen production by combinatorial modification of multiple genes.
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Affiliation(s)
- Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jingya Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Shenyang Functional Cordyceps militaris Industrial Technology Research Institute, Shenyang, 110034, China
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Shenghou Wang
- Shenyang Functional Cordyceps militaris Industrial Technology Research Institute, Shenyang, 110034, China
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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4
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Thomason LC, Court DL. Study of Ren, RexA, and RexB Functions Provides Insight Into the Complex Interaction Between Bacteriophage λ and Its Host, Escherichia coli. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:153-164. [PMID: 36204488 PMCID: PMC9529316 DOI: 10.1089/phage.2022.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The phage λ rexA and rexB genes are expressed from the P RM promoter in λ lysogens along with the cI repressor gene. RexB is also expressed from a second promoter, P LIT, embedded in rexA. The combined expression of rexA and rexB causes Escherichia coli to be more ultraviolet (UV) sensitive. Sensitivity is further increased when RexB levels are reduced by a defect in the P LIT promoter, thus the degree of sensitivity can be modulated by the ratio of RexA/RexB. Expression of the phage λ ren gene rescues this host UV sensitive phenotype; Ren also rescues an aberrant lysis phenotype caused by RexA and RexB. We screened an E. coli two-hybrid library to identify bacterial proteins with which each of these phage proteins physically interact. The results extend previous observations concerning λ Rex exclusion and show the importance of E. coli electron transport and sulfur assimilation pathways for the phage.
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Affiliation(s)
- Lynn C. Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, Maryland, USA
| | - Donald L. Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, Maryland, USA
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5
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Chou SC, Lai YJ, Zhuo XZ, Chen WY, Li SY. Increasing the λ-Red mediated gene deletion efficiency in Escherichia coli using methyl phosphotriester-modified DNA. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2022.104297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nat Cell Biol 2022; 24:268-278. [PMID: 35145221 PMCID: PMC8843813 DOI: 10.1038/s41556-021-00836-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022]
Abstract
Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering. Wang, Qu et al. developed a genome-editing system, utilizing catalytically inactive Cas9 fused to microbial single-strand annealing proteins, for kilobase-scale insertion in human cells without introducing DNA nicks or breaks.
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7
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Wang S, Zhang F, Mei M, Wang T, Yun Y, Yang S, Zhang G, Yi L. A split protease-E. coli ClpXP system quantifies protein-protein interactions in Escherichia coli cells. Commun Biol 2021; 4:841. [PMID: 34230602 PMCID: PMC8260793 DOI: 10.1038/s42003-021-02374-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/10/2021] [Indexed: 12/04/2022] Open
Abstract
Characterizing protein–protein interactions (PPIs) is an effective method to help explore protein function. Here, through integrating a newly identified split human Rhinovirus 3 C (HRV 3 C) protease, super-folder GFP (sfGFP), and ClpXP-SsrA protein degradation machinery, we developed a fluorescence-assisted single-cell methodology (split protease-E. coli ClpXP (SPEC)) to explore protein–protein interactions for both eukaryotic and prokaryotic species in E. coli cells. We firstly identified a highly efficient split HRV 3 C protease with high re-assembly ability and then incorporated it into the SPEC method. The SPEC method could convert the cellular protein-protein interaction to quantitative fluorescence signals through a split HRV 3 C protease-mediated proteolytic reaction with high efficiency and broad temperature adaptability. Using SPEC method, we explored the interactions among effectors of representative type I-E and I-F CRISPR/Cas complexes, which combining with subsequent studies of Cas3 mutations conferred further understanding of the functions and structures of CRISPR/Cas complexes. Wang et al. developed a fluorescence-assisted single-cell methodology (split protease-E. coli ClpXP (SPEC)) to characterise protein-protein interactions for both eukaryotic and prokaryotic species in E. coli cells. Their method can quantify these interactions with high sensitivity, easy manipulation, and broad temperature adaptability
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Affiliation(s)
- Shengchen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Faying Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Ting Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
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8
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Wang C, Cheng JKW, Zhang Q, Hughes NW, Xia Q, Winslow MM, Cong L. Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. Nucleic Acids Res 2021; 49:e36. [PMID: 33619540 PMCID: PMC8034634 DOI: 10.1093/nar/gkaa1264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/15/2022] Open
Abstract
Several existing technologies enable short genomic alterations including generating indels and short nucleotide variants, however, engineering more significant genomic changes is more challenging due to reduced efficiency and precision. Here, we developed RecT Editor via Designer-Cas9-Initiated Targeting (REDIT), which leverages phage single-stranded DNA-annealing proteins (SSAP) RecT for mammalian genome engineering. Relative to Cas9-mediated homology-directed repair (HDR), REDIT yielded up to a 5-fold increase of efficiency to insert kilobase-scale exogenous sequences at defined genomic regions. We validated our REDIT approach using different formats and lengths of knock-in templates. We further demonstrated that REDIT tools using Cas9 nickase have efficient gene-editing activities and reduced off-target errors, measured using a combination of targeted sequencing, genome-wide indel, and insertion mapping assays. Our experiments inhibiting repair enzyme activities suggested that REDIT has the potential to overcome limitations of endogenous DNA repair steps. Finally, our REDIT method is applicable across cell types including human stem cells, and is generalizable to different Cas9 enzymes.
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Affiliation(s)
- Chengkun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason K W Cheng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhe Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qiong Xia
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA
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9
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Filsinger GT, Wannier TM, Pedersen FB, Lutz ID, Zhang J, Stork DA, Debnath A, Gozzi K, Kuchwara H, Volf V, Wang S, Rios X, Gregg CJ, Lajoie MJ, Shipman SL, Aach J, Laub MT, Church GM. Characterizing the portability of phage-encoded homologous recombination proteins. Nat Chem Biol 2021; 17:394-402. [PMID: 33462496 PMCID: PMC7990699 DOI: 10.1038/s41589-020-00710-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 01/29/2023]
Abstract
Efficient genome editing methods are essential for biotechnology and fundamental research. Homologous recombination (HR) is the most versatile method of genome editing, but techniques that rely on host RecA-mediated pathways are inefficient and laborious. Phage-encoded single-stranded DNA annealing proteins (SSAPs) improve HR 1,000-fold above endogenous levels. However, they are not broadly functional. Using Escherichia coli, Lactococcus lactis, Mycobacterium smegmatis, Lactobacillus rhamnosus and Caulobacter crescentus, we investigated the limited portability of SSAPs. We find that these proteins specifically recognize the C-terminal tail of the host's single-stranded DNA-binding protein (SSB) and are portable between species only if compatibility with this host domain is maintained. Furthermore, we find that co-expressing SSAPs with SSBs can significantly improve genome editing efficiency, in some species enabling SSAP functionality even without host compatibility. Finally, we find that high-efficiency HR far surpasses the mutational capacity of commonly used random mutagenesis methods, generating exceptional phenotypes that are inaccessible through sequential nucleotide conversions.
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Affiliation(s)
- Gabriel T. Filsinger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Correspondence to: ,
| | - Timothy M. Wannier
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Felix B. Pedersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Isaac D. Lutz
- Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Julie Zhang
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Devon A. Stork
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Anik Debnath
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Tenza Inc., Cambridge, MA
| | - Kevin Gozzi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Helene Kuchwara
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Verena Volf
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Harvard University John A. Paulson School of Engineering and Applied Sciences, Cambridge, Massachusetts, USA
| | - Stan Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Xavier Rios
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Marc J. Lajoie
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Seth L. Shipman
- Gladstone Institutes, San Francisco, CA,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Correspondence to: ,
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10
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Fan YY, Tang Q, Li Y, Li FH, Wu JH, Li WW, Yu HQ. Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria. Environ Microbiol 2021; 23:1238-1255. [PMID: 33369000 DOI: 10.1111/1462-2920.15374] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022]
Abstract
The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real-world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the intron-encoded homing-endonuclease empowered genome editing (iEditing). The iEditing device enables rapid and efficient genome engineering in Shewanella oneidensis MR-1, the representative strain of the electroactive bacteria group. Moreover, combining with the Red or RecET recombination system, the genome-editing efficiency was greatly improved, up to approximately 100%. Significantly, the iEditing device itself is eliminated simultaneously when genome editing occurs, thereby requiring no follow-up to remove the encoding system. Then, we develop a new extracellular electron transfer (EET) engineering strategy by programming the parallel EET systems to enhance versatile EET. The engineered strains exhibit sufficiently enhanced electron output and pollutant reduction ability. Furthermore, this device has demonstrated its great potential to be extended for genome editing in other important microbes. This work provides a useful and efficient tool for the rapid generation of synthetic microorganisms for various environmental applications.
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Affiliation(s)
- Yang-Yang Fan
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Qiang Tang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang Li
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Feng-He Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Jing-Hang Wu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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11
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λ Recombineering Used to Engineer the Genome of Phage T7. Antibiotics (Basel) 2020; 9:antibiotics9110805. [PMID: 33202746 PMCID: PMC7697293 DOI: 10.3390/antibiotics9110805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage T7 and T7-like bacteriophages are valuable genetic models for lytic phage biology that have heretofore been intractable with in vivo genetic engineering methods. This manuscript describes that the presence of λ Red recombination proteins makes in vivo recombineering of T7 possible, so that single base changes and whole gene replacements on the T7 genome can be made. Red recombination functions also increase the efficiency of T7 genome DNA transfection of cells by ~100-fold. Likewise, Red function enables two other T7-like bacteriophages that do not normally propagate in E. coli to be recovered following genome transfection. These results constitute major technical advances in the speed and efficiency of bacteriophage T7 engineering and will aid in the rapid development of new phage variants for a variety of applications.
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12
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Liu H, Hou G, Wang P, Guo G, Wang Y, Yang N, Rehman MNU, Li C, Li Q, Zheng J, Zeng J, Li S. A double-locus scarless genome editing system in Escherichia coli. Biotechnol Lett 2020; 42:1457-1465. [PMID: 32130564 DOI: 10.1007/s10529-020-02856-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/27/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVE To develop a convenient double-locus scarless genome editing system in Escherichia coli, based on the type II Streptococcus pyogenes CRISPR/Cas9 and λ Red recombination cassette. RESULTS A two-plasmid genome editing system was constructed. The large-sized plasmid harbors the cas9 and λ Red recombination genes (gam, bet, and exo), while the small-molecular plasmid can simultaneously express two different gRNAs (targeting genome RNAs). The recombination efficiency was tested by targeting the galK, lacZ, and dbpA genes in E. coli with ssDNA or dsDNA. Resulting concurrent double-locus recombination efficiencies were 88 ± 5.5% (point mutation), 39.7 ± 4.3% (deletion/insertion), and 57.8 ± 3.4%-58.5 ± 4.1% (mixed point and deletion/insertion mutation), depending on 30 (ssDNA) or 40 bp (dsDNA) homologous side arms employed. In addition, the curing efficiency of the guide plasmid expressing gRNAs for negative selection was higher (96 ± 3% in 4 h) than the help plasmid carrying cas9 and λ Red (92 ± 2% in 9 h). CONCLUSIONS The new editing system is convenient and efficient for simultaneous double-locus recombination in the genome and should be favorable for high-throughput multiplex genome editing in synthetic biology and metabolic engineering.
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Affiliation(s)
- Haiqing Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Guofeng Hou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Peng Wang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Guiying Guo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Yu Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Nuo Yang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Muhammad Nafees Ur Rehman
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Changlong Li
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Science, Capital Medical University, Beijing, 100069, China
| | - Qian Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China
| | - Jiping Zheng
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China.
| | - Jifeng Zeng
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life Sciences and Pharmacy, Hainan University, Haikou, 570228, China.
| | - Shanhu Li
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, 100071, China.
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13
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Corts AD, Thomason LC, Gill RT, Gralnick JA. Efficient and Precise Genome Editing in Shewanella with Recombineering and CRISPR/Cas9-Mediated Counter-Selection. ACS Synth Biol 2019; 8:1877-1889. [PMID: 31277550 DOI: 10.1021/acssynbio.9b00188] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dissimilatory metal-reducing bacteria, particularly those from the genus Shewanella, are of importance for bioremediation of metal contaminated sites and sustainable energy production. However, studies on this species have suffered from a lack of effective genetic tools for precise and high throughput genome manipulation. Here we report the development of a highly efficient system based on single-stranded DNA oligonucleotide recombineering coupled with CRISPR/Cas9-mediated counter-selection. Our system uses two plasmids: a sgRNA targeting vector and an editing vector, the latter harboring both Cas9 and the phage recombinase W3 Beta. Following the experimental analysis of Cas9 activity, we demonstrate the ability of this system to efficiently and precisely engineer different Shewanella strains with an average efficiency of >90% among total transformed cells, compared to ≃5% by recombineering alone, and regardless of the gene modified. We also show that different genetic changes can be introduced: mismatches, deletions, and small insertions. Surprisingly, we found that use of CRISPR/Cas9 alone allows selection of recombinase-independent S. oneidensis mutations, albeit at lower efficiency and frequency. With synthesized single-stranded DNA as substrates for homologous recombination and Cas9 as a counter-selectable marker, this new system provides a rapid, scalable, versatile, and scarless tool that will accelerate progress in Shewanella genomic engineering.
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Affiliation(s)
- Anna D. Corts
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Lynn C. Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ryan T. Gill
- DTU BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
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14
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Corts AD, Thomason LC, Gill RT, Gralnick JA. A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides. Sci Rep 2019; 9:39. [PMID: 30631105 PMCID: PMC6328582 DOI: 10.1038/s41598-018-37025-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
Shewanella oneidensis MR-1 is an invaluable host for the discovery and engineering of pathways important for bioremediation of toxic and radioactive metals and understanding extracellular electron transfer. However, genetic manipulation is challenging due to the lack of genetic tools. Previously, the only reliable method used for introducing DNA into Shewanella spp. at high efficiency was bacterial conjugation, enabling transposon mutagenesis and targeted knockouts using suicide vectors for gene disruptions. Here, we describe development of a robust and simple electroporation method in S. oneidensis that allows an efficiency of ~4.0 x 106 transformants/µg DNA. High transformation efficiency is maintained when cells are frozen for long term storage. In addition, we report a new prophage-mediated genome engineering (recombineering) system using a λ Red Beta homolog from Shewanella sp. W3-18-1. By targeting two different chromosomal alleles, we demonstrate its application for precise genome editing using single strand DNA oligonucleotides and show that an efficiency of ~5% recombinants among total cells can be obtained. This is the first effective and simple strategy for recombination with markerless mutations in S. oneidensis. Continued development of this recombinant technology will advance high-throughput and genome modification efforts to engineer and investigate S. oneidensis and other environmental bacteria.
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Affiliation(s)
- Anna D Corts
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA
| | - Lynn C Thomason
- RNA Biology Laboratory, Basic Science Program, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80303, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA.
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15
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Efficient and Scalable Precision Genome Editing in Staphylococcus aureus through Conditional Recombineering and CRISPR/Cas9-Mediated Counterselection. mBio 2018; 9:mBio.00067-18. [PMID: 29463653 PMCID: PMC5821094 DOI: 10.1128/mbio.00067-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus aureus is an important human pathogen, but studies of the organism have suffered from the lack of a robust tool set for its genetic and genomic manipulation. Here we report the development of a system for the facile and high-throughput genomic engineering of S. aureus using single-stranded DNA (ssDNA) oligonucleotide recombineering coupled with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated counterselection. We identify recombinase EF2132, derived from Enterococcus faecalis, as being capable of integrating single-stranded DNA oligonucleotides into the S. aureus genome. We found that EF2132 can readily mediate recombineering across multiple characterized strains (3 of 3 tested) and primary clinical isolates (6 of 6 tested), typically yielding thousands of recombinants per transformation. Surprisingly, we also found that some S. aureus strains are naturally recombinogenic at measurable frequencies when oligonucleotides are introduced by electroporation, even without exogenous recombinase expression. We construct a temperature-sensitive, two-vector system which enables conditional recombineering and CRISPR/Cas9-mediated counterselection in S. aureus without permanently introducing exogenous genetic material or unintended genetic lesions. We demonstrate the ability of this system to efficiently and precisely engineer point mutations and large single-gene deletions in the S. aureus genome and to yield highly enriched populations of engineered recombinants even in the absence of an externally selectable phenotype. By virtue of utilizing inexpensive, commercially synthesized synthetic DNA oligonucleotides as substrates for recombineering and counterselection, this system provides a scalable, versatile, precise, inexpensive, and generally useful tool for producing isogenic strains in S. aureus which will enable the high-throughput functional assessment of genome variation and gene function across multiple strain backgrounds. Engineering genetic changes in bacteria is critical to understanding the function of particular genes or mutations but is currently a laborious and technically challenging process to perform for the important human pathogen Staphylococcus aureus. In an effort to develop methods which are rapid, easy, scalable, versatile, and inexpensive, here we describe a system for incorporating synthetic, mutagenic DNA molecules into the S. aureus genome and for eliminating cells that lack the engineered mutation. This method allows efficient, precise, and high-throughput genetic engineering of S. aureus strains and will facilitate studies seeking to address a variety of issues about the function of particular genes and specific mutations.
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Josephs EA, Marszalek PE. A 'Semi-Protected Oligonucleotide Recombination' Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches. Nucleic Acids Res 2017; 45:e63. [PMID: 28053122 PMCID: PMC5416779 DOI: 10.1093/nar/gkw1339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022] Open
Abstract
In Escherichia coli, a DNA mismatch repair (MMR) pathway corrects errors that occur during DNA replication by coordinating the excision and re-synthesis of a long tract of the newly-replicated DNA between an epigenetic signal (a hemi-methylated d(GATC) site or a single-stranded nick) and the replication error after the error is identified by protein MutS. Recent observations suggest that this 'long-patch repair' between these sites is coordinated in the same direction of replication by the replisome. Here, we have developed a new assay that uniquely allows us to introduce targeted 'mismatches' directly into the replication fork via oligonucleotide recombination, examine the directionality of MMR, and quantify the nucleotide-dependence, sequence context-dependence, and strand-dependence of their repair in vivo-something otherwise nearly impossible to achieve. We find that repair of genomic lagging strand mismatches occurs bi-directionally in E. coli and that, while all MutS-recognized mismatches had been thought to be repaired in a consistent manner, the directional bias of repair and the effects of mutations in MutS are dependent on the molecular species of the mismatch. Because oligonucleotide recombination is routinely performed in both prokaryotic and eukaryotic cells, we expect this assay will be broadly applicable for investigating mechanisms of MMR in vivo.
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Affiliation(s)
- Eric A Josephs
- Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, NC, USA
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, NC, USA
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