1
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy S. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. Nucleic Acids Res 2024; 52:e47. [PMID: 38709890 PMCID: PMC11162764 DOI: 10.1093/nar/gkae332] [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: 10/13/2023] [Revised: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
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2
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy SF. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562064. [PMID: 37873145 PMCID: PMC10592806 DOI: 10.1101/2023.10.13.562064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
- Present Address: BacStitch DNA, Los Altos, CA, USA
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3
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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4
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Jiang H, Meng F, Lu D, Chen Y, Luo G, Chen Y, Chen J, Chen C, Zhang X, Su D. High-throughput FastCloning technology: A low-cost method for parallel cloning. PLoS One 2022; 17:e0273873. [PMID: 36084059 PMCID: PMC9462701 DOI: 10.1371/journal.pone.0273873] [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: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
FastCloning, a reliable cloning technique for plasmid construction, is a widely used protocol in biomedical research laboratories. Only two-step molecular manipulations are required to add a gene (cDNA) of interest into the desired vector. However, parallel cloning of the gene into multiple vectors is still a labor-intensive operation, which requires a range of primers for different vectors in high-throughput cloning projects. The situation could even be worse if multiple fragments of DNA are required to be added into one plasmid. Here, we describe a high-throughput FastCloning (HTFC) method, a protocol for parallel cloning by adding an adaptor sequence into all vectors. The target gene and vectors were PCR amplified separately to obtain the insert product and linear vectors with 18-base overlapping at each end of the DNAs required for FastCloning. Furthermore, a method for generating polycistronic bacterial constructs based on the same strategy as that used for HTFC was developed. Thus, the HTFC technique is a simple, effective, reliable, and low-cost tool for parallel cloning.
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Affiliation(s)
- Hua Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Fan Meng
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Deren Lu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yanjuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Guilin Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yuejun Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Jun Chen
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Cheng Chen
- Department of Gynecology and Obstetrics, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P.R. China
| | - Xi Zhang
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, P.R. China
- * E-mail:
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5
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Oz N, Vayndorf EM, Tsuchiya M, McLean S, Turcios-Hernandez L, Pitt JN, Blue BW, Muir M, Kiflezghi MG, Tyshkovskiy A, Mendenhall A, Kaeberlein M, Kaya A. Evidence that conserved essential genes are enriched for pro-longevity factors. GeroScience 2022; 44:1995-2006. [PMID: 35695982 PMCID: PMC9616985 DOI: 10.1007/s11357-022-00604-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 02/02/2023] Open
Abstract
At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 21% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the ~ 3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.
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Affiliation(s)
- Naci Oz
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Mitsuhiro Tsuchiya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Samantha McLean
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jason N Pitt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin W Blue
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael Muir
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael G Kiflezghi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander Mendenhall
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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6
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Baas-Thomas MS, Oehm SB, Ostrov N, Church GM. Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli. ACS Synth Biol 2022; 11:2009-2014. [PMID: 35666547 PMCID: PMC9208019 DOI: 10.1021/acssynbio.2c00061] [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] [Indexed: 11/29/2022]
Abstract
![]()
Bacterial selection
is an indispensable tool for E. coli genetic
engineering. Marker genes allow for mutant isolation even
at low editing efficiencies. TolC is an especially
useful E. coli marker: its presence can be selected
for with sodium dodecyl sulfate, while its absence can be selected
for with the bactericidal protein ColE1. However, utilization of this
selection system is greatly limited by the lack of commercially available
ColE1 protein. Here, we provide a simple, plate-based, ColE1 negative-selection
protocol that does not require purification of ColE1. Using agar plates
containing a nonpurified lysate from a ColE1-production strain, we
achieved a stringent negative selection with an escape rate of 10–7. Using this powerful negative-selection assay, we
then performed the scarless deletion of multiple, large genomic loci
(>10 kb), screening only 12 colonies each. We hope this accessible
protocol for ColE1 production will lower the barrier of entry for
any lab that wishes to harness tolC’s dual
selection for genetic engineering.
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Affiliation(s)
| | - Sebastian B Oehm
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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7
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Strain-Damerell C, Mahajan P, Fernandez-Cid A, Gileadi O, Burgess-Brown NA. Screening and Production of Recombinant Human Proteins: Ligation-Independent Cloning. Methods Mol Biol 2021; 2199:23-43. [PMID: 33125643 DOI: 10.1007/978-1-0716-0892-0_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Structural genomics groups have identified the need to generate multiple truncated versions of each target to improve their success in producing a well-expressed, soluble, and stable protein and one that crystallizes and diffracts to a sufficient resolution for structural determination. At the Structural Genomics Consortium, we opted for the ligation-independent cloning (LIC) method which provides the throughput we desire to produce and screen many proteins in a parallel process. Here, we describe our LIC protocol for generating constructs in 96-well format and provide a choice of vectors suitable for expressing proteins in both E. coli and the baculovirus expression vector system (BEVS).
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Affiliation(s)
| | | | | | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford, UK
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8
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Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
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Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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9
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Geng Y, Yan H, Li P, Ren G, Guo X, Yin P, Zhang L, Qian Z, Zhao Z, Sun YC. A highly efficient in vivo plasmid editing tool based on CRISPR-Cas12a and phage λ Red recombineering. J Genet Genomics 2019; 46:455-458. [PMID: 31607505 PMCID: PMC7172145 DOI: 10.1016/j.jgg.2019.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/16/2019] [Accepted: 07/04/2019] [Indexed: 12/03/2022]
Affiliation(s)
- Yiman Geng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Haiqin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, 233030, China
| | - Pei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Gaixian Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaopeng Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Peiqi Yin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Leiliang Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Zhendong Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Yi-Cheng Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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10
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A Novel Cre Recombinase-Mediated In Vivo Minicircle DNA (CRIM) Vaccine Provides Partial Protection against Newcastle Disease Virus. Appl Environ Microbiol 2019; 85:AEM.00407-19. [PMID: 31053588 DOI: 10.1128/aem.00407-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Minicircle DNA (mcDNA), which contains only the necessary components for eukaryotic expression and is thus smaller than traditional plasmids, has been designed for application in genetic manipulation. In this study, we constructed a novel plasmid containing both the Cre recombinase under the phosphoglycerate kinase (PGK) promoter and recombinant lox66 and lox71 sites located outside the cytomegalovirus (CMV) expression cassette. The strictly controlled synthesis of Cre recombinase in vivo maintained the complete form of the plasmid in vitro, whereas the in vivo production of Cre transformed the parental plasmid to mcDNA after transfection. The newly designed Cre recombinase-mediated in vivo mcDNA platform, named CRIM, significantly increased the nuclear entry of mcDNA, followed by increased production of mRNA and protein, using enhanced green fluorescent protein (EGFP) as a model. Similar results were also observed in chickens when the vaccine was delivered by the regulated-delayed-lysis Salmonella strain χ11218, where significantly increased production of EGFP was observed in chicken livers. Then, we used the HN gene of genotype VII Newcastle disease virus as an antigen model to construct the traditional plasmid pYL43 and the novel mcDNA plasmid pYL47. After immunization, our CRIM vaccine provided significantly increased protection against challenge compared with that of the traditional plasmid, providing us with a novel mcDNA vaccine platform.IMPORTANCE Minicircle DNA (mcDNA) has been considered an attractive alternative to DNA vaccines; however, the relatively high cost and complicated process of purifying mcDNA dramatically restricts the application of mcDNA in the veterinary field. We designed a novel in vivo mcDNA platform in which the complete plasmid could spontaneously transform into mcDNA in vivo In combination with the regulated-delayed-lysis Salmonella strain, the newly designed mcDNA vaccine provides us with an elegant platform for veterinary vaccine development.
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11
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Garcia S, Trinh CT. Modular design: Implementing proven engineering principles in biotechnology. Biotechnol Adv 2019; 37:107403. [PMID: 31181317 DOI: 10.1016/j.biotechadv.2019.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/23/2019] [Accepted: 06/04/2019] [Indexed: 12/27/2022]
Abstract
Modular design is at the foundation of contemporary engineering, enabling rapid, efficient, and reproducible construction and maintenance of complex systems across applications. Remarkably, modularity has recently been discovered as a governing principle in natural biological systems from genes to proteins to complex networks within a cell and organism communities. The convergent knowledge of natural and engineered modular systems provides a key to drive modern biotechnology to address emergent challenges associated with health, food, energy, and the environment. Here, we first present the theory and application of modular design in traditional engineering fields. We then discuss the significance and impact of modular architectures on systems biology and biotechnology. Next, we focus on the very recent theoretical and experimental advances in modular cell engineering that seeks to enable rapid and systematic development of microbial catalysts capable of efficiently synthesizing a large space of useful chemicals. We conclude with an outlook towards theoretical and practical opportunities for a more systematic and effective application of modular cell engineering in biotechnology.
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Affiliation(s)
- Sergio Garcia
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, United States of America; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, United States of America; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America.
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12
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Liu X, Liu Z, Dziulko AK, Li F, Miller D, Morabito RD, Francois D, Levy SF. iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast. Cell Syst 2019; 8:338-344.e8. [PMID: 30954477 PMCID: PMC6483859 DOI: 10.1016/j.cels.2019.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/10/2019] [Accepted: 03/06/2019] [Indexed: 11/24/2022]
Abstract
We developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae, which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating, 15 barcoded plasmid libraries containing split selectable markers (URA3AI, KanMXAI, HphMXAI, and NatMXAI), and an array of ∼24,000 "double-barcoder" strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performing many new combinatorial screens by short-read sequencing.
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Affiliation(s)
- Xianan Liu
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794-5215, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA
| | - Zhimin Liu
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794-5215, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA
| | - Adam K Dziulko
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794-5215, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA
| | - Fangfei Li
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Robert D Morabito
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794-5215, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA
| | - Danielle Francois
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794-5215, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA
| | - Sasha F Levy
- Department of Biochemistry, Stony Brook University, Stony Brook, NY 11794-5215, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-5215, USA; Joint Initiative for Metrology in Biology, Stanford, CA 94305-4245, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
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13
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US3 Kinase-Mediated Phosphorylation of Tegument Protein VP8 Plays a Critical Role in the Cellular Localization of VP8 and Its Effect on the Lipid Metabolism of Bovine Herpesvirus 1-Infected Cells. J Virol 2019; 93:JVI.02151-18. [PMID: 30626671 DOI: 10.1128/jvi.02151-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 02/04/2023] Open
Abstract
Bovine herpesvirus 1 (BoHV-1) infects bovine species, causing respiratory infections, genital disorders and abortions. VP8 is the most abundant tegument protein of BoHV-1 and is critical for virus replication in cattle. In this study, the cellular transport of VP8 in BoHV-1-infected cells and its ability to alter the cellular lipid metabolism were investigated. A viral kinase, US3, was found to be involved in regulating these processes. In the early stages of infection VP8 was localized in the nucleus. Subsequently, presumably after completion of its role in the nucleus, VP8 was translocated to the cytoplasm. When US3 was deleted or the essential US3 phosphorylation site of VP8 was mutated in BoHV-1, the majority of VP8 was localized in the nuclei of infected cells. This suggests that phosphorylation by US3 may be critical for cytoplasmic localization of VP8. Eventually, the cytoplasmic VP8 was accumulated in the cis-Golgi apparatus but not in the trans-Golgi network, implying that VP8 was not involved in virion transport toward and budding from the cell membrane. VP8 caused lipid droplet (LD) formation in the nuclei of transfected cells and increased cellular cholesterol levels. Lipid droplets were not found in the nuclei of BoHV-1-infected cells when VP8 was cytoplasmic in the presence of US3. However, when US3 was deleted or phosphorylation residues in VP8 were mutated, nuclear VP8 and LDs appeared in BoHV-1-infected cells. The total cholesterol level was increased in BoHV-1-infected cells but not in ΔUL47-BoHV-1-infected cells, further supporting a role for VP8 in altering the cellular lipid metabolism during infection.IMPORTANCE Nuclear localization signals (NLSs) and nuclear export signals (NESs) are important elements directing VP8 to the desired locations in the BoHV-1-infected cell. In this study, a critical regulator that switches the nuclear and cytoplasmic localization of VP8 in BoHV-1-infected cells was identified. BoHV-1 used viral kinase US3 to regulate the cellular localization of VP8. Early during BoHV-1 infection VP8 was localized in the nucleus, where it performs various functions; once US3 was expressed, phosphorylated VP8 was cytoplasmic and ultimately accumulated in the cis-Golgi apparatus, presumably to be incorporated into virions. The Golgi localization of VP8 was only observed in virus-infected cells and not in US3-cotransfected cells, suggesting that this is mediated by other viral factors. Interestingly, VP8 was shown to cause increased cholesterol levels, which is a novel function for VP8 and a potential strategy to supply lipid for viral replication.
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Abstract
The Gateway recombinatorial cloning system was developed for cloning multiple DNA fragments in parallel (e.g., in 96-well formats) in a standardized manner using the same enzymes. Gateway cloning is based on the highly specific integration and excision reactions of bacteriophage λ into and out of the Escherichia coli genome. Because the sites of recombination ("att" sites) are much longer (25-242 bp) than restriction sites, they are extremely unlikely to occur by chance in DNA fragments. Therefore, the same recombination enzyme can be used to robustly clone many different fragments of variable size in parallel reactions.
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15
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Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes. Genetics 2017; 208:419-431. [PMID: 29127264 DOI: 10.1534/genetics.117.300377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
A single gene can partake in several biological processes, and therefore gene deletions can lead to different-sometimes unexpected-phenotypes. However, it is not always clear whether such pleiotropy reflects the loss of a unique molecular activity involved in different processes or the loss of a multifunctional protein. Here, using Saccharomyces cerevisiae metabolism as a model, we systematically test the null hypothesis that enzyme phenotypes depend on a single annotated molecular function, namely their catalysis. We screened a set of carefully selected genes by quantifying the contribution of catalysis to gene deletion phenotypes under different environmental conditions. While most phenotypes were explained by loss of catalysis, slow growth was readily rescued by a catalytically inactive protein in about one-third of the enzymes tested. Such noncatalytic phenotypes were frequent in the Alt1 and Bat2 transaminases and in the isoleucine/valine biosynthetic enzymes Ilv1 and Ilv2, suggesting novel "moonlighting" activities in these proteins. Furthermore, differential genetic interaction profiles of gene deletion and catalytic mutants indicated that ILV1 is functionally associated with regulatory processes, specifically to chromatin modification. Our systematic study shows that gene loss phenotypes and their genetic interactions are frequently not driven by the loss of an annotated catalytic function, underscoring the moonlighting nature of cellular metabolism.
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Wei Y, Deng P, Mohsin A, Yang Y, Zhou H, Guo M, Fang H. An electroporation-free method based on Red recombineering for markerless deletion and genomic replacement in the Escherichia coli DH1 genome. PLoS One 2017; 12:e0186891. [PMID: 29065183 PMCID: PMC5655456 DOI: 10.1371/journal.pone.0186891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022] Open
Abstract
The λ-Red recombination system is a popular method for gene editing. However, its applications are limited due to restricted electroporation of DNA fragments. Here, we present an electroporation-free λ-Red recombination method in which target DNA fragments are excised by I-CreI endonuclease in vivo from the landing pad plasmid. Subsequently, the I-SceI endonuclease-cutting chromosome and DNA double-strand break repair were required. Markerless deletion and genomic replacement were successfully accomplished by this novel approach. Eight nonessential regions of 2.4–104.4 kb in the Escherichia coli DH1 genome were deleted separately with selection efficiencies of 5.3–100%. Additionally, the recombination efficiencies were 2.5–45%, representing an order of magnitude improvement over the electroporation method. For example, for genomic replacement, lycopene expression flux (3.5 kb) was efficiently and precisely integrated into the chromosome, accompanied by replacement of nonessential regions separately into four differently oriented loci. The lycopene production level varied approximately by 5- and 10-fold, corresponding to the integrated position and expression direction, respectively, in the E. coli chromosome.
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Affiliation(s)
- Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Pingping Deng
- Institute of Health Sciences, Anhui University, Economic and Technology Development Zone, Hefei, Anhui, China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yan Yang
- Luoyang Vocational & Technical College, Luoyang, Henan, China
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Huayan Zhou
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- * E-mail: (MG); (HF)
| | - Hongqing Fang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Institute of Health Sciences, Anhui University, Economic and Technology Development Zone, Hefei, Anhui, China
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (MG); (HF)
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Characterization of Inducible ccdB Gene as a Counterselectable Marker in Escherichia coli Recombineering. Curr Microbiol 2017; 74:961-964. [PMID: 28573338 DOI: 10.1007/s00284-017-1273-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/27/2017] [Indexed: 02/04/2023]
Abstract
Recombineering is a homologous-based DNA cloning and modification technique. Recombineering-mediated chromosomal gene knock-in usually involves a selectable/counterselectable cassette. Though a variety of selectable/counterselectable cassettes were developed; however, a specifically designed gene deletion strain or minimal medium is often required. Herein, we describe a novel selectable/counterselectable cassette Plac-ccdB-aacC1 in which aacC1 (gentamicin resistance gene) is used as the selectable marker for the homologous arm-flanked cassette knock-in, while the IPTG inducible ccdB gene is used as the counterselectable marker for chromosomal gene knock-in. The counterselection is achieved via supplementing 1 mM IPTG in the LB agar medium. An oligonucleotide designed to evade the mismatch repair system was utilized to engineer an Escherichia coli DH10B-derived gyrA462 strain that was used to as the host for the plasmid harboring the Plac-ccdB-aacC1 cassette. By using the Plac-ccdB-aacC1 cassette, a linear-linear homologous recombination (LLHR) system was generated by knocking a 6.2 kb araC-PBAD-redγ-recET-recA DNA fragment into the E. coli DH10B chromosome. The functional of the LLHR recombineering system was characterized by cloning of the target DNA from PCR product as well as from the genomic DNA mixture. The Plac-ccdB-aacC1 cassette will be a useful tool in E. coli recombineering.
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MISSA 2.0: an updated synthetic biology toolbox for assembly of orthogonal CRISPR/Cas systems. Sci Rep 2017; 7:41993. [PMID: 28155921 PMCID: PMC5290471 DOI: 10.1038/srep41993] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023] Open
Abstract
Efficient generation of plants carrying mutations in multiple genes remains a challenge. Using two or more orthogonal CRISPR/Cas systems can generate plants with multi-gene mutations, but assembly of these systems requires a robust, high-capacity toolkit. Here, we describe MISSA 2.0 (multiple-round in vivo site-specific assembly 2.0), an extensively updated toolkit for assembly of two or more CRISPR/Cas systems. We developed a novel suicide donor vector system based on plasmid RK2, which has much higher cloning capacity than the original, plasmid R6K-based system. We validated the utility of MISSA 2.0 by assembling multiple DNA fragments into the E. coli chromosome, and by creating transgenic Arabidopsis thaliana that constitutively or inducibly overexpress multiple genes. We then demonstrated that the higher cloning capacity of the RK2-derived MISSA 2.0 donor vectors facilitated the assembly of two orthogonal CRISPR/Cas systems including SpCas9 and SaCas9, and thus facilitated the creation of transgenic lines harboring these systems. We anticipate that MISSA 2.0 will enable substantial advancements in multiplex genome editing based on two or more orthogonal CRISPR/Cas9 systems, as well as in plant synthetic biology.
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Chang Y, Nguyen BH, Xie Y, Xiao B, Tang N, Zhu W, Mou T, Xiong L. Co-overexpression of the Constitutively Active Form of OsbZIP46 and ABA-Activated Protein Kinase SAPK6 Improves Drought and Temperature Stress Resistance in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1102. [PMID: 28694815 PMCID: PMC5483469 DOI: 10.3389/fpls.2017.01102] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/07/2017] [Indexed: 05/07/2023]
Abstract
Drought is one of the major abiotic stresses threatening rice (Oryza sativa) production worldwide. Drought resistance is controlled by multiple genes, and therefore, a multi-gene genetic engineering strategy is theoretically useful for improving drought resistance. However, the experimental evidence for such a strategy is still lacking. In this study, a few drought-responsive genes from rice were assembled by a multiple-round site-specific assembly system, and the constructs were introduced into the rice cultivar KY131 via Agrobacterium-mediated transformation. The transgenic lines of the multi-gene and corresponding single-gene constructs were pre-evaluated for drought resistance. We found that the co-overexpression of two genes, encoding a constitutively active form of a bZIP transcription factor (OsbZIP46CA1) and a protein kinase (SAPK6) involved in the abscisic acid signaling pathway, showed significantly enhanced drought resistance compared with the single-gene transgenic lines and the negative transgenic plants. Single-copy lines of this bi-gene combination (named XL22) and the corresponding single-gene lines were further evaluated for drought resistance in the field using agronomical traits. The results showed that XL22 exhibited greater yield, biomass, spikelet number, and grain number under moderate drought stress conditions. The seedling survival rate of XL22 and the single-gene overexpressors after drought stress treatment also supported the drought resistance results. Furthermore, expression profiling by RNA-Seq revealed that many genes involved in the stress response were specifically up-regulated in the drought-treated XL22 lines and some of the stress-related genes activated in CA1-OE and SAPK6-OE were distinct, which could partially explain the different performances of these lines with respect to drought resistance. In addition, the XL22 seedlings showed improved tolerance to heat and cold stresses. Our results demonstrate that the multi-gene assembly in an appropriate combination may be a promising approach in the genetic improvement of drought resistance.
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Affiliation(s)
- Yu Chang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Ba Hoanh Nguyen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Institute of Natural Sciences Education, Vinh UniversityVinh, Vietnam
| | - Yongjun Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Benze Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Ning Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Wenliu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Lizhong Xiong, Tongmin Mou,
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Lizhong Xiong, Tongmin Mou,
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20
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Trinh CT, Mendoza B. Modular cell design for rapid, efficient strain engineering toward industrialization of biology. Curr Opin Chem Eng 2016. [DOI: 10.1016/j.coche.2016.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Chen Z, Ling W, Shang G. Recombineering and I-SceI-mediatedPseudomonas putidaKT2440 scarless gene deletion. FEMS Microbiol Lett 2016; 363:fnw231. [DOI: 10.1093/femsle/fnw231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/06/2016] [Accepted: 10/06/2016] [Indexed: 12/28/2022] Open
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22
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Celie PHN, Parret AHA, Perrakis A. Recombinant cloning strategies for protein expression. Curr Opin Struct Biol 2016; 38:145-54. [DOI: 10.1016/j.sbi.2016.06.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/10/2016] [Indexed: 11/30/2022]
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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24
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Pines G, Freed EF, Winkler JD, Gill RT. Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination. ACS Synth Biol 2015; 4:1176-85. [PMID: 25856528 DOI: 10.1021/acssynbio.5b00009] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ability to specifically modify bacterial genomes in a precise and efficient manner is highly desired in various fields, ranging from molecular genetics to metabolic engineering and synthetic biology. Much has changed from the initial realization that phage-derived genes may be employed for such tasks to today, where recombineering enables complex genetic edits within a genome or a population. Here, we review the major developments leading to recombineering becoming the method of choice for in situ bacterial genome editing while highlighting the various applications of recombineering in pushing the boundaries of synthetic biology. We also present the current understanding of the mechanism of recombineering. Finally, we discuss in detail issues surrounding recombineering efficiency and future directions for recombineering-based genome editing.
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Affiliation(s)
- Gur Pines
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Emily F. Freed
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - James D. Winkler
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Ryan T. Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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Two Polyhydroxyalkanoate Synthases from Distinct Classes from the Aromatic Degrader Cupriavidus pinatubonensis JMP134 Exhibit the Same Substrate Preference. PLoS One 2015; 10:e0142332. [PMID: 26544851 PMCID: PMC4636328 DOI: 10.1371/journal.pone.0142332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/19/2015] [Indexed: 12/04/2022] Open
Abstract
Cupriavidus pinatubonensis JMP134 utilizes a variety of aromatic substrates as sole carbon sources, including meta-nitrophenol (MNP). Two polyhydroxyalkanoate (PHA) synthase genes, phaC1 and phaC2, were annotated and categorized as class I and class II PHA synthase genes, respectively. In this study, both His-tagged purified PhaC1 and PhaC2 were shown to exhibit typical class I PHA synthase substrate specificity to make short-chain-length (SCL) PHA from 3-hydroxybutyryl-CoA and failed to make medium-chain-length (MCL) PHA from 3-hydroxyoctanoyl-CoA. The phaC1 or phaC2 deletion strain could also produce SCL PHA when grown in fructose or octanoate, but the double mutant of phaC1 and phaC2 lost this ability. The PhaC2 also exhibited substrate preference towards SCL substrates when expressed in Pseudomonas aeruginosa PAO1 phaC mutant strain. On the other hand, the transcriptional level of phaC1 was 70-fold higher than that of phaC2 in MNP-grown cells, but 240-fold lower in octanoate-grown cells. Further study demonstrated that only phaC1 was involved in PHA synthesis in MNP-grown cells. These findings suggested that phaC1 and phaC2 genes were differentially regulated under different growth conditions in this strain. Within the phaC2-containing gene cluster, a single copy of PHA synthase gene was present clustering with genes encoding enzymes in the biosynthesis of PHA precursors. This is markedly different from the genetic organization of all other previously reported class II PHA synthase gene clusters and this cluster likely comes from a distinct evolutionary path.
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26
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Peña-Castillo L, Badis G. Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast. Methods Mol Biol 2015; 1361:203-25. [PMID: 26483024 DOI: 10.1007/978-1-4939-3079-1_12] [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: 02/22/2023]
Abstract
Understanding how genes are regulated, decoding their "regulome", is one of the main challenges of the post-genomic era. Here, we describe the in vitro method we used to associate cis-regulatory sites with cognate trans-regulators by characterizing the DNA-binding specificity of the vast majority of yeast transcription factors using Protein Binding Microarrays. This approach can be implemented to any given organism.
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Affiliation(s)
- Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X5.,Department of Computer Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Gwenael Badis
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Paris, 75724, France.
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Tas H, Nguyen CT, Patel R, Kim NH, Kuhlman TE. An Integrated System for Precise Genome Modification in Escherichia coli. PLoS One 2015; 10:e0136963. [PMID: 26332675 PMCID: PMC4558010 DOI: 10.1371/journal.pone.0136963] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
We describe an optimized system for the easy, effective, and precise modification of the Escherichia coli genome. Genome changes are introduced first through the integration of a 1.3 kbp Landing Pad consisting of a gene conferring resistance to tetracycline (tetA) or the ability to metabolize the sugar galactose (galK). The Landing Pad is then excised as a result of double-strand breaks by the homing endonuclease I-SceI, and replaced with DNA fragments bearing the desired change via λ-Red mediated homologous recombination. Repair of the double strand breaks and counterselection against the Landing Pad (using NiCl2 for tetA or 2-deoxy-galactose for galK) allows the isolation of modified bacteria without the use of additional antibiotic selection. We demonstrate the power of this method to make a variety of genome modifications: the exact integration, without any extraneous sequence, of the lac operon (~6.5 kbp) to any desired location in the genome and without the integration of antibiotic markers; the scarless deletion of ribosomal rrn operons (~6 kbp) through either intrachromosomal or oligonucleotide recombination; and the in situ fusion of native genes to fluorescent reporter genes without additional perturbation.
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Affiliation(s)
- Huseyin Tas
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Cac T. Nguyen
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ravish Patel
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Neil H. Kim
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Thomas E. Kuhlman
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Zou Z, Hu Y, Liu Z, Zhong W, Cao H, Chen H, Jin M. Efficient strategy for constructing duck enteritis virus-based live attenuated vaccine against homologous and heterologous H5N1 avian influenza virus and duck enteritis virus infection. Vet Res 2015; 46:42. [PMID: 25889564 PMCID: PMC4397706 DOI: 10.1186/s13567-015-0174-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 03/23/2015] [Indexed: 01/01/2023] Open
Abstract
Duck is susceptible to many pathogens, such as duck hepatitis virus, duck enteritis virus (DEV), duck tembusu virus, H5N1 highly pathogenic avian influenza virus (HPAIV) in particular. With the significant role of duck in the evolution of H5N1 HPAIV, control and eradication of H5N1 HPAIV in duck through vaccine immunization is considered an effective method in minimizing the threat of a pandemic outbreak. Consequently, a practical strategy to construct a vaccine against these pathogens should be determined. In this study, the DEV was examined as a candidate vaccine vector to deliver the hemagglutinin (HA) gene of H5N1, and its potential as a polyvalent vaccine was evaluated. A modified mini-F vector was inserted into the gB and UL26 gene junction of the attenuated DEV vaccine strain C-KCE genome to generate an infectious bacterial artificial chromosome (BAC) of C-KCE (vBAC-C-KCE). The HA gene of A/duck/Hubei/xn/2007 (H5N1) was inserted into the C-KCE genome via the mating-assisted genetically integrated cloning (MAGIC) to generate the recombinant vector pBAC-C-KCE-HA. A bivalent vaccine C-KCE-HA was developed by eliminating the BAC backbone. Ducks immunized with C-KCE-HA induced both the cross-reactive antibodies and T cell response against H5. Moreover, C-KCE-HA-immunized ducks provided rapid and long-lasting protection against homologous and heterologous HPAIV H5N1 and DEV clinical signs, death, and primary viral replication. In conclusion, our BAC-C-KCE is a promising platform for developing a polyvalent live attenuated vaccine.
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Affiliation(s)
- Zhong Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yong Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Collaborative Innovation Center for Industrial Fermentation, Hubei University of Technology, Wuhan, 430068, China.
| | - Zhigang Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Life Sciences, AnQing Normal University, AnQing, 246011, China.
| | - Wei Zhong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hangzhou Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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Abstract
Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein−based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation.
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Guo YY, Shi ZY, Fu XZ, Chen JC, Wu Q, Chen GQ. A strategy for enhanced circular DNA construction efficiency based on DNA cyclization after microbial transformation. Microb Cell Fact 2015; 14:18. [PMID: 25896825 PMCID: PMC4455692 DOI: 10.1186/s12934-015-0204-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background With the rapid development of synthetic biology, the demand for assembling multiple DNA (genes) fragments into a large circular DNA structure in one step has dramatically increased. However, for constructions of most circular DNA, there are two contradictions in the ligation/assembly and transformation steps. The ligation/assembly consists of two different reactions: 1) the ligation/assembly between any two pieces of a linear form DNA; 2) the cyclization (or self-ligation) of a single linear form DNA. The first contradiction is that the bimolecular ligation/assembly requires a higher DNA concentration while the cyclization favors a lower one; the second contradiction is that a successful transformation of a ligation/assembly product requires a relatively high DNA concentration again. This study is the first attempt to use linear plasmid and Cyclization After Transformation (CAT) strategy to neutralize those contradictions systematically. Results The linear assembly combined with CAT method was demonstrated to increase the overall construction efficiency by 3–4 times for both the traditional ligation and for the new in vitro recombination-based assembly methods including recombinant DNA, Golden Gate, SLIC (Sequence and Ligation Independent Cloning) and Gibson Isothermal Assembly. Finally, the linear assembly combined with CAT method was successfully applied to assemble a pathway of 7 gene fragments responsible for synthesizing precorrin 3A which is an important intermediate in VB12 production. Conclusion The linear assembly combined with CAT strategy method can be regarded as a general strategy to enhance the efficiency of most existing circular DNA construction technologies and could be used in construction of a metabolic pathway consisting of multiple genes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0204-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ying-Ying Guo
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Zhen-Yu Shi
- Synthenome.com, Dingley Village, VIC3172, Australia.
| | - Xiao-Zhi Fu
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Qiong Wu
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Nano and Micro Mechanics, Tsinghua University, Beijing, 100084, China.
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Wang J, Xu R, Liu A. IRDL cloning: a one-tube, zero-background, easy-to-use, directional cloning method improves throughput in recombinant DNA preparation. PLoS One 2014; 9:e107907. [PMID: 25243603 PMCID: PMC4171505 DOI: 10.1371/journal.pone.0107907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and efficient construction of expression vectors and subsequent transformation are basic recombinant methods for the investigation of gene functionality. Although novel cloning methods have recently been developed, many laboratories worldwide continue to use traditional restriction digestion-ligation methods to construct expression vectors owing to financial constraints and the unavailability of appropriate vectors. We describe an improved restriction digestion-ligation (IRDL) cloning method that combines the advantage of directional cloning from double digestion-ligation with that of a low background observed by using a positive selection marker gene ccdB to facilitate digestion and ligation in a single tube. The IRDL cloning overcomes the time-consuming and laborious limits of traditional methods, thereby providing an easy-to-use, low-cost, and one-step strategy for directional cloning of target DNA fragments into an expression vector. As a proof-of-concept example, we developed two yeast vectors to demonstrate the feasibility and the flexibility of the IRDL cloning method. This method would provide an effective and easy-to-use system for gene cloning and functional genomics studies.
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Affiliation(s)
- Jiancai Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Ronghua Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Aizhong Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Kunming, People's Republic of China
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Efficient strategy to generate a vectored duck enteritis virus delivering envelope of duck Tembusu virus. Viruses 2014; 6:2428-43. [PMID: 24956180 PMCID: PMC4074935 DOI: 10.3390/v6062428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/16/2022] Open
Abstract
Duck Tembusu virus (DTMUV) is a recently emerging pathogenic flavivirus that has resulted in a huge economic loss in the duck industry. However, no vaccine is currently available to control this pathogen. Consequently, a practical strategy to construct a vaccine against this pathogen should be determined. In this study, duck enteritis virus (DEV) was examined as a candidate vaccine vector to deliver the envelope (E) of DTMUV. A modified mini-F vector was inserted into the SORF3 and US2 gene junctions of the attenuated DEV vaccine strain C-KCE genome to generate an infectious bacterial artificial chromosome (BAC) of C-KCE (vBAC-C-KCE). The envelope (E) gene of DTMUV was inserted into the C-KCE genome through the mating-assisted genetically integrated cloning (MAGIC) strategy, resulting in the recombinant vector, pBAC-C-KCE-E. A bivalent vaccine C-KCE-E was generated by eliminating the BAC backbone. Immunofluorescence and western blot analysis results indicated that the E proteins were vigorously expressed in C-KCE-E-infected chicken embryo fibroblasts (CEFs). Duck experiments demonstrated that the insertion of the E gene did not alter the protective efficacy of C-KCE. Moreover, C-KCE-E-immunized ducks induced neutralization antibodies against DTMUV. These results demonstrated, for the first time, that recombinant C-KCE-E can serve as a potential bivalent vaccine against DEV and DTMUV.
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Knockin’ on pHeaven’s Door: A Fast and Reliable High-Throughput Compatible Zero-Background Cloning Procedure. Mol Biotechnol 2014; 56:449-58. [DOI: 10.1007/s12033-014-9736-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Strain-Damerell C, Mahajan P, Gileadi O, Burgess-Brown NA. Medium-throughput production of recombinant human proteins: ligation-independent cloning. Methods Mol Biol 2014; 1091:55-72. [PMID: 24203324 DOI: 10.1007/978-1-62703-691-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Structural genomics groups have identified the need to generate multiple truncated versions of each target to improve their success in producing a well-expressed, soluble, and stable protein and one that crystallizes and diffracts to a sufficient resolution for structural determination. At the SGC, we opted for the Ligation-Independent Cloning (LIC) method which provides the medium throughput we desire to produce and screen many proteins in a parallel process. Here, we describe our LIC protocol for generating constructs in a 96-well format and provide a choice of vectors suitable for expressing proteins in both E. coli and the baculovirus expression vector system (BEVS).
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36
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Morioka Y, Fujihara Y, Okabe M. Generation of precise point mutation mice by footprintless genome modification. Genesis 2013; 52:68-77. [PMID: 24265262 DOI: 10.1002/dvg.22727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/28/2013] [Accepted: 11/09/2013] [Indexed: 11/09/2022]
Abstract
Point mutation mice are a key tool in the study of biological functions of genomic DNA sequences and the creation of human disease models. These mice are produced by homologous recombination combined with site-specific recombinase, which allows removal of drug selection cassettes. However, the methods currently available leave ectopic sequences in the "inactive" intron region of the targeted genome in addition to the desired mutation. Since recent research suggests that the intron region may actually have some functionality, these sequences could potentially interfere with neighboring gene expression and, as a result, affect the mouse phenotype. To completely avoid this issue, we used the PiggyBac transposon to remove selection cassettes and achieve precise genome modification without leaving behind a footprint. This PiggyBac system allowed us to successfully generate mice carrying an artificially introduced W(v) point mutation in the Kit gene, and these mice were confirmed to have phenotypes identical to spontaneous W(v) mutation mice. Generation of W(v) -mutation corrected mice was also possible, and phenotypes were completely restored. Our footprintless genome modification technology can generate precise point mutation mice with only the desired mutation, and they reflect an accurate phenotype that makes these mice a reliable and "worry-free" research resource.
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Affiliation(s)
- Yuka Morioka
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
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37
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Zhao W, Hu H, Zsak L, Yu Q, Yang Z. Application of the ligation-independent cloning (LIC) method for rapid construction of a minigenome rescue system for Newcastle disease virus VG/GA strain. Plasmid 2013; 70:314-20. [DOI: 10.1016/j.plasmid.2013.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
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38
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Sun Q, Liu J, Li Y, Zhang Q, Shan S, Li X, Qi B. Creation and validation of a widely applicable multiple gene transfer vector system for stable transformation in plant. PLANT MOLECULAR BIOLOGY 2013; 83:391-404. [PMID: 23839253 DOI: 10.1007/s11103-013-0096-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 06/16/2013] [Indexed: 05/09/2023]
Abstract
Multiple gene transfer (MGT) technology has become a powerful tool for basic and applied plant biology research in recent years. Despite some notable successes in obtaining plant lines harbouring multiple transgenes, these methods are still generally unwieldy and costly. We report here a straightforward and cost effective strategy, utilizing commonly available restriction enzymes for the transfer of multiple genes into plants, hence greatly widening the accessibility of MGT. This methodology exploits the specific 'nested' arrangement of a pair of isocaudomer restriction enzymes (for example XbaI-AvrII-XbaI) so that through the alternate use of these two enzymes in a reiterative fashion multiple genes/constructs (up to five in this study) could be 'stacked' together with ease. In a proof-of-concept experiment, we constructed a plant transformation vector containing three reporter gene expression cassettes flanked by two matrix attachment region sequences. The expression of all three genes was confirmed in transgenic Arabidopsis thaliana. The usefulness of this technology was further validated by the construction of a plant transformation vector containing five transgenes for the production of eicosapentaenoic acid (EPA, C20∆⁵,⁸,¹¹,¹⁴,¹⁷), a polyunsaturated essential fatty acid found in fish oils that is beneficial for health. In addition, we constructed four more vectors, incorporating one seed specific and three promoters conferring constitutive expression. These expression cassettes are flanked by a different isocaudomer pair (AvrII-SpeI-AvrII) and four other unique restriction sites, allowing the exchange of promoters and terminators of choice.
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Affiliation(s)
- Quanxi Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271000, China
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39
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Cobb RE, Ning JC, Zhao H. DNA assembly techniques for next-generation combinatorial biosynthesis of natural products. J Ind Microbiol Biotechnol 2013; 41:469-77. [PMID: 24127070 DOI: 10.1007/s10295-013-1358-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/25/2013] [Indexed: 12/30/2022]
Abstract
Natural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound's therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis.
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Affiliation(s)
- Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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40
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Baumann T, Arndt KM, Müller KM. Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V. BMC Biotechnol 2013; 13:81. [PMID: 24090222 PMCID: PMC3856533 DOI: 10.1186/1472-6750-13-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/25/2013] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. RESULTS A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. CONCLUSIONS The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
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Affiliation(s)
- Tobias Baumann
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Room UHG E2-143 Universitätsstr, 25, Bielefeld 33615, Germany.
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41
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Schoberle TJ, Nguyen-Coleman CK, May GS. Plasmids for increased efficiency of vector construction and genetic engineering in filamentous fungi. Fungal Genet Biol 2013; 58-59:1-9. [PMID: 23867711 PMCID: PMC3817716 DOI: 10.1016/j.fgb.2013.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/01/2013] [Accepted: 07/03/2013] [Indexed: 01/15/2023]
Abstract
Fungal species are continuously being studied to not only understand disease in humans and plants but also to identify novel antibiotics and other metabolites of industrial importance. Genetic manipulations, such as gene deletion, gene complementation, and gene over-expression, are common techniques to investigate fungal gene functions. Although advances in transformation efficiency and promoter usage have improved genetic studies, some basic steps in vector construction are still laborious and time-consuming. Gateway cloning technology solves this problem by increasing the efficiency of vector construction through the use of λ phage integrase proteins and att recombination sites. We developed a series of Gateway-compatible vectors for use in genetic studies in a range of fungal species. They contain nutritional and drug-resistance markers and can be utilized to manipulate different filamentous fungal genomes.
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Affiliation(s)
- Taylor J. Schoberle
- The University of Texas Graduate School of Biomedical
Sciences at Houston; The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
| | - C. Kim Nguyen-Coleman
- Microbiology and Molecular Genetics, Division of Pathology
and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
| | - Gregory S. May
- Program in Genes and Development, Division of Pathology and
Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
- Microbiology and Molecular Genetics, Division of Pathology
and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
- The University of Texas Graduate School of Biomedical
Sciences at Houston; The University of Texas MD Anderson Cancer Center, Houston,
Texas 77030
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42
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Sabri S, Steen JA, Bongers M, Nielsen LK, Vickers CE. Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microb Cell Fact 2013; 12:60. [PMID: 23799955 PMCID: PMC3706339 DOI: 10.1186/1475-2859-12-60] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/23/2013] [Indexed: 11/21/2022] Open
Abstract
Background Metabolic engineering projects often require integration of multiple genes in order to control the desired phenotype. However, this often requires iterative rounds of engineering because many current insertion approaches are limited by the size of the DNA that can be transferred onto the chromosome. Consequently, construction of highly engineered strains is very time-consuming. A lack of well-characterised insertion loci is also problematic. Results A series of knock-in/knock-out (KIKO) vectors was constructed for integration of large DNA sequences onto the E. coli chromosome at well-defined loci. The KIKO plasmids target three nonessential genes/operons as insertion sites: arsB (an arsenite transporter); lacZ (β-galactosidase); and rbsA-rbsR (a ribose metabolism operon). Two homologous ‘arms’ target each insertion locus; insertion is mediated by λ Red recombinase through these arms. Between the arms is a multiple cloning site for the introduction of exogenous sequences and an antibiotic resistance marker (either chloramphenicol or kanamycin) for selection of positive recombinants. The resistance marker can subsequently be removed by flippase-mediated recombination. The insertion cassette is flanked by hairpin loops to isolate it from the effects of external transcription at the integration locus. To characterize each target locus, a xylanase reporter gene (xynA) was integrated onto the chromosomes of E. coli strains W and K-12 using the KIKO vectors. Expression levels varied between loci, with the arsB locus consistently showing the highest level of expression. To demonstrate the simultaneous use of all three loci in one strain, xynA, green fluorescent protein (gfp) and a sucrose catabolic operon (cscAKB) were introduced into lacZ, arsB and rbsAR respectively, and shown to be functional. Conclusions The KIKO plasmids are a useful tool for efficient integration of large DNA fragments (including multiple genes and pathways) into E. coli. Chromosomal insertion provides stable expression without the need for continuous antibiotic selection. Three non-essential loci have been characterised as insertion loci; combinatorial insertion at all three loci can be performed in one strain. The largest insertion at a single site described here was 5.4 kb; we have used this method in other studies to insert a total of 7.3 kb at one locus and 11.3 kb across two loci. These vectors are particularly useful for integration of multigene cassettes for metabolic engineering applications.
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Affiliation(s)
- Suriana Sabri
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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43
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Shi Z, Wedd AG, Gras SL. Parallel in vivo DNA assembly by recombination: experimental demonstration and theoretical approaches. PLoS One 2013; 8:e56854. [PMID: 23468883 PMCID: PMC3585241 DOI: 10.1371/journal.pone.0056854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/17/2013] [Indexed: 01/10/2023] Open
Abstract
The development of synthetic biology requires rapid batch construction of large gene networks from combinations of smaller units. Despite the availability of computational predictions for well-characterized enzymes, the optimization of most synthetic biology projects requires combinational constructions and tests. A new building-brick-style parallel DNA assembly framework for simple and flexible batch construction is presented here. It is based on robust recombination steps and allows a variety of DNA assembly techniques to be organized for complex constructions (with or without scars). The assembly of five DNA fragments into a host genome was performed as an experimental demonstration.
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Affiliation(s)
- Zhenyu Shi
- School of Chemistry, University of Melbourne, Parkville, Victoria, Australia.
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Buntru M, Gärtner S, Staib L, Kreuzaler F, Schlaich N. Delivery of multiple transgenes to plant cells by an improved version of MultiRound Gateway technology. Transgenic Res 2013; 22:153-67. [PMID: 22972476 DOI: 10.1007/s11248-012-9640-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/27/2012] [Indexed: 11/30/2022]
Abstract
At present, only few methods for the effective assembly of multigene constructs have been described. Here we present an improved version of the MultiRound Gateway technology, which facilitates plant multigene transformation. The system consists of two attL-flanked entry vectors, which contain an attR cassette, and a transformation-competent artificial chromosome based destination vector. By alternate use of the two entry vectors, multiple transgenes can be delivered sequentially into the Gateway-compatible destination vector. Multigene constructs that carried up to seven transgenes corresponding to more than 26 kb were assembled by seven rounds of LR recombination. The constructs were successfully transformed into tobacco plants and were stably inherited for at least two generations. Thus, our system represents a powerful, highly efficient tool for multigene plant transformation and may facilitate genetic engineering of agronomic traits or the assembly of genetic pathways for the production of biofuels, industrial or pharmaceutical compounds in plants.
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Affiliation(s)
- Matthias Buntru
- Institute for Biology I, RWTH Aachen University, Worringer Weg 1, 52056, Aachen, Germany.
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45
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Transcriptional networks controlling the cell cycle. G3-GENES GENOMES GENETICS 2013; 3:75-90. [PMID: 23316440 PMCID: PMC3538345 DOI: 10.1534/g3.112.004283] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/07/2012] [Indexed: 01/09/2023]
Abstract
In this work, we map the transcriptional targets of 107 previously identified Drosophila genes whose loss caused the strongest cell-cycle phenotypes in a genome-wide RNA interference screen and mine the resulting data computationally. Besides confirming existing knowledge, the analysis revealed several regulatory systems, among which were two highly-specific and interconnected feedback circuits, one between the ribosome and the proteasome that controls overall protein homeostasis, and the other between the ribosome and Myc/Max that regulates the protein synthesis capacity of cells. We also identified a set of genes that alter the timing of mitosis without affecting gene expression, indicating that the cyclic transcriptional program that produces the components required for cell division can be partially uncoupled from the cell division process itself. These genes all have a function in a pathway that regulates the phosphorylation state of Cdk1. We provide evidence showing that this pathway is involved in regulation of cell size, indicating that a Cdk1-regulated cell size checkpoint exists in metazoans.
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46
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Geertsma ER. FX cloning: a versatile high-throughput cloning system for characterization of enzyme variants. Methods Mol Biol 2013; 978:133-148. [PMID: 23423894 DOI: 10.1007/978-1-62703-293-3_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Methods for the cloning of large numbers of open reading frames (ORFs) into expression vectors are of critical importance for diverse disciplines in biology. Here I describe a system termed FX cloning that facilitates the high-throughput generation of expression constructs. FX cloning combines attractive features of established recombination- and single-strand-annealing-based cloning methods that were thus far not unified in one single method. FX cloning allows the straightforward transfer of a sequence-verified ORF to a variety of expression vectors, and it avoids the common but undesirable feature of significantly extending target ORFs with cloning-related sequences. It leaves a minimal seam of only a single amino acid to either side of the protein. Furthermore, FX cloning is highly efficient and economic in its use. The method is based on a class IIS restriction enzyme and negative selection markers. The full procedure takes place in one pot and does not require intermediate purifications. The method has proven to be very robust and suitable for all common pro- and eukaryotic expression systems.
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Affiliation(s)
- Eric R Geertsma
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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47
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Kittleson JT, DeLoache W, Cheng HY, Anderson JC. Scalable plasmid transfer using engineered P1-based phagemids. ACS Synth Biol 2012; 1:583-9. [PMID: 23656280 DOI: 10.1021/sb300054p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Dramatic improvements to computational, robotic, and biological tools have enabled genetic engineers to conduct increasingly sophisticated experiments. Further development of biological tools offers a route to bypass complex or expensive mechanical operations, thereby reducing the time and cost of highly parallelized experiments. Here, we engineer a system based on bacteriophage P1 to transfer DNA from one E. coli cell to another, bypassing the need for intermediate DNA isolation (e.g., minipreps). To initiate plasmid transfer, we refactored a native phage element into a DNA module capable of heterologously inducing phage lysis. After incorporating known cis-acting elements, we identified a novel cis-acting element that further improves transduction efficiency, exemplifying the ability of synthetic systems to offer insight into native ones. The system transfers DNAs up to 25 kilobases, the maximum assayed size, and operates well at microliter volumes, enabling manipulation of most routinely used DNAs. The system's large DNA capacity and physical coupling of phage particles to phagemid DNA suggest applicability to biosynthetic pathway evolution, functional proteomics, and ultimately, diverse molecular biology operations including DNA fabrication.
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Affiliation(s)
- Joshua T. Kittleson
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
| | - Will DeLoache
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
| | - Hsiao-Ying Cheng
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
| | - J. Christopher Anderson
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
- Berkeley National Laboratory, Physical Biosciences Division, QB3: California
Institute for Quantitative Biological Research, 327 Stanley Hall,
Berkeley, California 94720, United States
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Curtis T, Daran JM, Pronk JT, Frey J, Jansson JK, Robbins-Pianka A, Knight R, Schnürer A, Smets BF, Smid EJ, Abee T, Vicente M, Zengler K. Crystal ball - 2013. Microb Biotechnol 2012. [PMCID: PMC3815379 DOI: 10.1111/1751-7915.12014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tom Curtis
- School of Civil Engineering and Geosciences; Newcastle University; Newcastle upon Tyne; NE17RU; UK
| | - Jean-Marc Daran
- Department of Biotechnology; Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation; Julianalaan 67; 2628; BC Delft; The Netherlands
| | - Jack T. Pronk
- Department of Biotechnology; Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation; Julianalaan 67; 2628; BC Delft; The Netherlands
| | - Joachim Frey
- Institute of Veterinary Bacteriology; Universität Bern; Laenggass-Str. 122; Postfach; CH; 3001; Bern; Switzerland
| | - Janet K. Jansson
- Department of Ecology; Earth Sciences Division; Lawrence Berkeley National, Laboratory; 1 Cyclotron Road; Berkeley; CA; 94720; USA
| | | | | | - Anna Schnürer
- Department of Microbiology; BioCenter; Swedish University of the Agricultural Sciences; Box 7025; 750 07; Uppsala; Sweden
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark; DK-2800 Kgs; Lyngby; Denmark
| | - E. J. Smid
- Laboratory of Food Microbiology; Wageningen University; 6700 EV; Wageningen; The Netherlands
| | - T. Abee
- Laboratory of Food Microbiology; Wageningen University; 6700 EV; Wageningen; The Netherlands
| | - Miguel Vicente
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas (CNB-CSIC); C/ Darwin n° 3; E-28049; Madrid; Spain
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Chang JJ, Ho CY, Ho FJ, Tsai TY, Ke HM, Wang CHT, Chen HL, Shih MC, Huang CC, Li WH. PGASO: A synthetic biology tool for engineering a cellulolytic yeast. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:53. [PMID: 22839502 PMCID: PMC3462719 DOI: 10.1186/1754-6834-5-53] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 06/28/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND To achieve an economical cellulosic ethanol production, a host that can do both cellulosic saccharification and ethanol fermentation is desirable. However, to engineer a non-cellulolytic yeast to be such a host requires synthetic biology techniques to transform multiple enzyme genes into its genome. RESULTS A technique, named Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO), that employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was developed. PGASO was applied to engineer Kluyveromycesmarxianus KY3, which is a thermo- and toxin-tolerant yeast. We obtained a recombinant strain, called KR5, that is capable of simultaneously expressing exoglucanase and endoglucanase (both of Trichodermareesei), a beta-glucosidase (from a cow rumen fungus), a neomycin phosphotransferase, and a green fluorescent protein. High transformation efficiency and accuracy were achieved as ~63% of the transformants was confirmed to be correct. KR5 can utilize beta-glycan, cellobiose or CMC as the sole carbon source for growth and can directly convert cellobiose and beta-glycan to ethanol. CONCLUSIONS This study provides the first example of multi-gene assembly in a single step in a yeast species other than Saccharomyces cerevisiae. We successfully engineered a yeast host with a five-gene cassette assembly and the new host is capable of co-expressing three types of cellulase genes. Our study shows that PGASO is an efficient tool for simultaneous expression of multiple enzymes in the kefir yeast KY3 and that KY3 can serve as a host for developing synthetic biology tools.
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Affiliation(s)
- Jui-Jen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Cheng-Yu Ho
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 115, Taiwan
| | - Feng-Ju Ho
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Tsung-Yu Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Microbial Genomics, National Chung Hsing University, Taichung, 402, Taiwan
| | | | - Hsin-Liang Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 115, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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Tsvetanova B, Peng L, Liang X, Li K, Hammond L, Peterson TC, Katzen F. Advanced DNA assembly technologies in drug discovery. Expert Opin Drug Discov 2012; 7:371-4. [PMID: 22468854 DOI: 10.1517/17460441.2012.672408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recombinant DNA technologies have had a fundamental impact on drug discovery. The continuous emergence of unique gene assembly techniques resulted in the generation of a variety of therapeutic reagents such as vaccines, cancer treatment molecules and regenerative medicine precursors. With the advent of synthetic biology there is a growing need for precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes. In this article, we summarize the highlights of the recombinant DNA technology since its inception in the early 1970s, emphasizing on the most recent advances, and underscoring their principles, advantages and shortcomings. Current and prior cloning trends are discussed in the context of sequence requirements and scars left behind. Our opinion is that despite the remarkable progress that has enabled the generation and manipulation of very large DNA sequences, a better understanding of the cell's natural circuits is needed in order to fully exploit the current state-of-the-art gene assembly technologies.
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