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Luan J, Song C, Liu Y, He R, Guo R, Cui Q, Jiang C, Li X, Hao K, Stewart AF, Fu J, Zhang Y, Wang H. Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method. Nat Protoc 2024:10.1038/s41596-024-01016-9. [PMID: 39009664 DOI: 10.1038/s41596-024-01016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activities and modifying genetic elements in multiple rounds because it can insert, delete or substitute nucleotides, DNA segments or even entire genes at the target site without introducing any unwanted change. To facilitate seamless site-directed mutagenesis in large plasmids and bacterial artificial chromosomes (BACs) with repetitive sequences, we recently developed the RedEx strategy. Compared with previous methods, our approach achieves the recovery of correct recombinants with high accuracy by circumventing unwanted recombination between repetitive sequences. RedEx readily yields more than 80% accuracy in seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters, which are among the most difficult targets due to the large number of repetitive DNA sequences in modules encoding almost identical enzymes. Here we present the RedEx method by describing in detail the seamless site-directed mutagenesis in a BAC vector. Overall, the process includes three parts: (1) insertion of the RedEx cassette containing the desired mutation together with selection-counterselection markers flanked by unique restriction sites and 20-bp overlapping sequences into the target site by recombineering, (2) removal of the selection-counterselection markers in the BAC by restriction digestion and (3) circularization of the linear BAC by exonuclease-mediated in vitro DNA annealing. This protocol can be performed within 3 weeks and will enable researchers with DNA cloning experience to master seamless site-directed mutagenesis to accelerate their research.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Yan Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruoting He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruofei Guo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Kexin Hao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China.
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Tan W, Miao Q, Jia X, Liu Y, Li S, Yang D. Research Progress on the Assembly of Large DNA Fragments. Chembiochem 2024; 25:e202400054. [PMID: 38477700 DOI: 10.1002/cbic.202400054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Synthetic biology, a newly and rapidly developing interdisciplinary field, has demonstrated increasing potential for extensive applications in the wide areas of biomedicine, biofuels, and novel materials. DNA assembly is a key enabling technology of synthetic biology and a central point for realizing fully synthetic artificial life. While the assembly of small DNA fragments has been successfully commercialized, the assembly of large DNA fragments remains a challenge due to their high molecular weight and susceptibility to breakage. This article provides an overview of the development and current state of DNA assembly technology, with a focus on recent advancements in the assembly of large DNA fragments in Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. In particular, the methods and challenges associated with the assembly of large DNA fragment in different hosts are highlighted. The advancements in DNA assembly have the potential to facilitate the construction of customized genomes, giving us the ability to modify cellular functions and even create artificial life. It is also contributing to our ability to understand, predict, and manipulate living organisms.
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Affiliation(s)
- Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Qing Miao
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Xuemei Jia
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Ying Liu
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
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3
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Bubnov DM, Yuzbashev TV, Khozov AA, Melkina OE, Vybornaya TV, Stan GB, Sineoky SP. Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs. Nucleic Acids Res 2022; 50:8947-8960. [PMID: 35920321 PMCID: PMC9410887 DOI: 10.1093/nar/gkac649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encoding whole metabolic pathways into the genome. This approach relies on the replacement of a counterselection marker with cargo DNA cassettes via λRed recombineering. We employed a counterselection strategy involving a genetic circuit based on the CI repressor of λ phage. Our design ensures elimination of most spontaneous mutants, and thus provides a counterselection stringency close to the maximum possible. We improved the efficiency of integrating long PCR-generated cassettes by exploiting the Ocr antirestriction function of T7 phage, which completely prevents degradation of unmethylated DNA by restriction endonucleases in wild-type bacteria. The employment of highly restrictive counterselection and ocr-assisted λRed recombineering allowed markerless integration of operon-sized cassettes into arbitrary genomic loci of four enterobacterial species with an efficiency of 50–100%. In the case of Escherichia coli, our strategy ensures simple combination of markerless mutations in a single strain via P1 transduction. Overall, the proposed approach can serve as a general tool for synthetic biology and metabolic engineering in a range of bacterial hosts.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
| | - Tigran V Yuzbashev
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Andrey A Khozov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills 1-12, Moscow 119234, Russia
| | - Olga E Melkina
- Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Laboratory of Bacterial Genetics, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Genomic Center, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
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Li X, Jin J, Xu W, Wang M, Liu L. Abortive ligation intermediate blocks seamless repair of double-stranded breaks. Int J Biol Macromol 2022; 209:1498-1503. [PMID: 35469952 DOI: 10.1016/j.ijbiomac.2022.04.098] [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: 02/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
Because indel results in frame-shift mutations, seamless repair of double-stranded break (DSB)s plays a pivotal role in synthetic biology, molecular biology, and genome integrity. However, DSB repair is not well documented. T4 DNA ligase (T4lig) served to ligate intra-molecularly a zero bp break-apart DSB linear plasmid DNA pET22b(28a)-xylanase. An ATP T4lig ligation reaction joined one single-stranded break (SSB) into a phosphodiester-bond, whereas the opposite SSB into an abortive ligation intermediate blocking the DSB sequential repair. The intermediate proved to be fluorescent Cy5-AMP-SSB by a T4lig ligation reaction in the aid of Alexa Fluor 647 ATP having Cy5-AMP fluorescence. The fluorescent Cy5-AMP-SSB was de-adenylated into SSB by an ATP-free T4lig or Mg2+-free T4ligL159L reaction. The de-adenylated SSB was re-joined into another phosphodiester-bond by a sequential ATP T4lig re-ligation reaction. Thereby, DSB repair proceeds an abortive ligation, a reverse de-adenylation, and a sequential re-ligation reaction. The result has a potential usage in synthetic biology, molecular biology, and cancer-curing.
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Affiliation(s)
- Xuegang Li
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiacheng Jin
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenxuan Xu
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Mingdao Wang
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China
| | - Liangwei Liu
- The Life Science College, Henan Agricultural University, Zhengzhou 450002, China; The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Henan Agricultural University, Zhengzhou 450002, China.
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5
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Chen W, Chen R, He L, Wu X. Development and optimization of Lysis gene E as a counter-selection marker with high stringency. Biotechnol J 2022; 17:e2100423. [PMID: 35373931 DOI: 10.1002/biot.202100423] [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: 08/10/2021] [Revised: 03/19/2022] [Accepted: 04/01/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Seamless modification of bacterial chromosomes is widely performed in both theoretical and practical research. For this purpose, excellent counter-selection marker genes with high stringency are needed. MAIN METHODS AND MAJOR RESULTS The lysis gene E was first constructed under the control of the PL promoter and the cI857 repressor. At 42°C, it could effectively kill Escherichia coli and seamless modification in this bacterium using E as a counter-selection marker was successfully conducted. It also works in another gram-negative strain, Serratia marcescens, under the control of the Arac/PBAD regulatory system. By combining lysis gene E and kil, the counter-selection frequencies of the PL -kil-sd-E cassette in E. coli reached 4.9 × 10-8 and 3.2 × 10-8 at two test loci, which are very close to frequencies observed with the best counter-selection systems reported, the inducible toxin systems. Under the control of the Arac/PBAD , the counter-selection frequency of PBAD -kil-sd-E in S. marcescens reached the level of 10-7 at four test loci. By expressing the araC gene from plasmid pKDsg-ack, 5- to 17-fold improvements in counter-selection stringency were observed at these loci. A surprisingly low counter-selection frequency of 4.9 × 10-9 was obtained at the marR-1 locus, which reflects the highest stringency for a counter-selection cassette reported thus far. Similarly, at the araB locus of E. coli, the counter-selection frequency of PBAD -kil-sd-E was 3 × 10-9 after introducing plasmid pKDsg-ack. CONCLUSIONS AND IMPLICATIONS We have developed and optimized a new universal counter-selection marker based on lysis gene E. The best counter-selection stringency of this new marker exceeds the inducible toxin system several fold. Our work can also provide inspiration for improving counter-selection stringency based on existing markers. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China.,Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ling He
- Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaotong Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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Yu D, Wang J. BAC Recombineering and Transgenesis to Study Cell Polarity and Polarized Tissue Morphogenesis in Mice. Methods Mol Biol 2022; 2438:197-216. [PMID: 35147944 PMCID: PMC9245493 DOI: 10.1007/978-1-0716-2035-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Planar cell polarity (PCP) signaling plays a critical role in coordinating cell polarity during various organogenesis processes in mammals, and its disruption is causal to numerous congenital disorders in humans. To elucidate its actions in mammals, mouse genetics is an indispensable approach. Given that both gain- and loss-of-function of many PCP genes often cause similar defects, the standard mouse transgenic approach may not always be ideal for studying PCP genes in their wild-type and mutant forms. Here we describe using BAC (bacterial artificial chromosomes) transgenes as a versatile and effective alternative. Transgenes made from BACs, which are genomic clones 100-200 kb in size, can more faithful recapitulate endogenous gene expression levels and patterns. Bacterial based recombination system can be used to efficiently introduce mutations, fluorescent protein tags, and LoxP sites for conditional expressions. Cre can also be inserted into BACs to map the contribution of cells expressing any PCP gene of interest, and study PCP mediated tissue morphogenesis.
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Affiliation(s)
- Deli Yu
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianbo Wang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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Rapid and Efficient BAC Recombineering: Gain & Loss Screening System. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
As the GroES/GroEL chaperonin system is the only bacterial chaperone that is essential under all conditions, we have been interested in the development of GroES/GroEL inhibitors as potential antibiotics. Using Escherichia coli GroES/GroEL as a surrogate, we have discovered several classes of GroES/GroEL inhibitors that show potent antibacterial activity against both Gram-positive and Gram-negative bacteria. However, it remains unknown if E. coli GroES/GroEL is functionally identical to other GroES/GroEL chaperonins and hence if our inhibitors will function against other chaperonins. Herein we report our initial efforts to characterize the GroES/GroEL chaperonins from clinically significant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). We used complementation experiments in GroES/GroEL-deficient and -null E. coli strains to report on exogenous ESKAPE chaperone function. In GroES/GroEL-deficient (but not knocked-out) E. coli, we found that only a subset of the ESKAPE GroES/GroEL chaperone systems could complement to produce a viable organism. Surprisingly, GroES/GroEL chaperone systems from two of the ESKAPE pathogens were found to complement in E. coli, but only in the strict absence of either E. coli GroEL (P. aeruginosa) or both E. coli GroES and GroEL (E. faecium). In addition, GroES/GroEL from S. aureus was unable to complement E. coli GroES/GroEL under all conditions. The resulting viable strains, in which E. coli groESL was replaced with ESKAPE groESL, demonstrated similar growth kinetics to wild-type E. coli, but displayed an elongated phenotype (potentially indicating compromised GroEL function) at some temperatures. These results suggest functional differences between GroES/GroEL chaperonins despite high conservation of amino acid identity.IMPORTANCE The GroES/GroEL chaperonin from E. coli has long served as the model system for other chaperonins. This assumption seemed valid because of the high conservation between the chaperonins. It was, therefore, shocking to discover ESKAPE pathogen GroES/GroEL formed mixed-complex chaperonins in the presence of E. coli GroES/GroEL, leading to loss of organism viability in some cases. Complete replacement of E. coli groESL with ESKAPE groESL restored organism viability, but produced an elongated phenotype, suggesting differences in chaperonin function, including client specificity and/or refolding cycle rates. These data offer important mechanistic insight into these remarkable machines, and the new strains developed allow for the synthesis of homogeneous chaperonins for biochemical studies and to further our efforts to develop chaperonin-targeted antibiotics.
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Zhang JJ, Moore BS. Site-Directed Mutagenesis of Large Biosynthetic Gene Clusters via Oligonucleotide Recombineering and CRISPR/Cas9 Targeting. ACS Synth Biol 2020; 9:1917-1922. [PMID: 32584552 DOI: 10.1021/acssynbio.0c00265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genetic engineering of natural product biosynthetic gene clusters represents an attractive approach to access new and complex bioactive small molecules. However, due to the large number and size of some genes involved in specialized metabolism, notably those encoding modular polyketide synthase and nonribosomal peptide synthetase megaproteins, it remains difficult to introduce precise genetic mutations to probe domain activity or alter chemical product formation. Here, we report the development and validation of a robust method combining oligonucleotide recombineering and CRISPR/Cas9 targeting for rapid site-directed mutagenesis of cloned pathways, which can be directly transferred to a heterologous host for expression. We rapidly generated 12 point mutations and identified several important determinants of successful mutagenesis, including the protospacer/PAM sequence and presence of regions of local homology. Our approach may be broadly applicable for researchers interested in probing natural product biosynthesis or performing pathway engineering.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92037, United States
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10
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Abbasi MN, Fu J, Bian X, Wang H, Zhang Y, Li A. Recombineering for Genetic Engineering of Natural Product Biosynthetic Pathways. Trends Biotechnol 2020; 38:715-728. [PMID: 31973879 DOI: 10.1016/j.tibtech.2019.12.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 01/21/2023]
Abstract
Microbial genomes encode many cryptic and uncharacterized biosynthetic gene clusters (BGCs). Exploiting this unexplored genetic wealth to discover microbial novel natural products (NPs) remains a challenging issue. We review homologous recombination (HR)-based recombineering, mediated by the recombinases RecE/RecT from Rac prophage and Redα/Redβ from lambda phage, which has developed into a highly inclusive tool for direct cloning of large DNA up to 100 kb, seamless mutation, multifragment assembly, and heterologous expression of microbial NP BGCs. Its utilization in the refactoring, engineering, and functional expression of long BGCs for NP biosynthesis makes it easy to elucidate NP-producing potential in microbes. This review also highlights various applications of recombineering in NP-derived drug discovery.
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Affiliation(s)
- Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jun Fu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Hailong Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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11
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Development of a rapid method for site-directed mutagenesis in Streptococcus zooepidemicus. J Biotechnol 2020; 324S:100025. [PMID: 34154731 DOI: 10.1016/j.btecx.2020.100025] [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: 03/04/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022]
Abstract
This paper describes the development of a straightforward method for site-directed gene mutagenesis in Streptococcus zooepidemicus, inspired by the mechanism of natural competence regulated by ComX in other streptococci. An alternative sigma factor comX gene was overexpressed from a plasmid in S. zooepidemicus and electrocompetent cells were prepared. As proof of concept, a DNA cassette with two targeting regions flanking a kanamycin resistance gene was spliced in an overlap extension PCR and electroporated. The cassette was then integrated in the genomic DNA by homologous recombination. Next, the gene SeseC_00180 (fibrinogen- and Ig-binding protein precursor) was selected as target for markerless gene deletion and the impact of its loss on the resulting hyaluronan production was determined. The new method of site-directed mutagenesis is significant because it is not necessary to clone the DNA cassette in an auxiliary vector, electroporating it in S. zooepidemicus cells is enough, which allows to bypass the problems with hard to clone DNA sequences and speeds up the whole process of mutation generation in S. zooepidemicus.
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12
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Piszczek L, Memoli S, Raggioli A, Viosca J, Rientjes J, Hublitz P, Czaban W, Wyrzykowska A, Gross C. Mouse model of the human serotonin transporter-linked polymorphic region. Mamm Genome 2019; 30:319-328. [PMID: 31667540 PMCID: PMC6884432 DOI: 10.1007/s00335-019-09815-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/21/2019] [Indexed: 11/27/2022]
Abstract
Genetic factors play a significant role in risk for mood and anxiety disorders. Polymorphisms in genes that regulate the brain monoamine systems, such as catabolic enzymes and transporters, are attractive candidates for being risk factors for emotional disorders given the weight of evidence implicating monoamines involvement in these conditions. Several common genetic variants have been identified in the human serotonin transporter (5-HTT) gene, including a repetitive sequence located in the promoter region of the locus called the serotonin transporter-linked polymorphic region (5-HTT-LPR). This polymorphism has been associated with a number of mental traits in both humans and primates, including depression, neuroticism, and harm avoidance. Some, but not all, studies found a link between the polymorphism and 5-HTT levels, leaving open the question of whether the polymorphism affects risk for mental traits via changes in 5-HTT expression. To investigate the impact of the polymorphism on gene expression, serotonin homeostasis, and behavioral traits, we set out to develop a mouse model of the human 5-HTT-LPR. Here we describe the creation and characterization of a set of mouse lines with single-copy human transgenes carrying the short and long 5-HTT-LPR variants. Although we were not able to detect differences in expression between the short and long variants, we encountered several technical issues concerning the design of our humanized mice that are likely to have influenced our findings. Our study serves as a cautionary note for future studies aimed at studying human transgene regulation in the context of the living mouse.
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Affiliation(s)
- Lukasz Piszczek
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
- Research Institute of Molecular Pathology, Vienna, Austria.
| | - Simone Memoli
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Angelo Raggioli
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - José Viosca
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
- Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Jeanette Rientjes
- Monash Genome Modification Platform (MGMP), Monash University, Clayton, Australia
| | - Philip Hublitz
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Weronika Czaban
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Anna Wyrzykowska
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Cornelius Gross
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
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13
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Chen W, Li Y, Wu G, Zhao L, Lu L, Wang P, Zhou J, Cao C, Li S. Simple and efficient genome recombineering using kil counter-selection in Escherichia coli. J Biotechnol 2019; 294:58-66. [PMID: 30768999 DOI: 10.1016/j.jbiotec.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 01/04/2019] [Accepted: 01/19/2019] [Indexed: 01/01/2023]
Abstract
Seamless modification of the Escherichia coli genome using positive selection / negative selection is widely used in metabolic engineering and functional genome analysis. Some excellent negative selection systems have been reported, of which tetA-sacB and inducible toxins system are prominent. To expand the existing negative selection toolkit, we constructed a new negative selection marker system based on kil gene of lambda prophage. The selection stringency of kil was measured and compared with the most widely used counter-selection gene, sacB, at the lacI, ack, and dbpa loci using different E. coli strains. At all these loci of tested strains, the selection stringency of kil significantly exceeds that of sacB by 2- to 28-fold. When dsDNA fragments were employed for recombination, the efficiency for isolating the correct recombinant of kil was significantly higher than that of sacB. This new negative selection system does not require special media or extended incubation time. However, our system cannot be used in host strains containing temperature-sensitive kil gene. A Red system providing plasmid without kil gene is recommended for use together with our system. Our counter-selection system is expected to be an addition to the engineering arsenal of E. coli.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China; Beijing Institute of Biotechnology, Beijing 100850, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guangjin Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lingfeng Zhao
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Li Lu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Peng Wang
- Beijing Institute of Biotechnology, Beijing 100850, China
| | - Jianguang Zhou
- Beijing Institute of Biotechnology, Beijing 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing 100850, China.
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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14
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Thi Thanh Hai N, Thuy LTT, Shiota A, Kadono C, Daikoku A, Hoang DV, Dat NQ, Sato-Matsubara M, Yoshizato K, Kawada N. Selective overexpression of cytoglobin in stellate cells attenuates thioacetamide-induced liver fibrosis in mice. Sci Rep 2018; 8:17860. [PMID: 30552362 PMCID: PMC6294752 DOI: 10.1038/s41598-018-36215-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Cytoglobin (CYGB), discovered in hepatic stellate cells (HSCs), is known to possess a radical scavenger function, but its pathophysiological roles remain unclear. Here, for the first time, we generated a new transgenic (TG) mouse line in which both Cygb and mCherry reporter gene expression were under the control of the native Cygb gene promoter. We demonstrated that the expression of Cygb-mCherry was related to endogenous Cygb in adult tissues by tracing mCherry fluorescence together with DNA, mRNA, and protein analyses. Administration of a single dose (50 mg/kg) of thioacetamide (TAA) in Cygb-TG mice resulted in lower levels of alanine transaminase and oxidative stress than those in WT mice. After 10 weeks of TAA administration, Cygb-TG livers exhibited reduced neutrophil accumulation, cytokine expression and fibrosis but high levels of quiescent HSCs. Primary HSCs isolated from Cygb-TG mice (HSCCygb-TG) exhibited significantly decreased mRNA levels of α-smooth muscle actin (αSMA), collagen 1α1, and transforming growth factor β-3 after 4 days in culture relative to WT cells. HSCsCygb-TG were resistant to H2O2-induced αSMA expression. Thus, cell-specific overexpression of Cygb attenuates HSC activation and protects mice against TAA-induced liver fibrosis presumably by maintaining HSC quiescence. Cygb is a potential new target for antifibrotic approaches.
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Affiliation(s)
- Nguyen Thi Thanh Hai
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
| | - Le Thi Thanh Thuy
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | | | - Chiho Kadono
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Atsuko Daikoku
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Dinh Viet Hoang
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Ninh Quoc Dat
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Misako Sato-Matsubara
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Katsutoshi Yoshizato
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
- PhoenixBio Co. Ltd., Hiroshima, Japan
- Endowed Laboratory of Synthetic Biology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Norifumi Kawada
- Departments of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan.
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15
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Ou B, Garcia C, Wang Y, Zhang W, Zhu G. Techniques for chromosomal integration and expression optimization in Escherichia coli. Biotechnol Bioeng 2018; 115:2467-2478. [PMID: 29981268 DOI: 10.1002/bit.26790] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 12/31/2022]
Abstract
Due to the inherent expression stability and low metabolic burden to the host cell, the expression of heterologous proteins in the bacterial chromosome in a precise and efficient manner is highly desirable for metabolic engineering and live bacterial applications. However, obtaining suitable chromosome expression levels is particularly challenging. In this minireview, we briefly present the technologies available for the integration of heterologous genes into Escherichia coli chromosomes and strategies to optimize the expression levels of heterologous proteins.
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Affiliation(s)
- Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.,Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Carolina Garcia
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Weiping Zhang
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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16
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Igarashi H, Ikeda K, Onimaru H, Kaneko R, Koizumi K, Beppu K, Nishizawa K, Takahashi Y, Kato F, Matsui K, Kobayashi K, Yanagawa Y, Muramatsu SI, Ishizuka T, Yawo H. Targeted expression of step-function opsins in transgenic rats for optogenetic studies. Sci Rep 2018; 8:5435. [PMID: 29615713 PMCID: PMC5882906 DOI: 10.1038/s41598-018-23810-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 03/20/2018] [Indexed: 12/12/2022] Open
Abstract
Rats are excellent animal models for experimental neuroscience. However, the application of optogenetics in rats has been hindered because of the limited number of established transgenic rat strains. To accomplish cell-type specific targeting of an optimized optogenetic molecular tool, we generated ROSA26/CAG-floxed STOP-ChRFR(C167A)-Venus BAC rats that conditionally express the step-function mutant channelrhodopsin ChRFR(C167A) under the control of extrinsic Cre recombinase. In primary cultured cortical neurons derived from this reporter rat, only Cre-positive cells expressing ChRFR(C167A) became bi-stable, that is, their excitability was enhanced by blue light and returned to the baseline by yellow~red light. In bigenic pups carrying the Phox2B-Cre driver, ChRFR(C167A) was specifically expressed in the rostral parafacial respiratory group (pFRG) in the medulla, where endogenous Phox2b immunoreactivity was detected. These neurons were sensitive to blue light with an increase in the firing frequency. Thus, this transgenic rat actuator/reporter system should facilitate optogenetic studies involving the effective in vivo manipulation of the activities of specific cell fractions using light of minimal intensity.
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Affiliation(s)
- Hiroyuki Igarashi
- Department of Physiology and Pharmacology, Tohoku University Graduate school of Medicine, Sendai, Japan. .,Research Fellow of the Japan Society for the Promotion of Science (JSPS Research Fellow), Tokyo, Japan.
| | - Keiko Ikeda
- Department of Physiology, International University of Health and Welfare, Narita, Chiba, Japan.,Division of Biology, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroshi Onimaru
- Department of Physiology, Showa University School of Medicine, Shinagawa, Tokyo, Japan
| | - Ryosuke Kaneko
- Department of Genetic and Behavioural Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kyo Koizumi
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan
| | - Kaoru Beppu
- Department of Super-network Brain Physiology, Tohoku University Graduate School of Life Sciences, Sendai, Japan
| | - Kayo Nishizawa
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yukari Takahashi
- Department of Neuroscience, The Jikei University School of Medicine, Tokyo, Japan
| | - Fusao Kato
- Department of Neuroscience, The Jikei University School of Medicine, Tokyo, Japan
| | - Ko Matsui
- Department of Super-network Brain Physiology, Tohoku University Graduate School of Life Sciences, Sendai, Japan
| | - Kazuto Kobayashi
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yuchio Yanagawa
- Department of Genetic and Behavioural Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Shin-Ichi Muramatsu
- Division of Neurology, Jichi Medical School, Tochigi, Japan.,Center for Gene & Cell Therapy, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Toru Ishizuka
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan
| | - Hiromu Yawo
- Department of Physiology and Pharmacology, Tohoku University Graduate school of Medicine, Sendai, Japan. .,Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan.
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17
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Hashimoto M, Asai A, Kawagishi H, Mikawa R, Iwashita Y, Kanayama K, Sugimoto K, Sato T, Maruyama M, Sugimoto M. Elimination of p19 ARF-expressing cells enhances pulmonary function in mice. JCI Insight 2016; 1:e87732. [PMID: 27699227 DOI: 10.1172/jci.insight.87732] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Senescent cells accumulate in many tissues as animals age and are considered to underlie several aging-associated pathologies. The tumor suppressors p19ARF and p16INK4a, both of which are encoded in the CDKN2A locus, play critical roles in inducing and maintaining permanent cell cycle arrest during cellular senescence. Although the elimination of p16INK4a-expressing cells extends the life span of the mouse, it is unclear whether tissue function is restored by the elimination of senescent cells in aged animals and whether and how p19ARF contributes to tissue aging. The aging-associated decline in lung function is characterized by an increase in compliance as well as pathogenic susceptibility to pulmonary diseases. We herein demonstrated that pulmonary function in 12-month-old mice was reversibly restored by the elimination of p19ARF-expressing cells. The ablation of p19ARF-expressing cells using a toxin receptor-mediated cell knockout system ameliorated aging-associated lung hypofunction. Furthermore, the aging-associated gene expression profile was reversed after the elimination of p19ARF. Our results indicate that the aging-associated decline in lung function was, at least partly, attributed to p19ARF and was recovered by eliminating p19ARF-expressing cells.
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Affiliation(s)
- Michihiro Hashimoto
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Azusa Asai
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Hiroyuki Kawagishi
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Ryuta Mikawa
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Yuji Iwashita
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | | | - Kazushi Sugimoto
- Department of Molecular and Laboratory Medicine, Mie University School of Medicine, Tsu, Mie, Japan
| | - Tadashi Sato
- Department of Respiratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Mitsuo Maruyama
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Masataka Sugimoto
- Department of Mechanism of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
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18
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RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression. Nat Protoc 2016; 11:1175-90. [PMID: 27254463 DOI: 10.1038/nprot.2016.054] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Full-length RecE and RecT from Rac prophage mediate highly efficient linear-linear homologous recombination that can be used to clone large DNA regions directly from genomic DNA into expression vectors, bypassing library construction and screening. Homologous recombination mediated by Redαβ from lambda phage has been widely used for recombinant DNA engineering. Here we present a protocol for direct cloning and engineering of biosynthetic gene clusters, large operons or single genes from genomic DNA using one Escherichia coli host that harbors both RecET and Redαβ systems. The pipeline uses standardized cassettes for horizontal gene transfer options, as well as vectors with different replication origins configured to minimize recombineering background through the use of selectively replicating templates or CcdB counterselection. These optimized reagents and protocols facilitate fast acquisition of transgenes from genomic DNA preparations, which are ready for heterologous expression within 1 week.
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19
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Genome modifications and cloning using a conjugally transferable recombineering system. ACTA ACUST UNITED AC 2015; 8:24-35. [PMID: 28352570 PMCID: PMC4980705 DOI: 10.1016/j.btre.2015.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/21/2022]
Abstract
The genetic modification of primary bacterial disease isolates is challenging due to the lack of highly efficient genetic tools. Herein we describe the development of a modified PCR-based, λ Red-mediated recombineering system for efficient deletion of genes in Gram-negative bacteria. A series of conjugally transferrable plasmids were constructed by cloning an oriT sequence and different antibiotic resistance genes into recombinogenic plasmid pKD46. Using this system we deleted ten different genes from the genomes of Edwardsiella ictaluri and Aeromonas hydrophila. A temperature sensitive and conjugally transferable flp recombinase plasmid was developed to generate markerless gene deletion mutants. We also developed an efficient cloning system to capture larger bacterial genetic elements and clone them into a conjugally transferrable plasmid for facile transferring to Gram-negative bacteria. This system should be applicable in diverse Gram-negative bacteria to modify and complement genomic elements in bacteria that cannot be manipulated using available genetic tools.
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20
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Ikeda K, Takahashi M, Sato S, Igarashi H, Ishizuka T, Yawo H, Arata S, Southard-Smith EM, Kawakami K, Onimaru H. A Phox2b BAC Transgenic Rat Line Useful for Understanding Respiratory Rhythm Generator Neural Circuitry. PLoS One 2015; 10:e0132475. [PMID: 26147470 PMCID: PMC4492506 DOI: 10.1371/journal.pone.0132475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/15/2015] [Indexed: 11/21/2022] Open
Abstract
The key role of the respiratory neural center is respiratory rhythm generation to maintain homeostasis through the control of arterial blood pCO2/pH and pO2 levels. The neuronal network responsible for respiratory rhythm generation in neonatal rat resides in the ventral side of the medulla and is composed of two groups; the parafacial respiratory group (pFRG) and the pre-Bötzinger complex group (preBötC). The pFRG partially overlaps in the retrotrapezoid nucleus (RTN), which was originally identified in adult cats and rats. Part of the pre-inspiratory (Pre-I) neurons in the RTN/pFRG serves as central chemoreceptor neurons and the CO2 sensitive Pre-I neurons express homeobox gene Phox2b. Phox2b encodes a transcription factor and is essential for the development of the sensory-motor visceral circuits. Mutations in human PHOX2B cause congenital hypoventilation syndrome, which is characterized by blunted ventilatory response to hypercapnia. Here we describe the generation of a novel transgenic (Tg) rat harboring fluorescently labeled Pre-I neurons in the RTN/pFRG. In addition, the Tg rat showed fluorescent signals in autonomic enteric neurons and carotid bodies. Because the Tg rat expresses inducible Cre recombinase in PHOX2B-positive cells during development, it is a potentially powerful tool for dissecting the entire picture of the respiratory neural network during development and for identifying the CO2/O2 sensor molecules in the adult central and peripheral nervous systems.
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Affiliation(s)
- Keiko Ikeda
- Division of Biology, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
- Division of Biology, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
- * E-mail:
| | - Masanori Takahashi
- Division of Biology, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Shigeru Sato
- Division of Biology, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroyuki Igarashi
- Department of Physiology, and Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Toru Ishizuka
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences and JST/CREST, Sendai, Miyagi, Japan
| | - Hiromu Yawo
- Department of Physiology, and Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences and JST/CREST, Sendai, Miyagi, Japan
| | - Satoru Arata
- Center for Biotechnology, Showa University, Shinagawa, Tokyo, Japan
| | - E. Michelle Southard-Smith
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Kiyoshi Kawakami
- Division of Biology, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Hiroshi Onimaru
- Department of Physiology, Showa University School of Medicine, Shinagawa, Tokyo, Japan
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21
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Making BAC transgene constructs with lambda-red recombineering system for transgenic animals or cell lines. Methods Mol Biol 2015; 1227:71-98. [PMID: 25239742 DOI: 10.1007/978-1-4939-1652-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The genomic DNA libraries based on Bacteria Artificial Chromosomes (BAC) are the foundation of whole genomic mapping, sequencing, and annotation for many species like mice and humans. With their large insert size, BACs harbor the gene-of-interest and nearby transcriptional regulatory elements necessary to direct the expression of the gene-of-interest in a temporal and cell-type specific manner. When replacing a gene-of-interest with a transgene in vivo, the transgene can be expressed with the same patterns and machinery as that of the endogenous gene. This chapter describes in detail a method of using lambda-red recombineering to make BAC transgene constructs with the integration of a transgene into a designated location within a BAC. As the final BAC construct will be used for transfection in cell lines or making transgenic animals, specific considerations with BAC transgenes such as genotyping, BAC coverage and integrity as well as quality of BAC DNA will be addressed. Not only does this approach provide a practical and effective way to modify large DNA constructs, the same recombineering principles can apply to smaller high copy plasmids as well as to chromosome engineering.
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22
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Recovery of an HMWP/hmwBP (pUL48/pUL47) complex from virions of human cytomegalovirus: subunit interactions, oligomer composition, and deubiquitylase activity. J Virol 2014; 88:8256-67. [PMID: 24829352 DOI: 10.1128/jvi.00971-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED We report that the human cytomegalovirus (HCMV) high-molecular-weight tegument protein (HMWP, pUL48; 253 kDa) and the HMWP-binding protein (hmwBP, pUL47; 110 kDa) can be recovered as a complex from virions disrupted by treatment with 50 mM Tris (pH 7.5), 0.5 M NaCl, 0.5% NP-40, and 10 mM dithiothreitol [DTT]. The subunit ratio of the complex approximates 1:1, with a shape and structure consistent with an elongated heterodimer. The HMWP/hmwBP complex was corroborated by reciprocal coimmunoprecipitation experiments using antipeptide antibodies and lysates from both infected cells and disrupted virus particles. An interaction of the amino end of pUL48 (amino acids [aa] 322 to 754) with the carboxyl end of pUL47 (aa 693 to 982) was identified by fragment coimmunoprecipitation experiments, and a head-to-tail self-interaction of hmwBP was also observed. The deubiquitylating activity of pUL48 is retained in the isolated complex, which cleaves K11, K48, and K63 ubiquitin isopeptide linkages. IMPORTANCE Human cytomegalovirus (HCMV, or human herpesvirus 5 [HHV-5]) is a large DNA-containing virus that belongs to the betaherpesvirus subfamily and is a clinically important pathogen. Defining the constituent elements of its mature form, their organization within the particle, and the assembly process by which it is produced are fundamental to understanding the mechanisms of herpesvirus infection and developing drugs and vaccines against them. In this study, we report isolating a complex of two large proteins encoded by HCMV open reading frames (ORFs) UL47 and UL48 and identifying the binding domains responsible for their interaction with each other and of pUL47 with itself. Our calculations indicate that the complex is a rod-shaped heterodimer. Additionally, we determined that the ubiquitin-specific protease activity of the ORF UL48 protein was functional in the complex, cleaving K11-, K48-, and K63-linked ubiquitin dimers. This information builds on and extends our understanding of the HCMV tegument protein network that is required to interface the HCMV envelope and capsid.
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23
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Ahn Y, Mullan HE, Krumlauf R. Long-range regulation by shared retinoic acid response elements modulates dynamic expression of posterior Hoxb genes in CNS development. Dev Biol 2014; 388:134-44. [PMID: 24525295 DOI: 10.1016/j.ydbio.2014.01.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/13/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Retinoic acid (RA) signaling plays an important role in determining the anterior boundary of Hox gene expression in the neural tube during embryogenesis. In particular, RA signaling is implicated in a rostral expansion of the neural expression domain of 5׳ Hoxb genes (Hoxb9-Hoxb5) in mice. However, underlying mechanisms for this gene regulation have remained elusive due to the lack of RA responsive element (RARE) in the 5׳ half of the HoxB cluster. To identify cis-regulatory elements required for the rostral expansion, we developed a recombineering technology to serially label multiple genes with different reporters in a single bacterial artificial chromosome (BAC) vector containing the mouse HoxB cluster. This allowed us to simultaneously monitor the expression of multiple genes. In contrast to plasmid-based reporters, transgenic BAC reporters faithfully recapitulated endogenous gene expression patterns of the Hoxb genes including the rostral expansion. Combined inactivation of two RAREs, DE-RARE and ENE-RARE, in the BAC completely abolished the rostral expansion of the 5׳ Hoxb genes. Knock-out of endogenous DE-RARE lead to significantly reduced expression of multiple Hoxb genes and attenuated Hox gene response to exogenous RA treatment in utero. Regulatory potential of DE-RARE was further demonstrated by its ability to anteriorize 5׳ Hoxa gene expression in the neural tube when inserted into a HoxA BAC reporter. Our data demonstrate that multiple RAREs cooperate to remotely regulate 5׳ Hoxb genes during CNS development, providing a new insight into the mechanisms for gene regulation within the Hox clusters.
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Affiliation(s)
- Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hillary E Mullan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA.
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24
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Parrish M, Ahn Y, Nolte C, De Kumar B, Krumlauf R. Hox complex analysis through BAC recombineering. Methods Mol Biol 2014; 1196:59-87. [PMID: 25151158 DOI: 10.1007/978-1-4939-1242-1_5] [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] [Indexed: 02/01/2023]
Abstract
BAC transgenesis in mice has proved to be useful in exploring the regulatory mechanisms and functions of the Hox complexes. The large constructs used may include most of the relevant components of the cis-regulatory landscape. Manipulations can be accomplished without compromising the integrity of the endogenous complex which reduces the likelihood of producing confounding phenotypic abnormalities. The development of recombineering tools has been critical in providing the means necessary to make many types of precise and varied manipulations of these large constructs. Here, we will discuss the methodologies necessary to manipulate Hox complex BACs, generation of transgenic animals bearing these constructs and the utilization of these resources to address fundamental aspects of Hox biology.
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Affiliation(s)
- Mark Parrish
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
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25
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Abstract
Piwi proteins and their small-RNA partners, piwi-interacting (pi)RNA, form a natural mechanism that prevents the deleterious activity of transposable elements in the germ line of metazoan species. The piRNA pathway relies on extended noncoding genomic regions, dubbed piRNA clusters, to produce long precursor transcripts that are subsequently processed into mature piRNAs. The large size and repetitive nature of piRNA clusters provide significant challenges for their dissection using common genetic tools. Here we describe an effective approach for manipulation of piRNA clusters using a combination of BAC recombineering in E. coli and phiC31-mediated transgenesis in Drosophila. Although the described approach is instrumental for manipulating piRNA clusters, it can also be implemented for other problems in functional genomics.
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Wang H, Bian X, Xia L, Ding X, Müller R, Zhang Y, Fu J, Stewart AF. Improved seamless mutagenesis by recombineering using ccdB for counterselection. Nucleic Acids Res 2013; 42:e37. [PMID: 24369425 PMCID: PMC3950717 DOI: 10.1093/nar/gkt1339] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombineering, which is the use of homologous recombination for DNA engineering in Escherichia coli, usually uses antibiotic selection to identify the intended recombinant. When combined in a second step with counterselection using a small molecule toxin, seamless products can be obtained. Here, we report the advantages of a genetic strategy using CcdB as the counterselectable agent. Expression of CcdB is toxic to E. coli in the absence of the CcdA antidote so counterselection is initiated by the removal of CcdA expression. CcdB counterselection is robust and does not require titrations or experiment-to-experiment optimization. Because counterselection strategies necessarily differ according to the copy number of the target, we describe two variations. For multi-copy targets, we use two E. coli hosts so that counterselection is exerted by the transformation step that is needed to separate the recombined and unrecombined plasmids. For single copy targets, we put the ccdA gene onto the temperature-sensitive pSC101 Red expression plasmid so that counterselection is exerted by the standard temperature shift to remove the expression plasmid. To reduce unwanted intramolecular recombination, we also combined CcdB counterselection with Redα omission. These options improve the use of counterselection in recombineering with BACs, plasmids and the E. coli chromosome.
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Affiliation(s)
- Hailong Wang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China, Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany, Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany and Gene Bridges GmbH, Building C2.3, Saarland University, 66123 Saarbrücken, Germany
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Familial Alzheimer's disease coding mutations reduce Presenilin-1 expression in a novel genomic locus reporter model. Neurobiol Aging 2013; 35:443.e5-443.e16. [PMID: 24011544 DOI: 10.1016/j.neurobiolaging.2013.07.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/28/2013] [Accepted: 07/31/2013] [Indexed: 01/13/2023]
Abstract
We have generated a physiologically relevant bacterial artificial chromosome (BAC)-based genomic DNA expression model to study PS1 gene expression and function. The PS1-WT-BAC construct restored γ-secretase function, whereas the mutant PS1 BACs demonstrated partial to complete loss of enzymatic activity when stably expressed in a PS double knock-out clonal cell line. We then engineered WT and mutant human PS1-BAC-Luciferase whole genomic locus reporter transgenes, which we transiently transduced in mouse and human non-neuronal and neuronal-like cells, respectively. PS1 ΔE9 and C410Y FAD were found to lower PS1 gene expression in both cell lines, whereas PS1-M146V showed a neuron-specific effect. The nonclinical γ-secretase inactive PS1-D257A mutation did not alter gene expression in either cell line. This is the first time that pathogenic coding mutations in the PS1 gene have been shown to lower PS1 gene expression. These findings may represent a pathologic mechanism for PS1 FAD mutations independent of their effects on γ-secretase activity and demonstrate how dominant PS1 mutations may exert their pathogenic effects by a loss-of-function mechanism.
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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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Nagase H, Nagasawa Y, Tachida Y, Sakakibara S, Okutsu J, Suematsu N, Arita S, Shimada K. Deiodinase 2 upregulation demonstrated in osteoarthritis patients cartilage causes cartilage destruction in tissue-specific transgenic rats. Osteoarthritis Cartilage 2013; 21:514-23. [PMID: 23296253 DOI: 10.1016/j.joca.2012.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Chondrocyte hypertrophy followed by cartilage destruction is a crucial step for osteoarthritis (OA) development, however, the underlying mechanism remains largely unknown. The objectives of this study are to identify the gene that may cause cartilage hypertrophy and to elucidate its role on OA pathogenesis. DESIGN Gene expression profiles of cartilages from OA patients and normal subjects were examined by microarray analysis. Expression of deiodinases, enzymes for regulation of triiodothyronine (T3) biosynthesis, in human and rat articular cartilage (AC) were examined by real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). Rat ACs and chondrocytes were treated with T3 to investigate its role on chondrocyte hypertrophy and inflammatory reaction. Cartilage-specific Type II deiodinase (DIO2) transgenic rats were generated using bacterial artificial chromosome harboring the entire rat Col2a1 and human DIO2 gene. An experimental OA model was created in the animal to examine the role of DIO2 on cartilage degeneration. RESULTS DIO2 is highly expressed in OA patient AC compared to normal control. In rat AC, DIO2 is specifically expressed among deiodinases and dominantly expressed the same as in brown adipose tissue. T3 induces hypertrophic markers in articular chondrocyte and cartilage explant culture, and enhances the effect of IL-1α on induction of cartilage degrading enzymes. Importantly, cartilage-specific DIO2 transgenic rats are more susceptible to knee joint destabilization and develop severe AC destruction. CONCLUSION Our findings demonstrate that upregulated expression of DIO2 in OA patient cartilage might be responsible for OA pathogenesis by enhancing the chondrocyte hypertrophy and inflammatory response.
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Affiliation(s)
- H Nagase
- Frontier Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Tokyo, Japan.
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Shyam K Sharan KB, Sharan SK. Manipulating the Mouse Genome Using Recombineering. ADVANCES IN GENETICS 2013; 2. [PMID: 31404315 DOI: 10.4172/2169-0111.1000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically engineered mouse models are indispensable for understanding the biological function of genes, understanding the genetic basis of human diseases and for preclinical testing of novel therapies. Generation of such mouse models has been possible because of our ability to manipulate the mouse genome. Recombineering is a highly efficient recombination-based method of genetic engineering that has revolutionized our ability to generate mouse models. Since recombineering technology is not dependent on the availability of restriction enzyme recognition sites, it allows us to modify the genome with great precision. It requires homology arms as short as 40 bases for recombination, which makes it relatively easy to generate targeting constructs to insert, change or delete either a single nucleotide or a DNA fragment several kb in size; insert selectable markers, reporter genes or add epitope tags to any gene of interest. In this review, we focus on the development of recombineering technology and its application in the generation of transgenic and knockout or knock-in mouse models. High throughput generation of gene targeting vectors, used to construct knockout alleles in mouse embryonic stem cells, is now feasible because of this technology. The challenge now is to use the "designer" mice to develop novel therapies to prevent, cure or effectively manage some the most debilitating human diseases.
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Affiliation(s)
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702
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Kropff B, Burkhardt C, Schott J, Nentwich J, Fisch T, Britt W, Mach M. Glycoprotein N of human cytomegalovirus protects the virus from neutralizing antibodies. PLoS Pathog 2012; 8:e1002999. [PMID: 23133379 PMCID: PMC3486915 DOI: 10.1371/journal.ppat.1002999] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022] Open
Abstract
Herpes viruses persist in the infected host and are transmitted between hosts in the presence of a fully functional humoral immune response, suggesting that they can evade neutralization by antiviral antibodies. Human cytomegalovirus (HCMV) encodes a number of polymorphic highly glycosylated virion glycoproteins (g), including the essential envelope glycoprotein, gN. We have tested the hypothesis that glycosylation of gN contributes to resistance of the virus to neutralizing antibodies. Recombinant viruses carrying deletions in serine/threonine rich sequences within the glycosylated surface domain of gN were constructed in the genetic background of HCMV strain AD169. The deletions had no influence on the formation of the gM/gN complex and in vitro replication of the respective viruses compared to the parent virus. The gN-truncated viruses were significantly more susceptible to neutralization by a gN-specific monoclonal antibody and in addition by a number of gB- and gH-specific monoclonal antibodies. Sera from individuals previously infected with HCMV also more efficiently neutralized gN-truncated viruses. Immunization of mice with viruses that expressed the truncated forms of gN resulted in significantly higher serum neutralizing antibody titers against the homologous strain that was accompanied by increased antibody titers against known neutralizing epitopes on gB and gH. Importantly, neutralization activity of sera from animals immunized with gN-truncated virus did not exhibit enhanced neutralizing activity against the parental wild type virus carrying the fully glycosylated wild type gN. Our results indicate that the extensive glycosylation of gN could represent a potentially important mechanism by which HCMV neutralization by a number of different antibody reactivities can be inhibited. Herpes viruses are transmitted between individuals in cell free form and successful spread benefits from mechanisms that limit the loss of infectivity by the activity of virus neutralizing antibodies. Human cytomegalovirus (HCMV) is an important pathogen and understanding how the virus can evade antiviral antibodies may be clinically relevant. HCMV particles contain a number of highly polymorphic, extensively glycosylated envelope proteins, one of which is glycoprotein N (gN). This protein is essential for replication of HCMV. We have hypothesized that the extensive glycosylation of gN may serve as a tool to evade neutralization by antiviral antibodies. Recombinant viruses were generated expressing gN proteins with reduced glycan modification. The loss of glycan modification had no detectable influence on the in vitro replication of the respective viruses. However, the recombinant viruses containing under-glycosylated forms of gN were significantly more susceptible to neutralization by a diverse array of antibody reactivities. Immunization of mice with viruses carrying fewer glycan modification induced significantly higher antibody titers against the homologous virus; however, the neutralization titers against the fully glycosylated virions, were not enhanced. Our results indicate that glycosylation of gN of HCMV represents a potentially important mechanism for evasion of antibody-mediated neutralization by a number of different antibody specificities.
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Affiliation(s)
- Barbara Kropff
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany
| | - Christiane Burkhardt
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany
| | - Juliane Schott
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany
| | - Jens Nentwich
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany
| | - Tanja Fisch
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany
| | - William Britt
- Department of Pediatrics, University of Alabama Birmingham, Birmingham, Alabama, United States of America
| | - Michael Mach
- Institut für Klinische und Molekulare Virologie, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany
- * E-mail:
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Akieda-Asai S, Sugiyama M, Miyazawa T, Koda S, Okano I, Senba K, Poleni PE, Hizukuri Y, Okamoto A, Yamahara K, Mutoh E, Aoyama F, Sawaguchi A, Furuya M, Miyazato M, Kangawa K, Date Y. Involvement of guanylin and GC-C in rat mesenteric macrophages in resistance to a high-fat diet. J Lipid Res 2012; 54:85-96. [PMID: 23081987 DOI: 10.1194/jlr.m029017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high-fat diet (HFD) is a well-known contributing factor in the development of obesity. Most rats fed HFDs become obese. Those that avoid obesity when fed HFDs are considered diet resistant (DR). We performed a microarray screen to identify genes specific to the mesenteric fat of DR rats and revealed high expression of guanylin and guanylyl cyclase C (GC-C) in some subjects. Our histologic studies revealed that the cellular source of guanylin and GC-C is macrophages. Therefore, we developed double-transgenic (Tg) rats overexpressing guanylin and GC-C in macrophages and found that they were resistant to the effects of HFDs. In the mesenteric fat of HFD-fed Tg rats, Fas and perilipin mRNAs were downregulated, and those of genes involved in fatty acid oxidation were upregulated, compared with the levels in HFD-fed wild-type rats. In vitro studies demonstrated that lipid accumulation was markedly inhibited in adipocytes cocultured with macrophages expressing guanylin and GC-C and that this inhibition was reduced after treatment with guanylin- and GC-C-specific siRNAs. Our results suggest that the macrophagic guanylin-GC-C system contributes to the altered expression of genes involved in lipid metabolism, leading to resistance to obesity.
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Affiliation(s)
- Sayaka Akieda-Asai
- Frontier Science Research Center, Ultrastructural Cell Biology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
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Hamilton G, Killick R, Lambert JC, Amouyel P, Carrasquillo MM, Pankratz VS, Graff-Radford NR, Dickson DW, Petersen RC, Younkin SG, Powell JF, Wade-Martins R. Functional and genetic analysis of haplotypic sequence variation at the nicastrin genomic locus. Neurobiol Aging 2012; 33:1848.e1-13. [PMID: 22405046 PMCID: PMC3683320 DOI: 10.1016/j.neurobiolaging.2012.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 01/19/2012] [Accepted: 02/04/2012] [Indexed: 11/23/2022]
Abstract
Nicastrin (NCSTN) is a component of the γ-secretase complex and therefore potentially a candidate risk gene for Alzheimer's disease. Here, we have developed a novel functional genomics methodology to express common locus haplotypes to assess functional differences. DNA recombination was used to engineer 5 bacterial artificial chromosomes (BACs) to each express a different haplotype of the NCSTN locus. Each NCSTN-BAC was delivered to knockout nicastrin (Ncstn(-/-)) cells and clonal NCSTN-BAC(+)/Ncstn(-/-) cell lines were created for functional analyses. We showed that all NCSTN-BAC haplotypes expressed nicastrin protein and rescued γ-secretase activity and amyloid beta (Aβ) production in NCSTN-BAC(+)/Ncstn(-/-) lines. We then showed that genetic variation at the NCSTN locus affected alternative splicing in human postmortem brain tissue. However, there was no robust functional difference between clonal cell lines rescued by each of the 5 different haplotypes. Finally, there was no statistically significant association of NCSTN with disease risk in the 4 cohorts. We therefore conclude that it is unlikely that common variation at the NCSTN locus is a risk factor for Alzheimer's disease.
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Affiliation(s)
- Gillian Hamilton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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Tuntufye HN, Goddeeris BM. Use of lambda Red-mediated recombineering and Cre/lox for generation of markerless chromosomal deletions in avian pathogenic Escherichia coli. FEMS Microbiol Lett 2012; 325:140-7. [PMID: 22029745 DOI: 10.1111/j.1574-6968.2011.02421.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) are bacteria associated with extraintestinal diseases in poultry. A method to generate markerless deletions of APEC genome is described. Lambda Red recombination is used to introduce a LoxP cassette (loxP-rpsL-neo-loxP) containing the rpsL gene for streptomycin sensitivity and the neo gene for kanamycin/neomycin resistance into the APEC genome, with attendant deletion of a desired chromosomal gene. The loxP sites are incorporated into primers used to amplify the rpsL-neo marker during the construction of the LoxP cassette, making the method rapid and efficient. The cassette is specifically integrated into the fiu gene or intergenic region 2051-52, and the Cre/lox system is used to remove the marker, hence deletion of the drug-resistance genes. The results demonstrate that the Cre/lox system can successfully be used to generate markerless deletions in APEC, and rpsL counter-selection can be used to select the deletions so that one does not have to pick and test to find the desired product.
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Affiliation(s)
- Huruma N Tuntufye
- Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Heverlee, Belgium.
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Sugitani H, Hirano E, Knutsen RH, Shifren A, Wagenseil JE, Ciliberto C, Kozel BA, Urban Z, Davis EC, Broekelmann TJ, Mecham RP. Alternative splicing and tissue-specific elastin misassembly act as biological modifiers of human elastin gene frameshift mutations associated with dominant cutis laxa. J Biol Chem 2012; 287:22055-67. [PMID: 22573328 DOI: 10.1074/jbc.m111.327940] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elastin is the extracellular matrix protein in vertebrates that provides elastic recoil to blood vessels, the lung, and skin. Because the elastin gene has undergone significant changes in the primate lineage, modeling elastin diseases in non-human animals can be problematic. To investigate the pathophysiology underlying a class of elastin gene mutations leading to autosomal dominant cutis laxa, we engineered a cutis laxa mutation (single base deletion) into the human elastin gene contained in a bacterial artificial chromosome. When expressed as a transgene in mice, mutant elastin was incorporated into elastic fibers in the skin and lung with adverse effects on tissue function. In contrast, only low levels of mutant protein incorporated into aortic elastin, which explains why the vasculature is relatively unaffected in this disease. RNA stability studies found that alternative exon splicing acts as a modifier of disease severity by influencing the spectrum of mutant transcripts that survive nonsense-mediated decay. Our results confirm the critical role of the C-terminal region of tropoelastin in elastic fiber assembly and suggest tissue-specific differences in the elastin assembly pathway.
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Affiliation(s)
- Hideki Sugitani
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Development of a bacterial artificial chromosome (BAC) recombineering procedure using galK-untranslated region (UTR) for the mutation of diploid genes. J Virol Methods 2012; 182:18-26. [PMID: 22407056 DOI: 10.1016/j.jviromet.2012.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 02/29/2012] [Indexed: 11/24/2022]
Abstract
Bacterial artificial chromosome (BAC) recombineering using galK selection allows DNA cloned in Escherichia coli to be modified without introducing an unwanted selectable marker at the modification site. Genomes of some herpesviruses have a pair of inverted repeat sequences that makes it very difficult to introduce mutations into diploid (duplicate) genes using the galK selection method. To mutate diploid genes, we developed a galK-UTR BAC recombineering procedure that blocks one copy of the target diploid gene by insertion of a galK untranslated region (UTR), which enables the simple mutation of the other copy. The blocked copy can then be replaced with an UTR-specific primer pair. The IR2 gene of equine herpesvirus 1 (EHV-1) maps within both the internal (IR) and terminal repeat (TR) of the genomic short region and is expressed at low levels because its promoter is TATA-less. Both IR2 promoters in EHV-1 BAC were replaced with a mutant IR2 promoter containing three Sp1-binding motifs and a consensus TATA box by galK-UTR BAC recombineering. The expression level of the IR2 protein controlled by the modified promoter increased approximately 4-fold as compared to that of wild-type EHV-1. The galK-UTR method will provide a useful tool in studies of herpesviruses.
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Karasawa F, Shiota A, Goso Y, Kobayashi M, Sato Y, Masumoto J, Fujiwara M, Yokosawa S, Muraki T, Miyagawa S, Ueda M, Fukuda MN, Fukuda M, Ishihara K, Nakayama J. Essential role of gastric gland mucin in preventing gastric cancer in mice. J Clin Invest 2012; 122:923-34. [PMID: 22307328 DOI: 10.1172/jci59087] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 12/21/2011] [Indexed: 02/06/2023] Open
Abstract
Gastric gland mucin secreted from the lower portion of the gastric mucosa contains unique O-linked oligosaccharides (O-glycans) having terminal α1,4-linked N-acetylglucosamine residues (αGlcNAc). Previously, we identified human α1,4-N-acetylglucosaminyltransferase (α4GnT), which is responsible for the O-glycan biosynthesis and characterized αGlcNAc function in suppressing Helicobacter pylori in vitro. In the present study, we engineered A4gnt(-/-) mice to better understand its role in vivo. A4gnt(-/-) mice showed complete lack of αGlcNAc expression in gastric gland mucin. Surprisingly, all the mutant mice developed gastric adenocarcinoma through a hyperplasia-dysplasia-carcinoma sequence in the absence of H. pylori infection. Microarray and quantitative RT-PCR analysis revealed upregulation of genes encoding inflammatory chemokine ligands, proinflammatory cytokines, and growth factors, such as Ccl2, Il-11, and Hgf in the gastric mucosa of A4gnt(-/-) mice. Further supporting an important role for this O-glycan in cancer progression, we also observed significantly reduced αGlcNAc in human gastric adenocarcinoma and adenoma. Our results demonstrate that the absence of αGlcNAc triggers gastric tumorigenesis through inflammation-associated pathways in vivo. Thus, αGlcNAc-terminated gastric mucin plays dual roles in preventing gastric cancer by inhibiting H. pylori infection and also suppressing tumor-promoting inflammation.
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Affiliation(s)
- Fumitoshi Karasawa
- Department of Molecular Pathology, Shinshu University Graduate School of Medicine, Matsumoto, Japan
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Back to BAC: the use of infectious clone technologies for viral mutagenesis. Viruses 2012; 4:211-35. [PMID: 22470833 PMCID: PMC3315213 DOI: 10.3390/v4020211] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 12/18/2022] Open
Abstract
Bacterial artificial chromosome (BAC) vectors were first developed to facilitate the propagation and manipulation of large DNA fragments in molecular biology studies for uses such as genome sequencing projects and genetic disease models. To facilitate these studies, methodologies have been developed to introduce specific mutations that can be directly applied to the mutagenesis of infectious clones (icBAC) using BAC technologies. This has resulted in rapid identification of gene function and expression at unprecedented rates. Here we review the major developments in BAC mutagenesis in vitro. This review summarises the technologies used to construct and introduce mutations into herpesvirus icBAC. It also explores developing technologies likely to provide the next leap in understanding these important viruses.
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Bird AW, Erler A, Fu J, Hériché JK, Maresca M, Zhang Y, Hyman AA, Stewart AF. High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes. Nat Methods 2011; 9:103-9. [PMID: 22138824 DOI: 10.1038/nmeth.1803] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 10/19/2011] [Indexed: 01/08/2023]
Abstract
Whereas bacterial artificial chromosomes (BACs) offer many advantages in studies of gene and protein function, generation of seamless, precisely mutated BACs has been difficult. Here we describe a counterselection-based recombineering method and its accompanying reagents. After identifying intramolecular recombination as the major problem in counterselection, we built a strategy to reduce these unwanted events by expressing Redβ alone at the crucial step. We enhanced this method by using phosphothioated oligonucleotides, using a sequence-altered rpsL counterselection gene and developing online software for oligonucleotide design. We illustrated this method by generating transgenic mammalian cell lines carrying small interfering RNA-resistant and point-mutated BAC transgenes. Using this approach, we generated mutated TACC3 transgenes to identify phosphorylation-specific spindle defects after knockdown of endogenous TACC3 expression. Our results highlight the complementary use of precisely mutated BAC transgenes and RNA interference in the study of cell biology at physiological expression levels and regulation.
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Affiliation(s)
- Alexander W Bird
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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40
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Watanabe M, Kurome M, Matsunari H, Nakano K, Umeyema K, Shiota A, Nakauchi H, Nagashima H. The creation of transgenic pigs expressing human proteins using BAC-derived, full-length genes and intracytoplasmic sperm injection-mediated gene transfer. Transgenic Res 2011; 21:605-18. [PMID: 22038447 DOI: 10.1007/s11248-011-9561-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 09/16/2011] [Indexed: 11/29/2022]
Abstract
In most transgenic (Tg) animals created to date, a transgene consisting of the minimum promoter region linked to a cDNA has been used. However, transgenes on small plasmids are susceptible to the position effect, increasing the difficulty of controlling transgene expression. In this study, we attempted to create Tg pigs by intracytoplasmic sperm injection-mediated gene transfer (ICSI-MGT) using two large genomic transgenes derived from a bacterial artificial chromosome (BAC) containing the full genomic region encoding two human proteins, type I collagen and albumin. The production efficiencies (Tg piglets/live offspring) of type I collagen and albumin Tg pigs were 11.8% (6/51) and 18.2% (2/11), respectively. In all of the Tg pigs examined by real-time PCR analysis, tissue-specific expression of the transgene was confirmed (type I collagen: skin, tendon, vessels, genitalia; albumin: liver). The production of human proteins derived from BAC transgenes was also confirmed. Fluorescence in situ hybridization analysis indicated that the BAC transgenes transferred into porcine oocytes by ICSI-MGT were integrated into single or multiple sites on the host chromosomes. These data demonstrate that Tg pigs expressing human proteins in a tissue-specific manner can be created using a BAC transgenic construct and the ICSI-MGT method.
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Affiliation(s)
- Masahito Watanabe
- Nakauchi Stem Cell and Organ Regeneration Project, Japan Science and Technology Agency (JST), ERATO, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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41
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Mutation of glutamine to arginine at position 548 of IE2 86 in human cytomegalovirus leads to decreased expression of IE2 40, IE2 60, UL83, and UL84 and increased transcription of US8-9 and US29-32. J Virol 2011; 85:11098-110. [PMID: 21865379 DOI: 10.1128/jvi.05315-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The IE2 86 protein of human cytomegalovirus (HCMV) is essential for productive infection. The mutation of glutamine to arginine at position 548 of IE2 86 causes the virus to grow both slowly and to very low titers, making it difficult to study this mutant via infection. In this study, Q548R IE2 86 HCMV was produced on the complementing cell line 86F/40HA, which allowed faster and higher-titer production of mutant virus. The main defects observed in this mutant were greatly decreased expression of IE2 40, IE2 60, UL83, and UL84. Genome replication and the induction of cell cycle arrest were found to proceed at or near wild-type levels, and there was no defect in transitioning to early or late protein expression. Q548R IE2 86 was still able to interact with UL84. Furthermore, Q548R IE2 40 maintained the ability to enhance UL84 expression in a cotransfection assay. Microarray analysis of Q548R IE2 HCMV revealed that the US8, US9, and US29-32 transcripts were all significantly upregulated. These results further confirm the importance of IE2 in UL83 and UL84 expression as well as pointing to several previously unknown regions of the HCMV genome that may be regulated by IE2.
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42
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Nedelkova M, Maresca M, Fu J, Rostovskaya M, Chenna R, Thiede C, Anastassiadis K, Sarov M, Stewart AF. Targeted isolation of cloned genomic regions by recombineering for haplotype phasing and isogenic targeting. Nucleic Acids Res 2011; 39:e137. [PMID: 21852329 PMCID: PMC3203589 DOI: 10.1093/nar/gkr668] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Studying genetic variations in the human genome is important for understanding phenotypes and complex traits, including rare personal variations and their associations with disease. The interpretation of polymorphisms requires reliable methods to isolate natural genetic variations, including combinations of variations, in a format suitable for downstream analysis. Here, we describe a strategy for targeted isolation of large regions (∼35 kb) from human genomes that is also applicable to any genome of interest. The method relies on recombineering to fish out target fosmid clones from pools and thereby circumvents the laborious need to plate and screen thousands of individual clones. To optimize the method, a new highly recombineering-efficient bacterial host, including inducible TrfA for fosmid copy number amplification, was developed. Various regions were isolated from human embryonic stem cell lines and a personal genome, including highly repetitive and duplicated ones. The maternal and paternal alleles at the MECP2/IRAK 1 loci were distinguished based on identification of novel allele-specific single-nucleotide polymorphisms in regulatory regions. Additionally, we applied further recombineering to construct isogenic targeting vectors for patient-specific applications. These methods will facilitate work to understand the linkage between personal variations and disease propensity, as well as possibilities for personal genome surgery.
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Affiliation(s)
- Marta Nedelkova
- Technische Universitaet Dresden, Genomics, BioInnovationsZentrum, Dresden, Germany
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43
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Hirota T, Ohta H, Shigeta M, Niwa H, Saitou M. Drug-Inducible Gene Recombination by the Dppa3-MER Cre MER Transgene in the Developmental Cycle of the Germ Cell Lineage in Mice1. Biol Reprod 2011; 85:367-77. [DOI: 10.1095/biolreprod.110.090662] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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44
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Madyagol M, Al-Alami H, Levarski Z, Drahovská H, Turňa J, Stuchlík S. Gene replacement techniques for Escherichia coli genome modification. Folia Microbiol (Praha) 2011; 56:253-63. [PMID: 21614539 DOI: 10.1007/s12223-011-0035-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/04/2011] [Indexed: 11/24/2022]
Abstract
The subject of this review covers modern experimental procedures for chromosomal gene replacement in Escherichia coli and related bacteria, which enable the specific substitution of targeted genome sequences with copies of those carrying defined mutations. Two principal methods for gene replacement were established. The first "in-out" method is based on integration of plasmid into bacterial chromosome and subsequent resolving of the cointegrate. The "linear fragment" method (recombineering) is based on homologous recombination mediated by short homology arms at the ends of linear DNA molecule. Many new protocols and improvements in targeted gene replacement were introduced during the last 10 years. These methods are well suited for high-throughput functional gene studies and for many biotechnological applications.
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Affiliation(s)
- Mahesh Madyagol
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 842 15, Bratislava, Slovak Republic
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45
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Costa JL, Forbes S, Brennan MB, Hochgeschwender U. Genetic modifications of mouse proopiomelanocortin peptide processing. Mol Cell Endocrinol 2011; 336:14-22. [PMID: 21195130 DOI: 10.1016/j.mce.2010.12.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 11/29/2022]
Abstract
Pro-opiomelanocortin (POMC) is a prohormone which undergoes extensive tissue and cell specific post-translational processing producing a number of active peptides with diverse biological roles ranging from control of adrenal function to pigmentation to the regulation of feeding. One approach to unraveling the complexities of the POMC system is to engineer mouse mutants which lack specific POMC peptides. We describe here the design, generation, validation, and preliminary analysis of one such partial POMC mutant specifically lacking α-MSH. In contrast to POMC null mutant mice, mice lacking α-MSH in the presence of all other POMC peptides maintain adrenal structures and produce corticosterone comparable to wildtype littermates; however, they still have decreased levels of aldosterone, as found in POMC null mutant mice. Our findings demonstrate that α-MSH is not needed for maintenance of adrenal structure or for corticosterone production, but is needed for aldosterone production. These data demonstrate that mouse strains generated with precise genetic modifications of POMC peptide processing can answer questions about POMC peptide function. Further analysis of this and additional strains of mice with modified POMC peptide processing patterns will open up a novel avenue for studying the roles of individual POMC peptides.
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Affiliation(s)
- Jessica L Costa
- Department of Medicine, University of Auckland, Auckland, New Zealand
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46
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Jacobs JS, Hong X, Eberl DF. A "mesmer"izing new approach to site-directed mutagenesis in large transformation-ready constructs: Mutagenesis via Serial Small Mismatch Recombineering. Fly (Austin) 2011; 5:162-9. [PMID: 21339708 DOI: 10.4161/fly.5.2.15092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Creating designer mutations in large genes is a challenge. Size limitations imposed by site-directed mutagenesis (SDM), coupled with the paucity of unique restriction enzyme sites, make subsequent cloning of these constructs extremely difficult. "Mutagenesis via Serial Small Mismatch Recombineering" (MSSMR) combines sequential recombineering steps with SDM to create seamless, pre-specified mutations as small as a single base pair. We demonstrate the simultaneous cloning of wild type and mutant constructs of a > 30 kb gene directly into attB transformation vectors. No post-transformation manipulations are required, and because the technique relies on recombineering methods, addition of undesired mutations via PCR is minimized.
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Affiliation(s)
- Julie S Jacobs
- Department of Biology, University of Iowa, Iowa City, IA, USA
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Bitrián M, Roodbarkelari F, Horváth M, Koncz C. BAC-recombineering for studying plant gene regulation: developmental control and cellular localization of SnRK1 kinase subunits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:829-42. [PMID: 21235649 DOI: 10.1111/j.1365-313x.2010.04462.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Recombineering, permitting precise modification of genes within bacterial artificial chromosomes (BACs) through homologous recombination mediated by lambda phage-encoded Red proteins, is a widely used powerful tool in mouse, Caenorhabditis and Drosophila genetics. As Agrobacterium-mediated transfer of large DNA inserts from binary BACs and TACs into plants occurs at low frequency, recombineering is so far seldom exploited in the analysis of plant gene functions. We have constructed binary plant transformation vectors, which are suitable for gap-repair cloning of genes from BACs using recombineering methods previously developed for other organisms. Here we show that recombineering facilitates PCR-based generation of precise translational fusions between coding sequences of fluorescent reporter and plant proteins using galK-based exchange recombination. The modified target genes alone or as part of a larger gene cluster can be transferred by high-frequency gap-repair into plant transformation vectors, stably maintained in Agrobacterium and transformed without alteration into plants. Versatile application of plant BAC-recombineering is illustrated by the analysis of developmental regulation and cellular localization of interacting AKIN10 catalytic and SNF4 activating subunits of Arabidopsis Snf1-related (SnRK1) protein kinase using in vivo imaging. To validate full functionality and in vivo interaction of tagged SnRK1 subunits, it is demonstrated that immunoprecipitated SNF4-YFP is bound to a kinase that phosphorylates SnRK1 candidate substrates, and that the GFP- and YFP-tagged kinase subunits co-immunoprecipitate with endogenous wild type AKIN10 and SNF4.
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Affiliation(s)
- Marta Bitrián
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
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48
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Yamaguchi S, Niwa R, Kazuki Y, Ohbayashi T. Application of a bacterial artificial chromosome modification system for a human artificial chromosome vector. Yonago Acta Med 2011; 54:21-31. [PMID: 24031125 PMCID: PMC3763799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 02/04/2011] [Indexed: 06/02/2023]
Abstract
Exactly controlled conditional gene expressing systems are crucial for genomic functional research, animal transgenesis and gene therapy. Bacterial artificial chromosomes (BACs) are optimal for harboring long fragments of genomic DNA or large cDNA up to 300 kb in size. Therefore, BACs are available to produce transgenic cells and animals for the functional studies of genes. However, BAC can insert DNA randomly into the host genome, possibly causing unpredicted expression. We previously developed a human artificial chromosome (HAC) vector from human chromosome 21 using chromosome engineering. The HAC vector has several important characteristics desired for an ideal gene delivery vector, including stable episomal maintenance, and the ability to carry large genomic DNA containing its own regulatory element, thus allowing physiological regulation of the transgene in a manner similar to that of the native chromosome. In this study, we develop a system fusing BAC library and HAC technology together to allow tight control of gene expression. This system enables BAC to be cloned into the defined locus on the HAC vector by the Cre/loxP system. In addition, the genome in the BAC is possible to be engineered freely by the BAC recombineering technology. This system is a highly efficient tool for the rapid generation of stringently controlled gene expression system on the HAC vector.
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Affiliation(s)
- Shigeyuki Yamaguchi
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, Yonago 683-8503, Japan ; †Division of Laboratory Animal Science, Research Center for Bioscience and Technology, Tottori University, Yonago 683-8503, Japan
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Isern E, Gustems M, Messerle M, Borst E, Ghazal P, Angulo A. The activator protein 1 binding motifs within the human cytomegalovirus major immediate-early enhancer are functionally redundant and act in a cooperative manner with the NF-{kappa}B sites during acute infection. J Virol 2011; 85:1732-46. [PMID: 21106746 PMCID: PMC3028895 DOI: 10.1128/jvi.01713-10] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 11/10/2010] [Indexed: 02/05/2023] Open
Abstract
Human cytomegalovirus (HCMV) infection causes a rapid induction of c-Fos and c-Jun, the major subunits of activator protein 1 (AP-1), which in turn have been postulated to activate the viral immediate-early (IE) genes. Accordingly, the major IE promoter (MIEP) enhancer, a critical control region for initiating lytic HCMV infection and reactivation from the latent state, contains one well-characterized AP-1 site and a second candidate interaction site. In this study we explored the role of these AP-1 elements in the context of the infection. We first show that the distal candidate AP-1 motif binds c-Fos/c-Jun heterodimers (AP-1 complex) and confers c-Fos/c-Jun-mediated activity to a core promoter. Site-directed mutagenesis studies indicate that both AP-1 response elements are critical for 12-O-tetradecanoylphorbol-13-acetate (TPA)-enhanced MIEP activity in transient-transfection assays. In marked contrast to the results obtained with the isolated promoter, disruption of the AP-1 recognition sites of the MIEP in the context of the infectious HCMV genome has no significant influence on the expression of the MIE protein IE1 or viral replication in different cell types. Moreover, a chimeric murine CMV driven by the HCMV MIEP (hMCMV-ES) with the two AP-1 binding sites mutated is not compromised in virulence, is able to grow and disseminate to different organs of the newborn mice as efficiently as the parental virus, and is competent in reactivation. We show, however, that combined inactivation of the enhancer AP-1 and NF-κB recognition sites leads to an attenuation of the hMCMV-ES in the neonatal murine infection model, not observed when each single element is abolished. Altogether, these results underline the functional redundancy of the MIEP elements, highlighting the plasticity of this region, which probably evolved to ensure maximal transcriptional performance across many diverse environments.
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Affiliation(s)
- Elena Isern
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain, Department of Virology, Hannover Medical School, 30625 Hannover, Germany, Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
| | - Montse Gustems
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain, Department of Virology, Hannover Medical School, 30625 Hannover, Germany, Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
| | - Martin Messerle
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain, Department of Virology, Hannover Medical School, 30625 Hannover, Germany, Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
| | - Eva Borst
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain, Department of Virology, Hannover Medical School, 30625 Hannover, Germany, Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
| | - Peter Ghazal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain, Department of Virology, Hannover Medical School, 30625 Hannover, Germany, Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
| | - Ana Angulo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain, Department of Virology, Hannover Medical School, 30625 Hannover, Germany, Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, United Kingdom
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50
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Recombineering BAC transgenes for protein tagging. Methods 2011; 53:113-9. [DOI: 10.1016/j.ymeth.2010.09.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/17/2010] [Accepted: 09/17/2010] [Indexed: 11/22/2022] Open
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