1
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Whitford CM, Gren T, Palazzotto E, Lee SY, Tong Y, Weber T. Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes. ACS Synth Biol 2023; 12:2353-2366. [PMID: 37402223 DOI: 10.1021/acssynbio.3c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
CRISPR tools, especially Cas9n-sgRNA guided cytidine deaminase base editors such as CRISPR-BEST, have dramatically simplified genetic manipulation of streptomycetes. One major advantage of CRISPR base editing technology is the possibility to multiplex experiments in genomically instable species. Here, we demonstrate scaled up Csy4 based multiplexed genome editing using CRISPR-mcBEST in Streptomyces coelicolor. We evaluated the system by simultaneously targeting 9, 18, and finally all 28 predicted specialized metabolite biosynthetic gene clusters in a single experiment. We present important insights into the performance of Csy4 based multiplexed genome editing at different scales. Using multiomics analysis, we investigated the systems wide effects of such extensive editing experiments and revealed great potentials and important bottlenecks of CRISPR-mcBEST. The presented analysis provides crucial data and insights toward the development of multiplexed base editing as a novel paradigm for high throughput engineering of Streptomyces chassis and beyond.
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Affiliation(s)
- Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Emilia Palazzotto
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Yaojun Tong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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2
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Milito A, Aschern M, McQuillan JL, Yang JS. Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3833-3850. [PMID: 37025006 DOI: 10.1093/jxb/erad100] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Microalgae hold enormous potential to provide a safe and sustainable source of high-value compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly progressing climate change. Bioengineering microalgal strains will be key to optimizing and modifying their metabolic outputs, and to render them competitive with established industrial biotechnology hosts, such as bacteria or yeast. To achieve this, precise and tuneable control over transgene expression will be essential, which would require the development and rational design of synthetic promoters as a key strategy. Among green microalgae, Chlamydomonas reinhardtii represents the reference species for bioengineering and synthetic biology; however, the repertoire of functional synthetic promoters for this species, and for microalgae generally, is limited in comparison to other commercial chassis, emphasizing the need to expand the current microalgal gene expression toolbox. Here, we discuss state-of-the-art promoter analyses, and highlight areas of research required to advance synthetic promoter development in C. reinhardtii. In particular, we exemplify high-throughput studies performed in other model systems that could be applicable to microalgae, and propose novel approaches to interrogating algal promoters. We lastly outline the major limitations hindering microalgal promoter development, while providing novel suggestions and perspectives for how to overcome them.
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Affiliation(s)
- Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Moritz Aschern
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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3
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Duran AG, Schwestka M, Nazari-Shafti TZ, Neuber S, Stamm C, Gossen M. Limiting Transactivator Amounts Contribute to Transgene Mosaicism in Tet-On All-in-One Systems. ACS Synth Biol 2022; 11:2623-2635. [PMID: 35815862 DOI: 10.1021/acssynbio.2c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MicroRNAs play an essential role in cell homeostasis and have been proposed as therapeutic agents. One strategy to deliver microRNAs is to genetically engineer target cells to express microRNAs of interest. However, to control dosage and timing, as well as to limit potential side-effects, microRNAs' expression should ideally be under exogenous, inducible control. Conditional expression of miRNA-based short hairpin RNAs (shRNAmirs) via gene regulatory circuits such as the Tet-system is therefore a promising strategy to control shRNAmirs' expression in research and therapy. Single vector approaches like Tet-On all-in-one designs are more compatible with potential clinical applications by providing the Tet-On system components in a single round of genetic engineering. However, all-in-one systems often come at the expense of heterogeneous and unstable expression. In this study, we aimed to understand the causes that lead to such erratic transgene expression. By using a reporter cell, we found that the degree of heterogeneity mostly correlated with reverse tetracycline transactivator (rtTA) expression levels. Moreover, the targeted integration of a potent rtTA expression cassette into a genomic safe harbor locus functionally rescued previously silenced rtTA-responsive transcription units. Overall, our results suggest that ensuring homogenous and stable rtTA expression is essential for the robust and reliable performance of future Tet-On all-in-one designs.
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Affiliation(s)
- Ana G Duran
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Timo Z Nazari-Shafti
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Sebastian Neuber
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Christof Stamm
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
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4
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Efficient expression of multiple guide RNAs for CRISPR/Cas genome editing. ABIOTECH 2020; 1:123-134. [PMID: 36304720 PMCID: PMC9590505 DOI: 10.1007/s42994-019-00014-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/21/2019] [Indexed: 01/16/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein system (CRISPR/Cas) has recently become the most powerful tool available for genome engineering in various organisms. With efficient and proper expression of multiple guide RNAs (gRNAs), the CRISPR/Cas system is particularly suitable for multiplex genome editing. During the past several years, different CRISPR/Cas expression strategies, such as two-component transcriptional unit, single transcriptional unit, and bidirectional promoter systems, have been developed to efficiently express gRNAs as well as Cas nucleases. Significant progress has been made to optimize gRNA production using different types of promoters and RNA processing strategies such as ribozymes, endogenous RNases, and exogenous endoribonuclease (Csy4). Besides being constitutively and ubiquitously expressed, inducible and spatiotemporal regulations of gRNA expression have been demonstrated using inducible, tissue-specific, and/or synthetic promoters for specific research purposes. Most recently, the emergence of CRISPR/Cas ribonucleoprotein delivery methods, such as engineered nanoparticles, further revolutionized transgene-free and multiplex genome editing. In this review, we discuss current strategies and future perspectives for efficient expression and engineering of gRNAs with a goal to facilitate CRISPR/Cas-based multiplex genome editing.
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5
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Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, Bader JS, Yun C, Boeke JD. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nat Struct Mol Biol 2020; 27:179-191. [PMID: 32042152 PMCID: PMC7082080 DOI: 10.1038/s41594-020-0374-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is the only autonomous retrotransposon active in human cells. Different host factors have been shown to influence L1 mobility however, systematic analyses of these factors are limited. Here, we developed a high-throughput microscopy-based retrotransposition assay that identified the Double-Stranded Break (DSB) repair and Fanconi Anemia factors active in the S/G2 phase as potent inhibitors and regulators of L1 activity. In particular BRCA1, an E3 ubiquitin ligase with a key role in several DNA repair pathways, directly affects L1 retrotransposition frequency and structure and also plays a distinct role in controlling L1 ORF2 protein translation through L1 mRNA binding. These results suggest the existence of a “battleground” at the DNA replication fork between HR factors and L1 retrotransposons, and revealing a potential role for L1 in the genotypic evolution of tumors characterized by BRCA1 and HR repair deficiencies.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Cellarity Inc., Cambridge, MA, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David J Kahler
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA.,Planet Pharma, Boston, MA, USA
| | - Donghui Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Flagship VL58, Inc., Cambridge, MA, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chi Yun
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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6
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Adney EM, Ochmann MT, Sil S, Truong DM, Mita P, Wang X, Kahler DJ, Fenyö D, Holt LJ, Boeke JD. Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function. Genetics 2019; 213:1401-1414. [PMID: 31666291 PMCID: PMC6893370 DOI: 10.1534/genetics.119.302601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a "copy-and-paste" mechanism. ORF1p is an RNA-binding protein, and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication, and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p; only 16% of trialanine mutants retained near-wild-type (WT) activity. All ORF1p mutants formed near-WT levels of mRNA transcripts and 75% formed near-WT levels of protein. Two ORF1p mutants presented a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins, and target DNA throughout the L1 life cycle.
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Affiliation(s)
- Emily M Adney
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Matthias T Ochmann
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Srinjoy Sil
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - David M Truong
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Paolo Mita
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Xuya Wang
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - David J Kahler
- High Throughput Biology Laboratory, NYU Langone Health, New York 10016
| | - David Fenyö
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Liam J Holt
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York 10016
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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7
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Kurata M, Wolf NK, Lahr WS, Weg MT, Kluesner MG, Lee S, Hui K, Shiraiwa M, Webber BR, Moriarity BS. Highly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays. PLoS One 2018; 13:e0198714. [PMID: 30222773 PMCID: PMC6141065 DOI: 10.1371/journal.pone.0198714] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
The CRISPR/Cas9 system is an RNA guided nuclease system that evolved as a mechanism of adaptive immunity in bacteria. This system has been adopted for numerous genome engineering applications in research and recently, therapeutics. The CRISPR/Cas9 system has been largely implemented by delivery of Cas9 as protein, RNA, or plasmid along with a chimeric crRNA-tracrRNA guide RNA (gRNA) under the expression of a pol III promoter, such as U6. Using this approach, multiplex genome engineering has been achieved by delivering several U6-gRNA plasmids targeting multiple loci. However, this approach is limited due to the efficiently of delivering multiple plasmids to a single cell at one time. To augment the capability and accessibility of multiplexed genome engineering, we developed an efficient golden gate based method to assemble gRNAs linked by optimal Csy4 ribonuclease sequences to deliver up to 10 gRNAs as a single gRNA array transcript. Here we report the optimal expression of our guide RNA array under a strong pol II promoter. This system can be implemented alongside the myriad of CRISPR applications, allowing users to model complex biological processes requiring numerous gRNAs.
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Affiliation(s)
- Morito Kurata
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Natalie K. Wolf
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Walker S. Lahr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Madison T. Weg
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Mitchell G. Kluesner
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Samantha Lee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Kai Hui
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States of America
| | - Masano Shiraiwa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Beau R. Webber
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Branden S. Moriarity
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States of America
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
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8
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Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD. LINE-1 protein localization and functional dynamics during the cell cycle. eLife 2018; 7:30058. [PMID: 29309036 PMCID: PMC5821460 DOI: 10.7554/elife.30058] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 01/04/2018] [Indexed: 01/12/2023] Open
Abstract
LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition. Only two percent of our genetic material or genome are occupied by genes, while between 60-70 percent are made up of hundreds of thousands of copies of very similar DNA sequences. These repetitive sequences evolved from genetic elements called transposons. Transposons are often referred to as ‘jumping genes’, as they can randomly move within the genome and thereby create dangerous mutations that may lead to cancer or other genetic diseases. LINE-1 is the only remaining active transposon in humans, and it expands by copying and pasting itself to new locations via a process called 'retrotransposition'. To do so, it is first transcribed into RNA – the molecules that help to make proteins – and then converted back into identical DNA sequences. Previous research has shown that LINE-1 can form complexes with a series of proteins, including the two encoded by LINE-1 RNA itself: ORF1p and ORF2p. The LINE-1 complexes can enter the nucleus of the cell and insert a new copy of LINE-1 into the genome. However, until now it was not known how they do this. To investigate this further, Mita et al. used human cancer cells grown in the lab and tracked LINE-1 during the different stages of the cell cycle. The results showed that LINE-1 enters the nucleus as the cell starts to divide and the membrane of the nucleus breaks down. The LINE-1 complexes are then retained in the nucleus while the membrane of the nucleus reforms. Later, as the cell duplicates its genetic material, LINE-1 starts to copy and paste itself. Mita et al., together with another group of researchers, also found that during this process, only LINE-1 RNA and ORF2p were found in the nucleus. This shows that the cell cycle dictates both where the LINE-1 complexes gather and when LINE-1 is active. A next step will be to further investigate how the ‘copy and paste’ mechanisms of LINE-1 and the two LINE-1 proteins are regulated during the cell cycle. In future, this may help to identify LINE-1’s role in processes like aging or in diseases such as cancer.
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Affiliation(s)
- Paolo Mita
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Aleksandra Wudzinska
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Xiaoji Sun
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Joshua Andrade
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - Shruti Nayak
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - David J Kahler
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - Sana Badri
- Department of Pathology, NYU Langone Health, New York, United States
| | - John LaCava
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Beatrix Ueberheide
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Proteomics laboratory, NYU Langone Health, New York, United States
| | - Chi Y Yun
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - David Fenyö
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Jef D Boeke
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
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9
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Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J. Dissection of affinity captured LINE-1 macromolecular complexes. eLife 2018; 7:30094. [PMID: 29309035 PMCID: PMC5821459 DOI: 10.7554/elife.30094] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mass spectrometry, and next generation RNA sequencing, we have characterized the proteins and nucleic acids associated with distinctive, enzymatically active L1 macromolecular complexes. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in target-primed reverse transcription.
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Affiliation(s)
- Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Paolo Mita
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Emily M Adney
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Aleksandra Wudzinska
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sana Badri
- Department of Pathology, NYU Langone Health, New York, United States
| | - Dmitry Ischenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - George Eng
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Kathleen H Burns
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | | | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
| | - John LaCava
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States.,Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
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10
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Site-specific chromosomal gene insertion: Flp recombinase versus Cas9 nuclease. Sci Rep 2017; 7:17771. [PMID: 29259215 PMCID: PMC5736728 DOI: 10.1038/s41598-017-17651-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/24/2017] [Indexed: 12/16/2022] Open
Abstract
Site-specific recombination systems like those based on the Flp recombinase proved themselves as efficient tools for cell line engineering. The recent emergence of designer nucleases, especially RNA guided endonucleases like Cas9, has considerably broadened the available toolbox for applications like targeted transgene insertions. Here we established a recombinase-mediated cassette exchange (RMCE) protocol for the fast and effective, drug-free isolation of recombinant cells. Distinct fluorescent protein patterns identified the recombination status of individual cells. In derivatives of a CHO master cell line the expression of the introduced transgene of interest could be dramatically increased almost 20-fold by subsequent deletion of the fluorescent protein gene that provided the initial isolation principle. The same master cell line was employed in a comparative analysis using CRISPR/Cas9 for transgene integration in identical loci. Even though the overall targeting efficacy was comparable, multi-loci targeting was considerably more effective for Cas9-mediated transgene insertion when compared to RMCE. While Cas9 is inherently more flexible, our results also alert to the risk of aberrant recombination events around the cut site. Together, this study points at the individual strengths in performance of both systems and provides guidance for their appropriate use.
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11
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Li S, Ma L, Ou M, Feng J, Liao Y, Wang G, Tang L. A novel inducible lentiviral system for multi-gene expression with human HSP70 promoter and tetracycline-induced promoter. Appl Microbiol Biotechnol 2017; 101:3689-3702. [PMID: 28160047 DOI: 10.1007/s00253-017-8132-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 01/04/2023]
Abstract
Despite lentiviral system's predominance, its ultimate potential for gene therapy has not been fully exploited. Currently, most lentivirus vectors are non-inducible expression system or single-gene-induced system, which limits the extensive application in gene therapy. In this study, we designed a novel lentiviral vector containing HSP70 promoter and TRE promoter. Compared to traditional lentiviral vectors and inducible vectors, our controllable system has many advantages. Firstly, it contains multiple gene or shRNA targets. Secondly, genes expression is on/off in response to heat shock and DOX induction in time of need respectively with high effectivity and sensitivity. Thirdly, TRE promoter and HSP70 promoter can work with no interference from each other in the same inducible lentiviral vector. In addition, our study also shows that our novel vector has a higher downstream gene expression efficiency than co-transfection method and can co-position multi-genes in single cell effectively. Finally, we propose four derived models based on our vector at the end, which may be useful in biological research and clinical research in the future. Therefore, we believe that this novel lentiviral system could be promising in gene therapy for tumor.
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Affiliation(s)
- Shun Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China
| | - Lunkun Ma
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China
| | - Mengting Ou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China
| | - Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, 646000, China
| | - Yi Liao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400044, China
| | - Guixue Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, 400044, China.
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Gebert J, Schnölzer M, Warnken U, Kopitz J. Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression. Methods Enzymol 2016; 585:295-327. [PMID: 28109436 DOI: 10.1016/bs.mie.2016.09.022] [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] [Indexed: 01/10/2023]
Abstract
Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified.
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Affiliation(s)
- J Gebert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - U Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Kopitz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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13
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Metabolic Disorders in the Transition Period Indicate that the Dairy Cows' Ability to Adapt is Overstressed. Animals (Basel) 2015; 5:978-1020. [PMID: 26479480 PMCID: PMC4693199 DOI: 10.3390/ani5040395] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/22/2015] [Accepted: 09/25/2015] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Metabolic disorders are a key problem in the transition period of dairy cows and often appear before the onset of further health problems. Problems derive from difficulties animals have to adapt to large variations and disturbances occurring both outside and inside the organism. A lack of success in solving these issues may be due to predominant approaches in farm management and agricultural science, dealing with such disorders as merely negative side effects. Instead, a successful adaptation of animals to their living conditions should be seen as an important end in itself. Both farm management and agricultural sciences should support animals in their ability to cope with nutritional and metabolic challenges by employing a functional and result-driven approach. Abstract Metabolic disorders are a key problem in the transition period of dairy cows and often appear before the onset of further health problems. They mainly derive from difficulties the animals have in adapting to changes and disturbances occurring both outside and inside the organisms and due to varying gaps between nutrient supply and demand. Adaptation is a functional and target-oriented process involving the whole organism and thus cannot be narrowed down to single factors. Most problems which challenge the organisms can be solved in a number of different ways. To understand the mechanisms of adaptation, the interconnectedness of variables and the nutrient flow within a metabolic network need to be considered. Metabolic disorders indicate an overstressed ability to balance input, partitioning and output variables. Dairy cows will more easily succeed in adapting and in avoiding dysfunctional processes in the transition period when the gap between nutrient and energy demands and their supply is restricted. Dairy farms vary widely in relation to the living conditions of the animals. The complexity of nutritional and metabolic processes and their large variations on various scales contradict any attempts to predict the outcome of animals’ adaptation in a farm specific situation. Any attempts to reduce the prevalence of metabolic disorders and associated production diseases should rely on continuous and comprehensive monitoring with appropriate indicators on the farm level. Furthermore, low levels of disorders and diseases should be seen as a further significant goal which carries weight in addition to productivity goals. In the long run, low disease levels can only be expected when farmers realize that they can gain a competitive advantage over competitors with higher levels of disease.
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Jarosinski KW, Vautherot JF. Differential expression of Marek's disease virus (MDV) late proteins during in vitro and in situ replication: role for pUL47 in regulation of the MDV UL46-UL49 gene locus. Virology 2015; 484:213-226. [PMID: 26117307 DOI: 10.1016/j.virol.2015.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 05/25/2015] [Accepted: 06/08/2015] [Indexed: 12/23/2022]
Abstract
Marek's disease virus (MDV) is a lymphotropic alphaherpesvirus that replicates in a highly cell-associated manner in vitro. Production of infectious cell-free virus only occurs in feather follicle epithelial (FFE) cells of infected chicken skins. Previously, we described differential expression for a core alphaherpesvirus protein, pUL47 that was found to be abundantly expressed in FFE cells of infected chickens, while barely detectable during in vitro propagation. Here, we further examined the dynamics of expression of four tegument proteins within the UL46-49 locus during in vitro and in situ replication. All four proteins examined were expressed abundantly in situ, whereas both pUL47 and pUL48 expression were barely detectable in vitro. Replacement of the putative UL47 and UL48 promoters with the minimal cytomegalovirus promoter enhanced mRNA and protein expression in vitro. Interestingly, enhanced expression of pUL47 resulted in increased UL46, UL48, and UL49 transcripts that resulted in increased pUL46 and pUL48 expression.
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Affiliation(s)
- Keith W Jarosinski
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa, IA, USA.
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15
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Heinz N, Hennig K, Loew R. Graded or threshold response of the tet-controlled gene expression: all depends on the concentration of the transactivator. BMC Biotechnol 2013; 13:5. [PMID: 23336718 PMCID: PMC3556329 DOI: 10.1186/1472-6750-13-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 01/14/2013] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Currently, the step-wise integration of tet-dependent transactivator and tet-responsive expression unit is considered to be the most promising tool to achieve stable tet-controlled gene expression in cell populations. However, disadvantages of this strategy for integration into primary cells led us to develop an "All-In-One" vector system, enabling simultaneous integration of both components. The effect on tet-controlled gene expression was analyzed for retroviral "All-In-One" vectors expressing the M2-transactivator either under control of a constitutive or a new type of autoregulated promoter. RESULTS Determination of luciferase activity in transduced cell populations indicated improvement of the dynamic range of gene expression for the autoregulated system. Further differences were observed regarding induction kinetics and dose-response. Most notably, introduction of the autoregulated system resulted in a threshold mode of induction, whereas the constitutive system exhibited pronounced effector-dose dependence. CONCLUSION Tet-regulated gene expression in the applied autoregulated system resembles a threshold mode, whereby full induction of the tet-unit can be achieved at otherwise limiting doxycycline concentrations.
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Botezatu L, Sievers S, Gama-Norton L, Schucht R, Hauser H, Wirth D. Genetic aspects of cell line development from a synthetic biology perspective. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:251-284. [PMID: 22068842 DOI: 10.1007/10_2011_117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Animal cells can be regarded as factories for the production of relevant proteins. The advances described in this chapter towards the development of cell lines with higher productivity capacities, certain metabolic and proliferation properties, reduced apoptosis and other features must be regarded in an integrative perspective. The systematic application of systems biology approaches in combination with a synthetic arsenal for targeted modification of endogenous networks are proposed to lead towards the achievement of a predictable and technologically advanced cell system with high biotechnological impact.
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Affiliation(s)
- L Botezatu
- Helmholtz Centre for Infection Research, Braunschweig, Germany
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17
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Nie L, Thakur MD, Wang Y, Su Q, Zhao Y, Feng Y. Regulation of U6 promoter activity by transcriptional interference in viral vector-based RNAi. GENOMICS PROTEOMICS & BIOINFORMATICS 2011; 8:170-9. [PMID: 20970745 PMCID: PMC5054135 DOI: 10.1016/s1672-0229(10)60019-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The direct negative impact of the transcriptional activity of one component on the second one in cis is referred to as transcriptional interference (TI). U6 is a type III RNA polymerase III promoter commonly used for driving small hairpin RNA (shRNA) expression in vector-based RNAi. In the design and construction of viral vectors, multiple transcription units may be arranged in close proximity in a space-limited vector. Determining if U6 promoter activity can be affected by TI is critical for the expression of target shRNA in gene therapy or loss-of-function studies. In this research, we designed and implemented a modified retroviral system where shRNA and exogenous gene expressions were driven by two independent transcriptional units. We arranged U6 promoter driving shRNA expression and UbiC promoter in two promoter arrangements. In primary macrophages, we found U6 promoter activity was inhibited by UbiC promoter when in the divergent arrangement but not in tandem. In contrast, PKG promoter had no such negative impact. Instead of enhancing U6 promoter activity, CMV enhancer had significant negative impact on U6 promoter activity in the presence of UbiC promoter. Our results indicate that U6 promoter activity can be affected by TI in a proximal promoter-specific and arrangement-dependent manner.
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Affiliation(s)
- Linghu Nie
- Key Laboratory of Genome Sciences and Information, Cancer Biology and Genetics Group, Beijing Institute of Genomics, Chinese Acadamy of Sciences, Beijing 100029, China
| | - Meghna Das Thakur
- Departments of Medicine and Cell Biology, Washington University, St. Louis, MO 63110, USA
| | - Yumei Wang
- Departments of Medicine and Cell Biology, Washington University, St. Louis, MO 63110, USA
| | - Qin Su
- Immunocore Limited, Abingdon, Oxon OX14 4RX, UK
| | - Yongliang Zhao
- Key Laboratory of Genome Sciences and Information, Cancer Biology and Genetics Group, Beijing Institute of Genomics, Chinese Acadamy of Sciences, Beijing 100029, China
| | - Yunfeng Feng
- Departments of Medicine and Cell Biology, Washington University, St. Louis, MO 63110, USA
- Corresponding author.
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18
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Bagh S, Mandal M, McMillen DR. Minimal genetic device with multiple tunable functions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:021911. [PMID: 20866841 DOI: 10.1103/physreve.82.021911] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 07/21/2010] [Indexed: 05/29/2023]
Abstract
The ability to design artificial genetic devices with predictable functions is critical to the development of synthetic biology. Given the highly variable requirements of biological designs, the ability to tune the behavior of a genetic device is also of key importance; such tuning will allow devices to be matched with other components into larger systems, and to be shifted into the correct parameter regimes to elicit desired behaviors. Here, we have developed a minimal synthetic genetic system that acts as a multifunction, tunable biodevice in the bacterium Escherichia coli. First, it acts as a biochemical AND gate, sensing the extracellular small molecules isopropyl β-D -1-thiogalactopyranoside and anhydrotetracycline as two input signals and expressing enhanced green fluorescent protein as an output signal. Next, the output signal of the AND gate can be amplified by the application of another extracellular chemical, arabinose. Further, the system can generate a wide range of chemically tunable single input-output response curves, without any genetic alteration of the circuit, by varying the concentrations of a set of extracellular small molecules. We have developed and parameterized a simple transfer function model for the system, and shown that the model successfully explains and predicts the quantitative relationships between input and output signals in the system.
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Affiliation(s)
- Sangram Bagh
- Department of Chemical and Physical Sciences, Institute for Optical Sciences, University of Toronto Mississauga, Ontario, Canada
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19
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Development of a BAC vector for integration-independent and tight regulation of transgenes in rodents via the Tet system. Transgenic Res 2010; 20:709-20. [PMID: 20640885 DOI: 10.1007/s11248-010-9427-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 07/03/2010] [Indexed: 01/02/2023]
Abstract
The establishment of functional transgenic mouse lines is often limited by problems caused by integration site effects on the expression construct. Similarly, tetracycline (Tet) controlled transcription units most commonly used for conditional transgene expression in mice are strongly influenced by their genomic surrounding. Using bacterial artificial chromosome (BAC) technology in constitutive expression systems, it has been shown that integration site effects resulting in unwanted expression patterns can be largely eliminated. Here we describe a strategy to minimize unfavourable integration effects on conditional expression constructs based on a 75 kb genomic BAC fragment. This fragment was derived from a transgenic mouse line, termed LC-1, which carries the Tet-inducible genes luciferase and cre (Schönig et al. 2002). Animals of this mouse line have previously been shown to exhibit optimal expression properties in terms of tightness in the off state and the absolute level of induction, when mated to appropriate transactivator expressing mice. Here we report the cloning and identification of the transgenic LC-1 integration site which was subsequently inserted into a bacterial artificial chromosome. We demonstrate that this vector facilitates the efficient generation of transgenic mouse and rat lines, where the Tet-controlled expression unit is shielded from perturbations caused by the integration site.
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20
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Nehlsen K, Schucht R, da Gama-Norton L, Krömer W, Baer A, Cayli A, Hauser H, Wirth D. Recombinant protein expression by targeting pre-selected chromosomal loci. BMC Biotechnol 2009; 9:100. [PMID: 20003421 PMCID: PMC2804664 DOI: 10.1186/1472-6750-9-100] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 12/14/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recombinant protein expression in mammalian cells is mostly achieved by stable integration of transgenes into the chromosomal DNA of established cell lines. The chromosomal surroundings have strong influences on the expression of transgenes. The exploitation of defined loci by targeting expression constructs with different regulatory elements is an approach to design high level expression systems. Further, this allows to evaluate the impact of chromosomal surroundings on distinct vector constructs. RESULTS We explored antibody expression upon targeting diverse expression constructs into previously tagged loci in CHO-K1 and HEK293 cells that exhibit high reporter gene expression. These loci were selected by random transfer of reporter cassettes and subsequent screening. Both, retroviral infection and plasmid transfection with eGFP or antibody expression cassettes were employed for tagging. The tagged cell clones were screened for expression and single copy integration. Cell clones producing > 20 pg/cell in 24 hours could be identified. Selected integration sites that had been flanked with heterologous recombinase target sites (FRTs) were targeted by Flp recombinase mediated cassette exchange (RMCE). The results give proof of principle for consistent protein expression upon RMCE. Upon targeting antibody expression cassettes 90-100% of all resulting cell clones showed correct integration. Antibody production was found to be highly consistent within the individual cell clones as expected from their isogenic nature. However, the nature and orientation of expression control elements revealed to be critical. The impact of different promoters was examined with the tag-and-targeting approach. For each of the chosen promoters high expression sites were identified. However, each site supported the chosen promoters to a different extent, indicating that the strength of a particular promoter is dominantly defined by its chromosomal context. CONCLUSION RMCE provides a powerful method to specifically design vectors for optimized gene expression with high accuracy. Upon considering the specific requirements of chromosomal sites this method provides a unique tool to exploit such sites for predictable expression of biotechnologically relevant proteins such as antibodies.
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21
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Powell A, Dupré J. From molecules to systems: the importance of looking both ways. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2009; 40:54-64. [PMID: 19268874 DOI: 10.1016/j.shpsc.2008.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype-phenotype relations had become apparent. Against this background we outline how a range of scientific developments and conceptual considerations can be regarded as enabling and perhaps necessitating contemporary systems approaches. We suggest that philosophical ideas have a valuable part to play in making sense of complex scientific and disciplinary issues.
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Affiliation(s)
- Alexander Powell
- ESRC Centre for Genomics in Society, University of Exeter, Byrne House, St German's Road, Exeter, Devon EX4 4PJ, UK.
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22
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Yang Y, Ho SCL, Yap MGS. Mutated polyadenylation signals for controlling expression levels of multiple genes in mammalian cells. Biotechnol Bioeng 2009; 102:1152-60. [PMID: 18973284 DOI: 10.1002/bit.22152] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A set of mutated SV40 early polyadenylation signals (SV40pA) with varying strengths is generated by mutating the AATAAA sequence in the wild-type SV40pA. They are shown to control the expression level of a gene over a 10-fold range using luciferase reporter genes in transient transfection assays. The relative strength of these SV40pA variants remains similar under three commonly used mammalian promoters and in five mammalian cell lines. Application of SV40pA variants for controlling expression level of multiple genes is demonstrated in a study of monoclonal antibody (mAb) synthesis in mammalian cells. By using SV40pA variants of different strengths, the expression of light chain (LC) and heavy chain (HC) genes encoded in a single vector is independently altered which results in different ratios of LC to HC expression spanning a range from 0.24 to 16.42. The changes in gene expression are determined by measuring mRNA levels and intracellular LC and HC polypeptides. It is found that a substantial decrease of HC expression, which increases the LC/HC mRNA ratio, only slightly reduces mAb production. However, reducing the LC expression by a similar magnitude, which decreases the LC/HC mRNA ratio results in a sharp decline of mAb production to trace amounts. This set of SV40pA variants offers a new tool for accurate control of the relative expression levels of multiple genes. It will have wide-ranging applications in fields related to the study of biosynthesis of multi-subunit proteins, proteomic research on protein interactions, and multi-gene metabolic engineering.
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Affiliation(s)
- Yuansheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore.
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Franck E, Hulsen T, Huynen MA, de Jong WW, Lubsen NH, Madsen O. Evolution of closely linked gene pairs in vertebrate genomes. Mol Biol Evol 2008; 25:1909-21. [PMID: 18566020 DOI: 10.1093/molbev/msn136] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos). We show here that a lack of head-to-tail (h2t) gene duos is an even more distinctive characteristic of mammalian genomes, with the platypus genome as the only exception. In nonmammalian vertebrate and in nonvertebrate genomes, the frequency of h2h, h2t, and tail-to-tail (t2t) gene duos is close to random. In tetrapod genomes, the h2t and t2t gene duos are more likely to be part of a larger gene cluster of closely spaced genes than h2h gene duos; in fish and urochordate genomes, the reverse is seen. In human and mouse tissues, the expression profiles of gene duos were skewed toward positive coexpression, irrespective of orientation. The organization of orthologs of both members of about 40% of the human gene duos could be traced in other species, enabling a prediction of the organization at the branch points of gnathostomes, tetrapods, amniotes, and euarchontoglires. The accumulation of h2h gene duos started in tetrapods, whereas that of h2t and t2t gene duos only started in amniotes. The apparent lack of evolutionary conservation of h2t and t2t gene duos relative to that of h2h gene duos is thus a result of their relatively late origin in the lineage leading to mammals; we show that once they are formed h2t and t2t gene duos are as stable as h2h gene duos.
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Affiliation(s)
- Erik Franck
- Biomolecular Chemistry, 271 Nijmegen Center of Molecular Life Science, Radboud University Nijmegen, Nijmegen, The Netherlands
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Wirth D, Gama-Norton L, Riemer P, Sandhu U, Schucht R, Hauser H. Road to precision: recombinase-based targeting technologies for genome engineering. Curr Opin Biotechnol 2007; 18:411-9. [PMID: 17904350 DOI: 10.1016/j.copbio.2007.07.013] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 07/30/2007] [Accepted: 07/31/2007] [Indexed: 02/07/2023]
Abstract
In the past years, recombinase-based approaches for integrating transgenes into defined chromosomal loci of mammalian cells have gained increasing attention. This method is attractive since it enables to precisely integrate transgenes of interest into pre-defined integration sites, thereby allowing to predict the expression properties of a genetically manipulated cell. This review focuses on the current state of targeting strategies including RMCE employing site-specific recombinases such as Cre, Flp and PhiC31. In particular, applications for protein expression, virus production, transgenic animals and chromosome engineering are described.
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Affiliation(s)
- Dagmar Wirth
- Helmholtz Centre for Infection Research, Department of Gene Regulation and Differentiation and Model Systems for Infection and Immunity, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
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25
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Klopotowska D, Strzadala L, Matuszyk J. Inducibility of doxycycline-regulated gene in neural and neuroendocrine cells strongly depends on the appropriate choice of a tetracycline-responsive promoter. Neurochem Int 2007; 52:221-9. [PMID: 17618706 DOI: 10.1016/j.neuint.2007.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 05/10/2007] [Accepted: 05/16/2007] [Indexed: 11/25/2022]
Abstract
Elucidation of the mechanisms underlying specific receptor activation of neural and neuroendocrine cells will require the establishment of cellular systems that permit the regulation of the expression of the protein of interest. In a tetracycline (Tet)-regulated system, the gene encoding the protein of interest is under the control of a Tet promoter and its transcription is activated in the presence of doxycycline (Dox) by the Tet transactivator rtTA. Acceptable inducibility of the gene's expression requires a high level of its expression in the presence of Dox and a minimal basal expression in the absence of Dox. Two Tet promoters are compared here, the original PhCMV*-1 and the second-generation Ptight, with respect to the inducibility of the gene of interest in neuroendocrine and neural cells genetically engineered to express rtTA, namely PC12-Tet-On cells and MB-G-18 cells (mouse brain-derived cells with the phenotype of neuron-restricted precursors). This study demonstrates that the use of Ptight provided a much higher Dox-induced maximal expression in both cell lines, while the basal activities of the two Tet promoters were at similar levels. The additional use of the Tet-controlled silencer (tTS) caused almost complete abrogation of the leakiness of the Ptight promoter and an increase in the inducibility of the regulated gene, but the maximal levels of gene expression driven in the presence of Dox were also markedly reduced.
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Affiliation(s)
- Dagmara Klopotowska
- Department of Experimental Oncology, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
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