1
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Li Y, Pinones M, Breeland A, Jiang P. Single-round QuikChange PCR for engineering multiple site-directed mutations in plasmid DNA. Anal Biochem 2024:115621. [PMID: 39019205 DOI: 10.1016/j.ab.2024.115621] [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: 04/16/2024] [Revised: 06/08/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
Mutational study is a cornerstone methodology in biochemistry and genetics, and many mutagenesis strategies have been invented to promote the efficiency of gene engineering. In this study, we developed a simple and timesaving approach to integrate simultaneous mutagenesis at discrete sites. By using plasmid as a template and compatible oligonucleotide primers per the QuikChange strategy, our method was able to introduce multiple nucleotide insertions, deletions and replacements in one round of polymerase chain reaction. The longest insertion and deletion were achieved with 28 bp and 16 bp mismatch respectively. For minor nucleotide replacements (mismatch no more than 4 bp), mutations were achieved at up to 4 discrete locations. Usually, a successful clone with all desired mutations was found by screening 5 colonies. Clones with a subset of mutations may be stocked into the library of mutants or used as templates in the next rounds of mutagenic PCR to accomplish the entire construction project. This method can be applied to build up a combinatory library of mutants through saturation mutagenesis at multiple sites. It is promising to facilitate the research of protein biochemistry, forward genetics and synthetic biology.
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Affiliation(s)
- Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, TX 76204 USA.
| | - Mileina Pinones
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, TX 76204 USA
| | - Alexis Breeland
- Division of Biology, Texas Woman's University, Denton, TX 76204 USA
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409 USA
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2
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Zhao Y, Coelho C, Lauer S, Majewski M, Laurent JM, Brosh R, Boeke JD. CREEPY: CRISPR-mediated editing of synthetic episomes in yeast. Nucleic Acids Res 2023:gkad491. [PMID: 37326023 PMCID: PMC10359617 DOI: 10.1093/nar/gkad491] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
Use of synthetic genomics to design and build 'big' DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, introducing designer variations to episomal assemblies with high efficiency and fidelity remains challenging. Here we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, a method for rapid engineering of large synthetic episomal DNA constructs. We demonstrate that CRISPR editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes. We optimize CREEPY for efficient and precise multiplex editing of >100 kb yeast episomes, providing an expanded toolkit for synthetic genomics.
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Affiliation(s)
- Yu Zhao
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Camila Coelho
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Miłosz Majewski
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
- Maastricht Science Programme, Maastricht University, Maastricht6200MD, The Netherlands
| | - Jon M Laurent
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY11201, USA
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3
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Wen K, Resch MD, Mazboudi R, Mulhall Maasz H, Galarza JM. Novel and efficient method for the reconstruction of adenoviruses through isothermal assembly and its potential applications. FRONTIERS IN MEDICAL TECHNOLOGY 2023; 5:1095198. [PMID: 36776626 PMCID: PMC9909595 DOI: 10.3389/fmedt.2023.1095198] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023] Open
Abstract
Adenovirus based vectors are useful tools for vaccine development, gene therapy, and oncolytic virotherapy. Here we describe a novel approach for the genetic engineering of any portion of the adenovirus genome and the reconstruction of either fully replication competent or defective virions. This innovative strategy is rapid, effective and suitable for the manipulation of the entire genome broadening the spectrum of potential applications for the adenovirus system. Our strategy involved insertion of restriction enzyme recognition sequences absent in the native virus into the termini of the adenovirus genome in order to facilitate recovery. These restriction enzyme sites, together with the two inverted terminal repeats and packaging sequences, were synthesized and then subcloned into the pBR322 vector. The remaining internal portion of the adenovirus genome was separated and amplified via PCR into six segments, of which groups of two were joined together by PCR and then subcloned into pBR322 plasmids. During the PCR reaction, an overlap of 30-40 bp was added to the termini of the adjacent fragments, allowing for the subsequent isothermal assembly and correct orientation of all fragments. This approach allows for the genetic modification of each genomic fragment according to the specific research goals, (e.g., deletion, substitution, addition, etc.) To recreate the entire viral genome, the four engineered fragments (each comprised of two adenovirus genomic sections) as well as the pBR322 backbone, were reassembled into a single construct utilizing an isothermal assembly reaction. Finally, the reassembled plasmid containing the entire genome was linearized and transfected into HEK293 cells to recover the complete reconstructed adenoviral vector. Using this approach, we have successfully generated two recombinant reporter adenoviruses, one of human adenovirus serotype 14 and another of serotype 55. The E3 region was replaced by the reporter genes (GFP and Luciferase) to visualize and track the recovery process. Subsequent infection of A549 cells with these reconstructed adenovirus vectors demonstrated that they were replication competent. This method shortens the viral reconstruction process because the one-step isothermal assembly requires less than 4 days, and recombinant adenovirus recovery occurs within 10 days. This new method allows for single or multiple genetic modifications within any portion of the viral genome and can be used to construct or manipulate any adenovirus whose complete genome sequence is known.
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4
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OverFlap PCR: A reliable approach for generating plasmid DNA libraries containing random sequences without a template bias. PLoS One 2022; 17:e0262968. [PMID: 35939421 PMCID: PMC9359533 DOI: 10.1371/journal.pone.0262968] [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: 01/03/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022] Open
Abstract
Over the decades, practical biotechnology researchers have aimed to improve naturally occurring proteins and create novel ones. It is widely recognized that coupling protein sequence randomization with various effect screening methodologies is one of the most powerful techniques for quickly, efficiently, and purposefully acquiring these desired improvements. Over the years, considerable advancements have been made in this field. However, developing PCR-based or template-guided methodologies has been hampered by resultant template sequence biases. Here, we present a novel whole plasmid amplification-based approach, which we named OverFlap PCR, for randomizing virtually any region of plasmid DNA without introducing a template sequence bias.
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5
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Yakobov N, Mahmoudi N, Grob G, Yokokawa D, Saga Y, Kushiro T, Worrell D, Roy H, Schaller H, Senger B, Huck L, Riera Gascon G, Becker HD, Fischer F. RNA-dependent synthesis of ergosteryl-3β-O-glycine in Ascomycota expands the diversity of steryl-amino acids. J Biol Chem 2022; 298:101657. [PMID: 35131263 PMCID: PMC8913301 DOI: 10.1016/j.jbc.2022.101657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/11/2022] Open
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6
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Abstract
DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , , .,Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, NY 11201, USA
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7
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Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J. LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mob DNA 2019; 11:1. [PMID: 31892958 PMCID: PMC6937734 DOI: 10.1186/s13100-019-0191-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. RESULTS We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. CONCLUSIONS Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.
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Affiliation(s)
- Daniel Ardeljan
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Xuya Wang
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Martin S. Taylor
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - David Husband
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Jared P. Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Mikhail Gorbounov
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Brandon Sie
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - H. Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065 USA
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Zhi Li
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Wilson McKerrow
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - David Fenyö
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Kathleen H. Burns
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, 9713 AV The Netherlands
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8
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Lončar N, van Beek HL, Fraaije MW. Structure-Based Redesign of a Self-Sufficient Flavin-Containing Monooxygenase towards Indigo Production. Int J Mol Sci 2019; 20:ijms20246148. [PMID: 31817552 PMCID: PMC6940849 DOI: 10.3390/ijms20246148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/12/2022] Open
Abstract
Indigo is currently produced by a century-old petrochemical-based process, therefore it is highly attractive to develop a more environmentally benign and efficient biotechnological process to produce this timeless dye. Flavin-containing monooxygenases (FMOs) are able to oxidize a wide variety of substrates. In this paper we show that the bacterial mFMO can be adapted to improve its ability to convert indole into indigo. The improvement was achieved by a combination of computational and structure-inspired enzyme redesign. We showed that the thermostability and the kcat for indole could be improved 1.5-fold by screening a relatively small number of enzyme mutants. This project not only resulted in an improved biocatalyst but also provided an improved understanding of the structural elements that determine the activity of mFMO and provides hints for further improvement of the monooxygenase as biocatalyst.
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Affiliation(s)
| | - Hugo L. van Beek
- Molecular Enzymology group, University of Groningen, 9747 AG Groningen, The Netherlands;
| | - Marco W. Fraaije
- Molecular Enzymology group, University of Groningen, 9747 AG Groningen, The Netherlands;
- Correspondence: ; Tel.: +31-50-3634345
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9
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Xia Y, Li K, Li J, Wang T, Gu L, Xun L. T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 2019; 47:e15. [PMID: 30462336 PMCID: PMC6379645 DOI: 10.1093/nar/gky1169] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
The assembly of DNA fragments with homologous arms is becoming popular in routine cloning. For an in vitro assembly reaction, a DNA polymerase is often used either alone for its 3'-5' exonuclease activity or together with a 5'-3' exonuclease for its DNA polymerase activity. Here, we present a 'T5 exonuclease DNA assembly' (TEDA) method that only uses a 5'-3' exonuclease. DNA fragments with short homologous ends were treated by T5 exonuclease and then transformed into Escherichia coli to produce clone colonies. The cloning efficiency was similar to that of the commercial In-Fusion method employing a proprietary DNA polymerase, but higher than that of the Gibson method utilizing T5 exonuclease, Phusion DNA polymerase, and DNA ligase. It also assembled multiple DNA fragments and did simultaneous site-directed mutagenesis at multiple sites. The reaction mixture was simple, and each reaction used 0.04 U of T5 exonuclease that cost 0.25 US cents. The simplicity, cost effectiveness, and cloning efficiency should promote its routine use, especially for labs with a budget constraint. TEDA may trigger further development of DNA assembly methods that employ single exonucleases.
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Affiliation(s)
- Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Kai Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China.,School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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10
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Fürst MJLJ, Boonstra M, Bandstra S, Fraaije MW. Stabilization of cyclohexanone monooxygenase by computational and experimental library design. Biotechnol Bioeng 2019; 116:2167-2177. [PMID: 31124128 PMCID: PMC6836875 DOI: 10.1002/bit.27022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 12/23/2022]
Abstract
Enzymes often by far exceed the activity, selectivity, and sustainability achieved with chemical catalysts. One of the main reasons for the lack of biocatalysis in the chemical industry is the poor stability exhibited by many enzymes when exposed to process conditions. This dilemma is exemplified in the usually very temperature‐sensitive enzymes catalyzing the Baeyer–Villiger reaction, which display excellent stereo‐ and regioselectivity and offer a green alternative to the commonly used, explosive peracids. Here we describe a protein engineering approach applied to cyclohexanone monooxygenase from Rhodococcus sp. HI‐31, a substrate‐promiscuous enzyme that efficiently catalyzes the production of the nylon‐6 precursor ε‐caprolactone. We used a framework for rapid enzyme stabilization by computational libraries (FRESCO), which predicts protein‐stabilizing mutations. From 128 screened point mutants, approximately half had a stabilizing effect, albeit mostly to a small degree. To overcome incompatibility effects observed upon combining the best hits, an easy shuffled library design strategy was devised. The most stable and highly active mutant displayed an increase in unfolding temperature of 13°C and an approximately 33x increase in half‐life at 30°C. In contrast to the wild‐type enzyme, this thermostable 8x mutant is an attractive biocatalyst for biotechnological applications.
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Affiliation(s)
| | - Marjon Boonstra
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Selle Bandstra
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
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11
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Fürst MJLJ, Kerschbaumer B, Rinnofner C, Migglautsch AK, Winkler M, Fraaije MW. Exploring the Biocatalytic Potential of a Self‐Sufficient Cytochrome P450 from
Thermothelomyces thermophila. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Bianca Kerschbaumer
- Austrian Centre of Industrial Biotechnology (ACIB) Petersgasse 14 8010 Graz Austria
| | - Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB) Petersgasse 14 8010 Graz Austria
- Bisy e.U. Wetzawinkel 20 8200 Hofstätten/Raab Austria
| | - Anna K. Migglautsch
- Institute of Organic Chemistry, Graz University of TechnologyNAWI Graz 8010 Graz Austria
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology (ACIB) Petersgasse 14 8010 Graz Austria
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands
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12
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Abstract
Protein engineering has an array of uses: whether you are studying a disease mutation, removing undesirable sequences, adding stabilizing mutations for structural purposes, or simply dissecting protein function. Protein engineering is almost exclusively performed using site-directed mutagenesis (SDM) as this provides targeted modification of specific amino acids, as well as the option of rewriting the native sequence to include or exclude certain regions. Despite its widespread use, SDM has often proved to be a bottleneck, requiring precision manipulation on a sample-by-sample basis to make it work. When dealing with large volumes of samples it is not possible to use such a low-throughput approach. Here we describe a high-throughput (HTP) method for SDM, optimized and used by the Structural Genomics Consortium (SGC) to complement structural studies.
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Affiliation(s)
- Claire Strain-Damerell
- Diamond Light Source Ltd., The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
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13
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Fürst MJLJ, Romero E, Gómez Castellanos JR, Fraaije MW, Mattevi A. Side-Chain Pruning Has Limited Impact on Substrate Preference in a Promiscuous Enzyme. ACS Catal 2018; 8:11648-11656. [PMID: 30687578 PMCID: PMC6345240 DOI: 10.1021/acscatal.8b03793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/26/2018] [Indexed: 01/02/2023]
Abstract
![]()
Detoxifying
enzymes such as flavin-containing monooxygenases deal
with a huge array of highly diverse xenobiotics and toxic compounds.
In addition to being of high physiological relevance, these drug-metabolizing
enzymes are useful catalysts for synthetic chemistry. Despite the
wealth of studies, the molecular basis of their relaxed substrate
selectivity remains an open question. Here, we addressed this issue
by applying a cumulative alanine mutagenesis approach to cyclohexanone
monooxygenase from Thermocrispum municipale, a flavin-dependent
Baeyer–Villiger monooxygenase which we chose as a model system
because of its pronounced thermostability and substrate promiscuity.
Simultaneous removal of up to eight noncatalytic active-site side
chains including four phenylalanines had no effect on protein folding,
thermostability, and cofactor loading. We observed a linear decrease
in activity, rather than a selectivity switch, and attributed this
to a less efficient catalytic environment in the enlarged active-site
space. Time-resolved kinetic studies confirmed this interpretation.
We also determined the crystal structure of the enzyme in complex
with a mimic of the reaction intermediate that shows an unaltered
overall protein conformation. These findings led us to propose that
this cyclohexanone monooxygenase may lack a distinct substrate selection
mechanism altogether. We speculate that the main or exclusive function
of the protein shell in promiscuous enzymes might be the stabilization
and accessibility of their very reactive catalytic intermediates.
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Affiliation(s)
- Maximilian J. L. J. Fürst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | | | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
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14
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Sanganna Gari RR, Seelheim P, Marsh B, Kiessling V, Creutz CE, Tamm LK. Quaternary structure of the small amino acid transporter OprG from Pseudomonas aeruginosa. J Biol Chem 2018; 293:17267-17277. [PMID: 30237175 DOI: 10.1074/jbc.ra118.004461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/13/2018] [Indexed: 02/01/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that causes nosocomial infections. The P. aeruginosa outer membrane contains specific porins that enable substrate uptake, with the outer membrane protein OprG facilitating transport of small, uncharged amino acids. However, the pore size of an eight-stranded β-barrel monomer of OprG is too narrow to accommodate even the smallest transported amino acid, glycine, raising the question of how OprG facilitates amino acid uptake. Pro-92 of OprG is critically important for amino acid transport, with a P92A substitution inhibiting transport and the NMR structure of this variant revealing that this substitution produces structural changes in the barrel rim and restricts loop motions. OprG may assemble into oligomers in the outer membrane (OM) whose subunit interfaces could form a transport channel. Here, we explored the contributions of the oligomeric state and the extracellular loops to OprG's function. Using chemical cross-linking to determine the oligomeric structures of both WT and P92A OprG in native outer membranes and atomic force microscopy, and single-molecule fluorescence of the purified proteins reconstituted into lipid bilayers, we found that both protein variants form oligomers, supporting the notion that subunit interfaces in the oligomer could provide a pathway for amino acid transport. Furthermore, performing transport assays with loop-deleted OprG variants, we found that these variants also can transport small amino acids, indicating that the loops are not solely responsible for substrate transport. We propose that OprG functions as an oligomer and that conformational changes in the barrel-loop region might be crucial for its activity.
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Affiliation(s)
| | - Patrick Seelheim
- From the Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology and
| | - Brendan Marsh
- the Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 OWA, United Kingdom
| | - Volker Kiessling
- From the Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology and
| | - Carl E Creutz
- the Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908 and
| | - Lukas K Tamm
- From the Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology and
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15
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Fürst MJLJ, Martin C, Lončar N, Fraaije MW. Experimental Protocols for Generating Focused Mutant Libraries and Screening for Thermostable Proteins. Methods Enzymol 2018; 608:151-187. [PMID: 30173762 DOI: 10.1016/bs.mie.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many proteins are rapidly deactivated when exposed to high or even ambient temperatures. This cannot only impede the study of a particular protein, but also is one of the major reasons why enzyme catalysis is still widely unable to compete with established chemical processes. Furthermore, differences in protein stability are a challenge in synthetic biology, when individual modules prove to be incompatible. The targeted stabilization of proteins can overcome these hurdles, and protein engineering techniques are more and more reliably supported by computational chemistry tools. Accordingly, algorithms to predict the differences in folding energy of a mutant compared to the wild-type, ΔΔGfold, are used in the highly successful FRESCO workflow. The resulting single mutant prediction library consists typically of a few hundred amino acid exchanges, and after combining the most successful hits we so far obtained stabilized mutants which exhibited increases in apparent melting temperature of 20-35°C and showed vastly increased half-lives, as well as resistance to cosolvents. Here, we report a detailed protocol to generate these mutant libraries experimentally, covering the entire workflow from primer design, through mutagenesis, protein production and screening, to mutation combination strategies. The individual parts of the method are furthermore applicable to many other scenarios besides protein stabilization, and these protocols are valuable for any project requiring individual or semi high-throughput site-directed mutagenesis, protein expression and purification, or generation of mutant combination libraries.
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Affiliation(s)
- Max J L J Fürst
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Caterina Martin
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Nikola Lončar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marco W Fraaije
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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16
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Construction of Designer Selectable Marker Deletions with a CRISPR-Cas9 Toolbox in Schizosaccharomyces pombe and New Design of Common Entry Vectors. G3-GENES GENOMES GENETICS 2018; 8:789-796. [PMID: 29321167 PMCID: PMC5844300 DOI: 10.1534/g3.117.300363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Vectors encoding selectable markers have been widely used in yeast to maintain or express exogenous DNA fragments. In the fission yeast Schizosaccharomyces pombe, several engineered markers have been reported and widely used, such as ura4+ and ScLEU2 from Saccharomyces cerevisiae, which complement ura4 and leu1 mutations, respectively. These two auxotrophic markers share no homology with the S. pombe genome; however, most others can recombine with the genome due to sequence homology shared between the genomic and plasmid-borne copies of the markers. Here, we describe a CRISPR-Cas9 toolbox that can be used to quickly introduce "designer" auxotrophic marker deletions into host strains, including leu1-Δ0, his3-Δ0, and lys9-Δ0 Together with ura4-D18, this brings the total number of available designer deletion auxotrophic markers to four. The toolbox consists of a Cas9-gRNA expression vector and a donor DNA plasmid pair for each designer deletion. Using this toolbox, a set of auxotrophic S. pombe strains was constructed. Further, we reorganized essential components in the commonly used pREP series of plasmids and assembled the corresponding auxotrophic marker gene onto these plasmids. This toolbox for producing designer deletions, together with the newly developed strains and plasmids, will benefit the whole yeast community.
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17
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Wehrmann M, Klebensberger J. Engineering thermal stability and solvent tolerance of the soluble quinoprotein PedE from Pseudomonas putida KT2440 with a heterologous whole-cell screening approach. Microb Biotechnol 2018; 11:399-408. [PMID: 29239114 PMCID: PMC5812247 DOI: 10.1111/1751-7915.13036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/18/2017] [Accepted: 11/12/2017] [Indexed: 12/16/2022] Open
Abstract
Due to their ability for direct electron transfer to electrodes, the utilization of rare earth metals as cofactor, and their periplasmic localization, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) represent an interesting class of biocatalysts for various biotechnological applications. For most biocatalysts protein stability is crucial, either to increase the performance of the protein under a given process condition or to maximize robustness of the protein towards mutational manipulations, which are often needed to enhance or introduce a functionality of interest. In this study, we describe a whole-cell screening assay, suitable for probing PQQ-ADH activities in Escherichia coli BL21(DE3) cells, and use this assay to screen smart mutant libraries for increased thermal stability of the PQQ-ADH PedE (PP_2674) from Pseudomonas putida KT2440. Upon three consecutive rounds of screening, we identified three different amino acid positions, which significantly improve enzyme stability. The subsequent combination of the beneficial mutations finally results in the triple mutant R91D/E408P/N410K, which not only exhibits a 7°C increase in thermal stability but also a twofold increase in residual activity upon incubation with up to 50% dimethyl sulfoxide (DMSO), while showing no significant difference in enzymatic efficiency (kcat /KM ).
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Affiliation(s)
- Matthias Wehrmann
- Institute of Technical BiochemistryUniversity of StuttgartStuttgartGermany
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18
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Zeng F, Zhang S, Hao Z, Duan S, Meng Y, Li P, Dong J, Lin Y. Efficient strategy for introducing large and multiple changes in plasmid DNA. Sci Rep 2018; 8:1714. [PMID: 29379085 PMCID: PMC5789069 DOI: 10.1038/s41598-018-20169-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/15/2018] [Indexed: 12/15/2022] Open
Abstract
While the QuikChange site-directed mutagenesis method and its later modifications are extremely useful and simple, they suffer from several drawbacks. Here, we propose a new method, named LFEAP mutagenesis (Ligation of Fragment Ends After PCR) for creating various mutations in plasmid by leveraging three existing concepts: inverse PCR, single primer PCR, and sticky-end assembly. The first inverse PCR on the target plasmid yielded linearized DNA fragments with mutagenic ends, and a second single primer PCR resulted in complementary single-stranded DNA fragments with the addition of overhangs at the 5' end of each strand. The resulting single strands were then annealed to produce double-stranded DNA with free 5' single-stranded DNA tails. These products with compatible sticky ends were efficiently assembled into a circular, mutagenized plasmid. With this strategy, multiple simultaneous changes (up to 15) and mutations in large plasmids (up to 50 kb) were achieved with high efficiency and fidelity. LFEAP mutagenesis is a versatile method that offers significant advantages for introducing large and multiple changes in plasmid DNA.
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Affiliation(s)
- Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Suhua Zhang
- Institute of Biophysics, Hebei University of Technology, Tianjin, 300401, China
| | - Zhimin Hao
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Shixin Duan
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Yanan Meng
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Pan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China
| | - Jingao Dong
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, China.
| | - Yibin Lin
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin Street, Houston, TX, 77030, USA.
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19
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Kalva S, Boeke JD, Mita P. Gibson Deletion: a novel application of isothermal in vitro recombination. Biol Proced Online 2018; 20:2. [PMID: 29375275 PMCID: PMC5774033 DOI: 10.1186/s12575-018-0068-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/12/2018] [Indexed: 11/10/2022] Open
Abstract
Background Recombinant DNA technology is today a fundamental tool for virtually all biological research fields. Among the many techniques available for the construction of a “custom DNA” molecule, the isothermal in vitro assembly, or Gibson assembly, allows for an efficient, one-step, scarless recombination-based assembly. Results Here, we apply and characterize the use of Gibson assembly for the deletion of DNA sequences around a DNA cut. This method, that we named “Gibson Deletion”, can be used to easily substitute or delete one or more restriction sites within a DNA molecule. We show that Gibson Deletion is a viable method to delete up to 100 nucleotides from the DNA ends of a cleavage site. In addition, we found that Gibson Deletion can be performed using single strand DNA with the same efficiency as using double strand DNA molecules. Conclusions Gibson Deletion is a novel, easy and convenient application of isothermal in vitro assembly, that performs with high efficiency and can be implemented for a broad range of applications. Electronic supplementary material The online version of this article (10.1186/s12575-018-0068-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swara Kalva
- 1The Bronx High School of Science, 75 West 205 Street, Bronx, NY 10468 USA
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, Institute of Systems Genetics (ISG), New York, NY 10016 USA
| | - Paolo Mita
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, Institute of Systems Genetics (ISG), New York, NY 10016 USA
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20
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Chuang J, Boeke JD, Mitchell LA. Coupling Yeast Golden Gate and VEGAS for Efficient Assembly of the Violacein Pathway in Saccharomyces cerevisiae. Methods Mol Biol 2018; 1671:211-225. [PMID: 29170962 DOI: 10.1007/978-1-4939-7295-1_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability to express non-native pathways in genetically tractable model systems is important for fields such as synthetic biology, genetics, and metabolic engineering. Here we describe a modular and hierarchical strategy to assemble multigene pathways for expression in S. cerevisiae. First, discrete promoter, coding sequence, and terminator parts are assembled in vitro into Transcription Units (TUs) flanked by adapter sequences using "yeast Golden Gate" (yGG), a type IIS restriction enzyme-dependent cloning strategy. Next, harnessing the natural capacity of S. cerevisiae for homologous recombination, TUs are assembled into pathways and expressed using the "Versatile Genetic Assembly System" (VEGAS) in yeast. Coupling transcription units constructed by yGG with VEGAS assembly is a generic and flexible workflow to achieve pathway expression in S. cerevisiae. This protocol describes assembly of a five TU pathway for yeast production of violacein, a pigment derived from Chromobacterium violaceum.
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Affiliation(s)
- James Chuang
- Department of Biomedical, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jef D Boeke
- School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Leslie A Mitchell
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, 10016, USA.
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21
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QuickLib, a method for building fully synthetic plasmid libraries by seamless cloning of degenerate oligonucleotides. PLoS One 2017; 12:e0175146. [PMID: 28406948 PMCID: PMC5390991 DOI: 10.1371/journal.pone.0175146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/21/2017] [Indexed: 11/19/2022] Open
Abstract
Incorporation of synthetic degenerate oligonucleotides into plasmids for building highly diverse genetic libraries requires efficient and quantitative DNA manipulation. We present a fast and seamless method for generating libraries of PCR-synthesized plasmids designed with a degenerate sequence and short overlapping ends. Our method called QuickLib should find many applications in synthetic biology; as an example, we easily prepared genetic libraries of Escherichia coli expressing billions of different backbone cyclic peptides.
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22
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23
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Ikushima S, Boeke JD. New Orthogonal Transcriptional Switches Derived from Tet Repressor Homologues for Saccharomyces cerevisiae Regulated by 2,4-Diacetylphloroglucinol and Other Ligands. ACS Synth Biol 2017; 6:497-506. [PMID: 28005347 DOI: 10.1021/acssynbio.6b00205] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we describe the development of tightly regulated expression switches in yeast, by engineering distant homologues of Escherichia coli TetR, including the transcriptional regulator PhlF from Pseudomonas and others. Previous studies demonstrated that the PhlF protein bound its operator sequence (phlO) in the absence of 2,4-diacetylphloroglucinol (DAPG) but dissociated from phlO in the presence of DAPG. Thus, we developed a DAPG-Off system in which expression of a gene preceded by the phlO-embedded promoter was activated by a fusion of PhlF to a multimerized viral activator protein (VP16) domain in a DAPG-free environment but repressed when DAPG was added to growth medium. In addition, we constructed a DAPG-On system with the opposite behavior of the DAPG-Off system; i.e., DAPG triggers the expression of a reporter gene. Exposure of DAPG to yeast cells did not cause any serious deleterious effect on yeast physiology in terms of growth. Efforts to engineer additional Tet repressor homologues were partially successful and a known mammalian switch, the p-cumate switch based on CymR from Pseudomonas, was found to function in yeast. Orthogonality between the TetR (doxycycline), CamR (d-camphor), PhlF (DAPG), and CymR (p-cumate)-based Off switches was demonstrated by evaluating all 4 ligands against suitably engineered yeast strains. This study expands the toolbox of "On" and "Off" switches for yeast biotechnology.
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Affiliation(s)
- Shigehito Ikushima
- High
Throughput Biology Center and Department of Molecular Biology and
Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Central
Laboratories for Key Technologies, KIRIN Company Limited, Yokohama, Kanagawa 236-0004, Japan
| | - Jef D. Boeke
- High
Throughput Biology Center and Department of Molecular Biology and
Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, New York, New York 10016, United States
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24
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Zeng F, Zhang Y, Zhang Z, Malik AA, Lin Y. Multiple-site fragment deletion, insertion and substitution mutagenesis by modified overlap extension PCR. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1279033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Fanli Zeng
- College of Life Sciences, Agricultural University of Hebei, Baoding, P.R. China
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Medical School, and Center of Biophysics, Autonomous University of Barcelona, Barcelona, Spain
| | - Yujie Zhang
- College of Life Sciences, Agricultural University of Hebei, Baoding, P.R. China
| | - Ze Zhang
- College of Life Sciences, Agricultural University of Hebei, Baoding, P.R. China
| | - Asrar Ahmad Malik
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Medical School, and Center of Biophysics, Autonomous University of Barcelona, Barcelona, Spain
| | - Yibin Lin
- Biophysics Unit, Department of Biochemistry and Molecular Biology, Medical School, and Center of Biophysics, Autonomous University of Barcelona, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Houston Medical School, Houston, TX, USA
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25
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Liu W, Tuck LR, Wright JM, Cai Y. Using Purified Tyrosine Site-Specific Recombinases In Vitro to Rapidly Construct and Diversify Metabolic Pathways. Methods Mol Biol 2017; 1642:285-302. [PMID: 28815507 DOI: 10.1007/978-1-4939-7169-5_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The site-specific recombinase Cre was previously reported to have in vitro activity. Here, we describe the method of purifying two new tyrosine site-specific recombinases VCre and Dre along with Cre by nickel affinity chromatography. We proved the in vitro function of the VCre and Dre on their respective conditional recombination sites. We also developed a methodology to one-step construct and optimize the productivity of a biosynthetic pathway through the combinatorial integration of promoters into a plasmid-encoded pathway by simply incubating a DNA mixture with recombinase system at 37 °C in vitro.
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Affiliation(s)
- Wei Liu
- School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Laura R Tuck
- School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jon Marles Wright
- School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3BF, UK.
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Yizhi Cai
- School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3BF, UK.
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26
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Taniguchi N, Murakami H. Multiple Site-Directed and Saturation Mutagenesis by the Patch Cloning Method. Methods Mol Biol 2017; 1498:339-347. [PMID: 27709586 DOI: 10.1007/978-1-4939-6472-7_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Constructing protein-coding genes with desired mutations is a basic step for protein engineering. Herein, we describe a multiple site-directed and saturation mutagenesis method, termed MUPAC. This method has been used to introduce multiple site-directed mutations in the green fluorescent protein gene and in the moloney murine leukemia virus reverse transcriptase gene. Moreover, this method was also successfully used to introduce randomized codons at five desired positions in the green fluorescent protein gene, and for simple DNA assembly for cloning.
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Affiliation(s)
| | - Hiroshi Murakami
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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27
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Xu JZ, Zhang WG. Strategies used for genetically modifying bacterial genome: site-directed mutagenesis, gene inactivation, and gene over-expression. J Zhejiang Univ Sci B 2016; 17:83-99. [PMID: 26834010 DOI: 10.1631/jzus.b1500187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
With the availability of the whole genome sequence of Escherichia coli or Corynebacterium glutamicum, strategies for directed DNA manipulation have developed rapidly. DNA manipulation plays an important role in understanding the function of genes and in constructing novel engineering bacteria according to requirement. DNA manipulation involves modifying the autologous genes and expressing the heterogenous genes. Two alternative approaches, using electroporation linear DNA or recombinant suicide plasmid, allow a wide variety of DNA manipulation. However, the over-expression of the desired gene is generally executed via plasmid-mediation. The current review summarizes the common strategies used for genetically modifying E. coli and C. glutamicum genomes, and discusses the technical problem of multi-layered DNA manipulation. Strategies for gene over-expression via integrating into genome are proposed. This review is intended to be an accessible introduction to DNA manipulation within the bacterial genome for novices and a source of the latest experimental information for experienced investigators.
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Affiliation(s)
- Jian-zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wei-guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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28
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Mingo J, Erramuzpe A, Luna S, Aurtenetxe O, Amo L, Diez I, Schepens JTG, Hendriks WJAJ, Cortés JM, Pulido R. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections. PLoS One 2016; 11:e0160972. [PMID: 27548698 PMCID: PMC4993582 DOI: 10.1371/journal.pone.0160972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/27/2016] [Indexed: 12/30/2022] Open
Abstract
Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis.
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Affiliation(s)
- Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Asier Erramuzpe
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Sandra Luna
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Olaia Aurtenetxe
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Laura Amo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Ibai Diez
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Jan T. G. Schepens
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Wiljan J. A. J. Hendriks
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Jesús M. Cortés
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail: ;
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29
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García-Nafría J, Watson JF, Greger IH. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly. Sci Rep 2016; 6:27459. [PMID: 27264908 PMCID: PMC4893743 DOI: 10.1038/srep27459] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022] Open
Abstract
In vivo homologous recombination holds the potential for optimal molecular cloning, however, current strategies require specialised bacterial strains or laborious protocols. Here, we exploit a recA-independent recombination pathway, present in widespread laboratory E.coli strains, to develop IVA (In Vivo Assembly) cloning. This system eliminates the need for enzymatic assembly and reduces all molecular cloning procedures to a single-tube, single-step PCR, performed in <2 hours from setup to transformation. Unlike other methods, IVA is a complete system, and offers significant advantages over alternative methods for all cloning procedures (insertions, deletions, site-directed mutagenesis and sub-cloning). Significantly, IVA allows unprecedented simplification of complex cloning procedures: five simultaneous modifications of any kind, multi-fragment assembly and library construction are performed in approximately half the time of current protocols, still in a single-step fashion. This system is efficient, seamless and sequence-independent, and requires no special kits, enzymes or proprietary bacteria, which will allow its immediate adoption by the academic and industrial molecular biology community.
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Affiliation(s)
- Javier García-Nafría
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Jake F. Watson
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ingo H. Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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30
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Guo W, Sun S, Xie B, Zhu XJ, Dai ZM. T4 DNA polymerase improves the efficiency of multiple site-directed mutagenesis. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1170630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Wei Guo
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
| | - Shuhui Sun
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
| | - Binghua Xie
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
| | - Xiao-Jing Zhu
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
| | - Zhong-Min Dai
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China
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31
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Yang Y, Chi Y, Tang X, Ertl HCJ, Zhou D. Rapid, Efficient, and Modular Generation of Adenoviral Vectors via Isothermal Assembly. ACTA ACUST UNITED AC 2016; 113:16.26.1-16.26.18. [PMID: 31773916 DOI: 10.1002/0471142727.mb1626s113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adenoviral vectors have yielded promising results as carriers for gene transfer and vaccines in basic research and clinical applications. However, most common procedures to construct adenoviral vectors and manipulate adenovirus (Ad) genomes are complex and labor-intensive. An easy and detailed protocol for the rapid, efficient, and modular generation of chimpanzee Ad serotype 68 (AdC68) as a molecular clone via isothermal assembly, which directionally assembles multiple DNA fragments in a single isothermal reaction without restriction enzymes or ligases, is presented. Any serotype of adenovirus with the sequence of genome known can be constructed as a molecular clone by this method. Recombinant adenoviral vectors can be created via one-step isothermal assembly in <3 days, and recombinant Ads can be rescued within 8 days. This protocol is practical for manipulations of Ad genomes, because an entire Ad genome can be divided into specific fragments within modular plasmids. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yong Yang
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yudan Chi
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xinying Tang
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | | | - Dongming Zhou
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product. G3-GENES GENOMES GENETICS 2015. [PMID: 26206350 PMCID: PMC4592980 DOI: 10.1534/g3.114.012765] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Here we describe the engineering of a distant homolog of the Tet repressor, CamR, isolated from Pseudomonas putida, that is regulated by camphor, a very inexpensive small molecule (at micromolar concentrations) for use in Saccharomyces cerevisiae. The repressor was engineered by expression from a constitutive yeast promoter, fusion to a viral activator protein cassette, and codon optimization. A suitable promoter responsive to the CamR fusion protein was engineered by embedding a P. putida operator binding sequence within an upstream activating sequence (UAS)-less CYC1 promoter from S. cerevisiae. The switch, named the Camphor-Off switch, activates expression of a reporter gene in camphor-free media and represses it with micromolar concentrations of camphor.
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Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, Zheng A, Choi WJ, Martin JA, Caravelli K, Stracquadanio G, Boeke JD. Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. ACS Synth Biol 2015; 4:853-9. [PMID: 25756291 DOI: 10.1021/sb500372z] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have adapted the Golden Gate DNA assembly method to the assembly of transcription units (TUs) for the yeast Saccharomyces cerevisiae, in a method we call yeast Golden Gate (yGG). yGG allows for the easy assembly of TUs consisting of promoters (PRO), coding sequences (CDS), and terminators (TER). Carefully designed overhangs exposed by digestion with a type IIS restriction enzyme enable virtually seamless assembly of TUs that, in principle, contain all of the information necessary to express a gene of interest in yeast. We also describe a versatile set of yGG acceptor vectors to be used for TU assembly. These vectors can be used for low or high copy expression of assembled TUs or integration into carefully selected innocuous genomic loci. yGG provides synthetic biologists and yeast geneticists with an efficient new means by which to engineer S. cerevisiae.
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Affiliation(s)
- Neta Agmon
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
| | - Leslie A. Mitchell
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
| | - Yizhi Cai
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JR, United Kingdom
| | - Shigehito Ikushima
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - James Chuang
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Allen Zheng
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Woo-Jin Choi
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - J. Andrew Martin
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
| | - Katrina Caravelli
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Giovanni Stracquadanio
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Jef D. Boeke
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
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34
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Mitchell LA, Chuang J, Agmon N, Khunsriraksakul C, Phillips NA, Cai Y, Truong DM, Veerakumar A, Wang Y, Mayorga M, Blomquist P, Sadda P, Trueheart J, Boeke JD. Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res 2015; 43:6620-30. [PMID: 25956652 PMCID: PMC4513848 DOI: 10.1093/nar/gkv466] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/27/2015] [Indexed: 11/14/2022] Open
Abstract
We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae. Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform homologous recombination and efficiently join sequences with terminal homology. In the VEGAS workflow, terminal homology between adjacent pathway genes and the assembly vector is encoded by 'VEGAS adapter' (VA) sequences, which are orthogonal in sequence with respect to the yeast genome. Prior to pathway assembly by VEGAS in S. cerevisiae, each gene is assigned an appropriate pair of VAs and assembled using a previously described technique called yeast Golden Gate (yGG). Here we describe the application of yGG specifically to building transcription units for VEGAS assembly as well as the VEGAS methodology. We demonstrate the assembly of four-, five- and six-gene pathways by VEGAS to generate S. cerevisiae cells synthesizing β-carotene and violacein. Moreover, we demonstrate the capacity of yGG coupled to VEGAS for combinatorial assembly.
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Affiliation(s)
- Leslie A Mitchell
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Chuang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Neta Agmon
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chachrit Khunsriraksakul
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nick A Phillips
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yizhi Cai
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David M Truong
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA
| | - Ashan Veerakumar
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yuxuan Wang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | - Praneeth Sadda
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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35
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Lin Q, Jia B, Mitchell LA, Luo J, Yang K, Zeller KI, Zhang W, Xu Z, Stracquadanio G, Bader JS, Boeke JD, Yuan YJ. RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synth Biol 2015; 4:213-20. [PMID: 24895839 DOI: 10.1021/sb500241e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe rapid assembly of DNA overlapping multifragments (RADOM), an improved assembly method via homologous recombination in Saccharomyces cerevisiae, which combines assembly in yeasto with blue/white screening in Escherichia coli. We show that RADOM can successfully assemble ∼3 and ∼10 kb DNA fragments that are highly similar to the yeast genome rapidly and accurately. This method was tested in the Build-A-Genome course by undergraduate students, where 125 ∼3 kb "minichunks" from the synthetic yeast genome project Sc2.0 were assembled. Here, 122 out of 125 minichunks achieved insertions with correct sizes, and 102 minichunks were sequenced verified. As this method reduces the time-consuming and labor-intensive efforts of yeast assembly by improving the screening efficiency for correct assemblies, it may find routine applications in the construction of DNA fragments, especially in hierarchical assembly projects.
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Affiliation(s)
- Qiuhui Lin
- Key
Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, PR China
- Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, 300072, PR China
| | - Bin Jia
- Key
Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, PR China
- Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, 300072, PR China
| | - Leslie A. Mitchell
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Institute
for Systems Genetics, New York University Langone Medical Center, 550 First Avenue, New York, New York 10016, United States
| | - Jingchuan Luo
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Institute
for Systems Genetics, New York University Langone Medical Center, 550 First Avenue, New York, New York 10016, United States
| | - Kun Yang
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Department
of Biomedical Engineering and Institute for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Karen I. Zeller
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Wenqian Zhang
- Key
Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, PR China
- Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, 300072, PR China
| | - Zhuwei Xu
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Institute
for Systems Genetics, New York University Langone Medical Center, 550 First Avenue, New York, New York 10016, United States
| | - Giovanni Stracquadanio
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Department
of Biomedical Engineering and Institute for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joel S. Bader
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Department
of Biomedical Engineering and Institute for Computational Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jef D. Boeke
- High
Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, United States
- Institute
for Systems Genetics, New York University Langone Medical Center, 550 First Avenue, New York, New York 10016, United States
| | - Ying-Jin Yuan
- Key
Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, PR China
- Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, 300072, PR China
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36
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Eckdahl TT, Campbell AM, Heyer LJ, Poet JL, Blauch DN, Snyder NL, Atchley DT, Baker EJ, Brown M, Brunner EC, Callen SA, Campbell JS, Carr CJ, Carr DR, Chadinha SA, Chester GI, Chester J, Clarkson BR, Cochran KE, Doherty SE, Doyle C, Dwyer S, Edlin LM, Evans RA, Fluharty T, Frederick J, Galeota-Sprung J, Gammon BL, Grieshaber B, Gronniger J, Gutteridge K, Henningsen J, Isom B, Itell HL, Keffeler EC, Lantz AJ, Lim JN, McGuire EP, Moore AK, Morton J, Nakano M, Pearson SA, Perkins V, Parrish P, Pierson CE, Polpityaarachchige S, Quaney MJ, Slattery A, Smith KE, Spell J, Spencer M, Taye T, Trueblood K, Vrana CJ, Whitesides ET. Programmed evolution for optimization of orthogonal metabolic output in bacteria. PLoS One 2015; 10:e0118322. [PMID: 25714374 PMCID: PMC4340930 DOI: 10.1371/journal.pone.0118322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy, pharmaceuticals, chemical commodities, biomining, and bioremediation.
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Affiliation(s)
- Todd T. Eckdahl
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
- * E-mail:
| | - A. Malcolm Campbell
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Laurie J. Heyer
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Jeffrey L. Poet
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - David N. Blauch
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America
| | - Nicole L. Snyder
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America
| | - Dustin T. Atchley
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erich J. Baker
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Micah Brown
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Elizabeth C. Brunner
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sean A. Callen
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jesse S. Campbell
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Caleb J. Carr
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - David R. Carr
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Spencer A. Chadinha
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Grace I. Chester
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Josh Chester
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Ben R. Clarkson
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kelly E. Cochran
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Shannon E. Doherty
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Catherine Doyle
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sarah Dwyer
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Linnea M. Edlin
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Rebecca A. Evans
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Taylor Fluharty
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Janna Frederick
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jonah Galeota-Sprung
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Betsy L. Gammon
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Brandon Grieshaber
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jessica Gronniger
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Katelyn Gutteridge
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Joel Henningsen
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Bradley Isom
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Hannah L. Itell
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erica C. Keffeler
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Andrew J. Lantz
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Jonathan N. Lim
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erin P. McGuire
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Alexander K. Moore
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jerrad Morton
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Meredith Nakano
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sara A. Pearson
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Virginia Perkins
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Phoebe Parrish
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Claire E. Pierson
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Sachith Polpityaarachchige
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Michael J. Quaney
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Abagael Slattery
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kathryn E. Smith
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Jackson Spell
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Morgan Spencer
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Telavive Taye
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kamay Trueblood
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Caroline J. Vrana
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - E. Tucker Whitesides
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
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37
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Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 2014; 155:1034-48. [PMID: 24267889 DOI: 10.1016/j.cell.2013.10.021] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
LINE-1s are active human DNA parasites that are agents of genome dynamics in evolution and disease. These streamlined elements require host factors to complete their life cycles, whereas hosts have developed mechanisms to combat retrotransposition's mutagenic effects. As such, endogenous L1 expression levels are extremely low, creating a roadblock for detailed interactomic analyses. Here, we describe a system to express and purify highly active L1 RNP complexes from human suspension cell culture and characterize the copurified proteome, identifying 37 high-confidence candidate interactors. These data sets include known interactors PABPC1 and MOV10 and, with in-cell imaging studies, suggest existence of at least three types of compositionally and functionally distinct L1 RNPs. Among the findings, UPF1, a key nonsense-mediated decay factor, and PCNA, the polymerase-delta-associated sliding DNA clamp, were identified and validated. PCNA interacts with ORF2p via a PIP box motif; mechanistic studies suggest that this occurs during or immediately after target-primed reverse transcription.
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38
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Li Y, Gu Q, Lin Z, Wang Z, Chen T, Zhao X. Multiplex iterative plasmid engineering for combinatorial optimization of metabolic pathways and diversification of protein coding sequences. ACS Synth Biol 2013; 2:651-61. [PMID: 24041030 DOI: 10.1021/sb400051t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineering complex biological systems typically requires combinatorial optimization to achieve the desired functionality. Here, we present Multiplex Iterative Plasmid Engineering (MIPE), which is a highly efficient and customized method for combinatorial diversification of plasmid sequences. MIPE exploits ssDNA mediated λ Red recombineering for the introduction of mutations, allowing it to target several sites simultaneously and generate libraries of up to 10(7) sequences in one reaction. We also describe "restriction digestion mediated co-selection (RD CoS)", which enables MIPE to produce enhanced recombineering efficiencies with greatly simplified coselection procedures. To demonstrate this approach, we applied MIPE to fine-tune gene expression level in the 5-gene riboflavin biosynthetic pathway and successfully isolated a clone with 2.67-fold improved production in less than a week. We further demonstrated the ability of MIPE for highly multiplexed diversification of protein coding sequence by simultaneously targeting 23 codons scattered along the 750 bp sequence. We anticipate this method to benefit the optimization of diverse biological systems in synthetic biology and metabolic engineering.
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Affiliation(s)
- Yifan Li
- Key Laboratory of Systems
Bioengineering,
Ministry of Education, and Department of Biochemical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Qun Gu
- Key Laboratory of Systems
Bioengineering,
Ministry of Education, and Department of Biochemical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Zhenquan Lin
- Key Laboratory of Systems
Bioengineering,
Ministry of Education, and Department of Biochemical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Zhiwen Wang
- Key Laboratory of Systems
Bioengineering,
Ministry of Education, and Department of Biochemical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Tao Chen
- Key Laboratory of Systems
Bioengineering,
Ministry of Education, and Department of Biochemical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xueming Zhao
- Key Laboratory of Systems
Bioengineering,
Ministry of Education, and Department of Biochemical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
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39
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Taniguchi N, Nakayama S, Kawakami T, Murakami H. Patch cloning method for multiple site-directed and saturation mutagenesis. BMC Biotechnol 2013; 13:91. [PMID: 24164925 PMCID: PMC3829206 DOI: 10.1186/1472-6750-13-91] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/23/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Various DNA manipulation methods have been developed to prepare mutant genes for protein engineering. However, development of more efficient and convenient method is still demanded. Homologous DNA assembly methods, which do not depend on restriction enzymes, have been used as convenient tools for cloning and have been applied to site-directed mutagenesis recently. This study describes an optimized homologous DNA assembly method, termed as multiple patch cloning (MUPAC), for multiple site-directed and saturation mutagenesis. RESULTS To demonstrate MUPAC, we introduced five back mutations to a mutant green fluorescent protein (GFPuv) with five deleterious mutations at specific sites and transformed Escherichia coli (E. coli) with the plasmids obtained. We observed that the over 90% of resulting colonies possessed the plasmids containing the reverted GFPuv gene and exhibited fluorescence. We extended the test to introduce up to nine mutations in Moloney Murine Leukemia Virus reverse transcriptase (M-MLV RT) by assembling 11 DNA fragments using MUPAC. Analysis of the cloned plasmid by electrophoresis and DNA sequencing revealed that approximately 30% of colonies had the objective mutant M-MLV RT gene. Furthermore, we also utilized this method to prepare a library of mutant GFPuv genes containing saturation mutations at five specific sites, and we found that MUPAC successfully introduced NNK codons at all five sites, whereas other site remained intact. CONCLUSIONS MUPAC could efficiently introduce various mutations at multiple specific sites within a gene. Furthermore, it could facilitate the preparation of experimental gene materials important to molecular and synthetic biology research.
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Affiliation(s)
| | | | | | - Hiroshi Murakami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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40
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Taylor MS, Ruch TR, Hsiao PY, Hwang Y, Zhang P, Dai L, Huang CRL, Berndsen CE, Kim MS, Pandey A, Wolberger C, Marmorstein R, Machamer C, Boeke JD, Cole PA. Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase. J Biol Chem 2013; 288:32211-32228. [PMID: 24045953 DOI: 10.1074/jbc.m113.510313] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ghrelin O-acyltransferase (GOAT) is a polytopic integral membrane protein required for activation of ghrelin, a secreted metabolism-regulating peptide hormone. Although GOAT is a potential therapeutic target for the treatment of obesity and diabetes and plays a key role in other physiologic processes, little is known about its structure or mechanism. GOAT is a member of the membrane-bound O-acyltransferase (MBOAT) family, a group of polytopic integral membrane proteins involved in lipid-biosynthetic and lipid-signaling reactions from prokaryotes to humans. Here we use phylogeny and a variety of bioinformatic tools to predict the topology of GOAT. Using selective permeabilization indirect immunofluorescence microscopy in combination with glycosylation shift immunoblotting, we demonstrate that GOAT contains 11 transmembrane helices and one reentrant loop. Development of the V5Glyc tag, a novel, small, and sensitive dual topology reporter, facilitated these experiments. The MBOAT family invariant residue His-338 is in the ER lumen, consistent with other family members, but conserved Asn-307 is cytosolic, making it unlikely that both are involved in catalysis. Photocross-linking of synthetic ghrelin analogs and inhibitors demonstrates binding to the C-terminal region of GOAT, consistent with a role of His-338 in the active site. This knowledge of GOAT architecture is important for a deeper understanding of the mechanism of GOAT and other MBOATs and could ultimately advance the discovery of selective inhibitors for these enzymes.
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Affiliation(s)
- Martin S Taylor
- From the Department of Pharmacology and Molecular Sciences,; the High Throughput Biology Center and Department of Molecular Biology and Genetics
| | | | - Po-Yuan Hsiao
- From the Department of Pharmacology and Molecular Sciences
| | - Yousang Hwang
- From the Department of Pharmacology and Molecular Sciences
| | - Pingfeng Zhang
- the Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania 19104
| | - Lixin Dai
- the High Throughput Biology Center and Department of Molecular Biology and Genetics
| | - Cheng Ran Lisa Huang
- the High Throughput Biology Center and Department of Molecular Biology and Genetics,; the McKusick-Nathans Institute of Genetic Medicine
| | - Christopher E Berndsen
- the Howard Hughes Medical Institute and Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Min-Sik Kim
- the McKusick-Nathans Institute of Genetic Medicine
| | | | - Cynthia Wolberger
- the Howard Hughes Medical Institute and Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Ronen Marmorstein
- the Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania 19104; the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | - Jef D Boeke
- the High Throughput Biology Center and Department of Molecular Biology and Genetics,.
| | - Philip A Cole
- From the Department of Pharmacology and Molecular Sciences,.
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