当前位置： SCI文献检索 > ACS Synthetic Biology期刊下所有文献 > A Novel Tool for Microbial Genome Editing Using the Restriction-Modification System.

A Novel Tool for Microbial Genome Editing Using the Restriction-Modification System.

Abstract：

:Scarless genetic manipulation of genomes is an essential tool for biological research. The restriction-modification (R-M) system is a defense system in bacteria that protects against invading genomes on the basis of its ability to distinguish foreign DNA from self DNA. Here, we designed an R-M system-mediated genome editing (RMGE) technique for scarless genetic manipulation in different microorganisms. For bacteria with Type IV REase, an RMGE technique using the inducible DNA methyltransferase gene, bceSIIM (RMGE-bceSIIM), as the counter-selection cassette was developed to edit the genome of Escherichia coli. For bacteria without Type IV REase, an RMGE technique based on a restriction endonuclease (RMGE-mcrA) was established in Bacillus subtilis. These techniques were successfully used for gene deletion and replacement with nearly 100% counter-selection efficiencies, which were higher and more stable compared to conventional methods. Furthermore, precise point mutation without limiting sites was achieved in E. coli using RMGE-bceSIIM to introduce a single base mutation of A128C into the rpsL gene. In addition, the RMGE-mcrA technique was applied to delete the CAN1 gene in Saccharomyces cerevisiae DAY414 with 100% counter-selection efficiency. The effectiveness of the RMGE technique in E. coli, B. subtilis, and S. cerevisiae suggests the potential universal usefulness of this technique for microbial genome manipulation.

journal_name

ACS Synth Biol

journal_title

ACS synthetic biology

authors

Bai H,Deng A,Liu S,Cui D,Qiu Q,Wang L,Yang Z,Wu J,Shang X,Zhang Y,Wen T

doi

10.1021/acssynbio.7b00254

subject

Has Abstract

pub_date

2018-01-19 00:00:00

pages

98-106

issue

1

issn

2161-5063

journal_volume

7

pub_type

杂志文章

相关文献

ACS Synthetic Biology文献大全
  • New Prodigiosin Derivatives Obtained by Mutasynthesis in Pseudomonas putida.

    abstract：:The deeply red-colored natural compound prodigiosin is a representative of the prodiginine alkaloid family, which possesses bioactivities as antimicrobial, antitumor, and antimalarial agents. Various bacteria including the opportunistic human pathogen Serratia marcescens and different members of the Streptomycetaceae ...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.7b00099

    authors： Klein AS,Domröse A,Bongen P,Brass HUC,Classen T,Loeschcke A,Drepper T,Laraia L,Sievers S,Jaeger KE,Pietruszka J

    更新日期：2017-09-15 00:00:00

  • Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression.

    abstract：:Feedback allows biological systems to control gene expression precisely and reliably, even in the presence of uncertainty, by sensing and processing environmental changes. Taking inspiration from natural architectures, synthetic biologists have engineered feedback loops to tune the dynamics and improve the robustness ...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.8b00040

    authors： Agrawal DK,Tang X,Westbrook A,Marshall R,Maxwell CS,Lucks J,Noireaux V,Beisel CL,Dunlop MJ,Franco E

    更新日期：2018-05-18 00:00:00

  • Exploiting Spermidine N-Hydroxycinnamoyltransferase Diversity and Substrate Promiscuity to Produce Various Trihydroxycinnamoyl Spermidines and Analogues in Engineered Yeast.

    abstract：:Trihydroxycinnamoyl spermidines (THCSpd) are plant specialized metabolites with promising pharmacological activities as antifungals, antibacterial, antiviral, and antidepressant drugs. However, their characterization and potential pharmaceutical exploitation are greatly impaired by the sourcing of these compounds, res...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.0c00391

    authors： Perrin J,Kulagina N,Unlubayir M,Munsch T,Carqueijeiro I,Dugé de Bernonville T,De Craene JO,Clastre M,St-Pierre B,Giglioli-Guivarc'h N,Gagneul D,Lanoue A,Courdavault V,Besseau S

    更新日期：2021-01-15 00:00:00

  • Structural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies.

    abstract：:Bacterial microcompartments are subcellular compartments found in many prokaryotes; they consist of a protein shell that encapsulates enzymes that perform a variety of functions. The shell protects the cell from potentially toxic intermediates and colocalizes enzymes for higher efficiency. Accordingly, it is of consid...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.9b00011

    authors： Sutter M,McGuire S,Ferlez B,Kerfeld CA

    更新日期：2019-04-19 00:00:00

  • Metabolic Engineering of Pseudomonas putida KT2440 for Complete Mineralization of Methyl Parathion and γ-Hexachlorocyclohexane.

    abstract：:Agricultural soils are often cocontaminated with multiple pesticides. Unfortunately, microorganisms isolated from natural environments do not possess the ability to simultaneously degrade different classes of pesticides. Currently, we can use the approaches of synthetic biology to create a strain endowed with various ...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.6b00025

    authors： Gong T,Liu R,Zuo Z,Che Y,Yu H,Song C,Yang C

    更新日期：2016-05-20 00:00:00

  • Design of a Temperature-Responsive Transcription Terminator.

    abstract：:RNA structures regulate various steps in gene expression. Transcription in bacteria is typically terminated by stable hairpin structures. Translation initiation can be modulated by metabolite- or temperature-sensitive RNA structures, called riboswitches or RNA thermometers (RNATs), respectively. RNATs control translat...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.7b00356

    authors： Roßmanith J,Weskamp M,Narberhaus F

    更新日期：2018-02-16 00:00:00

  • Metabolic Rewiring Improves the Production of the Fungal Active Targeting Molecule Fusarinine C.

    abstract：:Author: Recently, increasing research in siderophores has been dedicated to their possible medical applications in diagnostics and therapeutics for human pathogenic infections. Fusarinine C (FsC) is a natural hydroxamate siderophore that harbors three amino groups, which allow the easy chemical modification of FsC for...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.9b00026

    authors： Lu Y,Wang H,Wang Z,Cong Y,Zhang P,Liu G,Liu C,Chi Z,Chi Z

    更新日期：2019-08-16 00:00:00

  • Repurposing Synechocystis PCC6803 UirS-UirR as a UV-Violet/Green Photoreversible Transcriptional Regulatory Tool in E. coli.

    abstract：:We have previously engineered green/red and red/far red photoreversible E. coli phytochrome and cyanobacteriochrome (CBCR) two-component systems (TCSs) and utilized them to program tailor-made gene expression signals for gene circuit characterization. Here, we transport the UV-violet/green photoreversible CBCR TCS Uir...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.6b00068

    authors： Ramakrishnan P,Tabor JJ

    更新日期：2016-07-15 00:00:00

  • Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis.

    abstract：:In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnol...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/sb300102k

    authors： Carapezza G,Umeton R,Costanza J,Angione C,Stracquadanio G,Papini A,Lió P,Nicosia G

    更新日期：2013-05-17 00:00:00

  • A Designed A. vinelandii-S. elongatus Coculture for Chemical Photoproduction from Air, Water, Phosphate, and Trace Metals.

    abstract：:Microbial mutualisms play critical roles in a diverse number of ecosystems and have the potential to improve the efficiency of bioproduction for desirable chemicals. We investigate the growth of a photosynthetic cyanobacterium, Synechococcus elongatus PCC 7942, and a diazotroph, Azotobacter vinelandii, in coculture. F...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.6b00107

    authors： Smith MJ,Francis MB

    更新日期：2016-09-16 00:00:00

  • Toward Synthetic Spatial Patterns in Engineered Cell Populations with Chemotaxis.

    abstract：:A major force shaping form and patterns in biology is based in the presence of amplification mechanisms able to generate ordered, large-scale spatial structures out of local interactions and random initial conditions. Turing patterns are one of the best known candidates for such ordering dynamics, and their existence ...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.5b00254

    authors： Duran-Nebreda S,Solé RV

    更新日期：2016-07-15 00:00:00

  • Biosynthetic Routes for Producing Various Fucosyl-Oligosaccharides.

    abstract：:Fucosyl-oligosaccharides (FOSs) play physiologically important roles as prebiotics, neuronal growth factors, and inhibitors of enteropathogens. However, challenges in designed synthesis and mass production of FOSs hamper their industrial applications. Here, we report flexible biosynthetic routes to produce various FOS...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.8b00436

    authors： Yun EJ,Liu JJ,Lee JW,Kwak S,Yu S,Kim KH,Jin YS

    更新日期：2019-02-15 00:00:00

  • Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli.

    abstract：:Menthol isomers are high-value monoterpenoid commodity chemicals, produced naturally by mint plants, Mentha spp. Alternative clean biosynthetic routes to these compounds are commercially attractive. Optimization strategies for biocatalytic terpenoid production are mainly focused on metabolic engineering of the biosynt...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.5b00092

    authors： Toogood HS,Ní Cheallaigh A,Tait S,Mansell DJ,Jervis A,Lygidakis A,Humphreys L,Takano E,Gardiner JM,Scrutton NS

    更新日期：2015-10-16 00:00:00

  • Rapid Fabrication of Protein Microarrays via Autogeneration and on-Chip Purification of Biotinylated Probes.

    abstract：:A streamlined approach toward the rapid fabrication of streptavidin-biotin-based protein microarrays was investigated. First, using our engineered versatile plasmid (pBADcM-tBirA) and an optimal coexpression strategy for biotin ligase and biotin acceptor peptide (BAP) chimeric recombinant protein, an autogeneration sy...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.0c00343

    authors： Li BW,Zhang Y,Wang YC,Xue Y,Nie XY

    更新日期：2020-09-18 00:00:00

  • GeneORator: An Effective Strategy for Navigating Protein Sequence Space More Efficiently through Boolean OR-Type DNA Libraries.

    abstract：:Directed evolution requires the creation of genetic diversity and subsequent screening or selection for improved variants. For DNA mutagenesis, conventional site-directed methods implicitly utilize the Boolean AND operator (creating all mutations simultaneously), producing a combinatorial explosion in the number of ge...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.9b00063

    authors： Currin A,Kwok J,Sadler JC,Bell EL,Swainston N,Ababi M,Day P,Turner NJ,Kell DB

    更新日期：2019-06-21 00:00:00

  • Evolutionary stability of a refactored phage genome.

    abstract：:Engineered genetic systems are commonly unstable; if propagated, they evolve to reverse or modify engineered elements because the elements impair fitness. A goal of synthetic biology is thus to anticipate and avoid detrimental engineering, but little is yet known about which types of elements cause problems in differe...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/sb300040v

    authors： Springman R,Molineux IJ,Duong C,Bull RJ,Bull JJ

    更新日期：2012-09-21 00:00:00

  • Refactoring and optimization of light-switchable Escherichia coli two-component systems.

    abstract：:Light-switchable proteins enable unparalleled control of molecular biological processes in live organisms. Previously, we have engineered red/far-red and green/red photoreversible two-component signal transduction systems (TCSs) with transcriptional outputs in E. coli and used them to characterize and control syntheti...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/sb500273n

    authors： Schmidl SR,Sheth RU,Wu A,Tabor JJ

    更新日期：2014-11-21 00:00:00

  • Enhanced triterpene accumulation in Panax ginseng hairy roots overexpressing mevalonate-5-pyrophosphate decarboxylase and farnesyl pyrophosphate synthase.

    abstract：:To elucidate the function of mevalonate-5-pyrophosphate decarboxylase (MVD) and farnesyl pyrophosphate synthase (FPS) in triterpene biosynthesis, the genes governing the expression of these enzymes were transformed into Panax ginseng hairy roots. All the transgenic lines showed higher expression levels of PgMVD and Pg...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/sb400194g

    authors： Kim YK,Kim YB,Uddin MR,Lee S,Kim SU,Park SU

    更新日期：2014-10-17 00:00:00

  • Incorporation of a Synthetic Amino Acid into dCas9 Improves Control of Gene Silencing.

    abstract：:The CRISPR-Cas9 nuclease has been repurposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoter...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.8b00347

    authors： Koopal B,Kruis AJ,Claassens NJ,Nobrega FL,van der Oost J

    更新日期：2019-02-15 00:00:00

  • Multiplex iterative plasmid engineering for combinatorial optimization of metabolic pathways and diversification of protein coding sequences.

    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 media...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/sb400051t

    authors： Li Y,Gu Q,Lin Z,Wang Z,Chen T,Zhao X

    更新日期：2013-11-15 00:00:00

  • Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins.

    abstract：:Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vect...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.6b00354

    authors： Pasin F,Bedoya LC,Bernabé-Orts JM,Gallo A,Simón-Mateo C,Orzaez D,García JA

    更新日期：2017-10-20 00:00:00

  • Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides.

    abstract：:Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale-up by traditional phosphoram...

    journal_title：ACS synthetic biology

    pub_type： 信件

    doi：10.1021/sb5001565

    authors： Bonde MT,Kosuri S,Genee HJ,Sarup-Lytzen K,Church GM,Sommer MO,Wang HH

    更新日期：2015-01-16 00:00:00

  • Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production.

    abstract：:Type I modular polyketide synthases (PKSs) are polymerases that utilize acyl-CoAs as substrates. Each polyketide elongation reaction is catalyzed by a set of protein domains called a module. Each module usually contains an acyltransferase (AT) domain, which determines the specific acyl-CoA incorporated into each conde...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.6b00176

    authors： Yuzawa S,Deng K,Wang G,Baidoo EE,Northen TR,Adams PD,Katz L,Keasling JD

    更新日期：2017-01-20 00:00:00

  • Engineering Translational Activators with CRISPR-Cas System.

    abstract：:RNA parts often serve as critical components in genetic engineering. Here we report a design of translational activators which is composed of an RNA endoribonuclease (Csy4) and two exchangeable RNA modules. Csy4, a member of Cas endoribonuclease, cleaves at a specific recognition site; this cleavage releases a cis-rep...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.5b00130

    authors： Du P,Miao C,Lou Q,Wang Z,Lou C

    更新日期：2016-01-15 00:00:00

  • Conditional Recruitment to a DNA-Bound CRISPR-Cas Complex Using a Colocalization-Dependent Protein Switch.

    abstract：:To spatially control biochemical functions at specific sites within a genome, we have engineered a synthetic switch that activates when bound to its DNA target site. The system uses two CRISPR-Cas complexes to colocalize components of a de novo-designed protein switch (Co-LOCKR) to adjacent sites in the genome. Coloca...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.0c00012

    authors： Kirkpatrick RL,Lewis K,Langan RA,Lajoie MJ,Boyken SE,Eakman M,Baker D,Zalatan JG

    更新日期：2020-09-18 00:00:00

  • Single-Molecule Kinetics Show DNA Pyrimidine Content Strongly Affects RNA:DNA and TNA:DNA Heteroduplex Dissociation Rates.

    abstract：:The heteroduplex hybridization thermodynamics of DNA with either RNA or TNA are greatly affected by DNA pyrimidine content, where increased DNA pyrimidine content leads to significantly increased duplex stability. Little is known, however, about the effect that purine or pyrimidine content has on the hybridization kin...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.9b00471

    authors： Lackey HH,Chen Z,Harris JM,Peterson EM,Heemstra JM

    更新日期：2020-02-21 00:00:00

  • FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.

    abstract：:The measurement of gene expression using fluorescence markers has been a cornerstone of synthetic biology for the past two decades. However, the use of arbitrary units has limited the usefulness of these data for many quantitative purposes. Calibration of fluorescence measurements from flow cytometry and plate reader ...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.0c00296

    authors： Fedorec AJH,Robinson CM,Wen KY,Barnes CP

    更新日期：2020-09-18 00:00:00

  • Electrochemical Measurement of the β-Galactosidase Reporter from Live Cells: A Comparison to the Miller Assay.

    abstract：:In order to match our ability to conceive of and construct cells with enhanced function, we must concomitantly develop facile, real-time methods for elucidating performance. With these, new designs can be tested in silico and steps in construction incrementally validated. Electrochemical monitoring offers the above ad...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.5b00073

    authors： Tschirhart T,Zhou XY,Ueda H,Tsao CY,Kim E,Payne GF,Bentley WE

    更新日期：2016-01-15 00:00:00

  • Robust Characterization of Two Distinct Glutarate Sensing Transcription Factors of Pseudomonas putida l-Lysine Metabolism.

    abstract：:A significant bottleneck in synthetic biology involves screening large genetically encoded libraries for desirable phenotypes such as chemical production. However, transcription factor-based biosensors can be leveraged to screen thousands of genetic designs for optimal chemical production in engineered microbes. In th...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.9b00255

    authors： Thompson MG,Costello Z,Hummel NFC,Cruz-Morales P,Blake-Hedges JM,Krishna RN,Skyrud W,Pearson AN,Incha MR,Shih PM,Garcia-Martin H,Keasling JD

    更新日期：2019-10-18 00:00:00

  • Assembly of Multicomponent Protein Filaments Using Engineered Subunit Interfaces.

    abstract：:Exploiting the ability of proteins to self-assemble into architectural templates may provide novel routes for the positioning of functional molecules in nanotechnology. Here we report the engineering of multicomponent protein templates composed of distinct monomers that assemble in repeating orders into a dynamic func...

    journal_title：ACS synthetic biology

    pub_type： 杂志文章

    doi：10.1021/acssynbio.8b00241

    authors： Glover DJ,Lim S,Xu D,Sloan NB,Zhang Y,Clark DS

    更新日期：2018-10-19 00:00:00