The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes.

abstract：:Synthetic biology involves reprogramming and engineering of regulatory genes in innovative ways for the implementation of novel tasks. Transcriptional gene regulation systems induced by small molecules in prokaryotes provide a rich source for logic gates. Cross-regulation, whereby a promoter is activated by different ...

journal_title：ACS synthetic biology

authors： Zhang D,Zhao Y,He Y,Wang Y,Zhao Y,Zheng Y,Wei X,Zhang L,Li Y,Jin T,Wu L,Wang H,Davison PA,Xu J,Huang WE

更新日期：2012-07-20 00:00:00

abstract：:DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include ad...

journal_title：ACS synthetic biology

authors： Song T,Garg S,Mokhtar R,Bui H,Reif J

更新日期：2016-08-19 00:00:00

abstract：:Quantification of biology's central dogma (transcription and translation) is pursued by a variety of methods. Direct, immediate, and ongoing quantification of these events is difficult to achieve. Common practice is to use fluorescent or luminescent proteins to report indirectly on prior cellular events, such as turni...

journal_title：ACS synthetic biology

authors： Wick S,Walsh DI 3rd,Bobrow J,Hamad-Schifferli K,Kong DS,Thorsen T,Mroszczyk K,Carr PA

更新日期：2019-05-17 00:00:00

abstract：:A gene-directed chemical communication pathway between synthetic protocell signaling transmitters (lipid vesicles) and receivers (proteinosomes) was designed, built and tested using a bottom-up modular approach comprising small molecule transcriptional control, cell-free gene expression, porin-directed efflux, substra...

journal_title：ACS synthetic biology

authors： Tang TD,Cecchi D,Fracasso G,Accardi D,Coutable-Pennarun A,Mansy SS,Perriman AW,Anderson JLR,Mann S

更新日期：2018-02-16 00:00:00

abstract：:Biosensors are important components of many synthetic biology and metabolic engineering applications. Here, we report a second generation of Saccharomyces cerevisiae digoxigenin and progesterone biosensors based on destabilized dimeric ligand-binding domains that undergo ligand-induced stabilization. The biosensors, c...

journal_title：ACS synthetic biology

authors： Jester BW,Tinberg CE,Rich MS,Baker D,Fields S

更新日期：2018-10-19 00:00:00

abstract：:Phenazine-1-carboxamide (PCN) produced by multifarious Pseudomonas strains represents a promising candidate as a new metabolite pesticide due to its broad-spectrum antifungal activity and capacity to induce systemic resistance in plants. The rice rhizosphere Pseudomonas strain PA1201 contains two reiterated gene clust...

journal_title：ACS synthetic biology

authors： Jin ZJ,Zhou L,Sun S,Cui Y,Song K,Zhang X,He YW

更新日期：2020-07-17 00:00:00

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

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

abstract：:The cell contents are encapsulated within a compartment, the volume of which is a fundamental physical parameter that may affect intracompartmental reactions. However, there have been few studies to elucidate whether and how volume changes alone can affect the reaction kinetics. It is difficult to address these questi...

journal_title：ACS synthetic biology

authors： Matsuura T,Hosoda K,Kazuta Y,Ichihashi N,Suzuki H,Yomo T

更新日期：2012-09-21 00:00:00

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

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

abstract：:Living organisms employ endogenous negative feedback loops to maintain homeostasis despite environmental fluctuations. A pressing open challenge in Synthetic Biology is to design and implement synthetic circuits to control host cells' behavior, in order to regulate and maintain desired conditions. To cope with the hig...

journal_title：ACS synthetic biology

authors： Fiore G,Matyjaszkiewicz A,Annunziata F,Grierson C,Savery NJ,Marucci L,di Bernardo M

更新日期：2017-03-17 00:00:00

abstract：:Increasing protein expression levels is a key step in the commercial production of enzymes. Predicting promoter activity and translation initiation efficiency based solely on consensus sequences have so far met with mixed results. Here, we addressed this challenge using a "brute-force" approach by designing and synthe...

journal_title：ACS synthetic biology

authors： Sauer C,Ver Loren van Themaat E,Boender LGM,Groothuis D,Cruz R,Hamoen LW,Harwood CR,van Rij T

更新日期：2018-07-20 00:00:00

abstract：:Komagataeibacter xylinus has received increasing attention as an important microorganism for the conversion of several carbon sources to bacterial cellulose (BC). However, BC productivity has been impeded by the lack of efficient genetic engineering techniques. In this study, a lambda Red and FLP/FRT-mediated site-spe...

journal_title：ACS synthetic biology

authors： Liu LP,Yang X,Zhao XJ,Zhang KY,Li WC,Xie YY,Jia SR,Zhong C

更新日期：2020-11-20 00:00:00

abstract：:Many Gram-negative pathogens encode type 3 secretion systems, sophisticated nanomachines that deliver proteins directly into the cytoplasm of mammalian cells. These systems present attractive opportunities for therapeutic protein delivery applications; however, their utility has been limited by their inherent pathogen...

journal_title：ACS synthetic biology

authors： Reeves AZ,Spears WE,Du J,Tan KY,Wagers AJ,Lesser CF

更新日期：2015-05-15 00:00:00

abstract：:The ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems t...

journal_title：ACS synthetic biology

authors： Halleran AD,Swaminathan A,Murray RM

更新日期：2018-05-18 00:00:00

abstract：:Antimycins are a family of natural products generated from a hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line. Although they possess an array of useful biological activities, their structural complexity makes chemical synthesis challenging, and their biosynthesis has thus far been ...

journal_title：ACS synthetic biology

authors： Liu J,Zhu X,Seipke RF,Zhang W

更新日期：2015-05-15 00:00:00

abstract：:Although Escherichia coli has been a popular tool for plasmid construction, this bacterium was believed to be "unsuitable" for constructing a large plasmid whose size exceeds 500 kilobases. We assumed that traditional plasmid vectors may lack some regulatory DNA elements required for the stable replication and segrega...

journal_title：ACS synthetic biology

authors： Mukai T,Yoneji T,Yamada K,Fujita H,Nara S,Su'etsugu M

更新日期：2020-06-19 00:00:00

abstract：:Multidrug resistance (MDR) is a globally relevant problem that requires novel approaches. Two-component systems are a promising, yet untapped target for novel antibacterials. They are prevalent in bacteria and absent in mammals, and their activity can be modulated upon perception of various stimuli. Screening pre-exis...

journal_title：ACS synthetic biology

authors： Lehning CE,Heidelberger JB,Reinhard J,Nørholm MHH,Draheim RR

更新日期：2017-07-21 00:00:00

abstract：:The development of a synthetic transcription factor that responds to intracellular calcium signals enables analyzing cellular events at the single-cell level or "rewiring" the intracellular information networks. In this study, we developed the calcium-dependent transcription factor (CaTF), which was cleaved by calpain...

journal_title：ACS synthetic biology

authors： Suzuki S,Murotomi K,Nakajima Y,Kawai K,Ohta K,Warita K,Miki T,Takeuchi Y

更新日期：2014-10-17 00:00:00

abstract：:Melatonin is a commercially attractive tryptophan-derived hormone. Here we describe a bioprocess for the production of melatonin using Escherichia coli to high titers. The first engineered strain produced 0.13 g/L of melatonin from tryptophan under fed-batch fermentation conditions. A 4-fold improvement on melatonin t...

journal_title：ACS synthetic biology

authors： Luo H,Schneider K,Christensen U,Lei Y,Herrgard M,Palsson BØ

更新日期：2020-06-19 00:00:00

abstract：:An RNA-dependent RNA polymerase ribozyme that was highly optimized through in vitro evolution for the ability to copy a broad range of template sequences exhibits promiscuity toward other nucleic acids and nucleic acid analogues, including DNA, threose nucleic acid (TNA), and arabinose nucleic acid (ANA). By operating...

journal_title：ACS synthetic biology

authors： Horning DP,Bala S,Chaput JC,Joyce GF

更新日期：2019-05-17 00:00:00

abstract：:Synthetic biology and metabolic engineering offer potentially green and attractive routes to the production of high value compounds. The provision of high-quality parts and pathways is crucial in enabling the biosynthesis of chemicals using synthetic biology. While a number of regulatory parts that provide control at ...

journal_title：ACS synthetic biology

authors： Wilkes J,Scott-Tucker A,Wright M,Crabbe T,Scrutton NS

更新日期：2020-10-16 00:00:00

abstract：:Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequen...

journal_title：ACS synthetic biology

authors： Xiong X,Zhang Y,Yan J,Jain S,Chee S,Ren B,Zhao H

更新日期：2017-06-16 00:00:00

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

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

abstract：:Novel approaches are needed to combat antibiotic resistance. Here, we describe a computational-experimental framework for the discovery of novel cryptic antimicrobial peptides (AMPs). The computational platform, based on previously validated antimicrobial scoring functions, indicated the activation peptide of pepsin A...

journal_title：ACS synthetic biology

authors： Pane K,Cafaro V,Avitabile A,Torres MT,Vollaro A,De Gregorio E,Catania MR,Di Maro A,Bosso A,Gallo G,Zanfardino A,Varcamonti M,Pizzo E,Di Donato A,Lu TK,de la Fuente-Nunez C,Notomista E

更新日期：2018-09-21 00:00:00

abstract：:In this paper, we present a new strategy for microprinting dense bacterial communities with a prescribed organization on a substrate. Unlike conventional bioprinting techniques that require bioinks, through optogenetic manipulation, we directly manipulated the behaviors of Pseudomonas aeruginosa to allow these living ...

journal_title：ACS synthetic biology

authors： Huang Y,Xia A,Yang G,Jin F

更新日期：2018-05-18 00:00:00

abstract：:Strategies to optimize a metabolic pathway often involve building a large collection of strains, each containing different versions of sequences that regulate the expression of pathway genes. Here, we develop reagents and methods to carry out this process at high efficiency in the yeast Saccharomyces cerevisiae. We id...

journal_title：ACS synthetic biology

authors： Cuperus JT,Lo RS,Shumaker L,Proctor J,Fields S

更新日期：2015-07-17 00:00:00

abstract：:In the search for enzymatically processed RNA fragments, we found the novel three-way junction motif. The structure prediction suggested the arrangement of helices at acute angle approx. 60°. This allows the design of a trimeric RNA nanoparticle that can be functionalized with multiple regulatory fragments. Such RNA n...

journal_title：ACS synthetic biology

authors： Jedrzejczyk D,Chworos A

更新日期：2019-03-15 00:00:00

abstract：:Traditional enzyme characterization methods are low-throughput and therefore limit engineering efforts in synthetic biology and biotechnology. Here, we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor enzyme reactions in a high-throughput manner. Throughput is improved by removing the need for protein pur...

journal_title：ACS synthetic biology

authors： Sukovich DJ,Modavi C,de Raad M,Prince RN,Anderson JC

更新日期：2015-07-17 00:00:00

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

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

abstract：:Materials synthesized by organisms, such as bones and wood, combine the ability to self-repair with remarkable mechanical properties. This multifunctionality arises from the presence of living cells within the material and hierarchical assembly of different components across nanometer to micron scales. While creating ...

journal_title：ACS synthetic biology

authors： Charrier M,Li D,Mann VR,Yun L,Jani S,Rad B,Cohen BE,Ashby PD,Ryan KR,Ajo-Franklin CM

更新日期：2019-01-18 00:00:00