Resource Competition Shapes the Response of Genetic Circuits.

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：:Mycoplasma hominis is a minimal human pathogen that is responsible for genital and neonatal infections. Despite many attempts, there is no efficient genetic tool to manipulate this bacterium, limiting most investigations of its pathogenicity and its uncommon energy metabolism that relies on arginine. The recent clonin...

journal_title：ACS synthetic biology

authors： Rideau F,Le Roy C,Descamps ECT,Renaudin H,Lartigue C,Bébéar C

更新日期：2017-05-19 00:00:00

abstract：:Synthetic biology is today harnessing the design of novel and greener biosynthesis routes for the production of added-value chemicals and natural products. The design of novel pathways often requires a detailed selection of enzyme sequences to import into the chassis at each of the reaction steps. To address such desi...

journal_title：ACS synthetic biology

authors： Mellor J,Grigoras I,Carbonell P,Faulon JL

更新日期：2016-06-17 00:00:00

abstract：:Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes. Recent results show that TALE proteins consist of a central repeat domain, which ...

journal_title：ACS synthetic biology

authors： Moore R,Chandrahas A,Bleris L

更新日期：2014-10-17 00:00:00

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

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

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

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

更新日期：2020-09-18 00:00:00

abstract：:The Synthetic Biology Open Language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine-to-machine communication. However, manual editing of SBOL is generally difficult for nontrivial designs. Here, we describe ShortBOL, a lightweight SBOL scripting ...

journal_title：ACS synthetic biology

authors： Crowther M,Grozinger L,Pocock M,Taylor CPD,McLaughlin JA,Mısırlı G,Bartley BA,Beal J,Goñi-Moreno A,Wipat A

更新日期：2020-04-17 00:00:00

abstract：:Crossbreeding is a classical yeast hybridization procedure, where the mating of haploid cells of opposite mating-type, MATa and MATα cells, produces a new heterozygous diploid. Here, we describe a method to generate haploid MATa and MATα cells using mating-type conversion caused by expression of the HO gene, which enc...

journal_title：ACS synthetic biology

authors： Fukuda N,Matsukura S,Honda S

更新日期：2013-12-20 00:00:00

abstract：:Biosensors regulated by specific substrates are needed to develop genetic tools to meet the needs of engineering microbial cell factories. Here, a xylose-inducible biosensor (xylbiosensor), comprising the Escherichia coli activation factor XylR, fusion activation domain (AD) VPRH, and a hybrid promoter with operator x...

journal_title：ACS synthetic biology

authors： Wei W,Shang Y,Zhang P,Liu Y,You D,Yin B,Ye B

更新日期：2020-05-15 00:00:00

abstract：:Multitargeting small regulatory RNAs (sRNAs) represent a potentially useful tool for metabolic engineering applications. Natural multitargeting sRNAs govern bacterial gene expression by binding to the translation initiation regions of protein-coding mRNAs through base pairing. We designed an Escherichia coli based gen...

journal_title：ACS synthetic biology

authors： Lahiry A,Stimple SD,Wood DW,Lease RA

更新日期：2017-04-21 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：:In this work we report synthetic adhesins (SAs) enabling the rational design of the adhesion properties of E. coli. SAs have a modular structure comprising a stable β-domain for outer membrane anchoring and surface-exposed immunoglobulin domains with high affinity and specificity that can be selected from large repert...

journal_title：ACS synthetic biology

authors： Piñero-Lambea C,Bodelón G,Fernández-Periáñez R,Cuesta AM,Álvarez-Vallina L,Fernández LÁ

更新日期：2015-04-17 00:00:00

abstract：:Recent advances in the design and construction of synthetic multicelled systems in E. coli and S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing design frameworks for synthetic biology do not account for the unique ...

journal_title：ACS synthetic biology

authors： Jang SS,Oishi KT,Egbert RG,Klavins E

更新日期：2012-08-17 00:00:00

abstract：:Combinatorial metabolic engineering has been widely established for the development of efficient microbial cell factories to produce the products of interest by precisely regulating the expression levels of multiple genes simultaneously. Here, we report a novel multifunctional CRISPR system that enables simultaneous g...

journal_title：ACS synthetic biology

authors： Dong C,Jiang L,Xu S,Huang L,Cai J,Lian J,Xu Z

更新日期：2020-09-18 00:00:00

abstract：:The availability of different host chassis will greatly expand the range of applications in synthetic biology. Members of the Acetobacteraceae family of Gram-negative bacteria form an attractive class of nonmodel microorganisms that can be exploited to produce industrial chemicals, food and beverage, and biomaterials....

journal_title：ACS synthetic biology

authors： Teh MY,Ooi KH,Danny Teo SX,Bin Mansoor ME,Shaun Lim WZ,Tan MH

更新日期：2019-04-19 00:00:00

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

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

abstract：:Optogenetic control of endogenous signaling can be an important tool for probing cell behavior. Using the photoresponse of the LOV2 domain of Avena sativa phototropin 1, we developed analogues of kinase inhibitors whose activity is light dependent. Inhibitory peptides were appended to the Jα helix, where they potently...

journal_title：ACS synthetic biology

authors： Yi JJ,Wang H,Vilela M,Danuser G,Hahn KM

更新日期：2014-11-21 00:00:00

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

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

更新日期：2016-01-15 00:00:00

abstract：:Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large amounts of high-quality data to be parametrized and tested, which are not generally available. Here, ...

journal_title：ACS synthetic biology

authors： Morrell WC,Birkel GW,Forrer M,Lopez T,Backman TWH,Dussault M,Petzold CJ,Baidoo EEK,Costello Z,Ando D,Alonso-Gutierrez J,George KW,Mukhopadhyay A,Vaino I,Keasling JD,Adams PD,Hillson NJ,Garcia Martin H

更新日期：2017-12-15 00:00:00

abstract：:This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on t...

journal_title：ACS synthetic biology

authors： Sainz de Murieta I,Bultelle M,Kitney RI

更新日期：2016-08-19 00:00:00

abstract：:Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be describ...

journal_title：ACS synthetic biology

authors： Boemo MA,Lucas AE,Turberfield AJ,Cardelli L

更新日期：2016-08-19 00:00:00

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

authors： Roßmanith J,Weskamp M,Narberhaus F

更新日期：2018-02-16 00:00:00

abstract：:To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machiner...

journal_title：ACS synthetic biology

authors： Lentini R,Forlin M,Martini L,Del Bianco C,Spencer AC,Torino D,Mansy SS

更新日期：2013-09-20 00:00:00

abstract：:Most of the current methods for controlling the formation rate of a key protein or enzyme in cell factories rely on the manipulation of target genes within the pathway. In this article, we present a novel synthetic system for post-translational regulation of protein levels, FENIX, which provides both independent contr...

journal_title：ACS synthetic biology

authors： Durante-Rodríguez G,de Lorenzo V,Nikel PI

更新日期：2018-11-16 00:00:00

abstract：:The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since the...

journal_title：ACS synthetic biology

authors： Hafner J,MohammadiPeyhani H,Sveshnikova A,Scheidegger A,Hatzimanikatis V

更新日期：2020-06-19 00:00:00

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

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

更新日期：2012-09-21 00:00:00

abstract：:Bacteria of the order Actinomycetales are one of the most important sources of pharmacologically active and industrially relevant secondary metabolites. Unfortunately, many of them are still recalcitrant to genetic manipulation, which is a bottleneck for systematic metabolic engineering. To facilitate the genetic mani...

journal_title：ACS synthetic biology

authors： Tong Y,Charusanti P,Zhang L,Weber T,Lee SY

更新日期：2015-09-18 00:00:00

abstract：:The engineering of microbial metabolic pathways over the last two decades has led to numerous examples of cell factories used for the production of small molecules. These molecules have an array of utility in commercial industries and as in situ expressed biomarkers or therapeutics in microbial applications. While mos...

journal_title：ACS synthetic biology

authors： Chien T,Jones DR,Danino T

更新日期：2021-01-15 00:00:00

abstract：:Fluorescent proteins are widely used as fusion tags to detect protein expression in vivo. To become fluorescent, these proteins must undergo chromophore maturation, a slow process with a half-time of 5 to >30 min that causes delays in real-time detection of protein expression. Here, we engineer a genetically encoded f...

journal_title：ACS synthetic biology

authors： Eason MG,Pandelieva AT,Mayer MM,Khan ST,Garcia HG,Chica RA

更新日期：2020-11-20 00:00:00

abstract：:Feedback control allows cells to dynamically sense and respond to environmental changes. However, synthetic controller designs can be challenging because of implementation issues, such as determining optimal expression levels for circuit components within a feedback loop. Here, we addressed this by coupling rational d...

journal_title：ACS synthetic biology

authors： Siu Y,Fenno J,Lindle JM,Dunlop MJ

更新日期：2018-01-19 00:00:00