Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits.

abstract：:Engineered bacteria promise to revolutionize diagnostics and therapeutics, yet many applications are precluded by the limited number of detectable signals. Here we present a general framework to engineer synthetic receptors enabling bacterial cells to respond to novel ligands. These receptors are activated via ligand-...

journal_title：ACS synthetic biology

authors： Chang HJ,Mayonove P,Zavala A,De Visch A,Minard P,Cohen-Gonsaud M,Bonnet J

更新日期：2018-01-19 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：:Genetic switches in which the activity of T7 RNA polymerase (RNAP) is directly regulated by external signals are obtained with an engineering strategy of splitting the protein into fragments and using regulatory domains to modulate their reconstitutions. Robust switchable systems with excellent dark-off/light-on prope...

journal_title：ACS synthetic biology

authors： Han T,Chen Q,Liu H

更新日期：2017-02-17 00:00:00

abstract：:Noncanonical amino acids form a highly diverse pool of building blocks that can render unique physicochemical properties to peptides and proteins. Here, four methionine analogues with unsaturated and varying side chain lengths were successfully incorporated at four different positions in nisin in Lactococcus lactis th...

journal_title：ACS synthetic biology

authors： Deng J,Viel JH,Chen J,Kuipers OP

更新日期：2020-09-18 00:00:00

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

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

abstract：:Robust and precise ratio control of heterogeneous phenotypes within an isogenic population is an essential task, especially in the development and differentiation of a large number of cells such as bacteria, sensory receptors, and blood cells. However, the mechanisms of such ratio control are poorly understood. Here, ...

journal_title：ACS synthetic biology

authors： Menn D,Sochor P,Goetz H,Tian XJ,Wang X

更新日期：2019-06-21 00:00:00

abstract：:Phages are biological entities found in every ecosystem. Although much has been learned about them in past decades, significant knowledge gaps remain. Manipulating virulent phage genomes is challenging. To date, no efficient gene-editing tools exist for engineering virulent lactococcal phages. Lactococcus lactis is a ...

journal_title：ACS synthetic biology

authors： Lemay ML,Tremblay DM,Moineau S

更新日期：2017-07-21 00:00:00

abstract：:The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved fo...

journal_title：ACS synthetic biology

authors： Natarajan A,Haitjema CH,Lee R,Boock JT,DeLisa MP

更新日期：2017-05-19 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：: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

authors： Ramakrishnan P,Tabor JJ

更新日期：2016-07-15 00:00:00

abstract：:Prenylated aromatic compounds are important intermediates in the biosynthesis of bioactive molecules such as 3-chromanols from plants, ubiquinones from prokaryotes and meroterpenoids from sponges. Biosynthesis of prenylated aromatic compounds using prokaryotic microorganisms has attracted increasing attention in the f...

journal_title：ACS synthetic biology

authors： He BB,Bu XL,Zhou T,Li SM,Xu MJ,Xu J

更新日期：2018-09-21 00:00:00

abstract：:We study translation repression in bacteria by engineering a regulatory circuit that functions as a binding assay for RNA binding proteins (RBP) in vivo. We do so by inducing expression of a fluorescent protein-RBP chimera, together with encoding its binding site at various positions within the ribosomal initiation re...

journal_title：ACS synthetic biology

authors： Katz N,Cohen R,Solomon O,Kaufmann B,Atar O,Yakhini Z,Goldberg S,Amit R

更新日期：2018-12-21 00:00:00

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

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

更新日期：2014-10-17 00:00:00

abstract：:Microorganisms often use specific autoinducers other than common metabolites for quorum sensing (QS). Herein, we demonstrated that Escherichia coli produced sulfide (H2S, HS-, and S2-) with the concentrations proportionally correlated to its cell density. We then designed synthetic gene circuits that used H2S as an au...

journal_title：ACS synthetic biology

authors： Liu H,Fan K,Li H,Wang Q,Yang Y,Li K,Xia Y,Xun L

更新日期：2019-09-20 00:00:00

abstract：:The microbial ability to resist stressful environmental conditions and chemical inhibitors is of great industrial and medical interest. Much of the data related to mutation-based stress resistance, however, is scattered through the academic literature, making it difficult to apply systematic analyses to this wealth of...

journal_title：ACS synthetic biology

authors： Winkler JD,Halweg-Edwards AL,Erickson KE,Choudhury A,Pines G,Gill RT

更新日期：2016-12-16 00:00:00

abstract：:Exploiting simple types of symmetry common to many natural protein oligomers as a starting point, several recent studies have succeeded in engineering complex self-assembling protein architectures reminiscent but distinct from those evolved in the natural world. Designing symmetric protein cages with a wide range of p...

journal_title：ACS synthetic biology

authors： Cannon KA,Nguyen VN,Morgan C,Yeates TO

更新日期：2020-03-20 00:00:00

abstract：:2-Pyrone-4,6-dicarboxylic acid (PDC) is a pseudoaromatic dicarboxylic acid and is a promising biobased building block chemical that can be used to make diverse polyesters with novel functionalities. In this study, Escherichia coli was metabolically engineered to produce PDC from glucose. First, an efficient biosynthet...

journal_title：ACS synthetic biology

authors： Luo ZW,Kim WJ,Lee SY

更新日期：2018-09-21 00:00:00

abstract：:Movement of molecules across membranes in response to a stimulus is a key component of cellular programming. Here, we characterize and manipulate the response of a protein-based piston capable of puncturing membranes in a pH-dependent manner. Our protein actuator consists of modified R bodies found in a bacterial endo...

journal_title：ACS synthetic biology

authors： Polka JK,Silver PA

更新日期：2016-04-15 00:00:00

abstract：:Heterochiral DNA strand-displacement reactions enable sequence-specific interfacing of oligonucleotide enantiomers, making it possible to interface native d-nucleic acids with molecular circuits built using nuclease-resistant l-DNA. To date, all heterochiral reactions have relied on peptide nucleic acid (PNA), which p...

journal_title：ACS synthetic biology

authors： Young BE,Sczepanski JT

更新日期：2019-12-20 00:00:00

abstract：:We recently developed a technique for rapidly and reversibly inhibiting protein function through light-inducible sequestration of proteins away from their normal sites of action. Here, we adapt this method for inducible inactivation of Bem1, a scaffold protein involved in budding yeast polarity. We find that acute inh...

journal_title：ACS synthetic biology

authors： Jost AP,Weiner OD

更新日期：2015-10-16 00:00:00

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

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

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

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

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：: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：:Staphylococci are prevalent skin-dwelling bacteria that are also leading causes of antibiotic-resistant infections. Viruses that infect and lyse these organisms (virulent staphylococcal phages) can be used as alternatives to conventional antibiotics and represent promising tools to eliminate or manipulate specific spe...

journal_title：ACS synthetic biology

authors： Bari SMN,Walker FC,Cater K,Aslan B,Hatoum-Aslan A

更新日期：2017-12-15 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：:Cellobiose phosphorylase (CBP) cleaves cellobiose-abundant in plant biomass-to glucose and glucose 1-phosphate. However, the pentose sugar xylose, also abundant in plant biomass, acts as a mixed-inhibitor and a substrate for the reverse reaction, limiting the industrial potential of CBP. Preventing xylose, which lacks...

journal_title：ACS synthetic biology

authors： Chomvong K,Lin E,Blaisse M,Gillespie AE,Cate JH

更新日期：2017-02-17 00:00:00

abstract：:Owl ( www.owlcad.org ) is a biodesign automation tool that generates electronic datasheets for synthetic biological parts using common formatting. Data can be retrieved automatically from existing repositories and modified in the Owl user interface (UI). Owl uses the data to generate an HTML page with standard typeset...

journal_title：ACS synthetic biology

authors： Appleton E,Tao J,Wheatley FC,Desai DH,Lozanoski TM,Shah PD,Awtry JA,Jin SS,Haddock TL,Densmore DM

更新日期：2014-12-19 00:00:00

abstract：:As light-regulated actuators, sensory photoreceptors underpin optogenetics and numerous applications in synthetic biology. Protein engineering has been applied to fine-tune the properties of photoreceptors and to generate novel actuators. For the blue-light-sensitive light-oxygen-voltage (LOV) photoreceptors, mutation...

journal_title：ACS synthetic biology

authors： Diensthuber RP,Engelhard C,Lemke N,Gleichmann T,Ohlendorf R,Bittl R,Möglich A

更新日期：2014-11-21 00:00:00

abstract：:The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, ...

journal_title：ACS synthetic biology

authors： Opgenorth P,Costello Z,Okada T,Goyal G,Chen Y,Gin J,Benites V,de Raad M,Northen TR,Deng K,Deutsch S,Baidoo EEK,Petzold CJ,Hillson NJ,Garcia Martin H,Beller HR

更新日期：2019-06-21 00:00:00