Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Bacillus subtilis Spores for Time-Delayed Protein Expression Applications.

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：: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：:In many biotechnological applications, it is useful for gene expression to be regulated by multiple signals, as this allows the programming of complex behavior. Here we implement, in Escherichia coli, a system that compares the concentration of two signal molecules, and tunes GFP expression proportionally to their rel...

journal_title：ACS synthetic biology

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

更新日期：2017-10-20 00:00:00

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

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

abstract：:It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction-diffusion system with two morphogens in a monostable regime, inspire...

journal_title：ACS synthetic biology

authors： Diambra L,Senthivel VR,Menendez DB,Isalan M

更新日期：2015-02-20 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：:Due to autotrophic growing capacity and extremely rich secondary metabolism, plants should be preferred targets of synthetic biology. However, developments in plants usually run below those in other taxonomic groups. In this work we engineered genetic circuits capable of logic YES, OR and AND Boolean computation in pl...

journal_title：ACS synthetic biology

authors： Cordero T,Rosado A,Majer E,Jaramillo A,Rodrigo G,Daròs JA

更新日期：2018-10-19 00:00:00

abstract：:Directed evolution experiments designed to improve the activity of a biocatalyst have increased in sophistication from the early days of completely random mutagenesis. Sequence-based and structure-based methods have been developed to identify "hotspot" positions that when randomized provide a higher frequency of benef...

journal_title：ACS synthetic biology

authors： Moore JC,Rodriguez-Granillo A,Crespo A,Govindarajan S,Welch M,Hiraga K,Lexa K,Marshall N,Truppo MD

更新日期：2018-07-20 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：: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：: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：:In response to emergent antibiotic resistance, new strategies are needed to enhance the effectiveness of existing antibiotics. Here, we describe a phagemid-delivered, RNA-mediated system capable of directly knocking down antibiotic resistance phenotypes. Small regulatory RNAs (sRNAs) were designed to specifically inhi...

journal_title：ACS synthetic biology

authors： Libis VK,Bernheim AG,Basier C,Jaramillo-Riveri S,Deyell M,Aghoghogbe I,Atanaskovic I,Bencherif AC,Benony M,Koutsoubelis N,Löchner AC,Marinkovic ZS,Zahra S,Zegman Y,Lindner AB,Wintermute EH

更新日期：2014-12-19 00:00:00

abstract：:Genome engineering technologies now enable precise manipulation of organism genotype, but can be limited in scalability by their design requirements. Here we describe Merlin ( http://merlincad.org ), an open-source web-based tool to assist biologists in designing experiments using multiplex automated genome engineerin...

journal_title：ACS synthetic biology

authors： Quintin M,Ma NJ,Ahmed S,Bhatia S,Lewis A,Isaacs FJ,Densmore D

更新日期：2016-06-17 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：:Transform-MinER (Transforming Molecules in Enzyme Reactions) is a web application facilitating the exploration of chemical biosynthetic space, guiding the user toward promising start points for enzyme design projects or directed evolution experiments. Two types of search are possible: Molecule Search allows a user to ...

journal_title：ACS synthetic biology

authors： Tyzack JD,Ribeiro AJM,Borkakoti N,Thornton JM

更新日期：2019-11-15 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：: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

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

更新日期：2013-11-15 00:00:00

abstract：:Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin...

journal_title：ACS synthetic biology

authors： Seker UO,Chen AY,Citorik RJ,Lu TK

更新日期：2017-02-17 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：:Episodic gene expression, with periods of high expression separated by periods of no expression, is a pervasive biological phenomenon. This bursty pattern of expression draws from a finite reservoir of expression machinery in a highly time variant way, i.e., requiring no resources most of the time but drawing heavily ...

journal_title：ACS synthetic biology

authors： Caveney PM,Norred SE,Chin CW,Boreyko JB,Razooky BS,Retterer ST,Collier CP,Simpson ML

更新日期：2017-02-17 00:00:00

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

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

更新日期：2018-10-19 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：: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：: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

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

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：:Synthetic biology relies on the manufacture of large and complex DNA constructs from libraries of genetic parts. Golden Gate and other Type IIS restriction enzyme-dependent DNA assembly methods enable rapid construction of genes and operons through one-pot, multifragment assembly, with the ordering of parts determined...

journal_title：ACS synthetic biology

authors： Potapov V,Ong JL,Kucera RB,Langhorst BW,Bilotti K,Pryor JM,Cantor EJ,Canton B,Knight TF,Evans TC Jr,Lohman GJS

更新日期：2018-11-16 00:00:00

abstract：:Synonymous mutation of the N-terminal coding sequence (NCS) has been used to regulate gene expression. We here developed a statistical model to predict the effect of the NCSs on protein expression in Bacillus subtilis WB600. First, a synonymous mutation was performed within the first 10 residues of a superfolder green...

journal_title：ACS synthetic biology

authors： Xu K,Tong Y,Li Y,Tao J,Li J,Zhou J,Liu S

更新日期：2021-01-19 00:00:00

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

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

更新日期：2019-02-15 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：: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