Comprehensive Profiling of Four Base Overhang Ligation Fidelity by T4 DNA Ligase and Application to DNA Assembly.

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：:Carotenoids, a variety of natural products, have significant pharmaceutical and commercial potential. Phytoene dehydrogenase (CrtI) is the rate-limit enzyme for carotenoid synthesis, whose catalysis specificity results in various carotenoids. However, the structural characteristics of CrtI for controlling the catalysi...

journal_title：ACS synthetic biology

authors： Liang N,Chen C,Wang Y,Ding MZ,Yao MD,Xiao WH,Yuan YJ

更新日期：2020-07-17 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：:Erythromycin is necessary in medical treatment and known to be biosynthesized with propionyl-CoA as direct precursor. Oversupply of propionyl-CoA induced hyperpropionylation, which was demonstrated as harmful for erythromycin synthesis in Saccharopolyspora erythraea. Herein, we identified three propionyl-CoA synthetas...

journal_title：ACS synthetic biology

authors： You D,Wang MM,Yin BC,Ye BC

更新日期：2019-02-15 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：: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：: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：: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：: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：:Bacterial biofilms are three-dimensional networks of cells entangled in a self-generated extracellular polymeric matrix composed of proteins, lipids, polysaccharides, and nucleic acids. Biofilms can establish themselves on virtually any accessible surface and lead to varying impacts ranging from infectious diseases to...

journal_title：ACS synthetic biology

authors： Balasubramanian S,Aubin-Tam ME,Meyer AS

更新日期：2019-07-19 00:00:00

abstract：:Design and implementation of synthetic biological circuits highly depends on well-characterized, robust promoters with predictable input-output responses. While great progress has been made with heterotrophic model organisms such as Escherichia coli, the available variety of tunable promoter parts for phototrophic cya...

journal_title：ACS synthetic biology

authors： Behle A,Saake P,Germann AT,Dienst D,Axmann IM

更新日期：2020-04-17 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：:As fast terminators of G-protein coupled receptor (GPCR) signaling, regulators of G-protein signaling (RGS) serve critical roles in fine-tuning second messenger levels and, consequently, cellular responses to external stimuli. Here, we report the creation of an optogenetic RGS2 (opto-RGS2) that suppresses agonist-evok...

journal_title：ACS synthetic biology

authors： Hannanta-Anan P,Chow BY

更新日期：2018-06-15 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：: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：: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：:While predictable design of a genetic circuit's output is a major goal of synthetic biology, it remains a significant challenge because DNA binding sites in the cell affect the concentration of available transcription factors (TF). To mitigate this problem, we propose to use a TF that results from the (reversible) pho...

journal_title：ACS synthetic biology

authors： Nilgiriwala KS,Jiménez J,Rivera PM,Del Vecchio D

更新日期：2015-05-15 00:00:00

abstract：:Nanostructures formed by self-assembled peptides have been increasingly exploited as functional materials for a wide variety of applications, from biotechnology to energy. However, it is sometimes challenging to assemble free short peptides into functional supramolecular structures, since not all peptides have the abi...

journal_title：ACS synthetic biology

authors： Abdali Z,Aminzare M,Zhu X,DeBenedictis E,Xie O,Keten S,Dorval Courchesne NM

更新日期：2020-12-18 00:00:00

abstract：:Medium-chain fatty acids (MCFAs) are key intermediates in the synthesis of medium-chain chemicals including α-olefins and dicarboxylic acids. In bacteria, microbial production of MCFAs is limited by the activity and product profile of fatty acyl-ACP thioesterases. Here, we engineer a heterologous bacterial medium-chai...

journal_title：ACS synthetic biology

authors： Sarria S,Bartholow TG,Verga A,Burkart MD,Peralta-Yahya P

更新日期：2018-05-18 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：: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：: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：: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：: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：:Sporulated cells have potential as time-delayed expression chassis of proteins for applications such as "on-demand" biologics production, whole cell biosensors, or oral vaccines. However, the desired attributes of high expression rates and low product variances are difficult to maintain from germinated spores. In this...

journal_title：ACS synthetic biology

authors： Tamiev D,Lantz A,Vezeau G,Salis H,Reuel NF

更新日期：2019-10-18 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：:Streptomycetes are Gram-positive mycelial bacteria, which synthesize a wide range of natural products including over two-thirds of the currently available antibiotics. However, metabolic engineering in Streptomyces species to overproduce a vast of natural products are hampered by a limited number of genetic tools. Her...

journal_title：ACS synthetic biology

authors： Yi JS,Kim MW,Kim M,Jeong Y,Kim EJ,Cho BK,Kim BG

更新日期：2017-03-17 00:00:00

abstract：:Site directed RNA editing is an engineered tool for the posttranscriptional manipulation of RNA and proteins. Here, we demonstrate the inclusion of additional N- and C-terminal protein domains in an RNA editing-dependent manner to switch between protein isoforms in mammalian cell culture. By inclusion of localization ...

journal_title：ACS synthetic biology

authors： Vogel P,Hanswillemenke A,Stafforst T

更新日期：2017-09-15 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 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