Exploring Chemical Biosynthetic Design Space with Transform-MinER.

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：: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：: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：: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：:Allosteric proteins, which can sense different signals, are interesting biological parts for synthetic biology. In particular, the design of an artificial allosteric enzyme to sense an unnatural signal is both challenging and highly desired, for example, for a precise and dynamical control of fluxes of growth-essentia...

journal_title：ACS synthetic biology

authors： Chen Z,Rappert S,Zeng AP

更新日期：2015-02-20 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：: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：:Fucosyl-oligosaccharides (FOSs) play physiologically important roles as prebiotics, neuronal growth factors, and inhibitors of enteropathogens. However, challenges in designed synthesis and mass production of FOSs hamper their industrial applications. Here, we report flexible biosynthetic routes to produce various FOS...

journal_title：ACS synthetic biology

authors： Yun EJ,Liu JJ,Lee JW,Kwak S,Yu S,Kim KH,Jin YS

更新日期：2019-02-15 00:00:00

abstract：:Characterization of genetic control elements is essential for the predictable engineering of synthetic biology systems. The current standard for in vivo characterization of control elements is through the use of fluorescent reporter proteins such as green fluorescent protein (GFP). Gene expression, however, involves n...

journal_title：ACS synthetic biology

authors： Pothoulakis G,Ceroni F,Reeve B,Ellis T

更新日期：2014-03-21 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：: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：: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：: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：: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：:Type I modular polyketide synthases (PKSs) are polymerases that utilize acyl-CoAs as substrates. Each polyketide elongation reaction is catalyzed by a set of protein domains called a module. Each module usually contains an acyltransferase (AT) domain, which determines the specific acyl-CoA incorporated into each conde...

journal_title：ACS synthetic biology

authors： Yuzawa S,Deng K,Wang G,Baidoo EE,Northen TR,Adams PD,Katz L,Keasling JD

更新日期：2017-01-20 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：: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：:Optogenetic tools can provide direct and programmable control of gene expression. Light-inducible recombinases, in particular, offer a powerful method for achieving precise spatiotemporal control of DNA modification. However, to-date this technology has been largely limited to eukaryotic systems. Here, we develop opto...

journal_title：ACS synthetic biology

authors： Sheets MB,Wong WW,Dunlop MJ

更新日期：2020-02-21 00:00:00

abstract：:A negating functionality is fundamental to information processing of logic circuits within cells and computers. Aiming to adapt unutilized electronic concepts to the interrogation of signaling circuits in cells, we first took a bottom-up strategy whereby we created protein-based devices that perform negating Boolean l...

journal_title：ACS synthetic biology

authors： Razavi S,Su S,Inoue T

更新日期：2014-09-19 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：:A bacterial flavin transferase (ApbE) was recently employed for flavin mononucleotide (FMN) modification on the Na+-translocating NADH:quinone oxidoreductase C (NqrC) protein in the pathogenic Gram-negative bacterium Vibrio cholerae. We employed this unique post-translational modification in mammalian cells and found ...

journal_title：ACS synthetic biology

authors： Kang MG,Park J,Balboni G,Lim MH,Lee C,Rhee HW

更新日期：2017-04-21 00:00:00

abstract：:The cellular response to hypoxia is orchestrated by HIF-1, a heterodimeric transcription factor composed of an α and a β subunit that enables cell survival under low oxygen conditions by altering the transcription of over 300 genes. There is significant evidence that inhibition of HIF-1 would be beneficial for cancer ...

journal_title：ACS synthetic biology

authors： Mistry IN,Tavassoli A

更新日期：2017-03-17 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：: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：:Lactams are an important class of commodity chemicals used in the manufacture of nylons, with millions of tons produced every year. Biological production of lactams could be greatly improved by high-throughput sensors for lactam biosynthesis. To identify biosensors of lactams, we applied a chemoinformatic approach ins...

journal_title：ACS synthetic biology

authors： Zhang J,Barajas JF,Burdu M,Ruegg TL,Dias B,Keasling JD

更新日期：2017-03-17 00:00:00

abstract：:Top-down reduction of the bacterial genome to construct desired chassis cells is important for synthetic biology. However, the current progress in the field of genome reduction is greatly hindered by indispensable life-essential genes that are interspersed throughout the chromosomal loci. Here, we described a new meth...

journal_title：ACS synthetic biology

authors： Xue X,Wang T,Jiang P,Shao Y,Zhou M,Zhong L,Wu R,Zhou J,Xia H,Zhao G,Qin Z

更新日期：2015-06-19 00:00:00

abstract：:The structural complexity of nonribosomal peptides (NRPs) impeding economic chemical synthesis and poor cultivability of source organisms limits the development of bioprocesses for novel bioactive compounds. Since nonribosomal peptide synthetases (NRPSs) assemble NRPs from simple amino acid building blocks, heterologo...

journal_title：ACS synthetic biology

authors： Jaitzig J,Li J,Süssmuth RD,Neubauer P

更新日期：2014-07-18 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：: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：: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