1,277 results match your criteria Acs Synthetic Biology[Journal]


Core catalysis of the reductive glycine pathway demonstrated in yeast.

ACS Synth Biol 2019 Apr 19. Epub 2019 Apr 19.

One-carbon (C1) compounds are attractive microbial feedstocks as they can be efficiently produced from widely available resources. Formate, in particular, represents a promising growth substrate, as it can be generated from electrochemical reduction of CO2 and fed to microorganisms in a soluble form. We previously identified the synthetic reductive glycine pathway as the most efficient route for aerobic growth on formate. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00464
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http://dx.doi.org/10.1021/acssynbio.8b00464DOI Listing
April 2019
1 Read

Protein-programmed accumulation of yeast cytosine deaminase in cancer cells in response to mock-hypoxia.

ACS Synth Biol 2019 Apr 18. Epub 2019 Apr 18.

One limitation of gene-directed enzyme prodrug therapy (GDEPT) is the difficulty in selectively and efficiently transducing cancer cells with the gene encoding a prodrug-converting enzyme. To circumvent this issue, we sought to move the selectivity from the gene delivery level to the protein level. We developed fusion proteins of the prodrug-activating enzyme yeast cytosine deaminase (yCD) and the oxygen-dependent degradation domain (ODDD) of HIF-1α, a domain that regulates the accumulation of HIF-1α in an oxygen-dependent manner. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00036DOI Listing

Genetic incorporation of noncanonical amino acids using two mutually orthogonal quadruplet codons.

ACS Synth Biol 2019 Apr 17. Epub 2019 Apr 17.

Genetic incorporation of noncanonical amino acids has emerged as a powerful tool for the study of protein structure and function. While the three triplet nonsense codons have been widely explored, quadruplet codons have attracted attention for the potential of creating additional blank codons for noncanonical amino acid mutagenesis. Here we demonstrated for the first time that two orthogonal quadruplet codons could be used to simultaneously encode two different noncanonical amino acids within a single protein in bacterial cells. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00051DOI Listing

Biosynthesis and heterologous production of argyrins.

ACS Synth Biol 2019 Apr 17. Epub 2019 Apr 17.

Argyrins represent a family of cyclic octapeptides exhibiting promising antimicrobial, antitumorigenic and immunosuppressant activities. They derive from a nonribosomal peptide synthetase pathway, which was identified and characterized in this study from the myxobacterial producer strain Cystobacter sp. SBCb004. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.9b00023
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http://dx.doi.org/10.1021/acssynbio.9b00023DOI Listing
April 2019
1 Read

DNA sequencing method including unnatural bases for DNA aptamer generation by genetic alphabet expansion.

ACS Synth Biol 2019 Apr 17. Epub 2019 Apr 17.

The creation of unnatural base pairs (UBPs) has rapidly advanced the genetic alphabet expansion technology of DNA, requiring a new sequencing method for UB-containing DNAs with five or more letters. The hydrophobic UBP, Ds‒Px, exhibits high fidelity in PCR and has been applied to DNA aptamer generation involving Ds as a fifth base. Here, we present a sequencing method for Ds-containing DNAs, in which Ds bases are replaced with natural bases by PCR using intermediate UB substrates (replacement PCR) for conventional deep sequencing. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00087DOI Listing

Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications.

ACS Synth Biol 2019 Apr 17. Epub 2019 Apr 17.

Well-characterised promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterisation to expand the promoter toolkit, and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00061DOI Listing

Engineering an artificial membrane vesicle trafficking system (AMVTS) for the excretion of β-carotene in Escherichia coli.

ACS Synth Biol 2019 Apr 16. Epub 2019 Apr 16.

Large hydrophobic molecules, such as carotenoids, cannot be effectively excreted from cells by natural transportation systems. These products accumulate inside cells and affect normal cellular physiological functions, which hinders further improvement of carotenoid production by microbial cell factories. In this study, we proposed to construct a novel artificial transport system utilize membrane lipids to carry and transport hydrophobic molecules. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00472DOI Listing
April 2019
1 Read

Engineering a Synthetic, Catabolically-Orthogonal Co-Culture System for Enhanced Conversion of Lignocellulose-Derived Sugars to Ethanol.

ACS Synth Biol 2019 Apr 12. Epub 2019 Apr 12.

Fermentation of lignocellulosic sugar mixtures is often suboptimal due to inefficient xylose catabolism and sequential sugar utilization caused by carbon catabolite repression. Unlike in conventional applications employing a single engineered strain, the alternative development of synthetic microbial communities facilitates the execution of complex metabolic tasks by exploiting the unique community features, including modularity, division of labor and facile tunability. A series of synthetic, catabolically-orthogonal co-culture systems were systematically engineered, as derived from either wild-type Escherichia coli W or ethanologenic LY180. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00007DOI Listing

Fine-tuning native promoters of Synechococcus elongatus PCC 7942 to develop synthetic toolbox for heterologous protein expression.

ACS Synth Biol 2019 Apr 11. Epub 2019 Apr 11.

The cyanobacterium Synechococcus elongatus PCC 7942 is a potential photosynthetic cell-factory. In this study, two native promoters from S. elongatus PCC 7942 driving the expression of abundant cyanobacterial proteins phycocyanin (PcpcB7942) and RuBisCO (Prbc7942) were characterized in relation to their sequence features, expression levels, diurnal behaviour and regulation by light and CO2, major abiotic factors important for cyanobacterial growth. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00066DOI Listing

Combining protein and metabolic engineering strategies for high-level production of O-acetylhomoserine in Escherichia coli.

ACS Synth Biol 2019 Apr 11. Epub 2019 Apr 11.

O-acetylhomoserine (OAH) is a promising platform chemical for the production of L-methionine and other valuable compounds. However, the relative low titer and yield of OAH greatly limit its industrial production and cost-effective application. In this study, we successfully constructed an efficient OAH-producing strain with high titer and yield by combining protein and metabolic engineering strategies in E. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00042DOI Listing
April 2019
3.951 Impact Factor

Construction of Bacterial Cells with an Active Transport System for Unnatural Amino Acids.

ACS Synth Biol 2019 Apr 16. Epub 2019 Apr 16.

Department of Chemistry , Sogang University , Seoul 121-742 , Republic of Korea.

Engineered organisms with an expanded genetic code have attracted much attention in chemical and synthetic biology research. In this work, engineered bacterial organisms with enhanced unnatural amino acid (UAA) uptake abilities were developed by screening periplasmic binding protein (PBP) mutants for recognition of UAAs. A FRET-based assay was used to identify a mutant PBP (LBP-AEL) with excellent binding affinity ( K ≈ 500 nM) to multiple UAAs from 37 mutants. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00076DOI Listing

A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions.

ACS Synth Biol 2019 Apr 18. Epub 2019 Apr 18.

Department of Biochemistry Molecular Pharmacology and Institute for Systems Genetics , NYU Langone Health , New York , New York 10016 , United States.

The accurate determination of protein-protein interactions has been an important focus of molecular biology toward which much progress has been made due to the continuous development of existing and new technologies. However, current methods can have limitations, including scale and restriction to high affinity interactions, limiting our understanding of a large subset of these interactions. Here, we describe a modified bacterial-hybrid assay that employs combined selectable and scalable reporters that enable the sensitive screening of large peptide libraries followed by the sorting of positive interactions by the level of reporter output. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00499DOI Listing
April 2019
2 Reads
3.951 Impact Factor

Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.

ACS Synth Biol 2019 Apr 16. Epub 2019 Apr 16.

Division of Materials Science, Graduate School of Science and Technology , Nara Institute of Science and Technology , 8916-5 Takayama , Ikoma , Nara 630-0192 , Japan.

Self-assembled protein nanostructures have gained interest, owing to their potential applications in biomaterials; however, successful design and construction of protein nanostructures are limited. Herein, we constructed fusion protein 1 by linking the C-terminus of a dimerization domain and the N-terminus of another dimerization domain with a three-helix bundle protein, where it self-assembled mainly into tetramers. By replacing the C-terminal dimerization domain of 1 with a trimerization domain (fusion protein 2), hexamers were mainly obtained. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00019DOI Listing

Thermostability Trends of TNA:DNA Duplexes Reveal Strong Purine Dependence.

ACS Synth Biol 2019 Apr 17. Epub 2019 Apr 17.

Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States.

The development of high fidelity polymerases and streamlined synthesis of threose nucleic acid (TNA) triphosphates and phosphoramidites has made TNA accessible as a motif for generating nuclease-resistant high-affinity aptamers, antisense oligos, and synthetic genetic biopolymers. Little is known, however, about the thermostability trends of TNA:DNA duplexes. Here we investigate the thermostability of 14 TNA:DNA duplexes with the goal of elucidating the fundamental factors governing TNA:DNA duplex stability. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00028DOI Listing

Microfluidic Synchronizer Using a Synthetic Nanoparticle-Capped Bacterium.

ACS Synth Biol 2019 Apr 12. Epub 2019 Apr 12.

Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology , Chinese Academy of Sciences , Shenzhen 518055 , People's Republic of China.

Conventional techniques to synchronize bacterial cells often require manual manipulations and lengthy incubation lacking precise temporal control. An automated microfluidic device was recently developed to overcome these limitations. However, it exploits the stalk property of Caulobacter crescentus that undergoes asymmetric stalked and swarmer cell cycle stages and is therefore restricted to this species. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.9b00058
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http://dx.doi.org/10.1021/acssynbio.9b00058DOI Listing
April 2019
2 Reads

Optogenetic Downregulation of Protein Levels with an Ultrasensitive Switch.

ACS Synth Biol 2019 Apr 16. Epub 2019 Apr 16.

Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8 , Marburg , 35032 , Germany.

Optogenetic control of protein activity is a versatile technique to gain control over cellular processes, for example, for biomedical and biotechnological applications. Among other techniques, the regulation of protein abundance by controlling either transcription or protein stability found common use as this controls the activity of any type of target protein. Here, we report modules of an improved variant of the photosensitive degron module and a light-sensitive transcription factor, which we compared to doxycycline-dependent transcriptional control. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00471DOI Listing
April 2019
2 Reads

Knock-In Strategy for Editing Human and Zebrafish Mitochondrial DNA Using Mito-CRISPR/Cas9 System.

ACS Synth Biol 2019 Apr 10;8(4):621-632. Epub 2019 Apr 10.

Key Laboratory of Reservoir Aquatic Environment , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , China.

The mitochondria DNA (mtDNA) editing tool, zinc finger nucleases (ZFNs), transcription activator-like effector nuclease (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system, is a promising approach for the treatment of mtDNA diseases by eliminating mutant mitochondrial genomes. However, there have been no reports of repairing the mutant mtDNA with homologous recombination strategy to date. Here, we show a mito-CRISPR/Cas9 system that mito-Cas9 protein can specifically target mtDNA and reduce mtDNA copy number in both human cells and zebrafish. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00411DOI Listing

A CRISPR-Cas9 Strategy for Activating the Saccharopolyspora erythraea Erythromycin Biosynthetic Gene Cluster with Knock-in Bidirectional Promoters.

ACS Synth Biol 2019 Apr 15. Epub 2019 Apr 15.

Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China.

The regulation of biosynthetic pathways is a universal strategy for industrial strains that overproduce metabolites. Erythromycin produced by Saccharopolyspora erythraea has extensive clinical applications. In this study, promoters of the erythromycin biosynthesis gene cluster were tested by reporter mCherry. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.9b00024
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http://dx.doi.org/10.1021/acssynbio.9b00024DOI Listing
April 2019
4 Reads

Improved Optical Multiplexing with Temporal DNA Barcodes.

ACS Synth Biol 2019 Apr 16. Epub 2019 Apr 16.

Department of Electrical & Computer Engineering , Duke University , Durham , North Carolina 27701 , United States.

Many biochemical events of importance are complex and dynamic. Fluorescence microscopy offers a versatile solution to study the dynamics of biology at the mesoscale. An important challenge in the field is the simultaneous study of several objects of interest, referred to as optical multiplexing. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.9b00010
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http://dx.doi.org/10.1021/acssynbio.9b00010DOI Listing
April 2019
1 Read

Developing Riboswitch-Mediated Gene Regulatory Controls in Thermophilic Bacteria.

ACS Synth Biol 2019 Apr 5;8(4):633-640. Epub 2019 Apr 5.

Biosciences Center , National Renewable Energy Laboratory , Golden , Colorado 80401 , United states.

Thermophilic bacteria are attractive hosts to produce bio-based chemicals. While various genetic manipulations have been employed in the metabolic engineering of thermophiles, a robust means to regulate gene expression in these bacteria (∼55 °C) is missing. Our bioinformatic search for various riboswitches in thermophilic bacteria revealed that major classes of riboswitches are present, suggesting riboswitches' regulatory roles in these bacteria. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00487DOI Listing

Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics.

ACS Synth Biol 2019 Apr 9;8(4):647-654. Epub 2019 Apr 9.

FFCLRP , University of São Paulo , 14049-901 Ribeirão Preto , São Paulo , Brazil.

As the field of synthetic biology moves toward the utilization of novel bacterial chassis, there is a growing need for biological parts with enhanced performance in a wide number of hosts. Is not unusual that biological parts (such as promoters and terminators), initially characterized in the model bacterium Escherichia coli, do not perform well when implemented in alternative hosts, such as Pseudomonas, therefore limiting the construction of synthetic circuits in industrially relevant bacteria, for instance Pseudomonas putida. In order to address this limitation, we present here the mining of transcriptional terminators through functional metagenomics to identify novel parts with broad host-range activity. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00507DOI Listing

Rapid Assembly of gRNA Arrays via Modular Cloning in Yeast.

ACS Synth Biol 2019 Apr 11;8(4):906-910. Epub 2019 Apr 11.

Imperial College Centre for Synthetic Biology , Imperial College London , London , SW7 2AZ , U.K.

CRISPR is a versatile technology for genomic editing and regulation, but the expression of multiple gRNAs in S. cerevisiae has thus far been limited. We present here a simple extension to the Yeast MoClo Toolkit, which enables the rapid assembly of gRNA arrays using a minimal set of parts. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00041DOI Listing
April 2019
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Development of Whole-Porcine Monoclonal Antibodies with Potent Neutralization Activity against Classical Swine Fever Virus from Single B Cells.

ACS Synth Biol 2019 Apr 12. Epub 2019 Apr 12.

Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Science , Jilin University , Changchun 130062 , Jilin Province , People's Republic of China.

Classical swine fever (CSF) is a highly contagious swine disease that causes devastating economic losses. However, there are few efficacious therapeutic antibodies against the CSF virus (CSFV). Accordingly, we isolated two whole-porcine anti-CSFV neutralizing antibodies (NAbs) directly from single B cells sorted using the conserved linear epitope of the CSFV E2 protein and goat anti-pig IgG. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00365
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http://dx.doi.org/10.1021/acssynbio.8b00365DOI Listing
April 2019
6 Reads

Building an Inducible T7 RNA Polymerase/T7 Promoter Circuit in Synechocystis sp. PCC6803.

ACS Synth Biol 2019 Apr 3;8(4):655-660. Epub 2019 Apr 3.

Department of Plant Biology , Carnegie Institution for Science , Stanford , California 94305 , United States.

To develop tightly regulated orthogonal gene expression circuits in the photoautotrophic cyanobacterium Synechocystis sp. PCC6803 (Syn6803), we designed a circuit in which a native inducible promoter drives the expression of phage T7 RNA polymerase (T7RNAP). T7RNAP, in turn, specifically recognizes the T7 promoter that is designed to drive GFP expression. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00515DOI Listing

Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies.

ACS Synth Biol 2019 Apr 15. Epub 2019 Apr 15.

CEB - Centre of Biological Engineering , University of Minho, Campus de Gualtar , Braga 4710-057 , Portugal.

The uncertain relationship between genotype and phenotype can make strain engineering an arduous trial and error process. To identify promising gene targets faster, constraint-based modeling methodologies are often used, although they remain limited in their predictive power. Even though the search for gene knockouts is fairly established in constraint-based modeling, most strain design methods still model gene up/down-regulations by forcing the corresponding flux values to fixed levels without taking in consideration the availability of resources. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00248
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http://dx.doi.org/10.1021/acssynbio.8b00248DOI Listing
April 2019
4 Reads

BioBits Health: Classroom activities exploring engineering, biology, and human health with fluorescent readouts.

ACS Synth Biol 2019 Mar 29. Epub 2019 Mar 29.

Recent advances in synthetic biology have resulted in biological technologies with the potential to reshape the way we understand and treat human disease. Educating students about the biology and ethics underpinning these technologies is critical to empower them to make informed future policy decisions regarding their use and to inspire the next generation of synthetic biologists. However, hands-on, educational activities that convey emerging synthetic biology topics can be difficult to implement due to the expensive equipment and expertise required to grow living cells. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00381DOI Listing
March 2019
1 Read

PERSIA for Direct Fluorescence Measurements of Transcription, Translation, and Enzyme Activity in Cell-Free Systems.

ACS Synth Biol 2019 Mar 28. Epub 2019 Mar 28.

Quantification of biology's central dogma (transcription and translation) is pursued by a variety of methods. Direct, immediate and ongoing quantification of these events is difficult to achieve. Common practice is to use fluorescent or luminescent proteins to report indirectly on prior cellular events, such as turning on a gene in a genetic circuit. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00450DOI Listing

An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries.

ACS Synth Biol 2019 Apr 2;8(4):844-856. Epub 2019 Apr 2.

Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , California 94720 , United States.

We present an accessible, robust continuous-culture turbidostat system that greatly facilitates the generation and phenotypic analysis of highly complex libraries in yeast and bacteria. Our system has many applications in genomics and systems biology; here, we demonstrate three of these uses. We first measure how the growth rate of budding yeast responds to limiting nitrogen at steady state and in a dynamically varying environment. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00529
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http://dx.doi.org/10.1021/acssynbio.8b00529DOI Listing
April 2019
4 Reads

Structural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies.

ACS Synth Biol 2019 Apr 27;8(4):668-674. Epub 2019 Mar 27.

Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.

Bacterial microcompartments are subcellular compartments found in many prokaryotes; they consist of a protein shell that encapsulates enzymes that perform a variety of functions. The shell protects the cell from potentially toxic intermediates and colocalizes enzymes for higher efficiency. Accordingly, it is of considerable interest for biotechnological applications. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00011DOI Listing

A Yeast System for Discovering Optogenetic Inhibitors of Eukaryotic Translation Initiation.

ACS Synth Biol 2019 Apr 4;8(4):744-757. Epub 2019 Apr 4.

Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada.

The precise spatiotemporal regulation of protein synthesis is essential for many complex biological processes such as memory formation, embryonic development, and tumor formation. Current methods used to study protein synthesis offer only a limited degree of spatiotemporal control. Optogenetic methods, in contrast, offer the prospect of controlling protein synthesis noninvasively within minutes and with a spatial scale as small as a single synapse. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00386DOI Listing
April 2019
3.951 Impact Factor

The Generation of Thermostable Fungal Laccase Chimeras by SCHEMA-RASPP Structure-Guided Recombination in Vivo.

ACS Synth Biol 2019 Apr 1;8(4):833-843. Epub 2019 Apr 1.

Department of Biocatalysis , Institute of Catalysis, CSIC , Cantoblanco , 28049 Madrid , Spain.

Fungal laccases are biotechnologically relevant enzymes that are capable of oxidizing a wide array of compounds, using oxygen from the air and releasing water as the only byproduct. The laccase structure is comprised of three cupredoxin domains sheltering two copper centers-the T1Cu site and the T2/T3 trinuclear Cu cluster-connected to each other through a highly conserved internal electron transfer pathway. As such, the generation of laccase chimeras with high sequence diversity from different orthologs is difficult to achieve without compromising protein functionality. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00509
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http://dx.doi.org/10.1021/acssynbio.8b00509DOI Listing
April 2019
3 Reads

Combinatorial Sensor Design in Caulobacter crescentus for Selective Environmental Uranium Detection.

ACS Synth Biol 2019 Apr 3;8(4):807-817. Epub 2019 Apr 3.

Environmental Restoration Department (ERD), Operations and Business Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States.

The ability to detect uranium (U) through environmental monitoring is of critical importance for informing water resource protection and nonproliferation efforts. While technologies exist for environmental U detection, wide-area environmental monitoring, i.e. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00484DOI Listing

Systematic Evaluation of Genetic and Environmental Factors Affecting Performance of Translational Riboswitches.

Authors:
R Kent N Dixon

ACS Synth Biol 2019 Apr 2;8(4):884-901. Epub 2019 Apr 2.

Manchester Institute of Biotechnology, School of Chemistry , University of Manchester , Manchester M13 9PL , United Kingdom.

Since their discovery, riboswitches have been attractive tools for the user-controlled regulation of gene expression in bacterial systems. Riboswitches facilitate small molecule mediated fine-tuning of protein expression, making these tools of great use to the synthetic biology community. However, the use of riboswitches is often restricted due to context dependent performance and limited dynamic range. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00017DOI Listing

Modeling Genetic Circuit Behavior in Transiently Transfected Mammalian Cells.

ACS Synth Biol 2019 Apr 28;8(4):697-707. Epub 2019 Mar 28.

The Bioinformatics Graduate Program , Boston University , Boston , Massachusetts 02215 , United States.

Binning cells by plasmid copy number is a common practice for analyzing transient transfection data. In many kinetic models of transfected cells, protein production rates are assumed to be proportional to plasmid copy number. The validity of this assumption in transiently transfected mammalian cells is not clear; models based on this assumption appear unable to reproduce experimental flow cytometry data robustly. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00166
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http://dx.doi.org/10.1021/acssynbio.8b00166DOI Listing
April 2019
3 Reads

Membrane-Bound Protein Scaffolding in Diverse Hosts Using Thylakoid Protein CURT1A.

ACS Synth Biol 2019 Apr 22;8(4):611-620. Epub 2019 Mar 22.

Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences , University of Copenhagen , 1871 Frederiksberg C , Denmark.

Protein scaffolding is a useful strategy for controlling the spatial arrangement of cellular components via protein-protein interactions. Protein scaffolding has primarily been used to colocalize soluble proteins in the cytoplasm, but many proteins require membrane association for proper function. Scaffolding at select membrane domains would provide an additional level of control over the distribution of proteins within a cell and could aid in exploiting numerous metabolic pathways that contain membrane-associated enzymes. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00418DOI Listing

SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli.

ACS Synth Biol 2019 Mar 18. Epub 2019 Mar 18.

Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry , University of Manchester , Manchester M1 7DN , U.K.

The rapid prototyping and optimization of plasmid-based recombinant gene expression is one of the key steps in the development of bioengineered bacterial systems. Often, multiple genes or gene modules need to be coexpressed, and for this purpose compatible, inducible plasmid systems have been developed. However, inducible expression systems are not favored in industrial processes, due to their prohibitive cost, and consequently the conversion to constitutive expression systems is often desired. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00399DOI Listing

An Expanded Synthetic Biology Toolkit for Gene Expression Control in Acetobacteraceae.

ACS Synth Biol 2019 Apr 22;8(4):708-723. Epub 2019 Mar 22.

School of Chemical and Biomedical Engineering , Nanyang Technological University , 637459 Singapore.

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. One such biomaterial is bacterial cellulose, which is a strong and ultrapure natural polymer used in tissue engineering scaffolds, wound dressings, electronics, food additives, and other products. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00168DOI Listing
April 2019
2 Reads

Direct Aromatic Nitration System for Synthesis of Nitrotryptophans in Escherichia coli.

ACS Synth Biol 2019 Apr 25;8(4):857-865. Epub 2019 Mar 25.

Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy , University of Florida , Gainesville , Florida 32610 , United States.

Nitrotryptophan and its analogues are useful building blocks for synthesizing bioactive and biotechnologically relevant chemicals, materials, and proteins. However, synthetic routes to enantiopure nitro-containing tryptophan derivatives are either complex and polluting or even unestablished yet. Herein, we describe microbial production of 4-NO-l-tryptophan (Nitrotrp) and its analogues by designing and expressing the biosynthetic pathway in Escherichia coli. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00534
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http://dx.doi.org/10.1021/acssynbio.8b00534DOI Listing
April 2019
3 Reads

Spatiotemporal Gene Repression System in the Heterocyst-Forming Multicellular Cyanobacterium Anabaena sp. PCC 7120.

ACS Synth Biol 2019 Apr 19;8(4):641-646. Epub 2019 Mar 19.

Department of Biological Sciences, Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-Osawa , Hachioji , Tokyo 192-0397 , Japan.

The heterocyst-forming multicellular cyanobacterium Anabaena sp. PCC 7120 is often used as a model organism for prokaryotic cell differentiation. We recently demonstrated that heterocysts are suitable for photosynthetic production of valuable chemicals, such as ethanol, due to their active catabolism and microoxic conditions. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00496
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http://dx.doi.org/10.1021/acssynbio.8b00496DOI Listing
April 2019
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Metabolic Engineering of Main Transcription Factors in Carbon, Nitrogen, and Phosphorus Metabolisms for Enhanced Production of Bacitracin in Bacillus licheniformis.

ACS Synth Biol 2019 Apr 22;8(4):866-875. Epub 2019 Mar 22.

State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences , Hubei University , Wuhan 430062 , PR China.

Primary metabolism plays a key role in the synthesis of secondary metabolite. In this study, the main transcription factors in carbon, nitrogen, and phosphorus metabolisms (CcpA, CcpC, CcpN, CodY, TnrA, GlnR, and PhoP) were engineered to improve bacitracin yield in Bacillus licheniformis DW2, an industrial strain for bacitracin production. First, our results demonstrated that deletions of ccpC and ccpN improved ATP and NADPH supplies, and the bacitracin yields were respectively increased by 14. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00005DOI Listing
April 2019
3 Reads
3.951 Impact Factor

Desymmetrization of Cyclodepsipeptides by Assembly Mode Switching of Iterative Nonribosomal Peptide Synthetases.

ACS Synth Biol 2019 Apr 19;8(4):661-667. Epub 2019 Mar 19.

Institut für organische Chemie , Technische Universität Berlin , Strasse des 17. Juni 124/TC2 , Berlin , 10623 , Germany.

Nonribosomal peptide synthetases assemble a considerable number of structurally complex peptides of pharmacological importance. This turns them into important biosynthetic machineries for peptide diversification by engineering approaches. To date, manifold reprogramming approaches focus on employing module and domain exchanges, or the engineering of domains responsible for amino acid recognition. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00541DOI Listing

Sensor-Enabled Alleviation of Product Inhibition in Chorismate Pyruvate-Lyase.

ACS Synth Biol 2019 Apr 25;8(4):775-786. Epub 2019 Mar 25.

Bioscience Division, MS M888 , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States.

Product inhibition is a frequent bottleneck in industrial enzymes, and testing mutations to alleviate product inhibition via traditional methods remains challenging as many variants need to be tested against multiple substrate and product concentrations. Further, traditional screening methods are conducted in vitro, and resulting enzyme variants may perform differently in vivo in the context of whole-cell metabolism and regulation. In this study, we address these two problems by establishing a high-throughput screening method to alleviate product inhibition in an industrially relevant enzyme, chorismate pyruvate-lyase (UbiC). Read More

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http://dx.doi.org/10.1021/acssynbio.8b00465DOI Listing

Shunting Phenylacetic Acid Catabolism for Tropone Biosynthesis.

ACS Synth Biol 2019 Apr 26;8(4):876-883. Epub 2019 Mar 26.

Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing 100029 , China.

Tropone is a seven-membered ring nonbenzenoid aromatic compound. It is the core structure of tropolonoids, which have various biological activities. In this study, a hybrid tropone biosynthetic pathway was designed by connecting phenylacetic acid (PAA) degradation with its biosynthesis and reconstituted in Escherichia coli. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00013DOI Listing
April 2019
3.951 Impact Factor

Enhanced Pyruvate Production in Candida glabrata by Engineering ATP Futile Cycle System.

ACS Synth Biol 2019 Apr 28;8(4):787-795. Epub 2019 Mar 28.

Energy metabolism plays an important role in the growth and central metabolic pathways of cells. Manipulating energy metabolism is an efficient strategy to improve the formation of target products and to understand the effects of altering intracellular energy levels on global metabolic networks. Candida glabrata, as a dominant yeast strain for producing pyruvate, principally converts glucose to pyruvate through the glycolytic pathway. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00479DOI Listing

Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2.

ACS Synth Biol 2019 Apr 20;8(4):796-806. Epub 2019 Mar 20.

Merkin Institute of Transformative Technologies in Healthcare , Broad Institute of MIT and Harvard , Cambridge , Massachusetts 02142 , United States.

Synthetic methylotrophy, the modification of organisms such as E. coli to grow on methanol, is a longstanding goal of metabolic engineering and synthetic biology. The poor kinetic properties of NAD-dependent methanol dehydrogenase, the first enzyme in most methanol assimilation pathways, limit pathway flux and present a formidable challenge to synthetic methylotrophy. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00481DOI Listing
April 2019
3.951 Impact Factor

Measuring Amber Initiator tRNA Orthogonality in a Genomically Recoded Organism.

ACS Synth Biol 2019 Apr 15;8(4):675-685. Epub 2019 Mar 15.

Department of Molecular Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia.

Using engineered initiator tRNA for precise control of protein translation within cells has great promise within future orthogonal translation systems to decouple housekeeping protein metabolism from that of engineered genetic systems. Previously, E. coli strain C321. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00021DOI Listing

Construction of an Efficient and Robust Aspergillus terreus Cell Factory for Monacolin J Production.

ACS Synth Biol 2019 Apr 25;8(4):818-825. Epub 2019 Mar 25.

Marine Biology and Biotechnology Laboratory , Qingdao National Laboratory for Marine Science and Technology , Wenhai Rd 1, Aoshanwei , Qingdao 266003 , China.

Monacolin J is a key precursor for the synthesis of the cholesterol-lowering drug simvastatin. Industrially, monacolin J is manufactured through the alkaline hydrolysis of the fungal polyketide lovastatin, which is relatively complex and environmentally unfriendly. A cell factory for monacolin J production was created by heterologously introducing lovastatin hydrolase into Aspergillus terreus in our previous study. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00489DOI Listing
April 2019
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Designing of a Cofactor Self-Sufficient Whole-Cell Biocatalyst System for Production of 1,2-Amino Alcohols from Epoxides.

ACS Synth Biol 2019 Apr 12;8(4):734-743. Epub 2019 Mar 12.

The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , China.

Optically pure 1,2-amino alcohols are highly valuable products as intermediates for chiral pharmaceutical products. Here we designed an environmentally friendly non-natural biocatalytic cascade for efficient synthesis of 1,2-amino alcohols from cheaper epoxides. A redesignated ω-transaminase PAKω-TA was tested and showed good bioactivity at a lower pH than other reported transaminases. Read More

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http://dx.doi.org/10.1021/acssynbio.8b00364DOI Listing

Temporal Pattern Recognition through Analog Molecular Computation.

ACS Synth Biol 2019 Apr 14;8(4):826-832. Epub 2019 Mar 14.

The James Franck Institute and Department of Physics , University of Chicago , Chicago , Illinois 60637 , United States.

Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern of the molecular concentration over time. Such temporally coded information can be completely invisible to even state-of-the-art molecular sensors with high chemical specificity that respond only to the total amount of the signaling molecule. Read More

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00503
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http://dx.doi.org/10.1021/acssynbio.8b00503DOI Listing
April 2019
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A Self-Actuated Cellular Protein Delivery Machine.

ACS Synth Biol 2019 Apr 12;8(4):686-696. Epub 2019 Mar 12.

UNAM-National Nanotechnology Research Center , Bilkent University , 06800 Ankara , Turkey.

Engineered bacterial cells have great promise to solve global problems, yet they are hampered by a lack of convenient strategy for controlled protein release. A well-controlled protein translocation through cellular membranes is essential for cell-based protein delivery. Here we have developed a controlled protein release system by programming a bacterial autotransporter system named Ag43. Read More

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http://dx.doi.org/10.1021/acssynbio.9b00062DOI Listing