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ACS Synthetic Biology

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https://www.readbyqxmd.com/read/29343065/perfect-adaptation-and-optimal-equilibrium-productivity-in-a-simple-microbial-biofuel-metabolic-pathway-using-dynamic-integral-control
#1
Corentin Briat, Mustafa H Khammash
The production of complex biomolecules by genetically engineered organisms is one of the most promising applications of metabolic engineering and synthetic biology. To obtain processes with high productivity, it is therefore crucial to design and implement efficient dynamic in-vivo regulation strategies. We consider here the microbial biofuel production model of Dunlop et al. (2010) for which we demonstrate that an antithetic dynamic integral control strategy can achieve robust perfect adaptation for the intracellular biofuel concentration in presence of poorly known network parameters and implementation errors in certain rate parameters of the controller...
January 17, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29343061/analyzing-and-tuning-ribozyme-activity-by-deep-sequencing-to-modulate-gene-expression-level-in-mammalian-cells
#2
Shungo Kobori, Yohei Yokobayashi
Self-cleaving ribozymes, in combination with aptamers and various classes of RNAs, have been heavily engineered to create RNA devices to control gene expression. Although understanding of sequence-function relationships of ribozymes is critical for such efforts, our current knowledge of self-cleaving ribozymes is mostly limited to the results from small scale mutational studies performed under different conditions, or qualitative results of mutate-and-select experiments which may contain experimental biases...
January 17, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29343055/genetically-encoded-circuit-for-remote-regulation-of-cell-migration-by-magnetic-fields
#3
Abdullah Al Mosabbir, Kevin Truong
Magneto-reception can be generally defined as the ability to transduce the effects of a magnetic field into a cellular response. Magnetic stimulation at the cellular level is particularly attractive due to its ability for deep penetration and minimal invasiveness, allowing remote regulation of engineered biological processes. Previously, a magnetic-responsive genetic circuit was engineered using the transient receptor potential vanilloid 1 (TRPV1) and the iron containing ferritin protein (i.e. the TF circuit)...
January 17, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29320853/high-co2-requirement-as-a-mechanism-for-the-containment-of-genetically-modified-cyanobacteria
#4
Ryan L Clark, Gina C Gordon, Nathaniel R Bennett, Haoxiang Lyu, Thatcher W Root, Brian F Pfleger
As researchers engineer cyanobacteria for biotechnological applications, we must consider potential environmental release of these organisms. Previous theoretical work has considered cyanobacterial containment through elimination of the CO2-concentrating mechanism (CCM) to impose a high-CO2 requirement (HCR), which could be provided in the cultivation environment but not in the surroundings. In this work, we experimentally implemented an HCR containment mechanism in Synechococcus sp. PCC7002 (PCC7002) through deletion of carboxysome shell proteins and showed that this mechanism contained cyanobacteria in a 5% CO2 environment...
January 10, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29320851/stringency-of-synthetic-promoter-sequences-in-clostridium-revealed-and-circumvented-by-tuning-promoter-library-mutation-rates
#5
Pawel Mordaka, John T Heap
Collections of characterized promoters of different strengths are key resources for synthetic biology, but are not well established for many important organisms, including industrially-relevant Clostridium spp. When generating promoters, reporter constructs are used to measure expression, but classical fluorescent reporter proteins are oxygen-dependent and hence inactive in anaerobic bacteria like Clostridium. We directly compared oxygen-independent reporters of different types in Clostridium acetobutylicum and found that glucuronidase (GusA) from E...
January 10, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29316791/serine-integrases-advancing-synthetic-biology
#6
Christine Merrick, Jia Zhao, Susan Rosser
Serine integrases catalyze precise rearrangement of DNA through site-specific recombination of small sequences of DNA called attachment (att) sites. Unlike other site-specific recombinases, the recombination reaction driven by serine integrases is highly directional and can only be reversed in the presence of an accessory protein called a recombination directionality factor (RDF). The ability to control reaction directionality has led to the development of serine integrases as tools for controlled rearrangement and modification of DNA in synthetic biology, gene therapy, and biotechnology...
January 9, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29316788/synbiohub-a-standards-enabled-design-repository-for-synthetic-biology
#7
James Alastair McLaughlin, Chris J Myers, Zach Zundel, Goksel Misirli, Michael Zhang, Irina Dana Ofiteru, Angel Goñi Moreno, Anil Wipat
The SynBioHub repository (synbiohub.org) is an open-source software project which facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g. the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation...
January 9, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29316787/reprogramming-one-carbon-metabolic-pathways-to-decouple-l-serine-catabolism-from-cell-growth-in-corynebacterium-glutamicum
#8
Yun Zhang, Xiuling Shang, Shujuan Lai, Yu Zhang, Qitiao Hu, Xin Chai, Bo Wang, Shuwen Liu, Tingyi Wen
L-Serine, the principal one-carbon source for DNA biosynthesis, is difficult for microorganisms to accumulate due to the coupling of L-serine catabolism and microbial growth. Here, we reprogrammed the one-carbon unit metabolic pathways in Corynebacterium glutamicum to decouple L-serine catabolism from cell growth. In silico model-based simulation showed a negative influence on glyA-encoding serine hydroxymethyltransferase flux with L-serine productivity. Attenuation of glyA transcription resulted in increased L-serine accumulation, and a decrease in purine pools, poor growth and longer cell shapes...
January 9, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29304277/photosynthetic-production-of-sunscreen-shinorine-using-an-engineered-cyanobacterium
#9
Guang Yang, Monica A Cozad, Destin A Holland, Yi Zhang, Hendrik Luesch, Yousong Ding
Mycosporine-like amino acids (MAAs) are secondary metabolites of a variety of marine organisms including cyanobacteria and macroalgae. These compounds have strong ultraviolet (UV) absorption maxima between 310 and 362 nm and are biological sunscreens for counteracting the damaging effects of UV radiation in nature. The common MAA shinorine has been used as one key active ingredient of environmentally friendly sunscreen creams. Commercially used shinorine is isolated from one red algae that is generally harvested from the wild...
January 5, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29301074/genetically-incorporating-two-distinct-post-translational-modifications-into-one-protein-simultaneously
#10
Sumana Venkat, Jourdan Sturges, Alleigh Stahman, Caroline Gregory, Qinglei Gan, Chenguang Fan
Post-translational modifications (PTMs) play important roles in regulating a variety of biological processes. To facilitate PTM studies, the genetic code expansion strategy has been utilized to co-translationally incorporate individual PTMs such as acetylation and phosphorylation into proteins at specific sites. However, recent studies have demonstrated that PTMs actually work together to regulate protein functions and structures. Thus, simultaneous incorporation of multiple distinct PTMs into one protein is highly desirable...
January 4, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29301067/biosynthesis-of-orthogonal-molecules-using-ferredoxin-and-ferredoxin-nadp-reductase-systems-enables-genetically-encoded-phyb-optogenetics
#11
Phillip Kyriakakis, Marianne Catanho, Nicole Hoffner, Walter Thavarajah, Vincent Jian-Yu, Syh-Shiuan Chao, Athena Hsu, Vivian Pham, Ladan Naghavian, Lara E Dozier, Gentry Patrick, Todd Coleman
Transplanting metabolic reactions from one species into another has many uses as a research tool with applications ranging from optogenetics to crop production. Ferredoxin (Fd), the enzyme that most often supplies electrons to these reactions, is often overlooked when transplanting enzymes from one species to another because most cells already contain endogenous Fd. However, we have shown that the production of chromophores used in Phytochrome B (PhyB) optogenetics, is greatly enhanced in mammalian cells by expressing bacterial and plant Fds with ferredoxin-NADP+ reductases (FNR)...
January 4, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29301066/an-expanded-heterologous-i-gal-i-promoter-collection-for-diauxie-inducible-expression-in-saccharomyces-cerevisiae
#12
Bingyin Peng, Rebecca J Wood, Lars K Nielsen, Claudia E Vickers
The <i>GAL</i> promoters are applied in metabolic engineering and synthetic biology to control gene expression in the budding yeast <i>Saccharomyces cerevisiae</i>. In <i>gal80Δ</i> background strains, they show diauxie-inducible expression, a feature beneficial in metabolic pathway optimization. However, only a limited number of the <i>GAL</i> promoters have been characterized and are available for engineering purposes. Multiple use of the same promoters can result in genetic instability in engineered strains due to homologous recombination...
January 4, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29257878/tarsyn-tunable-antibiotic-resistance-devices-enabling-bacterial-synthetic-evolution-and-protein-production
#13
Maja Rennig, Virginia Martinez, Kiavash Mirzadeh, Finn Dunas, Belinda Röjsäter, Daniel O Daley, Morten H H Nørholm
Evolution can be harnessed to optimize synthetic biology designs. A prominent example is recombinant protein production-a dominating theme in biotechnology for more than three decades. Typically, a protein coding sequence (cds) is recombined with genetic elements, such as promoters, ribosome binding sites and terminators, which control expression in a cell factory. A major bottleneck during production is translational initiation. Previously we identified more effective translation initiation regions (TIRs) by creating sequence libraries and then selecting for a TIR that drives high-level expression-an example of synthetic evolution...
January 4, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29298053/an-expanded-plasmid-based-genetic-toolbox-enables-cas9-genome-editing-and-stable-maintenance-of-synthetic-pathways-in-phaeodactylum-tricornutum
#14
Samuel S Slattery, Andrew Diamond, Helen Wang, Jasmine Alyssa Therrien, Jeremy Thomas Lant, Teah Jazey, Kyle Lee, Zachary Klassen, Isabel Desgagné-Penix, Bogumil Jacek Karas, David R Edgell
With the completion of the genome sequence, and development of an efficient conjugation-based transformation system allowing the introduction of stable episomes, Phaeodactylum tricornutum has become an ideal platform for the study of diatom biology and synthetic biology applications. The development of plasmid-based genetic tools is the next step to improve manipulation of this species. Here, we report the identification of endogenous P. tricornutum promoters, terminators and introns allowing selective expression of antibiotic resistance markers from stably replicating plasmids in P...
January 3, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29298043/metabolic-feedback-circuits-provide-rapid-control-of-metabolite-dynamics
#15
Di Liu, Fuzhong Zhang
Metabolism constitutes the basis of life, and the dynamics of metabolism dictate various cellular processes. However, exactly how metabolite dynamics are controlled remains poorly understood. By studying an engineered fatty acid-producing pathway as a model, we found that upon transcription activation a metabolic product from an unregulated pathway required seven cell cycles to reach to its steady state level, with the speed mostly limited by enzyme expression dynamics. To overcome this limit, we designed metabolic feedback circuits (MeFCs) with three different architectures, and experimentally measured and modeled their metabolite dynamics...
January 3, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29295615/the-locational-impact-of-site-specific-pegylation-streamlined-screening-with-cell-free-protein-expression-and-coarse-grain-simulation
#16
Kristen M Wilding, Addison K Smith, Joshua W Wilkerson, Derek B Bush, Thomas Allen Knotts, Bradley Charles Bundy
Although polyethylene glycol (PEG) is commonly used to improve protein stability and therapeutic efficacy, the optimal location for attaching PEG onto proteins is not well understood. Here, we present a cell-free protein synthesis-based screening platform which facilitates site-specific PEGylation and efficient evaluation of PEG attachment efficiency, thermal stability, and activity for different variants of PEGylated T4 lysozyme, including a di-PEGylated variant. We also report developing a computationally-efficient coarse-grain simulation model as a potential tool to narrow experimental screening candidates...
January 2, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29258303/antibody-based-fusion-proteins-allow-ca2-rewiring-to-most-extracellular-ligands
#17
Anam Qudrat, Kevin Truong
The Ca2+ signaling toolkit is the set of proteins used by living systems to generate and respond to Ca2+ signals. The selective expression of these proteins in particular tissues, cell types and subcellular locations allows the Ca2+ signal to regulate a diverse set of cellular processes. Through synthetic biology, the Ca2+ signaling toolkit can be expanded beyond the natural repertoire to potentially allow a non-natural ligand to control downstream cellular processes. To realize this potential, we exploited the ability of an antibody to bind its antigen exclusively in combination with the ability of the cytoplasmic domain of vascular endothelial growth factor receptor 2 (VEGFR2) to generate a Ca2+ signal upon oligomerization...
January 2, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29284088/dynamic-engineering-of-1-alkenes-biosynthesis-and-secretion-in-yeast
#18
Yongjin J Zhou, Yating Hu, Zhiwei Zhu, Verena Siewers, Jens Nielsen
Microbial production of fatty acid-derived hydrocarbons offers a great opportunity to sustainably supply biofuels and oleochemicals. One challenge is to achieve a high production rate. Besides, low efficiency in secretion will cause high separation costs and it is therefore desirable to have product secretion. Here, we engineered the budding yeast Saccharomyces cerevisiae, to produce and secrete 1-alkenes by manipulation of the fatty acid metabolism, enzyme selection, engineering the electron transfer system and expressing a transporter...
December 28, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29284082/sporobeads-the-utilization-of-the-bacillus-subtilis-endospore-crust-as-a-protein-display-platform
#19
Julia Bartels, Sebastián López Castellanos, Jara Radeck, Thorsten Mascher
Upon starvation, the soil bacterium Bacillus subtilis forms an intracellular, metabolically inactive endospore. Its core contains the DNA, encased by three protein layers protecting it against a multitude of environmental threats. The outermost layer, the crust, harbors great potential as a protein-displaying platform: a gene of interest can be translationally fused to a crust protein gene, resulting in endospores displaying the desired protein on their surface. To unlock this potential in a standardized fashion, we designed a suite of twelve vectors (Sporovectors), based on the BioBrick cloning standard...
December 28, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29281883/establishing-an-artificial-pathway-for-efficient-biosynthesis-of-hydroxytyrosol
#20
Xianglai Li, Zhenya Chen, Yifei Wu, Yajun Yan, Xinxiao Sun, Qipeng Yuan
Hydroxytyrosol (HT) is a valuable natural phenolic compound with strong antioxidant activity and various physiological and pharmaceutical functions. In this study, we established an artificial pathway for biosynthesis of HT. First, efficient enzymes were selected to construct tyrosol biosynthetic pathway. ARO10 from Saccharomyces cerevisiae was shown to be a better ketoacid decarboxylase than Kivd from Lactococcus lactis for tyrosol production. While knockout of feaB significantly decreased accumulation of the byproduct 4-hydroxyphenylacetic acid, overexpression of alcohol dehydrogenase ADH6 further improved tyrosol production...
December 28, 2017: ACS Synthetic Biology
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