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ACS Synthetic Biology

Han Yang, Feixia Liu, Yin Li, Bo Yu
Epidemiological data confirmed a strong correlation between regular consumption of cruciferous vegetables and lower cancer risk. This cancer preventive property is mainly attributed to the glucosinolate products, such as glucoraphanin found in broccoli that is derived from methionine. Here we report the first successful reconstruction of the complete biosynthetic pathway of glucoraphanin from methionine in Escherichia coli via gene selection, pathway design, and protein engineering. We used branched-chain amino transferase 3 to catalyze two transamination steps to ensure the purity of precursor molecules and used cysteine as a sulfur donor to simplify the synthesis pathway...
November 17, 2017: ACS Synthetic Biology
Jens Mark Moll, Melanie Wehmöller, Nils Christopher Frank, Lisa Homey, Paul Baran, Christoph Garbers, Larissa Lamertz, Jonathan H Axelrod, Eithan Galun, Henning D Mootz, Jürgen Scheller
Trans-signaling of the major pro- and anti-inflammatory cytokines Interleukin (IL)-6 and IL-11 has the unique feature to virtually activate all cells of the body and is critically involved in chronic inflammation and regeneration. Hyper-IL-6 and Hyper-IL-11 are single chain designer trans-signaling cytokines, in which the cytokine and soluble receptor units are trapped in one complex via a flexible peptide linker. Albeit, Hyper-cytokines are essential tools to study trans-signaling in vitro and in vivo, the superior potency of these designer cytokines are accompanied by undesirable stress responses...
November 14, 2017: ACS Synthetic Biology
Lummy Maria Oliveira Monteiro, Letícia Magalhães Arruda, Rafael Silva-Rocha
Regulation of gene expression in bacteria results from the interplay between hundreds of transcriptional factors (TFs) at target promoters. However, how the arrangement of binding sites for TFs generates the regulatory logic of promoters is not well-known. Here, we generated and fully characterized a library of synthetic complex promoters for the global regulators, CRP and IHF, in Escherichia coli, which are formed by a weak -35/-10 consensus sequence preceded by four combinatorial binding sites for these two TFs...
November 14, 2017: ACS Synthetic Biology
Lingjun Yu, Wei Su, Paul D Fey, Fengquan Liu, Liangcheng Du
The cyclic lipodepsipeptides WAP-8294A are antibiotics with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). One member of this family, WAP-8294A2 (Lotilibcin), was in clinical trials due to its high activity and distinct chemistry. However, WAP-8294A compounds are produced in a very low yield by Lysobacter and only under very stringent conditions. Improving WAP-8294A yield has become very critical for research and application of these anti-MRSA compounds. Here, we report a strategy to increase WAP-8294A production...
November 10, 2017: ACS Synthetic Biology
Jonathan Lloyd, Claire H Tran, Krishen Wadhwani, Christian Cuba Samaniego, Hari K K Subramanian, Elisa Franco
Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within nonequilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex...
November 10, 2017: ACS Synthetic Biology
Andrew Halleran, Richard M Murray
Synthetic biologists have turned towards quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell-free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry...
November 9, 2017: ACS Synthetic Biology
Nicholas T Ong, Evan J Olson, Jeffrey J Tabor
Optogenetics is a technology wherein researchers combine light and genetically engineered photoreceptors to control biological processes with unrivaled precision. Near-infrared (NIR) wavelengths (>700 nm) are desirable optogenetic inputs due to their low phototoxicity and spectral isolation from most photoproteins. The bacteriophytochrome photoreceptor 1 (BphP1), found in several purple photosynthetic bacteria, senses NIR light and activates transcription of photosystem promoters by binding to and inhibiting the transcriptional repressor PpsR2...
November 9, 2017: ACS Synthetic Biology
Daniel D Lewis, Michael Chavez, Kwan Lun Chiu, Cheemeng Tan
Living cells are known for their capacity for versatile signal processing, particularly the ability to respond differently to the same stimuli using biochemical networks that integrate environmental signals and reconfigure their dynamic responses. However, the complexity of natural biological networks confounds the discovery of fundamental mechanisms behind versatile signaling. Here, we study one specific aspect of reconfigurable signal processing in which a minimal biological network integrates two signals, using one to reconfigure the network's transfer function with respect to the other, producing an emergent switch between induction and repression...
November 8, 2017: ACS Synthetic Biology
Yuichi Furuhata, Yuta Nihongaki, Moritoshi Sato, Keitaro Yoshimoto
Mesenchymal stem cells (MSCs) are of interest in regenerative medicine owing to their multilineage differentiation and self-renewal properties. Understanding the in vivo differentiation process is necessary for clinical applications including cell therapy and transplantation. This remains challenging owing to the lack of induction methods that imitate the natural programming process. Endogenous gene regulation of tissue-specific transcription factors is therefore desirable. In the present study, we demonstrated endogenous activation of adipogenic genes through the dCas9-based transcription system and achieved efficient induction of different types of adipocyte-like cells from MSCs...
November 7, 2017: ACS Synthetic Biology
Kyle V Butler, Anna M Chiarella, Jian Jin, Nathaniel A Hathaway
Epigenome editing is a powerful method for life science research and could give rise to new therapies for diseases initiated or maintained by epigenetic dysregulation, including several types of cancers and autoimmune disorders. In addition, much is still unknown about the mechanisms by which histone-modifying proteins work in concert to properly regulate gene expression. To investigate and manipulate complex epigenetic interactions in live cells, we have developed a small molecule platform for specifically inducing gene repression and histone deacetylation at a reporter gene...
November 7, 2017: ACS Synthetic Biology
Wenting Zhao, Lara Pferdehirt, Laura Segatori
Protein function is typically studied and engineered by modulating protein levels within the complex cellular environment. To achieve fast, targeted, and predictable control of cellular protein levels without genetic manipulation of the target, we developed a technology for post-translational depletion based on a bifunctional molecule (NanoDeg) consisting of the antigen-binding fragment from the Camelidae species heavy-chain antibody (nanobody) fused to a degron signal that mediates degradation through the proteasome...
November 7, 2017: ACS Synthetic Biology
Brian Thompson, Shawn Pugh, Michael Machas, David R Nielsen
Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production...
November 2, 2017: ACS Synthetic Biology
T-Y Dora Tang, Dario Cecchi, Giorgio Fracasso, Davide Accardi, Angelique Coutable, Sheref S Mansy, Adam W Perriman, John Leslie Ross Anderson, Stephen Mann
A gene-directed chemical communication pathway between synthetic protocell signaling transmitters (lipid vesicles) and receivers (proteinosomes) was designed, built and tested using a bottom-up modular approach comprising small molecule transcriptional control, cell-free gene expression, porin-directed efflux, substrate signaling, and enzyme cascade-mediated processing.
November 1, 2017: ACS Synthetic Biology
Chang Liu, Bo Zhang, Yi-Ming Liu, Keqian Yang, Shuang-Jiang Liu
The quantitative monitoring of intracellular metabolites with in vivo biosensors provides an efficient means of identifying high-yield strains and observing product accumulation in real time. In this study, a shikimic acid (SA) biosensor was constructed from a LysR-type transcriptional regulator (ShiR) of Corynebacterium glutamicum. The SA biosensor specifically responded to the increase of intracellular SA concentration over a linear range of 19.5 ± 3.6 to 120.9 ± 1.2 fmole at the single-cell level. This new SA biosensor was successfully used to 1) monitor the SA production of different C...
October 31, 2017: ACS Synthetic Biology
Shanshan Li, Junyang Wang, Wensheng Xiang, Keqian Yang, Zilong Li, Weishan Wang
Streptomycetes are well-known producers of biologically active secondary metabolites. Various efforts have endeavored to increase productions of these metabolites, while few approaches could well coordinate the biosynthesis of secondary metabolites and other physiological events of their hosts. Here we develop a universal autoregulated strategy for fine-tuning the expression of secondary metabolites biosynthetic gene clusters (BGCs) in Streptomyces species. First, inducible promoters were used to control the expression of secondary metabolites BGCs...
October 31, 2017: ACS Synthetic Biology
Hung-Ju Chang, Pauline Mayonove, Agustin Zavala, Angelique De Visch, Philippe Minard, Martin Cohen-Gonsaud, Jerome Bonnet
Engineered bacteria promise to revolutionize diagnostics and therapeutics, yet many applications are precluded by the limited number of detectable signals. Here we present a general framework to engineer synthetic receptors enabling bacterial cells to respond to novel ligands. These receptors are activated via ligand-induced dimerization of a single-domain antibody fused to monomeric DNA-binding domains (split-DBDs). Using E. coli as a model system, we engineer both transmembrane and cytosolic receptors using a VHH for ligand detection and demonstrate the scalability of our platform by using the DBDs of two different transcriptional regulators...
October 30, 2017: ACS Synthetic Biology
Sen Yang, Qingtao Liu, Yunfeng Zhang, Guocheng Du, Jian Chen, Zhen Kang
Characterization of genetic circuits and biosynthetic pathways in different hosts always requires promoter substitution and redesigning. Here, a strong, broad-spectrum promoter, Pbs, for Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae was constructed, and it was incorporated into the minimal E. coli-B. subtilis-S. cerevisiae shuttle plasmid pEBS (5.8 kb). By applying a random mutation strategy, three broad-spectrum promoters Pbs1, Pbs2, and Pbs3, with different strengths were generated and characterized...
October 23, 2017: ACS Synthetic Biology
Lu Pu, Shuai Yang, Aiguo Xia, Fan Jin
Synthetic biologists have attempted to solve real-world problems, such as those of bacterial biofilms, that are involved in the pathogenesis of many clinical infections and difficult to eliminate. To address this, we employed a blue light responding system and integrated it into the chromosomes of Pseudomonas aeruginosa. With making rational adaption and improvement of the light-activated system, we provided a robust and convenient means to spatiotemporally control gene expression and manipulate biological processes with minimal perturbation in P...
October 20, 2017: ACS Synthetic Biology
Yoshiki Murase, Hiroki Nakanishi, Gakushi Tsuji, Takeshi Sunami, Norikazu Ichihashi
One of the largest challenges in the synthesis of artificial cell that can reproduce is in vitro assembly of ribosomes from in vitro synthesized rRNAs and proteins. In this study, to circumvent the chemical modification of 16S rRNA for reconstitution of fully active 30S subunit, we performed artificial evolution of 16S rRNA, which forms the functional 30S subunit without chemical modifications. We first established an in vitro selection scheme by combining the integrated synthesis, assembly, and translation (iSAT) system with the liposome sorting technique...
October 20, 2017: ACS Synthetic Biology
Maxwell Bates, Joe Lachoff, Duncan Meech, Valentin Zulkower, Anaïs Moisy, Yisha Luo, Hille Tekotte, Cornelia Johanna Franziska Scheitz, Rupal Khilari, Florencio Mazzoldi, Deepak Chandran, Eli Groban
Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs...
October 20, 2017: ACS Synthetic Biology
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