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Synthetic Biology
Genome-wide primary transcriptome analysis of H
Feb 20, 2017   Scientific Reports
Cho S, Kim MS, Jeong Y, Lee BR, Lee JH, Kang SG, Cho BK
Genome-wide primary transcriptome analysis of H
Feb 20, 2017
Scientific Reports
UNASSIGNED: In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H
CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli
Feb 20, 2017   Metabolic Engineering
Liang L, Liu R, Garst AD, Lee T, Nogué VS, Beckham GT, Gill RT
CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli
Feb 20, 2017
Metabolic Engineering
UNASSIGNED: Isopropanol is an important target molecule for sustainable production of fuels and chemicals. Increases in DNA synthesis and synthetic biology capabilities have resulted in the development of a range of new strategies for the more rapid design, construction, and testing of production strains. Here, we report on the use of such capabilities to construct and test 903 different variants of the isopropanol production pathway in Escherichia coli. We first constructed variants to explore the effect of codon optimization, copy number, and translation initiation rates on isopropanol production. The best strain (PA06) produced isopropanol at titers of 17.5g/L, with a yield of 0.62 (mol/mol), and maximum productivity of 0.40g/L/h. We next integrated the isopropanol synthetic pathway into the genome and then used the CRISPR EnAbled Trackable genome Engineering (CREATE) strategy to generate an additional 640 individual RBS library variants for further evaluation. After testing each of these variants, we constructed a combinatorial library containing 256 total variants from four different RBS levels for each gene. The best producing variant, PA14, produced isopropanol at titers of 7.1g/L at 24h, with a yield of 0.75 (mol/mol), and maximum productivity of 0.62g/L/h (which was 0.22g/L/h above the parent strain PA07). We demonstrate the ability to rapidly construct and test close to ~1000 designer strains and identify superior performers. Copyright © 2017. Published by Elsevier Inc.
BioNano genome map resource for Oryza sativa ssp. japonica and indica and its application in rice genome sequence correction and gap filling
Feb 18, 2017   Molecular Plant
Chen P, Jing X, Liao B, Zhu Y, Xu J, Liu R, Zhao Y, Li X
Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy
Feb 12, 2017   Cell Systems
Mohammadi P, Beerenwinkel N, Benenson Y
Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy
Feb 12, 2017
Cell Systems
Cell classifiers are genetic logic circuits that transduce endogenous molecular inputs into cell-type-specific responses. Designing classifiers that achieve optimal differential response between specific cell types is a hard computational problem because it involves selection of endogenous inputs and optimization of both biochemical parameters and a logic function. To address this problem, we first derive an optimal set of biochemical parameters with the largest expected differential response over a diverse set of logic circuits, and second, we use these parameters in an evolutionary algorithm to select circuit inputs and optimize the logic function. Using this approach, we design experimentally feasible microRNA-based circuits capable of perfect discrimination for several real-world cell-classification tasks. We also find that under realistic cell-to-cell variation, circuit performance is comparable to standard cross-validation performance estimates. Our approach facilitates the generation of candidate circuits for experimental testing in therapeutic settings that require precise cell targeting, such as cancer therapy.Copyright © 2017 Elsevier Inc. All rights reserved.
Expanding the product portfolio of fungal type I fatty acid synthases
Feb 20, 2017   Nature Chemical Biology Add nature.com free-link Cancel
Zhu Z, Zhou YJ, Krivoruchko A, Grininger M, Zhao ZK, Nielsen J
Expanding the product portfolio of fungal type I fatty acid synthases
Feb 20, 2017
Nature Chemical Biology
UNASSIGNED: Fungal type I fatty acid synthases (FASs) are mega-enzymes with two separated, identical compartments, in which the acyl carrier protein (ACP) domains shuttle substrates to catalytically active sites embedded in the chamber wall. We devised synthetic FASs by integrating heterologous enzymes into the reaction chambers and demonstrated their capability to convert acyl-ACP or acyl-CoA from canonical fatty acid biosynthesis to short/medium-chain fatty acids and methyl ketones.
Engineering Iron Responses in Mammalian Cells by Signal-Induced Protein Proximity
Feb 21, 2017   ACS Synthetic Biology
Zeng G, Li H, Wei Y, Xuan W, Zhang R, Breden LE, Wang W, Liang FS
Engineering Iron Responses in Mammalian Cells by Signal-Induced Protein Proximity
Feb 21, 2017
ACS Synthetic Biology
UNASSIGNED: A new synthetic biology engineering strategy integrating chemical reactivity sensing and small molecule induced protein dimerization has been developed to generate artificial Fe
A novel DNAJB6 mutation causes dominantly-inherited distal-onset myopathy and compromises DNAJB6 function
Feb 24, 2017   Clinical Genetics
Tsai PC, Tsai YS, Soong BW, Huang YH, Wu HT, Chen YH, Lin KP, Liao YC, Lee YC
A novel DNAJB6 mutation causes dominantly-inherited distal-onset myopathy and compromises DNAJB6 function
Feb 24, 2017
Clinical Genetics
Mutations in the DNAJB6 gene have been identified as a rare cause of dominantly-inherited limb-girdle muscular dystrophy or distal-onset myopathy. To identify the genetic cause of distal-onset myopathy in a Taiwanese family of Han Chinese origin, we performed exome sequencing for the two affected individuals and identified a heterozygous mutation, c.287C>T (p.Pro96Leu) in the DNAJB6 gene that co-segregated with myopathy in the family. Notably, this mutation is novel and localizes within the glycine and phenylalanine-rich (G/F) domain and alters an amino acid residue previously reported with a different mutation. Furthermore, in vitro functional studies demonstrated that the c.287C>T (p.Pro96Leu) mutation possessed a dominant negative effect on the anti-aggregation function of DNAJB6 protein. Taken together, these findings expand the molecular spectrum of DNAJB6 mutations and also emphasize the pathogenic role of DNAJB6 dysfunction in distal-onset myopathy.This article is protected by copyright. All rights reserved.
An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy
Feb 23, 2017   Biochimica Et Biophysica Acta
Völler JS, Biava H, Hildebrandt P, Budisa N
An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy
Feb 23, 2017
Biochimica Et Biophysica Acta
BACKGROUND: To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW: This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS: ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics. GENERAL SIGNIFICANCE: Mapping the electrostatics in proteins will improve our understanding of natural catalytic processes and, in beyond, will be helpful for biocatalyst engineering. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017. Published by Elsevier B.V.
Tailoring Escherichia coli for the L-rhamnose P
Feb 22, 2017   ACS Synthetic Biology
Hjelm A, Karyolaimos A, Zhang Z, Rujas E, Vikström D, Slotboom DJ, de Gier JW
Tailoring Escherichia coli for the L-rhamnose P
Feb 22, 2017
ACS Synthetic Biology
UNASSIGNED: Membrane and secretory protein production in Escherichia coli requires precisely controlled production rates to avoid the deleterious saturation of their biogenesis pathways. Based on this requirement, the E. coli L-rhamnose P
Inducing circular RNA formation using the CRISPR endoribonuclease Csy4
Feb 22, 2017   RNA (New York, N.Y.)
Borchardt EK, Meganck RM, Vincent HA, Ball CB, Ramos SB, Moorman NJ, Marzluff WF, Asokan A
Inducing circular RNA formation using the CRISPR endoribonuclease Csy4
Feb 22, 2017
RNA (New York, N.Y.)
UNASSIGNED: Circular RNAs (circRNAs) are highly stable, covalently closed RNAs that are regulated in a spatiotemporal manner and whose functions are largely unknown. These molecules have the potential to be incorporated into engineered systems with broad technological implications. Here we describe a switch for inducing backsplicing of an engineered circRNA that relies on the CRISPR endoribonuclease, Csy4, as an activator of circularization. The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task. Co-expression of Csy4 and the circRNA switch allows for the removal of downstream competitive splice sites and stabilization of the 5' cleavage product. This subsequently results in backsplicing of the 5' cleavage product into a circRNA that can efficiently translate a reporter protein from an internal ribosomal entry site (IRES). Our platform outlines a straightforward approach towards regulating splicing and could find potential applications in synthetic biology as well as in studying the properties of different circRNAs. Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Mathematical modelling of clostridial acetone-butanol-ethanol fermentation
Feb 17, 2017   Applied Microbiology And Biotechnology
Millat T, Winzer K
Mathematical modelling of clostridial acetone-butanol-ethanol fermentation
Feb 17, 2017
Applied Microbiology And Biotechnology
UNASSIGNED: Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the production of industrial-relevant solvents, solventogensis. In recent decades, mathematical models have been employed to elucidate the complex interlinked regulation and conditions that determine these two distinct metabolic states and govern the transition between them. In this review, we discuss these models with a focus on the mechanisms controlling intra- and extracellular changes between acidogenesis and solventogenesis. In particular, we critically evaluate underlying model assumptions and predictions in the light of current experimental knowledge. Towards this end, we briefly introduce key ideas and assumptions applied in the discussed modelling approaches, but waive a comprehensive mathematical presentation. We distinguish between structural and dynamical models, which will be discussed in their chronological order to illustrate how new biological information facilitates the 'evolution' of mathematical models. Mathematical models and their analysis have significantly contributed to our knowledge of ABE fermentation and the underlying regulatory network which spans all levels of biological organization. However, the ties between the different levels of cellular regulation are not well understood. Furthermore, contradictory experimental and theoretical results challenge our current notion of ABE metabolic network structure. Thus, clostridial ABE fermentation still poses theoretical as well as experimental challenges which are best approached in close collaboration between modellers and experimentalists.
Antibody-controlled actuation of DNA-based molecular circuits
Feb 17, 2017   Nature Communications
Engelen W, Meijer LH, Somers B, de Greef TF, Merkx M
Antibody-controlled actuation of DNA-based molecular circuits
Feb 17, 2017
Nature Communications
UNASSIGNED: DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.
Draft Genome Sequence of
Feb 17, 2017   Genome Announcements
Palakawong Na Ayudthaya S, Strepis N, Pristaš P, Plugge CM
Draft Genome Sequence of
Feb 17, 2017
Genome Announcements
Copyright © 2017 Palakawong Na Ayudthaya et al.
A method for high-throughput production of sequence-verified DNA libraries and strain collections
Feb 14, 2017   Molecular Systems Biology
Smith JD, Schlecht U, Xu W, Suresh S, Horecka J,   . . . . . .   , Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP
A method for high-throughput production of sequence-verified DNA libraries and strain collections
Feb 14, 2017
Molecular Systems Biology
UNASSIGNED: The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site-specific recombination to index library DNA, and next-generation sequencing to identify desired clones. We used REDI to generate a library of ~3,300 DNA probes that exhibited > 96% purity and remarkable uniformity (> 95% of probes within twofold of the median abundance). Additionally, we created a collection of ~9,000 individually accessible CRISPR interference yeast strains for > 99% of genes required for either fermentative or respiratory growth, demonstrating the utility of REDI for rapid and cost-effective creation of strain collections from oligonucleotide pools. Our approach is adaptable to any complex DNA library, and fundamentally changes how these libraries can be parsed, maintained, propagated, and characterized. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.
Evolution of a split RNA polymerase as a versatile biosensor platform
Feb 13, 2017   Nature Chemical Biology Add nature.com free-link Cancel
Pu J, Zinkus-Boltz J, Dickinson BC
Evolution of a split RNA polymerase as a versatile biosensor platform
Feb 13, 2017
Nature Chemical Biology
UNASSIGNED: Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies are often limited by a low signal-to-noise ratio, the extensive optimization required for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE). We then applied the resulting activity-responsive RNAP (AR) system to create biosensors that can be activated by light and small molecules, demonstrating the 'plug-and-play' nature of the platform. Finally, we validated that ARs can interrogate multidimensional protein-protein interactions and trigger RNA nanostructure production, protein synthesis, and gene knockdown in mammalian systems, illustrating the versatility of ARs in synthetic biology applications.
Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit
Feb 13, 2017   Nature Biotechnology Add nature.com free-link Cancel
Gupta A, Reizman IM, Reisch CR, Prather KL
Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit
Feb 13, 2017
Nature Biotechnology
UNASSIGNED: Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We apply our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in titers of myo-inositol increased 5.5-fold and titers of glucaric acid increased from unmeasurable to >0.8 g/L, compared to the parent strains lacking dynamic flux control. Scaled-up production of these strains in benchtop bioreactors resulted in almost ten- and fivefold increases in specific titers of myo-inositol and glucaric acid, respectively. We also used our module to control flux into aromatic amino acid biosynthesis to increase titers of shikimate in E. coli from unmeasurable to >100 mg/L.
Characterization and application of endogenous phase-dependent promoters in Bacillus subtilis
Feb 15, 2017   Applied Microbiology And Biotechnology
Yang S, Du G, Chen J, Kang Z
Characterization and application of endogenous phase-dependent promoters in Bacillus subtilis
Feb 15, 2017
Applied Microbiology And Biotechnology
UNASSIGNED: Bacillus subtilis as an important host has been widely used in synthetic biology, metabolic engineering, and production of industrial enzymes. To fully take advantage of this organism, 114 endogenous putative promoters were measured with a green fluorescent protein reporter and four classes of phase-dependent promoters (class I: exponential phase; class II: middle-log and early stationary phases; class III: lag-log and stationary phases; class IV: stationary phase) with different strengths were identified. The transcriptional strengths ranged from 0.03 to 2.03-fold of that of the commonly used strong promoter P
Enzymatic N- and C-Protection in Cyanobactin RiPP Natural Products
Feb 14, 2017   Journal Of The American Chemical Society
Sardar D, Hao Y, Lin Z, Morita M, Nair SK, Schmidt EW
Enzymatic N- and C-Protection in Cyanobactin RiPP Natural Products
Feb 14, 2017
Journal Of The American Chemical Society
UNASSIGNED: Recent innovations in peptide natural product biosynthesis reveal a surprising wealth of previously uncharacterized biochemical reactions that have potential applications in synthetic biology. Among these, the cyanobactins are noteworthy because these peptides are protected at their N- and C-termini by macrocyclization. Here, we use a novel bifunctional enzyme AgeMTPT to protect linear peptides by attaching prenyl and methyl groups at their free N- and C-termini. Using this peptide protectase in combination with other modular biosynthetic enzymes, we describe the total synthesis of the natural product aeruginosamide B and the biosynthesis of linear cyanobactin natural products. Our studies help to define the enzymatic mechanism of macrocyclization, providing evidence against the water exclusion hypothesis of transpeptidation and favoring the kinetic lability hypothesis.
Stretchable living materials and devices with hydrogel-elastomer hybrids hosting programmed cells
Feb 16, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Liu X, Tang TC, Tham E, Yuk H, Lin S, Lu TK, Zhao X
Stretchable living materials and devices with hydrogel-elastomer hybrids hosting programmed cells
Feb 16, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
UNASSIGNED: Living systems, such as bacteria, yeasts, and mammalian cells, can be genetically programmed with synthetic circuits that execute sensing, computing, memory, and response functions. Integrating these functional living components into materials and devices will provide powerful tools for scientific research and enable new technological applications. However, it has been a grand challenge to maintain the viability, functionality, and safety of living components in freestanding materials and devices, which frequently undergo deformations during applications. Here, we report the design of a set of living materials and devices based on stretchable, robust, and biocompatible hydrogel-elastomer hybrids that host various types of genetically engineered bacterial cells. The hydrogel provides sustainable supplies of water and nutrients, and the elastomer is air-permeable, maintaining long-term viability and functionality of the encapsulated cells. Communication between different bacterial strains and with the environment is achieved via diffusion of molecules in the hydrogel. The high stretchability and robustness of the hydrogel-elastomer hybrids prevent leakage of cells from the living materials and devices, even under large deformations. We show functions and applications of stretchable living sensors that are responsive to multiple chemicals in a variety of form factors, including skin patches and gloves-based sensors. We further develop a quantitative model that couples transportation of signaling molecules and cellular response to aid the design of future living materials and devices.
Synthetic biology: Synthetic gene networks that smell
Feb 15, 2017   Nature Chemical Biology Add nature.com free-link Cancel
Farzadfard F, Lu TK
Specificity of genome evolution in experimental populations of
Feb 16, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE
Specificity of genome evolution in experimental populations of
Feb 16, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
UNASSIGNED: Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations of
Durable vesicles for reconstitution of membrane proteins in biotechnology
Feb 16, 2017   Biochemical Society Transactions
Beales PA, Khan S, Muench SP, Jeuken LJ
Durable vesicles for reconstitution of membrane proteins in biotechnology
Feb 16, 2017
Biochemical Society Transactions
UNASSIGNED: The application of membrane proteins in biotechnology requires robust, durable reconstitution systems that enhance their stability and support their functionality in a range of working environments. Vesicular architectures are highly desirable to provide the compartmentalisation to utilise the functional transmembrane transport and signalling properties of membrane proteins. Proteoliposomes provide a native-like membrane environment to support membrane protein function, but can lack the required chemical and physical stability. Amphiphilic block copolymers can also self-assemble into polymersomes: tough vesicles with improved stability compared with liposomes. This review discusses the reconstitution of membrane proteins into polymersomes and the more recent development of hybrid vesicles, which blend the robust nature of block copolymers with the biofunctionality of lipids. These novel synthetic vesicles hold great promise for enabling membrane proteins within biotechnologies by supporting their enhanced © 2017 The Author(s).
Ethylene production with engineered Synechocystis sp PCC 6803 strains
Feb 24, 2017   Microbial Cell Factories
Veetil VP, Angermayr SA, Hellingwerf KJ
Ethylene production with engineered Synechocystis sp PCC 6803 strains
Feb 24, 2017
Microbial Cell Factories
BACKGROUND: Metabolic engineering and synthetic biology of cyanobacteria offer a promising sustainable alternative approach for fossil-based ethylene production, by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene. RESULTS: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene production through the integration of a codon-optimized version of the efe gene under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5'-AGGAGG-3') as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased ethylene production twofold by RBS screening and further investigated improving ethylene production from a single gene copy of efe, using multiple tandem promoters and by putting our best construct on an RSF1010-based broad-host-self-replicating plasmid, which has a higher copy number than the genome. Moreover, to raise the intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene is formed, we constructed a glycogen-synthesis knockout mutant (ΔglgC) and introduced the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however, surprisingly, ethylene production was lower in this strain than in the wild-type background. CONCLUSION: Making use of different RBS sequences, production of ethylene ranging over a 20-fold difference has been achieved. However, a further increase of production through multiple tandem promoters and a broad-host plasmid was not achieved speculating that the transcription strength and the gene copy number are not the limiting factors in our system.
Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions
Feb 23, 2017   Conference Proceedings : ... Annual International Conference Of The IEEE Engineering In Medicine And Biology Society. IEEE Engineering In Medicine And Biology Society. Annual Conference
Foo M, Sawlekar R, Kulkarni VV, Bates DG, Foo M, Sawlekar R, Kulkarni VV, Bates DG, Kulkarni VV, Sawlekar R, Bates DG, Foo M
Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions
Feb 23, 2017
Conference Proceedings : ... Annual International Conference Of The IEEE Engineering In Medicine And Biology Society. IEEE Engineering In Medicine And Biology Society. Annual Conference
UNASSIGNED: The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators. Here, we propose an alternative design approach that utilises the abstract chemical reactions involved in cellular signalling cycles to implement a biomolecular controller - termed a signalling-cycle (SC) controller. We compare the performance of the PI and SC controllers in closed-loop with a nonlinear second-order chemical process. Our results show that the SC controller outperforms the PI controller in terms of both performance and robustness, and also requires fewer abstract chemical reactions to implement, highlighting its potential usefulness in the construction of biomolecular control circuits.
Cell-free synthetic biology for environmental sensing and remediation
Feb 22, 2017   Current Opinion In Biotechnology
Karig DK
Cell-free synthetic biology for environmental sensing and remediation
Feb 22, 2017
Current Opinion In Biotechnology
UNASSIGNED: The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

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