recent SynBio papers
Get flash to fully experience Pearltrees
Natural strategies for the spatial optimizatio... [Nat Chem Biol. 2012
Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources.
Using a newly synthesized gibberellin analog containing an acetoxymethyl group (GA(3)-AM) and its binding proteins, we developed an efficient chemically inducible dimerization (CID) system that is completely orthogonal to existing rapamycin-mediated protein dimerization . Combining the two systems should allow applications that have been difficult or impossible with only one CID system . By using both chemical inputs (rapamycin and GA(3)-AM), we designed and synthesized Boolean logic gates in living mammalian cells.
Rapid and orthogonal logic gating with a gibbe... [Nat Chem Biol. 2012
Reprogramming the Genetic Code
The genetic code provides rules by which a genome is decoded to produce proteins of defined amino acid composition and sequence. These rules, which specify 61 codons (triplets of nucleotides) that code for the 20 common amino acids, and 3 codons that signal the termination of protein synthesis, are near-universally conserved in living organisms. Despite conservation of this code and the translational machinery that enforces it, a growing body of work addresses the challenges in reprogramming the genetic code. Designer amino acids, created by synthetic chemistry, can now be incorporated into specific sites in proteins of interest in vitro, in cells, and most recently in a whole animal (see the figure).PLoS ONE: Synthetic Biology: Mapping the Scientific Landscape
This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved.
Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.
Synthetic Genetic Polymers Capable of Heredity and Evolution
Author Summary It is common belief that the properties of cells depend on their environment and on the genes they carry. Yet, many cases exist where individual cells in the same environment behave very differently, despite sharing the same genes. This creates a problem when we try to explain the behavior of a cell population based on the genes these cells carry. For example, it is difficult to predict how fast the overall number of cells increases based on the genes they all carry if some cells divide much faster than others. We addressed this problem using a synthetic gene circuit that could randomly allocate cells into drug resistant and drug sensitive states.
PLoS Computational Biology: Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit
RSS 1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Joint Bioenergy Institute, Emeryville, California, USA. [3] QB3-California Institute for Quantitative Sciences, Berkeley, California, USA. [4] [5]. Our ability to routinely engineer genetic networks for applications is limited by the scarcity of highly specific and non-cross-reacting ( orthogonal ) gene regulators with predictable behavior.
Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012] - PubMed - NCBI
Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame.
PLoS ONE: A Biobrick Library for Cloning Custom Eukaryotic Plasmids
Author Summary Although an amino acid can be encoded by multiple synonymous codons, these codons are not used equally frequently in a genome. Biased codon usage is believed to improve translational efficiency because it is thought that preferentially used codons are translated faster than unpreferred ones. Surprisingly, we find similar translational speeds among synonymous codons. We show that translational efficiency is optimized by a previously unknown mechanism that relies on proportional use of codons according to their cognate tRNA concentrations. Our results provide important molecular details of protein translation, answer why codon usage is unequal, demonstrate widespread natural selection for translational efficiency, and can guide designs of synthetic genomes and cells with efficient translation systems. Wenfeng Qian 1 , Jian-Rong Yang 1 , 2 , Nathaniel M.
PLoS Genetics: Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency
iSSB, Institute of Systems and Synthetic Biology, CNRS UPS3509, University of Evry-Val-d’Essonne EA4527, Genopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030 Evry Cedex, France De novo biosynthetic pathways are designed, assembled and optimized to produce high-value compounds such as drugs and chemical building blocks from renewable resources. Microorganisms are used as synthetic platforms of systems biology where biochemical pathways are engineered into the host metabolic network. Retrosynthetic biology offers a creative pathway design concept that has gained interest because of its potential to identify novel metabolic ways for therapeutic production.
Current Opinion in Biotechnology - A retrosynthetic biology approach to therapeutics: from conception to delivery
Engineering Molecular Circuits Usin... [Annu Rev Chem Biomol Eng. 2012] - PubMed - NCBI
Synthetic biology has made significant leaps over the past decade, and it now enables rational and predictable reprogramming of cells to conduct complex physiological activities. The bases for cellular reprogramming are mainly genetic control components affecting gene expression. A huge variety of these modules, ranging from engineered fusion proteins regulating transcription to artificial RNA devices affecting translation, is available, and they often feature a highly modular scaffold. First endeavors to combine these modules have led to autoregulated expression systems and genetic cascades. Analogous to the rational engineering of electronic circuits, the existing repertoire of artificial regulatory elements has further enabled the ambitious reprogramming of cells to perform Boolean calculations or to mimic the oscillation of circadian clocks.Integrated Electromicrobial Conversion of CO2 to Higher Alcohols
One of the major challenges in using electrical energy is the efficiency in its storage. Current methods, such as chemical batteries, hydraulic pumping, and water splitting, suffer from low energy density or incompatibility with current transportation infrastructure. Here, we report a method to store electrical energy as chemical energy in higher alcohols, which can be used as liquid transportation fuels.1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Joint Bioenergy Institute, Emeryville, California, USA. [3] QB3-California Institute for Quantitative Sciences, Berkeley, California, USA. [4] [5]. Our ability to routinely engineer genetic networks for applications is limited by the scarcity of highly specific and non-cross-reacting (orthogonal) gene regulators with predictable behavior. Though antisense RNAs are attractive contenders for this purpose, quantitative understanding of their specificity and sequence-function relationship sufficient for their design has been limited.
Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012] - PubMed - NCBI
Karmella A. Haynes * † , Francesca Ceroni ‡ , Daniel Flicker § , Andrew Younger § , and Pamela A. Silver §
A Sensitive Switch for Visualizing Natural Gene Silencing in Single Cells - ACS Synthetic Biology (ACS Publications)
RSS 1] Howard Hughes Medical Institute, Boston University, Boston, Massachusetts, USA. [2] Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA. [3] Center for BioDynamics, Boston University, Boston, Massachusetts, USA. Here we show that bacterial communication through indole signaling induces persistence, a phenomenon in which a subset of an isogenic bacterial population tolerates antibiotic treatment.