Automated design of synthetic ribosome binding sites to control protein expression.

PubWeight™: 5.86‹?› | Rank: Top 1%

🔗 View Article (PMC 2782888)

Published in Nat Biotechnol on October 04, 2009

Authors

Howard M Salis1, Ethan A Mirsky, Christopher A Voigt

Author Affiliations

1: Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.

Articles citing this

(truncated to the top 100)

Synthetic biology: applications come of age. Nat Rev Genet (2010) 6.96

Microbial engineering for the production of advanced biofuels. Nature (2012) 3.60

Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell (2014) 3.15

Next-generation synthetic gene networks. Nat Biotechnol (2009) 3.12

Engineering the perfect (bacterial) cancer therapy. Nat Rev Cancer (2010) 2.70

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol (2014) 2.63

Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods (2013) 2.61

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol (2012) 2.55

Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A (2012) 2.30

Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol (2012) 2.17

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat Commun (2011) 2.06

Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods (2013) 2.03

Rate-limiting steps in yeast protein translation. Cell (2013) 1.99

Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat Chem Biol (2013) 1.98

RNA processing enables predictable programming of gene expression. Nat Biotechnol (2012) 1.92

Engineering biological systems with synthetic RNA molecules. Mol Cell (2011) 1.80

Principles of genetic circuit design. Nat Methods (2014) 1.79

Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol (2012) 1.70

Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements. J Ind Microbiol Biotechnol (2012) 1.67

Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol (2012) 1.66

Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A (2012) 1.60

Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol (2015) 1.60

Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res (2010) 1.55

Creating small transcription activating RNAs. Nat Chem Biol (2015) 1.55

Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A (2013) 1.53

Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat Commun (2013) 1.52

A portable expression resource for engineering cross-species genetic circuits and pathways. Nat Commun (2015) 1.50

Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. PLoS Genet (2012) 1.46

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res (2012) 1.42

Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Nucleic Acids Res (2012) 1.41

The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab Eng (2012) 1.40

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res (2013) 1.38

De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc Natl Acad Sci U S A (2012) 1.31

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microb Cell Fact (2011) 1.29

Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res (2012) 1.28

Application of synthetic biology in cyanobacteria and algae. Front Microbiol (2012) 1.28

Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol (2013) 1.27

Quantitative dissection of the simple repression input-output function. Proc Natl Acad Sci U S A (2011) 1.23

Metabolic engineering for the production of natural products. Annu Rev Chem Biomol Eng (2011) 1.22

Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol (2010) 1.20

Fundamental relationship between operon organization and gene expression. Proc Natl Acad Sci U S A (2011) 1.19

Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Comput Biol (2012) 1.19

Optimization of gene expression through divergent mutational paths. Cell Rep (2012) 1.18

Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res (2013) 1.18

Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat Methods (2012) 1.17

Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay. Nucleic Acids Res (2013) 1.16

A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genet (2012) 1.14

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol Syst Biol (2014) 1.12

On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli. Genetics (2010) 1.11

A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol Syst Biol (2011) 1.10

Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc Natl Acad Sci U S A (2013) 1.10

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res (2010) 1.10

Genetic design automation: engineering fantasy or scientific renewal? Trends Biotechnol (2011) 1.08

Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res (2013) 1.08

A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli. Microb Cell Fact (2013) 1.08

Fine-tuning gene networks using simple sequence repeats. Proc Natl Acad Sci U S A (2012) 1.07

Regulatory consequences of gene translocation in bacteria. Nucleic Acids Res (2012) 1.07

Automatic design of digital synthetic gene circuits. PLoS Comput Biol (2011) 1.06

Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng (2013) 1.06

Combinatorial design of a highly efficient xylose-utilizing pathway in Saccharomyces cerevisiae for the production of cellulosic biofuels. Appl Environ Microbiol (2012) 1.05

Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng (2011) 1.05

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS One (2011) 1.05

Synthetic biology guides biofuel production. J Biomed Biotechnol (2010) 1.05

Evidence for induction of integron-based antibiotic resistance by the SOS response in a clinical setting. PLoS Pathog (2012) 1.05

Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst Biol (2010) 1.04

Strategies for protein synthetic biology. Nucleic Acids Res (2010) 1.04

A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol (2010) 1.04

Non-transcriptional regulatory processes shape transcriptional network dynamics. Nat Rev Microbiol (2011) 1.04

Evolution-guided optimization of biosynthetic pathways. Proc Natl Acad Sci U S A (2014) 1.03

One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy. Nucleic Acids Res (2013) 1.03

Programming stress-induced altruistic death in engineered bacteria. Mol Syst Biol (2012) 1.03

Tuning gene expression with synthetic upstream open reading frames. Proc Natl Acad Sci U S A (2013) 1.02

Tuning response curves for synthetic biology. ACS Synth Biol (2013) 1.01

Characterization of an inducible promoter in different DNA copy number conditions. BMC Bioinformatics (2012) 1.01

SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth Biol (2012) 1.01

Rapid optimization of gene dosage in E. coli using DIAL strains. J Biol Eng (2011) 1.01

Permanent genetic memory with >1-byte capacity. Nat Methods (2014) 1.00

Modulating membrane composition alters free fatty acid tolerance in Escherichia coli. PLoS One (2013) 1.00

The predictability of molecular evolution during functional innovation. Proc Natl Acad Sci U S A (2014) 1.00

Synthetic biology toolbox for controlling gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002. ACS Synth Biol (2014) 1.00

Tuning the dials of Synthetic Biology. Microbiology (2013) 1.00

Genome engineering for improved recombinant protein expression in Escherichia coli. Microb Cell Fact (2014) 0.99

Multiplex genome editing by natural transformation. Proc Natl Acad Sci U S A (2014) 0.99

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res (2014) 0.99

Directed evolution: an evolving and enabling synthetic biology tool. Curr Opin Chem Biol (2012) 0.99

Toward design-based engineering of industrial microbes. Curr Opin Microbiol (2010) 0.99

Comprehensive engineering of Escherichia coli for enhanced expression of IgG antibodies. Metab Eng (2010) 0.98

Designing and using RNA scaffolds to assemble proteins in vivo. Nat Protoc (2012) 0.98

Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices. PLoS One (2012) 0.98

Algorithms for automated DNA assembly. Nucleic Acids Res (2010) 0.98

Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng (2011) 0.97

Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol (2014) 0.97

Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res (2011) 0.96

Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells. PLoS Biol (2013) 0.96

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota. Cell Syst (2015) 0.95

Predicting the strength of UP-elements and full-length E. coli σE promoters. Nucleic Acids Res (2011) 0.95

Development of Synechocystis sp. PCC 6803 as a phototrophic cell factory. Mar Drugs (2013) 0.95

Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res (2013) 0.95

Engineered biosynthesis of natural products in heterologous hosts. Chem Soc Rev (2015) 0.95

Benchmarking various green fluorescent protein variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for live cell imaging. Appl Environ Microbiol (2013) 0.95

Articles cited by this

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science (2008) 10.90

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75

Coding-sequence determinants of gene expression in Escherichia coli. Science (2009) 8.38

A synthetic multicellular system for programmed pattern formation. Nature (2005) 6.93

A fast, robust and tunable synthetic gene oscillator. Nature (2008) 6.85

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature (2008) 6.68

Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol (2004) 5.07

Synthetic gene networks that count. Science (2009) 4.54

Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci U S A (1990) 4.45

Directed evolution of a genetic circuit. Proc Natl Acad Sci U S A (2002) 4.26

Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol (2009) 4.11

Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol (2009) 3.86

Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev (2005) 3.78

Environmental signal integration by a modular AND gate. Mol Syst Biol (2007) 3.25

The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol Microbiol (1992) 3.22

A synthetic genetic edge detection program. Cell (2009) 3.20

Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res (1994) 3.08

Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol (2006) 3.02

Thermodynamics of single mismatches in RNA duplexes. Biochemistry (1999) 2.36

Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell (2006) 2.26

Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat Chem Biol (2008) 2.19

Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol (2007) 2.18

Gene synthesis demystified. Trends Biotechnol (2008) 2.00

Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA. Proc Natl Acad Sci U S A (2001) 1.91

Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab Eng (2008) 1.81

Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA. J Mol Biol (2003) 1.55

Combinatorial pathway analysis for improved L-tyrosine production in Escherichia coli: identification of enzymatic bottlenecks by systematic gene overexpression. Metab Eng (2007) 1.36

Library of synthetic 5' secondary structures to manipulate mRNA stability in Escherichia coli. Biotechnol Prog (1999) 1.35

Computational design of orthogonal ribosomes. Nucleic Acids Res (2008) 1.04

Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches. Biochemistry (2008) 1.03

Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs. Nucleic Acids Res (2008) 1.00

Articles by these authors

Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature (2009) 6.74

Synthetic biology: engineering Escherichia coli to see light. Nature (2005) 4.58

Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol (2005) 4.25

Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature (2010) 3.69

Environmental signal integration by a modular AND gate. Mol Syst Biol (2007) 3.25

A synthetic genetic edge detection program. Cell (2009) 3.20

Genetic programs constructed from layered logic gates in single cells. Nature (2012) 2.35

Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A (2012) 2.30

Synthesis of methyl halides from biomass using engineered microbes. J Am Chem Soc (2009) 1.90

Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach. Chem Biol (2004) 1.88

The promise of optogenetics in cell biology: interrogating molecular circuits in space and time. Nat Methods (2010) 1.87

Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci U S A (2011) 1.75

Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol (2012) 1.70

Engineering synthetic signaling proteins with ultrasensitive input/output control. Nat Biotechnol (2007) 1.66

Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods (2013) 1.42

Multichromatic control of gene expression in Escherichia coli. J Mol Biol (2010) 1.39

Kinetic buffering of cross talk between bacterial two-component sensors. J Mol Biol (2009) 1.32

Modular control of multiple pathways using engineered orthogonal T7 polymerases. Nucleic Acids Res (2012) 1.28

Library analysis of SCHEMA-guided protein recombination. Protein Sci (2003) 1.28

Engineering the Salmonella type III secretion system to export spider silk monomers. Mol Syst Biol (2009) 1.26

De novo design of biocatalysts. Curr Opin Chem Biol (2002) 1.23

Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol (2010) 1.20

Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island 1. J Mol Biol (2007) 1.16

Prokaryotic gene clusters: a rich toolbox for synthetic biology. Biotechnol J (2010) 1.07

Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. Curr Opin Chem Biol (2013) 1.02

Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol Syst Biol (2013) 1.02

Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol (2010) 0.94

Characterization of combinatorial patterns generated by multiple two-component sensors in E. coli that respond to many stimuli. Biotechnol Bioeng (2010) 0.91

Genetic circuit performance under conditions relevant for industrial bioreactors. ACS Synth Biol (2012) 0.91

Genetic sensor for strong methylating compounds. ACS Synth Biol (2013) 0.84

Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol (2014) 0.79

Synthetic biology: Bacteria collaborate to sense arsenic. Nature (2012) 0.78

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota. Cell Syst (2016) 0.76

Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion. Microb Cell Fact (2010) 0.76

Synthetic biology. ACS Synth Biol (2012) 0.75

Life from information. Nat Methods (2008) 0.75