Synthetic biology for evolutionary engineering: from perturbation of genotype to acquisition of desired phenotype

Engineering global transcription to tune lipophilic properties in Yarrowia lipolytica

(2018) Man Wang et al.   Biotechnology for Biofuels

Modular Ligation Extension of Guide RNA Operons (LEGO) for Multiplexed dCas9 Regulation of Metabolic Pathways in Saccharomyces cerevisiae

(2018) Matthew Deaner et al.   Biotechnology Journal

Directed evolution to improve protein folding in vivo

(2018) Veronika Sachsenhauser et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo

(2018) Christopher L. Moore et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering

(2018) Rongming Liu et al.   METABOLIC ENGINEERING

Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device

(2018) Joo Yeon Seok et al.   METABOLIC ENGINEERING

Directed evolution of a synthetic phylogeny of programmable Trp repressors

(2018) Jared W. Ellefson et al.   Nature Chemical Biology

Synthetic addiction extends the productive life time of engineeredEscherichia colipopulations

(2018) Peter Rugbjerg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterozygous diploid and interspecies SCRaMbLEing

(2018) Michael J. Shen et al.   Nature Communications

L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast

(2018) Lena Hochrein et al.   Nature Communications

Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance

(2018) Tianmin Wang et al.   Nature Communications

Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria

(2018) Chen Dong et al.   Nature Communications

Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome

(2018) B. A. Blount et al.   Nature Communications

Precise control of SCRaMbLE in synthetic haploid and diploid yeast

(2018) Bin Jia et al.   Nature Communications

In vitro DNA SCRaMbLE

(2018) Yi Wu et al.   Nature Communications

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods

(2018) Wei Liu et al.   Nature Communications

Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES

(2018) Zhouqing Luo et al.   Nature Communications

Mutually Orthogonal DNA Replication Systems In Vivo

(2018) Garri A. Arzumanyan et al.   ACS Synthetic Biology

Modular Ligation Extension of Guide RNA Operons (LEGO) for Multiplexed dCas9 Regulation of Metabolic Pathways in Saccharomyces cerevisiae

(2018) Matthew Deaner et al.   Biotechnology Journal

CRISPRi allows optimal temporal control of N-acetylglucosamine bioproduction by a dynamic coordination of glucose and xylose metabolism in Bacillus subtilis

(2018) Yaokang Wu et al.   METABOLIC ENGINEERING

Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae

(2018) Manisha Wadhwa et al.   Microbial Cell Factories

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window

(2018) Shakked O. Halperin et al.   NATURE

Continuous directed evolution of proteins with improved soluble expression

(2018) Tina Wang et al.   Nature Chemical Biology

Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria

(2018) Dongsoo Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ring synthetic chromosome V SCRaMbLE

(2018) Juan Wang et al.   Nature Communications

Retroelement-based genome editing and evolution

(2018) Anna J. Simon et al.   ACS Synthetic Biology

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

(2018) Arjun Ravikumar et al.   CELL

A synthetic microbial biosensor for high-throughput screening of lactam biocatalysts

(2018) Soo-Jin Yeom et al.   Nature Communications

A novel cloning strategy for one-step assembly of multiplex CRISPR vectors

(2018) Marc Zuckermann et al.   Scientific Reports

Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae

(2017) Matthew Deaner et al.   METABOLIC ENGINEERING

Evolution of a split RNA polymerase as a versatile biosensor platform

(2017) Jinyue Pu et al.   Nature Chemical Biology

Continuous directed evolution of aminoacyl-tRNA synthetases

(2017) David I Bryson et al.   Nature Chemical Biology

Balancing gene expression without library construction via a reusable sRNA pool

(2017) Amar Ghodasara et al.   NUCLEIC ACIDS RESEARCH

Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes

(2017) Hoang Long Pham et al.   Nature Communications

Phage-assisted continuous evolution of proteases with altered substrate specificity

(2017) Michael S. Packer et al.   Nature Communications

Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli

(2017) Sabine Oesterle et al.   Scientific Reports

Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae

(2017) Matthew Deaner et al.   ACS Synthetic Biology

Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae

(2017) John M. Leavitt et al.   Biotechnology Journal

On-chip analysis, indexing and screening for chemical producing bacteria in a microfluidic static droplet array

(2016) Sungho Jang et al.   LAB ON A CHIP

Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance

(2016) Ahmed H. Badran et al.   NATURE

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Genetically encoded sensors enable real-time observation of metabolite production

(2016) Jameson K. Rogers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

(2016) K. Nishida et al.   SCIENCE

Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort

(2016) Markus Jeschek et al.   Nature Communications

In vivo continuous evolution of genes and pathways in yeast

(2016) Nathan Crook et al.   Nature Communications

Evolving Orthogonal Suppressor tRNAs To Incorporate Modified Amino Acids

(2016) Andre C. Maranhao et al.   ACS Synthetic Biology

CRMAGE: CRISPR Optimized MAGE Recombineering

(2016) Carlotta Ronda et al.   Scientific Reports

Ribosome Subunit Stapling for Orthogonal Translation inE. coli

(2015) Stephen D. Fried et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Engineering Synthetic Multistress Tolerance in Escherichia coli by Using a Deinococcal Response Regulator, DR1558

(2015) Deepti Appukuttan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolved strains of Scheffersomyces stipitis achieving high ethanol productivity on acid- and base-pretreated biomass hydrolyzate at high solids loading

(2015) Patricia J Slininger et al.   Biotechnology for Biofuels

Protein synthesis by ribosomes with tethered subunits

(2015) Cédric Orelle et al.   NATURE

Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors

(2015) Andreas Meyer et al.   Nature Chemistry

Comparative genome analysis of a thermotolerant Escherichia coli obtained by Genome Replication Engineering Assisted Continuous Evolution (GREACE) and its parent strain provides new understanding of microbial heat tolerance

(2015) Guodong Luan et al.   New Biotechnology

Development of potent in vivo mutagenesis plasmids with broad mutational spectra

(2015) Ahmed H. Badran et al.   Nature Communications

CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli

(2015) Brady F. Cress et al.   ACS Synthetic Biology

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

(2014) I. Farasat et al.   Molecular Systems Biology

An orthogonal DNA replication system in yeast

(2014) Arjun Ravikumar et al.   Nature Chemical Biology

Evolution-guided optimization of biosynthetic pathways

(2014) Srivatsan Raman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production

(2014) John Blazeck et al.   Nature Communications

Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels

(2014) Sang Woo Seo et al.   Scientific Reports

Genome replication engineering assisted continuous evolution (GREACE) to improve microbial tolerance for biofuels production

(2013) Guodong Luan et al.   Biotechnology for Biofuels

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

Directed evolution of genetic parts and circuits by compartmentalized partnered replication

(2013) Jared W Ellefson et al.   NATURE BIOTECHNOLOGY

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Programming adaptive control to evolve increased metabolite production

(2013) Howard H. Chou et al.   Nature Communications

Synthetic RNA devices to expedite the evolution of metabolite-producing microbes

(2013) Jina Yang et al.   Nature Communications

Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency

(2012) Sang Woo Seo et al.   METABOLIC ENGINEERING

Genome-scale promoter engineering by coselection MAGE

(2012) Harris H Wang et al.   NATURE METHODS

Significant Rewiring of the Transcriptome and Proteome of an Escherichia coli Strain Harboring a Tailored Exogenous Global Regulator IrrE

(2012) Tingjian Chen et al.   PLoS One

A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level

(2012) Stephan Binder et al.   GENOME BIOLOGY

gTME for Improved Adaptation of Saccharomyces cerevisiae to Corn Cob Acid Hydrolysate

(2011) Hongmei Liu et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

(2011) Jessica S. Dymond et al.   NATURE

Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion

(2011) H. H. Wang et al.   NUCLEIC ACIDS RESEARCH

Laboratory-Evolved Mutants of an Exogenous Global Regulator, IrrE from Deinococcus radiodurans, Enhance Stress Tolerances of Escherichia coli

(2011) Tingjian Chen et al.   PLoS One

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY