Adaptive laboratory evolution – principles and applications for biotechnology

Gene Copy-Number Alterations: A Cost-Benefit Analysis

(2013) Yun-Chi Tang et al.   CELL

Homofermentative production of optically pure L-lactic acid from xylose by genetically engineered Escherichia coli B

(2013) Jinfang Zhao et al.   Microbial Cell Factories

Dissection of Ire1 Functions Reveals Stress Response Mechanisms Uniquely Evolved in Candida glabrata

(2013) Taiga Miyazaki et al.   PLoS Pathogens

An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile

(2012) Yu Shen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Biotechnology of non-Saccharomyces yeasts—the ascomycetes

(2012) Eric A. Johnson   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics

(2012) José Luis Corchero et al.   BIOTECHNOLOGY ADVANCES

Evolutionary engineering strategies to enhance tolerance of xylose utilizing recombinant yeast to inhibitors derived from spruce biomass

(2012) Rakesh Koppram et al.   Biotechnology for Biofuels

Sex enhances adaptation by unlinking beneficial from detrimental mutations in experimental yeast populations

(2012) Jeremy C Gray et al.   BMC EVOLUTIONARY BIOLOGY

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

(2012) Gionata Scalcinati et al.   FEMS YEAST RESEARCH

Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1

(2012) Liat Avrahami-Moyal et al.   FEMS YEAST RESEARCH

Pilot-scale evaluation the enological traits of a novel, aromatic wine yeast strain obtained by adaptive evolution

(2012) Axelle Cadière et al.   FOOD MICROBIOLOGY

Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae

(2012) Hang Zhou et al.   METABOLIC ENGINEERING

Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli

(2012) Luis H. Reyes et al.   METABOLIC ENGINEERING

An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae

(2012) Bart Oud et al.   Microbial Cell Factories

Laboratory evolution of copper tolerant yeast strains

(2012) Giusy Adamo et al.   Microbial Cell Factories

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

(2012) B. Ryall et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Amplification of the CUP1 gene is associated with evolution of copper tolerance in Saccharomyces cerevisiae

(2012) G. M. Adamo et al.   MICROBIOLOGY-SGM

Yeast Adapts to a Changing Stressful Environment by Evolving Cross-Protection and Anticipatory Gene Regulation

(2012) Riddhiman Dhar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

(2012) JEREMY R. DETTMAN et al.   MOLECULAR ECOLOGY

Exploiting Adaptive Laboratory Evolution of Streptomyces clavuligerus for Antibiotic Discovery and Overproduction

(2012) Pep Charusanti et al.   PLoS One

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

(2012) S. Wielgoss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

(2012) Selwyn Quan et al.   PLoS Genetics

In vivo evolutionary engineering of a boron-resistant bacterium: Bacillus boroniphilus

(2011) Mustafa Şen et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Experimental Evolution of a Facultative Thermophile from a Mesophilic Ancestor

(2011) Ian K. Blaby et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Adaptive evolution for fast growth on glucose and the effects on the regulation of glucose transport system in Clostridium tyrobutyricum

(2011) Ling Jiang et al.   BIOTECHNOLOGY AND BIOENGINEERING

The role of cellular objectives and selective pressures in metabolic pathway evolution

(2011) Hojung Nam et al.   CURRENT OPINION IN BIOTECHNOLOGY

Mechanistic pathway modeling for industrial biotechnology: challenging but worthwhile

(2011) Wolfgang Wiechert et al.   CURRENT OPINION IN BIOTECHNOLOGY

Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering

(2011) Vasiliy A Portnoy et al.   CURRENT OPINION IN BIOTECHNOLOGY

Microbial production of building block chemicals and polymers

(2011) Jeong Wook Lee et al.   CURRENT OPINION IN BIOTECHNOLOGY

Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae

(2011) Jeremiah Wright et al.   FEMS YEAST RESEARCH

Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties

(2011) Z. Petek Çakar et al.   FEMS YEAST RESEARCH

Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast

(2011) Bart Oud et al.   FEMS YEAST RESEARCH

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

(2011) H. Bachmann et al.   GENOME RESEARCH

Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator

(2011) Zarath M Summers et al.   ISME Journal

Laboratory Evolution and Multi-platform Genome Re-sequencing of the Cellulolytic ActinobacteriumThermobifida fusca

(2011) Yu Deng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution

(2011) R. DHAR et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Evolutionary engineered Saccharomyces cerevisiae wine yeast strains with increased in vivo flux through the pentose phosphate pathway

(2011) Axelle Cadière et al.   METABOLIC ENGINEERING

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

(2011) Jeremy J Minty et al.   Microbial Cell Factories

Pre-expression of a sulfhydryl oxidase significantly increases the yields of eukaryotic disulfide bond containing proteins expressed in the cytoplasm of E.coli

(2011) Van Nguyen et al.   Microbial Cell Factories

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

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli

(2011) Dae-Hee Lee et al.   PLoS One

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

(2011) K.-K. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

(2011) Jared W. Wenger et al.   PLoS Genetics

Phosphoenolpyruvate Carboxykinase as the Sole Anaplerotic Enzyme in Saccharomyces cerevisiae

(2010) R. M. Zelle et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Anaplerotic Role for Cytosolic Malic Enzyme in EngineeredSaccharomyces cerevisiaeStrains

(2010) Rintze M. Zelle et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

(2010) D.-H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enatiomerically pure hydroxycarboxylic acids: current approaches and future perspectives

(2010) Qun Ren et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology

(2010) James M. Clomburg et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering

(2010) Rosa Garcia Sanchez et al.   Biotechnology for Biofuels

Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

(2010) Tim F Cooper et al.   BMC EVOLUTIONARY BIOLOGY

Whole-genome sequencing of a laboratory-evolved yeast strain

(2010) Carlos L Araya et al.   BMC GENOMICS

Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress

(2010) Takaaki Horinouchi et al.   BMC GENOMICS

A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution

(2010) Pier-Luc Tremblay et al.   ENVIRONMENTAL MICROBIOLOGY

Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

(2010) Lei Wang et al.   Genome Biology and Evolution

Evolution ofEscherichia colifor Growth at High Temperatures

(2010) Birgit Rudolph et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae

(2010) H. Wouter Wisselink et al.   METABOLIC ENGINEERING

Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

(2010) E. Crozat et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hsp90 and Environmental Stress Transform the Adaptive Value of Natural Genetic Variation

(2010) D. F. Jarosz et al.   SCIENCE

Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

(2010) Pep Charusanti et al.   PLoS Genetics

Microbial experimental evolution

(2009) Albert F. Bennett et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Phylogenetic diversity of stress signaling pathways in fungi

(2009) Elissavet Nikolaou et al.   BMC EVOLUTIONARY BIOLOGY

Isolation of cobalt hyper-resistant mutants of Saccharomyces cerevisiae by in vivo evolutionary engineering approach

(2009) Z. Petek Çakar et al.   JOURNAL OF BIOTECHNOLOGY

Degeneracy: A design principle for achieving robustness and evolvability

(2009) James Whitacre et al.   JOURNAL OF THEORETICAL BIOLOGY

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Microbial factories for recombinant pharmaceuticals

(2009) Neus Ferrer-Miralles et al.   Microbial Cell Factories

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Next-generation synthetic gene networks

(2009) Timothy K Lu et al.   NATURE BIOTECHNOLOGY

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

(2009) S. Maslov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal gene transfer in evolution: facts and challenges

(2009) L. Boto   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS

(2009) Daniel M. Stoebel et al.   PLoS Genetics

Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance

(2009) Anna M. Selmecki et al.   PLoS Genetics

Novel Evolutionary Engineering Approach for Accelerated Utilization of Glucose, Xylose, and Arabinose Mixtures by Engineered Saccharomyces cerevisiae Strains

(2008) H. W. Wisselink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fungal secretomes—nature’s toolbox for white biotechnology

(2008) Henning Bouws et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Strategies for systems-level metabolic engineering

(2008) Tae Yong Kim et al.   Biotechnology Journal

Aneuploidy Underlies Rapid Adaptive Evolution of Yeast Cells Deprived of a Conserved Cytokinesis Motor

(2008) Giulia Rancati et al.   CELL

Importance of systems biology in engineering microbes for biofuel production

(2008) Aindrila Mukhopadhyay et al.   CURRENT OPINION IN BIOTECHNOLOGY

Extremely thermophilic microorganisms for biomass conversion: status and prospects

(2008) Sara E Blumer-Schuette et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth

(2008) S. C. Sleight et al.   GENETICS

Microbial diversity and genomics in aid of bioenergy

(2008) Vipin Chandra Kalia et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Evolvability and hierarchy in rewired bacterial gene networks

(2008) Mark Isalan et al.   NATURE

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE

Microbial production of organic acids: expanding the markets

(2008) Michael Sauer et al.   TRENDS IN BIOTECHNOLOGY

Evolution of Evolvability in Gene Regulatory Networks

(2008) Anton Crombach et al.   PLoS Computational Biology

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL