Evolution of new enzymes by gene duplication and divergence

Protein engineering: the potential of remote mutations

(2019) Matthew Wilding et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism

(2019) Andrew F. Schober et al.   Cell Reports

Single point mutation in the transcriptional regulator PnpR renders Pseudomonas sp. strain WBC-3 capable of utilizing 2-chloro-4-nitrophenol

(2019) Shi-Kai Deng et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme

(2019) Gloria Yang et al.   Nature Chemical Biology

Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB

(2019) Juhan Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome

(2019) Andrew B Morgenthaler et al.   eLife

Mutational and transcriptional landscape of spontaneous gene duplications and deletions inCaenorhabditis elegans

(2018) Anke Konrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset

(2018) Charlotte M. Miton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Primordial-like enzymes from bacteria with reduced genomes

(2017) Matteo P. Ferla et al.   MOLECULAR MICROBIOLOGY

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

Structural and functional innovations in the real-time evolution of new (βα)8barrel enzymes

(2017) Matilda S. Newton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

Understanding Flavin-Dependent Halogenase Reactivity via Substrate Activity Profiling

(2017) Mary C. Andorfer et al.   ACS Catalysis

Conformational Tinkering Drives Evolution of a Promiscuous Activity through Indirect Mutational Effects

(2016) Gloria Yang et al.   BIOCHEMISTRY

A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate

(2016) Jamie P. Kershner et al.   JOURNAL OF BACTERIOLOGY

The role of protein dynamics in the evolution of new enzyme function

(2016) Eleanor Campbell et al.   Nature Chemical Biology

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans

(2015) James C. Farslow et al.   BMC GENOMICS

Early evolutionary history and genomic features of gene duplicates in the human genome

(2015) Lijing Bu et al.   BMC GENOMICS

Two-step Ligand Binding in a (βα)8Barrel Enzyme

(2015) Annika Söderholm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Panoramic view of a superfamily of phosphatases through substrate profiling

(2015) Hua Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of Gene Duplication and Amplification

(2015) Andrew B. Reams et al.   Cold Spring Harbor Perspectives in Biology

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio)

(2015) Jiong-Tang Li et al.   Scientific Reports

Novel Type II and Monomeric NAD+ Specific Isocitrate Dehydrogenases: Phylogenetic Affinity, Enzymatic Characterization and Evolutionary Implication

(2015) Peng Wang et al.   Scientific Reports

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

(2015) Param Priya Singh et al.   PLoS Computational Biology

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

The structure of the hexameric atrazine chlorohydrolase AtzA

(2015) T. S. Peat et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence

(2014) Casey L. McGrath et al.   GENETICS

High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms

(2014) M. Adler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential Effects of a Mutation on the Normal and Promiscuous Activities of Orthologs: Implications for Natural and Directed Evolution

(2014) Akhil Khanal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary meandering of intermolecular interactions along the drift barrier

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

(2013) Lavanya Kannan et al.   Biology Direct

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

(2013) Daniel R. Schrider et al.   GENETICS

The Evolutionary Origins of Detoxifying Enzymes

(2013) Hagit Bar-Rogovsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Influence of DNA copy number and mRNA levels on the expression of breast cancer related proteins

(2013) Simen Myhre et al.   Molecular Oncology

Fitness Costs of Synonymous Mutations in the rpsT Gene Can Be Compensated by Restoring mRNA Base Pairing

(2013) Peter A. Lind et al.   PLoS One

Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

(2013) Mario Alberto Martínez-Núñez et al.   PLoS One

Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree

(2013) Matthieu Chartier et al.   PeerJ

Intramolecular Epistasis and the Evolution of a New Enzymatic Function

(2012) Sajid Noor et al.   PLoS One

Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

(2012) J. Nasvall et al.   SCIENCE

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans

(2011) Kendra J. Lipinski et al.   CURRENT BIOLOGY

Divergent Evolution in Enolase Superfamily: Strategies for Assigning Functions

(2011) John A. Gerlt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide selection for increased copy number in Acinetobacter baylyi ADP1: locus and context-dependent variation in gene amplification

(2011) Sarah C. Seaton et al.   MOLECULAR MICROBIOLOGY

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

Catalytic Improvement and Evolution of Atrazine Chlorohydrolase

(2009) C. Scott et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to deregulate gene clusters involved in the neuronal phenotypic traits of Down syndrome

(2009) Aude-Marie Lepagnol-Bestel et al.   HUMAN MOLECULAR GENETICS

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA