Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening

Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters

(2014) Mónica Martínez-Martínez et al.   Microbial Biotechnology

Identification of a metagenome-derived prephenate dehydrogenase gene from an alkaline-polluted soil microorganism

(2013) Chengjian Jiang et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Biochemical Diversity of Carboxyl Esterases and Lipases from Lake Arreo (Spain): a Metagenomic Approach

(2013) Mónica Martínez-Martínez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Discovery of (hemi-) cellulase genes in a metagenomic library from a biogas digester using 454 pyrosequencing

(2013) Xing Yan et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases

(2013) Jin-Song Gong et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family

(2013) María Alcaide et al.   BIOCHEMICAL JOURNAL

Functional screening of enzymes and bacteria for the dechlorination of hexachlorocyclohexane by a high-throughput colorimetric assay

(2013) Pooja Sharma et al.   BIODEGRADATION

The metabolic cost of flagellar motion inPseudomonas putida KT2440

(2013) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of cold-active, acidic endocellulase from Ladakh soil by functional metagenomics

(2013) Archana Bhat et al.   EXTREMOPHILES

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

(2013) Sunghee Lee et al.   ISME Journal

Strategy for screening metagenomic resources for exocellulase activity using a robotic, high-throughput screening system

(2013) Kyong-Cheol Ko et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Design of orthogonal genetic switches based on a crosstalk map of  s, anti- s, and promoters

(2013) V. A. Rhodius et al.   Molecular Systems Biology

Synthetic circuits integrating logic and memory in living cells

(2013) Piro Siuti et al.   NATURE BIOTECHNOLOGY

Spanning high-dimensional expression space using ribosome-binding site combinatorics

(2013) Lior Zelcbuch et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows

(2013) Lingling Wang et al.   PLoS One

Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries

(2013) L. Terrón-González et al.   Scientific Reports

A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves

(2013) Claudia Thompson et al.   AMB Express

Phylogenetically Novel LuxI/LuxR-Type Quorum Sensing Systems Isolated Using a Metagenomic Approach

(2012) Eri Nasuno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biochemical analysis of a highly specific, pH stable xylanase gene identified from a bovine rumen-derived metagenomic library

(2012) X. Gong et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Role and significance of beta-glucosidases in the hydrolysis of cellulose for bioethanol production

(2012) Reeta Rani Singhania et al.   BIORESOURCE TECHNOLOGY

A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5

(2012) Hsin-Liang Chen et al.   Biotechnology for Biofuels

Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment

(2012) María-Eugenia Guazzaroni et al.   ENVIRONMENTAL MICROBIOLOGY

Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology

(2012) Markus Schmidt et al.   FEBS LETTERS

Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors

(2012) Pablo I. Nikel et al.   JOURNAL OF BIOTECHNOLOGY

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

(2012) Rafael Silva-Rocha et al.   NUCLEIC ACIDS RESEARCH

Functional Metagenomics Unveils a Multifunctional Glycosyl Hydrolase from the Family 43 Catalysing the Breakdown of Plant Polymers in the Calf Rumen

(2012) Manuel Ferrer et al.   PLoS One

Toward rational design of bacterial genomes

(2011) Guillaume Cambray et al.   CURRENT OPINION IN MICROBIOLOGY

A novel, extremely alkaliphilic and cold-active esterase from Antarctic desert soil

(2011) Xiao Ping Hu et al.   EXTREMOPHILES

Implementing an OR–NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli

(2011) Rafael Silva-Rocha et al.   Molecular BioSystems

Develop reusable and combinable designs for transcriptional logic gates

(2011) Jian Zhan et al.   Molecular Systems Biology

Regulation of Alternative Sigma Factor Use

(2010) Sofia Österberg et al.   Annual Review of Microbiology

Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria

(2010) J. W. Craig et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Product-Induced Gene Expression, a Product-Responsive Reporter Assay Used To Screen Metagenomic Libraries for Enzyme-Encoding Genes

(2010) T. Uchiyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity of Glycosyl Hydrolases from Cellulose-Depleting Communities Enriched from Casts of Two Earthworm Species

(2010) A. Beloqui et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments

(2010) Meng Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Mining metagenomes for novel cellulase genes

(2010) Cheng-Jie Duan et al.   BIOTECHNOLOGY LETTERS

Synthetic gene networks in mammalian cells

(2010) Wilfried Weber et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metagenomic era for biocatalyst identification

(2010) Lucía Fernández-Arrojo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context

(2010) Rita Bartossek et al.   ENVIRONMENTAL MICROBIOLOGY

Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli

(2010) Tae Seok Moon et al.   JOURNAL OF MOLECULAR BIOLOGY

A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion

(2010) Morten OA Sommer et al.   Molecular Systems Biology

Distributed biological computation with multicellular engineered networks

(2010) Sergi Regot et al.   NATURE

A synthetic three-color scaffold for monitoring genetic regulation and noise

(2010) Robert Cox et al.   Journal of Biological Engineering

Identification of a Novel Alkaliphilic Esterase Active at Low Temperatures by Screening a Metagenomic Library from Antarctic Desert Soil

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

Rapid Identification of Genes Encoding DNA Polymerases by Function-Based Screening of Metagenomic Libraries Derived from Glacial Ice

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

Abundance of Novel and Diverse tfdA-Like Genes, Encoding Putative Phenoxyalkanoic Acid Herbicide-Degrading Dioxygenases, in Soil

(2009) A. Zaprasis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Deep Sequencing of a Dimethylsulfoniopropionate-Degrading Gene (dmdA) by Using PCR Primer Pairs Designed on the Basis of Marine Metagenomic Data

(2009) V. A. Varaljay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

(2009) W. J. Sul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization and kinetic analysis of a thermostable GH3 β-glucosidase from Penicillium brasilianum

(2009) Kristian B. R. M. Krogh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking

(2009) Sho Morimoto et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Identification of Cellulase Genes from the Metagenomes of Compost Soils and Functional Characterization of One Novel Endoglucanase

(2009) Hao Pang et al.   CURRENT MICROBIOLOGY

Functional metagenomics for enzyme discovery: challenges to efficient screening

(2009) Taku Uchiyama et al.   CURRENT OPINION IN BIOTECHNOLOGY

The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome

(2009) Hikaru Suenaga et al.   FEMS MICROBIOLOGY ECOLOGY

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

(2009) Karin Hjort et al.   FEMS MICROBIOLOGY ECOLOGY

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

(2009) Hikaru Suenaga et al.   ISME Journal

A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts

(2009) Falk Warnecke et al.   JOURNAL OF BIOTECHNOLOGY

Characterization of a novel β-glucosidase-like activity from a soil metagenome

(2009) Chengjian Jiang et al.   JOURNAL OF MICROBIOLOGY

Lipase Diversity in Glacier Soil Based on Analysis of Metagenomic DNA Fragments and Cell Culture

(2009) Yuhong Zhang   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

The second wave of synthetic biology: from modules to systems

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

Lysine racemase: a novel non-antibiotic selectable marker for plant transformation

(2009) I-Chieh Chen et al.   PLANT MOLECULAR BIOLOGY

Functional Cloning and Expression of a Novel Endo-α-1,5-L-Arabinanase from a Metagenomic Library

(2009) Dominic Wong et al.   PROTEIN AND PEPTIDE LETTERS

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Characterization of a gene encoding cellulase from uncultured soil bacteria

(2008) Soo-Jin Kim et al.   FEMS MICROBIOLOGY LETTERS

Microbial carbohydrate esterases in cold adapted environments

(2008) Vincenzo Aurilia et al.   GENE

Advances in Recovery of Novel Biocatalysts from Metagenomes

(2008) Helen L. Steele et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomics for Mining New Genetic Resources of Microbial Communities

(2008) Manuel Ferrer et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomics

(2008) R.D. Sleator et al.   LETTERS IN APPLIED MICROBIOLOGY

The genome BLASTatlas—a GeneWiz extension for visualization of whole-genome homology

(2008) Peter F. Hallin et al.   Molecular BioSystems

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Setting the standard in synthetic biology

(2008) Adam Arkin   NATURE BIOTECHNOLOGY

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

Substrate-induced gene expression (SIGEX) screening of metagenome libraries

(2008) Taku Uchiyama et al.   Nature Protocols

Engineering BioBrick vectors from BioBrick parts

(2008) Reshma P Shetty et al.   Journal of Biological Engineering