Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering

Adaptation ofBacillus subtiliscarbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective

(2014) Michael Kohlstedt et al.   ENVIRONMENTAL MICROBIOLOGY

Overexpression of a non-native deoxyxylulose-dependent vitamin B6 pathway in Bacillus subtilis for the production of pyridoxine

(2014) Fabian M. Commichau et al.   METABOLIC ENGINEERING

Total Synthesis of a Functional Designer Eukaryotic Chromosome

(2014) N. Annaluru et al.   SCIENCE

Rapid and Reliable DNA Assembly via Ligase Cycling Reaction

(2014) Stefan de Kok et al.   ACS Synthetic Biology

Synthetic biology: Tools to design microbes for the production of chemicals and fuels

(2013) Sang Woo Seo et al.   BIOTECHNOLOGY ADVANCES

Metabolic engineering of Escherichia coli: A sustainable industrial platform for bio-based chemical production

(2013) Xianzhong Chen et al.   BIOTECHNOLOGY ADVANCES

Meeting report: The Cambridge BioDesign TechEvent - Synthetic Biology, a new “Age of Wonder”?

(2013) Mario Juhas et al.   Biotechnology Journal

Bacillus subtilis Mutants with Knockouts of the Genes Encoding Ribonucleases RNase Y and RNase J1 Are Viable, with Major Defects in Cell Morphology, Sporulation, and Competence

(2013) S. Figaro et al.   JOURNAL OF BACTERIOLOGY

Genetic manipulations restored the growth fitness of reduced-genome Escherichia coli

(2013) Yasutaka Hirokawa et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Improved production of secreted heterologous enzyme in Bacillus subtilis strain MGB874 via modification of glutamate metabolism and growth conditions

(2013) Kenji Manabe et al.   Microbial Cell Factories

Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis

(2013) K. Yano et al.   MICROBIOLOGY-SGM

In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol

(2013) Tong Hao et al.   Molecular BioSystems

Essential genes in Bacillus subtilis: a re-evaluation after ten years

(2013) Fabian M. Commichau et al.   Molecular BioSystems

Cyclic di-AMP: another second messenger enters the fray

(2013) Rebecca M. Corrigan et al.   NATURE REVIEWS MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

SubtiWiki–a database for the model organismBacillus subtilisthat links pathway, interaction and expression information

(2013) Raphael H. Michna et al.   NUCLEIC ACIDS RESEARCH

Selection-Driven Accumulation of Suppressor Mutants in Bacillus subtilis: The Apparent High Mutation Frequency of the Cryptic gudB Gene and the Rapid Clonal Expansion of gudB+ Suppressors Are Due to Growth under Selection

(2013) Katrin Gunka et al.   PLoS One

Moonlighting is mainstream: Paradigm adjustment required

(2012) Shelley D. Copley   BIOESSAYS

Improvement of d-lactate productivity in recombinant Escherichia coli by coupling production with growth

(2012) Li Zhou et al.   BIOTECHNOLOGY LETTERS

Programmable bacterial catalysis - designing cells for biosynthesis of value-added compounds

(2012) Carolyn M.C. Lam et al.   FEBS LETTERS

Inactivation of Ribosomal Protein Genes in Bacillus subtilis Reveals Importance of Each Ribosomal Protein for Cell Proliferation and Cell Differentiation

(2012) G. Akanuma et al.   JOURNAL OF BACTERIOLOGY

Cyclic Di-AMP Homeostasis inBacillus subtilis

(2012) Felix M. P. Mehne et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In the fast lane: Large-scale bacterial genome engineering

(2012) Tamás Fehér et al.   JOURNAL OF BIOTECHNOLOGY

Genetically switched d-lactate production in Escherichia coli

(2012) Li Zhou et al.   METABOLIC ENGINEERING

SLiCE: a novel bacterial cell extract-based DNA cloning method

(2012) Yongwei Zhang et al.   NUCLEIC ACIDS RESEARCH

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

(2012) Kosei Tanaka et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

High Confidence Prediction of Essential Genes in Burkholderia Cenocepacia

(2012) Mario Juhas et al.   PLoS One

Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network

(2012) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

(2012) J. M. Buescher et al.   SCIENCE

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

Essential genes as antimicrobial targets and cornerstones of synthetic biology

(2012) Mario Juhas et al.   TRENDS IN BIOTECHNOLOGY

Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability

(2012) Tobias Bergmiller et al.   PLoS Genetics

The Essential Function of B. subtilis RNase III Is to Silence Foreign Toxin Genes

(2012) Sylvain Durand et al.   PLoS Genetics

Combined Effect of Improved Cell Yield and Increased Specific Productivity Enhances Recombinant Enzyme Production in Genome-Reduced Bacillus subtilis Strain MGB874

(2011) Kenji Manabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biosynthesis of polyhydroxyalkanoates containing 2-hydroxybutyrate from unrelated carbon source by metabolically engineered Escherichia coli

(2011) Si Jae Park et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study

(2011) Martina Bielaszewska et al.   LANCET INFECTIOUS DISEASES

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries

(2011) Jiayuan Quan et al.   Nature Protocols

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

EcoliWiki: a wiki-based community resource for Escherichia coli

(2011) Brenley K. McIntosh et al.   NUCLEIC ACIDS RESEARCH

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

Synthetic Biology: Integrated Gene Circuits

(2011) N. Nandagopal et al.   SCIENCE

Essence of life: essential genes of minimal genomes

(2011) Mario Juhas et al.   TRENDS IN CELL BIOLOGY

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

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

Metabolic engineering of Escherichia coli for the production of 1,2-propanediol from glycerol

(2010) James M. Clomburg et al.   BIOTECHNOLOGY AND BIOENGINEERING

Update on designing and building minimal cells

(2010) Michael C Jewett et al.   CURRENT OPINION IN BIOTECHNOLOGY

Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

(2010) John P. McCutcheon et al.   Genome Biology and Evolution

Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Growth and Ribosome Function in Wild-Type Escherichia coli and Salmonella enterica

(2010) M. O'Connor et al.   JOURNAL OF BACTERIOLOGY

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing

(2010) Mark Matzas et al.   NATURE BIOTECHNOLOGY

A synthetic DNA transplant

(2010) Mitsuhiro Itaya   NATURE BIOTECHNOLOGY

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

(2010) Sriram Kosuri et al.   NATURE BIOTECHNOLOGY

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

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

(2010) Q. Wang et al.   SCIENCE

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli: Analysis of a Bar-Coded Mutant Collection

(2009) E. C. Hobbs et al.   JOURNAL OF BACTERIOLOGY

Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies

(2009) M. R. Hemm et al.   JOURNAL OF BACTERIOLOGY

Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production

(2009) Shuobo Shi et al.   METABOLIC ENGINEERING

Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production

(2009) Jun Lee et al.   Microbial Cell Factories

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways

(2009) Jiayuan Quan et al.   PLoS One

Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast

(2009) C. Lartigue et al.   SCIENCE

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses

(2008) C. T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Has nature already identified all useful antibacterial targets?

(2008) Dirk Bumann   CURRENT OPINION IN MICROBIOLOGY

Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis

(2008) T. Morimoto et al.   DNA RESEARCH

Superpositioning of Deletions Promotes Growth of Escherichia coli with a Reduced Genome

(2008) H. Mizoguchi et al.   DNA RESEARCH

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes

(2008) Jessica C Zweers et al.   Microbial Cell Factories

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

Large-scale transposon mutagenesis ofMycoplasma pulmonis

(2008) Christopher T. French et al.   MOLECULAR MICROBIOLOGY

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

Rapid and efficient construction of markerless deletions in the Escherichia coli genome

(2008) B. J. Yu et al.   NUCLEIC ACIDS RESEARCH