A navigation guide of synthetic biology tools for Pseudomonas putida

Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase

(2020) Javier García-Hidalgo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Regulatory systems for gene expression control in cyanobacteria

(2020) Petra Till et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Limited life cycle and cost assessment for the bioconversion of lignin‐derived aromatics into adipic acid

(2020) Jozef B. J. H. Duuren et al.   BIOTECHNOLOGY AND BIOENGINEERING

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

(2020) Milenko Tokic et al.   Biotechnology for Biofuels

Engineering Pseudomonas putida KT2440 for the production of isobutanol

(2020) Robert Nitschel et al.   ENGINEERING IN LIFE SCIENCES

Direct biosynthesis of adipic acid from lignin-derived aromatics using engineered Pseudomonas putida KT2440

(2020) Wei Niu et al.   METABOLIC ENGINEERING

An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida

(2020) Christos Batianis et al.   Microbial Biotechnology

Biotransformation of 2,4‐dinitrotoluene in a phototrophic co‐culture of engineered Synechococcus elongatus and Pseudomonas putida

(2020) Derek T. Fedeson et al.   Microbial Biotechnology

Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products

(2020) Isabel Bator et al.   Frontiers in Bioengineering and Biotechnology

Engineering the Osmotic State of Pseudomonas putida KT2440 for Efficient Cell Disruption and Downstream Processing of Poly(3-Hydroxyalkanoates)

(2020) Ignacio Poblete-Castro et al.   Frontiers in Bioengineering and Biotechnology

Bio-production of high-purity propionate by engineering l-threonine degradation pathway in Pseudomonas putida

(2020) Chao Ma et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Response of Pseudomonas putida to Complex, Aromatic‐Rich Fractions from Biomass

(2020) Mee‐Rye Park et al.   ChemSusChem

Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440

(2020) Gayle J. Bentley et al.   METABOLIC ENGINEERING

Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications

(2020) Peixin Liang et al.   Microbial Cell Factories

Tailor-made sRNAs: a plasmid tool to control the expression of target mRNAs in Pseudomonas putida

(2020) Patrícia Apura et al.   PLASMID

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis

(2020) Ove Øyås et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440

(2020) Matthias Wehrmann et al.   mBio

Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes

(2020) Lun Yao et al.   Nature Communications

Industrial biotechnology of Pseudomonas putida: advances and prospects

(2020) Anna Weimer et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metabolic engineering of Pseudomonas putida for the production of various types of short-chain-length polyhydroxyalkanoates from levulinic acid

(2020) Daegeun Cha et al.   BIORESOURCE TECHNOLOGY

Improving lysine production through construction of an Escherichia coli enzyme‐constrained model

(2020) Chao Ye et al.   BIOTECHNOLOGY AND BIOENGINEERING

Production of Substituted Styrene Bioproducts from Lignin and Lignocellulose Using Engineered Pseudomonas putida KT2440

(2020) James J. Williamson et al.   Biotechnology Journal

Environmental Performance of Pseudomonas putida with a Uracylated Genome

(2020) Elena Algar et al.   CHEMBIOCHEM

The Wsp intermembrane complex mediates metabolic control of the swim‐attach decision of Pseudomonas putida

(2020) Ángeles Hueso‐Gil et al.   ENVIRONMENTAL MICROBIOLOGY

Light-response of Pseudomonas putida KT2440 mediated by class II LitR, a photosensor homolog.

(2020) Satoru Sumi et al.   JOURNAL OF BACTERIOLOGY

Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

(2020) Sanjeev Dahal et al.   PROTEOMICS

Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial

(2020) Sirli Rosendahl et al.   Scientific Reports

The naked bacterium: emerging properties of a surfome-streamlined Pseudomonas putida strain

(2020) Esteban Martinez-García et al.   ACS Synthetic Biology

Characterization of Context-Dependent Effects on Synthetic Promoters

(2020) Sebastian Köbbing et al.   Frontiers in Bioengineering and Biotechnology

CRISPR-Assisted Multiplex Base Editing System in Pseudomonas putida KT2440

(2020) Jun Sun et al.   Frontiers in Bioengineering and Biotechnology

Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing

(2020) Mitchell G. Thompson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of Photocaged Isopropyl β‐ d ‐1‐thiogalactopyranoside Solubility on the Light Responsiveness of LacI‐controlled Expression Systems in Different Bacteria

(2020) Fabian Hogenkamp et al.   CHEMBIOCHEM

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

(2020) Deepanwita Banerjee et al.   Nature Communications

Resistance to Bipyridyls Mediated by the TtgABC Efflux System in Pseudomonas putida KT2440

(2020) Tania Henríquez et al.   Frontiers in Microbiology

Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production

(2020) Snorre Sulheim et al.   iScience

For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!

(2020) Víctor de Lorenzo et al.   New Biotechnology

Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

(2019) Ilaria Massaiu et al.   Microbial Cell Factories

Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida

(2019) Daniel C. Volke et al.   Microbial Biotechnology

Accelerated genome engineering of Pseudomonas putida by I-Sce I―mediated recombination and CRISPR-Cas9 counterselection

(2019) Nicolas T. Wirth et al.   Microbial Biotechnology

Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

(2019) Kyeong Rok Choi et al.   Microbial Biotechnology

A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae

(2019) Yueping Zhang et al.   Nature Communications

Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems

(2019) Lei Li et al.   BIOTECHNOLOGY ADVANCES

Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed

(2019) Lázaro Molina et al.   ENVIRONMENTAL MICROBIOLOGY

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics

(2019) Vanesa Amarelle et al.   ACS Synthetic Biology

Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning

(2019) Paul Opgenorth et al.   ACS Synthetic Biology

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency

(2019) Santiago Gisler et al.   Nature Communications

Pseudomonas putida KT 2440 is HV 1 certified, not GRAS

(2019) Linde F. C. Kampers et al.   Microbial Biotechnology

Cell density-dependent auto-inducible promoters for expression of recombinant proteins in Pseudomonas putida

(2019) Annika Meyers et al.   Microbial Biotechnology

CRISPR-Cas9 genome editing approaches in filamentous fungi and oomycetes

(2019) Mariana Schuster et al.   FUNGAL GENETICS AND BIOLOGY

Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing

(2019) Kutubuddin A. Molla et al.   TRENDS IN BIOTECHNOLOGY

Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium

(2019) Lázaro Molina et al.   ENVIRONMENTAL MICROBIOLOGY

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

(2019) Juan Nogales et al.   ENVIRONMENTAL MICROBIOLOGY

Recent advances in the CRISPR genome editing tool set

(2019) Su Bin Moon et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

(2019) Linde F. C. Kampers et al.   Microbial Cell Factories

Pass-back chain extension expands multimodular assembly line biosynthesis

(2019) Jia Jia Zhang et al.   Nature Chemical Biology

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

(2019) Esteban Martínez-García et al.   NUCLEIC ACIDS RESEARCH

Towards a fully automated algorithm driven platform for biosystems design

(2019) Mohammad HamediRad et al.   Nature Communications

CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria

(2019) Gaoyan Wang et al.   Nature Microbiology

Integration Host Factor IHF facilitates homologous recombination and mutagenic processes in Pseudomonas putida

(2019) Katren Mikkel et al.   DNA REPAIR

Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module

(2019) Belén Calles et al.   Molecular Systems Biology

Biotransformation of corn bran derived ferulic acid to vanillic acid using engineered Pseudomonas putida KT2440

(2019) Priya Upadhyay et al.   PREPARATIVE BIOCHEMISTRY & BIOTECHNOLOGY

Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineeredEscherichia coli

(2019) Christina V. Dinh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli

(2018) Guillaume Urtecho et al.   BIOCHEMISTRY

Building a genome engineering toolbox in nonmodel prokaryotic microbes

(2018) Emily Freed et al.   BIOTECHNOLOGY AND BIOENGINEERING

CRISPR/Cas9 Assisted Multiplex Genome Editing Technique in Escherichia coli

(2018) Xu Feng et al.   Biotechnology Journal

Genetic tools for reliable gene expression and recombineering in Pseudomonas putida

(2018) Taylor B. Cook et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

(2018) Kyeong Rok Choi et al.   METABOLIC ENGINEERING

Optimal bioprocess design through a gene regulatory network – Growth kinetic hybrid model: Towards replacing Monod kinetics

(2018) Argyro Tsipa et al.   METABOLIC ENGINEERING

Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose

(2018) Pavel Dvořák et al.   METABOLIC ENGINEERING

Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi)

(2018) Benjamin M. Woolston et al.   METABOLIC ENGINEERING

Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system

(2018) Jun Sun et al.   Microbial Cell Factories

The CRISPR tool kit for genome editing and beyond

(2018) Mazhar Adli   Nature Communications

Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors

(2018) Ye Chen et al.   Nature Communications

CRISPR/Cas9 Assisted Multiplex Genome Editing Technique in Escherichia coli

(2018) Xu Feng et al.   Biotechnology Journal

CRISPR for Crop Improvement: An Update Review

(2018) Deepa Jaganathan et al.   Frontiers in Plant Science

Simultaneous Improvements of Pseudomonas Cell Growth and Polyhydroxyalkanoate Production from a Lignin Derivative for Lignin-Consolidated Bioprocessing

(2018) Xiaopeng Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A new sRNA mediated post-transcriptional regulation system for Bacillus subtilis

(2018) Sen Yang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

Improved Thermotolerance of Genome-Reduced Pseudomonas putida EM42 Enables Effective Functioning of the PL /c I857 System

(2018) Tomás Aparicio et al.   Biotechnology Journal

Dynamic control of endogenous metabolism with combinatorial logic circuits

(2018) Felix Moser et al.   Molecular Systems Biology

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modelling

(2018) Isotta D'Arrigo et al.   Environmental Microbiology Reports

A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli

(2018) Gonzalo Durante-Rodríguez et al.   ACS Synthetic Biology

A Multiplex Genome Editing Method for Escherichia coli Based on CRISPR-Cas12a

(2018) Xiang Ao et al.   Frontiers in Microbiology

In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production

(2018) Annalisa Occhipinti et al.   PeerJ

A versatile one-step CRISPR-Cas9 based approach to plasmid-curing

(2017) Ida Lauritsen et al.   Microbial Cell Factories

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

(2017) Axel von Kamp et al.   Nature Communications

Characterizing a thermostable Cas9 for bacterial genome editing and silencing

(2017) Ioannis Mougiakos et al.   Nature Communications

Experimental validation of in silico estimated biomass yields of Pseudomonas putida KT2440

(2017) Sarah Beate Hintermayer et al.   Biotechnology Journal

CRISPR/Cas9-Based Counterselection Boosts Recombineering Efficiency in Pseudomonas putida

(2017) Tomás Aparicio et al.   Biotechnology Journal

Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering

(2017) Yang Liu et al.   Frontiers in Microbiology

The XylS/Pm regulator/promoter system and its use in fundamental studies of bacterial gene expression, recombinant protein production and metabolic engineering

(2017) Agnieszka Gawin et al.   Microbial Biotechnology

A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities

(2017) Deirdre E. Ricaurte et al.   Microbial Biotechnology

CRISPR/Cas9 in Genome Editing and Beyond

(2016) Haifeng Wang et al.   Annual Review of Biochemistry

Mechanisms of Bacterial Transcription Termination: All Good Things Must End

(2016) Ananya Ray-Soni et al.   Annual Review of Biochemistry

CRISPR technologies for bacterial systems: Current achievements and future directions

(2016) Kyeong Rok Choi et al.   BIOTECHNOLOGY ADVANCES

Efficient gene knockdown in Clostridium acetobutylicum by synthetic small regulatory RNAs

(2016) Changhee Cho et al.   BIOTECHNOLOGY AND BIOENGINEERING

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

(2016) Eugeni Belda et al.   ENVIRONMENTAL MICROBIOLOGY

Systems biology-guided biodesign of consolidated lignin conversion

(2016) Lu Lin et al.   GREEN CHEMISTRY

Metabolic engineering of Pseudomonas putida for production of docosahexaenoic acid based on a myxobacterial PUFA synthase

(2016) Katja Gemperlein et al.   METABOLIC ENGINEERING

Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol

(2016) Veronique Beckers et al.   Microbial Cell Factories

Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR

(2016) Michael Jahn et al.   Microbial Cell Factories

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

(2016) Jasper J. Koehorst et al.   Scientific Reports

Broad-Host-Range ProUSER Vectors Enable Fast Characterization of Inducible Promoters and Optimization of p-Coumaric Acid Production in Pseudomonas putida KT2440

(2016) Patricia Calero et al.   ACS Synthetic Biology

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs

(2015) Amit Kumar Chaudhary et al.   BIOTECHNOLOGY ADVANCES

Tn5/7-lux: a versatile tool for the identification and capture of promoters in Gram-negative bacteria

(2015) Steven T Bruckbauer et al.   BMC MICROBIOLOGY

The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism inPseudomonas putida

(2015) Ruggero La Rosa et al.   ENVIRONMENTAL MICROBIOLOGY

Modeling the Interplay of Pseudomonas putida EIIANtr with the Potassium Transporter KdpFABC

(2015) S. Wolf et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites

(2015) Irene M. Brockman et al.   METABOLIC ENGINEERING

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

(2015) Paulo Maia et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Enrichments of gene replacement events by Agrobacterium-mediated recombinase-mediated cassette exchange

(2015) Hiroyasu Ebinuma et al.   MOLECULAR BREEDING

A set of powerful negative selection systems for unmodified Enterobacteriaceae

(2015) Varnica Khetrapal et al.   NUCLEIC ACIDS RESEARCH

Harnessing CRISPR–Cas systems for bacterial genome editing

(2015) Kurt Selle et al.   TRENDS IN MICROBIOLOGY

The Glycerol-Dependent Metabolic Persistence of Pseudomonas putida KT2440 Reflects the Regulatory Logic of the GlpR Repressor

(2015) Pablo I. Nikel et al.   mBio

Targeted Large-Scale Deletion of Bacterial Genomes Using CRISPR-Nickases

(2015) Kylie Standage-Beier et al.   ACS Synthetic Biology

Tn7-Based Device for Calibrated Heterologous Gene Expression in Pseudomonas putida

(2015) Sebastian Zobel et al.   ACS Synthetic Biology

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

Functional Characterization of the Mannitol Promoter of Pseudomonas fluorescens DSM 50106 and Its Application for a Mannitol-Inducible Expression System for Pseudomonas putida KT2440

(2015) Jana Hoffmann et al.   PLoS One

The Functional Structure of Central Carbon Metabolism in Pseudomonas putida KT2440

(2014) Suresh Sudarsan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology

(2014) Zhen Kang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression

(2014) Esteban Martínez-García et al.   Microbial Cell Factories

Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks

(2014) A. A. Nielsen et al.   Molecular Systems Biology

Tunable protein degradation in bacteria

(2014) D Ewen Cameron et al.   NATURE BIOTECHNOLOGY

Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA

(2014) Ryan R Gallagher et al.   Nature Protocols

SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities

(2014) Esteban Martínez-García et al.   NUCLEIC ACIDS RESEARCH

Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets

(2014) Rienk A. Rienksma et al.   SEMINARS IN IMMUNOLOGY

Endogenous Small RNA Clusters in Plants

(2014) Yong-Xin Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Functional characterization and application of a tightly regulated MekR/P mekA expression system in Escherichia coli and Pseudomonas putida

(2013) Nadja Graf et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Expanding the scope of site-specific recombinases for genetic and metabolic engineering

(2013) Thomas Gaj et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition

(2013) Jozef BJH van Duuren et al.   BMC BIOTECHNOLOGY

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

(2013) Lei S. Qi et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress

(2013) S. M. Gaida et al.   NUCLEIC ACIDS RESEARCH

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

The transcriptional regulator CprK detects chlorination by combining direct and indirect readout mechanisms

(2013) L. R. Kemp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Tailored fatty acid synthesis via dynamic control of fatty acid elongation

(2013) J. P. Torella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory RNAs

(2013) Jorge Vazquez-Anderson et al.   RNA Biology

A High-Throughput Functional Complementation Assay for Classification of BRCA1 Missense Variants

(2013) P. Bouwman et al.   Cancer Discovery

Industrial biotechnology of Pseudomonas putida and related species

(2012) Ignacio Poblete-Castro et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida

(2012) Andreas Kremling et al.   BMC Systems Biology

Streamlining genomes: toward the generation of simplified and stabilized microbial systems

(2012) Audrey Leprince et al.   CURRENT OPINION IN BIOTECHNOLOGY

The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida

(2012) I. F. Escapa et al.   ENVIRONMENTAL MICROBIOLOGY

Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida

(2012) Audrey Leprince et al.   ENVIRONMENTAL MICROBIOLOGY

The TOL network ofPseudomonas putidamt-2 processes multiple environmental inputs into a narrowresponse space

(2012) Rafael Silva-Rocha et al.   ENVIRONMENTAL MICROBIOLOGY

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

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

(2012) Ignacio Poblete-Castro et al.   METABOLIC ENGINEERING

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

TREX: A Universal Tool for the Transfer and Expression of Biosynthetic Pathways in Bacteria

(2012) Anita Loeschcke et al.   ACS Synthetic Biology

Mechanisms of Resistance to Chloramphenicol in Pseudomonas putida KT2440

(2011) Matilde Fernández et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes

(2011) Esteban Martínez-García et al.   BMC MICROBIOLOGY

The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms

(2011) Rafael Silva-Rocha et al.   ENVIRONMENTAL MICROBIOLOGY

Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440

(2011) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Efficient production of soluble recombinant single chain Fv fragments by a Pseudomonas putida strain KT2440 cell factory

(2011) Thorben Dammeyer et al.   Microbial Cell Factories

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

In silicogenome-scale metabolic analysis ofPseudomonas putidaKT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

(2010) Seung Bum Sohn et al.   Biotechnology Journal

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

(2010) Stacey D Finley et al.   BMC Systems Biology

The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid

(2010) Michalis Koutinas et al.   ENVIRONMENTAL MICROBIOLOGY

A General Mechanism for Network-Dosage Compensation in Gene Circuits

(2010) M. Acar et al.   SCIENCE

(Re-)construction, characterization and modeling of systems for synthetic biology

(2009) María Suárez Diez et al.   Biotechnology Journal

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

Genetic noise control via protein oligomerization

(2008) Cheol-Min Ghim et al.   BMC Systems Biology

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology