Published in Nat Rev Microbiol on February 01, 2005
Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev (2010) 7.35
RNA processing enables predictable programming of gene expression. Nat Biotechnol (2012) 1.92
Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PLoS Genet (2007) 1.74
Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev (2009) 1.59
KIN-29 SIK regulates chemoreceptor gene expression via an MEF2 transcription factor and a class II HDAC. EMBO J (2006) 1.31
pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol (2011) 1.15
The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation. Nucleic Acids Res (2009) 1.14
The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PLoS One (2010) 1.08
Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci (2013) 1.08
Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. BMC Genomics (2011) 1.07
Whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls. Sensors (Basel) (2010) 1.03
The culturable soil antibiotic resistome: a community of multi-drug resistant bacteria. PLoS One (2013) 1.01
The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR transcriptional regulator. J Bacteriol (2007) 1.00
Evidence of in vivo cross talk between the nitrogen-related and fructose-related branches of the carbohydrate phosphotransferase system of Pseudomonas putida. J Bacteriol (2008) 0.96
Atrazine biodegradation in the lab and in the field: enzymatic activities and gene regulation. Microb Biotechnol (2008) 0.93
Characterization of novel carbazole catabolism genes from gram-positive carbazole degrader Nocardioides aromaticivorans IC177. Appl Environ Microbiol (2006) 0.92
Murine vaginal colonization model for investigating asymptomatic mucosal carriage of Streptococcus pyogenes. Infect Immun (2013) 0.92
Bacterial degradation of benzoate: cross-regulation between aerobic and anaerobic pathways. J Biol Chem (2012) 0.91
De novo evolution of complex, global and hierarchical gene regulatory mechanisms. J Mol Evol (2010) 0.90
Investigating antibiotic resistance in non-clinical environments. Front Microbiol (2013) 0.88
Census of solo LuxR genes in prokaryotic genomes. Front Cell Infect Microbiol (2015) 0.87
Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis. PLoS One (2011) 0.87
Integrated response to inducers by communication between a catabolic pathway and its regulatory system. J Bacteriol (2007) 0.86
Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125. Extremophiles (2006) 0.85
DNA linking number change induced by sequence-specific DNA-binding proteins. Nucleic Acids Res (2010) 0.85
The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Syst Biol (2011) 0.82
Gene regulatory network inference using fused LASSO on multiple data sets. Sci Rep (2016) 0.81
Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution. J Mol Evol (2010) 0.81
Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression. Biophys J (2015) 0.81
Chlorinated phenols control the expression of the multidrug resistance efflux pump MexAB-OprM in Pseudomonas aeruginosa by interacting with NalC. Mol Microbiol (2011) 0.80
Novel regulator MphX represses activation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR in Acinetobacter calcoaceticus. PLoS One (2011) 0.79
The interplay of StyR and IHF regulates substrate-dependent induction and carbon catabolite repression of styrene catabolism genes in Pseudomonas fluorescens ST. BMC Microbiol (2008) 0.79
Microbially derived biosensors for diagnosis, monitoring and epidemiology. Microb Biotechnol (2017) 0.78
Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. Adv Microb Physiol (2012) 0.78
The Multifaceted Activity of the VirF Regulatory Protein in the Shigella Lifestyle. Front Mol Biosci (2016) 0.78
Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res (2008) 0.77
Transcriptional activation of quinoline degradation operons of Pseudomonas putida 86 by the AraC/XylS-type regulator OxoS and cross-regulation of the PqorM promoter by XylS. Appl Environ Microbiol (2005) 0.76
Constitutive Expression of a Nag-Like Dioxygenase Gene through an Internal Promoter in the 2-Chloronitrobenzene Catabolism Gene Cluster of Pseudomonas stutzeri ZWLR2-1. Appl Environ Microbiol (2016) 0.76
Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil. Appl Environ Microbiol (2015) 0.76
Phenotypic robustness and the assortativity signature of human transcription factor networks. PLoS Comput Biol (2014) 0.76
Distinct Residues Contribute to Motility Repression and Autoregulation in the Proteus mirabilis Fimbria-Associated Transcriptional Regulator AtfJ. J Bacteriol (2016) 0.76
Nitrogen regulation of the xyl genes of Pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil. Microb Biotechnol (2016) 0.75
Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner. ISME J (2016) 0.75
Isolation of a non-genomic origin fluoroquinolone responsive regulatory element using a combinatorial bioengineering approach. Nucleic Acids Res (2016) 0.75
Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134. Appl Environ Microbiol (2015) 0.75
Essential is not irreplaceable: fitness dynamics of experimental E. coli RNase P RNA heterologous replacement. J Mol Evol (2014) 0.75
Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria. PLoS One (2017) 0.75
Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Environ Microbiol (2003) 1.61
Export of autotransported proteins proceeds through an oligomeric ring shaped by C-terminal domains. EMBO J (2002) 1.50
Microbial responses to environmental arsenic. Biometals (2009) 1.48
Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem (2006) 1.45
The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res (2012) 1.42
Production of functional single-chain Fv antibodies in the cytoplasm of Escherichia coli. J Mol Biol (2002) 1.39
Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution. FEMS Microbiol Rev (2002) 1.32
Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol (2006) 1.29
Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol (2011) 1.24
The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol (2011) 1.20
Tracing explosives in soil with transcriptional regulators of Pseudomonas putida evolved for responding to nitrotoluenes. Microb Biotechnol (2008) 1.17
pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol (2011) 1.15
The sigma54 regulon (sigmulon) of Pseudomonas putida. Environ Microbiol (2003) 1.14
Noise and robustness in prokaryotic regulatory networks. Annu Rev Microbiol (2010) 1.13
Functional transplantation of the sumoylation machinery into Escherichia coli. Protein Expr Purif (2004) 1.12
The environmental fate of organic pollutants through the global microbial metabolism. Mol Syst Biol (2007) 1.11
Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol (2005) 1.11
Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett (2012) 1.09
Structural tolerance of bacterial autotransporters for folded passenger protein domains. Mol Microbiol (2004) 1.07
Thioredoxin fusions increase folding of single chain Fv antibodies in the cytoplasm of Escherichia coli: evidence that chaperone activity is the prime effect of thioredoxin. J Mol Biol (2006) 1.06
The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol (2013) 1.02
Sinorhizobium meliloti fur-like (Mur) protein binds a fur box-like sequence present in the mntA promoter in a manganese-responsive manner. Appl Environ Microbiol (2007) 1.01
Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol (2005) 1.00
Engineering the soil bacterium Pseudomonas putida for arsenic methylation. Appl Environ Microbiol (2013) 1.00
The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida. J Bacteriol (2007) 0.99
Emergence of novel functions in transcriptional regulators by regression to stem protein types. Mol Microbiol (2007) 0.99
Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. MBio (2012) 0.98
Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma54 Pu promoter of Pseudomonas putida. J Bacteriol (2004) 0.98
Adaptation of the yeast URA3 selection system to gram-negative bacteria and generation of a {delta}betCDE Pseudomonas putida strain. Appl Environ Microbiol (2005) 0.98
Evidence of in vivo cross talk between the nitrogen-related and fructose-related branches of the carbohydrate phosphotransferase system of Pseudomonas putida. J Bacteriol (2008) 0.96
Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Lett (2008) 0.96
Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. Metab Eng (2012) 0.95
The metabolic cost of flagellar motion in Pseudomonas putida KT2440. Environ Microbiol (2013) 0.93
The interplay of the EIIA(Ntr) component of the nitrogen-related phosphotransferase system (PTS(Ntr)) of Pseudomonas putida with pyruvate dehydrogenase. Biochim Biophys Acta (2011) 0.92
Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol (2008) 0.92
Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation. Mol Microbiol (2011) 0.90
Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440. Environ Microbiol (2013) 0.90
Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol Rev (2010) 0.90
The ancestral role of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics. Res Microbiol (2007) 0.90
Functional coexistence of twin arsenic resistance systems in Pseudomonas putida KT2440. Environ Microbiol (2014) 0.89
Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol (2006) 0.89
Testing the limits of biological tolerance to arsenic in a fungus isolated from the River Tinto. Environ Microbiol (2003) 0.89
Accumulation of inorganic polyphosphate enables stress endurance and catalytic vigour in Pseudomonas putida KT2440. Microb Cell Fact (2013) 0.89
Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol (2012) 0.89
Subtractive hybridization reveals a high genetic diversity in the fish pathogen Photobacterium damselae subsp. piscicida: evidence of a SXT-like element. Microbiology (2005) 0.88
Fructose 1-phosphate is the preferred effector of the metabolic regulator Cra of Pseudomonas putida. J Biol Chem (2011) 0.86
Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria. Methods Mol Biol (2012) 0.85
Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors. J Biotechnol (2012) 0.85
Freeing Pseudomonas putida KT2440 of its proviral load strengthens endurance to environmental stresses. Environ Microbiol (2014) 0.85
Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. Environ Microbiol (2010) 0.85
The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes. Environ Microbiol (2006) 0.84
Why are chlorinated pollutants so difficult to degrade aerobically? Redox stress limits 1,3-dichloroprop-1-ene metabolism by Pseudomonas pavonaceae. Philos Trans R Soc Lond B Biol Sci (2013) 0.84
Growth-dependent phosphorylation of the PtsN (EIINtr) protein of Pseudomonas putida. J Biol Chem (2007) 0.83
The role of thiol species in the hypertolerance of Aspergillus sp. P37 to arsenic. J Biol Chem (2004) 0.83
Sigma 54 levels and physiological control of the Pseudomonas putida Pu promoter. J Bacteriol (2003) 0.82
Implementing an OR-NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli. Mol Biosyst (2011) 0.82
Cooperative amino acid changes shift the response of the σ⁵⁴-dependent regulator XylR from natural m-xylene towards xenobiotic 2,4-dinitrotoluene. Mol Microbiol (2011) 0.82
The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Syst Biol (2011) 0.82
Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma54-promoter Pu to the response regulator PprA. Mol Microbiol (2008) 0.82
The Standard European Vector Architecture (SEVA) plasmid toolkit. Methods Mol Biol (2014) 0.82
Endogenous stress caused by faulty oxidation reactions fosters evolution of 2,4-dinitrotoluene-degrading bacteria. PLoS Genet (2013) 0.82
The private life of environmental bacteria: pollutant biodegradation at the single cell level. Environ Microbiol (2014) 0.81
The grammar of (micro)biological diversity. Environ Microbiol (2002) 0.81
Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins. Environ Microbiol (2011) 0.81
In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Anal Bioanal Chem (2010) 0.81
The Crp regulator of Pseudomonas putida: evidence of an unusually high affinity for its physiological effector, cAMP. Environ Microbiol (2011) 0.81
Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains. J Bacteriol (2003) 0.81
A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations. Mol Biosyst (2011) 0.80
Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor. Mol Biosyst (2012) 0.80
Expanding the boolean logic of the prokaryotic transcription factor XylR by functionalization of permissive sites with a protease-target sequence. ACS Synth Biol (2013) 0.80
Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environ Microbiol Rep (2013) 0.80
Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate : phosphotransferase system of Pseudomonas putida. Environ Microbiol (2012) 0.80
Non-disruptive release of Pseudomonas putida proteins by in situ electric breakdown of intact cells. J Microbiol Methods (2007) 0.80
Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene. Mol Microbiol (2012) 0.79
Engineering whole-cell biosensors with no antibiotic markers for monitoring aromatic compounds in the environment. Methods Mol Biol (2012) 0.79
Inferring the genetic network of m-xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2. Mol Microbiol (2005) 0.79
The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in m-xylene biodegradation. Environ Microbiol (2014) 0.78
Secretion of proteins with dimerization capacity by the haemolysin type I transport system of Escherichia coli. Mol Microbiol (2004) 0.78
The IHF regulon of exponentially growing Pseudomonas putida cells. Environ Microbiol (2012) 0.78
Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo. Nucleic Acids Res (2003) 0.77
From the phosphoenolpyruvate phosphotransferase system to selfish metabolism: a story retraced in Pseudomonas putida. FEMS Microbiol Lett (2014) 0.77
Streamlining of a Pseudomonas putida genome using a combinatorial deletion method based on minitransposon insertion and the Flp-FRT recombination system. Methods Mol Biol (2012) 0.77
Osmotic stress limits arsenic hypertolerance in Aspergillus sp. P37. FEMS Microbiol Ecol (2007) 0.77
Confidence, tolerance, and allowance in biological engineering: the nuts and bolts of living things. Bioessays (2014) 0.77
A second chromosomal copy of the catA gene endows Pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environ Microbiol (2014) 0.77
Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2. ISME J (2012) 0.76
In vivo drafting of single-chain antibodies for regulatory duty on the sigma54-promoter Pu of the TOL plasmid. Mol Microbiol (2006) 0.76
Microbial systems biology: bottom up and top down. FEMS Microbiol Rev (2008) 0.76
Arsenate transport and reduction in the hyper-tolerant fungus Aspergillus sp. P37. Environ Microbiol (2003) 0.76
Towards a global biotechnology scenario. Curr Opin Biotechnol (2012) 0.76
The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Environ Microbiol (2012) 0.76
m-xylene-responsive Pu-PnifH hybrid sigma54 promoters that overcome physiological control in Pseudomonas putida KT2442. J Bacteriol (2005) 0.76
Chromosomal integration of transcriptional fusions. Methods Mol Biol (2014) 0.75
Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida. BMC Syst Biol (2012) 0.75
Functional analysis of the integration host factor site of the σ(54) Pu promoter of Pseudomonas putida by in vivo UV imprinting. Mol Microbiol (2011) 0.75
The upstream-activating sequences of the sigma54 promoter Pu of Pseudomonas putida filter transcription readthrough from upstream genes. J Biol Chem (2006) 0.75
An electro-optical device from a biofilm structure created by bacterial activity. Adv Mater (2010) 0.75
Widening functional boundaries of the σ(54) promoter Pu of Pseudomonas putida by defeating extant physiological constraints. Mol Biosyst (2015) 0.75
Production and characterization of a recombinant single-chain antibody (scFv) for tracing the σ54 factor of Pseudomonas putida. J Biotechnol (2011) 0.75
Beautiful is not (necessarily) right: overcoming the Phryne's trial syndrome. Bioessays (2010) 0.75