The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space (Q40076031)

17 September 2017

The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space (English)

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17 September 2017

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17 September 2017

Rafael Silva-Rocha

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language of work or name

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22 November 2012

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Environmental Microbiology

17 September 2017

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17 September 2017

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17 September 2017

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17 September 2017

271-286

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The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster

17 September 2017

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Network motifs: theory and experimental approaches

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Transcription analysis of rpoH in Pseudomonas putida

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Role of the ptsN gene product in catabolite repression of the Pseudomonas putida TOL toluene degradation pathway in chemostat cultures

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Structure and evolution of transcriptional regulatory networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Emergence of Scaling in Random Networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Activation of the toluene-responsive regulator XylR causes a transcriptional switch between sigma54 and sigma70 promoters at the divergent Pr/Ps region of the TOL plasmid.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Boolean network models of cellular regulation: prospects and limitations

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Promoters in the environment: transcriptional regulation in its natural context

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma54-dependent Pu promoter of the TOL plasmid

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Boolean network model predicts cell cycle sequence of fission yeast

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Information routing driven by background chatter in a signaling network

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

RNA polymerase holoenzymes can share a single transcription start site for the Pm promoter. Critical nucleotides in the -7 to -18 region are needed to select between RNA polymerase with sigma38 or sigma32.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

A SAT-based algorithm for finding attractors in synchronous Boolean networks.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Inducibility of the TOL catabolic pathway in Pseudomonas putida (pWW0) growing on succinate in continuous culture: evidence of carbon catabolite repression control

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The TACAN4TGCA motif upstream from the -35 region in the sigma70-sigmaS-dependent Pm promoter of the TOL plasmid is the minimum DNA segment required for transcription stimulation by XylS regulators

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The incoherent feedforward loop can provide fold-change detection in gene regulation

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Cellular XylS levels are a function of transcription of xylS from two independent promoters and the differential efficiency of translation of the two mRNAs

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Emergent decision-making in biological signal transduction networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Transcriptional regulation by competing transcription factor modules

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Modeling and simulation of genetic regulatory systems: a literature review

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The incoherent feed-forward loop can generate non-monotonic input functions for genes

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Modelling and analysis of gene regulatory networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Genetic evidence that the XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA-protein interactions

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

21 January 2018

Biological robustness

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

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.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Transcriptional regulatory networks in Saccharomyces cerevisiae

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The yeast cell-cycle network is robustly designed

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Bacterial regulatory networks are extremely flexible in evolution

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Structure and function of the feed-forward loop network motif

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Identifying global regulators in transcriptional regulatory networks in bacteria

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

High stability and fast recovery of expression of the TOL plasmid-carried toluene catabolism genes of Pseudomonas putida mt-2 under conditions of oxygen limitation and oscillation

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

A method for the generation of standardized qualitative dynamical systems of regulatory networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Network motifs: simple building blocks of complex networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12014

The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Levels and activity of the Pseudomonas putida global regulatory protein Crc vary according to growth conditions

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

ON/OFF and beyond--a boolean model of apoptosis

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Mining logic gates in prokaryotic transcriptional regulation networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

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

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

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

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The IHF regulon of exponentially growing Pseudomonas putida cells

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Intrinsic noise in gene regulatory networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

In vivo UV laser footprinting of the Pseudomonas putidasigma 54Pu promoter reveals that integration host factor couples transcriptional activity to growth phase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12014

The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12014

Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma54-promoter Pu to the response regulator PprA.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Genomic analysis of the hierarchical structure of regulatory networks

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma32 or sigma38 depending on the growth phase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12014

The organization of the Pm promoter of the TOL plasmid reflects the structure of its cognate activator protein XylS

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

Growth-dependent Phosphorylation of the PtsN (EIINtr) Protein ofPseudomonas putida

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12014

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12014

21 January 2018

Identifiers

DOI

10.1111/1462-2920.12014

1 reference

17 September 2017

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PubMed ID

23171249