[HTML][HTML] Mining logic gates in prokaryotic transcriptional regulation networks
R Silva-Rocha, V de Lorenzo - FEBS letters, 2008 - Elsevier
Prokaryotic transcriptional networks possess a large number of regulatory modules that
formally implement many of the logic gates that are typical of digital, Boolean circuits. Yet …
formally implement many of the logic gates that are typical of digital, Boolean circuits. Yet …
Compilation and analysis of σ54-dependent promoter sequences
Promoters recognized by the RNA-polymerase with the alternative sigma factor σ54 (Eσ54)
are unique in having conserved positions around-24 and-12 nucleotides upstream from the …
are unique in having conserved positions around-24 and-12 nucleotides upstream from the …
The function and organization of plasmids
F Hayes - E. coli Plasmid Vectors: Methods and Applications, 2003 - Springer
Abstract In 1952, Joshua Lederberg coined the term plasmid to describe any bacterial
genetic element that exists in an extrachromosomal state for at least part of its replication …
genetic element that exists in an extrachromosomal state for at least part of its replication …
The NorR Protein of Escherichia coli Activates Expression of the Flavorubredoxin Gene norV in Response to Reactive Nitrogen Species
MI Hutchings, N Mandhana, S Spiro - Journal of Bacteriology, 2002 - Am Soc Microbiol
The Escherichia coli norVW genes encode a flavorubredoxin and NADH:(flavo) rubredoxin
reductase, respectively, which are involved in nitric oxide detoxification under anaerobic …
reductase, respectively, which are involved in nitric oxide detoxification under anaerobic …
À la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer‐binding protein XylR to non‐natural effectors
J Garmendia, D Devos, A Valencia… - Molecular …, 2001 - Wiley Online Library
To investigate the activation mechanism of the enhancer‐binding protein XylR encoded by
the TOL plasmid of Pseudomonas putida mt‐2, a combinatorial library was generated …
the TOL plasmid of Pseudomonas putida mt‐2, a combinatorial library was generated …
The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
R Silva‐Rocha, J Tamames… - Environmental …, 2011 - Wiley Online Library
The regulatory and metabolic networks that rule biodegradation of pollutants by
environmental bacteria are wired to the rest of the cellular physiology through both …
environmental bacteria are wired to the rest of the cellular physiology through both …
Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR
Prokaryotic transcription factors (TFs) that bind small xenobiotic molecules (eg, TFs that
drive genes that respond to environmental pollutants) often display a promiscuous effector …
drive genes that respond to environmental pollutants) often display a promiscuous effector …
Regulation of the Carnitine Pathway inEscherichia coli: Investigation of the cai-fixDivergent Promoter Region
A Buchet, K Eichler… - Journal of …, 1998 - Am Soc Microbiol
The divergent structural operons caiTABCDE and fixABCX of Escherichia coli are required
for anaerobic carnitine metabolism. Transcriptional monocopy lacZ fusion studies showed …
for anaerobic carnitine metabolism. Transcriptional monocopy lacZ fusion studies showed …
Activation of the toluene‐responsive regulator XylR causes a transcriptional switch between σ54 and σ70 promoters at the divergent Pr/Ps region of the TOL plasmid
G Bertoni, S Marqués, V De Lorenzo - Molecular microbiology, 1998 - Wiley Online Library
The mechanism by which XylR, the toluene‐responsive activator of the σ54‐dependent Pu
and Ps promoters of the Pseudomonas TOL plasmid pWW0, downregulates its own σ70 …
and Ps promoters of the Pseudomonas TOL plasmid pWW0, downregulates its own σ70 …
Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt‐2 exposed to m‐xylene
R Silva‐Rocha, V de Lorenzo - Molecular microbiology, 2012 - Wiley Online Library
The expression dynamics of the catabolic promoters of the TOL plasmid pWW0 has been
examined in single cells of Pseudomonas putida mt‐2 exposed to m‐xylene. To this end, we …
examined in single cells of Pseudomonas putida mt‐2 exposed to m‐xylene. To this end, we …