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LETTERS A fast, robust and tunable synthetic gene oscillator
, 2008
"... One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to ‘design specifications’ generated from computational modelling 1–6. This approach provides a systematic framework for exploring how a given ..."
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Cited by 82 (3 self)
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One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to ‘design specifications’ generated from computational modelling 1–6. This approach provides a systematic framework for exploring how a given regulatory network generates a particular phenotypic behaviour. Several fundamental gene circuits have been developed using this approach, including toggle switches 7 and oscillators 8–10, and these have been applied in new contexts such as triggered biofilm development 11 and cellular population control 12. Here we describe an engineered genetic oscillator in Escherichia coli that is fast, robust and persistent, with tunable oscillatory periods as fast as 13 min. The oscillator was designed using a previously modelled network architecture comprising linked positive and negative feedback loops 1,13. Using a microfluidic platform tailored for single-cell
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet
- 2009
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Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli
- PLoS Biol
"... Bacteria induce stress responses that protect the cell from lethal factors such as DNA-damaging agents. Bacterial populations also form persisters, dormant cells that are highly tolerant to antibiotics and play an important role in recalcitrance of biofilm infections. Stress response and dormancy ap ..."
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Cited by 49 (1 self)
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Bacteria induce stress responses that protect the cell from lethal factors such as DNA-damaging agents. Bacterial populations also form persisters, dormant cells that are highly tolerant to antibiotics and play an important role in recalcitrance of biofilm infections. Stress response and dormancy appear to represent alternative strategies of cell survival. The mechanism of persister formation is unknown, but isolated persisters show increased levels of toxin/antitoxin (TA) transcripts. We have found previously that one or more components of the SOS response induce persister formation after exposure to a DNA-damaging antibiotic. The SOS response induces several TA genes in Escherichia coli. Here, we show that a knockout of a particular SOS-TA locus, tisAB/istR, had a sharply decreased level of persisters tolerant to ciprofloxacin, an antibiotic that causes DNA damage. Step-wise administration of ciprofloxacin induced persister formation in a tisABdependent manner, and cells producing TisB toxin were tolerant to multiple antibiotics. TisB is a membrane peptide that was shown to decrease proton motive force and ATP levels, consistent with its role in forming dormant cells. These results suggest that a DNA damage–induced toxin controls production of multidrug tolerant cells and thus provide a model of
Indole is an inter-species biofilm signal mediated by SdiA
- BMC Microbiology
, 2007
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Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS biology 7
, 2009
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Cited by 38 (1 self)
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See next page for additional authors Follow this and additional works at:
Srienc F: Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses
- Appl Environ Microbiol
"... This article cites 44 articles, 17 of which can be accessed free ..."
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Cited by 31 (5 self)
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This article cites 44 articles, 17 of which can be accessed free
Metabolic engineering to enhance bacterial hydrogen production. Microb Biotechnol 1: 30–39. 10 Y. Hu et al
, 2008
"... Hydrogen fuel is renewable, efficient and clean, and fermentative bacteria hold great promise for its gen-eration. Here we use the isogenic Escherichia coli K-12 KEIO library to rapidly construct multiple, precise deletions in the E. coli genome to direct the metabolic flux towards hydrogen producti ..."
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Cited by 24 (11 self)
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Hydrogen fuel is renewable, efficient and clean, and fermentative bacteria hold great promise for its gen-eration. Here we use the isogenic Escherichia coli K-12 KEIO library to rapidly construct multiple, precise deletions in the E. coli genome to direct the metabolic flux towards hydrogen production. Escherichia coli has three active hydrogenases, and the genes involved in the regulation of the formate hydrogen lyase (FHL) system for synthesizing hydrogen from formate via hydrogenase 3 were also manipulated to enhance hydrogen production. Specifically, we altered regulation of FHL by controlling the regulators HycA and FhlA, removed hydrogen consumption by hydro-genases 1 and 2 via the hyaB and hybC mutations, and re-directed formate metabolism using the fdnG, fdoG, narG, focA, fnr and focB mutations. The result was a 141-fold increase in hydrogen production from formate to create a bacterium (BW25113 hyaB hybC hycA fdoG/pCA24N-FhlA) that produces the largest amount of hydrogen to date and one that achieves the theoretical yield for hydrogen from formate. In addi-tion, the hydrogen yield from glucose was increased by 50%, and there was threefold higher hydrogen pro-duction from glucose with this strain.
Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microbiol 77: 5577–5583
, 2011
"... In many genomes, toxin-antitoxin (TA) systems have been identified; however, their role in cell physiology has been unclear. Here we examine the evidence that TA systems are involved in biofilm formation and persister cell formation and that these systems may be important regulators of the switch fr ..."
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Cited by 23 (7 self)
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In many genomes, toxin-antitoxin (TA) systems have been identified; however, their role in cell physiology has been unclear. Here we examine the evidence that TA systems are involved in biofilm formation and persister cell formation and that these systems may be important regulators of the switch from the planktonic to the biofilm lifestyle as a stress response by their control of secondary messenger 3,5-cyclic diguanylic acid. Specifically, upon stress, the sequence-specific mRNA interferases MqsR and MazF mediate cell survival. In addition, we propose that TA systems are not redundant, as they may have developed to respond to specific stresses. Toxin-antitoxin (TA) systems typically consist of two genes in an operon which encode a stable toxin that disrupts an essential cellular process (e.g., translation via mRNA degrada-tion) and a labile antitoxin (either RNA or a protein) that prevents toxicity (73). RNA antitoxins are known as type I if they inhibit toxin translation as antisense RNA or type III if they inhibit toxin activity; type II antitoxins are proteins that inhibit toxin activity (48). For type II systems (Fig. 1), the
The Escherichia coli RutR transcription factor binds
, 2008
"... at targets within genes as well as intergenic regions ..."
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Cited by 20 (7 self)
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at targets within genes as well as intergenic regions
