A comprehensive library of fluorescent transcriptional reporters for Escherichia coli

Zaslaver, Alon; Bren, Anat; Ronen, Michal; Itzkovitz, Shalev; Kikoin, Ilya; Shavit, Sara; Liebermeister, Wolfram; Surette, Michael G.; Alon, Uri

doi:10.1038/nmeth895

Cited by 717 publications

(905 citation statements)

References 30 publications

Supporting

Mentioning

898

Contrasting

Order By: Relevance

“…For inferring module networks in a biological context, we applied the TiWnet to a published dataset of promoter activity data from ≈ 1100 Escherichia coli operons (Zaslaver et al, 2006). The promoter activities were recorded with high temporal resolution as the bacteria progressed through a classical growth curve experiment experiencing a "diauxic shift".…”

Section: Methodsmentioning

confidence: 99%

Recovering networks from distance data

et al. 2013

View full text Add to dashboard Cite

A fully probabilistic approach to reconstructing Gaussian graphical models from distance data is presented. The main idea is to extend the usual central Wishart model in traditional methods to using a likelihood depending only on pairwise distances, thus being independent of geometric assumptions about the underlying Euclidean space. This extension has two advantages: the model becomes invariant against potential bias terms in the measurements, and can be used in situations which on input use a kernel-or distance matrix, without requiring direct access to the underlying vectors. The latter aspect opens up a huge new application field for Gaussian graphical models, as network reconstruction is now possible from any Mercer kernel, be it on graphs, strings, probabilities or more complex objects. We combine this likelihood with a suitable prior to enable Bayesian network inference. We present an efficient MCMC sampler for this model and discuss the estimation of module networks. Experiments depict the high quality and usefulness of the inferred networks.

show abstract

Section: Methodsmentioning

confidence: 99%

Recovering networks from distance data

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Background fluorescence of a strain without the reporter fusion, normalized to its OD, was subtracted from the fluorescence signal of the strain carrying the reporter fusion, also normalized to its OD, at the same time point. To determine the rate of lasB expression, we differentiated the fluorescent signal over time as described (Zaslaver et al, 2006). The change in GFP/OD within a 15-min timespan, corresponding to two successive measurements, was calculated (dGFP/dt/OD).…”

Section: This Studymentioning

confidence: 99%

Negative regulation of bacterial quorum sensing tunes public goods cooperation

Gupta

Schuster

2013

The ISME Journal

View full text Add to dashboard Cite

Bacterial quorum sensing (QS) often coordinates the expression of other, generally more costly public goods involved in virulence and nutrient acquisition. In many Proteobacteria, the basic QS circuitry consists of a synthase that produces a diffusible acyl-homoserine lactone and a cognate receptor that activates public goods expression. In some species, the circuitry also contains negative regulators that have the potential to modulate the timing and magnitude of activation. In this study, we experimentally investigated the contribution of this regulatory function to the evolutionary stability of public goods cooperation in the opportunistic pathogen Pseudomonas aeruginosa. We compared fitness and public goods expression rates of strains lacking either qteE or qscR, each encoding a distinct negative regulator, with those of the wild-type parent and a signalblind receptor mutant under defined growth conditions. We found that (1) qteE and qscR mutations behave virtually identically and have a stronger effect on the magnitude than on the timing of expression, (2) high expression in qteE and qscR mutants imposes a metabolic burden under nutrient conditions that advance induction and (3) high expression in qteE and qscR mutants increases population growth when QS is required, but also permits invasion by both wild-type and receptor mutant strains. Our data indicate that negative regulation of QS balances the costs and benefits of public goods by attenuating expression after transition to the induced state. As the cells cannot accurately assess the amount of cooperation needed, such bet-hedging would be advantageous in changing parasitic and nonparasitic environments.

show abstract

“…Progress in sequencing technologies, high throughput experimental techniques like chromatin immunoprecipitation, and advances such as noise filters [6] and oscillators that can combine repressor functionality with that of a two-component system [3], together with improvements in measuring cellular quantities at high resolution [69], should not only enable us to design synthetic circuits for maneuvering bacterial systems [11], but also enable us to address several fundamentally unanswered questions in the years to come. Network view of transcription regulation.…”

Section: Discussionmentioning

confidence: 99%

Structure and evolution of gene regulatory networks in microbial genomes

Janga¹,

Collado‐Vides²

2007

Research in Microbiology

View full text Add to dashboard Cite

With the availability of genome sequences for hundreds of microbial genomes, it has become possible to address several questions from a comparative perspective to understand the structure and function of regulatory systems, at least in model organisms. Recent studies have focused on topological properties and the evolution of regulatory networks and their components. Our understanding of natural networks is paving the way to embedding synthetic regulatory systems into organisms, allowing us to expand the natural diversity of living systems to an extent we had never before anticipated.

show abstract

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli

Cited by 717 publications

References 30 publications

Recovering networks from distance data

Recovering networks from distance data

Negative regulation of bacterial quorum sensing tunes public goods cooperation

Structure and evolution of gene regulatory networks in microbial genomes

Contact Info

Product

Resources

About