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The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

ABSTRACT: This SuperSeries is composed of the following SubSeries: GSE178278 [poor media] GSE178279 [rich media] GSE197447 [poor media time lapse]

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE178281 | GEO | 2022/06/07

REPOSITORIES: GEO

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The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.

Project description:The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

| S-EPMC9262627 | biostudies-literature

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

2022-06-07 | GSE178279 | GEO

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

2022-06-07 | GSE178278 | GEO

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

2022-06-07 | GSE197447 | GEO

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

| PRJNA810361 | ENA

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

| PRJNA738352 | ENA

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

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The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Project description:The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

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YAMAT-seq of mature tRNA pools in the bacterium Escherichia coli str. K-12 substr. MG1655 and derivatives

Project description:Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.

2022-12-02 | GSE198606 | GEO

Comparative genomics of Staphylococcus aureus and the application of a “pan-genome” for assigning RNA-Seq transcript reads from divergent strains and in vivo human nasal samples

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