Thymine starvation and limitation in Escherichia coli thyA- cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli
PROVIDER: GSE19879 | GEO | 2010/02/12
SECONDARY ACCESSION(S): PRJNA121979
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of responses of E. coli thymine auxotrophs to i) growth under sub-optimal thymine concentration (TLM) and ii) lethal conditions under complete thymine starvation (TLD). Thymine limitation: Time series following shift to limiting thymine concentrations (15, 30, 45, 60 and 90 mins) - single replicate. Thymine starvation: Time series following shift to zero thymine medium (15, 30, 45, 60 and 90 mins) - 2 biological replicates at each time point.
2010-05-14 | E-GEOD-19879 | biostudies-arrayexpress
Project description:In Escherichia coli, Lon is an ATP-dependent protease which degrades misfolded proteins and certain rapidly-degraded regulatory proteins. Given that oxidatively damaged proteins are generally degraded rather than repaired, we anticipated that Lon deficient cells would exhibit decreased viability during aerobic, but not anaerobic, carbon starvation. We found that the opposite actually occurs. Wild-type and Lon deficient cells survived equally well under aerobic conditions, but Lon deficient cells died more rapidly than the wild-type under anaerobiosis. Microarray analysis revealed that genes of the Clp family of ATP-dependent proteases were induced during aerobic growth but not during anaerobic growth. Thus, Clp may compensate for loss of Lon when cells are in an oxygen containing atmosphere. Under anaerobic carbon starvation conditions, Lon must be active to support survival. Keywords: Other
2007-11-01 | GSE6609 | GEO
Project description:Thymine starvation and limitation in Escherichia coli thyA- cells
| PRJNA121979 | ENA
Project description:Our laboratory has recently discovered that E. coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for Thymineless Death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses on actively growing optA1 gpt strains subjected to hypoxanthine deprivation for increasing periods of time. The data show that, upon Hx withdrawal, the optA1 gpt strain displays a diminished ability to de-repress the de novo purine biosynthesis genes, and this is likely due to internal guanine accumulation. The impairment to fully induce the purR regulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS is observed, supporting the concept of replication stress as a final cause of death. No evidence was observed for the participation of other stress responses, including the rpoS-mediated global stress response in the starved cells, and reinforcing the lack of feedback of replication stress into the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient is observed for expression of genes located nearby the replication origin relative to those located towards the replication terminus.
2016-04-06 | GSE80002 | GEO
Project description:Our laboratory has recently discovered that E. coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for Thymineless Death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses on actively growing optA1 gpt strains subjected to hypoxanthine deprivation for increasing periods of time. The data show that, upon Hx withdrawal, the optA1 gpt strain displays a diminished ability to de-repress the de novo purine biosynthesis genes, and this is likely due to internal guanine accumulation. The impairment to fully induce the purR regulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS is observed, supporting the concept of replication stress as a final cause of death. No evidence was observed for the participation of other stress responses, including the rpoS-mediated global stress response in the starved cells, and reinforcing the lack of feedback of replication stress into the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient is observed for expression of genes located nearby the replication origin relative to those located towards the replication terminus. The present study was aimed at understanding the metabolic changes in dGTP-starved cells. To do so, we designed two experiments. The first experiment was aimed at investigating the transcriptional consequences of loss of the Hx purine source in each of the four strains (wt, optA1, gpt, and optA1 gpt). Here, hypoxanthine was withdrawn from actively growing cells starting at OD 0.1, and periodic 2-fold dilutions were applied to keep to OD of the growing cultures below or only slightly above 0.20 (low-dilution protocol). Samples were taken for microarray analysis at 15, 30, 45, 60, and 120 min. At each time point RNA samples were taken and analyzed for gene expression changes using the Affymetrix GeneChip E. coli Genome 2.0 Array. This experiment was conducted three times, independently. A second experiment was aimed at following the transcriptional changes in the optA1 gpt strain during the entire 6-hour time course including the filamentation and cell death stage. Here, we used a slightly different dilution protocol (high-dilution protocol), in which the strain was initially highly diluted (OD630 = 0.01) and further diluted at strategic points to prevent the OD to rise above 0.1. These conditions optimize the cell death phenomenon. This experiment was also conducted three times independently.
2016-04-06 | E-GEOD-80002 | biostudies-arrayexpress
Project description:Here we report on an RNAseq method in combination with spike-in cells to measure global changes in the transcription pattern after valine-induced isoleucine starvation of a standard E. coli K12 strain. Due to the spike-in method we were able to show that ribosomal RNA is degraded during isoleucine starvation and we showed how this change in cellular RNA content affect the estimated regulation of mRNA levels compared to if spike-in were not utilized. Our analysis also showed that induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS and Lrp regulons
2019-11-19 | GSE136753 | GEO
Project description:A genome reduced E. coli strain MDS42ΔgalK::Ptet-gfp-kan were applied for the comparative transcriptome analysis. Genome-wide transcriptional changes under high osmotic prresure, high temperature condition and starvation were evaluated.
2013-11-04 | GSE49296 | GEO
Project description:RNA-seq was carried out to compare the transcriptomes of wild-type BW25133 E coli with a mutant lacking the conserved serine/threonine kinase, YeaG, with the aim of understanding how YeaG contributes to the transcriptional response to sustained nitrogen starvation, and identify pathways affected by YeaG. We also compare the wild-type transcriptome during nitrogen-replete, following nitrogen starvation, and under 24 h of sustained nitrogen starvation to identify pathways involved in the response to nitrogen run out, and also in adaptation to sustained nitrogen starvation.
2018-06-04 | E-MTAB-6481 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6382538 | biostudies-literature
Project description:Stochastic switching of a monostable circuit mediated the adaptation of the engineered OSU12-hisC Escherichia coli strain to histidine starvation. In this strain, the hisC gene was deleted from the His operon and placed under the control of a monostable foreign promoter. In response to histidine depletion, the OSU12-hisC population shifted to a higher HisC expression level, which are beneficial under starving conditions but are not favoured by the monostable circuit. Microarray analysis indicated that OSU12-hisC reorganised its transcriptome to reach the appropriate physiological state upon starvation. The study suggests that bacteria do not necessarily need to evolve signalling mechanisms to control gene expression appropriately, even for essential genes.
2011-03-29 | GSE28210 | GEO