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Type I restriction–modification systems regulate gene expression through DNA topology

ABSTRACT: RNA-seq analysis of wildtype Escherichia coli MG1655 versus a strain with knockout of the hsdM gene of the Type I restriction enzyme EcoKI

ORGANISM(S): Escherichia coli

PROVIDER: GSE328962 | GEO | 2026/04/28

REPOSITORIES: GEO

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Transcription profiling of E. coli cells during cell death programmed by a restriction-modification system

Project description:Genetically programmed deaths play important roles in the biology of unicellular prokaryotic cells. Some gene complexes force their maintenance on the host bacterial cells by killing cells that have lost them. This form of programmed death called post-segregational killing or genetic addiction is brought about by several Type II restriction-modification gene complexes, through restriction attack on the undermethylated chromosome, and underlie their behavior as selfish mobile elements. To learn the genetic steps to death, we examined how carriage and loss of PaeR7I restriction-modification gene complex affect host Escherichia coli cells through transcriptome and experimental analyses. The PaeR7I complex was on a temperature-sensitive plasmid so that the killing was induced by a temperature shift. We used microarrays to detail the global program of gene expression underlying cell death process mediated by PaeR7I restriction-modification system in E. coli. Experiment Overall Design: Post-segregational cell killing was induced by blocking replication of a temperature sensitive plasmid carrying PaeR7I RM gene complex by shifting up the cultivation temperature. At 30℃, the permissive temperature for the plasmid replication, growth as monitored by OD660, of MG1655/pTN9 (r+m+) was indistinguishable from those of MG1655/pTN11 (r-m+) and MG1655/pHSG415 (vector). Cell death was observed at least 4 h after the temperature shift only in MG1655/pTN9 (r+m+) as in the previous works; the increase in viable cell counts stopped and resulted in decrease of cell viability. To analyze global gene expression when cells went to death, we performed transcriptome analysis 0 h, 1h, 1 h 50 min, and 3h after the temperature shift. We used Affimetrix E. coli antisense genome array. Experiments were performed independently twice.

2009-07-04 | E-GEOD-7326 | biostudies-arrayexpress

Type I restriction–modification systems regulate gene expression through DNA topology

Project description:Type I restriction–modification systems regulate gene expression through DNA topology

| PRJNA1457089 | ENA

Expression profiles during cell death programmed by a restriction-modification system in E. coli

2009-06-23 | GSE7326 | GEO

ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases

Project description:We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains

2016-12-13 | GSE92255 | GEO

Stationary phase in LB, genomic DNA reference

Project description:Responses of Escherichia coli MG1655 in stationary phase in LB Keywords: time course

2006-03-08 | GSE4380 | GEO

Anaerobic growth in M9 + glucose, genomic DNA reference

Project description:Responses of Escherichia coli MG1655 as they grow anaerobically in M9 + glucose Keywords: time course

2006-03-08 | GSE4373 | GEO

Testing the impact of Type I Restriction Modification Systems on Gene Expression in Uropathogenic Escherichia coli

Project description:Background: DNA methylation influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. The regulatory role of DNA methylation and other epigenetic marks also extends to virulence; both orphan methyltransferases and those from restriction modification systems (RMSs) have been co-opted to regulate virulence in many bacteria. However, functional characterisation of DNA methylation mediated by archetypal Type I RMSs remains limited. Results: We elucidated the methylation specificity of the Type I RMS in UTI89, a prototypical cystitis strain of E. coli. Deletion of this RMS led to loss of methylation of >750 sites across the genome but no detectable effect on gene expression, virulence, or growth in a screen of 1190 conditions. Similarly, deletion of the endogenous Type I RMS in two other E. coli strains with different methylation specificities also had no effect on gene expression or any growth phenotype. Finally, introduction of these two different RMSs into UTI89 also resulted in no detectable change in gene expression or growth phenotypes. These results stand in sharp contrast with many reports of RMSs regulating gene expression in other bacteria, leading us to propose the concept of “regulation avoidance” for these E. coli Type I RMSs. We hypothesize that regulation avoidance is a consequence of evolutionary adaptation of both the RMSs and the E. coli genome. Conclusions: Our results provide a clear and currently rare example of regulation avoidance for Type I RMSs in multiple strains of E. coli, further study of which may provide deeper insights into the evolution of gene regulation and horizontal gene transfer.

2021-07-01 | GSE165421 | GEO

Anaerobic growth in M9 + glucose + fumarate,genomic DNA reference

Project description:Responses of Escherichia coli MG1655 as they grow anaerobically in M9 + glucose + fumarate Keywords: time course

2006-03-08 | GSE4374 | GEO

RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens

Project description:Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.

2019-06-17 | GSE126710 | GEO

Anaerobic growth in M9 + glucose

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