Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: 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.

ORGANISM(S): Escherichia coli

SUBMITTER: Yoko Asakura 

PROVIDER: E-GEOD-7326 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex.

Asakura Yoko Y   Kobayashi Ichizo I  

Nucleic acids research 20090320 9


Genetically programmed cell deaths play important roles in unicellular prokaryotes. In postsegregational killing, loss of a gene complex from a cell leads to its descendants' deaths. With type II restriction-modification gene complexes, such death is triggered by restriction endonuclease's attacks on under-methylated chromosomes. Here, we examined how the Escherichia coli transcriptome changes after loss of PaeR7I gene complex. At earlier time points, activation of SOS genes and sigma(E)-regulon  ...[more]

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