Transcriptomics,Genomics

Dataset Information

18

Expression profiling of E.coli K-12 wild-type vs. delta dksA cells upon amino acid starvation


ABSTRACT: Actively dividing cells perform robust and accurate DNA replication during fluctuating nutrient availability, yet factors that prevent disruption of replication remain largely unknown. Here we report that DksA, a nutrient-responsive transcription factor, ensures replication completion in Escherichia coli. In the absence of DksA, replication is rapidly arrested upon amino acid starvation. This replication arrest occurs independently of exogenous DNA damage, yet it induces the DNA damage response and recruits the main recombination protein RecA. This microarray experiment compares the transcriptional responses to amino acid starvation in wild-type and delta dksA cells. The SOS-regulated genes are highly induced in delta dksA cells. Overall design: Four-condition experiment: wt, wt+SHX, delta dksA, delta dksA+SHX. Biological replicates: 3 for each sample. Reference: a mixture of the same amount of the four RNA samples.

INSTRUMENT(S): Custom Agilent Escherichia coli 4 x 44k Gene Expression Array

SUBMITTER: Jue D. Wang  

PROVIDER: GSE19742 | GEO | 2010-06-01

SECONDARY ACCESSION(S): PRJNA122209

REPOSITORIES: GEO

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Publications

The transcription factor DksA prevents conflicts between DNA replication and transcription machinery.

Tehranchi Ashley K AK   Blankschien Matthew D MD   Zhang Yan Y   Halliday Jennifer A JA   Srivatsan Anjana A   Peng Jia J   Herman Christophe C   Wang Jue D JD  

Cell 20100501 4


Actively dividing cells perform robust and accurate DNA replication during fluctuating nutrient availability, yet factors that prevent disruption of replication remain largely unknown. Here we report that DksA, a nutrient-responsive transcription factor, ensures replication completion in Escherichia coli by removing transcription roadblocks. In the absence of DksA, replication is rapidly arrested upon amino acid starvation. This arrest requires active transcription and is alleviated by RNA polym  ...[more]

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