Unknown,Transcriptomics,Genomics,Proteomics

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Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

ABSTRACT: Comparative transcript abundance in E. Coli degradosome mutants and their parental strains. Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. Computed

ORGANISM(S): Escherichia coli

SUBMITTER: Sue Lin-Chao

PROVIDER: E-GEOD-3977 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global analysis of Escherichia coli RNA degradosome function using DNA microarrays.

Bernstein Jonathan A JA Lin Pei-Hsun PH Cohen Stanley N SN Lin-Chao Sue S

Proceedings of the National Academy of Sciences of the United States of America 20040223 9

RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB he ...[more]

PMID: 14981237

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Dataset Information

Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

Publications

Global analysis of Escherichia coli RNA degradosome function using DNA microarrays.

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