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PMID: 14981237 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 101 ·No. 9 ·2004-03-02 ·Pages 2758-63

Bernstein JA, Lin PH, Cohen SN, Lin-Chao S

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.

MeSH Terms
Bacterial Proteins/genetics,metabolism Endoribonucleases/genetics,metabolism Escherichia coli/genetics Escherichia coli Proteins/genetics,metabolism Half-Life Mutagenesis Oligonucleotide Array Sequence Analysis RNA, Bacterial/genetics,metabolism RNA, Messenger/genetics,metabolism Transcription, Genetic
Chemicals
Bacterial Proteins Escherichia coli Proteins RNA, Bacterial RNA, Messenger Endoribonucleases ribonuclease E
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Bernstein Jonathan A
Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Lin Pei-Hsun
Cohen Stanley N
Lin-Chao Sue
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0308747101
Published
2004-03-02
Epub
2004-00-23
Pages
2758-63
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC365694
Subset
IM
Grants
NIGMS NIH HHS · R01 GM054158 · United States
NIGMS NIH HHS · T32 GM007790 · United States
NIGMS NIH HHS · GM 07790 · United States
NIGMS NIH HHS · GM 54158 · United States
External Links
PubMed source DOI: 10.1073/pnas.0308747101 PMC Full Text View journal details
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