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<span style = 'font-size: large'> '''Bernstein, JA, Lin, PH, Cohen, SN and Lin-Chao, S'''  (2004) Global analysis of Escherichia coli RNA degradosome function using DNA microarrays.''Proc. Natl. Acad. Sci. U.S.A.'' '''101''':2758-63</span>
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|{{TableHeadingColor}} |'''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.
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'''Bernstein, JA, Lin, PH, Cohen, SN and Lin-Chao, S'''  (2004) Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. ''Proc. Natl. Acad. Sci. U.S.A.'' '''101''':2758-63
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!align=left  |Abstract
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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.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14981237 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC365694 PMC365694]
Online version:[http://dx.doi.org/10.1073/pnas.0308747101 10.1073/pnas.0308747101]
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|{{TableHeadingColor}} nowrap |'''Links''' ||  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14981237 PubMed]
!align=left  |Keywords
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Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Endoribonucleases/genetics; Endoribonucleases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Half-Life; Mutagenesis; Oligonucleotide Array Sequence Analysis; RNA, Bacterial/genetics; RNA, Bacterial/metabolism; RNA, Messenger/genetics; RNA, Messenger/metabolism; Transcription, Genetic
 
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==Significance {{HelpIcon|Help:Literature}} ==
==Significance {{HelpIcon|Help:Literature}} ==
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
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== Strains used in this paper ==
[[Strain:N3433|N3433]]
YHC012 = N3433 pnp::Tn5
SU02 = N3433 rhlB(del)::FRT-kan-FRT
SH3208 = W3110 (Lambda) trpE5(del) his
BZ453 = SH3208 zcb::Tn10 rne(truncated-missing aa 603-1061)<ref name='PMID:8682798'/>
[[Strain:K10|K10]] = Hfr(PO2A), garB10, fhuA22, ompF627(T2R), fadL701(R), relA1, pitA10, spoT1, rrnB-2, mcrB1, creC510 [http://cgsc.biology.yale.edu/Strain.php?ID=9448]
DF261 = K10 eno-2


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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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Latest revision as of 04:23, 15 September 2013

Citation

Bernstein, JA, Lin, PH, Cohen, SN and Lin-Chao, S (2004) Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 101:2758-63

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.

Links

PubMed PMC365694 Online version:10.1073/pnas.0308747101

Keywords

Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Endoribonucleases/genetics; Endoribonucleases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Half-Life; Mutagenesis; Oligonucleotide Array Sequence Analysis; RNA, Bacterial/genetics; RNA, Bacterial/metabolism; RNA, Messenger/genetics; RNA, Messenger/metabolism; Transcription, Genetic

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Significance

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Useful Materials and Methods

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Strains used in this paper

N3433

YHC012 = N3433 pnp::Tn5

SU02 = N3433 rhlB(del)::FRT-kan-FRT

SH3208 = W3110 (Lambda) trpE5(del) his

BZ453 = SH3208 zcb::Tn10 rne(truncated-missing aa 603-1061)[1]

K10 = Hfr(PO2A), garB10, fhuA22, ompF627(T2R), fadL701(R), relA1, pitA10, spoT1, rrnB-2, mcrB1, creC510 [1]

DF261 = K10 eno-2

Annotations

<annotationlinks/>


Accessions SMD Category SMD Subcategory SMD status
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References

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  1. ↑ Kido, M et al. (1996) RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J. Bacteriol. 178 3917-25 PubMed
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