Escherichia coli RNase E has a role in the decay of bacteriophage T4 mRNA.

Mudd, Elisabeth A.; Carpousis, Agamemnon J.; Krisch, Henry

doi:10.1101/gad.4.5.873

Cited by 86 publications

(47 citation statements)

References 40 publications

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“…The degradation of these stem-loop-protected messages is frequently initiated by upstream endonucleolytic cleavage. RNase E is the only endoribonuclease known, so far, to have a general role in mRNA decay (Mudd et al, 1990a;1990b;Babitzke and Kushner, 1991;Bouvet and Belasco, 1992;Cohen and McDowall, 1997).…”

Section: Introductionmentioning

confidence: 99%

Polyphosphate kinase is a component of the Escherichia coli RNA degradosome

Blum

Carpousis

et al. 1997

Molecular Microbiology

115

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SummaryThe Escherichia coli degradosome is a multienzyme complex with four major protein components: the endoribonuclease RNase E, the exoribonuclease PNPase, the RNA helicase RhlB and enolase. The first three of these proteins are known to have important functions in mRNA processing and degradation. In this work, we identify an additional component of the degradosome, polyphosphate kinase (PPK), which catalyses the reversible polymerization of the ␥-phosphate of ATP into polyphosphate (poly(P)). An E. coli strain deleted for the ppk gene showed increased stability of the ompA mRNA. Purified His-tagged PPK was shown to bind RNA, and RNA binding was prevented by hydrolysable ATP. Chemical modification of RNA by PPK, for example the addition or removal of 3Ј or 5Ј terminal phosphates, could not be detected. However, polyphosphate was found to inhibit RNA degradation by the degradosome in vitro. This inhibition was overcome by the addition of ADP, required for the degradation of polyphosphate and for the regeneration of ATP by PPK in the degradosome. Thus, PPK in the degradosome appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP.

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Section: Introductionmentioning

confidence: 99%

Polyphosphate kinase is a component of the Escherichia coli RNA degradosome

Blum

Carpousis

et al. 1997

Molecular Microbiology

115

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“…Investigations of the decay of individual transcripts (16)(17)(18)(19) and global investigations of mRNA abundance in rne mutants (20) have indicated a broadly important role for this enzyme. However, the RNase E region that provides a scaffold for degradosome formation is not essential for cell survival and growth (17,21,22), and truncated RNase E proteins lacking this domain are active in vivo as well as in vitro (8,23).…”

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Global analysis of Escherichia coli RNA degradosome function using DNA microarrays

Bernstein

Lin

Cohen

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

205

212

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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.RNase E ͉ rhlB helicase ͉ enolase ͉ polynucleotide phosphorylase T he turnover of mRNA is a necessary component of normal genetic regulation within cells. In eubacteria, mRNA degradation results from the combined action of endo-and exoribonucleases. In Escherichia coli, the exoribonuclease polynucleotide phosphorylase (PNPase), the RhlB RNA helicase, and the glycolytic enzyme enolase assemble on the C-terminal region of the endoribonuclease RNase E as constituents of a protein complex termed the RNA degradosome (refs. 1-4; for recent reviews, see refs. 5 and 6). Two heat shock proteins, GroEL and DnaK (4), and polyphosphate kinase (Ppk) (7) also are associated with degradosomes in substoichiometric amounts. The N-terminal half of RNase E, which contains the catalytic domain of the enzyme (8), is not sufficient for degradosome formation (3, 9) but can associate the degradosome protein complex with the cytoplasmic membrane (11).The E. coli ams͞rne locus, which encodes RNase E, is required for bulk RNA turnover (12, 13) as well as for the processing of 9S rRNA (14,15). Investigations of the decay of individual transcripts (16)(17)(18)(19) and global investigations of mRNA abundance in rne mutants (20) have indicated a broadly important role for this enzyme. However, the RNase E region that provides a scaffold for degradosome formation is not essential for cell survival and growth (17,21,22), and truncated RNase E proteins lacking this domain are active in vivo as well as in vitro (8,23).Although the degradosome commonly has been viewed as an RNA decay ''machine'' (e.g., ref. 24), until recently (11) it was not known whether assembled degradosomes actually exist as such in living cells. Moreover, whether degradosome formation is a significant factor in mRNA decay in vivo has been...

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“…RNA degradation ͉ processive ͉ RNase G T he multifunctional Escherichia coli ribonuclease, RNase E, has a demonstrated role in the processing of ribosomal RNA (1,2), the chemical degradation of bulk cellular RNA (3)(4)(5)(6)(7), the decay of specific regulatory, messenger, and structural RNAs (for recent reviews, see refs. 8 and 9), the control of plasmid DNA replication (10), and the removal of poly(A) tails from transcripts (11,12).…”

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The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection

Yin

Vickers

Cohen

2002

Proc. Natl. Acad. Sci. U.S.A.

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RNase E, a multifunctional endoribonuclease of Escherichia coli, attacks substrates at highly specific sites. By using synthetic oligoribonucleotides containing repeats of identical target sequences protected from cleavage by 2 -O-methylated nucleotide substitutions at specific positions, we investigated how RNase E identifies its cleavage sites. We found that the RNase E catalytic domain (i.e., N-Rne) binds selectively to 5 -monophosphate RNA termini but has an inherent mode of cleavage in the 3 to 5 direction. Target sequences made uncleavable by the introduction of 2 -O-methylmodified nucleotides bind to RNase E and impede cleavages at normally susceptible sites located 5 to, but not 3 to, the protected target. Our results indicate that RNase E can identify cleavage sites by a 3 to 5 ''scanning'' mechanism and imply that anchoring of the enzyme to the 5 -monophosphorylated end of these substrates orients the enzyme for directional cleavages that occur in a processive or quasiprocessive mode. In contrast, we find that RNase G, which has extensive structural homology with and size similarity to N-Rne, and can functionally complement RNase E gene deletions when overexpressed, has a nondirectional and distributive mode of action.has a demonstrated role in the processing of ribosomal RNA (1, 2), the chemical degradation of bulk cellular RNA (3-7), the decay of specific regulatory, messenger, and structural RNAs (for recent reviews, see refs. 8 and 9), the control of plasmid DNA replication (10), and the removal of poly(A) tails from transcripts (11,12). RNase E cleaves preferentially at specific sites in single-strand RNA segments rich in AϩU nucleotides (13)(14)(15)(16)). An inherent mode of action involving entry of RNase E at the 5Ј end of substrates followed by a 5Ј to 3Ј wave of cleavages has been inferred from the greater in vivo stability of fragments at the 3Ј ends of certain RNA substrates (17-20) together with evidence that (i) the enzyme prefers a free 5Ј end for endonucleolytic cleavage (18,20), (ii) RNase E degradation efficiency is affected by 5Ј-phosphorylation in vivo (10) and in vitro (19,20), and (iii) 5Ј regions of secondary structure can impede cleavages in vivo (21). However, RNA degradation in vivo also can occur in the opposite direction (e.g., ref. 22).As RNase E cleavage of complex substrates potentially can be affected by differences in the affinity of the enzyme for target sites having different sequences (15, 16), by secondary structure (23), and in vivo also by the attachment of ribosomes (24-26) and͞or RNA-binding proteins (27), conclusions about the inherent mode of action of RNase E from studies of long natural substrates may be problematical. We wished to elucidate the mechanism of target-site selection by RNase E in the absence of these confounding factors; to do this, we designed, and chemically synthesized, oligoribonucleotide substrates that contain repeats of identical target sequences and are devoid of regions able to engage in base paring. We found that the RNase E catalytic...

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Escherichia coli RNase E has a role in the decay of bacteriophage T4 mRNA.

Cited by 86 publications

References 40 publications

Polyphosphate kinase is a component of the Escherichia coli RNA degradosome

Polyphosphate kinase is a component of the Escherichia coli RNA degradosome

Global analysis of Escherichia coli RNA degradosome function using DNA microarrays

The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection

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