Processing enzyme ribonuclease E specifically cleaves RNA I

Tomcsányi, T; Apirion, David

doi:10.1016/0022-2836(85)90056-7

Cited by 132 publications

(31 citation statements)

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“…RNase E is also involved in the endonucleolytic processing of T4 gene 32 mRNA to a more stable form (17). One other known substrate of RNase E is RNA 1, an inhibitor of ColEl plasmid DNA synthesis (18).In this communication we show that both ams-1 and rne-3071 mutant strains exhibit increases in the chemical half-life of pulse-labeled mRNA, as well as an accumulation of apparently identical unprocessed 5S rRNA precursors. In addition, we demonstrate that in vitro a natural RNase E substrate is processed when incubated with wild-type but not rne-3071 or ams-1 cell extracts, and that when the Ams protein is overproduced, there is an increase in processing.…”

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confidence: 73%

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The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli.

Babitzke

Kushner

1991

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

194

138

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The in vitro and in vivo analysis of the ribonuclease E-deficient (rne-) and the altered mRNA stability protein-deficient (ams-) strains of Escherichia coli has demonstrated that they carry mutations in the same structural gene. Strains encoding either thermolabile RNase E (rne-3071) or Ams protein (ams-l) are defective in both rRNA processing and mRNA turnover. Immediately after a shift to the nonpermissive temperature, the chemical decay rate of bulk mRNA is slowed 2-to 3-fold, and within 70 min, precursors to 5S rRNA begin to accumulate. In addition, all of the phenotypes associated with either the rne-3071 or the ams-) alleles were complemented by a recombinant plasmid carrying ams+. When taken together with previous genetic studies, these results suggest that the role of ribonuclease E in mRNA turnover involves endonucleolytic cleavages at the proposed ACAG(A/U)AUUUG consensus sequence. mRNA decay in Escherichia coli is hypothesized to proceed through the action of both endonucleases and exonucleases (for review, see ref. 1). The involvement of two exonucleases, polynucleotide phosphorylase (2) and ribonuclease 11 (3), in mRNA decay has clearly been demonstrated (4). In contrast, little is currently known about the endonucleases involved in general mRNA turnover (1). Two possible candidates are the products of the ams and rne genes.The ams locus was identified by a temperature-sensitive mutation (ams-1) that mapped at 24 min on the E. coli linkage map (5, 6) and increased the chemical half-life of total pulse-labeled RNA (7). It has recently been shown in this laboratory that the absence of the altered mRNA stability (Ams) protein increases the chemical half-lives of specific mRNAs and stabilizes discrete mRNA decay intermediates in ams-1 pnp-7 rnb-500 triple mutants (8). In addition, the endonucleolytic cleavage sites involved in the decay of the trxA message, which encodes thioredoxin, have been identified in the same triple mutant (9). The Ams protein has been proposed to be either an RNase or a positive regulator of other RNases (8). The ams gene has been cloned (10), sequenced, and shown to encode a 91-kDa polypeptide (30).RNase E is the enzyme responsible for processing ofthe 5S rRNA from the primary rRNA transcript and was first identified by a temperature-sensitive mutation (rne-3071) (11) that resulted in the accumulation of a 9S RNA species containing 5S rRNA as well as additional upstream and downstream sequences (12). The processing of 9S RNA to the precursor of 5S rRNA (p5S rRNA), consisting of 3 additional nucleotides on both sides of the mature 5S rRNA (13), is believed to occur through two sequential endonucleolytic cleavages. First 9S RNA is processed to 7S RNA and 4S RNA, followed by the conversion of7S RNA to p5S rRNA (14). Genetic mapping studies have localized this gene at -24 min on the E. coli linkage map (5, 15). In addition to rRNA processing, there is now evidence that suggests RNase E is involved in mRNA metabolism as well. Recently it was shown that there was a 4-fold inc...

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confidence: 73%

Section: Introductionmentioning

confidence: 99%

The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli.

Babitzke

Kushner

1991

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

194

138

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“…shown to migrate as a single band in silver nitrate-stained gels (see above) was assayed for endoribonuclease activity on 9 S RNA, GGG⅐RNA I, and the BR13 and BR10 oligoribonucleotides, all of which are cleaved by purified RNase E at highly specific sites (18,19,22,(27)(28)(29). Control reactions that show the cleavages produced by RNase A, a common eukaryotic single-strand-specific endoribonuclease, were included for comparison; these controls demonstrated that the cleavage patterns of ARD-1 and RNase A are different, and also indicated the absence of RNase A activity in our purified ARD-1 preparations.…”

Section: Ard-1 Cleaves Oligoribonucleotides and Complex Rnas At The Smentioning

confidence: 99%

ARD-1 cDNA from Human Cells Encodes a Site-specific Single-strand Endoribonuclease That Functionally Resembles Escherichia coli RNase E

Claverie-Martı́n¹,

Wang²,

Cohen³

1997

Journal of Biological Chemistry

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The human ARD-1 (activator of RNA decay) cDNA sequence can rescue mutations in the Escherichia coli rne gene, which specifies the essential endoribonuclease RNase E, resulting in RNase E-like cleavages in vivo in rne-defective bacteria and in vitro in extracts isolated from these cells (Wang, RNA degradation in eukaryotes, as in bacteria, appears to be a regulated process that involves multiple enzymatic steps (for reviews, see . Although a variety of ribonucleases have been identified in eukaryotes, with few exceptions little or no information is available about the specific biological role of these enzymes or the genes that encode them (for reviews, see . This is especially true of nucleases that degrade the mRNA of mammalian cells.MThe Escherichia coli rne gene encodes an essential endoribonuclease, RNase E, which has a key role in the decay and processing of 9 S ribosomal RNA, RNA I, an antisense regulator of replication of ColE1-type plasmids, and a variety of messenger RNAs (for reviews, see Refs. 9 -11). A human cDNA sequence designated as ARD-1 (activator of RNA decay) was identified recently by its ability to reverse the pleiotropic effects of temperature-sensitive (ts) and deletion mutations in rne (1). Expression of ARD-1 cDNA in E. coli results in RNase E-like cleavages in vivo in rne ts cells shifted to a nonpermissive temperature, and extracts isolated from cells mutated in rne but expressing ARD-1 cDNA cleave 9 S RNA in vitro at locations attacked by RNase E (1). Collectively, these findings suggested that ARD-1 may encode an endoribonuclease activity similar to that of RNase E. Moreover, the 13.3-kDa ARD-1 protein sequence deduced from analysis of the cDNA has multiple structural features in common with the 118-kDa Rne protein, including similarity to domains of eukaryotic proteins implicated in endocytosis, macromolecular transport, and RNA binding (12)(13)(14).Recently, a peptide sequence almost identical to the protein encoded by human ARD-1 cDNA was found at the carboxyl terminus of bovine NIPP-1 (38.5 kDa), a nuclear inhibitor of protein phosphatase 1 (2).1 Comparison of the cloned cDNA sequences of ARD-1 and NIPP-1 showed that the 5Ј-untranslated region of ARD-1 contains a 470-bp 2 segment that is not present in NIPP-1 cDNA and that ARD-1 cDNA lacks a 220 bp segment of the coding region of NIPP-1 (2); these observations have led to the proposal by Van Eynde et al. (2) that ARD-1 and NIPP-1 mRNAs are generated by alternative splicing.Using ARD-1 protein overexpressed in E. coli and highly purified by affinity-column chromatography, we show here that ARD-1 is a single-strand-specific Mg 2ϩ -dependent endoribonuclease that binds to RNase E substrates, cleaves short oligoribonucleotides and complex substrates in AϩU-rich regions at the sites cut by RNase E, and generates 5Ј-phosphate termini. Thus, the amino acid residues comprising the ARD-1 sequence appear to function both as a domain of the protein phosphatase inhibitor NIPP-1 and a human analog of E. coli ribonuclease E. EXPERIMENTAL PROCE...

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“…Mutations in the rne/ams gene have a stabilizing effect on the bulk of mRNAs (4,37,44). This enzyme also cleaves RNAI (27,33,52), the antisense RNA regulating ColE1-type plasmid replication (53), and is involved in the processing and turnover of many bacterial and bacteriophage mRNAs (14, 16, 23, 28-30, 35, 42, 46) (for a review, see reference 11). The Escherichia coli rne/ams/hmp gene codes for the RNase E protein of 1,061 amino acids (8).…”

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confidence: 99%

RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli

et al. 1996

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We have isolated suppressor mutants that suppress temperature-sensitive colony formation and anucleate cell production of a mukB mutation. A linkage group (smbB) of the suppressor mutations is located in the rne/ams/hmp gene encoding the processing endoribonuclease RNase E. All of the rne (smbB) mutants code for truncated RNase E polypeptides lacking a carboxyl-terminal half. The amount of MukB protein was higher in these rne mutants than that in the rne ؉ strain. These rne mutants grew nearly normally in the mukB ؉ genetic background. The copy number of plasmid pBR322 in these rne mutants was lower than that in the rne ؉ isogenic strain. The results suggest that these rne mutations increase the half-lives of mukB mRNA and RNAI of pBR322, the antisense RNA regulating ColE1-type plasmid replication. We have demonstrated that the wild-type RNase E protein bound to polynucleotide phosphorylase (PNPase) but a truncated RNase E polypeptide lacking the C-terminal half did not. We conclude that the C-terminal half of RNase E is not essential for viability but plays an important role for binding with PNPase. RNase E and PNPase of the multiprotein complex presumably cooperate for effective processing and turnover of specific substrates, such as mRNAs and other RNAs in vivo.RNase E was first defined as a processing endoribonuclease that catalyzes the maturation of 5S rRNA (2,3,17). Mutations in the rne/ams gene have a stabilizing effect on the bulk of mRNAs (4,37,44). This enzyme also cleaves RNAI (27, 33, 52), the antisense RNA regulating ColE1-type plasmid replication (53), and is involved in the processing and turnover of many bacterial and bacteriophage mRNAs (14, 16, 23, 28-30, 35, 42, 46) (for a review, see reference 11). The Escherichia coli rne/ams/hmp gene codes for the RNase E protein of 1,061 amino acids (8). The RNase E protein migrates as a 170-to 180-kDa polypeptide in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) (7,12,35). Taraseviciene et al. (50) concluded that the RNA binding domain and catalytic functions overlap in the N-terminal half of the protein. The more precise mapping reported that, while the catalytic function of RNase E is in the N-terminal half, the RNA binding domain is located in the C-terminal half and does not overlap with the catalytic domain (31). It would be more accurate to state that the N-terminal half of Rne (residues 1 to 498) has the catalytic function of RNase E (31, 50) while a nonoverlapping RNA binding activity has been mapped near the start of the C-terminal half (50). RNase E, polynucleotide phosphorylase (PNPase), and 3Ј-to-5Ј exonucleases were found in the same multiprotein complex in E. coli cell extracts (6, 45).The MukB protein of E. coli has an important role in proper partitioning of the replicated sister chromosomes into two daughter cells (40,41,57,59,60). The MukB protein consists of 1,484 amino acid residues (57). MukB has been suggested to be a motor protein essential for chromosome partitioning (41) (for reviews, see references 18 and...

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Processing enzyme ribonuclease E specifically cleaves RNA I

Cited by 132 publications

References 31 publications

The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli.

The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli.

ARD-1 cDNA from Human Cells Encodes a Site-specific Single-strand Endoribonuclease That Functionally Resembles Escherichia coli RNase E

RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli

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