Gene rne affects the structure of the ribonucleic acid-processing enzyme ribonuclease E of Escherichia coli

Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates

RNA processing and degradation shape the transcriptome by generating stable molecules that are necessary for translation (rRNA and tRNA) and by facilitating the turnover of mRNA, which is necessary for the posttranscriptional control of gene expression. In bacteria and the plant chloroplast, RNA degradosomes are multienzyme complexes that process and degrade RNA. In many bacterial species, the endoribonuclease RNase E is the central component of the RNA degradosome. RNase E-based RNA degradosomes are inner membrane proteins in a large family of gram-negative bacteria (β- and γ-Proteobacteria). Until now, the reason for membrane localization was not understood. Here, we show that a mutant strain of Escherichia coli, in which the RNA degradosome is localized to the interior of the cell, has high levels of 20S and 40S particles that are defective intermediates in ribosome assembly. These particles have aberrant protein composition and contain rRNA precursors that have been cleaved by RNase E. After RNase E cleavage, rRNA fragments are degraded to nucleotides by exoribonucleases. In vitro, rRNA in intact ribosomes is resistant to RNase E cleavage, whereas protein-free rRNA is readily degraded. We conclude that RNA degradosomes in the nucleoid of the mutant strain interfere with cotranscriptional ribosome assembly. We propose that membrane-attached RNA degradosomes in wild-type cells control the quality of ribosome assembly after intermediates are released from the nucleoid. That is, the compact structure of mature ribosomes protects rRNA against cleavage by RNase E. Turnover of a proportion of intermediates in ribosome assembly explains slow growth of the mutant strain. Competition between mRNA and rRNA degradation could be the cause of slower mRNA degradation in the mutant strain. We conclude that attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA precursors, thus explaining the reason for conservation of membrane-attached RNA degradosomes throughout the β- and γ-Proteobacteria.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation

Ribonuclease E (RNAase E) was isolated in a complex that also contained polynucleotide phosphorylase (PNPase). Besides copurification, evidence for an association of these enzymes comes from sedimentation and immunoprecipitation experiments. Highly purified RNAase E correctly processed E. coli 5S ribosomal RNA, bacteriophage T4 gene 32 mRNA and E. coli ompA mRNA at sites known to depend on the rne gene for cleavage in vivo. The difference between previous smaller estimates of the size of RNAase E and that reported here apparently is due to the sensitivity of the enzyme to proteolysis during purification. The discovery of a specific association between RNAase E and PNPase raises the intriguing possibility that these enzymes act cooperatively in the processing and degradation of RNA.

The rne gene and ribonuclease E

The cloned rne+ gene complements temperature sensitive RNase E mutations and directs the synthesis of a polypeptide. In vitro the RNA transcribed from the rne gene directs the synthesis of a number of polypeptides, one of which is identical in size to the in vivo product of the rne gene. A rabbit reticulocyte cell free extract programmed with this RNA produced RNase E activity. Thus, it is evident that the rne gene is the structural gene for RNase E. However, the in vivo product of the cloned RNase E gene is more thermolabile than the chromosomal gene product. When cells containing the rne plasmid were treated with chloramphenicol, the pre-existing RNase E became less heat labile with time. This leads to the suggestion that in the cell RNase E undergoes post-translational modification(s).

Cloning and analysis of the entire Escherichia coli ams gene. ams is identical to hmp1 and encodes a 114 kDa protein that migrates as a 180 kDa protein

We have used an antibody to a previously identified 180 kDa (Hmp1) protein in Escherichia coli to clone the corresponding gene, which encodes a polypeptide of 114 kDa that has a mobility equivalent to 180 kDa in SDS/PAGE. We have demonstrated that the 180 kDa polypeptide is the primary gene product and not due to aggregation with other molecules. Moreover, our data indicate that the highly charged C-terminal region of the protein is responsible for its anomalous behaviour when analysed by SDS/PAGE. The hmp1 gene is in fact identical to ams (abnormal mRNA stability), also designated rne (RnaseE), and reported to have an ORF of 91 kDa. This discrepancy with the data in this paper can be ascribed to the omission of two bases in the previously reported sequence, generating an apparent stop codon. We previously demonstrated that the 180 kDa Hmp1/Ams protein cross reacted with both a polyclonal antibody and a monoclonal antibody raised against a yeast heavy chain myosin. However, we could detect no homology with myosin genes in the ams/hmp1 sequence. From the DNA sequence data, we identified a putative nucleotide binding site and a transmembrane domain in the N-terminal half of the molecule. In the C-terminal half, which appears to constitute a separate domain dominated by proline and charged amino acids, we also identified a region homologous to the highly conserved 70 kDa snRNP protein, involved in RNA splicing in eukaryotes. This feature would be consistent with reports that ams encodes RNaseE, an enzyme required for the processing of several stable RNAs in E. coli.

The rne gene is the structural gene for the processing endoribonuclease RNase E of Escherichia coli

Using T7 RNA polymerase and specific constructs derived from 5S rRNA and RNA I genes, we generated substrates for the RNA processing enzyme RNase E. Using these substrates we have shown that a 3.2 kb DNA fragment that complements the rne-3071 mutation can express RNase E activity. We also found that T7 RNA polymerase terminates within the 5S rRNA gene.

The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene

A DNA clone complementing the rne-3071 mutation has been expressed and localized in the physical map of Escherichia coli. The DNA fragment from this clone was localized to the region of the E. coli chromosome where the rne-3071 mutation has been mapped. The position of this DNA fragment in the E. coli chromosome, the size of the product directed by this DNA fragment (110,000 Da), the restriction map of this fragment, the fact that the same clone complements the ams mutation, and the observation that the rne-3071 and the ams mutations cause similar patterns of RNA synthesis, show that the rne gene--a gene specifying the processing endonuclease RNase E--and the ams gene--a gene that affects mRNA stability--are identical.

Sequencing and expression of the rne gene of Escherichia coli

RNase E is a major endonucleolytic RNA processing enzyme in Escherichia coli. We have sequenced a 3.2 kb EcoRI-BamHI fragment encoding the rne gene, and identified its reading frame. Upstream from the gene, there are appropriate consensus sequences for a putative promoter and a ribosome binding site. We have translated this gene using a T7 RNA polymerase/promoter system. We determined 25 amino acids from the N-terminal of the translated product and they are in full agreement with the DNA sequence. The translated product of the rne gene migrates in SDS containing polyacrylamide gels as a 110,000 Da polypeptide, but the open reading frame found in the sequenced DNA indicates a much smaller protein. The entity that migrates as a 110,000 Da contains RNA, which could account, at least partially, for the migration of the rne gene product in SDS containing polyacrylamide gels.

A precursor for a small stable RNA (10Sa RNA) of Escherichia coli

Strains carrying plasmids that code for 10Sa RNA synthesize a larger molecule when the RNA processing enzyme RNase E is inactivated. The T1 fingerprint of 10Sa RNA and the larger molecule is very similar, but the latter contains additional oligonucleotides. We show that the larger RNA is converted to the smaller, mature RNA. The precursor molecule starts with an adenosine triphosphate and is therefore a primary transcript. RNase E is not the enzyme that processes p10Sa (precursor 10Sa) RNA into 10Sa RNA. The cell extract contains an activity that carries out this conversion. This activity requires the dication Mn2+.

Purification and properties of ribonuclease E, an RNA-processing enzyme from Escherichia coli

The Escherichia coli RNA-processing enzyme RNAase E was purified through a number of steps including isoelectrofocusing. The final fraction contained mainly a single polypeptide of 66 kDa. However, while all the steps in the purification yielded the same qualitative activity, the specific activity of fractions was decreased in the last steps of the purification. By combining the most-purified enzyme with earlier fractions from the purification, we could show that the cells could contain a factor that enhances RNAase E activity. The purified enzyme showed the same characteristics with respect to temperature optimum, pH and ionic requirements as less-purified preparations. Testing specific inhibitors we concluded that the enzyme requires SH groups, free amino groups, and either of the amino acids tryptophan, tyrosine, histidine or methionine for its activity.

Initiation, processing and termination of ribosomal RNA from a hybrid 5 S ribosomal RNA gene in a plasmid

Transformation of an RNA-processing mutant (rne, RNase E-) of Escherichia coli with a recombinant plasmid containing the promoter region of the ribosomal cluster rrnA and portions from the 3' region of the rrnD cluster results in the accumulation of the precursors to 5 S ribosomal RNAs at the permissive as well as that of two full-length transcripts and a processing intermediate at the nonpermissive temperature. The two full-length transcripts start from the two rrnA promoters, which are about 120 nucleotides apart. This plasmid, pJR3 delta, contains an intact 5 S rRNA gene and portions from the 16 S and 23 S rRNA genes. Analysis of the major plasmid-specific RNA species revealed that RNA molecules initiated in vivo from the first promoter (P1) start with pppA, while transcripts from the second promoter (P2) contain either pppG or pppC at their 5' ends. Termination occurs mainly at the first available termination site. Full-length transcripts initiated from both promoters are processed to precursors of 5 S rRNAs in vivo at the permissive temperature, but only about 20% of these transcripts are processed to mature 5 S rRNA. RNA1 and RNA2 (the transcripts initiated from P1 and P2, respectively) and RNA3 (an RNA-processing intermediate containing the entire 5 S region and the 3' end of the transcripts) can be cleaved in vitro by cell extracts of wild type strains resulting in precursor and mature 5 S rRNAs in a reaction that is RNase E dependent but not ribosome dependent. The 5' end of the processed 5 S rRNA can correspond to the 5' end of mature 5 S rRNA or it can contain one to three additional nucleotides.

Maturation of 5-S rRNA: ribonuclease E cleavages and their dependence on precursor sequences

9-S RNA is a processing intermediate that accumulates in an RNase E- strain of Escherichia coli. It spans from the RNase III cleavage site, after 23-S rRNA, to the 3' end of the transcript and is derived from rRNA genes which do not contain tRNAs distal to 5-S rRNA. Here, we have studied the processing of 9-S RNA with ribonuclease E. RNase E cleaves 9-S RNA in two sites: one of these is three nucleotides upstream from the 5' end of 5-S rRNA, the other downstream from its 3' end. Both cleavages are probably introduced by the same enzyme, since both cleavages are thermolabile when an extract of a temperature-sensitive RNase E mutant was used for processing in vitro. In order to asses the role of 5' and 3' end precursor-specific sequences in the RNase E reaction, we isolated the molecules lacking nucleotides at the 5' or 3' end. Molecules having the 5' end of 9-S RNA but missing nucleotides from the 3' end (called 8-S RNA) were as good a substrate for RNase E as 9-S, RNA itself. However, molecules having the 3' end of 9-S RNA but the 5' end of p5 (called 7-S RNA), were less efficient substrates for RNase E. Finally, the removal of as little as seven nucleotides from the 5' end of 8-S RNA rendered it almost completely unsuitable as a substrate for RNase E.

Processing of procaryotic ribonucleic acid

Images

Inactivation of the ribonucleic acid-processing enzyme ribonuclease E blocks cell division

The Escherichia coli endoribonuclease ribonuclease E, the enzyme responsible for the processing of precursor 5S ribosomal ribonucleic acid (RNA) from the nascent ribosomal RNA transcript, is thermolabile in rne-3071 mutants. When cells of such a strain were shifted to a nonpermissive temperature, the function of ribonuclease E was almost instantaneously inactivated. However, a threefold linear increase in absorbance took place over a 3-h period, and similar linear increases occurred in all the macromolecules we measured, including deoxyribonucleic acid, RNA, protein, and lipopolysaccharides. Interestingly, during this period, the cells elongated but failed to divide. Thus, these experiments suggest that an early effect of inactivation of the RNA processing enzyme ribonuclease E is a block in cell division.

Transfer RNA precursors are accumulated in Escherichia coli in the absence of RNase E

A temperature-sensitive Escherichia coli mutant, which contains a heat-labile RNase E, fails to produce 5-S rRNA at a non-permissive temperature. It accumulates a number of RNA molecules in the 4-12-S range. One of these molecules, a 9-S RNA, is a precursor to 5-S rRNA [Ghora, B. K. and Apirion, D. (1978) Cell, 15, 1055-1056]. These molecules were purified and processed in a cell-free system. Some of these RNA molecules, after processing, give rise to products the size of transfer RNA, but not to 5-S-rRNA. Further characterization of the processed products of one such precursor molecule shows that it contains tRNA1Leu and tRNA1His. RNase E is necessary but not sufficient for the processing of this molecule to mature tRNAs in vitro. The accumulation of such tRNA precursors in an RNase E mutant cell and the obligatory participation of RNase E in its processing indicate that RNase E functions in the maturation of transfer RNAs as well as of 5-S rRNA.

Cloning the gene for ribonuclease E, an RNA processing enzyme

A transducing bacteriophage lambda Ch25rne+, which codes for ribonuclease E of E. coli, has been isolated. To achieve this a random library of Escherichia coli HindIII fragments was cloned in the lambda Charon 25 vector (prepared in F.R. Blattner's laboratory), and lambda Ch25rne+ was selected by its ability upon lysogenization to enable a temperature-sensitive (ts) rne-3071 mutant to grow and to exhibit normal RNA processing at the nonpermissive temperature of 45 degrees C. The level of RNase E was doubled in an rne+ strain lysogenized with lambda Ch25rne+. lambda Ch25rne+ directs the synthesis of a polypeptide of 71 000 m.wt., which is the size of RNase E. Restriction analysis and electron micrography of heteroduplexes suggested that the size of the host DNA insert is about 1.9 kb.