Identification of RNA molecules which contain 5 S ribosomal RNA and transfer RNA in an RNAase E-RNAase P- double mutant strain of Escherichia 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.

Processing of tRNA in prokaryotes and eukaryotes

Considerable progress has been made in defining the steps in the conversion of a tRNA precursor to a mature tRNA. These steps, which differ in different systems, include removal of precursor-specific residues from the 5' and 3' termini of the initial transcript, addition of the 3'-C-C-A terminus, splicing of intervening sequences, and modification of nucleotide residues. Despite these advances in defining the "pathways" of tRNA processing, relatively little is known about most of the enzymes actually involved in these processing steps. In this article I describe the sequence of reactions needed to convert the initial tRNA transcript to a functional, mature tRNA, and discuss the specificity and properties of enzymes known to be involved in this process. In addition, I speculate on the expected specificities of other enzymes involved in tRNA processing which have not yet been identified, and on the structural organization of the processing machinery.

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.

Primary and secondary structure in a precursor of 5 S rRNA

In order to shed some light on the mechanism of action of RNAase E, we studied primary and secondary structure in 9 S (a precursor of 5 S rRNA), p5 and 5 S rRNAs. These molecules were digested with RNAases A and T1 in the presence of a high salt concentration; conditions under which single-stranded RNA is differentially digested. The double-stranded RNA fragments were isolated and analyzed. The analyses suggested that p5 and 5 S rRNA contain a stem of ten basepairs which consists of sequences from the 5' and 3' regions of the molecule, while 9 S contains a similar stem which is three basepairs longer and includes also a bulge of three unpaired bases. The stem in the 9 S RNA contains four sites where RNA processing cleavages occur. One of the cleavage sites which leads to the formation of p5 is in a junction between single-stranded and double-stranded RNA. The 9 S RNA molecule contains another large stem of at least 15 basepairs which is derived from the 3' end of the 9 S precursor molecular; it is apparently the transcription termination stem.

Ribonuclease E is involved in the processing of 5-S rRNA from a number of rRNA transcription units

Strains of Escherichia coli having a thermosensitive RNase E produce a number of 5-S ribosomal RNA precursors at a non-permissive temperature. One of these precursors, 9-S RNA, was reported earlier [Ghora, B.K. and Apirion, D. (1978) Cell, 15, 1055-1066]. Here we show the existence of additional precursors to 5-S rRNA, originating from a number of rRNA genes. All the precursors are very similar in the first 200 nucleotides and the last part of this sequence contains the mature 5-S rRNA. Precursors that contain only these nucleotides (8-S RNA) accumulate. They probably originate from the rrn genes C, D and F which contain trailer tRNAs. The 9-S RNA precursors contain in addition a termination stem and loop structure and are derived from genes which do not contain trailer tRNA (Singh and Apirion, unpublished results). In addition, a 10-S precursor was identified. It contains distal to the 5-S rRNA a trailer tRNA, tRNAAsp, and a transcription termination signal. It is derived from the rrnF gene. The accumulation of an RNA precursor containing an RNase P site in an rne mutant suggests that the efficiency of one RNA processing enzyme depends on the activity of other RNA processing enzymes.

Processing of procaryotic ribonucleic acid

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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.