Structural characterization and in vitro processing of Escherichia coli ribosomal RNA transcripts containing 5- triphosphates, leader sequences, 16 S rRNA, and spacer tRNAs

Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3' stabilizing stem and loop structure

The transcripts of the rpsO-pnp operon of Escherichia coli, coding for ribosomal protein S15 and polynucleotide phosphorylase, are processed at four sites in the 249 nucleotides of the intercistronic region. The initial processing step in the decay of the pnp mRNA is made by RNase III, which cuts at two sites upstream from the pnp gene. The other two cleavages are dependent on the wild-type allele of the rne gene, which encodes the endonucleolytic enzyme RNase E. The cuts are made 37 nucleotides apart at the base of the stem-loop structure of the rho-independent attenuator located downstream from rpsO. The cleavage downstream from the attenuator generates an rpsO mRNA.nearly identical with the monocistronic attenuated transcript, while the cleavage upstream from the transcription attenuator gives rise to an rpsO mesage lacking the terminal 3' hairpin structure. The rapid degradation of the processed mRNA in an rne+ strain, compared to the slow degradation of the transcript that accumulates in an rne- strain, suggests that RNase E initiates the decay of the rpsO message by removing the stabilizing stem-loop at the 3' end of the RNA.

Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA

The metY gene coding for a minor form of the initiator tRNA is the first gene of a complex polycistronic operon also encoding the transcription termination factor NusA and the translation initiation factor IF2. The mixed tRNA-mRNA polycistronic transcript is cleaved by RNase III in a hairpin structure downstream from the tRNA. This cleavage separates the tRNA from the mRNA and initiates the rapid degradation of the 5' extremity of the downstream mRNA. Dissociation of the structural (tRNA) and informational (mRNA) RNAs from this operon is also achieved by independent transcription in vivo. The presence of two transcription terminators located downstream from metY produces a small tRNAMetf2 precursor transcript, whereas an internal promoter situated between metY and the first open reading frame directs the transcription of only the protein-coding part of the operon.

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+.

Electronic fingerprinting of RNA

Software has been developed to assist RNA fingerprinting analysis. One program generates, from a DNA sequence data file, the oligonucleotides resulting from digestion of an RNA transcript labeled with any specified nucleotide(s). Oligonucleotides are sorted according to their position on the fingerprint. Expected molar yields and products of secondary redigestion are also indicated. A second program facilitates calculation of experimental molar yields of oligonucleotides.

Processing enzyme ribonuclease E specifically cleaves RNA I. An inhibitor of primer formation in plasmid DNA synthesis

When the RNA processing enzyme RNAase E is inactivated in an Escherichia coli strain carrying derivatives of the colicin E1 plasmid, a small RNA, about 100 nucleotides long, accumulates. Structural analysis of this RNA showed that it is RNA I, the RNA that inhibits plasmid DNA synthesis. RNA I is a specific substrate for RNAase E and the cleavage takes place between the fifth and sixth nucleotides from the 5' end of the molecule. This is only the second natural RNA substrate that has been found, so far, for the RNA processing enzyme ribonuclease E, the other being a precursor for 5 S ribosomal RNA. It is remarkable that nine nucleotides around the cleavage sites are identical in both substrates: (Formula: see text). Therefore, we suggest that at least part of the interaction between RNAase E and its substrate is controlled by these nine nucleotides.

Synthesis and processing of 5 S rRNA from an rrnB minigene in a plasmid

A recombinant plasmid containing the promoters, terminators and only the intact 5 S rRNA gene of rrnB is expressed efficiently in Escherichia coli cells. In strains containing a thermolabile RNAase E (rne) full-length transcripts of the rrnB region from the plasmid and a partially processed intermediate product accumulate at non-permissive temperatures. Upon addition of chloramphenicol two additional plasmid-specific RNA molecules appear. They are shorter than the full-length transcripts. These species contain the 3'-end region of the full-length transcripts. Even though the 5' ends of these RNAs were most likely produced by degradative enzymes these 5' ends are not ragged. All these plasmid-specific RNAs are specific substrates for the two endonucleolytic RNA processing enzymes, RNAase E and RNAase III.

Accurate processing and pseudouridylation of chloroplast transfer RNA in a chloroplast transcription system

The trancription of a cloned trnV1-trnN1-trnR1 cluster from Euglena gracilis chloroplast (ct) DNA and the processing of a tRNA(Val)-tRNA(Asn)-tRNA(Arg) polycistronic precursor were studied in a spinach ct transcription extract. A soluble ct RNA polymerase selectively transcribes the trnV1-trnN1-trnR1-trnL1 locus in the EcoG fragment from the Euglena ct genome. Restriction enzyme modified templates and RNA fingerprint analysis were used to confirm that the tRNA genes were correctly transcribed. The tRNA(Val)-tRNA(Asn)-tRNA(Arg) polycistronic precursor transcribed by RNA polymerase III in a HeLa cell extract was used as a substrate to demonstrate that a ct tRNA precursor molecule is correctly processed by the ct tRNA processing enzymes. The oligonucleotide pattern of tRNAs processed in vitro from the tRNA(Val)-tRNA(Asn)-RNA(Arg) polycistronic precursor is indistinguishable from tRNA(Val), tRNA(Asn) and tRNA(Arg) transcribed by the ct RNA polymerase and processed in the ct transcription extract. The 3'-CCAOH is added to the tRNAs by a 3' nucleotidyltransferase after correct processing of the 3' terminus. Correct pseudouridylation was demonstrated for uridine residues in a tRNA(Met) m molecule transcribed from a spinach ct trnM1 locus. Thus, the enzymatic activities involved in tRNA biosynthesis in vitro include DNA-dependent (tDNA) RNA polymerase, a 5'-processing activity (RNase P-like), a 3'-exonuclease, an endoribonuclease involved in 3'-tRNA maturation, a tRNA nucleotidyltransferase, and pseudouridylate synthetase.

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.

Identification of a precursor molecular for the RNA moiety of the processing enzyme RNase P

A precursor molecule for 10Sb (M1) RNA, the RNA moiety of the RNA processing enzyme ribonuclease P (EC 3.1.26.5), is accumulated transiently in an Escherichia coli strain containing a plasmid that carries the 10Sb RNA gene. The same RNA precursor molecule is accumulated, in relatively large quantities, in a temperature-sensitive RNase E- mutant at the nonpermissive temperature. The RNA precursor includes 10Sb RNA and an extra 3' fragment that contains a termination stem and loop. It can be processed in vitro to a molecule the size of 10Sb RNA. None of the four endoribonucleases of E. coli--RNase III, RNase E, RNase F, or RNase P--takes part in this cleavage reaction. Therefore, we suggest that the processing of the precursor-10Sb RNA to 10Sb RNA is carried out by a thus-far unidentified endoribonuclease. The accumulation of a RNA molecule in a RNase E- mutant that does not contain a cleavage site for RNase E has been encountered previously and can be explained by assuming the existence of a RNA processing complex in the E. coli cell.

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.

Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease

Splicing of transfer RNA precursors containing intervening sequences proceeds in two distinct stages: endonucleolytic cleavage, followed by ligation. We have physically separated endonuclease and ligase activities from extracts of yeast cells, and we report properties of the partially purified endonuclease preparation. The endonuclease behaves as an integral membrane protein: it is purified from a membrane fraction from which it can be solubilized with nonionic detergents, and the activity of the endonuclease in the membrane fraction is stimulated by nonionic detergents. The endonuclease cleaves precursor tRNAs at two sites to excise the intervening sequence precisely. Both the extent and the accuracy of cleavage are enhanced by the presence of spermidine; the degree of stimulation varies with the pre-tRNA substrate. The cleavage products possess 5'-hydroxyl and 2',3'-cyclic phosphodiester termini. The cyclic phosphodiester termini can be opened to 2'-phosphates by a cyclic phosphodiesterase activity in the preparation.

Evidence for an internal promoter preceding tufA in the str operon of Escherichia coli

We constructed plasmids carrying tufA from which the major promoter for the rpsL-rpsG-fus-tufA operon (also called the str operon) had been removed. These plasmids continued to express tufA, as judged by the ability to complement mocimycin resistance and by electrophoretic analysis of synthesized proteins. Tn5 transpositions into fus, the gene for elongation factor G, which lies immediately on the 5' side of tufA, failed to obstruct the expression of tufA. The subcloning of a 2,000-base-pair PstI-SmaI DNA fragment (containing the intercistronic region between tufA and fus, the distal portion of fus, and the proximal portion of tufA) next to promoterless tetracycline resistance genes (tet) yielded a plasmid that was capable of bestowing resistance to 12 microgram of tetracycline per ml. The removal of an EcoRI fragment that lies within fus destroyed the ability of the 2,000-base-pair PstI-SmaI fragment to promote the transcription of tet. These data indicate that, in addition to the operon's major promoter rpsLp, there is an internal promoter, tufAp, which can be used for the transcription of tufA, tufAp probably lies within fus, about 50 base pairs upstream from its 3' end and 120 base pairs from the start codon of tufA. The relative activities of tufB and of tufA-from-tufAp were estimated by a comparison of beta-galactosidase activities of almost identical EF-Tu-beta-galactosidase protein fusions; they were approximately equal.

Location of the tufB promoter of E. coli: cotranscription of tufB with four transfer RNA genes

Previous nucleotide sequence studies have demonstrated that the structural genes for four transfer RNA species (thrU, tyrU, glyT and thrT) are positioned close to one another and near tufB, one of the structural genes for elongation factor Tu. We have carried out experiments to determine the position of the tufB promoter and thus to infer whether these five genes are in a single transcription unit. tufB cloned on plasmids was fused to Tc (in operon fusion) or to lacZ (in gene fusion). These plasmids were then subjected to in vitro deletion to locate the promoter responsible for tufB transcription. In addition, the ability of wild-type tufB to complement kirromycin resistance was determined with deletion plasmids. The results indicate that the major promoter for tufB lies upstream from the four transfer RNA genes, and that there might be at least one weak internal promotor, possibly adjacent to tufB. Assuming that the four tRNA genes that lie between the major promoter and tufB are also transcribed from that promoter, we suggest that all five genes lie in a single transcription unit (thrUp-thrU-tyrU-glyT-thrT-tufB-tufBt) whose primary transcript is thus both a transfer RNA precursor and messenger RNA.