Fusion of the tandem Escherichia coli rrnA promoters to a transcription termination signal from the end of rrnD

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

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-1) 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-1 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.

A repeated 18 bp sequence motif in the mouse rDNA spacer mediates binding of a nuclear factor and transcription termination

DNA sequences and protein factors directing termination of mouse rDNA transcription in a nuclear extract system were examined. Termination is specific and requires a sequence element AGGTCGACCAGATTANTCCG (the Sall box) that is present eight times in the spacer region downstream of the 3' end of pre-rRNA. Exonuclease III protection experiments reveal the binding of a nuclear protein to the Sall box. Deletions, insertions, and point mutations in the Sall box reduce or abolish the interaction with the nuclear factor and disrupt transcription termination. A synthetic oligonucleotide corresponding to the Sall box consensus sequence governs transcription termination in vitro, although with reduced activity. Therefore, other sequences normally surrounding the Sall box appear to contribute to the accuracy and efficiency of termination.

The sequence of the distal end of the E. coli ribosomal RNA rrnE operon indicates conserved features are shared by rrn operons

The 1440 nucleotides of the distal region of the E. coli ribosomal RNA operon found on the lambda aroE transducing phage has been sequenced. We show that the lambda aroE hybrid rrn operon ends after a solitary 5S RNA gene with rrnE distal sequence. A single terminator structure of dyad symmetry followed by a run of six T's have been identified and compared to other sequenced rrn terminator hairpins. Immediately adjacent to the hairpin is a region of interrupted but conserved sequence that is shared by rrnE, rrnB and rrnD. An open reading frame of 127 amino acids abuts the terminator structure. Another open reading frame of 147 amino acids is found on the opposite strand several hundred nucleotides downstream.

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.

Hybrid 5 S ribosomal RNA encoded by a multicopy plasmid is incorporated into ribosomes of Escherichia coli

The recombinant plasmid pJR3 delta contains a tandem pair of promoters from rrnA followed by a hybrid 5 S rRNA gene, derived from the two 5 S rRNA genes of the rrnD transcription unit, and a terminator. Escherichia coli cells transformed with this plasmid produce 2-3-times more 5 S rRNA compared to untransformed cells. The growth of cells containing this plasmid is not affected significantly. Although the sequence and the secondary structure of the plasmid-specific 5 S rRNA differ from those of its counterparts (e.g., from 5 S rRNA species encoded by chromosomal genes), it is processed properly and is incorporated into ribosomes.

Precursor nucleotides at the 5' end are not required for processing by RNase E at the 3' end of 5-S rRNA

7-S RNA, a single-site substrate for the processing enzyme RNase E of Escherichia coli, consists of p5 rRNA (the precursors of 5-S RNA) and the 3'-end region of the rRNA transcript which is mainly a termination stem and loop. The 7-S RNA studied here was derived mainly from the rRNA gene cluster rrnD, carried in a multicopy plasmid. It contains four different populations of molecules that differ from each other at their 5' ends only: the shortest species has the 5' end of the mature 5-S rRNA, while the others are one, two and three nucleotides longer. The four different 5'-end forms were separated in a long sequencing gel. Processing of these forms and unfractionated 7-S RNA by RNase E in vitro, showed that all forms, even the shortest one, can be processed to p5 rRNA. Since the extra nucleotides at the 5' end of the molecule could be base-paired with the region of 7-S RNA where RNase E cuts, it is concluded that this double-stranded structure is not required for the action of RNase E in separating the 3' end of p5 rRNA from the termination stem.