Effects of deletions in the spacer region of the rrnB operon on the transcription of the large ribosomal RNAs from Escherichia coli

Effects of base change mutations within an Escherichia coli ribosomal RNA leader region on rRNA maturation and ribosome formation

The effects of base change mutations in a highly conserved sequence (boxC) within the leader of bacterial ribosomal RNAs (rRNAs) was studied. The boxC sequence preceding the 16S rRNA structural gene constitutes part of the RNase III processing site, one of the first cleavage sites on the pathway to mature 16S rRNA. Moreover, rRNA leader sequences facilitate correct 16S rRNA folding, thereby assisting ribosomal subunit formation. Mutations in boxC cause cold sensitivity and result in 16S rRNA and 30S subunit deficiency. Strains in which all rRNA operons are replaced by mutant transcription units are viable. Thermodynamic studies by temperature gradient gel electrophoresis reveal that mutant transcripts have a different, less ordered structure. In addition, RNA secondary structure differences between mutant and wild-type transcripts were determined by chemical and enzymatic probing. Differences are found in the leader RNA sequence itself but also in structurally important regions of the mature 16S rRNA. A minor fraction of the rRNA transcripts from mutant operons is not processed by RNase III, resulting in a significantly extended precursor half-life compared to the wild-type. The boxC mutations also give rise to a new aberrant degradation product of 16S rRNA. This intermediate cannot be detected in strains lacking RNase III. Together the results indicate that the boxC sequence, although important for RNase III processing, is likely to serve additional functions by facilitating correct formation of the mature 16S rRNA structure. They also suggest that quality control steps are acting during ribosome biogenesis.

Multiple functions of the transcribed spacers in ribosomal RNA operons

rRNA operons contain about 25% transcribed spacer sequences in addition to the 16S, 23S, 5S and tRNA genes. The spacer sequences are removed from the primary rRNA transcript by a series of co-ordinated nucleolytic events. Besides the role in rRNA processing, the spacer sequences are also involved in transcription and the ribosome assembly. In this study we analyze the spacer between tRNA and 23S rRNA genes. Based on computer modeling and chemical probing data, a model for the transient secondary structure of the intergenic spacer is proposed. Mutational analysis has shown that the transient secondary structure around the 5' end of 23S rRNA is involved in ribosome assembly. We propose that the transient structure at the 5' end of 23S rRNA directs 23S rRNA folding into the mature structure and facilitates ribosomal large subunit assembly.

Base-pairing of 23 S rRNA ends is essential for ribosomal large subunit assembly

In ribosomal RNA precursors the spacer sequences bracketing mature 16 S and 23 S rRNA are base-paired to form long helices (processing stems). In pre-23 S rRNA, the processing stem is continued by eight base-pairs of mature 23 S rRNA known as helix 1. Recently, we have found that any part of 23 S rRNA between positions 40 and 2773 could be deleted without the loss of ribosome-like particle formation, while both end regions were indispensable. In this paper we have analyzed the role of the 5' and 3' end regions of 23 S rRNA during ribosomal 50 S assembly in vivo by using mutants of the 23 S rRNA gene. Deletions and substitutions in both strands of the helix 1 lead to the loss of plasmid derived 50 S formation. Compensatory mutations restoring helix 1 were assembled into functional 50 S subunits. We conclude that the helix 1 of 23 S rRNA is the main RNA determinant for ribosomal large-subunit assembly. Deletions in both the 5' and 3' strand of the processing stem reduced the ability of the 23 S rRNA to form ribosomal 50 S subunits. However, even the complete removal of either the 5' or the 3' strand of the processing stem did not abolish the 50 S assembly completely. Thus, processing stem facilitates, but is not essential for assembly.

Guanosine tetraphosphate as a global regulator of bacterial RNA synthesis: a model involving RNA polymerase pausing and queuing

A recently reported comparison of stable RNA (rRNA, tRNA) and mRNA synthesis rates in ppGpp-synthesizing and ppGpp-deficient (delta relA delta spoT) bacteria has suggested that ppGpp inhibits transcription initiation from stable RNA promoters, as well as synthesis of (bulk) mRNA. Inhibition of stable RNA synthesis occurs mainly during slow growth of bacteria when cytoplasmic levels of ppGpp are high. In contrast, inhibition of mRNA occurs mainly during fast growth when ppGpp levels are low, and it is associated with a partial inactivation of RNA polymerase. To explain these observations it has been proposed that ppGpp causes transcriptional pausing and queuing during the synthesis of mRNA. Polymerase queuing requires high rates of transcription initiation in addition to polymerase pausing, and therefore high concentrations of free RNA polymerase. These conditions are found in fast growing bacteria. Furthermore, the RNA polymerase queues lead to a promoter blocking when RNA polymerase molecules stack up from the pause site back to the (mRNA) promoter. This occurs most frequently at pause sites close to the promoter. Blocking of mRNA promoters diverts RNA polymerase to stable RNA promoters. In this manner ppGpp could indirectly stimulate synthesis of stable RNA at high growth rates. In the present work a mathematical analysis, based on the theory of queuing, is presented and applied to the global control of transcription in bacteria. This model predicts the in vivo distribution of RNA polymerase over stable RNA and mRNA genes for both ppGpp-synthesizing and ppGpp-deficient bacteria in response to different environmental conditions. It also shows how small changes in basal ppGpp concentrations can produce large changes in the rate of stable RNA synthesis.

Functional importance of the Escherichia coli ribosomal RNA leader box A sequence for post-transcriptional events

To shed more light on the controversial findings concerning the functional participation of the highly conserved nut-like leader box A sequence element in ribosomal RNA transcription antitermination we have carried out a mutational study. We have substituted the box A and combined this mutation with several deletions comprising the rRNA leader elements box B, box C and the tL region. The mutations are located within the genuine rrnB operon cloned on multicopy plasmids. We determined the effects of the mutations on cell growth, rRNA accumulation and ribosomal subunit stoichiometry. Cells transformed with the mutated plasmids were affected in their growth rate, and showed a surprising deficiency of the promoter-proximal 16S compared to the 23S RNA, indicative of a post-transcriptional degradation event. Accordingly, we could demonstrate a reduced amount of free 30S relative to 50S ribosomal subunits in exponentially growing cells. Similar stoichiometric aberrations in the ribosome pool were detected in conditionally Nus factor-defective strains. The results show that the leader box A sequence within rRNA operons has important post-transcriptional functions for 16S RNA stability and ribosomal subunit stoichiometry. A model is proposed, describing the biogenesis and quality control of ribosomes based on rRNA leader and Nus-factor interactions. It is compatible with the previously observed effects of box A in antitermination.

The tRNAGlu2 gene in the rrnB operon of E. coli is a prerequisite for correct RNase III processing in vitro

RNase III cleaves precursor 16S RNA and precursor 23S RNA from the ribosomal RNA transcript. In vitro transcription experiments, using plasmids with the rrnB operon truncated in the 16S RNA and with various deletions in the spacer tRNA region, showed that no matter what size of deletion if the tRNA gene was affected RNase III processing of 16S RNA became incomplete. In comparison to a control plasmid, where only the 16S RNA gene was truncated and that showed normal RNA processing, plasmids where the tRNA gene was deleted partially or totally either the 5' or the 3' end of 16S RNA was processed. This relation between RNase III processing and the 3-dimensional structure of tRNA suggests an interaction between RNase III and a tRNA processing enzyme most probably RNase P.