The Escherichia coli ribosomal RNA leader: a structural and functional investigation

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.

Characterization of transient RNA-RNA interactions important for the facilitated structure formation of bacterial ribosomal 16S RNA

The co-transcribed leader sequences of bacterial rRNA are known to affect the structure and function of the small ribosomal subunits. Base changes in the leader nut -like sequence elements have been shown to cause misfolded but correctly processed 16S rRNA structures at low growth temperature. Transient interactions of leader sequences with the nascent 16S rRNA are considered to guide rRNA folding and to facilitate correct structure formation. In order to understand this chaperone-like activity of the leader RNA we have analyzed the thermodynamic stabilities of wild-type and mutant leader transcripts. We show here that base changes cause subtle differences in the melting profiles of the corresponding leader transcripts. Furthermore, we show that direct interaction between leader transcripts and the 16S rRNA is limited to the 5'-domain of the 16S rRNA for both wild-type and mutant leaders. Binding studies of mutant and wild-type leader transcripts to 16S rRNA revealed small changes in the affinities and the thermal stabilities as a consequence of the base changes. Different complex stabilities as a function of the Mg(2+) ion concentration indicated that mutant and wild-type leader transcripts interact differently with the 16S rRNA, consistent with a less stable and tightly folded structure of the mutant leader. Employing time-resolved oligonucleotide hybridization assays we could show different folding kinetics for 16S rRNA molecules when linked to wild-type leader, mutant leader or in the absence of leader RNA. The studies help to understand how bacterial rRNA leader transcripts may affect the folding of the small subunit rRNA.

Mutations in the leader region of ribosomal RNA operons cause structurally defective 30 S ribosomes as revealed by in vivo structural probing

The biogenesis of functional ribosomes is regulated in a very complex manner, involving different proteins and RNA molecules. RNAs are not only essential components of both ribosomal subunits but also transiently interacting factors during particle formation. In eukaryotes snoRNAs act as molecular chaperones to assist maturation, modification and assembly. In a very similar way highly conserved leader sequences of bacterial rRNA operons are involved in the correct formation of 30 S ribosomal subunits. Certain mutations in the rRNA leader region cause severe growth defects due to malfunction of ribosomes which are assembled from such transcription units. To understand how the leader sequences act to facilitate the formation of the correct 30 S subunits we performed in vivo chemical probing to assess structural differences between ribosomes assembled either from rRNA transcribed from wild-type operons or from operons which contain mutations in the rRNA leader region. Cells transformed with plasmids containing the respective rRNA operons were reacted with dimethylsulphate (DMS). Ribosomes were isolated by sucrose gradient centrifugation and modified nucleotides within the 16 S rRNA were identified by primer extension reaction. Structural differences between ribosomes from wild-type and mutant rRNA operons occur in several clusters within the 16 S rRNA secondary structure. The most prominent differences are located in the central domain including the universally conserved pseudoknot structure which connects the 5', the central and the 3' domain of 16 S rRNA. Two other clusters with structural differences fall in the 5' domain where the leader had been shown to interact with mature 16 S rRNA and within the ribosomal protein S4 binding site. The other differences in structure are located in sites which are also known as sites for the action of several antibiotics. The data explain the functional defects of ribosomes from rRNA operons with leader mutations and help to understand the altered biogenesis pathway from mutations in an rRNA leader region to the formation of functionally defective ribosomes.

Transcriptional pausing of RNA polymerase in the presence of guanosine tetraphosphate depends on the promoter and gene sequence

We have studied the response of the effector molecule guanosine 3',5'-bisdiphosphate (ppGpp) on RNA polymerase pausing during in vitro transcription elongation. Pausing was followed during single round extension of stalled ternary complexes excluding possible ppGpp effects on initiation. The ppGpp dependences of early pausing sites within different transcription systems controlled by promoters with known response to enhanced ppGpp levels in vivo were quantitatively characterized. Transcription of stable RNAs and mRNA genes were analyzed. In addition, the in vitro pausing behavior of two promoter variants directing the same sequence but differing in their in vivo ppGpp sensitivity were compared. In the presence of ppGpp we noted a slight general enhancement of specific pauses in all transcription systems. However, genes known to be under stringent or growth rate control in vivo revealed a notably stronger pausing enhancement. The sites of pausing are not changed by the presence of ppGpp but appear to be sequence-specific. The effect of ppGpp on the extent of pausing depends on the particular promoter and closely adjacent sequences that the RNA polymerase has passed during initiation. Pausing enhancement requires the presence of ppGpp during elongation but not during initiation. The results underline the importance of pausing for transcription regulation and offer a plausible explanation for inhibition of stable RNA expression under conditions of elevated concentrations of ppGpp.

Processing of eukaryotic pre-rRNA: the role of the transcribed spacers

The 17-18S, 5.8S, and 25-28S rRNA species of eukaryotic cells are produced by a series of nucleolytic reactions that liberate the mature rRNAs from the large primary precursor transcript synthesized by RNA polymerase 1. Whereas the order of the cleavage reactions has long been established, until recently little information was available on their molecular details, such as the nature of the proteins, including the nucleolytic enzymes, involved and the signals directing the processing machinery to the correct sites. This situation is now rapidly changing, in particular where yeast is concerned. The use of recently developed systems for in vivo mutational analysis of yeast rDNA has considerably enhanced our knowledge of cis-acting structural features within the pre-rRNA, in particular the transcribed spacer sequences, that are critical for correct and efficient removal of these spacers. The same systems also allow a link to be forged between trans-acting processing factors and these cis-acting elements. In this paper, we will focus predominantly on the nature and role of the cis-acting processing elements as identified in the transcribed spacer regions of Saccharomyces cerevisiae pre-rRNA.

Point mutations in the leader boxA of a plasmid-encoded Escherichia coli rrnB operon cause defective antitermination in vivo

We have introduced point mutations into the leader boxA of a plasmid-encoded Escherichia coli rrnB operon to study the in vivo role of this regulatory element in the natural context of rRNA synthesis. The same mutations were previously shown to cause severe antitermination defects in vitro and in the context of a reporter gene assay. The plasmid-encoded rrnB mutant constructs studied here also contained point mutations in the 16S and 23S rRNA genes, which were used to distinguish rRNAs derived from plasmid and chromosomal rrn operons by primer extension analysis. Point mutations in boxA reduced the fraction of plasmid-derived rRNA in the cell from 75% to about 50%. The reduction was similar for both 30S and 50S subunits as well as 70S ribosomes, suggesting that no transcriptional polarity occurred between the expression of the 16S and 23S rRNA genes in plasmid rrnB operons carrying a mutant boxA. The boxA mutations do not affect the amount of transcription initiation, suggesting that a suboptimal leader boxA causes premature transcription termination at an early stage of transcription. Our results are consistent with a role for antitermination in the completion of full-length rrn transcripts but give no indications of posttranscriptional boxA functions.

The Escherichia coli ribosomal RNA leader nut region interacts specifically with mature 16S RNA

All ribosomal RNAs are preceded by leader sequences not present in the final ribosome particles. The highly conserved leader sequences of bacterial rRNAs are known to be important for the folding and assembly of functional ribosomes. Very likely transient binding of the leader to mature parts of the 16S RNA occurs during transcription. To better understand the mechanistic details of these functions we have performed a secondary structural analysis of E. coli ribosomal RNA leader transcripts by chemical modification and enzymatic hydrolysis studies. The data were combined with results from thermodynamic stability calculations to yield a generalized structural model. The same secondary structure of the leader core, comprising the nut-like sequences up to the mature 5' end of the 16S RNA, was deduced, irrespective if transcripts started at promoter P1 or 120 nucleotides downstream at P2. Employing gelshift and cross-linking studies we were able to demonstrate that a part of the leader core, namely the nut-like sequence elements bind directly to specific regions within the mature 16S RNA. The sites of RNA-RNA cross-linking could be localized by sequencing. They map in the 16S RNA 5' domain at nucleotide positions G27 to G42, C48, G68, G117 and G126. The results may explain the recently observed scaffolding function of the leader RNA during ribosome biogenesis.