Direct localization by cryo-electron microscopy of secondary structural elements in Escherichia coli 23 S rRNA which differ from the corresponding regions in Haloarcula marismortui

Interactions between terminal ribosomal RNA helices stabilize the E. coli large ribosomal subunit

The ribosome is a large ribonucleoprotein assembly that uses diverse and complex molecular interactions to maintain proper folding. In vivo assembled ribosomes have been isolated using MS2 tags installed in either the 16S or 23S ribosomal RNAs (rRNAs), to enable studies of ribosome structure and function in vitro. RNA tags in the Escherichia coli 50S subunit have commonly been inserted into an extended helix H98 in 23S rRNA, as this addition does not affect cellular growth or in vitro ribosome activity. Here, we find that E. coli 50S subunits with MS2 tags inserted in H98 are destabilized compared to wild-type (WT) 50S subunits. We identify the loss of RNA-RNA tertiary contacts that bridge helices H1, H94, and H98 as the cause of destabilization. Using cryogenic electron microscopy (cryo-EM), we show that this interaction is disrupted by the addition of the MS2 tag and can be restored through the insertion of a single adenosine in the extended H98 helix. This work establishes ways to improve MS2 tags in the 50S subunit that maintain ribosome stability and investigates a complex RNA tertiary structure that may be important for stability in various bacterial ribosomes.

Telomerase from yeast Saccharomyces cerevisiae is active in vitro as a monomer

A system for isolation of yeast telomerase via RNA affinity tag in TLC1 RNA was developed. Streptavidin aptamer was inserted at two different positions in TLC1 RNA. Telomerase with TLC1 RNA with one of these inserts is functional in vivo and can be isolated by affinity chromatography in vitro. A telomerase preparation isolated using this technique from a strain producing two distinguishable TLC1 RNA molecules (with and without aptameric insertion) resulted in isolation of active telomerase containing only TLC1 RNA with the aptamer. Our results indicate that yeast telomerase is active in vitro as a monomer.

'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target

In this study we describe a novel method to investigate the RNA–RNA interactions between a small RNA and its target that we termed ‘RNA walk’. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT–PCR or real-time PCR. Domains carrying the cross-linked adducts fail to efficiently amplify by PCR compared with non-cross-linked domains. This method was calibrated and used to study the interaction between a special tRNA-like molecule (sRNA-85) that is part of the trypanosome signal recognition particle (SRP) complex and the ribosome. Four contact sites between sRNA-85 and rRNA were identified by ‘RNA walk’ and were further fine-mapped by primer extension. Two of the contact sites are expected; one contact site mimics the interaction of the mammalian Alu domain of SRP with the ribosome and the other contact sites include a canonical tRNA interaction. The two other cross-linked sites could not be predicted. We propose that ‘RNA walk, is a generic method to map target RNA small RNAs interactions in vivo.

Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments

Ribosomal RNAs (rRNAs), assisted by ribosomal proteins, form the basic structure of the ribosome, and play critical roles in protein synthesis. Compared to prokaryotic ribosomes, eukaryotic ribosomes contain elongated rRNAs with several expansion segments and larger numbers of ribosomal proteins. To investigate architectural evolution and functional capability of rRNAs, we employed a Tn5 transposon system to develop a systematic genetic insertion of an RNA segment 31 nt in length into Escherichia coli rRNAs. From the plasmid library harboring a single rRNA operon containing random insertions, we isolated surviving clones bearing rRNAs with functional insertions that enabled rescue of the E. coli strain (Δ7rrn) in which all chromosomal rRNA operons were depleted. We identified 51 sites with functional insertions, 16 sites in 16S rRNA and 35 sites in 23S rRNA, revealing the architecture of E. coli rRNAs to be substantially flexible. Most of the insertion sites show clear tendency to coincide with the regions of the expansion segments found in eukaryotic rRNAs, implying that eukaryotic rRNAs evolved from prokaryotic rRNAs suffering genetic insertions and selections.

Analysis of the secondary structure of expansion segment 39 in ribosomes from fungi, plants and mammals

The structure of expansion segment 39, ES39, in eukaryotic 23 S-like ribosomal RNA was analysed using a combination of chemical and enzymic reagents. Ribosomes were isolated from yeast, wheat, mouse, rat and rabbit, five organisms representing three different eukaryotic kingdoms. The isolated ribosomes were treated with structure-sensitive chemical and enzymic reagents and the modification patterns analysed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The expansion segment was relatively accessible to modification by both enzymic and chemical probes, suggesting that ES39 was exposed on the surface of the ribosomes. The collected modification data were used in secondary structure modelling of the expansion segment. Despite considerable variation in both sequence and length between organisms from different kingdoms, the structure analysis of the expansion segment gave rise to structural fingerprints that allowed identification of homologous structures in ES39 from fungi, plants and mammals. The homologous structures formed an initial helix and an invariant hairpin connected to the initial helix via a long single-stranded loop. The remaining part of the ES39 sequences accounted for most of the length variation seen between the analysed species. This part could form additional, albeit less similar, hairpins. A comparison of ES39 sequences from other fungi, plants and mammals showed that identical structures could be formed in these organisms.

Site-specific labeling of the ribosome for single-molecule spectroscopy

Single-molecule fluorescence spectroscopy can reveal mechanistic and kinetic details that may not be observed in static structural and bulk biochemical studies of protein synthesis. One approach requires site-specific and stable attachment of fluorophores to the components of translation machinery. Fluorescent tagging of the ribosome is a prerequisite for the observation of dynamic changes in ribosomal conformation during translation using fluorescence methods. Modifications of the ribosomal particle are difficult due to its complexity and high degree of sequence and structural conservation. We have developed a general method to label specifically the prokaryotic ribosome by hybridization of fluorescent oligonucleotides to mutated ribosomal RNA. Functional, modified ribosomes can be purified as a homogenous population, and fluorescence can be monitored from labeled ribosomal complexes immobilized on a derivatized quartz surface.

Affinity purification of ribosomes with a lethal G2655C mutation in 23 S rRNA that affects the translocation

A method for preparation of Escherichia coli ribosomes carrying lethal mutations in 23 S rRNA was developed. The method is based on the site-directed incorporation of a streptavidin binding tag into functionally neutral sites of the 23 S rRNA and subsequent affinity chromatography. It was tested with ribosomes mutated at the 23 S rRNA position 2655 (the elongation factor (EF)-G binding site). Ribosomes carrying the lethal G2655C mutation were purified and studied in vitro. It was found in particular that this mutation confers strong inhibition of the translocation process but only moderately affects GTPase activity and binding of EF-G.

A protonated base pair participating in rRNA tertiary structural interactions

In the recently published X-ray crystallographic structure for the 50S subunit of Haloarcula marismortui ribosomes, residue U2546 of the 23S rRNA forms a non-Watson-Crick base pair with U2610. The corresponding residues in the secondary structure of the Escherichia coli 23S molecule are U2511 and C2575, and it follows that the latter base (C2575) should be protonated in order to form a base pair that is isostructural with its counterpart in H.marismortui. This prediction was demonstrated experimentally by reduction with sodium borohydride followed by primer extension analysis; borohydride is able to reduce positively charged bases, yielding products which block reverse transcription. In the course of the analysis a further charged base pair (AH(+)1528-G1543) was identified in the E.coli 23S molecule. Both charged pairs (U2511-CH(+)2575 and AH(+)1528-G1543) were only observed in the context of the intact ribosomal subunit and were not seen in deproteinized rRNA.