S1 nuclease as a probe of yeast ribosomal 5 S RNA conformation

Evolutionary changes in the higher order structure of the ribosomal 5S RNA

Comparative studies have been undertaken on the higher order structure of ribosomal 5S RNAs from diverse origins. Competitive reassociation studies show that 5S RNA from either a eukaryote or archaebacterium will form a stable ribonucleoprotein complex with the yeast ribosomal 5S RNA binding protein (YL3); in contrast, eubacterial RNAs will not compete in a similar fashion. Partial S1 ribonuclease digestion and ethylnitrosourea reactivity were used to probe the structural differences suggested by the reconstitution experiments. The results indicate a more compact higher order structure in eukaryotic 5S RNAs as compared to eubacteria and suggest that the archaebacterial 5S RNA contains features which are common to either group. The potential significance of these results with respect to a generalized model for the tertiary structure of the ribosomal 5S RNA and to the heterogeneity in the protein components of 5S RNA-protein complexes are discussed.

Identification and assignment of base pairs in three helical stems of Torulopsis utilis ribosomal 5S RNA and its RNase T1 and RNase T2 cleaved fragments via 500-MHz proton homonuclear overhauser enhancements

Imino proton resonances in the downfield region (10-14 ppm) of the 500-MHz 1H NMR spectrum of Torulopsis utilis 5S RNA are identified (A X U, G X C, or G X U) and assigned to base pairs in helices I, IV, and V via analysis of homonuclear Overhauser enhancements (NOE) from intact T. utilis 5S RNA, its RNase T1 and RNase T2 digested fragments, and a second yeast (Saccharomyces cerevisiae) 5S RNA whose nucleotide sequence differs at only six residues from that of T. utilis 5S RNA. The near-identical chemical shifts and NOE behavior of most of the common peaks from these four RNAs strongly suggest that helices I, IV, and V retain the same conformation after RNase digestion and that both T. utilis and S. cerevisiae 5S RNAs share a common secondary and tertiary structure. Of the four G X U base pairs identified in the intact 5S RNA, two are assigned to the terminal stem (helix I) and the other two to helices IV and V. Seven of the nine base pairs of the terminal stem have been assigned. Our experimental demonstration of a G X U base pair in helix V supports the 5S RNA secondary structural model of Luehrsen and Fox [Luehrsen, K. R., & Fox, G.E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 2150-2154]. Finally, the base-pair proton peak assigned to the terminal G X U in helix V of the RNase T2 cleaved fragment is shifted downfield from that in the intact 5S RNA, suggesting that helices I and V may be coaxial in intact T. utilis 5S RNA.

The secondary structure of oocyte and somatic 5S ribosomal RNAs of the fish Misgurnus fossilis L. from nuclease hydrolyses and chemical modification data

We have studied the accessibility of 5'- 32P labeled oocyte and somatic 5S rRNAs from the fish Misgurnus fossilis L. to S1, T1 and cobra venom nucleases and have found that the cleavage sites of 5S rRNAs closely related in primary structures differ in these molecules. The data of nuclease hydrolyses revealed the existence of two conformers corresponding to renatured and partially denatured somatic 5S rRNA and capable of mutual interconversions. The exposed cytosine residues were located in oocyte and somatic 5S rRNAs converted into uridine ones by sodium bisulfite treatment. The data have been used to construct the secondary structure models of somatic and oocyte 5S rRNAs by means of specially devised computer program. These models differ in their 5'-halves which contain all the nucleotide substitutions in the primary structure, all differences in location of the exposed cytosine residues, and finally, in the cleavage pattern by the nucleases used.

Dynamics of ribosomal RNA structure

The structural dynamics of ribosomal 5S RNAs have been investigated by probing single strandedness through enzymatic cleavage and chemical modification. This comparative study includes 5S rRNAs from E. coli, B. stearothermophilus, T. thermophilus, H. cutirubrum, spinach chloroplast, spinach cytomplasm, and Artemia salina. The structural studies support a unique tertiary interaction in eubacterial 5S rRNAs, involving nucleotides around positions 43 and 75. In addition long range structural effects are demonstrated in E. coli 5S rRNA due to the conversion of C to U at position 92.

Partial melting of the segment around pseudouridine in yeast 5S RNA

Pseudouridine in yeast 5S RNA was modified with 4-bromomethyl-7-methoxy-coumarin(BMC). Temperature dependence of fluorescence intensity was measured at various concentrations of Mg2+ and K+ cations. Hyperchromicity was also measured. At 100mM KCl and 10mM Mg2+, fluorescence intensity decreased with temperature as free BMC except a plateau at 45 degrees C. Withdrawal of Mg2+ from the buffer resulted in a large quenching at 20 degrees C and showed a gradual increase of fluorescence intensity with temperature, indicating a partial melting of the segment around pseudouridine. The temperature range agrees with the low melting temperature shown by hyperchromicity. In 10 mM KCl solution, the effects are more exaggerated.

Secondary structure of Bombyx mori and Dictyostelium discoideum 5S rRNA from S1 nuclease and cobra venom ribonuclease susceptibility, and computer assisted analysis

The 5S rRNAs from Bombyx mori and Dictyostelium discoideum were end-labeled with [32-P] at either the 5' or 3' end and sequenced using enzymatic digestion. The secondary structure of these molecules was studied using the single-strand specific S1 nuclease and the base-pair specific cobra venom ribonuclease. Computer analysis of these results was performed and was used to generate a consensus secondary structure for each molecule. A comparison of these results with those of other workers is presented.

A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes

A general secondary structure is proposed for the 5S RNA of prokaryotic ribosomes, based on helical energy filtering calculations. We have considered all secondary structures that are common to 17 different prokaryotic 5S RNAs and for each 5S sequence calculated the (global) minimum energy secondary structure (300,000 common structures are possible for each sequence). The 17 different minimum energy secondary structures all correspond, with minor differences, to a single, secondary structure model. This is strong evidence that this general 5S folding pattern corresponds to the secondary structure of the functional 5S rRNA. The general 5S secondary structure is forked and in analogy with the cloverleaf of tRNA is named the "wishbone" model. It constant 8 double helical regions; one in the stem, four in the first, or constant arm, and three in the second arm. Four of these double helical regions are present in a model earlier proposed (1) and four additional regions not proposed by them are presented here. In the minimum energy general structure, the four helices in the constant arm are exactly 15 nucleotide pairs long. These helices are stacked in the sequences from gram-positive bacteria and probably stacked in gram-negative sequences as well. In sequences from gram-positive bacteria the length of the constant arm is maintained at 15 stacked pairs by an unusual minimum energy interaction involving a C26-G57 base pair intercalated between two adjacent helical regions.

Influence of mRNA secondary structure on binding and migration of 40S ribosomal subunits

Reovirus messenger RNA was modified by reaction with bisulfite (in denaturing conditions) or by incorporation of IMP in place of GMP, thereby irreversibly unfolding the mRNA. Messenger RNA in which the secondary structure was weakened or abolished retained the ability to bind to wheat germ ribosomes, suggesting that conformational features around the AUG codon are not required for ribosome recognition of mRNA. Ribosomes were not able to attach (directly) to spurious internal sites, even in extensively unfolded RNA, indicating that the monocistronic character of eucaryotic messages (in which initiation is limited to a single 5' proximal site) is not simply due to conformational masking of all the internal AUG codons. The secondary structure in eucaryotic messages does contribute to the fidelity of the translation process, however, because when 40S ribosomal subunits were incubated with denatured mRNA they failed to stop at the 5' proximal AUG codon. Extensive migration beyond the 5' region occurred when 40S ribosomes (in the absence of 60S subunits) attached to unfolded mRNA, implying that the secondary structure in native mRNA facilitates correct translation by impeding migration of 40S subunits beyond the 5' proximal initiation region. Secondary structure in mRNA may also modulate the efficiency of translation. Studies with BrUMP-substituted mRNA, in which the secondary structure is enhanced, suggested that the efficiency of mRNA binding to ribosomes decreases as the stability of the secondary structure increases.