Conserved unpaired adenine residues are important for ordered structures of 5S ribosomal RNA. An infrared study of the secondary and tertiary structure of Thermus thermophilus 5S rRNA

Water (H2O and D2O) molar absorptivity in the 1000-4000 cm-1 range and quantitative infrared spectroscopy of aqueous solutions

Water (H2O and D2O) molar absorptivity was measured by Fourier transform infrared transmission spectroscopy in the 1000-4000 cm-1 range at 25 degrees C. A series of assembled cells with path lengths from 1.2 to 120.5 microns was used for these measurements. The optimal path length (the path length of aqueous solution at which the IR spectrum of solute, corrected for water absorbance, has the highest signal-to-noise ratio) was calculated for all water absorbance bands. The results presented here show that the optimal path length does not depend on solute properties and is inversely proportional to the solvent (water) molar absorptivity. The maximal signal-to-noise ratio for measurements of IR spectra of aqueous solution in the 1650 cm-1 spectral region, of primary interest in biological applications, can be obtained at an optimal cell path lengths of 3-4 microns (H2O) and 40-60 microns (D2O). As an example, the signal-to-noise ratio was calculated as a function of the cell path length for the amide I (H2O) and amide I' (D2O) bands of an aqueous lysozyme solution. The molar absorptivities of water bands are several orders of magnitude weaker than those of the strongest bands of biological macromolecules in the same spectral regions. High net water absorbance in aqueous solutions is due simply to the very high molar concentration of water. A method is proposed for the quantitative measuring of the path length of the cell which exploits the molar absorptivity of the strongest water bands (stretching vibrations) or of bands which do not overlap with solute absorbance. A path length in the range from approximately 0.01 micron to approximately 1.0 mm can be determined with high precision using this technique for a samples of known concentration. Problems involved in the proper correction of strong water absorbance in IR spectra of aqueous solutions of biomolecules are discussed, including multiple reflections within the cell, the effects of pH, temperature, and perturbation of water spectral properties by polar solutes, as well as the selection of optimal spectral regions in which one may obtain the most precise absorbance corrections.

Conformational comparisons among homologous bony fish 5S ribosomal RNAs

The reversible thermal melting of homologous 5S ribosomal RNAs of three bony fishes, rainbow trout (Salmo gairdneri), carp (Cyprinus carpio), and dog salmon (Onchorhynchus keta), were compared in aqueous salts (sodium chloride and/or divalent metal chlorides) by means of differential optical absorption at 260 and 280 nm, and c.d. at 265 nm. The melting parameters of the multiphasic melting process were conserved among the homologous RNAs, and it was shown that they did not depend on the methods of measurement but on concentrations of [Na+] and of [metal2+]. Other physicochemical methods, such as FT-IR absorption, gave the same melting profiles as the u.v. methods. The c.d. spectrum was homologous among the ribosomal RNAs. The melting is explained by changes in local structures in the 'consensus secondary structure model'. Also, stabilization of the secondary and tertiary structures by binding of Mg2+ and Ca2+, and the catalysed hydrolysis of the main chains by various divalent ions are discussed.

A 5 S rRNA-like secondary structure in the 7 SL RNA may define a ribosomal binding site of the signal recognition particle

A new secondary structure model for parts of the 7 SL RNA is proposed which indicates for a stretch of at least 40 bases a strong structural homology to the ribosomal protein L5 binding site of eukaryotic 5 S rRNA. It is suggested that the 5 S rRNA-like structural part of 7 SL RNA mediates binding of the signal recognition particle near to the peptidyl transferase center of the ribosome.

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.

Secondary structure of Tetrahymena thermophilia 5S ribosomal RNA as revealed by enzymatic digestion and microdensitometric analysis

The secondary structure of [32P] end-labeled 5S rRNA from Tetrahymena thermophilia (strain B) has been investigated using the enzymes S1 nuclease, cobra venom ribonuclease and T2 ribonuclease. The results, analyzed by scanning microdensitometry and illustrated by three-dimensional computer graphics, support the secondary structure model of Curtiss and Vournakis for 5S rRNA. Aberrent mobility of certain RNA fragments on sequencing gels was observed as regions of band compression. These regions are postulated to be caused by stable internal base-pairing. The molecule was probed with T2 RNase in neutral (pH 7.5) and acidic (pH 4.5) buffers and only minor structural differences were revealed. One of the helices was found to be susceptible to enzymatic attack by both the single-strand and double-strand specific enzymes. These observations are evidence for the existence of dynamic structural equilibria in 5S rRNA.

Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species

The secondary structure models of 5S rRNA have been constructed from the primary structure of 352 5S rRNA species available at present. All the 5S rRNAs examined can take essentially the same secondary structure, however they reveal characteristic differences between eukaryotes, metabacteria (= archaebacteria) and eubacteria. These three types of models can be further subgrouped by minor but characteristic differences. A phylogenic tree of organisms has been constructed using these 5S rRNA sequences by the weighted pairing method (WPG method). The tree reveals that there exist several major groups of eubacteria which seem to have diverged into different directions in the early stages of bacterial evolution. After emergence of eubacteria, metabacteria and eukaryotes separated from each other from their common ancestor. In the eukaryotic evolution, red algae (Rhodophyta) emerged first, and thereafter, thraustocytrids-Proctista, Ascomycota, green plants (green algae and land plants), Basidiomycota, Chromophyta (brown algae, diatoms and golden-yellow algae), slime- and water molds, various protozoans, and animals emerged in this order.