NUMEROUS attempts have been made to deduce a secondary structure of 5S RNA1–4. Differing approaches have yielded various structures, but each turns out to be inconsistent with either physical, chemical, biochemical, or comparative evidence. Clearly the situation is not analogous to that which obtained for transfer RNA (tRNA). There is, however, at least one fundamental difference between the two molecules. The functional 5S RNA molecule is at all times an integral part of the 50S ribosomal subunit, whereas tRNA is a transient inhabitant of the ribosome milieu. Thus, it is possible that functional conformations of the 5S RNA molecule need only exist in the context of the ribosome, and consequently, may only exist therein. Thus, the interpretation of experimental investigations on the isolated 5S RNA molecule may have inherent difficulties.

5S RNA Secondary Structure

Publisher Summary This chapter reviews that 5S RNA is a small ribonucleic acid associated with the large ribosomal subunits of eukaryotic (60 S) and prokaryotic (5O S) ribosomes. It was soon determined that its sequence did not contain modified nucleotides, such as found in tRNAs. The discovery of 5S RNA was followed by investigations concerning its sequence and physical properties, to obtain information concerning its structure and function. It reviews that the primary structures of 5S RNA cannot be folded in a single pattern, such as the cloverleaf structure of tRNA. After a method for the total reconstitution of bacterial 50S, ribosomal subunits were developed; it became possible to add a new approach to the research concerning the structure and function of 5S RNA. The chapter discusses that the information on eukaryotic 5S and especially 5.8S RNA is scarce and calls for more experimentation. For the near future, detailed investigations concerning the structure of 5S RNA protein complexes seem most promising, as they represent one of the best systems in which to study RNA–protein interactions. Certainly, attempts should be made to crystallize these complexes to obtain the intimate information required for knowing the forces that govern nucleic acid–protein interaction.

Structure and function of 5S and 5.8 S RNA.

INTRODUCTION ........................................................... 562 GENERAL FEATURES OF PROKARYOTIC RIBOSOMES ....... ............... 563 Diversity in Bacterial Ribosomes .................... ............................ 563 STRUCTURES OF THE PROKARYOTIC rRNA MOLECULES ...... ............ 564 Prokaryotic rRNA Molecules................................................... 564 rRNA Integrity and Ribosome Function ............ ............................. 565 Eukaryotic Analogy ........................................................... 565 Base Compositions ofrRNA from Prokaryotes .......... ......................... 565 Primary and Secondary Structures of the rRNA ......... ........................ 568 Question of Functional Heterogeneity in the rRNA Molecules ...... .............. 569 Phylogenetic Differences in the rRNA of Prokaryotes ........ .................... 570 Prokaryotic Origin for the Eukaryotic Organelles? ........ ...................... 572 GENES SPECIFYING rRNA ..................................................... 573 Gene Dosage for rRNA .......................................................... 573 Mapping the rRNA Genes in E. coli ...... ........ .............................. 573 Mapping the rRNA Genes in B. subtilis ......................................... 575 Isolation of the rDNA .......... ............................... 575 General Features of the Prokaryotic Ribosomes ................... .............. 591 Structures of the Prokaryotic rRNA Molecules .................................. 591 Genes Specifying rRNA ........... .............................. 591 Transcription of the rRNA Genes .......................................... 592 Post-Transcriptional Processing of rRNA ....................................... 592 TRANSCRIPTION OF THE rRNA GENES ....................................... 576 rRNA Transcriptional Unit ............... .......................... 576 Interaction of the RNA Polymerase with the rDNA .............. ................ 577 Initiation of rDNA Transcription .......................................... 578 Regulation ofrRNA Synthesis During Balanced Growth ....... ................. 579 Regulation of rRNA Synthesis During Perturbation of Balanced Growth ........ 581 Regulation ofrRNA Synthesis During Morphogenesis ....... .................... 582 POST-TRANSCRIPTIONAL PROCESSING OF rRNA ....... .................... 583 Hypothetical Tandem Transcript of the rDNA .......... ......................... 583 Immediate Precursors of the rRNA Molecules .......... ......................... 584 Function of the Precursor-Specific Sequences .......... ......................... 587 Post-Transcriptional Modification of Nucleosides ......... ...................... 588 Interaction of the rRNA with the Ribosomal Proteins ............................ 589 CONCLUDING COMMENTS ................... ........................ 590 SUMMARY ........................................... 591 ACKNOWLEDGMENTS .............. ............................. 592 ADDENDUM IN PROOF 593 LITERATURE CITED ............................................................ 593

Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes.

Isolation and characterization of a guanine insertion enzyme, a specific tRNA transglycosylase, from Escherichia coli.

Secale cereale DNA, of mean fragment length 500 bp, was fractionated by hydroxylapatite chromatography to allow recovery of a very rapidly renaturing fraction (C0t 0–0.02). This DNA fraction was shown to contain several families of highly repeated sequence DNA. Two highly repeated families were purified; (1) a fraction which renatured to a density of 1.701 g/ cc and comprised 2–4% of the total genome, and (2) polypyrimidine tract DNA which comprised 0.1% of the total genome. The 1.701 g/cc DNA consisted of short sequence repeat units (5–50 bp long) tandemly repeated in blocks 30 kb long, while a portion of the polypyrimidine tract DNA behaved as part of a much larger block of tandemly repeated sequences. The chromosomal location of these sequences was determined by the in situ hybridisation of radioactive, complementary RNA to root tip mitotic chromosomes and showed the 1.701 g/cc sequences to be largely limited to the telomeric blocks of heterochromatin, accounting for 25–50% of the DNA present in these parts of the chromosomes. The polypyrimidine tracts were distributed at interstitial locations with 20–30% of the sequences at three well defined sites. The combined distributions of the 1.701 g/cc DNA sequences and polypyrimidine tracts effectively “individualised” each rye chromosome thus providing a sensitive means of identifying these chromosomes. The B chromosomes present in Secale cereale cv. Unevita, did not show defined locations for the sequences analysed. — The data are discussed in terms of the structure of the rye genome and the generality of the observed genomic arrangement of highly repeated sequence DNA.

B.E. Griffin

Papers

5 s RNA Conformation. Studies of its Partial T1 Ribonuclease Digestion by Gel Electrophoresis and Two-dimensional Thin-layer Chromatography