THE SYNTHESIS OF 5S RNA AND ITS REGULATION DURING EARLY SEA URCHIN DEVELOPMENT

De novo synthesis of 5S RNA and of transfer RNA (tRNA) has been demonstrated previously to occur by mid-cleavage (128-cell stage) in sea urchin embryos (24). The present study focused on determining more precisely the time of onset of activity of the genes for 5S RNA and for tRNA during sea urchin embryogenesis by preloading the GTP precursor pools of unfertilized eggs. The results showed that newly-made 5S RNA and tRNA could be detected as early as the 32-cell stage. In order to determine whether newly-synthesized 5S RNA accumulates coordinately during development with newly-made 26S (34) and 18S ribosomal RNAs (rRNAs), the relative rates of accumulation of these three RNA molecules were measured and compared at each of several stages of sea urchin embryogenesis. In contrast to the coordinated accumulation of newly-synthesized 26S and 18S rRNAs, newly-made 5S RNA accumulated in excess at the mesenchyme blastula (9-fold excess), midgastrula (5-fold excess) and prism (3-fold excess) stages. The 5S RNA/26S RNA molar ratios only approached unity in advanced (48 hr) plutei. The non-coordinated accumulation of newly-made 5S RNA with that of 26S and 18S rRNAs suggests that the accumulation of these newly-synthesized RNAs is differentially regulated during early sea urchin development.     

Two 5S genes are expressed in chicken somatic cells.

Two 5S RNA species were detected in chicken cells. 5S I RNA has the nucleotide sequence of chicken 5S RNA previously published by Brownlee et al. (1) and 5S II RNA differs from it by 10 mutations. The secondary structure of both species is compatible with that proposed for other eukaryotic 5S RNAs. 5S II RNA represents 50-60% of 5S I RNA. Both species were found in total chicken liver and brain and were present in polysomes in the same relative proportions. Only one 5S RNA species could be detected in rat liver and HeLa cells. Chicken is the first vertebrate described so far in which two 5S RNA genes are expressed in somatic cells.     

Structural features of Bacillus precursor 5S RNA involved in the interaction with RNAase M5.

Mature 5S (m5S) RNA from Bacillus licheniformis specifically and almost completely inhibits in vitro maturation of bacillus precursor 5S (p5S) RNA, showing that the maturation enzyme RNAase M5 can recognize Bacillus m5S RNA. E. coli m5S RNA is a much less efficient inhibitor, whereas S. carlsbergensis 5S RNA inhibits maturation by about 70%. The differences in inhibition can be correlated with the position of the sequence UAGG (residues 101-104 in B. licheniformis m5S RNA) relative to the double-helical region formed by the 5'- and 3'-terminal sequences (molecular stalk) of m5S RNA. Recent experiments by Meyhack and Pace (Biochemistry 17 (1980) 5804-5810) demonstrated this UAGG sequence to be indispensable for processing of p5S RNA. Other elements of secondary and/or tertiary structure are also required, however. The effect of artificially constructed "5S RNA" molecules having defined disturbances in the base-pairing within the molecular stalk on in vitro maturation shows that base-pairing in the immediate neighbourhood of the bonds to be cleaved during maturation is crucial to recognition of p5S RNA by RNAase M5. G.U pairs are tolerated in this region, however, without loss of efficiency in maturation. Base-pairing does not have to extend throughout the complete molecular stalk. The introduction of an A/C combination at the end of the molecular stalk removed from the bonds cleaved by RNAase M5 does not significantly impair the efficiency of maturation.     

Phylogeny of the 5S ribosomal RNA from Synechococcus lividus II: the cyanobacterial/chloroplast 5S RNAs form a common structural class

The complete nucleotide sequence of the 5S ribosomal RNA from the cyanobacterium Synechococcus lividus II has been determined. The sequence is (sequence in text) This 5S RNA has the cyanobacterial- and chloroplast-specific nucleotide insertion between positions 30 and 31 (using the numbering system of the generalized eubacterial 5S RNA) and the chloroplast-specific nucleotide-deletion signature between positions 34 and 39. The 5S RNA of S. lividus II has 27 base differences compared with the 5S RNA of the related strain S. lividus III. This large difference may reflect an ancient divergence between these two organisms. The electrophoretic mobilities on nondenaturing polyacrylamide gels of renatured 5S RNAs from S. lividus II, S. lividus III, and spinach chloroplasts are identical, but differ considerably from that of Escherichia coli 5S RNA. This most likely reflects differences in higher-order structure between the 5S RNA of E. coli and these cyanobacterial and chloroplast 5S RNAs.     

The isolation and characterization of a second oocyte 5s DNA from Xenopus laevis

A second and minor DNA component containing 5s RNA genes has been purified from the genomic DNA of Xenopus laevis (XIt 5S DNA). Some of its physical and chemical characteristics are described. It contains a 5S RNA gene sequence which has some oocyte and some somatic-specific residues, as well as nucleotides which differ from both types of 5S RNA. There are about 2000 of these 5S RNA genes per haploid complement of DNA compared to about 24,000 of the principal oocyte 5S RNA genes. The multiple repeating units of XIt 5S DNA are homogeneous in length (about 350 base pairs). We present evidence that XIt 5S RNA is transcribed in ovaries but not in somatic cells; XIt 5S DNA may therefore be under the same control as the major oocyte 5S DNA.     

Two zinc finger proteins from Xenopus laevis bind the same region of 5S RNA but with different nuclease protection patterns.

Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatography. The purified p43-5S RNA migrates as a distinct species during electrophoresis on native polyacrylamide gels. Radiolabeled 5S RNA can be incorporated into the p43-5S complex by an RNA exchange reaction. The resulting complexes containing labeled 5S RNA have a mobility on polyacrylamide gels identical to that of purified p43-5S RNPs. RNP complexes containing 5S RNA labeled at either the 5' or 3' end were probed with a variety of nucleases in order to identify residues protected by p43. Nuclease protection assays performed with alpha-sarcin indicate that p43 binds primarily helices I, II, IV, and V of 5S RNA. This is the same general binding site observed for TFIIIA on 5S RNA. Direct comparison of the binding sites of p43 and TFIIIA with T1 and cobra venom nucleases reveals striking differences in the protection patterns of these two proteins.     

Unusual structural features of the 5S ribosomal RNA from Streptococcus cremoris

The nucleotide sequence of the 5S ribosomal RNA of Streptococcus cremoris has been determined. The sequence is 5' (sequence in text) 3'. Comparison of the S. cremoris 5S RNA sequence to an updated prokaryotic generalized 5S RNA structural model shows that this 5S RNA contains some unusual structural features. These features result largely from uncommon base substitutions in helices I, II and IV. Some of these unusual structural features are shared by several of the known 5S RNA sequences from mycoplasmas. However, the characteristic bloc of deletions found in helix V of these mycoplasma 5S RNAs is not present in the 5S RNA of S. cremoris.     

The relation between polyoma T-antigen and increased 5S RNA synthesis in cell-free extracts from polyoma-infected mouse kidney cell cultures.

In polyoma-infected mouse kidney cell cultures 5S RNA synthesis began to increase around 16 h, i.e. 7-9 h after the onset of polyoma T-antigen synthesis. The rate of polyoma-induced 5S RNA synthesis reached a maximum plateau around 25 h when it was 1.8-2.0 times higher than in mock-infected parallel cultures. Stimulation of 5S RNA synthesis in vivo thus coincided in time with the increase in total cellular RNA and protein. Cell-free extracts (S100) prepared at 15 h from mock-(S100-M) or polyoma-infected (S100-Py) mouse kidney cell cultures were indistinguishable with respect to protein concentration and 5S RNA synthesis, using a cloned somatic Xenopus borealis 5S gene as template. S100-Py extracted 25 h after infection contained 30% more protein and synthesized 1.5-2.0 times more 5S RNA than S100-M. Complete removal of the polyoma T-antigens from S100-Py by 3 cycles of immunoprecipitation with hamster anti-T serum remained without effect on stimulated 5S RNA synthesis. However, a linear relationship between 5S RNA synthesis and protein concentration of S100-M and S100-Py was observed.     

The role of the basic N-terminal region of protein L18 in 5S RNA-23S RNA complex formation.

Of the three proteins, L5, L18 and L25, which bind to 5S RNA, the former two effect the interaction of 5S RNA with 23S RNA. We have used trypsin as a probe to investigate the roles of the proteins in this RNA-RNA assembly, with the following results: (1) In complexes with 5S RNA, the highly basic N-terminal region of L18 is accessible to trypsin. This accessibility is unaffected by L25. However, its presence is essential for stimulating L5 binding. (2) In 5S RNA-protein-23S RNA complexes proteins L5 and L18 are both strongly resistant to proteolysis. (3) No 5S RNA-23S RNA complex formation occurs in the presence of L5 and the C-terminal L18 fragment. Two possible models for the mechanism of RNA-RNA assembly are proposed.     

Small Ribosomal Ribonucleic Acid Species of Saccharomyces cerevisiae

Yeast ribosomes contain two small molecular-weight species of ribonucleic acid (RNA), in addition to transiently associated transfer RNA. The 5S RNA species is part of the large ribosomal subunit and appears to be exactly the same size as 5S RNA from other organisms. There is another RNA molecule, approximately 5.8S or 150 nucleotides in size, which is noncovalently attached to the 25S ribosomal RNA and can be freed by gentle heating or urea treatment. Neither 5 nor 5.8S RNA are methylated. The 5.8S RNA is probably derived from a part of the 35S precursor RNA, whereas the 5S RNA is made de novo. These results substantiate the notion that ribosome biosynthesis in yeast is analogous to that of the higher eukaryotes.     

Accumulation and specific cleavage of 5S RNA in the isthmus of laying hen oviduct. Evidence for three chicken 5S RNA

RNA extracts from the isthmus of laying hen oviduct contain truncated 5S RNA molecules that were found to be shorter at their 5' terminus as compared to native 5S RNA I and II. Moreover one of the truncated species differs from 5S RNA I by the absence of the 3' end nucleotide. The truncated forms increase of about 70% the total 5S RNA (intact + truncated) in the isthmus, as compared to the other studied tissues. Furthermore 5S RNA I is heterogeneous: 25% have A instead of U at the 3' end, and some evidence was obtained for the existence of two 5S RNA I conformers.     

RNA-protein interactions of stored 5S RNA with TFIIIA and ribosomal protein L5 during Xenopus oogenesis

We studied the pathway of 5S RNA during oogenesis in Xenopus laevis from its storage in the cytoplasm to accumulation in the nucleus, the sequence requirements for the 5S RNA to follow that pathway, and the 5S RNA-protein interactions that occur during the mobilization of stored 5S RNA for assembly into ribosomes. In situ hybridization to sections of oocytes indicates that 5S RNA first becomes associated with the amplified nucleoli during vitellogenesis when the nucleoli are activity synthesizing ribosomal RNA and assembling ribosomes. When labeled 5S RNA is microinjected into the cytoplasm of stage V oocytes, it migrates into the nucleus, whether microinjected naked or complexed with the protein TFIIIA as a 7S RNP storage particle. During vitellogenesis, a nonribosome bound pool of 5S RNA complexed with ribosomal protein L5 (5S RNPs) is formed, which is present throughout the remainder of oogenesis. Immunoprecipitation assays on homogenates of microinjected oocytes showed that labeled 5S RNA can become complexed either with L5 or with TFIIIA. Nucleotides 11 through 108 of the 5S RNA molecule provide the necessary sequence and conformational information required for the formation of immunologically detectable complexes with TFIIIA or L5 and for nuclear accumulation. Furthermore, labeled 5S RNA from microinjected 7S RNPs can subsequently become associated with L5. Such labeled 5S RNA is found in both 5S RNPs and 7S RNPs in the cytoplasm, but only in 5S RNPs in the nucleus of microinjected oocytes. These data suggest that during oogenesis a major pathway for incorporation of 5S RNA into nascent ribosomes involves the migration of 5S RNA from the nucleus to the cytoplasm for storage in an RNP complex with TFIIIA, exchange of that protein association for binding with ribosomal protein L5, and a return to the nucleus for incorporation into ribosomes as they are being assembled in the amplified nucleoli.