In vitro synthesis of a 5S RNA precursor by isolated nuclei of rat liver and HeLa cells

Cerastodermaglaucum5S ribosomal DNA: characterization of the repeat unit, divergence with respect toCerastoderma edule, and PCR–RFLPs for the identification of both cockles

The 5S rDNA repeat unit of the cockle Cerastoderma glaucum from the Mediterranean and Baltic coasts was PCR amplified and sequenced. The length of the units was 539–568 bp, of which 120 bp were assigned to the 5S rRNA gene and 419–448 bp to the spacer region, and the G/C content was 46%–49%, 54%, and 44%–47%, respectively. Two types of units (A and B), differing in the spacer, were distinguished based on the percentage of differences and clustering in phylogenetic trees. A PCR assay with specific primers for each unit type indicated that the occurrence of both units is not restricted to the sequenced individuals. The 5S rDNA units of C. glaucum were compared with new and previously reported sequences of Cerastoderma edule. The degree of variation observed in C. edule was lower than that in C. glaucum and evidence for the existence of units A and B in C. edule was not found. The two cockles have the same coding region but displayed numerous fixed differences in the spacer region and group separately in the phylogenetic trees. Digestion of the 5S rDNA PCR product with the restriction enzymes HaeIII and EcoRV revealed two RFLPs useful for cockle identification.Key words: Cerastoderma, cockle identification, 5S ribosomal DNA, nontranscribed spacer variation, PCR-RFLP.

Ischemia induces early expression of a new transcription factor (6A3-5) in kidney vascular smooth muscle cells: studies in rat and human renal pathology

Acute renal failure, characterized by rapid decline in glomerular filtration rate, is a major cause of morbidity and mortality. During the evolution of renal diseases chronic ischemia develops. Indeed, acute or chronic renal failure may occur as a result of renal ischemia, which induces cells to dedifferentiate, proliferate, or become apoptotic. In this study, we have investigated the expression of a newly identified transcription factor, 6A3-5, under in vitro and in vivo conditions. Proliferating vascular smooth muscle were investigated in response to different mitogenic agents. The 6A3-5 expression was then studied in ischemic rat kidney, induced by renal pedicle clamping, followed, or not, by reperfusion. Subsequently human renal biopsies from early kidney grafts and chronic renal diseases were also investigated for 6A3-5 protein expression by immunohistochemistry. In vitro study shows an over-expression of 6A3-5 following 2 to 4 hours stimulation by serum or Angiotensin II, of rat proliferating aortic smooth muscle cell. Moreover, in vivo study shows that this new protein is over expressed in rat kidney submitted to 45 minutes ischemia. An anti-6A3-5 antibody shows the protein to be expressed in smooth muscle cells of the arterioles and intermediate size arteries, in mesangial cells and interstitial myofibroblasts. In human biopsies of early kidney grafts and renal disease, the same up-regulation of 6A3-5, as in acute ischemic situation, is observed. This 6A3-5 expression is intimately associated with alpha-smooth muscle cell actin expression in mesangial cells, arteriolar smooth muscle cells as well as interstitial myofibroblasts. Transcription factor 6A3-5 could potentially be a novel early vascular marker of acute and chronic renal ischemic stress implicated in tissue remodeling.

Ribosomal 5 S rRNA maturation in Saccharomyces cerevisiae

The maturation of the ribosomal 5 S RNA in Saccharomyces cerevisiae is examined based on the expression of mutant 5 S rRNA genes, in vivo, and a parallel analysis of RNA processing, in vitro. Both types of analysis indicate that 5 S rRNA processing is not dependent on the nucleotide sequence of either the external transcribed spacer or the mature 5 S rRNA. The results further indicate the RNA is processed by an exonuclease activity which is limited primarily or entirely by helix I, the secondary structure formed between the mature and interacting termini. The 5 S RNA binding protein (YL3) also appears not to influence directly the maturation process, but rather to play a role in protecting the rRNA from further degradation by "housekeeping" nucleases. Taken together, the results continue to support a "quality control" function which helps to ensure that during maturation only normal precursors are processed and assembled into active ribosomes.

Termination as a factor in "quality control" during ribosome biogenesis

In eukaryotes, nascent rDNA and 5 S rRNA gene transcripts undergo 3'-end processing after termination. Mutations in which terminator sequences in these ribosomal RNA genes are deleted completely result in highly unstable transcripts, which are not properly processed and integrated into stable ribosome structure. Mutations that retard RNA processing by extending the 3' external transcribed spacer or by introducing additional secondary structure in the spacers have a similar effect on stable transcript integration. The results indicate that proper termination coupled with efficient rRNA processing acts as a "quality control" process, which helps to ensure that only normal rRNA precursors are effectively processed and assembled into active ribosomes.

A 3' exonuclease activity degrades the pseudogene 5S RNA transcript and processes the major oocyte 5S RNA transcript in Xenopus oocytes

Transcription of the major oocyte 5S RNA gene (o) and pseudogene (psi) of Xenopus laevis yields different RNAs with three different homologous systems: oocyte microinjection, whole oocyte extract, and fractionated TFIIIA + TFIIIB + TFIIIC components. Those peculiar results are caused by a 3' RNA exonuclease activity, which is inhibited in the oocyte extract, that rapidly degrades the pseudogene 5S RNA but does not degrade as readily the chimeric RNA transcripts generated by HindIII-truncated 5S RNA pseudogenes. The same, or a similar, RNase activity processes the 130- and the 142-base-long transcripts of the major oocyte 5S RNA gene into mature 120-base-long 5S RNA. We performed site-specific mutagenesis on the somatic 5S RNA gene and changed specific nucleotides on the somatic 5S RNA. These studies indicated that the structure that confers stability to the 5S RNA in vivo and in vitro is the 9-bp helix formed in 5S RNA, but not in psi 5S RNA, by the complementary 5' and 3' ends of the molecule.

Processing of the 3' sequence extensions upon the 5S rRNA of a mutant yeast in Xenopus laevis germinal vesicle extract

A processing endonuclease acts to remove a short sequence from the 3' end of transcripts of the Saccharomyces cerevisiae 5S ribosomal RNA gene in generating the mature sequence of 5S RNA. Cells bearing the nuclear mutation rna82 .1 lack this activity and accumulate 5S forms with additional nucleotides at their 3' termini. 5S RNAs labelled during short pulse- labellings of the mutant are essentially primary transcripts that mostly have the sequence U-U-A-U-U-U-C[U-U-U-U(U-U)] added to the 3' end of normal yeast 5S RNA. They are subjected in vivo to a series of slow processing events whereby this sequence is ultimately replaced by: U-U(A)1-9 in a substantial proportion of the 5S RNA molecules of the mutant [Piper, P. W., Bellatin , J. A. and Lockheart , A. (1983) EMBO J. 2, 353-359]. In higher eukaryotes no endonuclease cleavage occurs during 5S RNA maturation, yet processing at the 3' ends of certain transcripts made by RNA polymerase III, most notably transfer RNA precursors, is still important. Since the enzymes involved in this processing have not been well characterised, we investigated how the additional sequences upon rna82 .1 yeast 5S RNA are processed in vitro in a system from a higher eukaryote that is often used for studying transcription by RNA polymerase III, the Xenopus laevis germinal vesicle extract. Our results are consistent with slow digestion of these 5S molecules by a 3'----5' exonuclease until they become 122-123 nucleotides in length, whereupon digestion ceases. This activity probably participates in the processing of certain Xenopus RNA polymerase III transcripts.

Effect of triiodothyronine (T3) on ribonucleic acid polymerase activity in developing tadpole hindlimb

Optimum conditions were studied for the determination of RNA polymerase activity in nuclei isolated from Rana catesbeiana tadpole hindlimbs. Tadpole nuclei were tested at 15 degrees C in the presence of spermidine (1.5 mM) bovine serum albumin (1.0%) and a high concentration of nucleoside triphosphates (1.0 mM). Tadpole nuclei exhibited a 60-70% higher total RNA polymerase activity with maximum activity of RNA polymerase I at 4 hr and RNA polymerase II at 8 hr after triiodothyronine injection. The results support a nuclear mechanism for the differentiation of tadpole hindlimbs induced by triiodothyronine.

Liposome-mediated insertion of intact DNA into isolated nuclei. Potential for a new in vitro transcription system

DNA molecules sequestered within negatively charged liposomes became nuclei-associated following interaction between isolated mouse plasmacytoma nuclei and liposomes. Few if any liposomes appeared to adhere to washed nuclei following their interaction with liposomes, suggesting that DNA was internalized. Liposome-delivered, radioactive pBR322 DNA re-extracted from nuclei appeared intact, whereas DNA from nuclei incubated with naked DNA was degraded. Up to 2 X 10(10) D of DNA were inserted into each nucleus. DNA delivered into nuclei via liposome was transcribed as shown by the fact that about 1% of the RNA synthesized in nuclei injected with pBR322 or E. coli DNA hybridized with moderate excess of homologous DNA. pBR322-specific RNA synthesized in isolated nuclei consisted of large MW transcripts. Experiments in which SV40 DNA and pBR322 DNA were delivered simultaneously in equimolar amounts into nuclei indicated that SV40 DNA was transcribed as efficiently as pBR322 DNA.

A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes

By Southern blotting and hybridization analysis using 32P-labeled poly(dT-dG) . poly(dC-dA) as a probe, we have found, in eukaryotic genomes, a huge number of stretches of dT-dG alternating sequence, a sequence that has been shown to adopt the Z-DNA conformation under some conditions. This sequence was found in all eukaryotic genomes examined from yeast to human, indicating extraordinary evolutionary conservation. The number of the sequence ranged from about 100 in yeast to tens of thousands in higher eukaryotes. Comparison of nucleotide sequences of dT-dG alternating regions and its flanking regions in several cloned genes showed that the repeated element [the Z(T-G) element]] consists only of dT-dG alternating sequence with variable length. The presence of another purine-pyrimidine alternating sequence was also surveyed in eukaryotic genomes by Southern blot hybridization using 32P-labeled poly(dG-dC) . poly(dG-dC) as the probe. The stretches of dC-dG alternating sequence [the Z(C-G) element] were found to be moderately repetitive in human, mouse, and salmon genomes. However, a few and no copies of the Z(C-G) element were found in yeast and calf genomes, respectively. These results provide evidence for the abundance of potential Z-DNA-forming sequences in nature.

Precursor molecules of both human 5S ribosomal RNA and transfer RNAs are bound by a cellular protein reactive with anti-La lupus antibodies

The small ribonucleoproteins recognized by anti-La autoantibodies contain a heterogeneous mixture of small RNAs from uninfected mammalian cells. The identity of many of these has now been established by the discovery of precursor forms of 5S rRNA and of certain tRNAs among La RNAs from HeLa cells. The small fraction of 5S rRNA molecules that exist as La ribonucleoproteins in vivo possess 1 or 2 additional U residues at their 3' ends. Such 5S molecules bound to the La protein have also been identified with in vitro nuclear transcription systems. Pulse-chase experiments performed both in vivo and in vitro support the idea that most newly synthesized 5S rRNA molecules are transiently associated with the La protein. Cell extracts contain a processing activity that converts longer in vitro-synthesized 5S RNA transcripts into molecules of mature size. The presence of in vivo tRNA precursors in the heterogeneous mixture of La RNAs is demonstrated by the identification of precursor forms of five different specific tRNAs (Meti, Asp, Gly, Glu, Asn). After in vitro transcription of a tRNA gene (tRNAiMet), only products the size of precursor molecules are precipitable by anti-La antibodies. The realization that virtually every known RNA polymerase III product associates at least initially with the La antigen suggests that this protein plays an essential role in the synthesis or maturation of all class III transcripts.

In vitro transcription of cloned 5S RNA genes of the newt Notophthalmus

Recombinant plasmids that carried genes coding for 5S ribosomal RNA of the newt, Notophthalmus viridescens, were transcribed in vitro with extracts of Xenopus laevis oocyte nuclei. Plasmids containing multiple repeats of the 5S gene and spacer directed accurate transcription of 5S RNA (120 bases). Individual repeat units were recloned by inserting Sau 3A restriction fragments into the Bam HI site of plasmid pBR322. Because each repeat was cut by the enzyme within the coding region, the inserts had incomplete coding regions at their ends and spacer sequences in the middle. The DNA of these subclones directed synthesis of a 5S-size RNA that contained both plasmid and 5S RNA sequences. Transcription initiated in the vector, proceeded through the gene segment coding for nucleotides 41-120, and terminated at the end of the gene. The initiation of in vitro transcription required neither the original 5' flanking sequences of the spacer nor the first third of the gene. We conclude that intragenic DNA sequences control the initiation of transcription. Other subclones that include pseudogenes gave rise to some transcripts 156 nucleotides long. These long transcripts represented continuation of transcription through the 36-base-pair pseudogene that is located immediately downstream from the 5S gene. However, most transcripts of these subclones terminated at the end of the normal gene before the beginning of the pseudogene. It is probable that a run of four or more Ts serves as part of the termination signal.

Intracellular distribution of low molecular weight RNA species in HeLa cells

Intracellular distributions of the low molecular weight RNA species of HeLa cells were determined by a nonaqueous method of cell fractionation, in which lyophilized cells were homogenized and centrifuged in anhydrous glycerol. The nonaqueous method was used to avoid artifactual extraction of weakly bound nuclear RNA during cell fractionation. We found that the mature small RNA species K, A, C, and D were almost entirely (greater than 95%) nuclear, and that mature 4S tRNA was partially (5-10%) nuclear. Our results gave higher nuclear content of the mature species K, A, C, and 4S than was shown previously with conventional aqueous cell fractionation. The nonaqueous method also gave higher nuclear proportions of some short-lived precursors to mature small RNAs. We found that approximately one-half of recently synthesized pre-4S RNA and more than one-half of recently synthesized 5S RNA were nuclear, whereas these species had been thought to be cytoplasmic from previous work. The species C' and D', precursors to the stable nuclear species C and D respectively, were found to be partially nuclear, also in contrast to earlier work. The stable cytoplasmic species L (oncornavirus 7S RNA) was found to be mostly nuclear shortly after synthesis.

Structure of the 5-S ribosomal RNA gene and its adjacent regions in Torulopsis utilis

A DNA segment spanning one repeating unit of ribosomal RNA(rRNA) genes in a yeast strain, Torulopsis utilis, has been cloned on a bacterial plasmid pBR322. The size of the cloned segment was about Mr = 8.0 x 10(6). All of the genes for the four species of rRNA were linked on it, and there was a long spacer between the 5-S and 18-S rRNA coding regions. The nucleotide sequences of the regions flanking the 5-S rRNA gene were determined and compared with those in the corresponding regions of Sacharomyces cerevisiae [Valenzuela, P., Bell, G. I., Masiarz, F. R., DeGennaro, L. J., and Rutter, W. J. (1977) Nature, 267, 641-643; Maxam A. M., Tizard, R., Skryabin, K. G., and Gilbert, W. (1977) Nature, 267, 643-645]. The sequence of the T. utilis 5-S rRNA is identical with that of S. cerevisiae except for two residues at positions 18 and 61. However, its upstream region contained a quite different sequence, and a sequence which showed some homology was only found at positions -21 to -28. The sequences were d(T-G-T-A-A-C-C-T) in T. utilis and d(T-A-T-C-A-C-C-T) in S. cerevisiae. Although the presence of various repeat sequences having the same or opposite directions was noted, these repeats occurred at different positions in the two yeast species. In the downstream region, the common sequence was only seven dT deoxynucleotides, which occurred immediately after the 5-S rRNA coding sequence. Significant direct and inverted repeat sequences were found in T. utilis, but such repeats are not seen in S. cerevisiae.

Transcription of a cloned Bombyx mori tRNA2Ala gene: nucleotide sequence of the tRNA precursor and its processing in vitro

We have analyzed the transcription of a cloned silkworm tRNA2Ala gene in germinal vesicle extracts of X. laevis oocytes. The primary transcript was sequenced; it is 98 nucleotides long, beginning with a 5' triphosphate nucleotide and ending in a 3' oligouridine stretch. After transcription for long periods of time, enzymes in the frog extract also process the tRNA2Ala precursor to remove extra 5' and 3' nucleotides and to add a CCA end. The twenty-two extra nucleotides at the 3' end of this precursor are recovered as an intact fragment, implicating a new site of endoribonuclease cleavage in eucaryotic tRNA processing. This enzyme activity has also been demonstrated by reincubation of isolated pre-tRNA2Ala with a germinal vesicle extract. The products of in vitro cleavage are the same as those seen in the transcription reactions. The tRNA2Ala precursor molecules are made faithfully in the system with as few as 6 bp of Bombyx morti DNA upstream of the transcription initiation site of the tRNA2Ala gene. This result narrows down the minimal amount of DNA adjacent to the 5' end of a eucaryotic tRNA gene needed to support proper initiation by RNA polymerase III.