Pinhal, Danillo; Yoshimura, Tatiana S.; Araki, Carlos S.; Martins, Cesar
Fonte: Biomed Central Ltd.Publicador: Biomed Central Ltd.
Tipo: Artigo de Revista CientíficaFormato: 14
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Background: Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates.Results: We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms...
We have developed a system to transcribe the yeast 5S rRNA gene in the absence of the transcription factor TFIIIA. A long transcript was synthesized both in vitro and in vivo from a hybrid gene in which the tRNA-like promoter sequence of the RPR1 gene was fused to the yeast 5S RNA gene. No internal initiation directed by the endogenous 5S rDNA promoter or any processing of the hybrid transcript was observed in vitro. Yeast cells devoid of transcription factor TFIIIA, which, therefore, could not synthesize any 5S rRNA from the endogenous chromosomal copies of 5S rDNA, could survive if they carried the hybrid RPR1-5S construct on a multicopy plasmid. In this case, the only source of 5S rRNA was the precursor RPR1-5S transcript that gave rise to two RNA species slightly larger than wild-type 5S rRNA. This establishes that the only essential function of TFIIIA is to promote the synthesis of 5S rRNA. However, cells devoid of TFIIIA and surviving with these two RNAs grew more slowly at 30 degrees C compared with wild-type cells and were thermosensitive at 37 degrees C.
Endotoxin has long been implicated as an inducer for the development and progression of gram-negative sepsis. Accordingly, antiendotoxin therapy has been considered one of the major targets for the treatment of sepsis. To investigate the influence of a human immunoglobulin G (IgG) derivative, the 5S fragment of IgG (5S-IgG; Gamma-Venin, Centeon Pharma GmbH, Frankfurt-Niederrad, Germany), on endotoxin release during bacterial proliferation and under antibiotic bactericidal action, time-kill studies were performed by using Escherichia coli ATCC 25922 starting inocula of 10(3), 10(5), and 10(7) CFU/ml with cefotaxime (120 microg/ml) alone and in combination with 5S-IgG (2,100 microg/ml). Samples were collected for bacterial colony count and endotoxin concentration determinations; the area under the free endotoxin concentration curve (AUFEC) was calculated by using the trapezoidal rule. Colony counts showed that cefotaxime had a rapid bactericidal effect because it achieved greater than a 4-log decrease in the numbers of E. coli CFU per milliliter over the first 2 h; the addition of 5S-IgG did not appear to alter the kinetics of killing. Comparison of the AUFEC revealed that the addition of 5S-IgG resulted in a mean reduction of 50, 66...
In the Arabidopsis accession Columbia, 5S rDNA is located in the pericentromeric heterochromatin of chromosomes 3, 4, and 5. Both a major and some minor 5S rRNA species are expressed from chromosomes 4 and 5, whereas the genes on chromosome 3 are not transcribed. Here, we show that 5S rDNA methylation is reduced in 2-day-old seedlings versus 4-day-old or older aerial plant tissues, and the minor 5S rRNA species are expressed most abundantly at this stage. Similarly, when 5S rDNA is demethylated by 5-azacytidine treatment or via the decrease in DNA methylation1 (ddm1) mutation, the expression of minor 5S rRNA species is increased. We also show that in leaf nuclei of mature wild-type plants, the transcribed fraction of 5S rDNA forms loops that emanate from chromocenters. These loops, which are enlarged in nuclei of mature ddm1 plants, are enriched for histone H3 acetylated at Lys-9 and methylated at Lys-4 compared with the heterochromatic chromocenters. Up to 4 days after germination, heterochromatin is not fully developed: the 5S rDNA resides in prechromocenters, does not form conspicuous loops, and shows the lowest transcription level. Our results indicate that the expression and chromatin organization of 5S rRNA genes change during heterochromatin establishment.
In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in lambda gt for 5S rRNA genes whose flanking sequences differed from those adjacent to 5S rRNA genes of the rDNA repeat. Three variant 5S rRNA genes were isolated on the basis of such dissimilarity to rDNA repeat sequences. They display a remarkable conservation of their DNA in the vicinity of the 5S coding region, and are examples of a minor form of 5S rRNA coding sequence present in a small number of copies in the yeast genome. These variant sequences appear to be transcribed as efficiently as 5S rRNA genes of the rDNA repeat. In one of our isolates of the variant sequence a Ty transposable element is inserted 145bp upstream of the initiation point for 5S rRNA synthesis.
In order to study the binding of the eukaryotic transcription factor IIIA to heterologous 5S rRNAs with a low degree of overall sequence conservation (less than 20%) we have utilized a transcription competition assay involving eubacterial, archaebacterial and eukaryotic 5S rRNAs. All the molecules inhibit Xenopus 5S rRNA transcription specifically, which suggests that only a small amount of specific conserved RNA sequences, if indeed any, are essential for the interaction of the transcription factor with the 5S rRNA molecule, whereas universal 5S rRNA secondary structure elements seem to be required. A fragment of Xenopus laevis oocyte 5S rRNA (nucleotides 41-120), which partially maintains the original 5S rRNA structure, also competes for TF III A. In vitro transcription of a naturally occurring mutant of the Xenopus laevis oocyte 5S rRNA gene, the pseudogene, which carries several point mutations within the TF III A binding domain is equally inhibited by exogenous Xenopus 5S rRNA.
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.
Previtellogenic oocytes of Triturus cristatus accumulate a free cytoplasmic RNP which sediments at 40S and contain 5S RNA and tRNA in association with two proteins of MW 45,000 and 39,000 daltons (P45 and P39). The 40S particle has a buoyant density of 1.53 g . cm-3 in CsCl and consists of four identical RNP subunits. Each monomeric subunit contains one molecule of 5S RNA, three molecules of tRNA, two molecules of P45 and one molecule of P39. The 40S particle can be completely dissociated by SDS treatment into its individual components, and the subunits, and even the complete 40S particle, can be reformed by removal of SDS in the presence of 0.2 M NaCl. RNA/protein binding experiments with isolated components, and analysis of reformed RNP complexes in CsCl gradients, demonstrate that the stable interactions are: 5S RNA/P45, 3(tRNA)/P45, 5S RNA/P39 and 5S RNA/P45/P39. Immunological studies show that P45 has also a nuclear location and may bind to the 5S RNA transcript in the chromatin, whereas P39 is predominantly cytoplasmic and is possibly related to proteins associated with 5S RNA in the ribosomal 60S subunit. It is suggested that the 40S RNP particle not only stores 5S RNA and tRNA but also provides a means for the exchange of the 5S RNA transcript binding protein (P45) for the 5S RNA ribosome associated protein (P39).
4.5S RNAH (4.5S RNA associated with poly A containing RNA) has extensive homology to major interspersed repeat B1 in rodent genomes. We developed a new cloning technique for screening genomic library that eliminates the signal produced by repeated sequences or pseudogenes and applied it to cloning of 4.5S RNAH genes. Six phage clones (2, 3, 6, 9, 10 and 15) which hybridize with 4.5S RNAH were isolated from a rat gene library by this method. The restriction fragments containing the 4.5S RNAH locus were subcloned into plasmids and sequenced. Clones 2, 3, 9 and 15 contained one to five base substitutions in the coding region for 4.5S RNAH and were probably pseudogenes. In clone 2, the 4.5S RNAH locus was linked directly with the identifier sequence. Clone 6 contained three copies of the 4.5S RNAH gene (6a, b and c) which were clustered in the same direction within 455 base pairs. 6b was linked directly with 6c and ubiquitous repetitive DNA sequences B2 were inserted immediately after 6a and 6c. These three sequences as well as the sequence in clone 10 were colinear with rat 4.5S RNAH. In an in vitro transcription system, only clone 10 gave intact 4.5S RNAH.
We describe the chromosomal organization of the major oocyte and somatic 5S RNA genes of Xenopus laevis in chromatin isolated from erythrocyte nuclei. Both major oocyte and somatic 5S DNA repeats are associated with nucleosomes; however, differences exist in the organization of chromatin over the oocyte and somatic 5S RNA genes. The repressed oocyte 5S RNA gene is protected from nuclease digestion by incorporation into a nucleosome, and the entire oocyte 5S DNA repeat is assembled into a loosely positioned array of nucleosomes. In contrast, the potentially active somatic 5S RNA gene is accessible to nuclease digestion, and the majority of somatic 5S RNA genes appear not to be incorporated into positioned nucleosomes. Evidence is presented supporting the stable association of transcription factors with the somatic 5S RNA genes. Histone H1 is shown to have a role both in determining the organization of nucleosomes over the oocyte 5S DNA repeat and in repressing transcription of the oocyte 5S RNA genes.
About 100 genes coding for 5S RNA in Neurospora crassa are dispersed throughout the genome (Selker et al., Cell 24:815-818, 1981; R. L. Metzenberg, J. N. Stevens, E. U. Selker, and E. Morzycka-Wroblewska, manuscript in preparation). The majority of them correspond to the most abundant species (alpha) of 5S RNA found in the cell. Gene conversion, gene transposition, or both may be responsible for the maintenance of sequence homogeneity (concerted evolution) of alpha-type 5S genes. To explore these possibilities, we isolated and characterized separate 5S regions from two distantly related laboratory strains of N. crassa. Restriction and sequence analyses revealed no differences in molecular location of allelic 5S genes between the two strains. However, the DNA sequences around the 5S genes are ca. 10% divergent. We concluded that transposition is not frequent enough to account for the concerted evolution of N. crassa alpha-5S genes. In contrast to sequence divergence in the flanking regions between the two strains, the 5S transcribed regions are identical (with one exception), suggesting that these genes are being corrected. We have found that flanking sequences of various N. crassa 5S genes within each strain are largely different. Thus...
In Xenopus laevis there are two multigene families of 5S RNA genes: the oocyte-type 5S RNA genes which are expressed only in oocytes and the somatic-type 5S RNA genes which are expressed throughout development. The Xenopus 5S RNA replication-expression model of Gottesfeld and Bloomer (Cell 28:781-791, 1982) and Wormington et al. (Cold Spring Harbor Symp. Quant. Biol. 47:879-884, 1983) predicts that the somatic-type 5S RNA genes replicate earlier in the cell cycle than do the oocyte-type genes. Hence, the somatic-type 5S RNA genes have a competitive advantage in binding the transcription factor TFIIIA in somatic cells and are thereby expressed to the exclusion of the oocyte-type genes. To test the replication-expression model, we determined the order of replication of the oocyte- and somatic-type 5S RNA genes. Xenopus cells were labeled with bromodeoxyuridine, stained for DNA content, and then sorted into fractions of S phase by using a fluorescence-activated cell sorter. The newly replicated DNA containing bromodeoxyuridine was separated from the lighter, unreplicated DNA by equilibrium centrifugation and was hybridized with DNA probes specific for the oocyte- and somatic-type 5S RNA genes. In this way we found that the somatic-type 5S RNA genes replicate early in S phase...
DNA containing the multiple genes for 5S RNA has been isolated from the genome of Xenopus laevis. Whereas 5S RNA is about 57% G + C, the 5S DNA has a base composition of about 33-35% GC and consists of two alternating regions that differ in base composition by at least 20% GC. A denaturation map of 5S DNA analyzed by electron microscopy demonstrates that the repeating pattern is regular and each repeating unit has a mass of about 500,000 daltons. If one gene for 5S RNA (84,000 daltons native) were present in each repeat, it should comprise about 16.8% of 5S DNA. This arrangement is confirmed, since 6.8% of pure 5S DNA (13.6% of its base pairs) hybridized with 5S RNA. The remaining 83% of each repeating unit is considered to be “spacer” DNA. The 5S RNA hybridizes with about 0.05% of the bulk DNA of X. laevis, so that 5S DNA comprises about 0.7% of the total nuclear DNA. This is equivalent to about 24,000 repeating units for each haploid complement of DNA. These repeats are highly clustered; as many as 86 have been visualized along a single DNA molecule.
Single and multiple repeating units of three types of Xenopus 5S DNA recombined with the plasmid pMB9 serve as templates for the accurate synthesis of 5S RNA after their injection into Xenopus laevis oocyte nuclei. All 15 cloned single repeating units of X. laevis oocyte 5S DNA that were tested supported 5S RNA synthesis. Three cloned fragments of X. borealis oocyte 5S DNA and one cloned single repeating unit of X. borealis somatic 5S DNA were templates for 5S RNA synthesis. We conclude that the majority of repeating units of 5S DNA in these multigene families contain the information for accurate initiation and termination of 5S RNA synthesis. The ability of this system to detect sequence changes that affect transcription is demonstrated.
5S rRNA is an integral component of the large ribosomal subunit in virtually all living organisms. Polyamine binding to 5S rRNA was investigated by cross-linking of N1-azidobenzamidino (ABA)-spermine to naked 5S rRNA or 50S ribosomal subunits and whole ribosomes from Escherichia coli cells. ABA-spermine cross-linking sites were kinetically measured and their positions in 5S rRNA were localized by primer extension analysis. Helices III and V, and loops A, C, D and E in naked 5S rRNA were found to be preferred polyamine binding sites. When 50S ribosomal subunits or poly(U)-programmed 70S ribosomes bearing tRNAPhe at the E-site and AcPhe-tRNA at the P-site were targeted, the susceptibility of 5S rRNA to ABA-spermine was greatly reduced. Regardless of 5S rRNA assembly status, binding of spermine induced significant changes in the 5S rRNA conformation; loop A adopted an apparent ‘loosening’ of its structure, while loops C, D, E and helices III and V achieved a more compact folding. Poly(U)-programmed 70S ribosomes possessing 5S rRNA cross-linked with spermine were more efficient than control ribosomes in tRNA binding, peptidyl transferase activity and translocation. Our results support the notion that 5S rRNA serves as a signal transducer between regions of 23S rRNA responsible for principal ribosomal functions.
We have examined the association, dissociation, and exchange of the 5S specific transcription factor (TFIIIA) with somatic- and oocyte-type 5S DNA. The factor associates faster with somatic than with oocyte 5S DNA, and the rate of complex formation is accelerated by vector DNA. Once formed, the TFIIIA-5S DNA complex is stable for greater than 4 h in the absence of free 5S DNA, and its dissociation is identical for somatic and for oocyte 5S DNA. In the presence of free 5S DNA, the factor transfers promptly from the complex to the free 5S DNA site. Unexpectedly, the direct exchange of factor between 5S DNA sites leads to proteolysis at the C-terminal arm of TFIIIA.
RNA import into mitochondria is a widespread phenomenon. Studied in details for yeast, protists, and plants, it still awaits thorough investigation for human cells, in which the nuclear DNA-encoded 5S rRNA is imported. Only the general requirements for this pathway have been described, whereas specific protein factors needed for 5S rRNA delivery into mitochondria and its structural determinants of import remain unknown. In this study, a systematic analysis of the possible role of human 5S rRNA structural elements in import was performed. Our experiments in vitro and in vivo show that two distinct regions of the human 5S rRNA molecule are needed for its mitochondrial targeting. One of them is located in the proximal part of the helix I and contains a conserved uncompensated G:U pair. The second and most important one is associated with the loop E-helix IV region with several noncanonical structural features. Destruction or even destabilization of these sites leads to a significant decrease of the 5S rRNA import efficiency. On the contrary, the β-domain of the 5S rRNA was proven to be dispensable for import, and thus it can be deleted or substituted without affecting the 5S rRNA importability. This finding was used to demonstrate that the 5S rRNA can function as a vector for delivering heterologous RNA sequences into human mitochondria. 5S rRNA-based vectors containing a substitution of a part of the β-domain by a foreign RNA sequence were shown to be much more efficiently imported in vivo than the wild-type 5S rRNA.
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.
The maturation of 5S RNA in Escherichia coli is poorly understood. Although it is known that large precursors of 5S RNA accumulate in mutant cells lacking the endoribonuclease-RNase E, almost nothing is known about how the mature 5' and 3' termini of these molecules are generated. We have examined 5S RNA maturation in wild-type and single- or multiple-exoribonuclease-deficient cells by Northern blot and primer-extension analysis. Our results indicate that no mature 5S RNA is made in RNase T-deficient strains. Rather, 5S RNA precursors containing predominantly 2 extra nucleotides at the 3' end accumulate. Apparently, these 5S RNAs are functional inasmuch as mutant cells are viable, growing only slightly slower than wild type. Purified RNase T can remove the extra 3' residues, showing that it is directly involved in the trimming reaction. In contrast, mutations affecting other 3' exoribonucleases have no effect on 5S RNA maturation. Approximately 90% of the 5S RNAs in both wild-type and RNase T- cells contain mature 5' termini, indicating that 5' processing is independent of RNase T action. These data identify the enzyme responsible for generating the mature 3' terminus of 5S RNA molecules and also demonstrate that a completely processed 5S RNA molecule is not essential for cell survival.
Nietfeld, W; Digweed, M; Mentzel, H; Meyerhof, W; Köster, M; Knöchel, W; Erdmann, V A; Pieler, T
Fonte: PubMedPublicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 26/09/1988EN
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We have investigated the structure of oocyte and somatic 5S ribosomal RNA and of 5S RNA encoding genes in Xenopus tropicalis. The sequences of the two 5S RNA families differ in four positions, but only one of these substitutions, a C to U transition in position 79 within the internal control region of the corresponding 5S RNA encoding genes, is a distinguishing characteristic of all Xenopus somatic and oocyte 5S RNAs characterized to date, including those from Xenopus laevis and Xenopus borealis. 5S RNA genes in Xenopus tropicalis are organized in clusters of multiple repeats of a 264 base pair unit; the structural and functional organization of the Xenopus tropicalis oocyte 5S gene is similar to the somatic but distinct from the oocyte 5S DNA in Xenopus laevis and Xenopus borealis. A comparative sequence analysis reveals the presence of a strictly conserved pentamer motif AAAGT in the 5'-flanking region of Xenopus 5S genes which we demonstrate in a separate communication to serve as a binding signal for an upstream stimulatory factor.