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At least 109 records · Page 6Linked to original sources

PubMed1994

The dynamic conformation of plant cytoplasmic 5S rRNAs.

Recently we have proposed a new three-dimensional model of plant 5S rRNAs structure. To verify this proposal we present here new data on RNase T1 digestion and hydroxyl radical hydrolysis of lupin and wheat germ 5S rRNAs at various buffer and temperature conditions. Interestingly, the guanosine residues 85-87 in the loop D of these RNAs, are resistant to RNase T1 at native but not at denaturating conditions. On the other hand, the reaction of 5S rRNA with the hydroxyl radicals showed different reactivity of many nucleotides in various parts of the molecule and suggest conformational changes, which occur mostly in the loops. The experimental data clearly support involvement of the nucleotides occupying conserved positions in the loops in the tertiary interactions in plant 5S rRNA structure.

Base Sequence↗

PubMed1995

Susceptibility mutations in the mitochondrial small ribosomal RNA gene in aminoglycoside induced deafness.

Aminoglycoside induced deafness has been linked recently to a predisposing homoplasmic mutation in the 3' end of the small ribosomal RNA (rRNA) gene of the human mitochondria (1555 A-->G) that makes the mitochondrial rRNA structurally more similar to its bacterial counterpart. This mitochondrial DNA mutation was consistently found in families in which the susceptibility to develop ototoxic deafness was inherited through the maternal lineage. However, the 1555 A-->G mutation was rarely found in sporadic patients in China, where a significant proportion of the population has been exposed to aminoglycosides. To further characterize the mutations predisposing to aminoglycoside ototoxicity, we analysed the 12S rRNA gene in 35 Chinese sporadic patients without the 1555 A-->G mutation. Using single stranded conformational polymorphism (SSCP) analysis, heteroduplex (HD) analysis, sequencing, and allele specific oligonucleotide hybridization, we found three out of 35 sporadic patients with unique sequence changes in the 12S rRNA gene. Two of the patients had homoplasmic mutations. One patient displayed localized heteroplasmy around nt 961, with an absence of the thymidine at this position and different populations of mitochondrial DNA with varying numbers of inserted cytosines. The description of these putative susceptibility mutations, in particular the heteroplasmic mutation around nt 961, provides further support for the important role of the mitochondrial 12S rRNA in genetic predisposition to aminoglycoside induced ototoxic deafness.

Aminoglycosides↗

PubMed1981

The structure of the yeast ribosomal RNA genes. 3. Precise mapping of the 18 S and 25 S rRNA genes and structure of the adjacent regions.

The 5'-terminal of Saccharomyces cerevisiae 18 S and 25 S rRNA are precisely mapped within the sequence of the rDNA repeating unit. The 3'-terminal of 25 S rRNA and 37 S pre-rRNA are located within a 548 bp segment of the rDNA repeating unit by the use of a DNA polymerase I extension technique. The analysis of the rDNA sequences at the structural gene boundaries reveals the presence of oligonucleotide repeats which may be involved in transcription or processing control mechanisms. The sequence of rDNA in the transcription termination region is determined and possible mechanisms shaping the 3'-end of 25 S rRNA are discussed.

Base Sequence↗

PubMed1996

The phylogeny of intestinal porcine spirochetes (Serpulina species) based on sequence analysis of the 16S rRNA gene.

Four type or reference strains and twenty-two field strains of intestinal spirochetes isolated from Swedish pig herds were subjected to phylogenetic analysis based on 16S rRNA sequences. Almost complete (>95%) 16S rRNA sequences were obtained by solid-phase DNA sequencing of in vitro-amplified rRNA genes. The genotypic patterns were compared with a previously proposed biochemical classification scheme, comprising beta-hemolysis, indole production, hippurate hydrolysis, and alpha-galactosidase, alpha-glucosidase, and beta-glucosidase activities. Comparison of the small-subunit rRNA sequences showed that the strains of the genus Serpulina were closely related. Phylogenetic trees were constructed, and three clusters were observed. This was also confirmed by signature nucleotide analysis of the serpulinas. The indole-producing strains, including the strains of S. hyodysenteriae and some weakly beta-hemolytic Serpulina strains, formed one cluster. A second cluster comprised weakly beta-hemolytic strains that showed beta-galactosidase activity but lacked indole production and hippurate-hydrolyzing capacity. The second cluster contained two subclusters with similar phenotypic profiles. A third cluster involved strains that possessed a hippurate-hydrolyzing capacity which was distinct from that of the former two clusters, because of 17 unique nucleotide positions of the 16S rRNA gene. Interestingly, the strains of this third cluster were found likely to have a 16S rRNA structure in the V2 region of the molecule different from that of the serpulinas belonging to the other clusters. As a consequence of these findings, we propose that the intestinal spirochetes of this phenotype (i.e., P43/6/78-like strains) should be regarded as a separate Serpulina species. Furthermore, this cluster was found to be by far the most homogeneous one. In conclusion, the biochemical classification of porcine intestinal spirochetes was comparable to that by phylogenetic analysis based on 16S rRNA sequences..

Animals↗

PubMed2002

Mutations in the GTPase center of Escherichia coli 23S rRNA indicate release factor 2-interactive sites.

Mutations in the GTPase center of Escherichia coli 23S rRNA were characterized in vivo as UGA-specific nonsense suppressors. Some site-directed mutations did not exhibit suppressor activity and were interspersed among suppressor mutations. Our results demonstrate the involvement of the two adjacent loops of this conserved rRNA structure in UGA-dependent translation termination and, taken with previous in vitro analyses and with consideration of the crystal structure of the GTPase center RNA, indicate that nucleotides 1067, 1093, 1094, and 1095 are sites of interaction with release factor 2.

Binding Sites↗

PubMed2006

Potential regulatory elements in the Trypanosoma cruzi rRNA gene promoter.

The Trypanosoma cruzi rRNA gene promoter was characterized by deletion and point mutation analyses. A core of 89 bp was identified as the minimal region with full promoter activity. This core region is flanked upstream by a control element that stimulates its activity, and downstream by a novel down regulating region of about 200 bp. A point mutation analysis of the transcription start region evidenced 7 contiguous nucleotides where individual substitutions produced in all cases a defective promoter. It is generally accepted that the anciently speciated trypanosomatids lack strict promoters for protein coding genes transcribed by RNA polymerase II. The occurrence of a well structured rRNA gene promoter in these species suggests an early appearance of the RNA polymerase I promoters in the evolution of eukaryotic cells.

Animals↗

PubMed2004

Ribosomal protein L3: influence on ribosome structure and function.

Early studies demonstrated roles for ribosomal protein L3 in peptidyltransferase center formation and the ability of cells to propagate viruses. More recent studies have linked these two processes via the effects of mutants and drugs on programmed -1 ribosomal frameshifting. Here, we show that mutant forms of L3 result in ribosomes having increased affinities for both aminoacyl- and peptidyl-tRNAs. These defects potentiate the effects of sparsomycin, which promotes increased aminoalcyl-tRNA binding at the P-site, while antagonizing the effects anisomycin, a drug that promotes decreased peptidyl-tRNA binding at the A-site. The changes in ribosome affinities for tRNAs also correlate with decreased peptidyltransferase activities of mutant ribosomes, and with decreased rates of cell growth and protein synthesis. In vivo dimethylsulfate (DMS) protection studies reveal that small changes in L3 primary sequence also have significant effects on rRNA structure as far away as 100 A, supporting an allosteric model of ribosome function.

Allosteric Site↗

PubMed1991

Alternative secondary structures in the 5' exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA.

The natural splice junction of the Tetrahymena large ribosomal RNA is flanked by hairpins that are phylogenetically conserved. The stem immediately preceding the splice junction involves nucleotides that also base pair with the internal guide sequence of the intervening sequence during splicing. Thus, precursors which contain wild-type exons can form two alternative helices. We have constructed a series of RNAs where the stem-loop in the 5' exon is more or less stable than in the wild-type precursor, and tested them in both forward and reverse self-splicing reactions. The presence of a stable hairpin in ligated exon substrates interferes with the ability of the intervening sequence to integrate at the splice junction. Similarly, the presence of the wild-type hairpin in the 5' exon reduces the rate of splicing 20-fold in short precursors. The data are consistent with a competition between unproductive formation of a hairpin in the 5' exon and productive pairing of the 5' exon with the internal guide sequence. The reduction of splicing by a hairpin that is a normal feature of rRNA structure is surprising; we propose that this attenuation is relieved in the natural splicing environment.

Animals↗

PubMed2005

Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution.

Mitochondrial DNA (mtDNA) of multicellular animals (Metazoa) is typically a small ( approximately 16 kbp), circular-mapping molecule that encodes 37 tightly packed genes. The structures of mtDNA-encoded transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are usually highly unorthodox, and proteins are translated with multiple deviations from the standard genetic code. In contrast, mtDNA of the choanoflagellate Monosiga brevicollis, the closest unicellular relative of animals, is four times larger, contains 1.5 times as many genes, and lacks mentioned peculiarities of animal mtDNA. To investigate the evolutionary transition that led to the specific organization of metazoan mtDNA, we determined complete mitochondrial sequences from the demosponges Geodia neptuni and Tethya actinia, two representatives of the most basal animal phylum, the Porifera. We found that poriferan mtDNAs resemble those of other animals in their compact organization, lack of introns, and a well-conserved animal-like gene order. Yet, they contain several extra genes, encode bacterial-like rRNAs and tRNAs, and use a minimally derived genetic code. Our findings suggest that the evolution of the typical metazoan mtDNA has been a multistep process in which the compact genome organization and the reduced gene content were established prior to the reduction of tRNA and rRNA structures and the introduction of multiple changes of the translation code.

Amino Acid Sequence↗

PubMed1985

The chloroplast genome of Carthamus tinctorius.

A physical map of safflower (Carthamus tinctorius L.) chloroplast DNA has been generated using SalI, PstI, KpnI and HindIII restriction endonucleases. Southern blots to single and double digests by these enzymes were hybridized with 32P-dCTP nick-translated KpnI probes, which were individually isolated from agarose gels. The plastid genome was found to be circular (151 kbp), to contain a repeated sequence of about 25 kbp, and to have small and large single copy regions of approximately 20 and 81 kbp, respectively. Heterologous probes from spinach and Euglena containing psbA, rbcL, atpA or rrnA structural genes were also hybridized with such single and double restriction enzyme digests and mapped on this circular chloroplast genome. The genetic map was found to be co-linear with that of spinach and many other higher plants.

Autoradiography↗

PubMed1997

Equally parsimonious pathways through an RNA sequence space are not equally likely.

An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid. As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement and that, in at least limited cases, this conjecture can be tested experimentally.

Base Sequence↗

PubMed1996

RNA: RNA interactions in the large subunit ribosomal RNA of Euglena gracilis.

In Euglena gracilis, the cytoplasmic large subunit (LSU) rRNA is composed of 14 discrete small RNA species that must somehow interact in the functional ribosome. We have isolated native complexes of Euglena rRNA and show here that the largest of these complexes contains eight of the 14 LSU rRNA species. Several of these small rRNA species are able to associate in vitro to reform an isolated domain of LSU rRNA structure.

Animals↗

PubMed2006

The ribosomal protein L32-2 (RPL32-2) of S. pombe exhibits a novel extraribosomal function by acting as a potential transcriptional regulator.

Ribosomal proteins play important roles in stabilizing the rRNA structure to facilitate protein synthesis in ribosome. In the present study, we analyzed the potential extraribosomal function of the ribosomal protein L32-2 (RPL32-2), which was expressed by a gene clone isolated from a cDNA library of Schizosaccharomyces pombe (S. pombe). RPL32-2 fused with the GAL4 DNA-bind domain or the GAL4 transcriptional activating domain could, respectively, activate transcriptions of reporter genes in yeast strain AH109. The RPL32-2 mutants with truncation of either the N- or the C-terminal domain resulted in abolishment of this regulatory effect. The DNA binding site for RPL32-2 of S. pombe was identified by using a random oligonucleotide selection strategy and gel motility shift assay and Western blotting confirmed its binding specificity. Moreover, we found RPL32-2 was also able to interact with a to-be-identified AT sequence binding protein. These data suggest that RPL32-2 of S. pombe, besides its ribosomal function, may also act as a potential transcriptional regulator in nucleus.

Binding Sites↗

PubMed1997

A study of the dielectric properties of E. coli ribosomal RNA and proteins in solution.

The permittivity of ribosomal proteins and ribosomal RNA (rRNA) in solution was measured in the range 100 kHz to 1 GHz at four different temperatures (5, 15, 25 and 35 degrees C). The experimental dielectric relaxation was analysed by the Cole-Cole equation and, from the best-fit parameters, the average values of the dipole moment and molecular radius of the proteins were obtained. The activation enthalpy was calculated from an Arrhenius plot of the relaxation time. The energy involved in the dielectric polarization of free proteins has a magnitude of about one hydrogen bond. The data on RNA were analysed according to the Mandel model. This analysis allowed the calculation of the "subunit b" as defined by Mandel. This parameter is dependent on the temperature and therefore the relaxation time does not follow the Arrhenius law. Our data thus show that, in solution, the rRNA structure is thermally rather unstable and highly flexible.

Bacterial Proteins↗

PubMed1994

The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations.

The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G + C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other spore-forming and non-spore-forming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov.

Base Sequence↗

PubMed1991

Development and application of oligonucleotide probes for identification of Lactococcus lactis subsp. cremoris.

Lactococcus lactis subsp. cremoris is of considerable interest to the dairy industry, which relies upon the few available strains for the manufacture of cheddar cheese free of fermented and fruity flavors. The subspecies cremoris differs from related subspecies by the lack of a few phenotypic traits. Our purpose was to identify unique rRNA sequences that could be used to discriminate L. lactis subsp. cremoris from related subspecies. The 16S rRNAs from 13 Lactococcus strains were partially sequenced by using reverse transcriptase to identify domains unique to L. lactis subsp. cremoris. All five strains of the subspecies cremoris had a unique base sequence in a hypervariable region located 70 to 100 bases from the 5' terminus. In this region, all L. lactis subsp. lactis biovar diacetylactis strains examined had a sequence identical to that of L. lactis subsp. lactis 7962, which was different from other strains of the subspecies lactis by only one nucleotide at position 90 (Escherichia coli 16S rRNA structural model) (J. Brosius, J. L. Palmer, J. P. Kennedy, and H. F. Noller, Proc. Natl. Acad. Sci. USA 75:4801-4805, 1978). Oligonucleotide probes specific for the genus Lactococcus (212RLa) and for the subspecies cremoris (68RCa) were synthesized and evaluated by hybridization to known rRNAs as well as fixed whole cells. Efficient and specific hybridization to the genus-specific probe was observed for the 13 Lactococcus strains tested. No hybridization was seen with the control species. All five strains of the subspecies cremoris hybridized to the subspecies-specific probe.

Base Sequence↗

PubMed2001

Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing.

Dbp2p, a member of the large family of DEAD-box proteins and a yeast homolog of human p68, was shown to interact with Upf1p, an essential component of the nonsense-mediated mRNA decay pathway. Dbp2p:Upf1p interaction occurs within a large conserved region in the middle of Upf1p that is largely distinct from its Nmd2p and Sup35/45p interaction domains. Deletion of DBP2, or point mutations within its highly conserved DEAD-box motifs, increased the abundance of nonsense-containing transcripts, leading us to conclude that Dbp2p also functions in the nonsense-mediated mRNA decay pathway. Dbp2p, like Upf1p, acts before or at decapping, is predominantly cytoplasmic, and associates with polyribosomes. Interestingly, Dbp2p also plays an important role in rRNA processing. In dbp2Delta cells, polyribosome profiles are deficient in free 60S subunits and the mature 25S rRNA is greatly reduced. The ribosome biogenesis phenotype, but not the mRNA decay function, of dbp2Delta cells can be complemented by the human p68 gene. We propose a unifying model in which Dbp2p affects both nonsense-mediated mRNA decay and rRNA processing by altering rRNA structure, allowing specific processing events in one instance and facilitating dissociation of the translation termination complex in the other.

Blotting, Northern↗

PubMed1984

The ribosomal 5.8S RNA: eukaryotic adaptation or processing variant?

A striking difference between the cytoplasmic ribosomes of eukaryotes and prokaryotes is the presence (in eukaryotes) of one additional RNA component, the 5.8S rRNA. This RNA, which is hydrogen bonded to the cognate high molecular weight RNA of the large subunit, is about 160 nucleotides in length, and is cotranscribed with the high molecular weight rRNA as part of a much larger precursor molecule, the nucleolar 36S-45S rRNA. Because of its relatively small size the 5.8S RNA is considered a good model for studies on rRNA structure, synthesis, maturation, ribosomal integration, function, and even evolution. Over the last decade numerous studies have examined these questions with many interesting results, including the probability that this RNA sequence may actually be present in all ribosomes, although not necessarily as a separate RNA component. Their findings are summarized in this review.

Animals↗