PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “rRNA structure”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed2003

Identification of 13 novel human modification guide RNAs.

Members of the two expanding RNA subclasses termed C/D and H/ACA RNAs guide the 2'-O-methylations and pseudouridylations, respectively, of rRNA and spliceosomal RNAs (snRNAs). Here, we report on the identification of 13 novel human intron-encoded small RNAs (U94-U106) belonging to the two subclasses of modification guides. Seven of them are predicted to direct 2'-O-methylations in rRNA or snRNAs, while the remainder represent novel orphan RNA modification guides. From these, U100, which is exclusively detected in Cajal bodies (CBs), is predicted to direct modification of a U6 snRNA uridine, U(9), which to date has not been found to be pseudouridylated. Hence, within CBs, U100 might function in the folding pathway or other aspects of U6 snRNA metabolism rather than acting as a pseudouridylation guide. U106 C/D snoRNA might also possess an RNA chaperone activity only since its two conserved antisense elements match two rRNA sequences devoid of methylated nucleotides and located remarkably close to each other within the 18S rRNA secondary structure. Finally, we have identified a retrogene for U99 snoRNA located within an intron of the Siat5 gene, supporting the notion that retro-transposition events might have played a substantial role in the mobility and diversification of snoRNA genes during evolution.

Base Sequence↗
PubMed1995

Positions of multiple insertions in SSU rDNA of lichen-forming fungi.

Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-forming fungi Calicium tricolor and Porpidia crustulata each contain one insertion. Insertions are not limited to fungi that form lichens; the lichen ally Mycocalicium albonigrum also contains two insertions. Of the 11 insertion positions now reported for lichen-forming fungi and this ally, 6 positions are known only from lichen-forming fungi. Including the 4 newly reported in this study, insertions are now known from at least 17 positions among all reported SSU rDNA sequences. Insertions, most of which are Group I introns, are reported in fungal and protistan lineages and occur at corresponding positions in genomes as phylogenetically distant as the nuclei of fungi, green algae, and red algae. Many of these positions are exposed in the mature rRNA tertiary structure and may be subject to independent insertion of introns. Insertion of introns, accompanied by their sporadic loss, accounts for the scattered distribution of insertions observed within the SSU rDNA of these diverse organisms.

Base Sequence↗
PubMed1988

Complete sequences of the rRNA genes of Drosophila melanogaster.

In this, the first of three papers, we present the sequence of the ribosomal RNA (rRNA) genes of Drosophila melanogaster. The gene regions of D. melanogaster rDNA encode four individual rRNAs: 18S (1,995 nt), 5.8S (123 nt), 2S (30 nt), and 28S (3,945 nt). The ribosomal DNA (rDNA) repeat of D. melanogaster is AT rich (65.9% overall), with the spacers being particularly AT rich. Analysis of DNA simplicity reveals that, in contrast to the intergenic spacer (IGS) and the external transcribed spacer (ETS), most of the rRNA gene regions have been refractory to the action of slippage-like events, with the exception of the 28S rRNA gene expansion segments. It would seem that the 28S rRNA can accommodate the products of slippage-like events without loss of activity. In the following two papers we analyze the effects of sequence divergence on the evolution of (1) the 28S gene "expansion segments" and (2) the 28S and 18S rRNA secondary structures among eukaryotic species, respectively. Our detailed analyses reveal, in addition to unequal crossing-over, (1) the involvement of slippage and biased mutation in the evolution of the rDNA multigene family and (2) the molecular coevolution of both expansion segments and the nucleotides involved with compensatory changes required to maintain secondary structures of RNA.

Animals↗
PubMed1999

Phylogenic and phenotypic evidence for the transfer of Eubacterium fossor to the genus Atopobium as Atopobium fossor comb. nov.

The 16S rRNA primary structure of Eubacterium fossor was determined by sequencing in vitro amplified rDNA. Sequence comparisons indicated that E. fossor has a specific phylogenetic association with the Atopobium species and is far from E. limosum, the type species of the genus Eubacterium. Phenotypic characters of E. fossor resemble those of the genus Atopobium. Therefore, we propose that E. fossor should be transferred to the genus Atopobium as Atopobium fossor comb. nov.

Bacterial Typing Techniques↗
PubMed2005

Insights into the genomes of archaea mediating the anaerobic oxidation of methane.

The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate-reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large-insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME-1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME-2a, ANME-2c and ANME-3 group. Genome walking for ANME-1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME-2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10-methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl-CoA synthase enzyme complex.

Amino Acid Sequence↗
PubMed1983

Efficient read-through of Tn9 and IS1 by RNA polymerase molecules that initiate at rRNA promoters.

Transcription and translation are coupled in most Escherichia coli operons. As a consequence, ribosomes must be present on an mRNA molecule while transcription of the mRNA is in progress or else premature termination of transcription may result. This requirement is most clearly manifested when premature nonsense codons result in polarity in multicistronic operons. Polarity can also result from insertions of transposons and insertion sequences. However, since rRNA operons are not translated, some property of these operons must allow transcription to be uncoupled from translation. In this paper we demonstrate that transposon Tn9 and insertion sequence IS1 are nonpolar or incompletely polar in rRNA operons during normal growth. We also show that essentially all expression of rrn sequences distal to IS1 and Tn9 results from transcripts that originate at rRNA promoters. These results suggest either that rRNA operons possess some mechanism which reduces or prevents termination within rRNA operons or that Tn9 and IS1 can be very inefficient at blocking normal transcription. Insertions of Tn10 in rRNA operons are substantially but incompletely polar. We could not determine whether the residual downstream transcription observed results from promoters within Tn10 or from read-through of Tn10. We discuss the meaning of read-through of Tn9 and IS1 and the residual expression of genes downstream from Tn10 with regard to rRNA operon structure and previous experiments in which polarity of transposons or insertion sequences was observed in protein-encoding operons.

DNA Transposable Elements↗
PubMed2005

Paenibacillus macerans possesses two types of 16S rDNA copies in a genome with a length difference of twelve base pairs.

Two Paenibacillus macerans strains, JCM 2500T and MCRI 12, exhibited two types of 16S rDNA copies in their genomes, accompanied by a length difference of 12 bp at positions 203 to 214 (Escherichia coli numbering). The long-type sequences were newly identified for P. macerans 16S rDNA, and the copy numbers were different between the two strains. Both types of 16S rRNA were expressed in each strain, and it was predicted that the polymorphism at this position is located in helix H10, based on a comparison with the E. coli 16S rRNA secondary structure model.

Bacillus↗
PubMedDate not supplied

[Affinity modification of 80S ribosomes from human placenta by derivatives of tri- and hexauridylates as mRNA analogs].

Derivatives of 5'-32P]labeled (pU)3 and (pU)6 bearing 4-(N-2-chloroethyl-N-methylamino)benzylmethylamine residues attached to 5'-phosphates via phosphamide bond were applied to the affinity labeling of 80S ribosomes from human placenta. The reagents had normal coding properties and were fixed in the ribosomal mRNA-binding region by codon-anticodon interaction with cognate Phe-tRNA(Rhe) at P site (in the case of (pU)3 derivative) or at both A and P sites (in the case of (pU)6 one). Both reagents were found to modify only the 40S subunit. The sites of the reagents attachment to 18S ribosomal RNA were identified by blot-hybridization of the modified 18S rRNA with restriction fragments of the corresponding rDNA. They were found to be located within positions 976-1057 for (pU)6 derivative and within 976-1164 for (pU)3 one. These sites are located presumably within highly conserved parts of the eukaryotic small subunit rRNA secondary structure.

Alkylating Agents↗
PubMedDate not supplied

[Affinity modification of 80S ribosomes from human placenta with mRNA analogs--derivatives of oligouridylates with alkylating groups at the 3'-end].

2',3'-O-[4-(N-2-chloroethyl-N-methylamino)]benzylidene derivatives of oligoribonucleotides (Up)5U[32P]pC and (Up)11U[32P]pC were used for affinity labeling of 80S ribosomes from human placenta in the presence of cognate Phe-tRNA(Phe). The derivatives retained the ability of tRNA(Phe)-dependent binding with 80S ribosomes and within the corresponding complexes were cross-linked to 40S subunits (preferentially to 18S rRNA). Sites of the mRNA analogs attachment were identified by blot-hybridization of the modified rRNA with restriction fragments of corresponding rDNA. They are located within positions 1610-1747 and 1748-1865 for both analogs. These fragments are situated at the 3'-end region of 18S rRNA in a highly conserved part of eukaryotic small subunit rRNA secondary structure.

Affinity Labels↗
PubMed2006

[Rapid identification of Riemerella anatipestifer on the basis of specific PCR amplifying 16S rDNA].

Riemerella anatipestifer (RA) infection is the main disease causing severe losses in duck production. Because RA is characterized more by the absence than by the presence of specific phenotypic properties and different scholar had the different results of biochemical detection, it can't always be identified quickly and correctly only by the phenotypic properties or biochemical characteristics. The research object was to develop a species specific PCR method for RA detection. Because of the conserved structure of rRNA and appropriate size of 16S rRNA, a multiple alignment of 16S rDNA (gene coding 16S rRNA) was processed among RA, Escherichia coli, Pasteurella multocida, Salmonella enteritidis and Salmonella gallinarum, which are the main bacteria causing duck diseases. A pair of species specific primers named 190f and 843r were selected from the variable regions of 16S rDNA depending on the result of multiple alignment. Using BLAST on NCBI website for a sequence similarity search, the results showed that this pair of primers had very high specificity, except for having a lower sequence similarity with some species of Flavobacterium and Chryseobacterium. A PCR assay was performed and the template was extracted using the bacteria genomic DNA extraction kit and boiling method respectively. A chelate resin named Chelex 100 was used in the boiling method at the same time. Under the annealing temperature of 60 degrees C, all the 26 RA strains, including 19 representative strains of serotypes 1 to approximately 19 and 7 domestic isolated strains, showed the same 654bp fragment after PCR, while there was no amplification with isolates of other bacterial species. Also a series of sensitivity experiments were performed and proved that the detection limit of this method was 50pg genomic DNA, 1.5 x 10(6) CFU/mL and 15 CFU/mL, when the template was prepared with genomic DNA extraction kit, only boiling method and boiling method with Chelex 100 respectively. 12 clinical cases which were probably infected with RA were chosen to identify the accuracy and sensitivity of this PCR method. Several other conventional detecting methods including bacteria isolating, differentiating culture, biochemical experiments and serotyping were used at the same time. The templates of PCR were extracted from brains or livers by boiling method with Chelex 100. Finally, 3 cases were identified as RA infection by the conventional methods and 4 by the PCR method, which proved the good accuracy and sensitivity of the PCR method. Thus, this PCR assay provides a rapid and accurate method for identification of Riemerella anatipestifer. It will help to make the final decision in clinical diagnose or species identification, especially when a new serotype or sub-serotype of RA comes up.

Animals↗
PubMed1981

Structure of the Tetrahymena pyriformis rRNA gene. Nucleotide sequence of the transcription initiation region.

Portions of rRNA gene repeat from Tetrahymena pyriformis were cloned in pBR322, and a subclone containing the transcription initiation site was isolated. The promoter region was identified by S1 nuclease mapping of a portion of the HindIIIB fragment of the rRNA gene, using the 35 S rRNA primary transcript as a probe. The nucleotide sequence of the initiation site and the 5'-flanking region reveals three sets of highly conserved repeat sequences. A model of the promoter region is presented in which the rDNA is wrapped around a series of histone octamers. In this model the families of repeat sequences are brought in close proximity and suggest several possible mechanisms for the regulation of rRNA synthesis in T. pyriformis.

Animals↗
PubMed1982

Structure and organization of tRNA, rRNA, and protein genes in neurospora crassa mitochondria.

Our studies on Neurospora crassa mitochondria have included sequence analysis of tRNAs, mapping and cloning of the tRNA, rRNA, and protein genes and the DNA sequence analysis of these genes. Results from tRNA sequence analyses explain how the mitochondrial protein synthesizing system can function with a much smaller number of tRNAs than other systems. Mapping studies have shown that the two rRNA genes and almost all of the tRNA genes are clustered onto a third of the mitochondrial genome. The two rRNA genes and all of the tRNA genes are coded for by the same DNA strand. DNA sequence analysis has provided several interesting results. Twenty-four tRNA genes have been identified. Highly conserved GC rich palindromic sequences flank tRNA genes. The intervening sequence within the large rRNA gene has a long open reading frame capable of coding for a protein 426 amino acids long. The gene for cytochrome oxidase subunit 3 has been localized within the tRNA-rRNA gene cluster and has been sequenced. This gene is also flanked by the highly conserved GC rich palindromic DNA sequences.

Amino Acid Sequence↗
PubMed1993

Phylogenetic relationships of Baikalian species of Prorhynchidae turbellarian worms as inferred by partial 18S rRNA gene sequence comparisons (preliminary report).

The polymerase chain reaction (PCR) and direct sequencing of RNA genes were applied for phylogenetic relationship analysis among Turbellaria (flatworms). Representatives of 10 species of the genus Geocentrophora (Prorhynchidae family) were used to establish homology between nucleotides in the 5'-end portion of the 18S rRNA gene sequences. Sequence data were subdivided into 3 subsets--unpaired and basepaired (according to rRNA secondary structure) and transversion, including only transversion substitutions--that were independently analyzed to construct phylogenetic trees. Distance matrix and maximum parsimony approaches were applied to infer phylogenies. Trees were examined in terms of morphological taxonomy. The DNA sequences support the taxonomy and systematics of Baikalian flatworms. The hypothesis of Geocentrophora origin in Baikal is discussed.

Animals↗
PubMed1996

Dissociation rates of peptidyl-tRNA from the P-site of E.coli ribosomes.

We studied the dissociation rates of peptidyl-tRNA from the P-site of poly(U)-programmed wild-type Escherichia coli ribosomes, hyperaccurate variants altered in S12 (SmD, SmP) and error-prone variants (Ram) altered in S4 or S5. The experiments were carried out in the presence and absence of streptomycin, and the effects of neomycin were tested in the wild-type ribosomes. Binding of peptidyl-tRNA to the P-site of wild-type ribosomes is much stronger than to their A-site. Addition of streptomycin dramatically reduces its affinity for the P-site. The S12 alternations make the P-site binding of peptidyl-tRNA much tighter, and the S4, S5 alterations make it weaker than in the case of the wild-type. We find that when binding of peptidyl-tRNA to the A-site is weak, then the affinity for the P-site is stronger, and vice versa. From these results, we formulate a hypothesis for the actions of streptomycin and neomycin based on deformations of the 16S rRNA tertiary structure. The results are also used to interpret some in vivo experiments on translational processivity.

Amino Acid Sequence↗
PubMed1988

The E. coli 16S rRNA binding site of ribosomal protein S15: higher-order structure in the absence and in the presence of the protein.

We have investigated in detail the secondary and tertiary structures of E. coli 16S rRNA binding site of protein S15 using a variety of enzymatic and chemical probes. RNase T1 and nuclease S1 were used to probe unpaired nucleotides and RNase V1 to monitor base-paired or stacked nucleotides. Bases were probed with dimethylsulfate (at A(N-1), C(N-3) and G(N-7)), with 1-cyclohexyl-3 (2-(1-methylmorpholino)-ethyl)-carboiimide-p- toluenesulfonate (at U(N-3) and G(N-1)) and with diethylpyrocarbonate (at A(N-7)). The RNA region corresponding to nucleotides 652 to 753 was tested within: (1) the complete 16S rRNA molecule; (2) a 16S rRNA fragment corresponding to nucleotides 578 to 756 obtained by transcription in vitro; (3) the S15-16S rRNA complex; (4) the S15-fragment complex. Cleavage and modification sites were detected by primer extension with reverse transcriptase. Our results show that: (1) The synthetized fragment folds into the same overall secondary structure as in the complete 16S rRNA, with the exception of the large asymmetrical internal loop (nucleotides 673-676/714-733) which is fully accessible in the fragment while it appears conformationally heterogeneous in the 16S rRNA; (2) the reactivity patterns of the S15-16S rRNA and S15-fragment complexes are identical; (3) the protein protects defined RNA regions, located in the large interior loop and in the 3'-end strand of helix [655-672]-[734-751]; (4) the protein also causes enhanced chemical reactivity and enzyme accessibility interpreted as resulting from a local conformational rearrangement, induced by S15 binding.

Base Sequence↗
PubMed1999

DNA localization in the nucleoli of sea urchin Paracentrotus lividus oocytes.

It is known that in oocytes of P. lividus the nucleus contains a single giant nucleolus of unusual structure where intensive rRNA synthesis occurs. However, the questions of structural and functional relationships between the nucleolar compartments and the sites of active rRNA transcription still remain open. In the present work, we studied the chromatin organization in the nucleoli of P. lividus oocytes using Feulgen's and osmium amine staining procedures. Our results indicate that nucleolar chromatin of small (immature) oocytes differs from that in large mature oocytes. At the early stage of development, the DNA filamentous network 0.2-0.5 microm in diameter is formed in the nucleoli. Profound changes in the structure of the nucleolar DNA are observed in the course of oogenesis. Thus, at the late stage of development, the nucleolar chromatin forms characteristic ring-like structures, which indicates a non-uniform distribution of active ribosomal genes. A model of structural organization of the P. lividus nucleolus is discussed.

Animals↗
PubMed2001

Recognition of nucleotide G745 in 23 S ribosomal RNA by the rrmA methyltransferase.

Methylation of the N1 position of nucleotide G745 in hairpin 35 of Escherichia coli 23 S ribosomal RNA (rRNA) is mediated by the methyltransferase enzyme RrmA. Lack of G745 methylation results in reduced rates of protein synthesis and growth. Addition of recombinant plasmid-encoded rrmA to an rrmA-deficient strain remedies these defects. Recombinant RrmA was purified and shown to retain its activity and specificity for 23 S rRNA in vitro. The recombinant enzyme was used to define the structures in the rRNA that are necessary for the methyltransferase reaction. Progressive truncation of the rRNA substrate shows that structures in stem-loops 33, 34 and 35 are required for methylation by RrmA. Multiple contacts between nucleotides in these stem-loops and RrmA were confirmed in footprinting experiments. No other RrmA contact was evident elsewhere in the rRNA. The RrmA contact sites on the rRNA are inaccessible in ribosomal particles and, consistent with this, 50 S subunits or 70 S ribosomes are not substrates for RrmA methylation. RrmA resembles the homologous methyltransferase TlrB (specific for nucleotide G748) as well as the Erm methyltransferases (nucleotide A2058), in that all these enzymes methylate their target nucleotides only in the free RNA. After assembly of the 50 S subunit, nucleotides G745, G748 and A2058 come to lie in close proximity lining the peptide exit channel at the site where macrolide, lincosamide and streptogramin B antibiotics bind.

Anti-Bacterial Agents↗