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At least 19 recordsLinked to original sources

PubMed1992

Loss of transfer RNA genes from the plastid 16S-23S ribosomal RNA gene spacer in a parasitic plant.

The plastid 16S-23S intergenic spacer region in Conopholis americana, a totally heterotrophic angiosperm in the family Orobanchaceae, has undergone large deletions, including the entire tRNA(Ile) gene and all but small remnants of the tRNA(Ala) gene. The length of the region is less than 20% of that of other land plants which have been investigated, making it the smallest 16S-23S intergenic spacer reported thus far for any land plant. The remaining sequences in the spacer are 90.1% identical to tobacco, indicating that, while the region is well conserved at the sequence level, it is evolving rapidly by deletion. Experiments using the polymerase chain reaction and hybridization to DNA gel blots have failed to reveal either of the two missing tRNA genes elsewhere in the Conopholis cell.

Base Sequence↗

PubMed1995

Complete sequences and organization of the rrnA operon from campylobacter jejuni TGH9011 (ATCC43431).

The rrnA ribosomal RNA (rRNA) operon of Campylobacter jejuni (Cj) TGH9011 (ATCC43431) was cloned and sequenced to completion. rRNAs were then characterized by primer extension and S1 nuclease mapping analysis. The secondary structure models of Cj 16S and 23S rRNAs were constructed, and the models were compared to the corresponding models from other eubacterial rRNA. The analysis presented a typical 5'-promoter-16S-tRNAs-23S-5S-terminator-3' prokaryotic rRNA operon structure. However, an unusual organization of the intercistronic tRNAs was observed where the two tRNAs, tRNA(Ala) and tRNA(Ile), were present in the order 5'-16S-tRNA(Ala)-tRNA(Ile)-23S-3', which is opposite of the typical 5'-16S-tRNA(Ile)-tRNA(Ala)-23S-3' structure observed in other bacteria.

Base Sequence↗

PubMed1996

A single base change prevents import of cytosolic tRNA(Ala) into mitochondria in transgenic plants.

Plant mitochondria do not contain a full set of tRNA genes, and the additional tRNAs needed for protein synthesis (including tRNA(Ala) are imported from the cytosol. The import process appears to be highly specific for certain tRNAs, and it has been suggested that the cognate amino-acyl-tRNA synthetases may be responsible for this specificity. In order to test this, we have grown transgenic tobacco plants expressing Arabidopsis thaliana tRNA(Ala) carrying a U70 to C70 mutation, which we have previously shown blocks aminoacylation by the plant alanyl-tRNA synthetase. Unlike the wild-type tRNA(Ala), the mutant tRNA is not present in the mitochrondrial tRNA fraction. This is the first report of a tRNA mutation which prevents mitochondrial import and strongly supports the hypothesis that aminoacyl-tRNA synthetases are involved in this process in plants. Insertion of four bases into the anticodon loop of tRNA(Ala) does not prevent mitochondrial import, implying that the tRNA might not need to participate in translation to be imported.

Arabidopsis↗

PubMed1993

Mosaic tile model for tRNA-enzyme recognition.

An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucleotide and its neighbours as they are defined by the tertiary structure of the molecule. Informational content of each tile is calculated as its probability to occur exclusively in a set of cognate tRNAs. Based on this algorithm the identity sites of E. coli tRNA(Ala) and tRNA(Gln) were determined. The results are in a good agreement with the biochemical data and provide new information about identity sites of these tRNAs.

Algorithms↗

PubMed1994

Characterization of the 16S-23S rRNA intergenic spacer of Bartonella bacilliformis.

The 16S-23S intergenic spacer region from the ribosomal RNA (rRNA) operon of Bartonella bacilliformis was cloned and characterized. The spacer is 906 nucleotides (nt) in length and contains the genes encoding isoleucine-tRNA (tRNA(Ile)) and alanine-tRNA (tRNA(Ala)). The tRNA-encoding genes are separated by 122 nt and are centrally located in the 16S-23S spacer region, with approx. 300 flanking nt. Genes encoding tRNA(Ile) and tRNA(Ala) have 88.3 and 93.4% sequence identity, respectively, to the homologous genes of Rhodobacter sphaeroides.

Bartonella↗

PubMed1995

tRNA intergenic spacers reveal polymorphisms diagnostic for Xanthomonas albilineans.

A PCR-based detection system was developed for Xanthomonas albilineans, a pathogen of sugarcane, and other related xanthomonads, using the conserved sequence of two adjacent tRNA genes and the variable length and sequence of the spacer region between them. An appropriate region was identified as follows: tRNA genes with the same anticodon from a wide variety of bacteria were aligned and the most frequent base at each position was chosen to derive primers that would anneal to the gene in either orientation. Pairs of such primers were screened against various Xanthomonas species and members of related genera using PCR at low to moderate annealing stringency. A subset of these pairs of tRNA consensus primers gave one or more PCR products which generally displayed interspecific length variability. The primer pair 5'-3' tRNA(ala) and 3'-5' tRNA(ile) showed interspecific length polymorphisms between X. albilineans and all other Xanthomonas species examined. These PCR products were cloned and sequenced from four isolates of X. albilineans and four isolates from different pathovars of X. campestris, and the spacer length variation confirmed. Specific tRNA gene primers were derived from the tRNA gene sequences. These primers yielded a PCR product of a characteristic length within most Xanthomonas species and pathovars tested. When a primer that projected from tRNA(ala) into the 3' end of the variable intergenic spacer was used with a tRNA(ile)-specific primer, PCR was a very sensitive diagnostic test for X. albilineans-infected sugarcane and gave no product or only a faint product with other species of bacteria. The specificity of this PCR-based detection system was further enhanced by a nested PCR reaction that took advantage of the fact that the tRNA(ala)-tRNA(ile) region was found to be embedded in a 16S rRNA-23S rRNA gene spacer. By amplifying the region between the 16S rRNA gene and tRNA(ile) or between the tRNA(ala) and the 23S rRNA gene, the subsequent nested PCR product was shown to be X. albilineans-specific.

Base Sequence↗

PubMed1995

The 16S-23S rRNA intergenic spacer region of Bartonella (Rochalimaea) species is longer than usually described in other bacteria.

We amplified by polymerase chain reaction (PCR) and sequenced using an automated laser fluorescent DNA sequencer (Pharmacia) the intergenic spacer region (ITS) between the 16S and 23S rRNAs of the four species of Rochalimaea which were recently renamed Bartonella sp. We obtained DNA fragments of 1211, 1262, 1258 and 1529 bp for the reference species of B. quintana, B. henselae, B. vinsonii and B. elizabethae, respectively. The ITS of the four species are longer than previously reported in prokaryotes and contained the genes encoding isoleucine-tRNA (tRNA(Ile)) and alanine-tRNA (tRNA(Ala)). The sequences of the tRNA(Ala) genes are identical for the four Bartonella species, but the tRNA(Ile) gene sequence of B. quintana presents one mutation in comparison with the other species.

Bartonella↗

PubMed1996

Two 16S-23S ribosomal DNA intergenic regions in different Treponema pallidum subspecies contain tRNA genes.

The 16S-23S intergenic spacers of Treponema pallidum subspecies pallidum, Nichols strain, and Treponema pallidum subspecies pertenue, Gauthier strain, have been cloned, characterized and sequenced. Isoleucine and alanine tRNA genes have been identified within the 16S-23S intergenic regions on separate alleles of 293 and 303 bases, respectively. The two alleles are present in both T.p.pallidum and T.p. pertenue, and show no sequence differences between the bacterial subspecies. The ile-tRNA and ala-tRNA genes show 65% and 84% sequence identity, respectively, with the homologous genes of the related spirochete, Borrelia burgdorferi.

Alleles↗

PubMed1997

Comparison of the 16S/23S ribosomal intergenic regions of "Candidatus Liberobacter asiaticum" and "Candidatus Liberobacter africanum," the two species associated with citrus huanglongbing (greening) disease.

16S/23S intergenic spacer regions from the rRNA operons of two strains of "Candidatus Liberobacter asiaticum" and one strain of "Candidatus Liberobacter africanum" were cloned and sequenced. The intergenic spacers of the two "Candidatus L. asiaticum" strains studied are identical and contain the genes for isoleucine tRNA (tRNA(Ile)) and alanine tRNA (tRNA(Ala)) separated by 11 nucleotides. The intergenic spacer of the "Candidatus L. africanum" strain contains only one tRNA gene (tRNA(Ala)). The level of homology between the intergenic spacers of the two liberobacter species is 79.46%. Ribosomal operons with 16S/23S spacer regions other than those studied might be present in the two "Candidatus Liberobacter" species.

Base Sequence↗

PubMed1994

The 16S/23S ribosomal spacer region of Coxiella burnetti.

The 16S/23S spacer region of Coxiella burnetti isolate Nine Nile, phase 1, was sequenced. Sequence analysis revealed two tRNA coding regions for tRNA(Ile) and tRNA(Ala). DNA sequence alignment demonstrated significant homology with tRNA species from Pseudomonas aeruginosa and Rhodobacter sphaeroides, respectively. The non-coding tRNA spacer region was unique to Coxiella burnetti, based on database alignment.

Cloning, Molecular↗

PubMed1995

A new factor from Escherichia coli affects translocation of mRNA.

Reconstitution of protein synthesis from purified translation factors on ribosomes from Escherichia coli has revealed the requirement for a protein, W, that affects chain elongation and is essential to reconstitute the process (Ganoza, M. C., Cunningham, C., and Green, R. M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 1648-1652). We report that W has no effect on initiation complex formation by 30 or 70 S ribosomes or on the association of ribosomal subunits, peptide bond synthesis, or binding Ala-tRNA, which is the second amino acid of the coat protein of the MS2 RNA virion. W has a pronounced effect on tripeptide synthesis, and is obligatory for the synthesis of the coat protein or of the hexapeptide encoded by f2am3 RNA. Extracts from a temperature-sensitive mutant of the translocase, EF-G, were purified free of the W protein and were used to score for translocation defects. W is required for binding Ser-tRNA, the third N-terminal amino acid of the MS2 or f2 RNA coat protein to ribosomes bearing fMet-Ala-tRNA, as well as for the ejection of deacyl-tRNA from ribosomes, which occurred concomitant with the binding of the Ser-tRNA. We propose that W functions by ejecting tRNAs from ribosomes in a step that precedes the movement of mRNA during translocation.

Bacterial Proteins↗

PubMed1991

Structural features of the plastid ribosomal RNA operons of two red algae: Antithamnion sp. and Cyanidium caldarium.

The nucleotide sequences of the plastid 16S rDNA of the multicellular red alga Antithamnion sp. and the 16S rDNA/23S rDNA intergenic spacers of the plastid DNAs of the unicellular red alga Cyanidium caldarium and of Antithamnion sp. were determined. Sequence comparisons support the idea of a polyphyletic origin of the red algal and the higher-plant chloroplasts. Both spacer regions include the unsplit tRNA(Ile)(GAU) and tRNA(Ala)(UGC) genes and so the plastids of both algae form a homogeneous group with those of chromophytic algae and Cyanophora paradoxa characterized by 'small-sized' rDNA spacers in contrast to green algae and higher plants. Nevertheless, remarkable sequence differences within the rRNA and the tRNA genes give the plastids of Cyanidium caldarium a rather isolated position.

Base Sequence↗

PubMed1994

Sequence analysis of the ribosomal RNA operon of the Lyme disease spirochete, Borrelia burgdorferi.

An 11,955-bp region of the Borrelia burgdorferi chromosome containing all the genes encoding ribosomal RNA (rRNA) has been sequenced. The region contains a single gene encoding 16S rRNA and two genes encoding the 23S and 5S rRNAs. The sizes of the 16S, 23S and 5S rRNAs encoded by these genes are 1537, 2926 and 112 nucleotides, respectively. In addition, the genes encoding tRNA(Ala) and tRNA(Ile) are located in the intergenic spacer between the 16S and 23S rDNAs. The tDNAs do not encode the common CCA 3' end which presumably must be added posttranscriptionally. All the genes are present in the same orientation, except for that encoding tRNA(Ile), which is transcribed from the opposite strand. The latter implies that the rDNAs are not transcribed as a single unit. The location of putative promoters and termination signals in the sequence suggest that the 16S rRNA and tRNA(Ala) are transcribed as a single unit, tRNA(Ile) is produced as an individual transcript and the 23S and 5S rDNAs are co-transcribed. Several of the features of this rDNA organization are unique, not having been described previously in any other eubacteria.

Base Sequence↗

PubMed1995

Defining a smaller RNA substrate for elongation factor Tu.

A nuclease protection assay was used to obtain equilibrium dissociation constants of Thermus thermophilus EF-Tu with two well-characterized internal deletions of Escherichia coli Ala-tRNA(Ala) and yeast Phe-tRNA(Phe). Aminoacylated tRNAs with the anticodon hairpin substituted by a tetranucleotide bind to EF-Tu as well as the corresponding full-sized tRNAs. However, the Ala minihelix, where residue A7 is joined directly to A49, binds to EF-Tu less well than the full-sized Ala-tRNA(Ala). Similar data were obtained for Escherichia coli EF-Tu. An in vitro selection strategy was used to isolate a substrate for EF-Tu from an RNA library where nine random nucleotides inserted between A7 and A49 in the Ala minihelix. After six rounds of enrichment, two groups of RNA were obtained that bound T. thermophilus EF-Tu as well as Ala-tRNA(Ala). Group I molecules have the consensus sequence UNDUGACUY (N = U, C, A, G; D = U, G; Y = U, C) in the randomized region, and Group II molecules generally have 5'-terminal GUG, but are more variable in the remaining six nucleotides. The selected RNAs bind EF-Tu better than the minihelix either because they provide additional function groups for protein binding or because they have a structure more similar to the aminoacyl acceptor branch of tRNA.

Base Sequence↗

PubMed1995

A single rRNA gene region in Bradyrhizobium japonicum.

Bradyrhizobium japonicum contains only a single rRNA (rrn) gene region, despite its comparatively large genome size of 8,700 kb. The nucleotide sequence revealed an organization of rRNA and tRNA genes that is frequently found in bacteria: 5'-rrs (16S rRNA)-ileT (tRNA(Ile))-alaT (tRNA(Ala))-rrl (23S rRNA)-rrf (5S rRNA)-3'. The 5' end of the primary transcript, one of the 16S rRNA processing sites, and the 5' end of the mature 16S rRNA were determined by primer extension. DNA hybridization experiments showed that the slowly growing Bradyrhizobium strains generally have only a single copy of the 16S rRNA gene, whereas the faster-growing Rhizobium species contain three rrs copies.

Base Sequence↗

PubMed1994

A tRNA gene mapping within the chloroplast rDNA cluster is differentially expressed during the development of Daucus carota.

In vivo analysis of expression of the chloroplast rDNA cluster during somatic embryogenesis of Daucus carota (D.carota) was performed by Northern-blot analysis with different DNA probes, spanning both the 16S rRNA gene, the 16S-23S rRNA spacer, which contains the two mosaic tRNA genes tRNA(Ile) and tRNA(Ala), and the region upstream of the 16S rRNA gene, where a tRNA(Val) maps. We show that expression both of the spacer tRNAs tRNA(Ile) and tRNA(Ala) is not significantly regulated during development whereas the amount of the transcript corresponding to tRNA(Val) is not detectable during early embryonic stages and progressively accumulates during late phases. Multiple transcription start sites have been identified upstream of the tRNA(Val) gene by S1 mapping analysis, which are activated late during the embryogenesis. These data indicate that developmental control mechanisms act on plastid gene expression during embryogenesis in carrot.

Base Sequence↗

PubMed1998

Characterization of oligonucleotide probes for the identification of Acinetobacter spp., A. baumannii and Acinetobacter genomic species 3.

The 16S-23S intergenic spacer regions of four Acinetobacter genomic species belonging to the A. calcoaceticus-A. baumannii (Acb) complex, i.e. genomic species 1 (A. calcoaceticus), genomic species 2 (A. baumannii), genomic species 3 and Tjernberg and Ursing (TU) genomic species 13, have been cloned and sequenced. Sequence analysis led to the discovery of a single copy of IIe and Ala tRNA genes within each spacer. Sequence comparison allowed the identification of a 192-base-pair long highly conserved sequence between the 3' end of the 16S rRNA and the 5' end of the tRNA(Ala) genes. Moreover, two short regions, which were specific to, respectively, genomic species 2 and 3, could be identified. Oligonucleotides corresponding to these sequences were constructed and tested for the ability to hybridize with chromosomal DNA extracted from Acinetobacter belonging to different genomic species and with chromosomal DNA of other bacterial genera. One of these oligonucleotides was demonstrated to be useful as a sensitive and specific probe for A. baumannii. A less sensitive probe for Acinetobacter genomic species 3 was also developed.

Acinetobacter↗

PubMed1995

Phylogenetic relationship of the green alga Nanochlorum eukaryotum deduced from its chloroplast rRNA sequences.

The marine green coccoidal alga Nanochlorum eukaryotum (N.e.) is of small size with an average diameter of 1.5 microns. It is characterized by primitive-appearing biochemical and morphological properties, which are considerably different from those of other green algae. Thus, it has been proposed that N.e. may be an early developed algal form. To prove this hypothesis, DNA of N.e. was isolated by a phenol extraction procedure, and the chloroplast DNA separated by preparative CsCl density-gradient centrifugation. The kinetic complexity of the nuclear and of the chloroplast DNA was evaluated by reassociation kinetics to 3 x 10(7) bp and 9 x 10(4) bp, respectively. Several chloroplast genes, including the rRNA genes, were cloned on distinct fragments. The order of the rRNA genes corresponds to the common prokaryotic pattern. The 16S rRNA gene comprises 1,548 bases and is separated from the 23S rRNA gene with its 2,920 bases by a short spacer of 460 bases, which also includes the tRNA(Ile) and tRNA(Ala) genes. The 5S rRNA gene has not been found; it must start further than 500 bases downstream from the 3'-end of the 23S rRNA gene. From the chloroplast rRNA sequences, we have deduced secondary structures of the 16S and 23S rRNAs, which are in agreement with standard models. The rRNA sequences were aligned with corresponding chloroplast sequences; phylogenetic relationships were calculated by several methods. From these calculations, we conclude that N.e. is most closely related to Chlorella vulgaris. Therefore, N.e. does not represent an early developed algal species; the primitive-appearing morphological and biochemical characteristics of N.e. must rather be explained by secondary losses.

Chlorella↗