Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences

Küntzel, Hans; Heidrich, Meinhard; Piechulla, Birgit

doi:10.1093/nar/9.6.1451

Cited by 65 publications

(35 citation statements)

References 22 publications

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“…These have been shown to be highly homologous to the bacterial 16 S rRNA with strong conservation of their 3'-terminal sequences [18]. In Figs 2A and 3 the 3'-terminal sequences of the depicted rRNA is identical between E. colt rRNA and chloroplast 16 S rRNA [14,15].…”

Section: Resultsmentioning

confidence: 87%

Occurrence of chloroplast ribosome recognition sites within conserved elements of the RNA genomes of carlaviruses

Foster

Mills

1991

FEBS Letters

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The nucl¢otide sequences upstream from the ,=~rlavirus olin reading frames wcrc exan~ined for direct sequence homology, Blocks of homology were evident upstream from the 25 K ORFs eF potato virus S (PVS), potato virus M (PVM} and lily symptomless virus (LSV), and upstream from th,= coast protein initiation codons of PVS, PVM, LSV. carnation latent virus and Hdenium virus S, Then,= blocks, which correspond to the Y.terminal resions of the subjenomic RNAs. were sl~own to contain potential ribosome rcco~,nitlon sequences, The distances between tit,= bindtn8 sites and initiation codons ransed from 20 to 40 nucleotides on the viral RNAs, Whilsl tit,= m.'tjority of chloroplasts mRNAs have a distance of 8 nucleotides between bindin8 site and initiation codon, the remaininB have a distance o1" 23 nucleotides which is similar to that reported here for the carlaviru~s.Subgenomic promoter: Seq nonce homology; Carlavirus; Ribosome bindin6 sit'=

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Section: Resultsmentioning

confidence: 87%

Occurrence of chloroplast ribosome recognition sites within conserved elements of the RNA genomes of carlaviruses

Foster

Mills

1991

FEBS Letters

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“…rRNA genes are widely used for estimation of evolutionary history and taxonomic assignment of individual organisms (14,26,(50)(51)(52). The choice of rRNA genes as optimal tools for such purposes is based on both observations and assumptions of ribosomal conservation (13,50).…”

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confidence: 99%

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei

Oberdorf²,

Nossa³

et al. 2010

Appl Environ Microbiol

238

181

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Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 ؎ 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% ؎ 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2°structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in "Candidatus Protochlamydia amoebophila." Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.

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“…Comparison of the primary structures of eukaryotic and prokaryotic 5S RNAs led to a universal four-helix model (4) that is generally accepted to be a minimal secondary structure model. For eukaryotic 5S RNA, the model can be extended to a five-helix model (10)(11)(12)(13).Although they have a common ancestry, prokaryotic and eukaryotic 5S RNAs are structurally distinct. Moreover, 50S ribosomal reconstitution experiments showed that different prokaryotic 5S RNAs are functionally interchangeable whereas eukaryotic 5S RNAs cannot replace the prokaryotic molecule in bacterial ribosomes (14).…”

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confidence: 99%

Three-dimensional structural model of eubacterial 5S RNA that has functional implications.

Pieler¹,

Erdmann²

1982

Proc. Natl. Acad. Sci. U.S.A.

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Escherichia coli 5S RNA and its specific protein complexes were hydrolyzed with the single-strand-specific nuclease SI. Based on the results, a tertiary structural model for E. coli 5S RNA is proposed in which ribosomal proteins E-L5, E-L18, and E-L25 influence the conformation of the RNA. This may be of significance for ribosomal function. Comparison ofthe proposed E. coli 5S RNA structure with those of 18 other prokaryotic 5S RNAs led to a generalized eubacterial 5S RNA tertiary structure in which the majority ofthe conserved nucleotides are in non-basepaired regions and several conserved "looped-out" adenines (in E. coli, adenines -52, -53, -57, -58, and -66) are implied to be important for protein recognition or interaction or both.The structure ofribosomal 5S RNA has been studied extensively for more than a decade (1), and these studies have led to the proposal of a large number of structural models (some of them are summarized in refs. 1-3 and others are described in refs. 4-12). Comparison of the primary structures of eukaryotic and prokaryotic 5S RNAs led to a universal four-helix model (4) that is generally accepted to be a minimal secondary structure model. For eukaryotic 5S RNA, the model can be extended to a five-helix model (10)(11)(12)(13).Although they have a common ancestry, prokaryotic and eukaryotic 5S RNAs are structurally distinct. Moreover, 50S ribosomal reconstitution experiments showed that different prokaryotic 5S RNAs are functionally interchangeable whereas eukaryotic 5S RNAs cannot replace the prokaryotic molecule in bacterial ribosomes (14). The question of whether the small ribosomal RNA is just a static structural component of the ribosome or whether it takes part in the dynamic process of protein biosynthesis, such as interacting with tRNA (for review, see refs. 1, 15, and 16) or the two large ribosomal RNAs (17, 18),can not yet be answered satisfactorily.The precise function of the 5S RNA can be determined only after its structure is known. Therefore, we analyzed Escherichia coli 5S RNA and its specific protein complexes by nuclease S1 digestion, previous studies with tRNA having established that this nuclease is single-strand specific (19). Based on similar nuclease S1 digestion studies, we here present a structural model for E. coli 5S RNA including tertiary interactions that leads to an extended four-helix model for eubacterial 5S RNA. Furthermore, we report experimental evidence for a conformational switch in E. coli 5S RNA mediated by its ribosomal binding proteins E-L5, E-L18, and E-L25. This could facilitate interactions between 5S RNA and tRNA, 16S RNA, and 23S RNA.MATERIAL AND METHODS Material. Uniformly 32P-labeled E. coli MRE600 50S ribosomal subunits were a gift from R. Brimacombe. Nuclease S1was from Boehringer Mannheim, RNases Ti and A were from Sankyo (Tokyo), and polyethyleneimine-cellulose plates were from Macherey and Nagel (Dfiren, Federal Republic of Germany). All other chemicals were purchased from Merck (Darmstadt, Federal Republic of Germany).Isol...

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Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences

Cited by 65 publications

References 22 publications

Occurrence of chloroplast ribosome recognition sites within conserved elements of the RNA genomes of carlaviruses

Occurrence of chloroplast ribosome recognition sites within conserved elements of the RNA genomes of carlaviruses

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Three-dimensional structural model of eubacterial 5S RNA that has functional implications.

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