Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species

Zwieb, Christian W; Glotz, Carola; Brimacombe, Richard

doi:10.1093/nar/9.15.3621

Cited by 179 publications

(85 citation statements)

References 22 publications

(64 reference statements)

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“…Our data indicate that homologous recombination is highly effective in maintenance of 16S rRNA homogeneity, as the diversity is confined within 1% in all but only 24 of the 425 species. The exceptionally high diversity in the 24 species does not violate the ribosomal constraints, as they can be explained at the 2°structure level, the ultimate line of ribosomal constraint (56). For example, in T. tengcongensis, the 2°structure is well conserved despite 6.70% diversity in the primary structure (Table 3).…”

Section: Discussionmentioning

confidence: 94%

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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Section: Discussionmentioning

confidence: 94%

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei

Oberdorf²,

Nossa³

et al. 2010

Appl Environ Microbiol

238

181

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“…As measured on the basis of secondary structures that have been proposed (32,40,42) for fungal 15S and animal 12S mitochondrial rRNAs, wheat mitochondrial 18S and E. coli 16S rRNAs share a substantially higher degree of positional homology with each other (and with plastid 16S rRNAs) than either does with the mitochondrial small subunit rRNAs of other eukaryotes. Within the universal core, wheat mitochondrial 18S rRNA also displays a distinctly higher level of primary sequence homology with eubacterial/ plastid 16S rRNAs than with the corresponding fungal and animal mitochondrial sequences (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Pronounced structural similarities between the small subunit ribosomal RNA genes of wheat mitochondria and Escherichia coli.

Spencer¹,

Schnare²,

Gray³

1984

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

116

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We present here the nucleotide sequence of the small subunit (18S) rRNA gene from wheat mitochondria. Aside from five discrete variable domains, this gene and the analogous (16S) rRNA gene in Escherichia coli show essentially a one-to-one correspondence in their potential secondary structures, with regions accounting for 86% of the bacterial 16S rRNA having a strict secondary structure counterpart in the mitochondrial 18S rRNA. Primary sequence identity between the two rRNAs ranges from 73% to 85% (76% overall) within regions of conserved secondary structure. Within a smaller secondary structure core common to all small subunit rRNAs, the wheat mitochondrial sequence shares substantially more primary sequence identity with the E. coli (eubacterial) sequence (88%) than with the small subunit rRNA sequences of Halobacterium vokcanii (an archaebacterium) (71%) or Xenopus laevis cytoplasm (61%). Moreover, the wheat mitochondrial sequence contains a very high proportion of certain lineage-specific residues that distinguish eubacterial/plastid 16S rRNAs from archaebacterial 16S and eukaryotic cytoplasmic 18S rRNAs. These data establish that the ancestry of the wheat mitochondrial 18S rRNA gene can be traced directly and specifically to the eubacterial primary kingdom, and the data provide compelling support for a relatively recent xenogenous (endosymbiotic) origin of plant mitochondria from eubacterialike organisms.The question of the origin of mitochondria continues to spark spirited debate (1, 2). Strong biochemical and structural similarities between mitochondria and bacteria lend support to an endosymbiotic (xenogenous) origin (3, 4) from organisms resembling, in respiratory metabolism (5) and cytochrome c structure (6), contemporary nonsulfur purple bacteria. On the other hand, mitochondrial genomes display patterns of gene arrangement and expression that differ substantially from characteristic bacterial patterns and that incorporate deviations from the universal genetic code (1, 2, 7). Such "nonbacterial" features, coupled with the fact that most of the "bacterial" traits of mitochondria are a manifestation of nuclear and not mitochondrial genes, have prompted a number of proposals (e.g., see refs. 8-10) that mitochondria had an autogenous origin, developing within a protoeukaryotic cell that gave rise to the genomes of both nucleus and organelles.In contrast to respiratory chain genes, rRNA genes are present in nuclear, bacterial (prokaryotic), and mitochondrial genomes, and considerable emphasis has been placed on rRNA sequence data as a means of distinguishing between autogenous and xenogenous hypotheses of mitochondrial origin (1, 2, 7). Moreover, since prokaryotes appear to be divided into two primary kingdoms, eubacteria and archaebacteria (11), any rRNA sequence data supporting a xenogenous origin should also indicate which of these two bacterial lineages has given rise to mitochondria. Sequence data supporting an endosymbiotic, eubacterial origin of wheat mitochondrial small subunit (18S) rRNA (...

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“…Even though the sequence of 16s RNA is known (Brosius et al, 1978;Carbon et al, 1979) and much of its secondary structure is agreed on (Noller and Woese, 1981;Stiegler et al, 1981;Zwieb et al, 1981) little progress has been made towards linking specific structures with function. Recent work with psoralen crosslinking of 16s RNA (Thompson and Hearst, 1983) has confirmed parts of the secondary structure, and has also provided evidence for new interactions that appear to be functionally important.…”

Section: Introductionmentioning

confidence: 99%