Conservation of secondary structure in 5 S ribosomal RNA : a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable

Wächter, Rupert De; Chen, Min-Wei; Vandenberghe, Antoon

doi:10.1016/s0300-9084(82)80436-7

Cited by 115 publications

(71 citation statements)

References 68 publications

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“…Judging from the SI cleavage data this region might also be folded in an alternative, 5S rRNA untypical fashion, as shown in Figure 10. De Wachter et al (23) have proposed a dynamic equilibrium involving a migration of the bulge in helix III for Lemna minor chloroplastic 5S rRNA.…”

Section: Discussionmentioning

confidence: 99%

Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach

Pieler¹,

Digweed²,

Bartsch

et al. 1983

Nucl Acids Res

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ABSTRACT5S rRNAs from Spinacea oleracea cytoplasmic and chloroplastic ribosomes have been subjected to digestion with the single strand specific nuclease Si and to chemical modification of cytidines by sodium bisulphite in order to probe the RNA structure. According to these data, cytoplasmic 5S rRNA can be folded as proposed in the general eukaryotic 5S rRNA structure (1) and 5S rRNA from chloroplastides is shown to be more related to the general eubacterial structure (2). INTRODUCTIONRibosomal 5S rRNA, a unique component of the protein synthesizing complex, is ideally suited as a model system for phylogenetic studies by comparative structural analysis. Heterologous reconstitution experiments (3) using 5S rRNAs of eukaryotic, eubacterial and archaebacterial origin for the incorporation into B. stearothermophilus 50S ribosomal subunits and protein binding studies (4,5) gave rise to the idea of at least two functionally distinct classes of 5S rRNA. Woese and Fox (6) introduced a general secondary structure for eukaryotic as well as for eubacterial 5S rRNAs on the basis of comparative sequence analyses. This model is considered to represent the minimal number of base pairs in any 5S rRNA structure. Recently, a general eukaryotic (1) and a general eubacterial (2,7) 5S rRNA model have been proposed. By analyzing the structure of cytoplasmic and chloroplastic 5S RNA from spinach using the single strand specific nuclease Si we would like to answer the question as to whether the chloroplast species is of eukaryotic character or of eubacterial origin, as proposed by the endosymbiotic hypothesis.5S rRNA molecules are supposed to be able to undergo confor-

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Section: Discussionmentioning

confidence: 99%

Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach

Pieler¹,

Digweed²,

Bartsch

et al. 1983

Nucl Acids Res

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“…Similar, although not necessarily identical, sets of equilibrium forms can be considered in this area of other bacterial 5s RNAs. Thus it seems that the flexibility of this part of the secondary structure is even greater than previously suspected [6,7]. In eukaryotic 5s RNAs, on the contrary, the flexibility of area D-12-E seems to be more developed [7].…”

Section: Secondary Structurementioning

confidence: 76%

“…1 are engaged in base pairing. This model is now accepted by most investigators [6,. The existence in eubacterial 5 s RNAs of the base pairs A .…”

Section: Secondary Structurementioning

confidence: 86%

“…The newly determined sequences were fitted [6] in an existing alignment of 5 s RNA sequences [12]. A tree was constructed from the eubacterial and organelle sequences by a clustering method known as weighted painvise grouping [13], starting from a difference matrix corrected for multiple mutation, as previously described [14].…”

Section: Construction Of Phylogenetic Treesmentioning

confidence: 99%

“…The presence in all eubacterial 5 S RNAs of an equal number of bases in both strands of loop I2 tends to support this view. The potential of an equilibrium between two structures in area I1-C, originally proposed [6] on the basis of a comparison of some 80 structures, can be shown to be applicable to all of the 300-odd presently known 5 s RNA structures of eukaryotic and archaebacterial as well as eubacterial origin.…”

Section: Secondary Structurementioning

confidence: 99%

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Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species

Vandenberghe¹,

Wassink²,

Raeymaekers³

et al. 1985

European Journal of Biochemistry

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The nucleotide sequences of the 5 S ribosomal RNAs of the bacteria Agrobacterium tumefaciens, Alcaligenes faecalis, Pseudomonas cepacia, Aquaspirillum serpens and Acinetobacter calcoaceticus have been determined. The sequences fit in a generally accepted model for 5 s RNA secondary structure. However, a closer comparative examination of these and other bacterial 5 S RNA primary structures reveals the potential of additional base pairing and of multiple equilibria between a set of slightly different alternative secondary structures in one area of the molecule. The phylogenetic position of the examined bacteria is derived from a 5 S RNA sequence alignment by a clustering method and compared with the position derived on the basis of 16s ribosomal RNA oligonucleotide catalogs.

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Solution conformations of B. subtilis ribosomal 5S RNA: A calorimetric study

Chang

Marshall

1986

Biopolymers

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SynopsisThe unfolding of B. subtilis 5s RNA is examined by direct calorimetric measurement in the presence of various concentrations of N a + and Mg2+. The composite differential scanning calorimetry (DSC) curve is analyzed into 3-5 individual two-state melting transitions. In the absence of added Na + or Mgz+ , the 55 RNA segments melt together at T , = 40°C. Addition of Na+ stabilizes the molecular structure (T, = 56°C) and widens the melting temperature range, so that up to five component transitions are observed. Addition of Mg2+ alone produces a very stable structure (T, = 75°C) with highly cooperative melting. Finally, addition of both N a + and Mg2+ produces the highest stability ( T , = 76'C). The results are interpreted according to hypothetical secondary and tertiary base-pairing schemes. The conformational changes demonstrated here may facilitate the movement of the protein synthesis machinery during RNA translation.

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Conservation of secondary structure in 5 S ribosomal RNA : a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable

Cited by 115 publications

References 68 publications

Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach

Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach

Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species

Solution conformations of B. subtilis ribosomal 5S RNA: A calorimetric study

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