Equilibria in 5-S ribosomal RNA secondary structure. Bulges and interior loops in 5-S RNA secondary structure may serve as articulations for a flexible molecule

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

doi:10.1111/j.1432-1033.1984.tb08356.x

Cited by 27 publications

(10 citation statements)

References 35 publications

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“…It is likely that the protein composition of our photo-induced 5 S-RNA -protein complex was heterogenous as we recently observed with the RNPH (Reboud, unpublished results). A heterogeneity of the 5 S-RNA -protein complex prepared from irradiated subunits might be related to the existence of slightly different forms of 5s RNA within ribosomes, as strongly suggested by other reports [28].…”

Section: Discussionsupporting

confidence: 61%

Photo‐induced protein cross‐linking to 5S RNA and 28–5.8S RNA within rat‐liver 60S ribosomal subunits

Paleologue

Reboud

1985

European Journal of Biochemistry

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Rat liver 60s ribosomal subunits were irradiated with 254-nm ultraviolet light (1.26 x lo4 quanta/subunit), under conditions which preserved their functional activity. Cross-linked RNA-protein complexes were recovered after unreacted proteins had been removed by repeated acetic acid extractions. Proteins linked to the whole rRNA, to 5 S RNA and to 28 -5.8 S RNAs were identified by two-dimensional gel electrophoresis after RNA hydrolysis by ribonucleases TI and A. Our results showed that numerous proteins interact with rRNAs (at least ten with 28-5.8s RNA, eight with 5 s RNA and among these three are common to both) and have been discussed in the light of all the available data.The proteins and rRNAs in ribosomes are arranged in a specific configuration to form functional domains. In the case of large ribosomal subunits it has been postulated that the 5 s RNA binding area has specific roles in the ribosomal peptidyltransferase and GTPase/ATPase activities, in tRNAbinding and subunit association [I]. As for the large RNA (23 -28 S), recent developments of nucleotide sequence data and phylogenetic sequence comparison show that it contains highly conserved RNA sequences that should be important in peptidyltransferase and GTPase activities [2], most likely with their contacting proteins. The identification of the proteins that interact directly with 5 s RNA and large RNA within the active large subunit is, then, a prerequisite task for understanding the ribosome function. While all published studies agree and show the existence of multiple well-defined 5 s RNA and 23s RNA binding proteins in prokaryotes, there is still controversy about the number and nature of the proteins interacting with eukaryotic 5 s and 28s RNAs (see Discussion).In order to elucidate this question we identified the proteins that were cross-linked to 5s RNA and 28 S RNA within 60s subunits submitted to low doses of short-wave ultraviolet radiations (254nm). A large amount of work done on Escherichia coli ribosomes has shown that protein-RNA cross-linking is induced by these radiations with a high degree of specifity [3-61. Our study, which is a complement to an earlier one [7], allowed us to draw conclusions as to the arrangement of the proteins and rRNAs in the 60s subunits. MATERIALS AND METHODS ChemicalsNalz5I(14 Ci/mg) was obtained from New England Nuclear, ribonucleases TI and A were supplied by Worthington.Correspondence to J. P. Reboud, Laboratoire de Biochimie Medicale, Universite Claude Bernard, U.E.R. Lyon-Nord, 43, Boulevard du 11 Novembre 191 8, F-69622 Villeurbanne-Cedex, FranceAbbreviations. RNPEoTA and RNP", the 5 S-RNA -protein complexes that are released from 60 S subunits by EDTA and heating, respectively; SDS, sodium dodecyl sulfate. Ultraviolet irradiation and analysis of proteins cross-linked to rRNAs60s subunits were prepared from free polysomes, as previously described [S]. They were subjected to reductive methylation prior to irradiation, since we found this procedure effective for diminishing aggregation of irradiated su...

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Section: Discussionsupporting

confidence: 61%

Photo‐induced protein cross‐linking to 5S RNA and 28–5.8S RNA within rat‐liver 60S ribosomal subunits

Paleologue

Reboud

1985

European Journal of Biochemistry

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“…Specific conformational 'switches' (a switch being defined as the existence of two mutually exclusive secondary structural elements) have been proposed by various authors for 16S and 23S RNA (e.g. Glotz & Brimacombe, 1980;Glotz et al, 1981;Thompson & Hearst, 1983a;Atmadja et al, 1984) and also for 5S RNA (Trifonov & Bolshoi, 1983;De Wachter et al, 1984).…”

Section: Function Of Rrnamentioning

confidence: 99%

Structure and function of ribosomal RNA

Brimacombe¹,

Stiege²

1985

Biochemical Journal

108

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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: T C O \ Y U C C G C a G U G U P G A A G A * U C G A A C U mentioning

confidence: 91%

“…Two bulges on complementary strands can converge by migrating in opposite directions and fuse to form a small internal loop or odd base pair. This mechanism, one of those previously proposed [7] to be responsible for secondary structure equilibria, is illustrated in Fig. 3.…”

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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Equilibria in 5-S ribosomal RNA secondary structure. Bulges and interior loops in 5-S RNA secondary structure may serve as articulations for a flexible molecule

Cited by 27 publications

References 35 publications

Photo‐induced protein cross‐linking to 5S RNA and 28–5.8S RNA within rat‐liver 60S ribosomal subunits

Photo‐induced protein cross‐linking to 5S RNA and 28–5.8S RNA within rat‐liver 60S ribosomal subunits

Structure and function of ribosomal RNA

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

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