Structure of eukaryotic 5S ribonucleic acid: a study of Saccharomyces cerevisiae 5S RNA with ribonucleases

Garrett, Roger A.; Olesen, Svend Ole

doi:10.1021/bi00262a047

Cited by 33 publications

(16 citation statements)

References 25 publications

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“…It is important to note that V 1 does not cleave at every base pair in the U5-IR stem. This is particularly noteworthy for the extended RDS U5-IR stem and is consistent with other studies showing that RNase V 1 cleaves selected base pairs (16,24,31) in the center of a helix consisting of a minimum of four to six contiguous stacked base pairs (4,25). In addition, the structure of the helix may change once the initial V 1 cut is made in the helical backbone, significantly reducing the affinity of the enzyme for substrate (13).…”

Section: Discussionsupporting

confidence: 90%

“…In addition, the structure of the helix may change once the initial V 1 cut is made in the helical backbone, significantly reducing the affinity of the enzyme for substrate (13). V 1 has also been shown to asymmetrically cleave certain helices so that one side is preferentially cleaved over the other (4,16,24). An alternative explanation for the RDS stem cleavage pattern is that the extended RDS U5-IR stem may participate in a tertiary interaction which sterically blocks the access of RNase V 1 to the stem.…”

Section: Discussionmentioning

confidence: 99%

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Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA ^Trp Primer Annealing

Morris

Leis

1999

J Virol

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Predicted secondary-structure elements encompassing the primer binding site in the 5′ untranslated region of Rous sarcoma virus (RSV) RNA play an integral role in multiple viral replications steps including reverse transcription, DNA integration, and RNA packaging (A. Aiyar, D. Cobrinik, Z. Ge, H. J. Kung, and J. Leis, J. Virol. 66:2464–2472, 1992; D. Cobrinik, A. Aiyar, Z. Ge, M. Katzman, H. Huang, and J. Leis, J. Virol. 65:3864–3872, 1991; J. T. Miller, Z. Ge, S. Morris, K. Das, and J. Leis, J. Virol. 71:7648–7656, 1997). These elements include the U5-Leader stem, U5-IR stem-loop, and U5-TΨC interaction region. Limited digestion of the 5′ untranslated region of wild-type and mutant RSV RNAs with structure- and/or sequence-specific RNases detects the presence of the U5-Leader stem and the U5-IR stem-loop. When a tRNATrp primer is annealed to wild-type RNAs in vitro, limited nuclease mapping indicates that the U5-IR stem becomes partially unwound. This is not observed when mutant RNAs with altered U5-IR stem-loop structures are substituted for wild-type RNAs. The U5-Leader stem also becomes destabilized when the tRNA primer is annealed to either wild-type or mutant RNA fragments. Nuclease mapping studies of tRNATrp, as well as the viral RNA, indicate that the U5-TΨC helix does form in vitro upon primer annealing. Collectively, these data suggest that the various structural elements near the RSV primer binding site undergo significant changes during the process of primer annealing.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA ^Trp Primer Annealing

Morris

Leis

1999

J Virol

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“…VA RNAs of all other groups have at least six ostensibly unmatched nucleotides on each side, but it is likely that these nucleotides are organized in some kind of compact structure because in most cases they are relatively insensitive to attack by singlestrand-specific nucleases. Precedents for such compact arrangements exist in 5S RNA (21,75) and the Rev response element RNA (4).…”

Section: Discussionmentioning

confidence: 99%

Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach

Mathews

1996

J Virol

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To explore the structure and function of a small regulatory RNA, we examined the virus-associated (VA) RNA species of all 47 known human adenovirus serotypes and of one simian virus, SA7. The VA RNA gene regions of 43 human adenoviruses were amplified and sequenced, and the structures of 10 representative VA RNAs were probed by nuclease sensitivity analysis. Most human viruses have two VA RNA species, VA RNA I and VA RNA II , but nine viruses (19%) have a single VA RNA gene. Sequence alignments classified the RNAs into eight families, corresponding broadly to the known virus groups, and three superfamilies. One superfamily contains the single VA RNAs of groups A and F and the VA RNA I species of group C; the second contains the VA RNA I species of groups B1, D, and E and the unclassified viruses (adenovirus types 42 to 47), as well as the single VA RNAs of group B2; and the third contains all VA RNA II species. Fourteen regions of homology occur throughout the molecule. The longest of these correspond to transcription signals; most of the others participate in RNA secondary structure. The previously identified tetranucleotide pair, GGGU:ACCC, is nearly invariant, diverging slightly (to GGGU:ACCU) only in the two group F viruses and forming a stem in the central domain that is critical for VA RNA structure and function. Secondary structure models which accommodate the nuclease sensitivity data and sequence variations within each family were generated. The major structural features-the terminal stem, apical stem-loop, and central domain-are conserved in all VA RNAs, but differences exist in the apical stem and central domains, especially of the VA RNA II species. Sequence analysis suggests that an ancestral VA RNA gene underwent duplication during the evolution of viruses containing two VA RNA genes. Although the VA RNA II gene seems to have been lost or inactivated by secondary deletion events in some viruses, the high degree of homology among the VA RNA II species implies that this RNA may play an undiscovered role in virus survival. We speculate that the VA RNA genes originated from cellular sequences containing multiple tRNA genes.

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“…The fact that all 5S rRNA sequences can be folded into a common structure argues for highly conserved structural and functional roles in the ribosome. The solution structures of 5S rRNAs from both prokaryotic and eukaryotic sources have been studied with enzymatic or chemical probes [14][15][16][17][18][19].A crystal structure of 5S rRNA has not yet been obtained. Several tentative tertiary structure models have been © I R L Press Limited, Oxford, England.…”

mentioning

confidence: 99%

A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs ofXenopus laevis

Romaniuk¹,

Stevenson²,

Ehresmann³

et al. 1988

Nucl Acids Res

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The secondary and tertiary structures of Xenopus oocyte and somatic 5S rRNAs were investigated using chemical and enzymatic probes. The accessibility of both RNAs towards single-strand specific nucleases (T1, T2, A and S1) and a helix-specific ribonuclease from cobra venom (RNase V1) was determined. The reactivity of nucleobase N7, N3 and N1 positions towards chemical probes was investigated under native (5 mM MgCl2, 100 mM KCl, 20 degrees C) and semi-denaturing (1 mM EDTA, 20 degrees C) conditions. Ethylnitrosourea was used to identify phosphates not reactive towards alkylation under native conditions. The results obtained confirm the presence of the five helical stems predicted by the consensus secondary structure model of 5S rRNA. The chemical reactivity data indicate that loops C and D are involved in a number of tertiary interactions, and loop E folds into an unusual secondary structure. A comparison of the data obtained for the two types of Xenopus 5S rRNA indicates that the conformations of the oocyte and somatic 5S rRNAs are very similar. However, the data obtained with nucleases under native conditions, and chemical probes under semi-denaturing conditions, reveal that helices III and IV in the somatic 5S rRNA are less stable than the same structures in oocyte 5S rRNA. Using chimeric 5S rRNAs, it was possible to demonstrate that the relative resistance of oocyte 5S rRNA to partial denaturation in 4 M urea is conferred by the five oocyte-specific nucleotide substitutions in loop B/helix III. In contrast, the superior stability of oocyte 5S rRNA in the presence of EDTA is related to a single C substitution at position 79.

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Structure of eukaryotic 5S ribonucleic acid: a study of Saccharomyces cerevisiae 5S RNA with ribonucleases

Cited by 33 publications

References 25 publications

Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA ^Trp Primer Annealing

Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA ^Trp Primer Annealing

Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach

A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs ofXenopus laevis

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Structure of eukaryotic 5S ribonucleic acid: a study of Saccharomyces cerevisiae 5S RNA with ribonucleases

Cited by 33 publications

References 25 publications

Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA Trp Primer Annealing

Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA Trp Primer Annealing

Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach

A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs ofXenopus laevis

Contact Info

Product

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Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA ^Trp Primer Annealing

Changes in Rous Sarcoma Virus RNA Secondary Structure near the Primer Binding Site upon tRNA ^Trp Primer Annealing