Mutations in the leader region of ribosomal RNA operons cause structurally defective 30 S ribosomes as revealed by in vivo structural probing

Balzer, Monika; Wagner, Rolf

doi:10.1006/jmbi.1997.1556

Cited by 17 publications

(10 citation statements)

References 31 publications

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“…The short ncRNA is often an anti-sense transcript of the corresponding mRNA, the trans RNA-RNA interaction typically involves a short stretch of near-complementarity, and a protein is often required as a third ingredient for the regulatory mechanism to be functional. Yet another example of a functionally relevant trans RNA-RNA interaction is the formation of the 30S ribosomal subunit in bacteria, which requires the transient interaction with the leader sequence of the rRNA operons (Balzer and Wagner 1998).…”

Section: Chaperone-rna Interactionsmentioning

confidence: 99%

On the importance of cotranscriptional RNA structure formation

Lai

Proctor

Meyer

2013

RNA

154

132

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The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.

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Section: Chaperone-rna Interactionsmentioning

confidence: 99%

On the importance of cotranscriptional RNA structure formation

Lai

Proctor

Meyer

2013

RNA

154

132

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“…For example, refolding of a metastable structure regulates translation in Escherichia coli phage MS2 (Groeneveld et al 1995;Poot et al 1997) and the activity of antisense RNAs expressed by plasmidborne killer genes (Nagel et al 1999). In bacterial prerRNA, a metastable interaction with leader sequences promotes proper assembly of 30 S ribosome and maturation of the 16 S rRNA (Balzer and Wagner 1998;Besancon and Wagner 1999).…”

Section: Introductionmentioning

confidence: 99%

Effect of transcription on folding of the Tetrahymena ribozyme

Heilman-Miller

Woodson²

2003

RNA

102

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Sequential formation of RNA interactions during transcription can bias the folding pathway and ultimately determine the functional state of a transcript. The kinetics of cotranscriptional folding of the Tetrahymena L-21 ribozyme was compared with refolding of full-length transcripts under the same conditions. Sequential folding after transcription by phage T7 or Escherichia coli polymerase is only twice as fast as refolding, and the yield of native RNA is the same. By contrast, a greater fraction of circularly permuted variants folded correctly at early times during transcription than during refolding. Hybridization of complementary oligonucleotides suggests that cotranscriptional folding enables a permuted RNA beginning at G303 to escape nonnative interactions in P3 and P9. We propose that base pairing of upstream sequences during transcription elongation favors branched secondary structures that increase the probability of forming the native ribozyme structure.

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“…It is known, for example, that the temporary interaction with highly conserved leader sequences of bacterial rRNA-operons is needed for the proper formation of 30S ribosomal subunits and the maturation of 16S rRNA [33,34]. …”

Section: Introductionmentioning

confidence: 99%

Co-transcriptional folding is encoded within RNA genes

Meyer

Miklós

2004

BMC Molecular Biol

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Background: Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription.

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Mutations in the leader region of ribosomal RNA operons cause structurally defective 30 S ribosomes as revealed by in vivo structural probing

Cited by 17 publications

References 31 publications

On the importance of cotranscriptional RNA structure formation

On the importance of cotranscriptional RNA structure formation

Effect of transcription on folding of the Tetrahymena ribozyme

Co-transcriptional folding is encoded within RNA genes

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