RNA stem-loop enhanced expression of previously non-expressible genes

Paulus, Michael J.

doi:10.1093/nar/gnh076

Cited by 36 publications

(37 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…34 When stable hairpins where introduced in close proximity to the ribosome binding site of a highly expressed gfp-reporter construct, translation was drastically reduced. Positioning of the same hairpin outside of the TIR resulted in high expression.…”

Section: Resultsmentioning

confidence: 99%

“…This position does not interfere with ribosome binding as the contact region spans nucleotides -35 to +20 relative to the AUG. 35 It has been suggested that a stable hairpin prevents long range interaction of the TIR with the 3'-end of the corresponding mRNA. 34 It is possible that hairpins I and II of ROSE ibpA not only serve as a folding scaffold for hairpin III but also prevent the TIR from undesired downstream interactions.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

TheEscherichia coliibpA thermometer is comprised of stable and unstable structural elements

Waldminghaus¹,

Gaubig

Klinkert

et al. 2009

RNA Biology

View full text Add to dashboard Cite

Translation of many small heat shock genes in α-and γ-proteobacteria is controlled by the ROSE (Repression Of heat Shock gene Expression) element, a thermo-responsive RNA structure in the 5'-untranslated region. ROSE ibpA regulates translation of the Escherichia coli ibpA gene coding for an inclusion body-associated protein. We present first structural insights into a full-length ROSE element by examining the temperatureinduced conformational changes of ROSE ibpA using detailed enzymatic and lead probing experiments between 20 and 50°C. The initial two hairpins are stable at all temperatures tested and might assist in proper folding of the third temperature-responsive stem-loop structure, which restricts access to the Shine-Dalgarno sequence at temperatures below 35°C. Toeprinting (primer extension inhibition) experiments show that binding of the 30S ribosome to ROSE ibpA is enhanced at high temperatures. In contrast to other ROSE-like elements, the final hairpin is rather short. Single point mutations result in alternative structures with positive or negative effects on translation efficiency. Our study demonstrates how the combination of stable and unstable modules controls translation efficiency in a complete RNA thermometer.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

TheEscherichia coliibpA thermometer is comprised of stable and unstable structural elements

Waldminghaus¹,

Gaubig

Klinkert

et al. 2009

RNA Biology

View full text Add to dashboard Cite

show abstract

“…The effects of mRNA secondary structure modification on bacterial translation, for instance, are studied in [56]. Inhibition of ribozymes by means of oligonucleotide directed RNA misfolding has been demonstrated e.g.…”

Section: Introductionmentioning

confidence: 99%

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model

Hackermüller¹,

Meisner²,

Auer³

et al. 2005

Gene

View full text Add to dashboard Cite

RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural feature on the binding affinities follows directly from this approach. The formalism is extended to describing the effects of hybridizing small "modifier RNAs" to a target RNA molecule outside its ligand binding site. We illustrate the applicability of our approach by quantitatively describing the interaction of the mRNA stabilizing protein HuR with AU-rich elements [Meisner et al. (2004), Chem. Biochem. in press]. We discuss our model and recent experimental findings demonstrating the effectivity of modifier RNAs in vitro in the context of the current research activities in the field of non-coding RNAs. We speculate that modifier RNAs might also exist in nature; if so, they present an additional regulatory layer for fine-tuning gene expression that could evolve rapidly, leaving no obvious traces in the genomic DNA sequences.

show abstract

“…(5) Synthetic "modifier RNAs" have been used as experimental techniques for changing the gene expression patterns independent of the RNAi pathway 10,54,62 . One possible mechanism is the modification of (m)RNA structure as a consequence of the duplex formation between modifier and its target (m)RNA, which in turn can dramatically affect the binding affinity of the (m)RNA and a protein 25 .…”

Section: Regulation By Rnamentioning

confidence: 99%

A Story of Growing Confusion: Genes and Their Regulation

Prohaska

Stadler

2008

Biophys. Rev. Lett.

View full text Add to dashboard Cite

High-throughput experiments have produced convicing evidence for an extensive contribution of diverse classes of RNAs in the expression of genetic information. Instead of a simple arrangement of mostly protein-coding genes, the human transcriptome features a complex arrangement of overlapping transcripts, many of which do not code for proteins at all, while others "sample" exons from several different "genes". The complexity of the transcriptome and the prevalence of noncoding transcripts forces us to reconsider both the concept of the "gene" itself and our understanding of the mechanisms that regulate "gene expression".

show abstract

RNA stem-loop enhanced expression of previously non-expressible genes

Cited by 36 publications

References 57 publications

TheEscherichia coliibpA thermometer is comprised of stable and unstable structural elements

TheEscherichia coliibpA thermometer is comprised of stable and unstable structural elements

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model

A Story of Growing Confusion: Genes and Their Regulation

Contact Info

Product

Resources

About