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Journal Article

Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons97374

Scharff,  L. B.
Organelle Biology and Biotechnology, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97105

Childs,  L.
BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97467

Walther,  D.
BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons97077

Bock,  R.
Organelle Biology and Biotechnology, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Scharff, L. B., Childs, L., Walther, D., & Bock, R. (2011). Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites. PLoS Genetics, 7(6), e1002155. doi:10.1371/journal.pgen.1002155.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-20D4-4
Abstract
The initiation of translation is a fundamental and highly regulated process in gene expression. Translation initiation in prokaryotic systems usually requires interaction between the ribosome and an mRNA sequence upstream of the initiation codon, the so-called ribosome-binding site (Shine-Dalgarno sequence). However, a large number of genes do not possess Shine-Dalgarno sequences, and it is unknown how start codon recognition occurs in these mRNAs. We have performed genome-wide searches in various groups of prokaryotes in order to identify sequence elements and/or RNA secondary structural motifs that could mediate translation initiation in mRNAs lacking Shine-Dalgarno sequences. We find that mRNAs without a Shine-Dalgarno sequence are generally less structured in their translation initiation region and show a minimum of mRNA folding at the start codon. Using reporter gene constructs in bacteria, we also provide experimental support for local RNA unfoldedness determining start codon recognition in Shine-Dalgarno-independent translation. Consistent with this, we show that AUG start codons reside in single-stranded regions, whereas internal AUG codons are usually in structured regions of the mRNA. Taken together, our bioinformatics analyses and experimental data suggest that local absence of RNA secondary structure is necessary and sufficient to initiate Shine-Dalgarno-independent translation. Thus, our results provide a plausible mechanism for how the correct translation initiation site is recognized in the absence of a ribosome-binding site.