Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites.
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 s...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-06-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3121790?pdf=render |
| _version_ | 1818015709099196416 |
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| author | Lars B Scharff Liam Childs Dirk Walther Ralph Bock |
| author_facet | Lars B Scharff Liam Childs Dirk Walther Ralph Bock |
| author_sort | Lars B Scharff |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T07:01:32Z |
| format | Article |
| id | doaj.art-89043296d91e4aa4b73267dc5026d1a6 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-14T07:01:32Z |
| publishDate | 2011-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-89043296d91e4aa4b73267dc5026d1a62022-12-22T02:06:45ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-06-0176e100215510.1371/journal.pgen.1002155Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites.Lars B ScharffLiam ChildsDirk WaltherRalph BockThe 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.http://europepmc.org/articles/PMC3121790?pdf=render |
| spellingShingle | Lars B Scharff Liam Childs Dirk Walther Ralph Bock Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. PLoS Genetics |
| title | Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. |
| title_full | Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. |
| title_fullStr | Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. |
| title_full_unstemmed | Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. |
| title_short | Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. |
| title_sort | local absence of secondary structure permits translation of mrnas that lack ribosome binding sites |
| url | http://europepmc.org/articles/PMC3121790?pdf=render |
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