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Structure probing of tmRNA in distinct stages of trans-translation
Södertörn University, School of Life Sciences.
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2007 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 13, no 5, 713-722 p.Article in journal (Refereed) Published
Abstract [en]

Ribosomes stalled on problematic mRNAs in bacterial cells can be rescued by transfer-messenger RNA ( tmRNA), its helper protein ( small protein B, SmpB), and elongation factor Tu (EF-Tu) through a mechanism called trans-translation. In this work we used lead(II) footprinting to probe the interactions of tmRNA with SmpB and other components of the translation machinery at different steps of the trans-translation cycle. Ribosomes with a short nascent peptide stalled on a truncated mRNA were reacted with Ala-tmRNAdEF-TudGTP, SmpB, and other translation components to initiate and execute trans-translation. Free tmRNA was probed with lead( II) acetate with and without SmpB, and ribosome bound tmRNA was probed in one of four different trans-translation states stabilized by antibiotic addition or selective exclusion of translation components. For comparison, we also analyzed lead( II) cleavage patterns of tmRNA in vivo in a wild-type as well as in an SmpB-deficient Escherichia coli strain. We observed some specific cleavages/protections in tmRNA for the individual steps of trans-translation, but the overall tmRNA conformation appeared to be similar in the stages analyzed. Our findings suggest that, in vivo, a dominant fraction of tmRNA is in complex with SmpB and that, in vitro, SmpB remains tmRNA bound at the initial steps of trans-translation.

Place, publisher, year, edition, pages
2007. Vol. 13, no 5, 713-722 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:sh:diva-14226DOI: 10.1261/rna.451507ISI: 000245882400010PubMedID: 17400816Scopus ID: 2-s2.0-34247338538OAI: oai:DiVA.org:sh-14226DiVA: diva2:467807
Available from: 2011-12-19 Created: 2011-12-19 Last updated: 2017-07-18Bibliographically approved

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf