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The ribosome, stringent factor and the bacterial stringent response
Stockholm University, Faculty of Science, Wenner-Gren Institute for Experimental Biology.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The stringent response plays a significant role in the survival of bacteria during different environmental conditions. It is activated by the binding of stringent factor (SF) to stalled ribosomes that have an unacylated tRNA in the ribosomal A-site which leads to the synthesis of (p)ppGpp. ppGpp binds to the RNA polymerase, resulting in a rapid down-regulation of rRNA and tRNA transcription and up-regulation of mRNAs coding for enzymes involved in amino acid biosynthesis. The importance of the A-site and unacylated tRNA in the activation of SF was confirmed by chemical modification and subsequent primer extension experiments (footprinting experiments) which showed that binding of SF to ribosomes resulted in the protection of regions in 23S rRNA, the A-loop and helix 89 that are involved in the binding of the A-site tRNA. An in vitro assay showed that the ribosomal protein L11 and its flexible N-terminal part was important in the activation of SF. Interestingly the N-terminal part of L11 was shown to activate SF on its own and this activation was dependent on both ribosomes and an unacylated tRNA in the A-site. The N-terminal part of L11 was suggested to mediate an interaction between ribosome-bound SF and the unacylated tRNA in the A-site or interact with SF and the unacylated tRNA independently of each other. Footprinting experiments showed that SF bound to the ribosome protected bases in the L11 binding domain of the ribosome that were not involved in an interaction with ribosomal protein L11. The sarcin/ricin loop, in close contact with the L11 binding domain on the ribosome and essential for the binding and activation of translation elongation factors was also found to be protected by the binding of SF. Altogether the presented results suggest that SF binds to the factor-binding stalk of the ribosome and that activation of SF is dependent on the flexible N-terminal domain of L11 and an interaction of SF with the unacylated tRNA in the A-site of the 50S subunit.

Place, publisher, year, edition, pages
Stockholm: Wenner-Grens institut för experimentell biologi , 2007. , 55 p.
Keyword [en]
Ribosome, stringent factor, stringent response, tRNA, ribosomal protein L11, pppGpp
National Category
Cell Biology
Research subject
Cellbiology
Identifiers
URN: urn:nbn:se:su:diva-6739ISBN: 978-91-7155-414-7 (print)OAI: oai:DiVA.org:su-6739DiVA: diva2:196962
Public defence
2007-04-20, sal MA331, Södertörns högskola, Alfred Nobels allé 7, Huddinge, 13:00
Opponent
Supervisors
Available from: 2007-03-29 Created: 2007-03-20Bibliographically approved
List of papers
1. Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli
Open this publication in new window or tab >>Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli
2005 In: FEBS Journal, ISSN 1742-464X, Vol. 272, no 3, 685-695 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24182 (URN)
Note
Part of urn:nbn:se:su:diva-6739Available from: 2007-03-29 Created: 2007-03-20Bibliographically approved
2. The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor
Open this publication in new window or tab >>The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor
2007 In: Journal of molecular biology, ISSN 0022-2836, Vol. 365, no 3, 764-772 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24183 (URN)000243561500021 ()
Note
Part of urn:nbn:se:su:diva-6739Available from: 2007-03-29 Created: 2007-03-20Bibliographically approved
3. Mapping the interaction between stringent factor and the ribosome by footprinting of ribosomal RNA
Open this publication in new window or tab >>Mapping the interaction between stringent factor and the ribosome by footprinting of ribosomal RNA
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-24184 (URN)
Note
Part of urn:nbn:se:su:diva-6739Available from: 2007-03-29 Created: 2007-03-20 Last updated: 2010-01-13Bibliographically approved

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