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Structural features of the tmRNA-ribosome interaction
Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
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2009 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 15, no 12, 2312-2320 p.Article in journal (Refereed) Published
Abstract [en]

Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA-ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation.

Place, publisher, year, edition, pages
RNA Society , 2009. Vol. 15, no 12, 2312-2320 p.
URN: urn:nbn:se:su:diva-31967DOI: 10.1261/rna.1584209ISI: 000272169000020PubMedID: 19861420OAI: diva2:279072
9 authorsAvailable from: 2009-12-01 Created: 2009-12-01 Last updated: 2010-08-04Bibliographically approved
In thesis
1. Studies on Translation Initiation and trans-Translation
Open this publication in new window or tab >>Studies on Translation Initiation and trans-Translation
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

 Translation initiation factor 1 (IF1) is an essential bacterial protein, without any clearly defined function in translation initiation. Same point mutants in this protein exhibit cold-sensitivity. In addition, a sequence specific increase in test protein expression has been observed for these mutants. Here in Paper I we analyze the parts of mRNA translation initiation region (TIR) involved in this effect, showing that Shine-Dalgarno sequence (SD), upstream enhancer region as well as linker between the initiation codon and SD are important. The similarity in action between the mutated IF1 and the antibiotic kasugamycin leads us to the suggestion that it occurs during the recently discovered proof-reading stage after the subunit joining step in the translation initiation. Deletion of yggJ and cspA genes involved in mRNA translation partially suppresses the cold-sensitivity phenotype of the R40D IF1 mutant. Deletion of the bipA gene confers even higher suppression confirming the previously assigned function of this protein in initiation of translation. In Paper II of this thesis proteome analysis of the IF1 mutation and kasugamycin action reveals some interesting features, such as increase in S6 polyglutamylation in the IF1 mutant cells or high level of GroEL-GroES protein in the cells treated with kasugamycin. A subset of genes having a similar TIR-specific increase in the expression under both conditions confirms previously made observations. Finally, in the Paper III we use cryo-electron tomography as well as chemical probing and computational modeling to address the question, how tmRNA moves on the ribosome during trans-translation. We observe that the tmRNA pseudoknots remain intact, while the mRNA part moves in the mRNA channel, allowing translation elongation to proceed.

Place, publisher, year, edition, pages
Stockholm: Department of Genetics, Microbiology and Toxicology,Stockholm university, 2010. 96 p.
E. coli, ribosome, IF1, tmRNA, trans-translaton
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Genetics
urn:nbn:se:su:diva-39304 (URN)978-91-7447-099-4 (ISBN)
Public defence
2010-06-18, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
At the time of doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: In press.Available from: 2010-05-27 Created: 2010-05-17 Last updated: 2010-08-04Bibliographically approved

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Surkov, SerhiyIsaksson, Leif A
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