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Studies on the functional interaction of translation initiation factor IF1 with ribosomal RNA
Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Translation initiation factor IF1 is a small, essential and ubiquitous protein factor encoded by a single infA gene in bacteria. Although several important functions have been attributed to IF1, the precise reason for its indispensability is yet to be defined. It is known that IF1 binds to the ribosomal A-site during initiation, where it primarily contacts ribosomal RNA (rRNA) and induces large scale conformational changes in the small ribosomal subunit. To shed more light on the function of IF1 and its interaction with the ribosome, we have employed a genetic approach to elucidate structure-function interactions between IF1 and rRNA. A selection has been used to isolate second site suppressor mutations in rRNA that restore the growth of a cold sensitive mutant IF1 with an arginine to leucine substitution in position 69 (R69L).  This yielded two classes of suppressors – one class that mapped to the processing stem of 23S rRNA – a transient structure important for proper maturation of 23S rRNA; and the other class to the functional sequence of 16S rRNA. Suppressor mutations in the processing stem of 23S rRNA were shown to disrupt efficient processing of 23S rRNA. In addition, we report that at least one of the manifestations of cold sensitivity associated with the mutant IF1 is at the level of ribosomal subunit association. These results led to a model whereby the cold sensitive R69L mutant IF1 results in aberrant ribosomal subunit association properties, while the 23S processing stem mutations indirectly suppress this effect by decreasing the pool of mature 50S subunits available for association.  Spontaneous suppressor mutations in 16S rRNA were diverse in position and phenotypic properties, but all mutations affected ribosomal subunit association, in most cases by directly decreasing the affinity of the 30S for 50S subunits. Site directed mutagenesis of select positions in 16S rRNA yielded additional suppressor mutations that were localized to the mRNA and streptomycin binding sites on the small ribosomal subunit. We suggest that the 16S rRNA suppressors occur in positions that affect the conformational dynamics brought about by IF1. Taken together, this work indicates that the major function of IF1 is the modulation of ribosomal subunit association brought about through conformational changes of the 30S subunit.

Place, publisher, year, edition, pages
Stockholm: Department of Genetics, Microbiology and Toxicology, Stockholm University , 2012. , 44 p.
Keyword [en]
Escherichia coli, ribosome, rRNA mutation
National Category
Genetics
Research subject
Molecular Genetics
Identifiers
URN: urn:nbn:se:su:diva-75363ISBN: 978-91-7447-520-3 (print)OAI: oai:DiVA.org:su-75363DiVA: diva2:516680
Public defence
2012-05-30, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

Available from: 2012-05-08 Created: 2012-04-17 Last updated: 2013-04-16Bibliographically approved
List of papers
1. Suppression of a cold-sensitive mutant initiation factor 1 by alterations in the 23S rRNA maturation region
Open this publication in new window or tab >>Suppression of a cold-sensitive mutant initiation factor 1 by alterations in the 23S rRNA maturation region
2011 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 278, no 10, 1745-1756 p.Article in journal (Refereed) Published
Abstract [en]

Genetic selection has been used to isolate second-site suppressors of a defective cold-sensitive initiation factor I (IF1) R69L mutant of Escherichia coli. The suppressor mutants specifically map to a single rRNA operon on a plasmid in a strain with all chromosomal rRNA operons deleted. Here, we describe a set of suppressor mutations that are located in the processing stem of precursor 23S rRNA. These mutations interfere with processing of the 23S rRNA termini. A lesion of RNase III also suppresses the cold sensitivity. Our results suggest that the mutant IF1 strain is perturbed at the level of ribosomal subunit association, and the suppressor mutations partially compensate for this defect by disrupting rRNA maturation. These results support the notion that IF1 is an RNA chaperone and that translation initiation is coupled to ribosomal maturation.

Keyword
Escherichia coli, RNase III, rRNA mutation, rRNA processing, translation
National Category
Genetics
Research subject
Molecular Genetics
Identifiers
urn:nbn:se:su:diva-68511 (URN)10.1111/j.1742-4658.2011.08099.x (DOI)000290169300014 ()
Note
3Available from: 2012-01-07 Created: 2012-01-04 Last updated: 2017-12-08Bibliographically approved
2. Mutations in 16S rRNA that suppress cold-sensitive initiation factor 1 affect ribosomal subunit association
Open this publication in new window or tab >>Mutations in 16S rRNA that suppress cold-sensitive initiation factor 1 affect ribosomal subunit association
2011 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 278, no 18, 3508-3517 p.Article in journal (Refereed) Published
Abstract [en]

A mutation in the infA gene encoding initiation factor 1 (IF1) gives rise to a cold-sensitive phenotype. An Escherichia coli strain with this mutation was used as a tool to select for second-site suppressors that compensate for the cold sensitivity and map specifically to rRNA. Several suppressor mutants with altered 16S rRNA that partially restore growth of an IF1 mutant strain in the cold were isolated and characterized. Suppressor mutations were found in helix (h) 18, h32, h34 and h41 in 16S rRNA. These mutations are not clustered to any particular region in 16S rRNA and none overlap previously reported sites of interaction with IF1. While the isolated suppressors are structurally diverse, they are functionally related because all affect ribosomal subunit association in vivo. Furthermore, in vitro subunit-association experiments indicate that most of the suppressor mutations directly influence ribosomal subunit association even though none of these are confined to any of the known intersubunit bridges. These results are consistent with the model that IF1 is an rRNA chaperone that induces large-scale conformational changes in the small ribosomal subunit, and as a consequence modulates initiation of translation by affecting subunit association.

Keyword
16S rRNA mutant, Escherichia coli, IF1, rRNA maturation, translation
National Category
Genetics
Research subject
Molecular Genetics
Identifiers
urn:nbn:se:su:diva-68008 (URN)10.1111/j.1742-4658.2011.08272.x (DOI)000294810600027 ()
Note
3Available from: 2012-01-03 Created: 2012-01-02 Last updated: 2017-12-08Bibliographically approved
3. Mutations in the streptomycin and mRNA binding sites on 16S rRNA suppress a cold sensitive initiation factor IF1
Open this publication in new window or tab >>Mutations in the streptomycin and mRNA binding sites on 16S rRNA suppress a cold sensitive initiation factor IF1
(English)Manuscript (preprint) (Other academic)
Keyword
16S rRNA mutation, IF1, Escherichia coli, translation, streptomycin
National Category
Genetics
Research subject
Molecular Genetics
Identifiers
urn:nbn:se:su:diva-75374 (URN)
Available from: 2012-04-19 Created: 2012-04-17 Last updated: 2012-04-25Bibliographically approved

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