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The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits.
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
Umeå University, Faculty of Medicine, Molecular Biology.
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology.
Umeå University, Faculty of Medicine, Molecular Biology.
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2004 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 10, no 11, 1798-1812 p.Article in journal (Refereed) Published
Abstract [en]

The RimM protein in Escherichia coli is associated with free 30S ribosomal subunits but not with 70S ribosomes. A DeltarimM mutant is defective in 30S maturation and accumulates 17S rRNA. To study the interaction of RimM with the 30S and its involvement in 30S maturation, RimM amino acid substitution mutants were constructed. A mutant RimM (RimM-YY-->AA), containing alanine substitutions for two adjacent tyrosines within the PRC beta-barrel domain, showed a reduced binding to 30S and an accumulation of 17S rRNA compared to wild-type RimM. The (RimM-YY-->AA) and DeltarimM mutants had significantly lower amounts of polysomes and also reduced levels of 30S relative to 50S compared to a wild-type strain. A mutation in rpsS, which encodes r-protein S19, suppressed the polysome- and 16S rRNA processing deficiencies of the RimM-YY-->AA but not that of the DeltarimM mutant. A mutation in rpsM, which encodes r-protein S13, suppressed the polysome deficiency of both rimM mutants. Suppressor mutations, found in either helices 31 or 33b of 16S rRNA, improved growth of both the RimM-YY-->AA and DeltarimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY-->AA mutant more efficiently than that of the DeltarimM mutant. Helices 31 and 33b are known to interact with S13 and S19, respectively, and S13 is known to interact with S19. A GST-RimM but not a GST-RimM(YY-->AA) protein bound strongly to S19 in 30S. Thus, RimM likely facilitates maturation of the region of the head of 30S that contains S13 and S19 as well as helices 31 and 33b.

Place, publisher, year, edition, pages
2004. Vol. 10, no 11, 1798-1812 p.
Keyword [en]
Alanine/metabolism, Amino Acid Sequence, Amino Acid Substitution, Bacterial Proteins/*chemistry/genetics/*metabolism, Escherichia coli/genetics/growth & development, Escherichia coli Proteins/*chemistry/genetics/*metabolism, Gene Expression Regulation; Bacterial, Glutathione Transferase/metabolism, Models; Molecular, Molecular Sequence Data, Mutagenesis; Site-Directed, Mutation, Protein Structure; Tertiary, RNA Processing; Post-Transcriptional, RNA; Ribosomal; 16S/genetics/metabolism, RNA-Binding Proteins, Recombinant Proteins/metabolism, Ribosomal Proteins/*chemistry/genetics/*metabolism, Ribosomes/*metabolism, Sequence Homology; Amino Acid, Tyrosine/metabolism
National Category
Medical and Health Sciences
URN: urn:nbn:se:umu:diva-16783DOI: 10.1261/rna.7720204PubMedID: 15496525OAI: diva2:156456
Available from: 2007-10-11 Created: 2007-10-11 Last updated: 2010-08-06Bibliographically approved
In thesis
1. Accessory factors for ribosomal assembly
Open this publication in new window or tab >>Accessory factors for ribosomal assembly
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The assembly of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) into ribosomal subunits (30S and 50S) is a complex process. Transcription of rRNA requires antitermination proteins and the primary transcripts are processed by ribonucleases. R-proteins and rRNAs are chemically modified, the r-proteins bind to the rRNAs and the formed RNA-protein complexes are folded into mature ribosomal subunits. All these processes are well-coordinated and overlapping. Non-ribosomal factors are required for proper assembly and maturation of the ribosomal subunits. Two of these factors are the RimM and RbfA proteins, which bind to 30S subunits and are important for efficient processing of 16S rRNA. Lack of either RimM or RbfA results in a reduced amount of polysomes and a lower growth rate. An increased amount of RbfA can partially compensate for deficiencies shown by a RimM lacking mutant.

Here, mutations that alter phylogenetically conserved amino acids in RimM have been constructed. One of these (rimM120), which resulted in the replacement of two adjacent tyrosines by alanines, reduced the growth rate three-fold and also decreased the processing efficiency of 16S rRNA. The RimM120 mutant protein showed a much reduced binding to the 30S subunits. Suppression of the rimM120 mutant was achieved by increased amount of the RimM120 protein, by overexpression of rbfA, or by mutations that changed r-protein S19 or 16S rRNA. A variant of r-protein S13, which was previously isolated as a suppressor to a deletion of rimM (∆rimM), suppressed also the rimM120 mutation. The wild-type RimM protein, but not the RimM120 protein, was shown to bind r-protein S19 in the 30S subunits. The changes in S13, S19 and 16S rRNA that compensated for the deficiencies shown by the rimM mutants are all located within a small region of the head of the 30S subunit, suggesting that this region is the likely target for the RimM action.

To isolate RbfA variants that show reduced association with the 30S subunits, phylogenetically conserved, surface exposed amino acid residues of RbfA were changed to alanines or, in some instances, to amino acids of the opposite charge to that in the wild-type protein. Alterations of F5, R31, D46 and D100 had the largest effect on growth.

Mutations in the metY-nusA-infB operon, isolated as suppressors to the ∆rimM mutant, were shown to increase the amounts of RbfA. In a ∆rimM mutant, all RbfA protein was found associated with the 30S subunits and no free RbfA was detected.

The RlmB protein was shown to be the methyltransferase responsible for the formation of Gm2251 in 23S rRNA in Escherichia coli. Unlike a Saccharomyces cerevisiae mutant that lacks the orthologue to RlmB, Pet56p, which methylates mitochondrial rRNA, a ∆rlmB mutant did not show any defects in ribosomal assembly.

Place, publisher, year, edition, pages
Umeå: Molekylärbiologi (Teknisk-naturvetenskaplig fakultet), 2004. 57 p.
Molecular biology, RimM, RbfA, RlmB, ribosomal assembly, rRNA processing, Molekylärbiologi
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
urn:nbn:se:umu:diva-385 (URN)91-7305-783-5 (ISBN)
Public defence
2005-01-14, major groove, 6L, NUS, Institutionen för molekylärbiologi, 901 87 Umeå, Umeå, 13:00
Available from: 2004-12-15 Created: 2004-12-15 Last updated: 2010-08-06Bibliographically approved

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Lövgren, MattiasBylund, GöranLundberg, CarinaPersson, OlofWikström, Mikael
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