A mitochondrial rRNA dimethyladenosine methyltransferase in Arabidopsis

Institut für Biologie/Genetik, Humboldt-Universität, Chausseestr. 117, 10115 Berlin, Germany.
The Plant Journal (Impact Factor: 6.82). 11/2009; 61(4):558-69. DOI: 10.1111/j.1365-313X.2009.04079.x
Source: PubMed

ABSTRACT S-adenosyl-L-methionine-dependent rRNA dimethylases mediate the methylation of two conserved adenosines near the 3' end of the rRNA in the small ribosomal subunits of bacteria, archaea and eukaryotes. Proteins related to this family of dimethylases play an essential role as transcription factors (mtTFBs) in fungal and animal mitochondria. Human mitochondrial rRNA is methylated and human mitochondria contain two related mtTFBs, one proposed to act as rRNA dimethylase, the other as transcription factor. The nuclear genome of Arabidopsis thaliana encodes three dimethylase/mtTFB-like proteins, one of which, Dim1B, is shown here to be imported into mitochondria. Transcription initiation by mitochondrial RNA polymerases appears not to be stimulated by Dim1B in vitro. In line with this finding, phylogenetic analyses revealed Dim1B to be more closely related to a group of eukaryotic non-mitochondrial rRNA dimethylases (Dim1s) than to fungal and animal mtTFBs. We found that Dim1B was capable of substituting the E. coli rRNA dimethylase activity of KsgA. Moreover, we observed methylation of the conserved adenines in the 18S rRNA of Arabidopsis mitochondria; this modification was not detectable in a mutant lacking Dim1B. These data provide evidence: (i) for rRNA methylation in Arabidopsis mitochondria; and (ii) that Dim1B is the enzyme catalyzing this process.

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Available from: Uwe Richter, Oct 16, 2014
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    • "In contrast, three TFB2M-like genes were found in the Arabidopsis nuclear genome, one of which coded for a mitochondrial protein named DIM1B (Richter et al., 2010). Unlike TFB2M, DIM1B was found to function as a mitochondrial rRNA dimethyl transferase rather than transcriptional cofactor, and phylogenetic analyses placed DIM1B and its plant orthologues next to nucleolar rRNA dimethyl transferases rather than yeast Mtf1 or mammalian TFB2M (Richter et al., 2010). "
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    ABSTRACT: The structural complexity of plant mitochondrial genomes correlates with the variety of single-strand DNA-binding proteins found in plant mitochondria. Most of these are plant-specific and have roles in homologous recombination and genome maintenance. Mitochondrial nucleoids thus differ fundamentally between plants and yeast or animals, where the principal nucleoid protein is a DNA-packaging protein that binds double-stranded DNA. Major transcriptional cofactors identified in mitochondria of non-plant species are also seemingly absent from plants. This article reviews current knowledge on plant mitochondrial DNA-binding proteins and discusses that those may affect the accessibility and conformation of transcription start sites, thus functioning as transcriptional modulators without being dedicated transcription factors.
    Mitochondrion 11/2014; 19. DOI:10.1016/j.mito.2014.02.004 · 3.52 Impact Factor
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    • "The plant mitoribosome contains three rRNA molecules encoded in the mitochondrial DNA, 26S and 5S for the LSU, and 18S for the SSU. The rRNAs undergo several important posttranscriptional modifications (pseudouridylation and methylation ; Bonen, 2004), and an rRNA methyltransferase required for the dimethylation of two conserved adenines in the mitochondrial 18S rRNA of Arabidopsis was characterized (Richter et al., 2010). "
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    ABSTRACT: The ribosome filter hypothesis posits that ribosomes are not simple non-selective translation machines but may also function as regulatory elements in protein synthesis. Recent data supporting ribosomal filtering come from plant mitochondria where it has been shown that translation of mitochondrial transcripts encoding components of oxidative phosphorylation complexes (OXPHOS) and of mitoribosomes can be differentially affected by alterations in mitoribosomes. The biogenesis of mitoribosome was perturbed by silencing of a gene encoding a small-subunit protein of the mitoribosome in Arabidopsis thaliana. As a consequence, the mitochondrial OXPHOS and ribosomal transcripts were both upregulated, but only the ribosomal proteins were oversynthesized, while the OXPHOS subunits were actually depleted. This finding implies that the heterogeneity of plant mitoribosomes found in vivo could contribute to the functional selectivity of translation under distinct conditions. Furthermore, global analysis indicates that biogenesis of OXPHOS complexes in plants can be regulated at different levels of mitochondrial and nuclear gene expression, however, the ultimate coordination of genome expression occurs at the complex assembly level.
    Frontiers in Plant Science 03/2014; 5:79. DOI:10.3389/fpls.2014.00079 · 3.95 Impact Factor
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    • "Confocal imaging revealed that DIM1A-GFP was localized primarily in root cell nuclei, most strongly in subnuclear regions presumed to be the nucleolus (Figures 6A to 6C). This result is consistent with recent work showing nucleolar localization of DIM1A-GFP transiently expressed in Arabidopsis protoplasts (Richter et al., 2010) and predominantly nucleolar localization of Dim1p in yeast (Lafontaine et al., 1998). At an organ-wide level, DIM1A-GFP was observed in all tissue types in the developing root (Figure 6F). "
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    ABSTRACT: Position-dependent patterning of hair and non-hair cells in the Arabidopsis thaliana root epidermis is a powerful system to study the molecular basis of cell fate specification. Here, we report an epidermal patterning mutant affecting the ADENOSINE DIMETHYL TRANSFERASE 1A (DIM1A) rRNA dimethylase gene, predicted to participate in rRNA posttranscriptional processing and base modification. Consistent with a role in ribosome biogenesis, DIM1A is preferentially expressed in regions of rapid growth, and its product is nuclear localized with nucleolus enrichment. Furthermore, DIM1A preferentially accumulates in the developing hair cells, and the dim1A point mutant alters the cell-specific expression of the transcriptional regulators GLABRA2, CAPRICE, and WEREWOLF. Together, these findings suggest that establishment of cell-specific gene expression during root epidermis development is dependent upon proper ribosome biogenesis, possibly due to the sensitivity of the cell fate decision to relatively small differences in gene regulatory activities. Consistent with its effect on the predicted S-adenosyl-l-Met binding site, dim1A plants lack the two 18S rRNA base modifications but exhibit normal pre-rRNA processing. In addition to root epidermal defects, the dim1A mutant exhibits abnormal root meristem division, leaf development, and trichome branching. Together, these findings provide new insights into the importance of rRNA base modifications and translation regulation for plant growth and development.
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