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Ribosomal RNA is methylated in all organisms. The list of ribosomal RNA methyltransferases of E. coli and yeast has been completed few years ago. However, the set of enzymes responsible for modification of mammalian mitochondrial rRNA still miss several entities. We applied a homology search to find genes potentially responsible for modification of mice mitochondrial 12S rRNA residues m5U429 and m4C839 (human numbering). While bacterial counterpart of the modified nucleotide m4C839 of the mitochondrial 12S rRNA is the modified nucleotide m4Cm1402 of the 16S rRNA, m5U429 modification is unique for mammalian mitochondria. We applied CRISPR/Cas9 system to inactivate genes presumably responsible for modification of mitochondrial 12S rRNA residues m5U429 and m4C839 in mice cell line. Purification and mass-spectrometry analysis of the mitochondrial rRNA fragments containing modification sites revealed loss of methylation upon inactivation of target genes. An analysis of knockout phenotype will be presented. Updating of the rRNA methyltransferases list allows highlighting the ways of the evolution of ribosome modification machinery.