title: The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel.
abstract: N(6)-Methyladenosine 1618 of Escherichia coli 23 S rRNA is located in a cluster of modified nucleotides 12 A away from the nascent peptide tunnel of the ribosome. Here, we describe the identification of gene ybiN encoding an enzyme responsible for methylation of A1618. Knockout of the ybiN gene leads to loss of modification at A1618. The modification is restored if ybiN knock-out strain has been co-transformed with a plasmid expressing the ybiN gene. On the basis of these results we suggest that ybiN gene should be renamed to rlmF in accordance with the accepted nomenclature for rRNA methyltransferases. Recombinant YbiN protein is able to methylate partially deproteinized 50 S ribosomal subunit, so-called 3.5 M LiCl core particle in vitro, but neither the completely assembled 50 S subunits nor completely deproteinized 23 S rRNA. Both lack of the ybiN gene and it's over-expression leads to growth retardation and loss of cell fitness comparative to the parental strain. It might be suggested that A1618 modification could be necessary for the exit tunnel interaction with some unknown regulatory peptides.
authors.affiliation: Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia.
authors.forename: Petr V
authors.initials: PV
authors.lastname: Sergiev
authors.forename: Marina V
authors.initials: MV
authors.lastname: Serebryakova
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Bogdanov
authors.forename: Olga A
authors.initials: OA
authors.lastname: Dontsova
mesh_terms: D000225:Adenine / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D004925:Escherichia / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D005798:Genes, Bacterial; D008745:Methylation; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009154:Mutation; D010957:Plasmids; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000378:metabolism*; D011994:Recombinant Proteins / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D011994:Recombinant Proteins; D008780:Methyltransferases; D000225:Adenine