title: Circular code motifs near the ribosome decoding center.
abstract: A maximal C(3) self-complementary trinucleotide circular code X is identified in genes of bacteria, eukaryotes, plasmids and viruses (Michel, 2015; Arquès and Michel, 1996). A translation (framing) code based on the circular code was proposed in Michel (2012) with the identification of several X circular code motifs (X motifs shortly) in both ribosomal RNAs (rRNAs) and their decoding center, and transfer RNAs (tRNAs). We extended these results in two ways. First, three universal X motifs were determined in the ribosome decoding center: the X motif mAA containing the conserved nucleotides A1492 and A1493, the X motif mG containing the conserved nucleotide G530 and the X motif m with unknown biological function (El Soufi and Michel, 2014). Secondly, statistical analysis of X motifs of greatest lengths performed on different and large tRNA populations according to taxonomy, tRNA length and tRNA score showed that these X motifs have occurrence probabilities in the 5' and/or 3' regions of 16 isoaccepting tRNAs of prokaryotes and eukaryotes greater than the random case (Michel, 2013). We continue here the previous works with the identification of X motifs in rRNAs of prokaryotes and eukaryotes near the ribosome decoding center. Seven X motifs PrRNAXm conserved in 16S rRNAs of prokaryotes P and four X motifs ErRNAXm conserved in 18S rRNAs of eukaryotes E are identified near the ribosome decoding center. Furthermore, four very large X motifs of length greater than or equal to 20 nucleotides, 14 large X motifs of length between 16 and 19 nucleotides and several X motifs of length greater or equal to 9 nucleotides are found in tRNAs of prokaryotes. Some properties of these X motifs in tRNAs are described. These new results strengthen the concept of a translation code based on the circular code (Michel, 2012).
authors.affiliation: Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France. Electronic address: kelsoufi@unistra.fr.
authors.forename: Karim
authors.initials: K
authors.lastname: El Soufi
authors.affiliation: Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France. Electronic address: c.michel@unistra.fr.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology; D059372:Nucleotide Motifs / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D012343:RNA, Transfer
keywords: Circular code motif; Ribosomal RNA; Transfer RNA; Translation code