title: Circular code motifs in the ribosome decoding center.
abstract: A translation (framing) code based on the circular code was proposed in Michel (2012) with the identification of X circular code motifs (X motifs shortly) in the bacterial rRNA of Thermus thermophilus, in particular in the ribosome decoding center. Three classes of X motifs are now identified in the rRNAs of bacteria Escherichia coli and Thermus thermophilus, archaea Pyrococcus furiosus, nuclear eukaryotes Saccharomyces cerevisiae, Triticum aestivum and Homo sapiens, and chloroplast Spinacia oleracea. The universally conserved nucleotides A1492 and A1493 in all studied rRNAs (bacteria, archaea, nuclear eukaryotes, and chloroplasts) belong to X motifs (called mAA). The conserved nucleotide G530 in rRNAs of bacteria and archaea belongs to X motifs (called mG). Furthermore, the X motif mG is also found in rRNAs of nuclear eukaryotes and chloroplasts. Finally, a potentially important X motif, called m, is identified in all studied rRNAs. With the available crystallographic structures of the Protein Data Bank PDB, we also show that these X motifs mAA, mG, and m belong to the ribosome decoding center of all studied rRNAs with possible interaction with the mRNA X motifs and the tRNA X motifs. The three classes of X motifs identified here in rRNAs of several and different organisms strengthen the concept of translation code based on the circular code.
authors.affiliation: Theoretical Bioinformatics, Icube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, Illkirch 67400, 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, Illkirch 67400, France. Electronic address: c.michel@unistra.fr.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000235:genetics; D005815:Genetic Code; D006801:Humans; D059372:Nucleotide Motifs / Q000235:genetics*; D020027:Pyrococcus furiosus / Q000235:genetics; D019642:RNA, Archaeal / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D018747:RNA, Chloroplast / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D018724:Spinacia oleracea / Q000235:genetics; D013824:Thermus / Q000235:genetics; D014908:Triticum / Q000235:genetics
chemical_list: D019642:RNA, Archaeal; D012329:RNA, Bacterial; D018747:RNA, Chloroplast; D012331:RNA, Fungal; D012335:RNA, Ribosomal
keywords: Circular code motif; Ribosomal RNA; Ribosome decoding center; Translation code; Trinucleotide