El Soufi Karim, Michel Christian J
Theoretical Bioinformatics, Icube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, Illkirch 67400, France.
Comput Biol Chem. 2014 Oct;52:9-17. doi: 10.1016/j.compbiolchem.2014.08.001. Epub 2014 Aug 5.
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.
米歇尔（2012年）提出了一种基于循环码的翻译（框架）码，在嗜热栖热菌的细菌rRNA中，特别是在核糖体解码中心，鉴定出了X个循环码基序（简称X基序）。目前在大肠杆菌、嗜热栖热菌、激烈火球菌、核真核生物酿酒酵母、普通小麦和智人的rRNA中，以及叶绿体菠菜的rRNA中，都鉴定出了三类X基序。在所有研究的rRNA（细菌、古细菌、核真核生物和叶绿体）中普遍保守的核苷酸A1492和A1493属于X基序（称为mAA）。细菌和古细菌rRNA中保守的核苷酸G530属于X基序（称为mG）。此外，在核真核生物和叶绿体的rRNA中也发现了X基序mG。最后，在所有研究的rRNA中鉴定出一个潜在重要的X基序，称为m。利用蛋白质数据库PDB中现有的晶体结构，我们还表明，这些X基序mAA、mG和m属于所有研究的rRNA的核糖体解码中心，可能与mRNA X基序和tRNA X基序相互作用。在几种不同生物体的rRNA中鉴定出的这三类X基序，强化了基于循环码的翻译码概念。
