The maximal C-3 self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses

摘要

In 1996, a set X of 20 trinucleotides is identified in genes of both prokaryotes and eukaryotes which has in average the highest occurrence in reading frame compared to the two shifted frames (Argues and Michel, 1996). Furthermore, this set X has an interesting mathematical property as X is a maximal C-3 self-complementary trinucleotide circular code (Arques and Michel, 1996). In 2014, the number of trinucleotides in prokaryotic genes has been multiplied by a factor of 527. Furthermore, two new gene kingdoms of plasmids and viruses contain enough trinucleotide data to be analysed. The approach used in 1996 for identifying a preferential frame for a trinucleotide is quantified here with a new definition analysing the occurrence probability of a complementary/permutation (CP) trinudeotide set in a gene kingdom. Furthermore, in order to increase the statistical significance of results compared to those of 1996, the circular code X is studied on several gene taxonomic groups in a kingdom. Based on this new statistical approach, the circular code X is strengthened in genes of prokaryotes and eukaryotes, and now also identified in genes of plasmids. A subset of X with 18 or 16 trinucleotides is identified in genes of viruses. Furthermore, a simple probabilistic model based on the independent occurrence of trinucleotides in reading frame of genes explains the circular code frequencies and asymmetries observed in the shifted frames in all studied gene kingdoms. Finally, the developed approach allows to identify variant X codes in genes, i.e. trinucleotide codes which differ from X. In genes of bacteria, eukaryotes and plasmids, 14 among the 47 studied gene taxonomic groups (about 30%) have variant X codes. Seven variant X codes are identified with at least 16 trinucleotides of X. Two variant X codes X-A in cyanobacteria and plasmids of cyanobacteria, and X-D in birds are self-complementary, without permuted trinucleotides but non-circular. Five variant X codes X-B in deinococcus, plasmids of chloroflexi and deinococcus, mammals and kinetoplasts, X-C in elusimicrobia and apicomplexans, X-E in fishes, X-F in insects, and X-G in basidiomycetes and plasmids of spirochaetes are C-3 self-complementary circular. In genes of viruses, no variant X code is found. (C) 2015 Elsevier Ltd. All rights reserved.