Global analysis of genomic texts: the distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes.
Present availability of the genomic text of bacteria allows assignment of biological known functions to many genes (typically, half of the genome's gene content). It is now time to try and predict new unexpected functions, using inductive procedures that allow correlating the content of the genomic text to possible biological functions. We show here that analysis of the genomes of Escherichia coli and Bacillus subtilis for the distribution of AGCT motifs predicts that genes exist for which the mRNA molecule can be translated as several different proteins synthesized after ribosomal frameshifting or hopping. Among these genes we found that several coded for the same function in E. coli and B. subtilis. We analyzed in depth the situation of the infB gene (experimentally known to specify synthesis of several proteins differing in their translation starts), the aceF/pdhC gene, the eno gene, and the rplI gene. In addition, genes specific to E. coli were also studied: ompA, ompFand tolA (predicting epigenetic variation that could help escape infection by phages or colicins).
Hénaut
A
A
Université de Versailles Saint Quentin, France.
Lisacek
F
F
Nitschké
P
P
Moszer
I
I
Danchin
A
A
D000123:Acetyltransferases / Q000235:genetics; D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000235:genetics*; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D016384:Consensus Sequence; D051047:Dihydrolipoyllysine-Residue Acetyltransferase; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins; D018965:Frameshifting, Ribosomal; D016680:Genome, Bacterial; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000235:genetics; D008432:Mathematical Computing; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010448:Peptide Initiation Factors / Q000235:genetics; D010751:Phosphopyruvate Hydratase / Q000235:genetics; D018272:Porins / Q000235:genetics; D039881:Prokaryotic Initiation Factor-2; D011768:Pyruvate Dehydrogenase Complex / Q000235:genetics; D012333:RNA, Messenger; D012269:Ribosomal Proteins / Q000235:genetics; D017386:Sequence Homology, Amino Acid
D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C109237:OmpF protein; D010448:Peptide Initiation Factors; D018272:Porins; D039881:Prokaryotic Initiation Factor-2; D011768:Pyruvate Dehydrogenase Complex; D012333:RNA, Messenger; D012269:Ribosomal Proteins; C062093:tolA protein, E coli; C078167:OMPA outer membrane proteins; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases; D000123:Acetyltransferases; D051047:Dihydrolipoyllysine-Residue Acetyltransferase; D010751:Phosphopyruvate Hydratase