In silico prediction of the origin of replication among bacteria: a case study of Bacteroides thetaiotaomicron.
The initiation of chromosomal replication occurs only once during the prokaryote cell cycle. Some origins of replication have been experimentally determined and have led to the development of in silico approaches to find the origin of replication among other prokaryotes. DNA base composition asymmetry is the basis of numerous in silico methods used to detect the origin and terminus of replication in prokaryotes. However, the composition asymmetry does not allow us to locate precisely the positions of the origin and terminus. Since DNA replication is a key step in the cell cycle it is important to determine properly the origin and terminus regions. Therefore, we have reviewed here the methods, tools, and databases for predicting the origins and terminuses of replication, and we have proposed some complementary analyses to reinforce these predictions. These analyses include finding the dnaA gene and its binding sites; making BLAST analyses of the intergenic sequences compared to related species; studying the gene order around the origin sequence; and studying the distribution of the genes encoded in the leading versus the lagging strand.
Pallejà
Albert
A
Department of Biochemistry and Biotechnology, Evolutionary Genomics Group, Rovira i Virgili University, Tarragona, Catalunya, Spain. albert.palleja@urv.cat
Guzman
Eduard
E
Garcia-Vallvé
Santiago
S
Romeu
Antoni
A
D001419:Bacteria / Q000235:genetics*; D001439:Bacteroides / Q000235:genetics*; D001483:Base Sequence; D002453:Cell Cycle / Q000502:physiology; D002876:Chromosomes, Bacterial / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D004261:DNA Replication; D006801:Humans; D008969:Molecular Sequence Data; D018741:Replication Origin / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software