title: Origin and length distribution of unidirectional prokaryotic overlapping genes.
abstract: Prokaryotic unidirectional overlapping genes can be originated by disrupting and replacing of the start or stop codon of one protein-coding gene with another start or stop codon within the adjacent gene. However, the probability of disruption and replacement of a start or stop codon may differ significantly depending on the number and redundancy of the start and stop codons sets. Here, we performed a simulation study of the formation of unidirectional overlapping genes using a simple model of nucleotide change and contrasted it with empirical data. Our results suggest that overlaps originated by an elongation of the 3'-end of the upstream gene are significantly more frequent than those originated by an elongation of the 5'-end of the downstream gene. According to this, we propose a model for the creation of unidirectional overlaps that is based on the disruption probabilities of start codon and stop codon sets and on the different probabilities of phase 1 and phase 2 overlaps. Additionally, our results suggest that phase 2 overlaps are formed at higher rates than phase 1 overlaps, given the same evolutionary time. Finally, we propose that there is no need to invoke selection to explain the prevalence of long phase 1 unidirectional overlaps. Rather, the overrepresentation of long phase 1 relative to long phase 2 overlaps might occur because it is highly probable that phase 2 overlaps are retained as short overlaps by chance. Such a pattern is stronger if selection against very long overlaps is included in the model. Our model as a whole is able to explain to a large extent the empirical length distribution of unidirectional overlaps in prokaryotic genomes.
authors.affiliation: Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
authors.forename: Miguel M
authors.initials: MM
authors.lastname: Fonseca
authors.forename: D James
authors.initials: DJ
authors.lastname: Harris
authors.forename: David
authors.initials: D
authors.lastname: Posada
mesh_terms: D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D001482:Base Composition; D018387:Codon, Initiator; D018388:Codon, Terminator; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D005807:Genes, Overlapping / Q000235:genetics*; D008957:Models, Genetic; D017354:Point Mutation
chemical_list: D018387:Codon, Initiator; D018388:Codon, Terminator
keywords: overlap length distribution; overlapping genes; prokaryotic genomes; unidirectional genes