title: Novel overlapping coding sequences in Chlamydia trachomatis.
abstract: Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853 that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes. The data suggest the presence of overlapping active genes in C. trachomatis.
authors.affiliation: Laboratory of Infectious Diseases Immunology, Chlamydia Vaccine Unit, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark. ksa@ssi.dk
authors.forename: Klaus T
authors.initials: KT
authors.lastname: Jensen
authors.forename: Lise
authors.initials: L
authors.lastname: Petersen
authors.forename: Søren
authors.initials: S
authors.lastname: Falk
authors.forename: Pernille
authors.initials: P
authors.lastname: Iversen
authors.forename: Peter
authors.initials: P
authors.lastname: Andersen
authors.forename: Michael
authors.initials: M
authors.lastname: Theisen
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
mesh_terms: D002692:Chlamydia trachomatis / Q000235:genetics*; D005798:Genes, Bacterial; D005807:Genes, Overlapping; D016680:Genome, Bacterial; D006801:Humans; D016366:Open Reading Frames / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D015533:Transcriptional Activation