title: Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene.
abstract: In this work we described a bacterial open reading frame with two different directions of nucleotide usage biases in its two parts. The level of GC-content in third codon positions (3GC) is equal to 40.17 ± 0.22% during the most of the length of Corynebacterium diphtheriae spaC gene. However, in the 3'-end of the same gene (from codon #1600 to codon #1873) 3GC level is equal to 64.61 ± 0.91%. Using original methodology ('VVTAK Sliding window' and 'VVTAK VarInvar') we approved that there is an ongoing mutational AT-pressure during the most of the length of spaC gene (up to codon #1599), and there is an ongoing mutational G-pressure in the 3&prime;-end of spaC. Intragenic promoters predicted by three different methods may be the cause of the differences in preferable types of nucleotide mutations in spaC parts because of their autonomous transcription.
authors.affiliation: 1 Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus.
authors.forename: Vladislav Victorovich
authors.initials: VV
authors.lastname: Khrustalev
authors.affiliation: 2 Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus.
authors.forename: Eugene Victorovich
authors.initials: EV
authors.lastname: Barkovsky
authors.affiliation: 3 Vaccine Preventable Diseases Laboratory, Republican Research and Practical Centre for Epidemiology and Microbiology, Filimonova 23, Minsk, Belarus.
authors.forename: Valentina Leonidovna
authors.initials: VL
authors.lastname: Kolodkina
authors.affiliation: 4 Laboratory of Cellular Technologies, Institute of Physiology of the National Academy of Sciences of Belarus, Academicheskaya 28, Minsk, Belarus.
authors.forename: Tatyana Aleksandrovna
authors.initials: TA
authors.lastname: Khrustaleva
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D001482:Base Composition / Q000235:genetics; D003062:Codon / Q000235:genetics*; D003353:Corynebacterium diphtheriae / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics*; D023281:Genomics; D008565:Membrane Proteins / Q000235:genetics*; D009154:Mutation; D016366:Open Reading Frames
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D008565:Membrane Proteins; C104625:SpaC protein, bacteria
keywords: Corynebacterium diphtheriae; Corynebacterium ulcerans; adhesion; asymmetric mutational pressure; autonomous transcription; bioinformatics; genomic islands; intragenic promoters; intragenic terminators; nucleotide mutations; nucleotide usage bias; pathogenicity islands; pili; promoter prediction; spaC genes; terminator prediction; transcription-associated mutational pressure