Title: Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene

Authors: Vladislav Victorovich Khrustalev; Eugene Victorovich Barkovsky; Valentina Leonidovna Kolodkina; Tatyana Aleksandrovna Khrustaleva

Addresses: Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus ' Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus ' Vaccine Preventable Diseases Laboratory, Republican Research and Practical Centre for Epidemiology and Microbiology, Filimonova 23, Minsk, Belarus ' Laboratory of Cellular Technologies, Institute of Physiology of the National Academy of Sciences of Belarus, Academicheskaya 28, Minsk, Belarus

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′-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.

Keywords: transcription-associated mutational pressure; asymmetric mutational pressure; genomic islands; pathogenicity islands; Corynebacterium diphtheriae; Corynebacterium ulcerans; spaC genes; adhesion; pili; nucleotide mutations; promoter prediction; terminator prediction; intragenic promoters; intragenic terminators; bioinformatics; nucleotide usage bias; autonomous transcription.

DOI: 10.1504/IJBRA.2015.070140

International Journal of Bioinformatics Research and Applications, 2015 Vol.11 No.4, pp.347 - 365

Received: 03 Jan 2014
Accepted: 06 Mar 2015
Published online: 27 Jun 2015 *

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