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

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...

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Vydané v:International journal of bioinformatics research and applications Ročník 11; číslo 4; s. 347
Hlavní autori: Khrustalev, Vladislav Victorovich, Barkovsky, Eugene Victorovich, Kolodkina, Valentina Leonidovna, Khrustaleva, Tatyana Aleksandrovna
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Switzerland 2015
Predmet:
Bacterial Proteins - genetics
Base Composition - genetics
Codon - genetics
Corynebacterium diphtheriae - genetics
Genes, Bacterial - genetics
Genomics
Membrane Proteins - genetics
Mutation
Open Reading Frames
pili
intragenic promoters
autonomous transcription
genomic islands
nucleotide usage bias
nucleotide mutations
spaC genes
adhesion
Corynebacterium diphtheriae
Corynebacterium ulcerans
transcription-associated mutational pressure
intragenic terminators
terminator prediction
pathogenicity islands
bioinformatics
asymmetric mutational pressure
promoter prediction
ISSN:1744-5485
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Popis
Shrnutí: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.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1744-5485
DOI:10.1504/IJBRA.2015.070140