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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| Published in: | International journal of bioinformatics research and applications Vol. 11; no. 4; p. 347 |
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| Main Authors: | , , , |
| Format: | Journal Article |
| Language: | English |
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Switzerland
2015
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| ISSN: | 1744-5485 |
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| 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. |
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| AbstractList | 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.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. 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. |
| Author | Khrustalev, Vladislav Victorovich Kolodkina, Valentina Leonidovna Barkovsky, Eugene Victorovich Khrustaleva, Tatyana Aleksandrovna |
| Author_xml | – sequence: 1 givenname: Vladislav Victorovich surname: Khrustalev fullname: Khrustalev, Vladislav Victorovich organization: 1 Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus – sequence: 2 givenname: Eugene Victorovich surname: Barkovsky fullname: Barkovsky, Eugene Victorovich organization: 2 Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus – sequence: 3 givenname: Valentina Leonidovna surname: Kolodkina fullname: Kolodkina, Valentina Leonidovna organization: 3 Vaccine Preventable Diseases Laboratory, Republican Research and Practical Centre for Epidemiology and Microbiology, Filimonova 23, Minsk, Belarus – sequence: 4 givenname: Tatyana Aleksandrovna surname: Khrustaleva fullname: Khrustaleva, Tatyana Aleksandrovna organization: 4 Laboratory of Cellular Technologies, Institute of Physiology of the National Academy of Sciences of Belarus, Academicheskaya 28, Minsk, Belarus |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26561319$$D View this record in MEDLINE/PubMed |
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| Keywords | 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 |
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| SubjectTerms | Bacterial Proteins - genetics Base Composition - genetics Codon - genetics Corynebacterium diphtheriae - genetics Genes, Bacterial - genetics Genomics Membrane Proteins - genetics Mutation Open Reading Frames |
| Title | Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene |
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