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Strand compositional asymmetry in bacterial and large viral genomes
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| Zeitschriftentitel: | Proceedings of the National Academy of Sciences |
|---|---|
| Personen und Körperschaften: | , |
| In: | Proceedings of the National Academy of Sciences, 95, 1998, 7, S. 3720-3725 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Proceedings of the National Academy of Sciences
|
| Schlagwörter: |
| author_facet |
Mrázek, Jan Karlin, Samuel Mrázek, Jan Karlin, Samuel |
|---|---|
| author |
Mrázek, Jan Karlin, Samuel |
| spellingShingle |
Mrázek, Jan Karlin, Samuel Proceedings of the National Academy of Sciences Strand compositional asymmetry in bacterial and large viral genomes Multidisciplinary |
| author_sort |
mrázek, jan |
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Mrázek, Jan Karlin, Samuel 0027-8424 1091-6490 Proceedings of the National Academy of Sciences Multidisciplinary http://dx.doi.org/10.1073/pnas.95.7.3720 <jats:p> Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of <jats:italic>Escherichia coli</jats:italic> , <jats:italic>Mycoplasma genitalium</jats:italic> , <jats:italic>Bacillus subtilis</jats:italic> , and marginally in <jats:italic>Haemophilus influenzae</jats:italic> , <jats:italic>Mycoplasma pneumoniae</jats:italic> , and <jats:italic>Helicobacter pylori</jats:italic> . Strand compositional asymmetry is not observed in the cyanobacterium <jats:italic>Synechocystis</jats:italic> sp. genome nor in the archaeal genomes of <jats:italic>Methanococcus jannaschii</jats:italic> , <jats:italic>Methanobacterium thermoautotrophicum</jats:italic> , and <jats:italic>Archaeoglobus fulgidus</jats:italic> . A strong strand compositional asymmetry is observed in β-type but not α- or γ-type human herpesviruses featuring G > C downstream of oriL and C > G upstream of oriL. Dinucleotide relative abundances (i.e., dinucleotide representations normalized by the component nucleotide frequencies) are consonant with respect to the leading and lagging strands. Strand compositional asymmetry may reflect on differences in replication synthesis of the leading versus lagging strand, on differences between template and coding strand associated with transcription-coupled repair mechanisms, on differences in gene density between the two strands, on differences in residue and codon biases in relation to gene function, expression level, or operon organization, or on differences in single or context-dependent base mutational rates. The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of replication. </jats:p> Strand compositional asymmetry in bacterial and large viral genomes Proceedings of the National Academy of Sciences |
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Proceedings of the National Academy of Sciences, 1998 |
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Proceedings of the National Academy of Sciences, 1998 |
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0027-8424 1091-6490 |
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1998 |
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Proceedings of the National Academy of Sciences |
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Proceedings of the National Academy of Sciences |
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49 |
| title |
Strand compositional asymmetry in bacterial and large viral genomes |
| title_unstemmed |
Strand compositional asymmetry in bacterial and large viral genomes |
| title_full |
Strand compositional asymmetry in bacterial and large viral genomes |
| title_fullStr |
Strand compositional asymmetry in bacterial and large viral genomes |
| title_full_unstemmed |
Strand compositional asymmetry in bacterial and large viral genomes |
| title_short |
Strand compositional asymmetry in bacterial and large viral genomes |
| title_sort |
strand compositional asymmetry in bacterial and large viral genomes |
| topic |
Multidisciplinary |
| url |
http://dx.doi.org/10.1073/pnas.95.7.3720 |
| publishDate |
1998 |
| physical |
3720-3725 |
| description |
<jats:p>
Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of
<jats:italic>Escherichia coli</jats:italic>
,
<jats:italic>Mycoplasma genitalium</jats:italic>
,
<jats:italic>Bacillus subtilis</jats:italic>
, and marginally in
<jats:italic>Haemophilus influenzae</jats:italic>
,
<jats:italic>Mycoplasma pneumoniae</jats:italic>
, and
<jats:italic>Helicobacter pylori</jats:italic>
. Strand compositional asymmetry is not observed in the cyanobacterium
<jats:italic>Synechocystis</jats:italic>
sp. genome nor in the archaeal genomes of
<jats:italic>Methanococcus jannaschii</jats:italic>
,
<jats:italic>Methanobacterium thermoautotrophicum</jats:italic>
, and
<jats:italic>Archaeoglobus fulgidus</jats:italic>
. A strong strand compositional asymmetry is observed in β-type but not α- or γ-type human herpesviruses featuring G > C downstream of oriL and C > G upstream of oriL. Dinucleotide relative abundances (i.e., dinucleotide representations normalized by the component nucleotide frequencies) are consonant with respect to the leading and lagging strands. Strand compositional asymmetry may reflect on differences in replication synthesis of the leading versus lagging strand, on differences between template and coding strand associated with transcription-coupled repair mechanisms, on differences in gene density between the two strands, on differences in residue and codon biases in relation to gene function, expression level, or operon organization, or on differences in single or context-dependent base mutational rates. The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of replication.
</jats:p> |
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| description | <jats:p> Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of <jats:italic>Escherichia coli</jats:italic> , <jats:italic>Mycoplasma genitalium</jats:italic> , <jats:italic>Bacillus subtilis</jats:italic> , and marginally in <jats:italic>Haemophilus influenzae</jats:italic> , <jats:italic>Mycoplasma pneumoniae</jats:italic> , and <jats:italic>Helicobacter pylori</jats:italic> . Strand compositional asymmetry is not observed in the cyanobacterium <jats:italic>Synechocystis</jats:italic> sp. genome nor in the archaeal genomes of <jats:italic>Methanococcus jannaschii</jats:italic> , <jats:italic>Methanobacterium thermoautotrophicum</jats:italic> , and <jats:italic>Archaeoglobus fulgidus</jats:italic> . A strong strand compositional asymmetry is observed in β-type but not α- or γ-type human herpesviruses featuring G > C downstream of oriL and C > G upstream of oriL. Dinucleotide relative abundances (i.e., dinucleotide representations normalized by the component nucleotide frequencies) are consonant with respect to the leading and lagging strands. Strand compositional asymmetry may reflect on differences in replication synthesis of the leading versus lagging strand, on differences between template and coding strand associated with transcription-coupled repair mechanisms, on differences in gene density between the two strands, on differences in residue and codon biases in relation to gene function, expression level, or operon organization, or on differences in single or context-dependent base mutational rates. The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of replication. </jats:p> |
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| imprint | Proceedings of the National Academy of Sciences, 1998 |
| imprint_str_mv | Proceedings of the National Academy of Sciences, 1998 |
| institution | DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15 |
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| spelling | Mrázek, Jan Karlin, Samuel 0027-8424 1091-6490 Proceedings of the National Academy of Sciences Multidisciplinary http://dx.doi.org/10.1073/pnas.95.7.3720 <jats:p> Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of <jats:italic>Escherichia coli</jats:italic> , <jats:italic>Mycoplasma genitalium</jats:italic> , <jats:italic>Bacillus subtilis</jats:italic> , and marginally in <jats:italic>Haemophilus influenzae</jats:italic> , <jats:italic>Mycoplasma pneumoniae</jats:italic> , and <jats:italic>Helicobacter pylori</jats:italic> . Strand compositional asymmetry is not observed in the cyanobacterium <jats:italic>Synechocystis</jats:italic> sp. genome nor in the archaeal genomes of <jats:italic>Methanococcus jannaschii</jats:italic> , <jats:italic>Methanobacterium thermoautotrophicum</jats:italic> , and <jats:italic>Archaeoglobus fulgidus</jats:italic> . A strong strand compositional asymmetry is observed in β-type but not α- or γ-type human herpesviruses featuring G > C downstream of oriL and C > G upstream of oriL. Dinucleotide relative abundances (i.e., dinucleotide representations normalized by the component nucleotide frequencies) are consonant with respect to the leading and lagging strands. Strand compositional asymmetry may reflect on differences in replication synthesis of the leading versus lagging strand, on differences between template and coding strand associated with transcription-coupled repair mechanisms, on differences in gene density between the two strands, on differences in residue and codon biases in relation to gene function, expression level, or operon organization, or on differences in single or context-dependent base mutational rates. The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of replication. </jats:p> Strand compositional asymmetry in bacterial and large viral genomes Proceedings of the National Academy of Sciences |
| spellingShingle | Mrázek, Jan, Karlin, Samuel, Proceedings of the National Academy of Sciences, Strand compositional asymmetry in bacterial and large viral genomes, Multidisciplinary |
| title | Strand compositional asymmetry in bacterial and large viral genomes |
| title_full | Strand compositional asymmetry in bacterial and large viral genomes |
| title_fullStr | Strand compositional asymmetry in bacterial and large viral genomes |
| title_full_unstemmed | Strand compositional asymmetry in bacterial and large viral genomes |
| title_short | Strand compositional asymmetry in bacterial and large viral genomes |
| title_sort | strand compositional asymmetry in bacterial and large viral genomes |
| title_unstemmed | Strand compositional asymmetry in bacterial and large viral genomes |
| topic | Multidisciplinary |
| url | http://dx.doi.org/10.1073/pnas.95.7.3720 |