Abstract：
:In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered. Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably between genomes.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
McVean GA,Hurst GDdoi
10.1007/s002399910031keywords:
subject
Has Abstractpub_date
2000-03-01 00:00:00pages
264-75issue
3eissn
0022-2844issn
1432-1432pii
10.1007/s002399910031journal_volume
50pub_type
杂志文章abstract：:Rooted phylogenetic trees for a total of 34 genes encoding the stimulatory (s alpha), inhibitory (i alpha), transducin (t alpha), Gx (x alpha), Gz (z alpha), G11 (alpha 11), G12 (alpha 12), G13 (alpha 13), G16 (alpha 16), Gq (q alpha), and other (o alpha) G protein alpha subunits have been constructed. The analysis sh...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00178599
更新日期：1992-09-01 00:00:00
abstract：:To understand the process and mechanism of protein evolution, it is important to know what types of amino acid substitutions are more likely to be under selection and what types are mostly neutral. An amino acid substitution can be classified as either conservative or radical, depending on whether it involves a change...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002399910007
更新日期：2000-01-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0016-z
更新日期：2006-08-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173165
更新日期：1995-12-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2420-3
更新日期：2003-05-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-012-9491-6
更新日期：2012-04-01 00:00:00
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pub_type： 杂志文章
doi：10.1007/s00239-003-2539-x
更新日期：2004-01-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-015-9665-0
更新日期：2015-02-01 00:00:00
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pub_type： 杂志文章
doi：10.1007/s00239-003-2533-3
更新日期：2003-12-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160429
更新日期：1993-11-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00178851
更新日期：1994-05-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173183
更新日期：1995-12-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01795752
更新日期：1981-01-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2472-z
更新日期：2003-10-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100629
更新日期：1984-01-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/pl00013145
更新日期：1997-12-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0196-y
更新日期：2006-08-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006257
更新日期：1997-11-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0120-x
更新日期：2005-02-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
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更新日期：1989-07-01 00:00:00
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pub_type： 杂志文章
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更新日期：1990-02-01 00:00:00
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pub_type： 杂志文章
doi：10.1007/BF01732666
更新日期：1980-05-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/s00239-015-9694-8
更新日期：2015-10-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732374
更新日期：1979-12-01 00:00:00
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pub_type： 杂志文章
doi：10.1007/s00239-005-0002-x
更新日期：2006-06-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102477
更新日期：1989-03-01 00:00:00
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更新日期：2008-03-01 00:00:00
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pub_type： 杂志文章
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更新日期：1999-01-01 00:00:00
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pub_type： 杂志文章
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更新日期：2003-06-01 00:00:00
abstract：:A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon...
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更新日期：2021-01-24 00:00:00
