Strand compositional asymmetry in bacterial and large viral genomes
Strand compositional asymmetry in bacterial and large viral genomes
复制标题
DOI：
10.1073/pnas.95.7.3720
复制
发表时间：
1998-03-31
影响因子：
11.1
通讯作者：
Karlin, S
中科院分区：
文献类型：
--
作者：
Mrázek, J;Karlin, S
在大肠杆菌、生殖支原体、枯草芽孢杆菌的基因组中，一些细菌基因组在从复制起点延伸到ter区域的DNA前导链上表现出对G的偏好，而在流感嗜血杆菌、肺炎支原体和幽门螺杆菌中则表现出对C的偏好。链组成不对称在蓝细菌中没有观察到，在jannaschii甲烷球菌、热自养甲烷细菌和fulgidarchaeglobus的古细菌基因组中也没有观察到。在β型人疱疹病毒中观察到强烈的链组成不对称，而在α型或γ型人疱疹病毒中则没有，其特征是g> C位于oriL下游，而c> G位于oriL上游。二核苷酸相对丰度（即，由组成核苷酸频率归一化的二核苷酸表示）相对于前导链和滞后链是一致的。链组成的不对称可能反映了前导链和滞后链复制合成的差异，与转录偶联修复机制相关的模板链和编码链之间的差异，两条链之间基因密度的差异，与基因功能、表达水平或操纵子组织相关的残基和密码子偏差的差异，或单个与上下文相关的碱基突变率的差异。古细菌基因组中链不对称的缺失可能反映了多重复制起源的存在。
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 Escherichia coli, Mycoplasma genitalium, Bacillus subtilis, and marginally in Haemophilus influenzae, Mycoplasma pneumoniae, and Helicobacter pylori. Strand compositional asymmetry is not observed in the cyanobacterium Synechocystis sp. genome nor in the archaeal genomes of Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus. A strong strand compositional asymmetry is observed in beta-type but not alpha- or gamma-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 as context dependent base mutational rates. The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of replication.