Lineage-specific differences in the amino acid substitution process.
Lineage-specific differences in the amino acid substitution process.
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氨基酸取代过程中谱系特异性的差异。
DOI：
10.1016/j.jmb.2009.11.075
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发表时间：
2010-03-12
影响因子：
5.6
通讯作者：
Liberles, David A.
中科院分区：
文献类型：
--
作者：
Huzurbazar, Snehalata;Kolesov, Grigory;Massey, Steven E.;Harris, Katherine C.;Churbanov, Alexander;Liberles, David A.
关键词：
在达尔文进化论中，基因中的突变几乎是随机发生的，由遗传密码转变为氨基酸突变。一些突变被固定为替代，另一些则从种群中消除。根据每对物种的平均种群大小，对具有完整基因组序列的密切相关物种对进行划分，我们查看了为这些划分生成的替换矩阵，并比较了物种之间的替换模式。我们估计了一个群体遗传模型，该模型将不同类型突变的相对固定概率与选择压力和种群大小联系起来。用贝叶斯框架生成了不同群体规模比较中不同氨基酸替代类型的选择压力的平均值和分布的参数。我们发现，需要在种群大小和替代类型上的划分来解释替代数据。选择系数随着氨基酸自由基取代度的增加和有效种群规模的增大而降低。为了进一步探索潜在过程在氨基酸替代中的作用，我们分析了来自TAED(适应性进化数据库)的胚芽(植物)基因家族，其中至少一个成员的已解决结构存在于蛋白质数据库中。使用PAML，我们将分支分为三类：强烈的负面选择、中等的负面选择/中性和积极的多样化选择。针对第一类和第三类，我们确定了沿着基因家族谱系变化的位置，并观察了替换的空间模式。在正向多样化选择下，选择性扫描有望产生初级序列聚类。通过直接物理相互作用的共同进化有望导致三级结构聚集。在正选择和负选择下，替换模式都是非随机的。在正向多样化选择下，一级和三级序列聚类存在显著的独立信号，表明选择性扫描和直接物理相互作用都起到了作用。在强负选择条件下，信号不是独立的。总而言之，提出了种群遗传和蛋白质热力学力量的复杂相互作用。
In Darwinian evolution, mutations occur approximately at random in a gene, turned into amino acid mutations by the genetic code. Some mutations are fixed to become substitutions and some are eliminated from the population. Partitioning pairs of closely related species with complete genome sequences by average population size of each pair, we looked at the substitution matrices generated for these partitions and compared the substitution patterns between species. We estimated a population genetic model that relates the relative fixation probabilities of different types of mutations to the selective pressure and population size. Parameterizations of the average and distribution of selective pressures for different amino acid substitution types in different population size comparisons were generated with a Bayesian framework. We found that partitions in population size as well as in substitution type are required to explain the substitution data. Selection coefficients were found to decrease with increasingly radical amino acid substitution and with increasing effective population size. To further explore the role of underlying processes in amino acid substitution, we analyzed embryophyte (plant) gene families from TAED (The Adaptive Evolution Database), where solved structures for at least one member exist in the Protein Data Bank. Using PAML, we assigned branches to three categories: strong negative selection, moderate negative selection/ neutrality, and positive diversifying selection. Focusing on the first and third categories, we identified sites changing along gene family lineages and observed the spatial patterns of substitution. Selective sweeps were expected to create primary sequence clustering under positive diversifying selection. Co-evolution through direct physical interaction was expected to cause tertiary structural clustering. Under both positive and negative selection, the substitution patterns were found to be nonrandom. Under positive diversifying selection, significant independent signals were found for primary and tertiary sequence clustering, suggesting roles for both selective sweeps and direct physical interaction. Under strong negative selection, the signals were not found to be independent. All together, a complex interplay of population genetic and protein thermodynamics forces is suggested.
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影响因子：
3.9
作者：
Berglund, AC;Wallner, B;Liberles, DA
通讯作者：
Liberles, DA
DOI：
10.1073/pnas.94.22.11911
发表时间：
1997-10-28
影响因子：
11.1
作者：
Gerstein, M;Levitt, M
通讯作者：
Levitt, M
影响因子：
2.9
作者：
Illergard, Kristoffer;Ardell, David H.;Elofison, Arne
通讯作者：
Elofison, Arne
DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
DOI：
10.1093/protein/7.11.1323
发表时间：
1994-11-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
BENNER, SA;COHEN, MA;GONNET, GH
通讯作者：
GONNET, GH