Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.
Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.
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DOI：
10.3389/fmicb.2014.00354
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发表时间：
2014
影响因子：
5.2
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Makarova KS;Krupovic M;Koonin EV
精致的真核DNA复制机制是从远古祖先进化而来的，而远古祖先本身就表现出相当的复杂性。在这里，我们讨论比较基因组和系统发育分析的核心复制酶，DNA聚合酶，以及它们与真核聚合酶的关系。在古生菌中，有三组B家族DNA聚合酶，历史上被称为PolB1、PolB2和PolB3。这三个群体似乎都是现存古生物的最后一个共同祖先的后代，但他们随后的进化轨迹似乎有很大的不同。尽管PolB3存在于所有古生菌中，除了塔乌姆考古群，并且似乎直接参与滞后的链复制，但该基因的进化并不遵循古生菌的系统发育，可以想象是由于多次水平转移和/或进化速度的巨大差异。相比之下，PolB1在Eurya chaeota中缺失，但在其他方面似乎已经垂直进化。第三个古老的B家族聚合酶，PolB2，主要包括聚合酶和核酸外切酶结构域的催化中心被破坏的蛋白质，因此这些酶似乎是失活的。PolB2组的成员散布在古生菌中，可能与RADA家族ATPase的失活成员和编码在同一预测操纵子内的另一种未鉴定的蛋白一起参与复制的修复或调节。除了B家族聚合酶外，所有古生菌都编码一个独特的D家族的酶，其来源尚不清楚。我们考察了与D家族聚合酶是B家族高度衍生的同系物的可能性相一致的多种考虑。真核DNA聚合酶与其古生菌祖先显示出高度复杂的关系，包括来自B家族和D家族古生菌聚合酶的蛋白质和结构域的贡献。
The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.
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影响因子：
14.9
作者：
Jokela, M;Eskelinen, A;Syväoja, JE
通讯作者：
Syväoja, JE
影响因子：
7.2
作者：
Koonin, Eugene V.;Yutin, Natalya
通讯作者：
Yutin, Natalya
影响因子：
13.8
作者：
Dandekar, T;Snel, B;Bork, P
通讯作者：
Bork, P
影响因子：
14.9
作者：
Aravind, L;Koonin, EV
通讯作者：
Koonin, EV
DOI：
10.1073/pnas.96.7.3600
发表时间：
1999-03-30
影响因子：
11.1
作者：
Hopfner, KP;Eichinger, A;Angerer, B
通讯作者：
Angerer, B