A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
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DOI：
10.1093/nar/30.2.482
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发表时间：
2002-01-15
影响因子：
14.9
通讯作者：
Koonin, EV
中科院分区：
文献类型：
--
作者：
Makarova, KS;Aravind, L;Koonin, EV
在对原核基因组中保守基因背景进行系统分析时，在大多数古细菌中发现了一个以前未检测到的、复杂的、部分保守的邻域，由 20 多个基因组成。 （嗜酸热原体和盐杆菌 NRC-1 除外）和一些细菌，包括超嗜热菌、海栖热袍菌和。 Aquifex aeolicus。该邻域的基因组成和基因顺序在物种之间差异很大，但所有版本都有一个由五个基因组成的稳定、保守的核心。其中一个核心基因编码预测的 DNA 解旋酶，通常与预测的 HD 超家族水解酶融合，另一个核心基因编码 RecB 家族核酸外切酶；三个核心基因仍未被表征，但其中一个可能编码一个新家族的核酸酶。另外两个基因属于该邻域并且存在于检测到该邻域的大多数基因组中，分别编码预测的不同家族的 HD 超家族水解酶（可能是核酸酶）和预测的新型 DNA 聚合酶。该邻域的另一个特征是旁系同源、未表征的蛋白质超家族的扩展，这些蛋白质由邻域中至少 20-30% 的基因编码。该邻域编码的蛋白质的功能特征表明它们包含以前未检测到的 DNA 修复系统，据我们所知，这是第一个主要针对嗜热菌的修复系统。这种假设的修复系统在功能上可能类似于细菌真核的跨损伤、诱变修复系统，其核心成分是 UmuC-DinB-Rad30-Rev1 超家族的 DNA 聚合酶，而该酶通常在嗜热菌中缺失。
During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most Archaea. (with the exception of Thermoplasma acidophilum and Halobacterium NRC-1) and some bacteria, including the hyperthermophiles, Thermotoga maritima and. Aquifex aeolicus. The gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conserved core that consists of five genes. One of the core genes encodes a predicted DNA helicase, often fused to a predicted HD-superfamily hydrolase, and another encodes a RecB family exonuclease; three core genes remain uncharacterized, but one of these might encode a nuclease of a new family. Two more genes that belong to this neighborhood and are present in most of the genomes in which the neighborhood was detected encode, respectively, a predicted HD-superfamily hydrolase (possibly a nuclease) of a distinct family and a predicted, novel DNA polymerase. Another characteristic feature of this neighborhood is the expansion of a superfamily of paralogous, uncharacterized proteins, which are encoded by at least 20-30% of the genes in the neighborhood. The functional features of the proteins encoded in this neighborhood suggest that they comprise a previously undetected DNA repair system, which, to our knowledge, is the first repair system largely specific for thermophiles to be identified. This hypothetical repair system might be functionally analogous to the bacterial-eukaryotic system of translesion, mutagenic repair whose central components are DNA polymerases of the UmuC-DinB-Rad30-Rev1 superfamily, which typically are missing in thermophiles.