Departement d'Immunologie, Unité de Génétique Moléculaire des Levures, Institut Pasteur, 75015 Paris, France.
Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2141-6. doi: 10.1073/pnas.0906355107. Epub 2010 Jan 19.
Bridging broken DNA ends via nonhomologous end-joining (NHEJ) contributes to the evolution and stability of eukaryote genomes. Although some bacteria possess a simplified NHEJ mechanism, the human commensal Escherichia coli is thought to rely exclusively on homology-directed mechanisms to repair DNA double-strand breaks (DSBs). We show here that laboratory and pathogenic E. coli strains possess a distinct end-joining activity that repairs DSBs and generates genome rearrangements. This mechanism, named alternative end-joining (A-EJ), does not rely on the key NHEJ proteins Ku and Ligase-D which are absent in E. coli. Differently from classical NHEJ, A-EJ is characterized by extensive end-resection largely due to RecBCD, by overwhelming usage of microhomology and extremely rare DNA synthesis. We also show that A-EJ is dependent on the essential Ligase-A and independent on Ligase-B. Importantly, mutagenic repair requires a functional Ligase-A. Although generally mutagenic, accurate A-EJ also occurs and is frequent in some pathogenic bacteria. Furthermore, we show the acquisition of an antibiotic-resistance gene via A-EJ, refuting the notion that bacteria gain exogenous sequences only by recombination-dependent mechanisms. This finding demonstrates that E. coli can integrate unrelated, nonhomologous exogenous sequences by end-joining and it provides an alternative strategy for horizontal gene transfer in the bacterial genome. Thus, A-EJ contributes to bacterial genome evolution and adaptation to environmental challenges. Interestingly, the key features of A-EJ also appear in A-NHEJ, an alternative end-joining mechanism implicated in chromosomal translocations associated with human malignancies, and we propose that this mutagenic repair might have originated in bacteria.
通过非同源末端连接（NHEJ）桥接断裂的 DNA 末端有助于真核生物基因组的进化和稳定性。尽管一些细菌具有简化的 NHEJ 机制，但人类共生菌大肠杆菌被认为仅依赖同源定向机制来修复 DNA 双链断裂（DSB）。我们在这里表明，实验室和致病性大肠杆菌菌株具有独特的末端连接活性，可修复 DSB 并产生基因组重排。这种机制称为替代末端连接（A-EJ），不依赖于关键的 NHEJ 蛋白 Ku 和 Ligase-D，而大肠杆菌中不存在这些蛋白。与经典的 NHEJ 不同，A-EJ 的特征是广泛的末端切除，主要由 RecBCD 引起，大量使用微同源性，并且极少量的 DNA 合成。我们还表明，A-EJ 依赖于必需的 Ligase-A，而不依赖于 Ligase-B。重要的是，诱变修复需要功能正常的 Ligase-A。尽管通常是诱变的，但准确的 A-EJ 也会发生，并且在一些致病菌中很常见。此外，我们通过 A-EJ 显示了获得抗生素抗性基因的现象，这反驳了细菌仅通过依赖重组的机制获得外源序列的观点。这一发现表明，大肠杆菌可以通过末端连接整合无关的、非同源的外源序列，为细菌基因组中的水平基因转移提供了一种替代策略。因此，A-EJ 有助于细菌基因组的进化和适应环境挑战。有趣的是，A-EJ 的关键特征也出现在 A-NHEJ 中，A-NHEJ 是一种替代的末端连接机制，与人类恶性肿瘤相关的染色体易位有关，我们提出这种诱变修复可能起源于细菌。
