Bacterial natural transformation by highly fragmented and damaged DNA
Bacterial natural transformation by highly fragmented and damaged DNA
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DOI：
10.1073/pnas.1315278110
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发表时间：
2013-12-03
影响因子：
11.1
通讯作者：
Willerslev, Eske
中科院分区：
文献类型：
--
作者：
Overballe-Petersen, Soren;Harms, Klaus;Willerslev, Eske
DNA 分子通过有机物的分解不断释放，在大多数环境中普遍存在。此类 DNA 会变得片段化和受损（通常 < 100 bp），并可能在环境中持续存在超过 50 万年。 DNA片段被认为是微生物的营养源，但不是细菌进化的潜在底物。在这里，我们表明，环境细菌贝氏不动杆菌通过自然转化获得了可能含有脱碱基位点、交联或错误编码损伤的片段化 DNA 分子（> = 20 bp）。通过从 43,000 年前的猛犸象骨骼中提取 DNA，我们进一步证明这种自然转化事件包括古代 DNA 分子。我们发现 DNA 重组不依赖于 RecA 重组酶，并且与 DNA 复制直接相关。我们发现，通过摄取短 DNA 片段产生的相邻核苷酸变异可以逃脱错配修复。此外，双核苷酸多态性在可转化细菌的基因组中似乎比不可转化细菌更常见。我们的研究结果表明，细菌可以通过自然转化获得大量存在于环境中的短DNA分子和受损DNA分子，包括真正古老的DNA分子。我们的研究结果表明，长达数十万年的 DNA 可能会发生自然遗传交换。
DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often < 100 bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (>= 20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake of short DNA fragments escape mismatch repair. Moreover, doublenucleotide polymorphisms appear more common among genomes of transformable than nontransformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.