Ngan Wing Y, Parab Lavisha, Bertels Frederic, Gallie Jenna
Microbial Evolutionary Dynamics Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
Microbial Molecular Evolution Group, Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
mBio. 2025 Jan 8;16(1):e0305224. doi: 10.1128/mbio.03052-24. Epub 2024 Dec 5.
Insertion sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element and a short duplication at the target site. It has been noted that, for some extant IS copies, no target site duplications (TSDs) are readily identifiable. TSD absence has been attributed to degeneration of the TSD after the insertion event, recombination between identical ISs, or adjacent deletions. Indeed, the latter two-recombination between ISs and adjacent deletions-are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long-term evolution experiment. Furthermore, we propose that some IS movements-namely, those that occur in association with large-scale genomic rearrangements-do not generate TSDs, and occur without evidence for recombination between ISs or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS movement plus a large deletion in C, and an IS movement occurring with a large duplication in SBW25. Although unlikely, it is possible that the observed deletion and associated IS movement occurred in two successive events in one overnight culture. However, an IS at the center of a large-scale duplication is not readily explained, suggesting that IS element activity may promote both large-scale deletions and duplications.
Insertion sequences are the most common mobile genetic elements found in bacterial genomes, and hence they significantly impact bacterial evolution. We observe insertion sequence movement at the center of large-scale deletions and duplications that occurred during laboratory evolution experiments with and , involving three distinct types of transposase. We raise the possibility that the transposase does not mediate DNA cleavage but instead inserts into existing DNA breaks. Our research highlights the importance of insertion sequences for the generation of large-scale genomic rearrangements and raises questions concerning the mechanistic basis of these mutations.
插入序列（ISs）是广泛存在于细菌基因组中的可移动DNA片段。IS的移动通常涉及（i）IS元件的切除，（ii）靶位点DNA的切割，以及（iii）IS元件的插入。这个过程会产生一个IS元件的新拷贝，并在靶位点产生一个短重复序列。已经注意到，对于一些现存的IS拷贝，没有容易识别的靶位点重复序列（TSD）。TSD的缺失被归因于插入事件后TSD的退化、相同IS之间的重组或相邻缺失。事实上，后两者——IS之间的重组和相邻缺失——是TSD缺失的常见原因，我们在对来自伦斯基长期进化实验的基因组序列数据的分析中证明了这一点。此外，我们提出一些IS的移动——即那些与大规模基因组重排相关的移动——不会产生TSD，并且发生时没有IS之间重组或相邻缺失的证据。为支持这一假设，我们提供了对这种IS转座事件的两个直接的实证观察结果：在C中发生的一次IS移动加上一次大缺失，以及在SBW25中发生的一次IS移动伴随着一次大重复。虽然不太可能，但观察到的缺失和相关的IS移动有可能在一个过夜培养物中相继发生在两个事件中。然而，一个位于大规模重复中心的IS不容易解释，这表明IS元件的活性可能促进大规模缺失和重复。
插入序列是在细菌基因组中发现的最常见的可移动遗传元件，因此它们对细菌进化有重大影响。我们观察到在使用和进行的实验室进化实验期间发生的大规模缺失和重复中心的插入序列移动，涉及三种不同类型的转座酶。我们提出转座酶不介导DNA切割而是插入到现有DNA断裂处的可能性。我们的研究强调了插入序列对大规模基因组重排产生的重要性，并提出了关于这些突变的机制基础的问题。
