Barth Zachary K, Dunham Drew T, Seed Kimberley D
Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA.
bioRxiv. 2023 Mar 23:2023.03.23.533998. doi: 10.1101/2023.03.23.533998.
Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4’s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.
归巢内切酶基因（HEGs）是普遍存在的自私元件，可产生靶向双链DNA断裂，促进HEG DNA序列重组到断裂位点，并影响编码HEG的基因组的进化动态。噬菌体携带HEGs已有充分记载，对HEGs的最重要表征集中在由大肠杆菌噬菌体T4编码的那些基因上。最近，有人观察到，被大量采样的弧菌噬菌体ICP1同样富含与T4不同的HEGs。在这里，我们研究了ICP1和多种噬菌体编码的HEGs，提出了有助于噬菌体进化的HEG驱动机制。相对于ICP1和T4，我们发现HEGs在噬菌体中的分布是可变的，HEGs经常在必需基因附近或内部编码。我们鉴定出由HEGs侧翼的高核苷酸同一性的大片段区域（>10kb），称为HEG岛，我们假设它们是由侧翼HEGs的活性所驱动。最后，我们发现了噬菌体编码的HEGs与其他噬菌体和噬菌体卫星编码的基因之间结构域交换的例子。我们预计，HEGs对噬菌体进化轨迹的影响比以前认为的更大，并且未来研究HEGs在噬菌体进化中作用的工作将继续突出这些观察结果。
