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Abstract：
Salmonella enterica Serovar Typhimurium (Salmonella) and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, the P22 DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, sequences similar to the pac site in the host genome, called pseudo-pac sites, lead to erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the Salmonella pseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequences. We built a regular expression (sequence match pattern) from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains-LT2 and 14028S-for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to initiate generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the Salmonella pseudo-pac sites in this study could be applied to other phage-host systems.
摘要：
肠沙门氏菌（沙门氏菌）及其噬菌体P22是通过广义转导研究水平基因转移的模型系统。通常,P22DNA包装机械启动包装时，短序列的DNA，被称为PAC网站，在P22基因组上被识别。然而,与宿主基因组中的pac位点相似的序列，称为伪pac网站，导致沙门氏菌DNA的错误包装和随后的广泛转导。虽然沙门氏菌假pac位点的一般基因组位置是已知的，序列本身尚未确定。我们使用映射到宿主沙门氏菌基因组的P22测序读数的可视化来定义广义转导起始区域和伪pac位点的可能位置。我们在每个基因组区域中搜索与P22pac位点具有最高相似性的序列,并比对所得序列。我们从比对中建立了正则表达式（序列匹配模式），并将其用于搜索两个P22易感沙门氏菌菌株LT2和14028S的基因组以进行序列匹配。最终的正则表达式成功地鉴定了LT2和14028S中的伪pac位点，其与映射的读段覆盖中的广义转导起始位点相对应。本研究中鉴定的伪pac位点序列可用于预测其他P22易感宿主中的广义转导位置，或通过基因工程在P22易感宿主的特定位置启动广义转导。此外，本研究中用于鉴定沙门氏菌假pac位点的生物信息学方法可应用于其他噬菌体宿主系统。
