Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.
Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella.
复制标题
噬菌体 P22 在沙门氏菌广义转导中使用的伪 pac 位点序列。
DOI：
10.1101/2024.03.25.586692
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发表时间：
2024
期刊：
影响因子：
--
通讯作者：
Kleiner,Manuel
中科院分区：
文献类型：
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作者：
Maier,JessieL;Gin,Craig;Callahan,Ben;Sheriff,EmmaK;Duerkop,BreckA;Kleiner,Manuel
沙门氏菌及其噬菌体P22是研究广义转导水平基因转移的模型系统。通常，当P22基因组上识别出称为pac位点的DNA短序列时，P22 DNA包装机器启动包装。然而，与宿主基因组中的pac位点相似的序列，称为假pac位点，导致沙门氏菌DNA的错误包装和随后的普遍转导。虽然一般的基因组位置的thesSalmonellaplactodo-pac网站是已知的，序列本身尚未确定。我们使用映射到宿主Salmonellagenomes的P22测序读数的可视化来定义广义转导起始的区域和假pac位点的可能位置。我们在每个基因组区域搜索与P22 pac位点具有最高相似性的序列，并将所得序列进行比对。我们从比对中构建了一个正则表达式（序列匹配模式），并使用它来搜索两个P22-耐药沙门氏菌株-LT 2和14028 S-的基因组序列匹配。最终的正则表达式成功地鉴定了LT 2和14028 S中的伪pac位点，其对应于映射的读段覆盖率中的广义转导起始位点。本研究中鉴定的pseudo-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do-pac位点的生物信息学方法可应用于其他噬菌体-宿主系统。
Salmonella entericaSerovar 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 ofSalmonellaDNA. While the general genomic locations of theSalmonellapseudo-pac sites are known, the sequences themselves have not been determined. We used visualization of P22 sequencing reads mapped to hostSalmonellagenomes 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-susceptibleSalmonellastrains—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 theSalmonellapseudo-pac sites in this study could be applied to other phage—host systems.