Introducing differential RNA-seq mapping to track the early infection phase for <i>Pseudomonas</i> phage ɸKZ

As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of <i>Pseudomonas aeruginosa</i> jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (<i>cdrAB</i>) and iron storage (<i>bfrB</i>), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (<i>atpCDGHF</i> and <i>cyoABCDE</i>). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.随着噬菌体生物学研究的持续复兴，越来越多的噬菌体基因组通过DNA测序技术得以解析。但目前学界对噬菌体在宿主感染过程中实现基因组表达所需的转录组架构的认知仍较为匮乏。目前仅极少数噬菌体完成了转录起始位点（Transcription start sites, TSSs）与操纵子的定位，且尚未有针对单株噬菌体——或其与感染宿主的组合——的注释化全局RNA图谱公开报道。本研究针对作为病毒遗传学与结构研究模式菌株的铜绿假单胞菌（Pseudomonas aeruginosa）巨型噬菌体ɸKZ，应用差异RNA测序（differential RNA-seq, dRNA-seq）技术，解析其感染宿主早期的宿主接管阶段的转录组结构。该转录组图谱大幅扩充了早期表达的病毒基因数量，明确了ɸKZ感染10分钟后激活的转录起始位点。与此同时，我们还记录了该关键代谢转换阶段中宿主转录组的基因表达变化情况。除此前已报道的氨基酸代谢相关基因上调外，我们还观察到生物膜形成相关基因（cdrAB）、铁储存相关基因（bfrB）的显著激活，以及抗毒素ParD的表达激活。与之相反，ɸKZ感染会快速下调氧化磷酸化复合物IV与V的相关基因（atpCDGHF与cyoABCDE）。综上，本研究数据为巨型噬菌体ɸKZ的转录组织模式与感染过程提供了全新认知，同时为噬菌体-宿主相互作用的全基因组转录组分析提供了研究框架。