Integrated omics reveal time-resolved insights into T4 phage infection of E. coli on proteome and transcriptome level

Bacteriophages are highly abundant viruses of bacteria. The major role of phages in microbial ecology to shape bacterial communities and their emerging medical potential as antibacterial agents have triggered a rebirth of phage research. It is of particular interest to understand the molecular mechanisms by which phages gain control over their host. Omics technologies such as next-generation sequencing and protein-profiling technologies can provide novel insights into transcriptional and translational events occurring during the infection process. Thereby, the temporal organization of the transcriptome and proteome of the phage and their bacterial hosts can be monitored. In this study, we performed next-generation sequencing and proteomics to study the transcriptome and proteome of the T4 phage and its host during the infection in a time-resolved manner. Our data shows the temporally resolved appearance of bacteriophage T4 transcripts and proteins, confirming previously described subgrouping of T4 gene products into early, middle and late infection phases. We observe specific early transcripts giving rise to middle or late proteins indicating the existence of previously not reported post-transcriptional regulatory mechanisms controlling the translation of T4 mRNAs. Moreover, we investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying degradation of E. coli transcripts and preservation of the host proteome. This study provides the first comprehensive insights into the transcriptomic and proteomic takeover by the bacteriophage T4, exemplifying the power and value of high-throughput technologies to simultaneously characterize multiple gene expression events. Moreover, we created a user-friendly application available to the entire scientific community to access gene expression patterns for their host and phage genes of interest.

噬菌体（Bacteriophages）是一类丰度极高的细菌病毒。噬菌体在微生物生态系统中塑造细菌群落的核心功能，以及其作为抗菌制剂的新兴医学潜力，共同推动了噬菌体研究的复兴。解析噬菌体调控宿主的分子机制，是该领域的核心研究热点。组学技术（如下一代测序（next-generation sequencing）与蛋白表达谱分析技术）可针对感染过程中的转录与翻译事件提供全新研究视角，借此可实现噬菌体与宿主细菌的转录组、蛋白质组的时间动态监测。本研究采用时间分辨率实验设计，利用下一代测序与蛋白质组学技术，对T4噬菌体（T4 phage）感染宿主过程中的转录组与蛋白质组进行了系统分析。本研究的数据清晰展示了T4噬菌体转录本与蛋白质的时间动态表达模式，验证了此前报道的T4基因产物按感染早期、中期、晚期进行分组的结论。研究发现部分早期转录本可翻译为中期或晚期蛋白质，这表明存在此前未被报道的、调控T4信使RNA（mRNA）翻译的转录后调控机制。此外，本研究还探究了感染过程中大肠杆菌（E. coli）来源的转录本与蛋白质的稳定性，发现大肠杆菌的转录本发生降解，而宿主蛋白质组得以保留。本研究首次全面解析了T4噬菌体对宿主转录组与蛋白质组的接管过程，充分体现了高通量技术可同时表征多基因表达事件的优势与应用价值。此外，本研究还开发了一款易用的应用程序，可供全球科研群体查询目标宿主与噬菌体基因的表达模式。