Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage‐bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA‐Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non‐coding RNAs (ncRNAs) and 93 virion‐associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA‐Seq revealed a gradual take‐over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA‐pncB1‐nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene‐sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage‐encoded hijacking mechanisms.

中文翻译：

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铜绿假单胞菌病毒 PA5oct 的综合组学分析凸显了巨型噬菌体的分子复杂性。


假单胞菌病毒 vB_PaeM_PA5oct 被提议作为巨型噬菌体模型来研究噬菌体-细菌相互作用，并且是噬菌体治疗应用的候选者。结合混合测序、RNA-Seq 和质谱分析，我们能够准确注释其 286,783 bp 基因组和 461 个编码区，包括 4 个非编码 RNA (ncRNA) 和 93 个病毒体相关蛋白。 PA5oct 在感染周期中依赖于宿主 RNA 聚合酶，RNA-Seq 揭示了总细胞转录组的逐渐接管，从早期感染的 21% 到晚期感染的 93%。 PA5oct 并未组织成严格连续的时间转录区域，但可以区分在感染的早期、中期和晚期转录的一些基因组区域。有趣的是，我们观察到在整个感染周期中转录活性有限的区域。我们发现 PA5oct 在感染过程中上调特定的细菌操纵子，包括参与 NAD 生物合成的操纵子pncA-pncB1-nadE 、用于胞外多糖生物合成的psl和用于周质硝酸还原酶生产的nap 。我们还观察到 T4P 基因产物的下调，表明重复感染排除机制。我们使用 PA5oct 的蛋白质组通过基因共享网络将我们的分离物定位在其他噬菌体中。这项综合组学研究阐明了巨型病毒的分子多样性，并对细胞调节和噬菌体编码的劫持机制提出了新的问题。