Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
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DOI：
10.1111/1462-2920.14979
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发表时间：
2020-06-01
影响因子：
5.1
通讯作者：
Lavigne, Rob
中科院分区：
文献类型：
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作者：
Lood, Cedric;Danis-Wlodarczyk, Katarzyna;Lavigne, Rob
假单胞菌病毒vB_PAM_PA5oct被提出作为研究噬菌体-细菌相互作用的模型巨型噬菌体，并且是噬菌体治疗应用的候选者。结合杂交测序，RNA-Seq和质谱分析，我们可以准确地注释其286，783 bp的基因组，其中包括461个编码区，包括4个非编码RNA（ncRNA）和93个病毒体相关蛋白。PA 5 oct依赖于宿主RNA聚合酶进行感染周期，RNA-Seq显示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%。PA 5 oct没有被组织成严格连续的时间转录区域，但是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显示有限转录活性的区域。我们发现，PA 5 oct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-pncB 1-nadE，用于胞外多糖生物合成的操纵子psl和用于周质硝酸还原酶生产的操纵子nap。我们还观察到T4 P基因产物的下调，提示双重感染排除机制。我们使用PA 5 oct的蛋白质组，使用基因共享网络将我们的分离株定位在其他菌株中。这项综合组学研究阐明了巨型病毒的分子多样性，并对细胞调控和噬菌体编码的劫持机制提出了新的问题。
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.