Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome
Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome
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DOI：
10.1016/j.jsb.2017.08.005
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发表时间：
2017-12-01
影响因子：
3
通讯作者：
Jones, Kathryn M.
中科院分区：
文献类型：
--
作者：
Johnson, Matthew C.;Sena-Velez, Marta;Jones, Kathryn M.
固氮根瘤菌噬菌体显示出丰富的新结构、多样的酶组合和基因组特征。在这里，我们报道了在4.9-5.7 a分辨率下噬菌体衣壳的冷冻电镜结构，噬菌体颗粒蛋白质组，以及侵染中华根瘤菌的Podovirus Phi M5的基因组。这是具有衣壳和衣壳相关结构蛋白的噬菌体的第一个结构，与感染铜绿假单胞菌的luz24样病毒的结构相关。像许多其他足病毒一样，Phi M5是一个T=7的二十面体，有光滑的衣壳和短的、相对没有特征的尾巴。尽管如此，这一组在系统发育上与已被充分表征的T7、P22和epsilon 15超群的podovirus完全不同。在结构上，一个独特的密度桥，似乎是Phi M5独有的，向下延伸到外壳蛋白的主体，与六聚体中的下一个单体相互作用，可能稳定成熟的衣壳。此外，预测的Phi M5的尾巴纤维与肠道细菌噬菌体的尾巴纤维有很大的不同，但与其他根茎噬菌体有共同的结构域。在基因组上，Phi M5是高度镶嵌的。Phi M5基因组全长44005bp，有357bp的直接末端重复序列（DTRs）和58个独特的orf。令人惊讶的是，衣壳结构模块、尾部模块、DNA包装终止酶、DNA复制模块和整合酶似乎都来自不同的谱系。Phi M5最不寻常的特征之一是其末端酶，其大亚基与先前描述的短dtr生成包装机完全不同，并且不适合任何已建立的系统发育组。
Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage capsid at 4.9-5.7A-resolution, the phage particle proteome, and the genome of the Sinorhizobium meliloti-infecting Podovirus Phi M5. This is the first structure of a phage with a capsid and capsid-associated structural proteins related to those of the LUZ24-like viruses that infect Pseudomonas aeruginosa. Like many other Podoviruses, Phi M5 is a T=7 icosahedron with a smooth capsid and short, relatively featureless tail. Nonetheless, this group is phylogenetically quite distinct from Podoviruses of the well-characterized T7, P22, and epsilon 15 supergroups. Structurally, a distinct bridge of density that appears unique to Phi M5 reaches down the body of the coat protein to the extended loop that interacts with the next monomer in a hexamer, perhaps stabilizing the mature capsid. Further, the predicted tail fibers of Phi M5 are quite different from those of enteric bacteria phages, but have domains in common with other rhizophages. Genomically, Phi M5 is highly mosaic. The Phi M5 genome is 44,005bp with 357bp direct terminal repeats (DTRs) and 58 unique ORFs. Surprisingly, the capsid structural module, the tail module, the DNA-packaging terminase, the DNA replication module and the integrase each appear to be from a different lineage. One of the most unusual features of Phi M5 is its terminase whose large subunit is quite different from previously-described short-DTR-generating packaging machines and does not fit into any of the established phylogenetic groups.