State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China.
Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA.
Environ Microbiol. 2018 Feb;20(2):477-491. doi: 10.1111/1462-2920.13937. Epub 2017 Oct 13.
Viral concentrates (VCs), containing bioinformative DNA and proteins, have been used to study viral diversity, viral metagenomics and virus-host interactions in natural ecosystems. Besides viruses, VCs also contain many noncellular biological components including diverse functional proteins. Here, we used a shotgun proteomic approach to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum (DCM) of the South China Sea. Proteins of viruses infecting picophytoplankton, that is, cyanobacteria and prasinophytes, and heterotrophic bacterioplankton, such as SAR11 and SAR116, dominated the viral proteome. Almost no proteins from RNA viruses or known gene transfer agents were detected, suggesting that they were not abundant at the sampling site. Remarkably, nonviral proteins made up about two thirds of VC proteins, including overwhelmingly abundant periplasmic transporters for nutrient acquisition and proteins for diverse cellular processes, that is, translation, energy metabolism and one carbon metabolism. Interestingly, three 56 kDa selenium-binding proteins putatively involved in peroxide reduction from gammaproteobacteria were abundant in the VCs, suggesting active removal of peroxide compounds at DCM. Our study demonstrated that metaproteomics provides a valuable avenue to explore the diversity and structure of the viral community and also the pivotal biological functions affiliated with microbes in the natural environment.
病毒浓缩物 (VCs) 含有具有生物信息学意义的 DNA 和蛋白质，已被用于研究自然生态系统中的病毒多样性、病毒宏基因组学和病毒-宿主相互作用。除了病毒，VCs 还包含许多非细胞生物成分，包括多种功能蛋白。在这里，我们使用一种鸟枪法蛋白质组学方法来描述从南海贫营养层的叶绿素最大值（DCM）中收集的 VCs 的蛋白质。感染微微型浮游植物（即蓝细菌和甲藻）和异养细菌浮游生物（如 SAR11 和 SAR116）的病毒的蛋白质，主导了病毒蛋白质组。几乎没有检测到感染 RNA 病毒或已知基因转移剂的蛋白质，这表明它们在采样地点并不丰富。值得注意的是，非病毒蛋白质约占 VC 蛋白质的三分之二，包括用于获取营养的大量丰富的周质转运蛋白以及用于各种细胞过程的蛋白质，即翻译、能量代谢和一碳代谢。有趣的是，三个假定参与从γ变形菌中还原过氧化物的 56 kDa 硒结合蛋白在 VCs 中丰富，表明在 DCM 处积极去除过氧化物化合物。我们的研究表明，宏蛋白质组学为探索病毒群落的多样性和结构以及与自然环境中微生物相关的关键生物学功能提供了有价值的途径。
