Proteomic Characterization of Cellular and Molecular Processes that Enable the <em>Nanoarchaeum equitans-Ignicoccus hospitalis</em> Relationship

Nanoarchaeum equitans, the only cultured representative of the Nanoarchaeota, is dependent on direct physical contact with its host, the hyperthermophile Ignicoccus hospitalis. The molecular mechanisms that enable this relationship are unknown. Using whole-cell proteomics, differences in the relative abundance of >75% of predicted protein-coding genes from both Archaea were measured to identify the specific response of I. hospitalis to the presence of N. equitans on its surface. A purified N. equitans sample was also analyzed for evidence of interspecies protein transfer. The depth of cellular proteome coverage achieved here is amongst the highest reported for any organism. Based on changes in the proteome under the specific conditions of this study, I. hospitalis reacts to N. equitans by curtailing genetic information processing (replication, transcription) in lieu of intensifying its energetic, protein processing and cellular membrane functions. We found no evidence of significant Ignicoccus biosynthetic enzymes being transported to N. equitans. These results suggest that, under laboratory conditions, N. equitans diverts some of its host's metabolism and cell cycle control to compensate for its own metabolic shortcomings, thus appearing to be entirely dependent on small, transferable metabolites and energetic precursors from I. hospitalis.骑移纳米古菌（Nanoarchaeum equitans）是纳米古菌门（Nanoarchaeota）目前唯一可培养的代表类群，其生存必须依赖与宿主——超嗜热古菌医院火球菌（Ignicoccus hospitalis）的直接物理接触。介导这种共生关系的分子机制迄今仍不明确。本研究采用全细胞蛋白质组学（whole-cell proteomics）技术，对两种古菌中超过75%的预测蛋白质编码基因的相对丰度差异进行定量检测，以解析医院火球菌（I. hospitalis）在其表面定植骑移纳米古菌（N. equitans）时的特异性应答反应。同时还对纯化的骑移纳米古菌样本开展了分析，以寻找跨物种蛋白质转移的相关证据。本研究实现的细胞蛋白质组覆盖深度，位列已报道的多数生物体的较高水平。基于本研究特定培养条件下的蛋白质组变化特征，医院火球菌对骑移纳米古菌的应答策略为：抑制遗传信息加工过程（包括DNA复制、转录），转而强化其能量代谢、蛋白质加工及细胞膜相关功能。本研究未发现有显著量的医院火球菌生物合成酶被转运至骑移纳米古菌体内的相关证据。上述结果表明，在实验室培养条件下，骑移纳米古菌会劫持宿主的部分代谢通路与细胞周期调控机制，以弥补自身的代谢缺陷，提示其完全依赖于从医院火球菌获取可转移的小分子代谢物与能量前体物。