Membrane changes during syntrophic interactions of an archaeal-bacterial coculture

Abstract Syntrophic interactions between bacteria and archaea are vital for anaerobic processes, relying on close cell-to-cell contact for efficient metabolite and electron transfer. Membrane-associated proteins and lipids likely play key roles in stabilizing these contacts, though little is known about membrane changes during syntrophy. These interactions are also central to theories of eukaryogenesis, where a symbiosis between an archaeal host—likely an Asgard archaeon—and a bacterial partner may have arisen from prior syntrophic interactions. Model systems of syntrophic microbes provide valuable insights into how such intimate associations could have led to the emergence of eukaryotic life. Here, we used syntrophic cocultures of the sulfate-reducing bacterium Desulfovibrio vulgaris and the methanogenic archaeon Methanococcus maripaludis to investigate membrane changes during a syntrophic interaction involving cell-to-cell contact. Evolved cocultures after several generations under syntrophic conditions were analyzed by proteomics and transcriptomics to identify differentially expressed proteins connected to cell-to-cell interactions, as well as by lipid analyses to determine changes in the cell membrane of both syntrophic partners. These data suggest a higher impact on the archaeon M. maripaludis, affecting transmembrane, signaling, and lipid biosynthesis proteins. To investigate the impact of evolutionary adaptation, both partners were re-isolated from a non-evolved ancestral coculture (coculture after mixing species), as well as from evolved (several generations) cocultures. While lipid profiles had changed in the coculture due to evolutionary adaptation, isolates were found to revert their lipid composition to the wildtype profile when growing independent again. This in-depth analysis of a model syntrophic coculture provides clues on how interdomain cell-to-cell interactions might have led to membrane changes during early eukaryogenesis. Description of .tar files containing data of intact polar lipid analysis: 1) Lipid_data_coculture_vs_monocultures.tar: Folders for each type of analysed culture (wildtype monocultures of D. vulgaris and M. maripaludis and cocultures Co-Anc, Co-300 and Co-1000) Raw data files of mass spectrometry runs of 5 biological replicates Folder with raw data files of mass spectrometry runs of growth medium blanks for all three different used growth media 2) Lipid_data_isolates_vs_cocultures.tar: Folders for each type of analysed culture (isolated monocultures of D. vulgaris and M. maripaludis and cocultures mixed with these isolates) Raw data files of mass spectrometry runs of 3 biological replicates Folder with raw data files of mass spectrometry runs of growth medium blanks for all three different used growth media### 摘要 细菌与古菌之间的互养相互作用（syntrophic interactions）对厌氧过程至关重要，此类相互作用依赖紧密的细胞间接触以实现高效的代谢物与电子传递。膜相关蛋白与脂质可能在稳定这类接触中发挥关键作用，但目前对互养过程中的膜变化仍知之甚少。 此类相互作用同时也是真核生物起源（eukaryogenesis）理论的核心内容：古菌宿主（极有可能为阿斯加德古菌（Asgard archaeon））与细菌共生体之间的共生关系，可能源自此前的互养相互作用。互养微生物的模式体系，可为解析这类紧密关联如何推动真核生命起源提供宝贵见解。 本研究利用硫酸盐还原菌普通脱硫弧菌（*Desulfovibrio vulgaris*）与产甲烷古菌马氏甲烷球菌（*Methanococcus maripaludis*）的互养共培养体系，探究涉及细胞间接触的互养相互作用过程中的膜变化。研究对互养条件下传代多代后的进化共培养样本，分别通过蛋白质组学与转录组学分析，筛选与细胞间相互作用相关的差异表达蛋白；同时通过脂质分析，确定两种互养伙伴的细胞膜变化。分析数据显示，马氏甲烷球菌（*M. maripaludis*）受到的影响更为显著，其跨膜蛋白、信号蛋白及脂质生物合成相关蛋白均发生改变。 为解析进化适应的影响，研究人员分别从未进化的祖先共培养体系（即物种混合后的初始共培养物）以及传代多代的进化共培养体系中，重新分离得到两种互养伙伴。尽管共培养体系的脂质谱因进化适应发生改变，但当分离得到的菌株重新独立培养时，其脂质组成会恢复至野生型谱型。 本研究对模式互养共培养体系的深度分析，为解析域间细胞间相互作用如何在早期真核生物起源过程中引发膜变化提供了线索。 ### 含完整极性脂质分析数据的.tar压缩包说明 1. `Lipid_data_coculture_vs_monocultures.tar` - 包含各分析培养类型的文件夹：普通脱硫弧菌（*D. vulgaris*）与马氏甲烷球菌（*M. maripaludis*）的野生型单培养体系，以及共培养体系Co-Anc、Co-300与Co-1000； - 包含5次生物学重复的质谱检测原始数据文件； - 包含三种不同使用培养基的空白培养基质谱检测原始数据文件的文件夹。 2. `Lipid_data_isolates_vs_cocultures.tar` - 包含各分析培养类型的文件夹：普通脱硫弧菌与马氏甲烷球菌的分离单培养体系，以及与这些分离菌株混合的共培养体系； - 包含3次生物学重复的质谱检测原始数据文件； - 包含三种不同使用培养基的空白培养基质谱检测原始数据文件的文件夹。