Azhieh Amirahmad, Hernandez Paul, Anderson Alexander C, Sychantha David, Verster Adrian J, Whitney John C, Ross Benjamin D
Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada.
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.
bioRxiv. 2025 May 4:2025.05.03.651265. doi: 10.1101/2025.05.03.651265.
Bacteria encode diverse mechanisms for mediating interbacterial antagonism through the exchange of toxic effector proteins. Although the structure, function, and regulation of these pathways has been well established for many organisms, an understanding of their ecological and evolutionary dynamics lags behind. Type VI secretion systems (T6SS) deliver effectors between competing Gram-negative bacteria, including among mammalian gut Bacteroidales, resulting in the evolution of elaborate defense mechanisms that protect against T6SS attack. One such mechanism is the recombinase-associated acquired interbacterial defence (rAID) system, which harbors arrays of orphan immunity genes that diverge in sequence from T6SS-associated cognate immunity genes. It is not known if such sequence divergence impacts rAID orphan immunity function, or how rAID distribution across microbiomes relates to the T6SS. Here, we show that divergent rAID orphan immunity factors that possess SUKH domains allow bacteria to survive intoxication by cognate effectors. Such protection is due to high affinity protein-protein interactions between orphan immunity and effector that are comparable to that of cognate effector-immunity. Unlike other examples of T6SS effector-immunity interactions, we find that the binding interface is comprised of electrostatic interactions with a high degree of redundancy underlying its protective capacity. Finally, we quantify orphan immunity and effector gene abundance and dynamics across human gut metagenomes, revealing patterns of co-occurrence indicative of positive selection. Population genetic analyses of longitudinal data suggests that orphan immunity genes accumulate non-synonymous mutations that lie at the predicted effector-immunity interface. Together, our findings establish rAID orphan immunity genes as important bacterial fitness determinants in the human gut.
细菌通过交换有毒效应蛋白编码了多种介导细菌间拮抗作用的机制。尽管这些途径的结构、功能和调控在许多生物体中已得到充分确立，但对其生态和进化动态的理解仍滞后。VI型分泌系统（T6SS）在竞争性革兰氏阴性细菌之间传递效应蛋白，包括在哺乳动物肠道拟杆菌中，这导致了精心设计的防御机制的进化，以抵御T6SS攻击。一种这样的机制是重组酶相关的获得性细菌间防御（rAID）系统，它含有一系列孤儿免疫基因，其序列与T6SS相关的同源免疫基因不同。尚不清楚这种序列差异是否会影响rAID孤儿免疫功能，或者rAID在微生物群落中的分布与T6SS有何关系。在这里，我们表明具有SUKH结构域的不同rAID孤儿免疫因子使细菌能够在同源效应蛋白中毒后存活。这种保护是由于孤儿免疫和效应蛋白之间的高亲和力蛋白质-蛋白质相互作用，这与同源效应蛋白-免疫相互作用相当。与T6SS效应蛋白-免疫相互作用的其他例子不同，我们发现结合界面由静电相互作用组成，其保护能力具有高度冗余性。最后，我们量化了人类肠道宏基因组中孤儿免疫和效应蛋白基因的丰度和动态，揭示了共生模式，表明存在正选择。对纵向数据的群体遗传分析表明，孤儿免疫基因积累了位于预测的效应蛋白-免疫界面的非同义突变。总之，我们的研究结果确立了rAID孤儿免疫基因是人类肠道中重要的细菌适应性决定因素。
