Global mapping of Salmonella enterica-host protein-protein interactions during infection

Summary of the study:
Intracellular bacterial pathogens inject effector proteins into host cells to hijack diverse cellular processes and promote their survival and proliferation. To systematically map effector-host protein-protein interactions (PPIs) during infection, we generated a library of 32 Salmonella enterica serovar Typhimurium (STm) strains expressing chromosomally encoded affinity-tagged effectors, and quantified PPIs in macrophages and epithelial cells by Affinity-Purification Quantitative Mass-Spectrometry. Thereby, we identified 25 previously described and 421 novel effector-host PPIs. While effectors converged on the same host cellular processes, most had multiple targets, which often differed between cell types. Using reciprocal co-immunoprecipitations, we validated 13 out of 22 new PPIs. We used this PPI resource to further demonstrate that SseJ, SseL and SifA modulate cholesterol accumulation at the Salmonella Containing Vacuole (SCV) partially via the cholesterol transporter Niemann-Pick C1 protein (NPC1), PipB recruits the organelle contact site protein PDZD8 to the SCV, and SteC promotes actin bundling by phosphorylating formin-like proteins.

Annotation to this repository:
This collection of supplementary and original data completes the associated manuscript of the same title. It comprises:
(01-04) The enrichment plots of the large scale AP/QMS study (related to figures 2, 3 and S2)
(05-06) The abundances of all proteins in the AP/QMS study, alongside the full limma results (Figures 2, 3, S2 and S4)
(07) The data at the basis of all plots shown in the manuscript (Figures 4, 5, 6, 7, S6 and S7)
(08) All original Western Blot scans (Figures 4, 6, 7, S1, S3, S5, S7 and S8)
(09) The limma results of the validation in pBMDMs (Figure S5)
(10) The limma results of the separate TMT-run to assess the interaction partners of SseJ (Figures 5 and S6)
(11-12) Additional information about the antibodies and primers used in this study (KRT and Experimental Procedures)

本研究摘要：
细胞内细菌病原体通过注入效应蛋白进入宿主细胞，以篡夺多种细胞过程并促进其生存和增殖。为系统性地绘制感染过程中效应蛋白-宿主蛋白-蛋白相互作用（PPIs），我们构建了一个包含32种不同菌株的Salmonella enterica serovar Typhimurium（STm）菌株库，这些菌株表达的是染色体重编码的亲和标签效应蛋白，并通过亲和纯化定量质谱分析（Affinity-Purification Quantitative Mass-Spectrometry）对巨噬细胞和上皮细胞中的PPIs进行量化。据此，我们鉴定出25个已描述和421个新的效应蛋白-宿主PPIs。尽管效应蛋白聚焦于相同的宿主细胞过程，但大多数效应蛋白具有多个靶点，这些靶点在不同细胞类型之间往往存在差异。通过互作共免疫沉淀，我们验证了22个新PPIs中的13个。利用这一PPI资源，我们进一步证实了SseJ、SseL和SifA通过胆固醇转运蛋白Niemann-Pick C1蛋白（NPC1）部分调节了Salmonella Containing Vacuole（SCV）中的胆固醇积累，PipB通过招募器室接触位点蛋白PDZD8至SCV，而SteC通过磷酸化形成素样蛋白促进肌动蛋白束的形成。
关于本仓库的说明：
本数据集收集了补充数据和原始数据，完整地补充了相关研究论文。其内容包括：(01-04) 大规模AP/QMS研究的富集图（与图2、3和S2相关）；(05-06) AP/QMS研究中所有蛋白的丰度，以及完整的limma结果（图2、3、S2和S4）；(07) 手稿中所有图表的基础数据（图4、5、6、7、S6和S7）；(08) 所有原始的Western Blot扫描图（图4、6、7、S1、S3、S5、S7和S8）；(09) pBMDMs验证的limma结果（图S5）；(10) 用于评估SseJ相互作用伙伴的单独TMT运行的limma结果（图5和S6）；(11-12) 关于本研究中使用的抗体和引物的附加信息（KRT和实验步骤）。