Table_3_Transcriptomic, Functional, and Network Analyses Reveal Novel Genes Involved in the Interaction Between Caenorhabditis elegans and Stenotrophomonas maltophilia.xlsx

The bacterivorous nematode Caenorhabditis elegans is an excellent model for the study of innate immune responses to a variety of bacterial pathogens, including the emerging nosocomial bacterial pathogen Stenotrophomonas maltophilia. The study of this interaction has ecological and medical relevance as S. maltophilia is found in association with C. elegans and other nematodes in the wild and is an emerging opportunistic bacterial pathogen. We identified 393 genes that were differentially expressed when exposed to virulent and avirulent strains of S. maltophilia and an avirulent strain of E. coli. We then used a probabilistic functional gene network model (WormNet) to determine that 118 of the 393 differentially expressed genes formed an interacting network and identified a set of highly connected genes with eight or more predicted interactions. We hypothesized that these highly connected genes might play an important role in the defense against S. maltophila and found that mutations of six of seven highly connected genes have a significant effect on nematode survival in response to these bacteria. Of these genes, C48B4.1, mpk-2, cpr-4, clec-67, and lys-6 are needed for combating the virulent S. maltophilia JCMS strain, while dod-22 was solely involved in response to the avirulent S. maltophilia K279a strain. We further found that dod-22 and clec-67 were up regulated in response to JCMS vs. K279a, while C48B4.1, mpk-2, cpr-4, and lys-6 were down regulated. Only dod-22 had a documented role in innate immunity, which demonstrates the merit of our approach in the identification of novel genes that are involved in combating S. maltophilia infection.

食细菌线虫秀丽隐杆线虫（Caenorhabditis elegans）是研究针对多种细菌病原体固有免疫应答的优秀模型，其中包括新兴的院内感染细菌病原体嗜麦芽窄食单胞菌（Stenotrophomonas maltophilia）。该互作体系的研究兼具生态与医学意义，因为嗜麦芽窄食单胞菌在野外可与秀丽隐杆线虫及其他线虫共生，且属于新兴的机会性致病细菌。我们鉴定出393个差异表达基因，这些基因在暴露于嗜麦芽窄食单胞菌的强毒株、弱毒株以及大肠杆菌（E. coli）弱毒株时呈现表达差异。随后我们借助概率性功能基因网络模型（WormNet）分析发现，393个差异表达基因中有118个构成了互作网络，并鉴定出一组具备8个及以上预测互作的高连接度基因。我们推测这类高连接度基因可能在抗嗜麦芽窄食单胞菌的宿主防御中发挥关键作用，后续实验证实，7个高连接度基因中的6个发生突变后，会对秀丽隐杆线虫应对这类细菌的存活率产生显著影响。其中，C48B4.1、mpk-2、cpr-4、clec-67及lys-6参与抵御强毒株嗜麦芽窄食单胞菌JCMS，而dod-22仅参与应答弱毒株嗜麦芽窄食单胞菌K279a。我们进一步发现，相较于K279a，JCMS可诱导dod-22与clec-67上调表达，而C48B4.1、mpk-2、cpr-4及lys-6则呈现下调表达。目前仅dod-22被报道与固有免疫相关，这证实了本研究方法在鉴定抗嗜麦芽窄食单胞菌感染新基因方面的应用价值。