利用系统作图(Systems mapping)研究大肠埃希菌和金黄色葡萄球菌的互作遗传机制

【背景】物种间相互作用是物种进化的重要推动力,然而如何将基因型和表型关联以及确定在物种相互作用过程中起重要作用的基因均面临挑战。【目的】通过系统作图(Systems mapping)得到两种微生物在相互作用过程中起重要作用的SNPs (Single nucleotide polymorphism),以及随着时间的变化,这些SNPs是如何相互联系进而影响大肠埃希菌和金黄色葡萄球菌的相互作用。【方法】分别对45株大肠埃希菌、45株金黄色葡萄球菌进行单独培养和混合共培养,通过实时荧光定量PCR(Real-time quantitative PCR,qPCR)进行绝对定量,得到一定时间内各个菌株的生长量,比较相同菌株在不同培养条件下生长情况,以各个菌株重测序结果为基础,结合系统作图得到在相互作用过程中起重要作用的显著SNPs及其相互联系。【结果】通过系统作图分析,获得具有54对显著SNPs组合的三维曼哈顿图,这些组合中41个显著SNPs来自大肠埃希菌,12个显著SNPs来自金黄色葡萄球菌。在上述SNPs中已有6个SNPs所在的候选基因都可以直接或者间接影响微生物的生长量变化,从而影响两种微生物相互作用方式。它们分别是nhaR(E19056)参与生物膜的形成,rhlE(E832164)与核糖体的组装有关,csiD (E2789300)的表达可以使细胞面对恶劣环境,alk B (E2309274)可以参与DNA的损伤修复,sucA(E759230)和yjjW(E4614704)都参与细胞的代谢过程。【结论】系统作图可以检测到物种在相互作用过程中显著SNPs;物种相互作用过程中不同SNPs遗传效应随着时间变化;细菌的相互作用过程是直接遗传效应、间接遗传效应和上位性效应共同产生的结果。

Analysis of interaction mode between Escherichia coli and Staphylococcus aureus by systems mapping

Background] The interaction between species is an important driving force for the evolution of species. But it is challenging to determine the single nucleotide polymorphism (SNPs) that play an important role in the process of interaction between species and establish an accurate genotype-phenotype map. Objective] To obtain the significant SNPs that play an important role in the interaction between Escherichia coli and Staphylococcus aureus and to detect how do these SNPs relate to each other over time. Methods] Real-time quantitative PCR (qPCR) was used to determine the abundance of all strains. We reared E. coli and S. aureus in monoculture and compared to the difference of growth between the same strain in monoculture and co-culture. The phenotypes and genotypes of all strains were analyzed by systems mapping and the significant SNPs were found out. Results] We obtained a three-dimensional Manhattan plot that identifies 54 significant combinations of SNPs derived from 41 SNPs in E. coli and 12 SNPs in S. aureus. Among them, 6 genes we obtained by annotation can directly or indirectly affect the growth of microorganisms, nhaR (E19056) was involved in the formation of biofilm, rhlE (E832164) is related to ribosome assembly, the expression of csiD (E2789300) can make cells face stress environment, alkB (E2309274) can participate in DNA damage repair, sucA (E759230) and yjjW (E4614704) are involved in the metabolic process of cells. Conclusion] Systems mapping can detect the significant SNPs. The genetic effects of different SNPs are variable in the process of species interaction. Bacterial interaction was found to exert direct genetic effects, indirect genetic effects and interspecific epistatic effects.