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
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摘要
【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。
[Background] The interaction between species is an important driving force for the evolution ofspecies. But it is challenging to determine the single nucleotide polymorphism(SNPs) that play animportant role in the process of interaction between species and establish an accurate genotype-phenotypemap. [Objective] To obtain the significant SNPs that play an important role in the interaction betweenEscherichia coli and Staphylococcus aureus and to detect how do these SNPs relate to each other overtime. [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 thesame strain in monoculture and co-culture. The phenotypes and genotypes of all strains were analyzed bysystems mapping and the significant SNPs were found out. [Results] We obtained a three-dimensionalManhattan plot that identifies 54 significant combinations of SNPs derived from 41 SNPs in E. coli and 12 SNPsin S. aureus. Among them, 6 genes we obtained by annotation can directly or indirectly affect the growthof microorganisms, nhaR(E19056) was involved in the formation of biofilm, rhlE(E832164) is related toribosome 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 inthe metabolic process of cells. [Conclusion] Systems mapping can detect the significant SNPs. Thegenetic effects of different SNPs are variable in the process of species interaction. Bacterial interactionwas found to exert direct genetic effects, indirect genetic effects and interspecific epistatic effects.
[Background] The interaction between species is an important driving force for the evolution ofspecies. But it is challenging to determine the single nucleotide polymorphism(SNPs) that play animportant role in the process of interaction between species and establish an accurate genotype-phenotypemap. [Objective] To obtain the significant SNPs that play an important role in the interaction betweenEscherichia coli and Staphylococcus aureus and to detect how do these SNPs relate to each other overtime. [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 thesame strain in monoculture and co-culture. The phenotypes and genotypes of all strains were analyzed bysystems mapping and the significant SNPs were found out. [Results] We obtained a three-dimensionalManhattan plot that identifies 54 significant combinations of SNPs derived from 41 SNPs in E. coli and 12 SNPsin S. aureus. Among them, 6 genes we obtained by annotation can directly or indirectly affect the growthof microorganisms, nhaR(E19056) was involved in the formation of biofilm, rhlE(E832164) is related toribosome 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 inthe metabolic process of cells. [Conclusion] Systems mapping can detect the significant SNPs. Thegenetic effects of different SNPs are variable in the process of species interaction. Bacterial interactionwas found to exert direct genetic effects, indirect genetic effects and interspecific epistatic effects.
引文
[1]Lawrence D,Fiegna F,Behrends V,et al.Species interactions alter evolutionary responses to a novel environment[J].PLoSBiology,2012,10(5):e1001330
[2]Davey JW,Hohenlohe PA,Etter PD,et al.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J].Nature Reviews Genetics,2011,12(7):499-510
[3]Whitham TG,Bailey JK,Schweitzer JA,et al.A framework for community and ecosystem genetics:from genes to ecosystems[J].Nature Reviews Genetics,2006,7(7):510-523
[4]Lander ES,Botstein D.Mapping mendelian factors underlying quantitative traits using RFLP linkage maps[J].Genetics,1989,121(1):185-199
[5]Mackay TFC,Stone EA,Ayroles JF.The genetics of quantitative traits:challenges and prospects[J].Nature Reviews Genetics,2009,10(8):565-577
[6]Wu RL,Lin M.Functional mapping-how to map and study the genetic architecture of dynamic complex traits[J].Nature Reviews Genetics,2006,7(3):229-237
[7]Li ZT,Sillanp??MJ.Dynamic quantitative trait locus analysis of plant phenomic data[J].Trends in Plant Science,2015,20(12):822-833
[8]Wang Z,Pang XM,Lv YF,et al.A dynamic framework for quantifying the genetic architecture of phenotypic plasticity[J].Briefings in Bioinformatics,2013,14(1):82-95
[9]Wang Z,Wang NT,Wu RL,et al.f GWAS:an R package for genome-wide association analysis with longitudinal phenotypes[J].Journal of Genetics and Genomics,2018,45(7):411-413
[10]Sun LD,Wu RL.Mapping complex traits as a dynamic system[J].Physics of Life Reviews,2015,13:155-185
[11]Wu RL,Cao JG,Huang ZW,et al.Systems mapping:how to improve the genetic mapping of complex traits through design principles of biological systems[J].BMC Systems Biology,2011,5:84
[12]Chen N,Zhu J,Ye MX,et al.Interactions between Escherichia coli and Staphylococcus aureus determined by genome-wide association analysis[J].Acta Microbiologica Sinica,2017,57(4):526-538(in Chinese)陈南,朱璟,叶梅霞,等.GWAS研究大肠杆菌和金黄色葡萄球菌种间互作进化机制[J].微生物学报,2017,57(4):526-538
[13]He XQ,Jin Y,Ye MX,et al.Bacterial genetic architecture of ecological interactions in co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an example[J].Frontiers in Microbiology,2017,8:2332
[14]Jiang LB,He XQ,Jin Y,et al.A mapping framework of competition-cooperation QTLs that drive community dynamics[J].Nature Communications,2018,9:3010
[15]Thompson JN.The evolution of species interactions[J].Science,1999,284(5423):2116-2118
[16]Goller C,Wang X,Itoh Y,et al.The cation-responsive protein NhaR of Escherichia coli activates pgaABCD transcription,required for production of the biofilm adhesin Poly-β-1,6-N-Acetyl-D-glucosamine[J].Journal of Bacteriology,2007,188(23):8022-8032
[17]Hall-Stoodley L,Costerton JW,Stoodley P.Bacterial biofilms:from the natural environment to infectious diseases[J].Nature Reviews Microbiology,2004,2(2):95-108
[18]Bizebard T,Ferlenghi I,Iost I,et al.Studies on three E.coli DEAD-Box helicases point to an unwinding mechanism different from that of model DNA helicases[J].Biochemistry,2004,43(24):7857-7866
[19]Jain C.The E.coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly[J].RNA,2008,14(2):381-389
[20]Metzner M,Germer J,Hengge R.Multiple stress signal integration in the regulation of the complexσS-dependent csiD-ygaF-gabDTP operon in Escherichia coli[J].Molecular Microbiology,2004,51(3):799-811
[21]Huisman GW,Kolter R.Sensing starvation:a homoserine lactone--dependent signaling pathway in Escherichia coli[J].Science,1994,265(5171):537-539
[22]Falnes P?,Johansen RF,Seeberg E.AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli[J].Nature,2002,419(6903):178-182
[23]Li M,Ho PY,Yao SJ,et al.Effect of sucA or sucC gene knockout on the metabolism in Escherichia coli based on gene expressions,enzyme activities,intracellular metabolite concentrations and metabolic fluxes by 13C-labeling experiments[J].Biochemical Engineering Journal,2006,30(3):286-296
[24]Kolker E,Makarova KS,Shabalina S,et al.Identification and functional analysis of‘hypothetical’genes expressed in Haemophilus influenzae[J].Nucleic Acids Research,2004,32(8):2353-2361
[2]Davey JW,Hohenlohe PA,Etter PD,et al.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J].Nature Reviews Genetics,2011,12(7):499-510
[3]Whitham TG,Bailey JK,Schweitzer JA,et al.A framework for community and ecosystem genetics:from genes to ecosystems[J].Nature Reviews Genetics,2006,7(7):510-523
[4]Lander ES,Botstein D.Mapping mendelian factors underlying quantitative traits using RFLP linkage maps[J].Genetics,1989,121(1):185-199
[5]Mackay TFC,Stone EA,Ayroles JF.The genetics of quantitative traits:challenges and prospects[J].Nature Reviews Genetics,2009,10(8):565-577
[6]Wu RL,Lin M.Functional mapping-how to map and study the genetic architecture of dynamic complex traits[J].Nature Reviews Genetics,2006,7(3):229-237
[7]Li ZT,Sillanp??MJ.Dynamic quantitative trait locus analysis of plant phenomic data[J].Trends in Plant Science,2015,20(12):822-833
[8]Wang Z,Pang XM,Lv YF,et al.A dynamic framework for quantifying the genetic architecture of phenotypic plasticity[J].Briefings in Bioinformatics,2013,14(1):82-95
[9]Wang Z,Wang NT,Wu RL,et al.f GWAS:an R package for genome-wide association analysis with longitudinal phenotypes[J].Journal of Genetics and Genomics,2018,45(7):411-413
[10]Sun LD,Wu RL.Mapping complex traits as a dynamic system[J].Physics of Life Reviews,2015,13:155-185
[11]Wu RL,Cao JG,Huang ZW,et al.Systems mapping:how to improve the genetic mapping of complex traits through design principles of biological systems[J].BMC Systems Biology,2011,5:84
[12]Chen N,Zhu J,Ye MX,et al.Interactions between Escherichia coli and Staphylococcus aureus determined by genome-wide association analysis[J].Acta Microbiologica Sinica,2017,57(4):526-538(in Chinese)陈南,朱璟,叶梅霞,等.GWAS研究大肠杆菌和金黄色葡萄球菌种间互作进化机制[J].微生物学报,2017,57(4):526-538
[13]He XQ,Jin Y,Ye MX,et al.Bacterial genetic architecture of ecological interactions in co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an example[J].Frontiers in Microbiology,2017,8:2332
[14]Jiang LB,He XQ,Jin Y,et al.A mapping framework of competition-cooperation QTLs that drive community dynamics[J].Nature Communications,2018,9:3010
[15]Thompson JN.The evolution of species interactions[J].Science,1999,284(5423):2116-2118
[16]Goller C,Wang X,Itoh Y,et al.The cation-responsive protein NhaR of Escherichia coli activates pgaABCD transcription,required for production of the biofilm adhesin Poly-β-1,6-N-Acetyl-D-glucosamine[J].Journal of Bacteriology,2007,188(23):8022-8032
[17]Hall-Stoodley L,Costerton JW,Stoodley P.Bacterial biofilms:from the natural environment to infectious diseases[J].Nature Reviews Microbiology,2004,2(2):95-108
[18]Bizebard T,Ferlenghi I,Iost I,et al.Studies on three E.coli DEAD-Box helicases point to an unwinding mechanism different from that of model DNA helicases[J].Biochemistry,2004,43(24):7857-7866
[19]Jain C.The E.coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly[J].RNA,2008,14(2):381-389
[20]Metzner M,Germer J,Hengge R.Multiple stress signal integration in the regulation of the complexσS-dependent csiD-ygaF-gabDTP operon in Escherichia coli[J].Molecular Microbiology,2004,51(3):799-811
[21]Huisman GW,Kolter R.Sensing starvation:a homoserine lactone--dependent signaling pathway in Escherichia coli[J].Science,1994,265(5171):537-539
[22]Falnes P?,Johansen RF,Seeberg E.AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli[J].Nature,2002,419(6903):178-182
[23]Li M,Ho PY,Yao SJ,et al.Effect of sucA or sucC gene knockout on the metabolism in Escherichia coli based on gene expressions,enzyme activities,intracellular metabolite concentrations and metabolic fluxes by 13C-labeling experiments[J].Biochemical Engineering Journal,2006,30(3):286-296
[24]Kolker E,Makarova KS,Shabalina S,et al.Identification and functional analysis of‘hypothetical’genes expressed in Haemophilus influenzae[J].Nucleic Acids Research,2004,32(8):2353-2361