植物青枯菌Po82菌株致病力分化相关基因的分离及其功能研究
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摘要
青枯菌(Ralstonia solanacearum)，是一种地域分布广且寄主范围非常大的毁灭性植物病原细菌。本实验室保存的Po82菌株与香蕉青枯菌及NPB菌株同属于演化型II/序列变种4，且兼具青枯菌2号和3号小种的致病力。
本论文以Po82菌株作为研究对象，利用抑制性差减杂交技术筛选差异基因；完成了该菌株的全基因组序列测定工作，利用生物信息学分析手段，依据泛基因组学的概念，从3个层面上共筛选出8个致病相关候选基因进行功能研究。旨在揭示青枯菌在进化过程中不同小种(或菌株)间致病力分化及寄主适应性的分子机理，从而为进一步有针对性的进行植物青枯病防控提供理论依据。
1.比较基因组学方法筛选Po82菌株特异基因以青枯菌Po82菌株为待测菌株，进行抑制性差减杂交文库的构建。以NPB菌株RUN292构建的差减文库中，共筛选获得6类46个差异基因。鉴于抑制性差减杂交的局限性，本实验室对Po82菌株的全基因组序列进行了测定。比较基因组学研究表明，该菌株中共存在有390个菌株特异基因以及53个基因岛。
2. Po82菌株III型分泌系统hrpB调控基因的功能研究构建Po82菌株hrpB基因突变株及其互补菌株。结果表明，青枯菌hrpB基因缺失突变株的致病力较Po82野生型菌株显著下降,互补菌株可恢复突变菌株的致病力；在营养贫瘠型培养基中，hrpB基因缺失突变株的生长速率较野生型青枯菌Po82菌株更快。因此，hrpB基因与青枯菌的致病力显著相关。
3. Po82菌株III型分泌系统效应子编码基因hopAF1的功能研究Po82菌株中存在与丁香假单胞菌DC3000中III型效应子HopAF1编码基因同源的基因。构建了Po82菌株hopAF1基因突变株及其互补菌株。接种香蕉和番茄进行致病力测定结果表明，hopAF1基因突变株接种植株的病情指数较野生型菌株下降，而互补菌株能够恢复突变菌株的致病力。半定量RT-PCR结果表明，hopAF1基因的表达趋势与hrpB基因相一致；腺苷酸环化酶转导实验结果表明，该基因产物可通过III型分泌系统进入植物细胞中。
4.四个重要Po82菌株特异基因的功能研究c00283和m00778基因为可能的III型分泌系统效应子编码基因；m00553基因属于MarR基因家族；c01536基因与海洋细菌Oceanicolabatsensis所具有Fis转录因子家族编码基因具有较高一致性。构建了c00283、m00553和m00778基因相应的突变菌株和互补菌株，c01536基因突变菌株发生致死突变。致病力测定结果表明，c00283、m00553和m00778基因突变株的病情指数相对于野生型菌株均显著下降，相应互补菌株的病情指数则与野生型菌相接近。半定量RT-PCR结果显示，c00283基因和m00778基因的表达趋势与III型分泌系统调控基因hrpB相一致。
5. Po82菌株III型效应子AvrPtoB和XopX类似物的功能初步研究在Po82菌株中，编号为c01857和m00718的基因编码产物为III型效应子AvrptoB和XopX类似物。构建了2个基因相应的突变株和互补菌株。致病力测定结果表明，c01857和m00718基因突变株的病情指数相对于野生型菌株均显著下降；半定量RT-PCR结果表明，上述2个基因的表达趋势与hrpB基因相一致。
Ralstonia solanacearum is one of the most important phytopathogenic bacteria worldwide, bothin terms of host range and destructive capability. A new hierarchical classification scheme wasestablished to distinguish the genetic diversity within the R. solanacearum species complex. Underthis classification, the phylotyping scheme was used to determine the genetic diversity of286strainsof R. solanacearum from17plant species in13Chinese provinces in previous study. Po82, areference strain, isolated from potato in Mexico, was resolve into phylotype II/sequevar4, in groupwith phylotype II/sequevar4NPB strain and banana disease-causing strains. Pathogenicity testrevealed that Po82possess pathogenic traits of both NPB and moko strains, thereby proving that itwas a pathogenicity variation strain.
In order to elucidate the molecular mechanism of pathogenicity variation, the method ofcomparative genomics was used; Suppressive subtractive hybridization (SSH) approach was used toinvestigate the differential genes of the Po82strain; the complete genome of Po82has been sequenced,annotated, and compared to the genomes of sequenced R. solanacearum strains; In this paper,candidate pathogenicity-related genes were selected for further analysis based on the pan-genomeconcept.
1. Screening strain-specific genes of Po82strain by comparative genomics
Suppressive subtractive hybridization (SSH) approach was used to investigate the pathogenicitydeterminant of the Po82strain. By comparison of the genome sequences of the Po82strain and mokostrain RUN92, there was no specific sequences were obtained. When using the Po82strain as thetester and NPB strain RUN292as driver,46differential genes were identified.
The R. solanacearum strain Po82chromosome and megaplasmid sequences have been depositedin GenBank with accession numbers CP002819and CP002820. In comparison to the six sequenced R.solanacearum strains,390strain-specific genes were identified within the genome of strain Po82,most of which encoded hypothetical and conserved hypothetical proteins. Fifty-three genomic islandswere predicted by Islandsviewer website. Using bioinformatics to analyze the46differential genesand the390strain-specific genes, five candidate genes were selected for further study.
2. Study on role of type III seretion system regulator hrpB gene of Po82strain
The mutant of hrpB gene was constructed by using homologous recombination and namedPo82ΔhrpB. Based on the mutant strain, the complement strain was also constructed. Thepathogenicity and the biological function of wild type, mutant strain and the complement strain weretested. Pathogenicity test showed that disease index of the mutant Po82ΔhrpB was decreasedcompared with the wild type Po82. Growth curve analysis indicated that Po82ΔhrpB mutant grew asfast as the Po82strain in rich medium, whereas, in Boucher‘s minimal medium, Po82ΔhrpB mutantgrew faster than the Po82. There were no significant differences between the mutants and wild typestrain in the ability of the mobility.
3. The Po82strain-specific hopAF1gene encoding putative T3SS effector
The hopAF1gene was one of strain-specific genes and had high consistency with the T3SSeffector of Pseudomonas syringae pv. tomato DC3000. The hopAF1gene mutant strain and itscomplement strain were constructed. The pathogenicity test revealed that hopAF1gene mutant strainwas significantly reduced in pathogenicity. The results of semi RT-PCR showed that hopAF1expression was increased in hrp-inducing conditions in a manner similar to hrpB. To determine ifHopAF1is translocated into plant cells by the T3SS, the adenylate cyclase (CyaA) fusion assay wasemployed. These data confirm that HopAF1-CyaA was translocated into plant cells by the T3SS ofPo82. The expression pattern and translocation of HopAF1are all hallmarks of a T3E. There were nosignificant differences among the wild-type, mutant and the complement strain in the ability of thegrowth condition, mobility and the biofilm formation.
4. Functional analysis of four strain-specific genes in Po82strain
The bioinformatic analysis found that the c00283and m00778genes were speculated to beputative T3SS effectors and m00553gene belonged to MarR gene family. In the process ofconstructing the mutant strain of c01536gene, there was no colony appeared. So we speculated thatthe lethal mutant occurred. Compared with the wild-type strain, the pathogenicity test results showedthat disease index of the mutant strains of c00283, m00553, m00778genes were decreased by15.8%,28.5%and17.2%, respectively. The results of semi RT-PCR suggested that the c00283and m00778genes expression were increased in hrp-inducing conditions in a manner similar to hrpB. Finally, toanalyze the basic biological function of three genes above, there were no significant differencesamong the wild-type, mutant and the complement strain in the ability of the growth condition,mobility and the biofilm formation.
5. Functional analysis of type III effectors AvrPtoB and XopX analogues in strain Po82
According to the related studies, two genes encongding type III effectors AvrPtoB and XopXanalogues were founded in the moko-strain Molk2. Both the two genes above were screened from thecomplete genome of Po82strain. The c01857gene had homology with the avrPtoB gene of P.syringae and the m00718genes had homology with the xopx gene of Xanthomonas campestris pv.vesicatoria. The c01857gene product had an E3ubiquitin ligase domain in the C-terminal. Thepathogenicity test suggested that the two genes played important role in pathogenicity of Po82strain.Semi RT-PCR results showed that two genes expression were increased in hrp-inducing conditions ina manner similar to hrpB. Basic biological function experiment demonstrated that c01857andm00718genes had no effects on the growth condition, mobility and the biofilm formation.
本论文以Po82菌株作为研究对象，利用抑制性差减杂交技术筛选差异基因；完成了该菌株的全基因组序列测定工作，利用生物信息学分析手段，依据泛基因组学的概念，从3个层面上共筛选出8个致病相关候选基因进行功能研究。旨在揭示青枯菌在进化过程中不同小种(或菌株)间致病力分化及寄主适应性的分子机理，从而为进一步有针对性的进行植物青枯病防控提供理论依据。
1.比较基因组学方法筛选Po82菌株特异基因以青枯菌Po82菌株为待测菌株，进行抑制性差减杂交文库的构建。以NPB菌株RUN292构建的差减文库中，共筛选获得6类46个差异基因。鉴于抑制性差减杂交的局限性，本实验室对Po82菌株的全基因组序列进行了测定。比较基因组学研究表明，该菌株中共存在有390个菌株特异基因以及53个基因岛。
2. Po82菌株III型分泌系统hrpB调控基因的功能研究构建Po82菌株hrpB基因突变株及其互补菌株。结果表明，青枯菌hrpB基因缺失突变株的致病力较Po82野生型菌株显著下降,互补菌株可恢复突变菌株的致病力；在营养贫瘠型培养基中，hrpB基因缺失突变株的生长速率较野生型青枯菌Po82菌株更快。因此，hrpB基因与青枯菌的致病力显著相关。
3. Po82菌株III型分泌系统效应子编码基因hopAF1的功能研究Po82菌株中存在与丁香假单胞菌DC3000中III型效应子HopAF1编码基因同源的基因。构建了Po82菌株hopAF1基因突变株及其互补菌株。接种香蕉和番茄进行致病力测定结果表明，hopAF1基因突变株接种植株的病情指数较野生型菌株下降，而互补菌株能够恢复突变菌株的致病力。半定量RT-PCR结果表明，hopAF1基因的表达趋势与hrpB基因相一致；腺苷酸环化酶转导实验结果表明，该基因产物可通过III型分泌系统进入植物细胞中。
4.四个重要Po82菌株特异基因的功能研究c00283和m00778基因为可能的III型分泌系统效应子编码基因；m00553基因属于MarR基因家族；c01536基因与海洋细菌Oceanicolabatsensis所具有Fis转录因子家族编码基因具有较高一致性。构建了c00283、m00553和m00778基因相应的突变菌株和互补菌株，c01536基因突变菌株发生致死突变。致病力测定结果表明，c00283、m00553和m00778基因突变株的病情指数相对于野生型菌株均显著下降，相应互补菌株的病情指数则与野生型菌相接近。半定量RT-PCR结果显示，c00283基因和m00778基因的表达趋势与III型分泌系统调控基因hrpB相一致。
5. Po82菌株III型效应子AvrPtoB和XopX类似物的功能初步研究在Po82菌株中，编号为c01857和m00718的基因编码产物为III型效应子AvrptoB和XopX类似物。构建了2个基因相应的突变株和互补菌株。致病力测定结果表明，c01857和m00718基因突变株的病情指数相对于野生型菌株均显著下降；半定量RT-PCR结果表明，上述2个基因的表达趋势与hrpB基因相一致。
Ralstonia solanacearum is one of the most important phytopathogenic bacteria worldwide, bothin terms of host range and destructive capability. A new hierarchical classification scheme wasestablished to distinguish the genetic diversity within the R. solanacearum species complex. Underthis classification, the phylotyping scheme was used to determine the genetic diversity of286strainsof R. solanacearum from17plant species in13Chinese provinces in previous study. Po82, areference strain, isolated from potato in Mexico, was resolve into phylotype II/sequevar4, in groupwith phylotype II/sequevar4NPB strain and banana disease-causing strains. Pathogenicity testrevealed that Po82possess pathogenic traits of both NPB and moko strains, thereby proving that itwas a pathogenicity variation strain.
In order to elucidate the molecular mechanism of pathogenicity variation, the method ofcomparative genomics was used; Suppressive subtractive hybridization (SSH) approach was used toinvestigate the differential genes of the Po82strain; the complete genome of Po82has been sequenced,annotated, and compared to the genomes of sequenced R. solanacearum strains; In this paper,candidate pathogenicity-related genes were selected for further analysis based on the pan-genomeconcept.
1. Screening strain-specific genes of Po82strain by comparative genomics
Suppressive subtractive hybridization (SSH) approach was used to investigate the pathogenicitydeterminant of the Po82strain. By comparison of the genome sequences of the Po82strain and mokostrain RUN92, there was no specific sequences were obtained. When using the Po82strain as thetester and NPB strain RUN292as driver,46differential genes were identified.
The R. solanacearum strain Po82chromosome and megaplasmid sequences have been depositedin GenBank with accession numbers CP002819and CP002820. In comparison to the six sequenced R.solanacearum strains,390strain-specific genes were identified within the genome of strain Po82,most of which encoded hypothetical and conserved hypothetical proteins. Fifty-three genomic islandswere predicted by Islandsviewer website. Using bioinformatics to analyze the46differential genesand the390strain-specific genes, five candidate genes were selected for further study.
2. Study on role of type III seretion system regulator hrpB gene of Po82strain
The mutant of hrpB gene was constructed by using homologous recombination and namedPo82ΔhrpB. Based on the mutant strain, the complement strain was also constructed. Thepathogenicity and the biological function of wild type, mutant strain and the complement strain weretested. Pathogenicity test showed that disease index of the mutant Po82ΔhrpB was decreasedcompared with the wild type Po82. Growth curve analysis indicated that Po82ΔhrpB mutant grew asfast as the Po82strain in rich medium, whereas, in Boucher‘s minimal medium, Po82ΔhrpB mutantgrew faster than the Po82. There were no significant differences between the mutants and wild typestrain in the ability of the mobility.
3. The Po82strain-specific hopAF1gene encoding putative T3SS effector
The hopAF1gene was one of strain-specific genes and had high consistency with the T3SSeffector of Pseudomonas syringae pv. tomato DC3000. The hopAF1gene mutant strain and itscomplement strain were constructed. The pathogenicity test revealed that hopAF1gene mutant strainwas significantly reduced in pathogenicity. The results of semi RT-PCR showed that hopAF1expression was increased in hrp-inducing conditions in a manner similar to hrpB. To determine ifHopAF1is translocated into plant cells by the T3SS, the adenylate cyclase (CyaA) fusion assay wasemployed. These data confirm that HopAF1-CyaA was translocated into plant cells by the T3SS ofPo82. The expression pattern and translocation of HopAF1are all hallmarks of a T3E. There were nosignificant differences among the wild-type, mutant and the complement strain in the ability of thegrowth condition, mobility and the biofilm formation.
4. Functional analysis of four strain-specific genes in Po82strain
The bioinformatic analysis found that the c00283and m00778genes were speculated to beputative T3SS effectors and m00553gene belonged to MarR gene family. In the process ofconstructing the mutant strain of c01536gene, there was no colony appeared. So we speculated thatthe lethal mutant occurred. Compared with the wild-type strain, the pathogenicity test results showedthat disease index of the mutant strains of c00283, m00553, m00778genes were decreased by15.8%,28.5%and17.2%, respectively. The results of semi RT-PCR suggested that the c00283and m00778genes expression were increased in hrp-inducing conditions in a manner similar to hrpB. Finally, toanalyze the basic biological function of three genes above, there were no significant differencesamong the wild-type, mutant and the complement strain in the ability of the growth condition,mobility and the biofilm formation.
5. Functional analysis of type III effectors AvrPtoB and XopX analogues in strain Po82
According to the related studies, two genes encongding type III effectors AvrPtoB and XopXanalogues were founded in the moko-strain Molk2. Both the two genes above were screened from thecomplete genome of Po82strain. The c01857gene had homology with the avrPtoB gene of P.syringae and the m00718genes had homology with the xopx gene of Xanthomonas campestris pv.vesicatoria. The c01857gene product had an E3ubiquitin ligase domain in the C-terminal. Thepathogenicity test suggested that the two genes played important role in pathogenicity of Po82strain.Semi RT-PCR results showed that two genes expression were increased in hrp-inducing conditions ina manner similar to hrpB. Basic biological function experiment demonstrated that c01857andm00718genes had no effects on the growth condition, mobility and the biofilm formation.
引文
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