鼠疫耶尔森氏菌毒力相关转录调控子Zur和PhoP的研究
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摘要
鼠疫是一种古老的自然疫源性疾病,其病原菌鼠疫耶尔森氏菌(以下简称鼠疫菌)是多宿主寄生菌,体现在:鼠疫菌以蚤类为传播媒介寄居在特定的宿主(主要是啮齿动物),并在自然界宿主中造成鼠疫疫情的周期性爆发,该过程中偶然与患畜接触或被带菌跳蚤叮咬而感染到人。面对上述的复杂因素,鼠疫菌必须能够感应并快速适应每个环节的变化,才能在宿主体内存活并在自然界中传播最终致病,而每个适应性反应也必然伴随着鼠疫菌基因转录改变,这体现在:很多特定的调控子,分别感应特定的外界信号,介导特定基因(包括毒力基因)表达的上调和下调,最终组成复杂的毒力调控网络,控制鼠疫菌在媒介和贮存宿主中生存能力和致病力。
病原菌从感应信号刺激到表达毒力因子的过程中,毒力调控子起着不可替代的作用。广谱或特异性的调控子,控制着毒力基因的表达;另外,若干个毒力调控基因的表达产物可组成一个复杂系统,执行毒力调控的功能,常称作毒力调控系统。一直作为研究热点的细菌毒力调控系统主要有QS系统、二元调控系统、Fur系统等等。这些系统又分成许多子调控系统,控制着不同类型毒力基因的表达,在细菌表现毒力的不同阶段起着调控作用。
Zur阻遏蛋白属于Fur家族,可以调控锌离子的转运,锌离子在所有生物细胞中是一种重要的蛋白质功能组分。PhoP-PhoQ是一种二元调控系统(two-component system),可以调控细菌的毒力,参与细菌对Mg2+限制性生长环境的适应,从而有利于鼠疫菌在巨噬细胞内的存活和繁殖。为了鉴定鼠疫菌毒力调控子Zur和PhoP的靶基因,尤其是直接调控的靶基因,并进一步研究Zur和PhoP对其下游直接靶基因的精细调控机制,本研究首先利用基于Red系统的一步法突变技术缺失替换鼠疫菌的zur和phoP基因,进而利用鼠疫菌全基因组DNA芯片进行基因转录谱分析。通过比较突变株和野生株在特定条件下的转录水平差异,界定表达上调和下调的基因,这些基因组成了Zur或PhoP调控元。这一分析可从全基因组水平筛选出所有受Zur或PhoP直接或间接调控的靶基因。转录谱的分析结果可以通过Real time RT-PCR进行验证。凝胶阻滞实验技术的应用,可以鉴定直接调控的靶基因,选择若干关键毒力相关基因,采用DNA酶I足迹实验技术、引物延伸实验技术,深入研究Zur和PhoP是如何直接调控这些基因的转录和表达,将毒力表型和分子实验数据结合起来,认识Zur和PhoP如何通过激活或抑制特定基因的表达,控制着鼠疫菌的宿主适应力和致病力。
与野生株相比,敲除了zur基因的鼠疫菌在锌离子刺激下有154个基因发生了转录丰度改变,其中64个基因转录上调,90个基因转录下调。汇总文献预测的Zur结合位点,通过consensus-matrix和convert-matrix程序计算Zur结合序列每个位置四个碱基出现的权重,得到Zur结合序列的Matrix,进而用WebLogo软件展示序列logo,最终预测得到Zur结合box:GAAATGTTATAWTATAACATTTC。基于上述Zur基序分析和Zur调控子的转录谱分析,我们通过Matrix scan程序查找Zur保守基序,选取weight值较高的4个基因ykgM、znuC、znuA、astA进行进一步的分子生化实验。通过凝胶阻滞实验明确了ykgM、znuC、znuA 3个转录单元直接受Zur调控。为了明确Zur的精细调控机制,本研究对这三个转录单元的启动子进行了足迹实验,得到了精确的Zur结合保护区域,在这个区域内存在着预测的Zur box,Zur蛋白直接调控的这三个转录单元,其Zur box均覆盖-10序列,这样就阻碍了RNA聚合酶的结合,可能正因为如此,使Zur表现出对它们的抑制特性。对锌离子刺激下的野生株和?zur突变株同时进行引物延伸实验,不仅可以明确受Zur转录调控的鼠疫菌ykgM、znuC和znuA的转录起始位点,也可以确定Zur对其转录的影响。同时结合足迹实验得到的Zur结合位点,推断出每个启动子内的RNA聚合酶结合位点(-10序列)以及-35序列,丰富了Zur调控元启动子区的分子特性。
前期对于?phoP突变株和野生株在低镁条件下的转录谱分析,已经初步界定了PhoP调控元,同样,我们用Real time RT-PCR对转录谱的分析结果进行验证。凝胶阻滞实验确定了30个转录单元直接受PhoP的转录调控,对其中17个基因的启动子区做了足迹实验,得到19个PhoP结合保护区域。通过生物信息学分析将鼠疫菌的PhoP box归纳为TGTTTAW七核苷酸同向重复序列,结合引物延伸实验得到的基因转录起始位点的位置信息,根据鼠疫菌的PhoP box在靶基因启动子内的位置以及是否含有-35序列,我们将PhoP启动子结构特征归纳为三类:PhoP结合位点在-35序列上游;PhoP结合位点覆盖-35序列;PhoP结合位点在-10序列的下游。
本研究首次较全面地鉴定了鼠疫菌Zur和PhoP直接调控的调控元,同时从分子水平上明确了鼠疫菌Zur box和PhoP box的特性,探究了Zur和PhoP转录调控机制,为Zur和PhoP这类毒力调控子调控网络的构建,以及这些调控元功能的进一步明确提供了实验证据,这些机制的系统阐述将为鼠疫菌致病机制和疫苗的研究奠定重要基础。
Plague has ravaged human populations for many centuries and claimed hundred millions of lives in history. Plague normally cycles between fleas and rodent hosts, with humans providing an unproductive alternative. Yersinia pestis is the etiologic agent of plague. Since Y. pestis undergoes various types of environmental changes during transmission and infection, a wide range of rapid, adaptive responses to the changing niches are required. There are specific regulators responsing to the environmentally specific signals and controlling the expression of their specific target genes (including virulence genes). Finally, the complex regulating network of virulence genes is composed of them, and the viability and pathgenicity of Yersinia pestis is controlled by this virulence-related regulating network.
Pathogen responses to signal stimulation, and expresses virulence-related regulators. These regulators play irreplaceable role during this process. The global or specific regulators control the expression of virulence genes. Additionally, the products that are expressed by some virulence regulated genes build up a complex system. The system in charge of virulence regulating functions is refered to virulence regulated system, which is always taken as research hotspot in pathogen bacteriology, incluing quorum sensing (QS) system, two-component system and Fur system etc.These systems are divided into many subsystems to control expression of different type of virulence genes and play the regulation role at different virulence-related stage of bacteria.
Zur belongs to the Fur family and regulates the transport of zinc ions. Zinc is an essential component of protein and has function in all living cells. The two-component system PhoP-PhoQ can govern bacterial virulence, helps bacteria to adapt to Mg2+-limiting environments, survival and proliferation in macrophage. For further indentifing target genes of Zur and PhoP, especially the directly regulated target genes, and investigating the mechanism of Zur or PhoP regulation, we employed gene knockout method, microarray-based gene expression profiling and conventional biochemical techniques to study the gene regulating targets of Zur and PhoP. The zur and phoP gene in Y. pestis were replaced, respectively, with kanamycin resistance cassette using one-step disruption protocol in this study. The whole-genome DNA microarray of Y. pestis was used to investigate global transcriptional responses. The transcription profile of the wild-type Y. pestis was then compared with that of the mutant for determining upregulated and downregulated genes. These genes composed of Zur or PhoP regulons. Then, the results of transcriptome analysis were proved by real-time reverse-transcription (RT-PCR). Electrophoretic mobility shift assay (EMSA), helped to identify direct target genes of the regulators. DNase I footprinting assay and primer extension analysis were used to study how the transcription and expression of these genes are regulated directly by Zur and PhoP. This will help us to understand the mechanism of how Zur and PhoP can help to control the adaptative ability and pathgenicity of Yersinia pestis in hosts.
Through transcriptome analysis, under stimulation of zinc ions, those strains with zur gene deletion had totally 154 genes changed their transcription level comparing with the wild type ones. Among them, 64 genes were upregulated, whereas 90 genes downregulated. We also collected data from published lituratures to predict Zur binding sites.
Presenting frequency of four bases at each site of Zur binding sequence was obtained by consensus-matrix and convert-matrix program, then the sequence logo were shown by WebLogo software. Finally, Zur binding box in Yersinia pestis was confirmed to be GAAATGTTATAWTATAACATTTC. Based on the above result and transcriptome analysis of Zur, we screened the conserved sequences of Zur by Matrix scan program and selected four genes(ykgM、znuC、znuA、astA) for further confirming by biochemical experiments. EMSA confirmed three transcriptional units, ykgM、znuC、znuA were regulated by Zur directly. In order to get the precise mechanism of Zur regulation, we used footprinting assay to study the promotors of these transcriptional units. The Zur bingding sequence was obtained, and the predicted conserved Zur box was present in this region. All the three Zur boxes covered -10 elements for blocking RNA polymerase binding. It is possible that this is why Zur inhibits their transcription. By using primer extension analysis, we compared the wild type with ?zur mutant under the stimulation of low zinc ions. Not only determined the transcription start sites of ykgM、znuC and znuA under the regulation of Zur, but also determined the effect of Zur to their transcription. Combined with the result of footprinting assay, -10 and -35 elements for RNA polymerase binding were localized. It was helpful to get more complete information of the promoter region of Zur regulon.
In our previous work, the transcriptome analysis of ?phoP mutant and wild type strains under low Mg2+ environments had confirmed PhoP regulon. In the present study, real time RT-PCR were used to test the result of transcriptome analysis. EMSA elucidated that 30 transcriptional units were regulated directly by PhoP. The promotor region of 17 genes were tested by footprinting assay, 19 PhoP conserved binding regions were obtained. Through bioinformatics analysis, PhoP box in Yersinia pestis was confirmed to be TGTTTAWN4TGTTTAW. Primer extension analysis was used to obtain the transcription start sites of these PhoP regulons. Finally, the promoters of the target genes of PhoP were classified into three types: PhoP binding sites lie in upstream of -35 elements, cover -35 elements, and lie in downstream of -35 elements.
This study firstly identified the regulons of Zur and PhoP of Yersinia pestis. At the same time, the result confirmed the Zur box and PhoP box of Yersinia pestis and explored the precise mechanism of Zur and PhoP regulation. It is helpful for building up virulence regulators networks and elucidating functional knowledge of these regulons. And further, these resluts will be helpful to investigating pathgenicity of Yersinia pestis.
病原菌从感应信号刺激到表达毒力因子的过程中,毒力调控子起着不可替代的作用。广谱或特异性的调控子,控制着毒力基因的表达;另外,若干个毒力调控基因的表达产物可组成一个复杂系统,执行毒力调控的功能,常称作毒力调控系统。一直作为研究热点的细菌毒力调控系统主要有QS系统、二元调控系统、Fur系统等等。这些系统又分成许多子调控系统,控制着不同类型毒力基因的表达,在细菌表现毒力的不同阶段起着调控作用。
Zur阻遏蛋白属于Fur家族,可以调控锌离子的转运,锌离子在所有生物细胞中是一种重要的蛋白质功能组分。PhoP-PhoQ是一种二元调控系统(two-component system),可以调控细菌的毒力,参与细菌对Mg2+限制性生长环境的适应,从而有利于鼠疫菌在巨噬细胞内的存活和繁殖。为了鉴定鼠疫菌毒力调控子Zur和PhoP的靶基因,尤其是直接调控的靶基因,并进一步研究Zur和PhoP对其下游直接靶基因的精细调控机制,本研究首先利用基于Red系统的一步法突变技术缺失替换鼠疫菌的zur和phoP基因,进而利用鼠疫菌全基因组DNA芯片进行基因转录谱分析。通过比较突变株和野生株在特定条件下的转录水平差异,界定表达上调和下调的基因,这些基因组成了Zur或PhoP调控元。这一分析可从全基因组水平筛选出所有受Zur或PhoP直接或间接调控的靶基因。转录谱的分析结果可以通过Real time RT-PCR进行验证。凝胶阻滞实验技术的应用,可以鉴定直接调控的靶基因,选择若干关键毒力相关基因,采用DNA酶I足迹实验技术、引物延伸实验技术,深入研究Zur和PhoP是如何直接调控这些基因的转录和表达,将毒力表型和分子实验数据结合起来,认识Zur和PhoP如何通过激活或抑制特定基因的表达,控制着鼠疫菌的宿主适应力和致病力。
与野生株相比,敲除了zur基因的鼠疫菌在锌离子刺激下有154个基因发生了转录丰度改变,其中64个基因转录上调,90个基因转录下调。汇总文献预测的Zur结合位点,通过consensus-matrix和convert-matrix程序计算Zur结合序列每个位置四个碱基出现的权重,得到Zur结合序列的Matrix,进而用WebLogo软件展示序列logo,最终预测得到Zur结合box:GAAATGTTATAWTATAACATTTC。基于上述Zur基序分析和Zur调控子的转录谱分析,我们通过Matrix scan程序查找Zur保守基序,选取weight值较高的4个基因ykgM、znuC、znuA、astA进行进一步的分子生化实验。通过凝胶阻滞实验明确了ykgM、znuC、znuA 3个转录单元直接受Zur调控。为了明确Zur的精细调控机制,本研究对这三个转录单元的启动子进行了足迹实验,得到了精确的Zur结合保护区域,在这个区域内存在着预测的Zur box,Zur蛋白直接调控的这三个转录单元,其Zur box均覆盖-10序列,这样就阻碍了RNA聚合酶的结合,可能正因为如此,使Zur表现出对它们的抑制特性。对锌离子刺激下的野生株和?zur突变株同时进行引物延伸实验,不仅可以明确受Zur转录调控的鼠疫菌ykgM、znuC和znuA的转录起始位点,也可以确定Zur对其转录的影响。同时结合足迹实验得到的Zur结合位点,推断出每个启动子内的RNA聚合酶结合位点(-10序列)以及-35序列,丰富了Zur调控元启动子区的分子特性。
前期对于?phoP突变株和野生株在低镁条件下的转录谱分析,已经初步界定了PhoP调控元,同样,我们用Real time RT-PCR对转录谱的分析结果进行验证。凝胶阻滞实验确定了30个转录单元直接受PhoP的转录调控,对其中17个基因的启动子区做了足迹实验,得到19个PhoP结合保护区域。通过生物信息学分析将鼠疫菌的PhoP box归纳为TGTTTAW七核苷酸同向重复序列,结合引物延伸实验得到的基因转录起始位点的位置信息,根据鼠疫菌的PhoP box在靶基因启动子内的位置以及是否含有-35序列,我们将PhoP启动子结构特征归纳为三类:PhoP结合位点在-35序列上游;PhoP结合位点覆盖-35序列;PhoP结合位点在-10序列的下游。
本研究首次较全面地鉴定了鼠疫菌Zur和PhoP直接调控的调控元,同时从分子水平上明确了鼠疫菌Zur box和PhoP box的特性,探究了Zur和PhoP转录调控机制,为Zur和PhoP这类毒力调控子调控网络的构建,以及这些调控元功能的进一步明确提供了实验证据,这些机制的系统阐述将为鼠疫菌致病机制和疫苗的研究奠定重要基础。
Plague has ravaged human populations for many centuries and claimed hundred millions of lives in history. Plague normally cycles between fleas and rodent hosts, with humans providing an unproductive alternative. Yersinia pestis is the etiologic agent of plague. Since Y. pestis undergoes various types of environmental changes during transmission and infection, a wide range of rapid, adaptive responses to the changing niches are required. There are specific regulators responsing to the environmentally specific signals and controlling the expression of their specific target genes (including virulence genes). Finally, the complex regulating network of virulence genes is composed of them, and the viability and pathgenicity of Yersinia pestis is controlled by this virulence-related regulating network.
Pathogen responses to signal stimulation, and expresses virulence-related regulators. These regulators play irreplaceable role during this process. The global or specific regulators control the expression of virulence genes. Additionally, the products that are expressed by some virulence regulated genes build up a complex system. The system in charge of virulence regulating functions is refered to virulence regulated system, which is always taken as research hotspot in pathogen bacteriology, incluing quorum sensing (QS) system, two-component system and Fur system etc.These systems are divided into many subsystems to control expression of different type of virulence genes and play the regulation role at different virulence-related stage of bacteria.
Zur belongs to the Fur family and regulates the transport of zinc ions. Zinc is an essential component of protein and has function in all living cells. The two-component system PhoP-PhoQ can govern bacterial virulence, helps bacteria to adapt to Mg2+-limiting environments, survival and proliferation in macrophage. For further indentifing target genes of Zur and PhoP, especially the directly regulated target genes, and investigating the mechanism of Zur or PhoP regulation, we employed gene knockout method, microarray-based gene expression profiling and conventional biochemical techniques to study the gene regulating targets of Zur and PhoP. The zur and phoP gene in Y. pestis were replaced, respectively, with kanamycin resistance cassette using one-step disruption protocol in this study. The whole-genome DNA microarray of Y. pestis was used to investigate global transcriptional responses. The transcription profile of the wild-type Y. pestis was then compared with that of the mutant for determining upregulated and downregulated genes. These genes composed of Zur or PhoP regulons. Then, the results of transcriptome analysis were proved by real-time reverse-transcription (RT-PCR). Electrophoretic mobility shift assay (EMSA), helped to identify direct target genes of the regulators. DNase I footprinting assay and primer extension analysis were used to study how the transcription and expression of these genes are regulated directly by Zur and PhoP. This will help us to understand the mechanism of how Zur and PhoP can help to control the adaptative ability and pathgenicity of Yersinia pestis in hosts.
Through transcriptome analysis, under stimulation of zinc ions, those strains with zur gene deletion had totally 154 genes changed their transcription level comparing with the wild type ones. Among them, 64 genes were upregulated, whereas 90 genes downregulated. We also collected data from published lituratures to predict Zur binding sites.
Presenting frequency of four bases at each site of Zur binding sequence was obtained by consensus-matrix and convert-matrix program, then the sequence logo were shown by WebLogo software. Finally, Zur binding box in Yersinia pestis was confirmed to be GAAATGTTATAWTATAACATTTC. Based on the above result and transcriptome analysis of Zur, we screened the conserved sequences of Zur by Matrix scan program and selected four genes(ykgM、znuC、znuA、astA) for further confirming by biochemical experiments. EMSA confirmed three transcriptional units, ykgM、znuC、znuA were regulated by Zur directly. In order to get the precise mechanism of Zur regulation, we used footprinting assay to study the promotors of these transcriptional units. The Zur bingding sequence was obtained, and the predicted conserved Zur box was present in this region. All the three Zur boxes covered -10 elements for blocking RNA polymerase binding. It is possible that this is why Zur inhibits their transcription. By using primer extension analysis, we compared the wild type with ?zur mutant under the stimulation of low zinc ions. Not only determined the transcription start sites of ykgM、znuC and znuA under the regulation of Zur, but also determined the effect of Zur to their transcription. Combined with the result of footprinting assay, -10 and -35 elements for RNA polymerase binding were localized. It was helpful to get more complete information of the promoter region of Zur regulon.
In our previous work, the transcriptome analysis of ?phoP mutant and wild type strains under low Mg2+ environments had confirmed PhoP regulon. In the present study, real time RT-PCR were used to test the result of transcriptome analysis. EMSA elucidated that 30 transcriptional units were regulated directly by PhoP. The promotor region of 17 genes were tested by footprinting assay, 19 PhoP conserved binding regions were obtained. Through bioinformatics analysis, PhoP box in Yersinia pestis was confirmed to be TGTTTAWN4TGTTTAW. Primer extension analysis was used to obtain the transcription start sites of these PhoP regulons. Finally, the promoters of the target genes of PhoP were classified into three types: PhoP binding sites lie in upstream of -35 elements, cover -35 elements, and lie in downstream of -35 elements.
This study firstly identified the regulons of Zur and PhoP of Yersinia pestis. At the same time, the result confirmed the Zur box and PhoP box of Yersinia pestis and explored the precise mechanism of Zur and PhoP regulation. It is helpful for building up virulence regulators networks and elucidating functional knowledge of these regulons. And further, these resluts will be helpful to investigating pathgenicity of Yersinia pestis.
引文
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