RpoS在大肠杆菌自然遗传转化中的功能研究
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摘要
大肠杆菌人工转化是分子生物学研究中的常规操作,但大肠杆菌自然遗传转化,是近年新发现的一种细菌转化模式,包括自然感受态的建立、外源DNA摄取以及外源基因表达等步骤。它的发现打破了传统上认为大肠杆菌不具备在自然状态下建立感受态并摄取外源DNA能力的观点,在遗传学上具有相当重要的意义。同时,作为基因工程最常用的实验材料之一,大肠杆菌通过自然遗传转化发生基因转移会严重影响其生物安全性。因此,研究大肠杆菌自然遗传转化的调控机理对于深入了解细菌遗传转化机理及评估大肠杆菌的生物安全性具有重要的理论及应用意义。
普遍压力应答因子σs,又称RpoS,是一种可激活大量RpoS依赖基因转录的选择性σ因子,它在压力环境下可以一定程度上替代管家6因子RpoD (σ70)启动特定压力抗逆基因的表达,使细菌应对不利环境。RpoS蛋白自身的表达具有“在快速生长的对数期很低,面对压力环境迅速升高”的特点。同时RpoS也被报道可能参与了大肠杆菌自然遗传转化调控过程。
本研究采用了开放系统下的大肠杆菌自然遗传转化体系,研究了RpoS在大肠杆菌自然遗传转化中的功能。
要研究RpoS在大肠杆菌自然遗传转化中的作用首先需要进一步确定RpoS在大肠杆菌自然遗传转化中是否发挥功能。本研究采用基因缺失及回补的方法,比较发现,在RpoS缺失的情况下,大肠杆菌自然遗传转化频率下降至野生型的10%以下,回补RpoS后转化频率得到恢复；通过比较RpoS缺陷株在不同筛选条件下的成活率可以发现,RpoS缺失不影响转化子的生存能力。因此,RpoS在大肠杆菌自然遗传转化中发挥作用。那么,RpoS是否参与大肠杆菌其他遗传转化过程?通过比较研究发现,RpoS缺失,大肠杆菌人工转化能力没有明显变化,此结果表明,RpoS对转化的作用为大肠杆菌自然遗传转化独有。因此,RpoS对大肠杆菌自然遗传转化确实存在影响,研究RpoS参与大肠杆菌自然遗传转化调控机理探究有助于对细菌转化机制的认识。
大肠杆菌自然遗传转化的过程包括：液体振荡培养和静置培养建立感受态以及固体培养完成DNA摄取两个阶段,明确RpoS在哪一个环节发挥功能,有助于了解其对自然遗传转化的调控机理。
发生在固相基质表面(培养平板)的DNA摄取过程是开放系统下的大肠杆菌自然遗传转化的特点之一。首先,通过DNA酶实验中断外源DNA供给的方法检测了自然遗传转化中DNA摄取发生的具体时间,结果表明,大肠杆菌细胞接触固相基质表面的瞬间即可完成DNA摄取,而且RpoS缺失不影响DNA摄取时期。随后,为检测在固相基质表面RpoS的转录水平,采用了PrpoS融合lacZ标记PrpoS的方法,结果示PrpoS活性在感受态细胞与固相基质接触瞬间并未明显上调;采用Western Blotting测量蛋白质水平的变化,发现RpoS在感受态与固相基质接触瞬间非但没有上升还有所下降。最后,通过诱导表达改变胞内RpoS含量发现RpoS表达量的高低不能显著影响转化频率。综合上述结果可以得出,RpoS是大肠杆菌发生高水平自然转化的必要因素,依旧不是充分条件；大肠杆菌完成自然遗传转化过程,需含有RpoS的的细胞与固相基质的接触,但RpoS的调控作用对固体培养以及DNA摄取过程无明显影响。
‘开放系统”大肠杆菌自然遗传转化不同于其他细菌自然转化的另一个特征是“自然感受态的建立经过了液体振荡培养和开放静置培养两个培养阶段”。本研究通过诱导表达调节胞内RpoS含量分别检测了不同培养时期诱导RpoS表达对自然转化能力的影响。结果显示,振荡培养期诱导RpoS表达能使转化频率上升约70%,静置培养期诱导RpoS表达可使转化频率上升约20%,而在两个培养时期均诱导RpoS表达使转化频率上升了140%,由此可见,通过诱导表达RpoS可以显著提高大肠杆菌自然遗传转化能力,胞内RpoS的含量可能与大肠杆菌自然遗传转化能力高低有关。而且,振荡培养期诱导作用明显表明大肠杆菌自然遗传感受态建立在振荡培养期。经过一步比较分析发现,在振荡培养对数前期诱导RpoS表达对自然遗传转化影响显著,对数中后期至稳定期诱导RpoS表达对于转化的影响不显著,结果显示,在振荡培养过程中对数前期细胞内RpoS含量决定转化能力的强弱。在静置培养过程中,通过对比不同胞内RpoS含量的大肠杆菌的转化频率变化规律发现,静置培养可以在一定程度上提升转化能力,该提升过程需要时间的积累(约8h完成),而在该培养阶段提高胞内RpoS的水平,可缩短积累所耗的时间(约4～6h即可完成),结合转化频率总体上升20%的结果,证明了静置培养阶段的胞内RpoS表达量对自然转化具有促进作用,但并不起决定作用。综上所述,胞内RpoS的含量对于大肠杆菌自然遗传感受态的建立很重要；对数前期的RpoS含量决定自然转化频率的高低；静置培养期的RpoS含量对转化能力具有促进作用。
核苷酸及其衍生物可作为营养物质被处于营养饥饿的大肠杆菌细胞所吸收,有报道单核苷酸参与流感嗜血杆菌等细菌自然转化的调控。那么,大肠杆菌自然遗传转化过程是否受到单核苷酸的影响呢?
单磷酸腺苷(AMP)在流感嗜血杆菌的自然转化中,通过抑制一些转化基因的转录而抑制遗传转化的发生,但在大肠杆菌的遗传转化中,是否也有类似的作用未见报道。鉴于人工转化的机制研究较为系统,本工作首先研究了AMP对大肠杆菌人工转化的作用。本研究比较研究了外源单核苷酸衍生物对大肠杆菌人工转化能力的影响,结果显示,外源AMP可能通过能量流动改变了胞内的能量状态,从而抑制了人工转化的发生。而在大肠杆菌的自然遗传转化中,外源AMP却有促进作用,是否也是通过能量流动引起的改变有待进一步验证。
综上所述,本研究工作借助分子生物学和遗传学的手段,揭示了普遍压力应答因子RpoS与大肠杆菌自然遗传转化能力相关性,并对参与大肠杆菌自然转化的AMP等因素进行了探讨,为更好的理解大肠杆菌自然遗传转化的调控机理以及RpoS在大肠杆菌中的功能提供了实验依据；另外,对单核苷酸AMP在大肠杆菌自然遗传转化中作用的研究,为进一步认识大肠杆菌自然转化的调控机理提供了依据。本工作为探讨细菌自然遗传转化的普遍规律提供了新的线索。
As a novel transformation system reported these years, Escherichia coli natural transformation contains these processes:natural competence development, DNA uptake and transformants determination. The finding of E. coli natural transformation was of good biology value, since it breaks the traditional view that E. coli could not take exogenous DNA and transform without artificial treatment. Moreover, because E. coli is also one of the most common used materials in genetic engineering, its biosecurity comes under question for its ability of natural gene transfer. So there is extensive space and requirement in the study of mechanism of this transformation system.
The general stress response factor σS, so-called RpoS, is an alternative σ factor of RNA polymerase in Escherichia coli. It can partially replace the "housekeeping" σ factor σ70(RpoD) under many stress conditions. RpoS intacts with the core RNA polymerase (RNAP) and controls the expression of a specific but large set of genes. Directly or indirectly, RpoS regulates10%of the E. coli genome (approximately500genes). With the characteristic of "low-expression in exponential phase and high-expression under stress conditions", RpoS was mentioned as a regulator of E. coli natural transformation.
In this study, we investigate the effect of RpoS on E. coli natural transformation in an "open system". Some regulation mechanisms was discussed in detail too.
In order to make sure whether RpoS has influence exactly on natural transformation process, we continuously exclude the interference of RpoS regulation on other transformation system and the disturbation of transformants survival. The results expressed that, RpoS affects the natural transformation frequency in E. coli, while has no effect on artificial transformation. The transformant survival was not interrupted by RpoS. So the RpoS regulation was exactly on the process of natural transformation.
E. coli natural transformation process contains natural competence development and DNA uptake. The RpoS's effects on which step determin the transformation frequency were investigated in the following work.
DNA uptake carried out on plate is one characteristic in natural transformation different from the classical artificial transformation with Ca2+. In order to determine the relationship between RpoS expression and the DNA uptake, three questions should be answered:whether the RpoS deletion would disturb the time that DNA uptake takes place, whether the RpoS expression was changed by the plating which promotes DNA uptake and if the transformation frequency would be changed by the RpoS expression changing in DNA uptake. We finally demonstrate that, although RpoS positive controls the natural transformation, it is not sufficient for transformation complete. The contact of natural competence with solid substrate was necessary for DNA uptake, but this process has nothing to do with RpoS expression.
Another characteristic of open system natural transformation is that the process of natural competence development contains two parts:shaking culture and static cultivation. In which step RpoS plays the major role on natural transformation was discussed in the following work. The results demonstrate that the intracellular RpoS content of cells in the process of natural competence development, especially in the early exponential phase, determines the level of transformation frequency. Although not as important as in early exponential phase, the RpoS content in static cultivation enhances the natural transformation.
In order to investigate the natural transformation regulation from various angles, besides the function research of single gene rpoS on the natural transformation, another factor AMP, which has been reported to inhibit the natural transformation of Haemophilus influenza, was discussed both in E. coli artificial and natural transformations. We found that intracellular AMP could changes the flow of energy by breaking the energy charge of the competence. This flow of energy blocks the E. coli artificial transformation. However, it enhances the natural transformation at the early exponential phase just like the RpoS regulation.
In conclusion, we demonstrate that the intracellular RpoS content in early exponential phase determines the level of transformation frequency, which has not been studies in previous work. Then one regulatory factor in H. influenza natural transformation AMP was found has different effect on E. coli natural transformation. These findings provide detailed understanding of RpoS effect on natural transformation.
普遍压力应答因子σs,又称RpoS,是一种可激活大量RpoS依赖基因转录的选择性σ因子,它在压力环境下可以一定程度上替代管家6因子RpoD (σ70)启动特定压力抗逆基因的表达,使细菌应对不利环境。RpoS蛋白自身的表达具有“在快速生长的对数期很低,面对压力环境迅速升高”的特点。同时RpoS也被报道可能参与了大肠杆菌自然遗传转化调控过程。
本研究采用了开放系统下的大肠杆菌自然遗传转化体系,研究了RpoS在大肠杆菌自然遗传转化中的功能。
要研究RpoS在大肠杆菌自然遗传转化中的作用首先需要进一步确定RpoS在大肠杆菌自然遗传转化中是否发挥功能。本研究采用基因缺失及回补的方法,比较发现,在RpoS缺失的情况下,大肠杆菌自然遗传转化频率下降至野生型的10%以下,回补RpoS后转化频率得到恢复；通过比较RpoS缺陷株在不同筛选条件下的成活率可以发现,RpoS缺失不影响转化子的生存能力。因此,RpoS在大肠杆菌自然遗传转化中发挥作用。那么,RpoS是否参与大肠杆菌其他遗传转化过程?通过比较研究发现,RpoS缺失,大肠杆菌人工转化能力没有明显变化,此结果表明,RpoS对转化的作用为大肠杆菌自然遗传转化独有。因此,RpoS对大肠杆菌自然遗传转化确实存在影响,研究RpoS参与大肠杆菌自然遗传转化调控机理探究有助于对细菌转化机制的认识。
大肠杆菌自然遗传转化的过程包括：液体振荡培养和静置培养建立感受态以及固体培养完成DNA摄取两个阶段,明确RpoS在哪一个环节发挥功能,有助于了解其对自然遗传转化的调控机理。
发生在固相基质表面(培养平板)的DNA摄取过程是开放系统下的大肠杆菌自然遗传转化的特点之一。首先,通过DNA酶实验中断外源DNA供给的方法检测了自然遗传转化中DNA摄取发生的具体时间,结果表明,大肠杆菌细胞接触固相基质表面的瞬间即可完成DNA摄取,而且RpoS缺失不影响DNA摄取时期。随后,为检测在固相基质表面RpoS的转录水平,采用了PrpoS融合lacZ标记PrpoS的方法,结果示PrpoS活性在感受态细胞与固相基质接触瞬间并未明显上调;采用Western Blotting测量蛋白质水平的变化,发现RpoS在感受态与固相基质接触瞬间非但没有上升还有所下降。最后,通过诱导表达改变胞内RpoS含量发现RpoS表达量的高低不能显著影响转化频率。综合上述结果可以得出,RpoS是大肠杆菌发生高水平自然转化的必要因素,依旧不是充分条件；大肠杆菌完成自然遗传转化过程,需含有RpoS的的细胞与固相基质的接触,但RpoS的调控作用对固体培养以及DNA摄取过程无明显影响。
‘开放系统”大肠杆菌自然遗传转化不同于其他细菌自然转化的另一个特征是“自然感受态的建立经过了液体振荡培养和开放静置培养两个培养阶段”。本研究通过诱导表达调节胞内RpoS含量分别检测了不同培养时期诱导RpoS表达对自然转化能力的影响。结果显示,振荡培养期诱导RpoS表达能使转化频率上升约70%,静置培养期诱导RpoS表达可使转化频率上升约20%,而在两个培养时期均诱导RpoS表达使转化频率上升了140%,由此可见,通过诱导表达RpoS可以显著提高大肠杆菌自然遗传转化能力,胞内RpoS的含量可能与大肠杆菌自然遗传转化能力高低有关。而且,振荡培养期诱导作用明显表明大肠杆菌自然遗传感受态建立在振荡培养期。经过一步比较分析发现,在振荡培养对数前期诱导RpoS表达对自然遗传转化影响显著,对数中后期至稳定期诱导RpoS表达对于转化的影响不显著,结果显示,在振荡培养过程中对数前期细胞内RpoS含量决定转化能力的强弱。在静置培养过程中,通过对比不同胞内RpoS含量的大肠杆菌的转化频率变化规律发现,静置培养可以在一定程度上提升转化能力,该提升过程需要时间的积累(约8h完成),而在该培养阶段提高胞内RpoS的水平,可缩短积累所耗的时间(约4～6h即可完成),结合转化频率总体上升20%的结果,证明了静置培养阶段的胞内RpoS表达量对自然转化具有促进作用,但并不起决定作用。综上所述,胞内RpoS的含量对于大肠杆菌自然遗传感受态的建立很重要；对数前期的RpoS含量决定自然转化频率的高低；静置培养期的RpoS含量对转化能力具有促进作用。
核苷酸及其衍生物可作为营养物质被处于营养饥饿的大肠杆菌细胞所吸收,有报道单核苷酸参与流感嗜血杆菌等细菌自然转化的调控。那么,大肠杆菌自然遗传转化过程是否受到单核苷酸的影响呢?
单磷酸腺苷(AMP)在流感嗜血杆菌的自然转化中,通过抑制一些转化基因的转录而抑制遗传转化的发生,但在大肠杆菌的遗传转化中,是否也有类似的作用未见报道。鉴于人工转化的机制研究较为系统,本工作首先研究了AMP对大肠杆菌人工转化的作用。本研究比较研究了外源单核苷酸衍生物对大肠杆菌人工转化能力的影响,结果显示,外源AMP可能通过能量流动改变了胞内的能量状态,从而抑制了人工转化的发生。而在大肠杆菌的自然遗传转化中,外源AMP却有促进作用,是否也是通过能量流动引起的改变有待进一步验证。
综上所述,本研究工作借助分子生物学和遗传学的手段,揭示了普遍压力应答因子RpoS与大肠杆菌自然遗传转化能力相关性,并对参与大肠杆菌自然转化的AMP等因素进行了探讨,为更好的理解大肠杆菌自然遗传转化的调控机理以及RpoS在大肠杆菌中的功能提供了实验依据；另外,对单核苷酸AMP在大肠杆菌自然遗传转化中作用的研究,为进一步认识大肠杆菌自然转化的调控机理提供了依据。本工作为探讨细菌自然遗传转化的普遍规律提供了新的线索。
As a novel transformation system reported these years, Escherichia coli natural transformation contains these processes:natural competence development, DNA uptake and transformants determination. The finding of E. coli natural transformation was of good biology value, since it breaks the traditional view that E. coli could not take exogenous DNA and transform without artificial treatment. Moreover, because E. coli is also one of the most common used materials in genetic engineering, its biosecurity comes under question for its ability of natural gene transfer. So there is extensive space and requirement in the study of mechanism of this transformation system.
The general stress response factor σS, so-called RpoS, is an alternative σ factor of RNA polymerase in Escherichia coli. It can partially replace the "housekeeping" σ factor σ70(RpoD) under many stress conditions. RpoS intacts with the core RNA polymerase (RNAP) and controls the expression of a specific but large set of genes. Directly or indirectly, RpoS regulates10%of the E. coli genome (approximately500genes). With the characteristic of "low-expression in exponential phase and high-expression under stress conditions", RpoS was mentioned as a regulator of E. coli natural transformation.
In this study, we investigate the effect of RpoS on E. coli natural transformation in an "open system". Some regulation mechanisms was discussed in detail too.
In order to make sure whether RpoS has influence exactly on natural transformation process, we continuously exclude the interference of RpoS regulation on other transformation system and the disturbation of transformants survival. The results expressed that, RpoS affects the natural transformation frequency in E. coli, while has no effect on artificial transformation. The transformant survival was not interrupted by RpoS. So the RpoS regulation was exactly on the process of natural transformation.
E. coli natural transformation process contains natural competence development and DNA uptake. The RpoS's effects on which step determin the transformation frequency were investigated in the following work.
DNA uptake carried out on plate is one characteristic in natural transformation different from the classical artificial transformation with Ca2+. In order to determine the relationship between RpoS expression and the DNA uptake, three questions should be answered:whether the RpoS deletion would disturb the time that DNA uptake takes place, whether the RpoS expression was changed by the plating which promotes DNA uptake and if the transformation frequency would be changed by the RpoS expression changing in DNA uptake. We finally demonstrate that, although RpoS positive controls the natural transformation, it is not sufficient for transformation complete. The contact of natural competence with solid substrate was necessary for DNA uptake, but this process has nothing to do with RpoS expression.
Another characteristic of open system natural transformation is that the process of natural competence development contains two parts:shaking culture and static cultivation. In which step RpoS plays the major role on natural transformation was discussed in the following work. The results demonstrate that the intracellular RpoS content of cells in the process of natural competence development, especially in the early exponential phase, determines the level of transformation frequency. Although not as important as in early exponential phase, the RpoS content in static cultivation enhances the natural transformation.
In order to investigate the natural transformation regulation from various angles, besides the function research of single gene rpoS on the natural transformation, another factor AMP, which has been reported to inhibit the natural transformation of Haemophilus influenza, was discussed both in E. coli artificial and natural transformations. We found that intracellular AMP could changes the flow of energy by breaking the energy charge of the competence. This flow of energy blocks the E. coli artificial transformation. However, it enhances the natural transformation at the early exponential phase just like the RpoS regulation.
In conclusion, we demonstrate that the intracellular RpoS content in early exponential phase determines the level of transformation frequency, which has not been studies in previous work. Then one regulatory factor in H. influenza natural transformation AMP was found has different effect on E. coli natural transformation. These findings provide detailed understanding of RpoS effect on natural transformation.
引文
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