烟草花叶病毒的修饰和调控及其与安托芬类似物的相互作用研究
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摘要
烟草花叶病毒(Tobacco mosaic virus, TMV)作为一种模式病毒,人们对它的研究已经有一百五十年的历史了,它是一种对农业生产有极大危害的植物病毒病原体,同时也是植物病毒中研究的最为详细的一种,在形态、粒体结构、化学组成、组装、外壳、亚基组成、基因组结构、核酸复制、蛋白翻译、病毒在细胞间的运动等方面常作为病毒学研究的经典范例,几乎所有关于病毒的研究都是从烟草花叶病毒起步的。由于烟草花叶病毒独特的组装性质及其处于纳米尺度的天然优势,近年来它已经成为了一种良好的植物病毒载体,并且在纳米科学领域也有日益广泛的应用,可以说,对烟草花叶病毒的研究不仅具有重大的理论价值和现实意义,同时具有十分广阔的应用前景。
本文从两大方面关注烟草花叶病毒：第一方面是抗烟草花叶病毒的研究,主要集中于安托芬(Antofine)与烟草花叶病毒之间的相互作用。以Antofine为生物活性探针,研究它发挥生物功能的靶标和作用模式,在前人工作的基础上,进一步揭示Antofine抑制烟草花叶病毒的机制,探索抗病毒药物开发的新途径和新思路；另一方面,以烟草花叶病毒为靶标,对其进行颗粒修饰和粒度调控,在加深对烟草花叶病毒自身性质认识的同时,实现人为调控病毒的表面特征和颗粒大小,为进一步利用它作为基因药物载体和制备可调控生物纳米材料奠定基础。
本文的工作分为以下四个部分：
一、烟草花叶病毒与Antofine及其类似物的相互作用研究。Antofine是一种具有显著抗烟草花叶病毒活性的天然产物,这种天然产物具有潜在的细胞毒性和抗癌活性,因此,一直以来都受到科学家们的关注。Antofine是个具有近似平面结构的分子,本课题组过去的研究发现Antofine与带有凸起结构的DNA具有特异性相互作用。本文利用荧光光谱、紫外可见光谱等方法,进一步确定了Antofine与带有凸起结构DNA之间的作用模式,并设计合成了一系列具有更细微结构和序列特征的DNA,测定了它们与Antofine相互作用的解离常数,获得了更完整的结论。
Antofine具有良好的抗烟草花叶病毒性质,但是关于它作用靶标的研究却十分有限。本课题组张偌瑜博士已经证实Antofine与TMV RNA之间存在强的相互作用(表观解离常数在nM级别)。本文在此工作基础上测定了Antofine与TMV壳蛋白之间的解离常数,通过荧光滴定的方法测定了一系列Antofine的类似物与TMV RNA之间的相互作用常数以及通过核酸酶抗性实验测定了它们抑制烟草花叶病毒组装的百分比。我们发现,Antofine与TMV壳蛋白的解离常数较之与TMV RNA的解离常数高了四个数量级,说明在抑制TMV组装的过程中,Antofine与TMV RNA之间的结合具有绝对的竞争力。Antofine类似物和核酸之间的结合能力与它们抑制病毒组装的能力呈现正相关关系,从而进一步确认TMV RNA是Antofine抑制病毒的靶标,Antofine及其类似物通过与TMV RNA相互作用抑制病毒组装,实现抗病毒活性。
二、体外筛选TMV起始组装序列文库的结果分析。烟草花叶病毒起始组装位点在病毒组装过程中具有重要的作用,Antofine对TMV组装的抑制很大程度上都来源于对起始组装位点的识别。为了更深入的了解起始组装位点的组装特性,本课题组利用SELEX技术,对含有～109种不同序列的起始组装位点文库进行了筛选。本文将筛选得到的全部序列进行了测序,并对测序结果进行了分析和归纳,总结了其中的规律。我们发现：顶端loop结构“NNG”的特征并不明显,但N具有嘌呤碱基偏好且对于C碱基的排斥很明显；apex最顶端的G碱基对于组装有重要的作用；靠近茎环顶部stem区域碱基对的熔链能力对于组装至关重要；G-U wobble碱基配对对于OriRNA和壳蛋白的识别可能具有重要作用。从序列出现的丰度来看,野生型序列出现的次数最多,说明人工进化和自然选择得到了相同的结果。
三、烟草花叶病毒的颗粒修饰与粒度调控。近年的研究趋势表明,越来越多的关注集中于烟草花叶病毒本身极其规律的螺旋堆积方式。很多科学家利用烟草花叶病毒作为氧化物、金属附着的模板,通过修饰病毒内外表面壳蛋白上特殊的氨基酸,使病毒带有诸如导电性,聚合性等特征。因此,烟草花叶病毒在纳米科学领域有着广泛的应用前景,另外,由于病毒可以利用宿主细胞表达外源蛋白,使它成为了良好的植物病毒载体。TMV在其他科学领域的应用日益广泛,要想更好的拓展TMV的应用,最基本的还是要增强对其本身特性的了解。无论在纳米科技领域还是生物医药领域,对TMV的应用都离不开对其表面性质以及组装与解组装过程的认识。本文采用光化学交联法对病毒颗粒表面的酪氨酸进行了交联,测定了交联对于病毒颗粒稳定性、完整性和侵染性的影响。利用锍盐烷基化结合"Click"反应的方法对烟草花叶病毒进行了荧光标记,开辟了一种新的生物连接途径,对实时监测烟草花叶病毒在细胞内的定位提供了有效的手段。
烟草花叶病毒具有简单而规律的组装特性,它的组装只需要起始组装位点与壳蛋白的识别,对延伸的RNA链并没有序列和长度的限制,这一特性使它成为了植物病毒载体,同时,也使其具备了构建生物纳米材料的可能。但是,天然病毒的尺度固定在300nm,极大的限制了它的可利用范围,我们希望能够人为的控制它的长度。本文采取两种方法进行病毒颗粒的调控：(1)尝试利用起始组装位点来引导DNA的组装。DNA分子在自然界分布广泛,相比于RNA分子,DNA分子更稳定,也更容易得到任意长度的核酸链。我们利用T4 RNA连接酶将RNA片段和DNA片段连接在一起,构建了153个核苷酸的杂合链,并检测了它们被TMV壳蛋白包裹的能力。(2)通过控制体外重组的RNA的长度来实现精确控制病毒颗粒的粒度。我们通过PCR得到不同长度的DNA分子,利用体外转录的方法得到其对应的RNA片段,这些片段都含有起始组装位点序列,进一步与壳蛋白进行体外组装,形成具有均一长度的纳米颗粒,实现对颗粒粒度的精确调控。
四、烟草花叶病毒壳蛋白的体外表达。TMV的表面修饰手段多种多样,但是无论通过酶法还是化学法都很难实现定点修饰。我们考虑在大肠杆菌中对烟草花叶病毒的壳蛋白进行体外表达。利用表达出来的壳蛋白进行组装,能够实现多方面,多位点的修饰,这对于TMV组装机制的研究有极大的促进作用。我们成功的在大肠杆菌中表达了TMV壳蛋白,并检测了它组装核酸的能力。
研究Antofine与烟草花叶病毒的作用模式,对病毒进行表面修饰和粒度的精确控制以及实现壳蛋白的体外表达,开拓了开发抗病毒药物的思路,加深了对其特性的认识,丰富了调控它的手段。总而言之,病毒防治是医药和农药研发领域中极其重要的课题,对Antofine抑制TMV组装靶点的寻找、对烟草花叶病毒组装机制的了解以及对于TMV表面修饰和粒度调控的深入研究和广泛利用能够促进多个科学和技术领域的发展。
Research on tobacco mosaic virus (TMV) has played a leading role in the development of virology for more than a century. TMV is one of the most harmful plant virus found worldwide, meanwhile, also the most deeply studied on the configuration, structure, chemical composition, assembly, subunit, DNA replication, protein translation, and cell to cell movement, et al. TMV exhibits most of its popularity as a model virus to the investigation on regular assembly mode and nano-dimension character. Studies on TMV have been last for a long period, and its prominent position in both fundamental and applied research will still continue to occupy. Our study interests focused on two major aspects:one, prevention and inhibition of TMV, which is a hot subject with practical significance in the field of research and development of new pesticides. Based on our previous work, we wondered the exact interaction model between TMV and Antofine; another, regulation of TMV. We hope to increase the understanding of the character and application of TMV, by means of its modification and length control.
This article is mainly focus on the following four parts:
First:Antofine is reported to have shown remarkable inhibition on TMV, and its analogs have pronounced activities including cytotoxicity, antitumor activity et al, which attracts many attentions. Our group has reported that high order of molecular recognition to bulged hairpin DNA afforded by Antofine, also got some deduction on Antofine's basic mode of its interaction with DNA by means of fluorescence and UV-Vis spectroscopy. On the basis of these work, herein, we designed and synthesized a series of bulged DNA containing much more subtle differences in comparison with HT3AGT which has the best affinity with Antofine in previous study. We ascertained the exact interaction mode between Antofine and bulged hairpin DNA.
Antofine is a well-known inhibitor for TMV, but its target is still unknown. Dr. Ruoyu Zhang has found the strong affinity between Antofine and TMV RNA. Herein, we determined the Kd value of Antofine and TMV CP by equilibrium dialysis. Combined with the determination of affinity with TMV RNA and assembly inhibition ability of Antofine analogs, we found that the activities of antofine and its analogs to inhibit TMV assembly may correlate with their binding affinity to TMV RNA. So we deduced antofine analogs inhibit TMV assembly mostly by virtue of interacting with TMV RNA.
Second:OriRNA plays a dominate role in TMV lifecycle and total assembly inhibition, thus, our group using SELEX, constructed a library of-109 different RNA sequences with 16 random sites. We sequenced all the members in the final library after 7 cycles'selection, and conclusions could be drawn from the analysis of the mutations:results from the statistical point of view, it is not obvious of the feature that the apex contains the specific trinucleotide 'NNG', but N prefer A and G, while C is dislike; G in the second 'NNG' of the apex maybe important to the assembly ability; the melting ability of the base pair closed to the apex is crucial to the assembly; G-U wobble pair may play a certain role in the recognition between OriRNA and TMV CP. From the view of the abundance of sequence, we found that wild-type OriRNA has the maximum frequency of its appearance, which indicated that both artificial evolution and natural selection got the same result.
Third:TMV has a hollow cylindrical structure with a high aspect ratio and formed through the periodical self-assembly of the TMV CP and TMV RNA. Because of its well-characterized nanosacle structure, TMV has been utilized as a template for functionalization with inorganic and organic molecules both in the inner cavity and on the exterior surface. TMV has also been used in the biotechnological sphere:as the source of transgenic sequences conferring virus resistance, in vaccines consisting of TMV particles genetically and in systems for expressing foreign genes. In order to better understanding these applications of TMV, we need to get much more information on its assembly mechanism while the character of TMV surface. We described the application of photochemical crosslinking of coat protein of TMV particle and its effect on infectivity and stability of TMV. Compared to native TMV, the crosslinked TMV showed lower thermostability and resistance to dilute alkaline, though it remains physical integrity; crosslinked TMV nearly lost its infectivity on tobacco leaves. On the other hand, Alkylsulfonium salts (ASS) have been reported as powerful alkylation agents. We use a tandem method of sulfonium alkylation and "click" chemistry (CuAAC) for TMV modification. This facile modification should be useful in bionanoscience.
Although TMV has such promising features for its application to nanoscale materials, the length of wild-type TMV rod which is limited to 300nm restricts its further application. We may replace the rod structure by other different lengths of RNA or DNA using suitable methods to realize length control and functional reconstruction. We adopted two methods as follow:first, we wondered whether the OriRNA can lead the assembly of DNA. If it works, we can be free to control the rod length, so we constructed a 153nt RNA-DNA hybrid in which the RNA part comprised the OriRNA of TMV, then determined the assembly ability of this hybrid; second, using PCR and transcription in vitro to construct different lengths of TMV RNA strands, during assembly procedure with TMV CP, we may get different lengths of virus rod evenly, to realize precise controlling of nano-scale particles of TMV.
Finally:people try many methods to achieve the modification of TMV, but neither by enzyme nor by chemistry can realize site-directed modification. So we considered to express TMV coat protein in E.coli, then assemble reconstituted or modified CP with TMV RNA into particles. Herein we successfully expressed the TMV CP in E. coli and checked its assembly ability at the same time.
Research on the interaction mode of Antofine and tobacco mosaic virus has opened up our thinking about the development of new antiviral strategies. Modification of TMV surface has deepened our understanding of its properties. Precise control of nano-scale particles of TMV has laid the foundation for TMV as a drug carrier. In vitro expression of TMV CP has enriched our means to control it. Virus infection is a severe public health problem related to serious personal, social, and economical consequences, herein, we ascertained the target of Antofine, developed some methods to modify TMV surface, which can be beneficial to the anti-viral research and application of TMV.
本文从两大方面关注烟草花叶病毒：第一方面是抗烟草花叶病毒的研究,主要集中于安托芬(Antofine)与烟草花叶病毒之间的相互作用。以Antofine为生物活性探针,研究它发挥生物功能的靶标和作用模式,在前人工作的基础上,进一步揭示Antofine抑制烟草花叶病毒的机制,探索抗病毒药物开发的新途径和新思路；另一方面,以烟草花叶病毒为靶标,对其进行颗粒修饰和粒度调控,在加深对烟草花叶病毒自身性质认识的同时,实现人为调控病毒的表面特征和颗粒大小,为进一步利用它作为基因药物载体和制备可调控生物纳米材料奠定基础。
本文的工作分为以下四个部分：
一、烟草花叶病毒与Antofine及其类似物的相互作用研究。Antofine是一种具有显著抗烟草花叶病毒活性的天然产物,这种天然产物具有潜在的细胞毒性和抗癌活性,因此,一直以来都受到科学家们的关注。Antofine是个具有近似平面结构的分子,本课题组过去的研究发现Antofine与带有凸起结构的DNA具有特异性相互作用。本文利用荧光光谱、紫外可见光谱等方法,进一步确定了Antofine与带有凸起结构DNA之间的作用模式,并设计合成了一系列具有更细微结构和序列特征的DNA,测定了它们与Antofine相互作用的解离常数,获得了更完整的结论。
Antofine具有良好的抗烟草花叶病毒性质,但是关于它作用靶标的研究却十分有限。本课题组张偌瑜博士已经证实Antofine与TMV RNA之间存在强的相互作用(表观解离常数在nM级别)。本文在此工作基础上测定了Antofine与TMV壳蛋白之间的解离常数,通过荧光滴定的方法测定了一系列Antofine的类似物与TMV RNA之间的相互作用常数以及通过核酸酶抗性实验测定了它们抑制烟草花叶病毒组装的百分比。我们发现,Antofine与TMV壳蛋白的解离常数较之与TMV RNA的解离常数高了四个数量级,说明在抑制TMV组装的过程中,Antofine与TMV RNA之间的结合具有绝对的竞争力。Antofine类似物和核酸之间的结合能力与它们抑制病毒组装的能力呈现正相关关系,从而进一步确认TMV RNA是Antofine抑制病毒的靶标,Antofine及其类似物通过与TMV RNA相互作用抑制病毒组装,实现抗病毒活性。
二、体外筛选TMV起始组装序列文库的结果分析。烟草花叶病毒起始组装位点在病毒组装过程中具有重要的作用,Antofine对TMV组装的抑制很大程度上都来源于对起始组装位点的识别。为了更深入的了解起始组装位点的组装特性,本课题组利用SELEX技术,对含有～109种不同序列的起始组装位点文库进行了筛选。本文将筛选得到的全部序列进行了测序,并对测序结果进行了分析和归纳,总结了其中的规律。我们发现：顶端loop结构“NNG”的特征并不明显,但N具有嘌呤碱基偏好且对于C碱基的排斥很明显；apex最顶端的G碱基对于组装有重要的作用；靠近茎环顶部stem区域碱基对的熔链能力对于组装至关重要；G-U wobble碱基配对对于OriRNA和壳蛋白的识别可能具有重要作用。从序列出现的丰度来看,野生型序列出现的次数最多,说明人工进化和自然选择得到了相同的结果。
三、烟草花叶病毒的颗粒修饰与粒度调控。近年的研究趋势表明,越来越多的关注集中于烟草花叶病毒本身极其规律的螺旋堆积方式。很多科学家利用烟草花叶病毒作为氧化物、金属附着的模板,通过修饰病毒内外表面壳蛋白上特殊的氨基酸,使病毒带有诸如导电性,聚合性等特征。因此,烟草花叶病毒在纳米科学领域有着广泛的应用前景,另外,由于病毒可以利用宿主细胞表达外源蛋白,使它成为了良好的植物病毒载体。TMV在其他科学领域的应用日益广泛,要想更好的拓展TMV的应用,最基本的还是要增强对其本身特性的了解。无论在纳米科技领域还是生物医药领域,对TMV的应用都离不开对其表面性质以及组装与解组装过程的认识。本文采用光化学交联法对病毒颗粒表面的酪氨酸进行了交联,测定了交联对于病毒颗粒稳定性、完整性和侵染性的影响。利用锍盐烷基化结合"Click"反应的方法对烟草花叶病毒进行了荧光标记,开辟了一种新的生物连接途径,对实时监测烟草花叶病毒在细胞内的定位提供了有效的手段。
烟草花叶病毒具有简单而规律的组装特性,它的组装只需要起始组装位点与壳蛋白的识别,对延伸的RNA链并没有序列和长度的限制,这一特性使它成为了植物病毒载体,同时,也使其具备了构建生物纳米材料的可能。但是,天然病毒的尺度固定在300nm,极大的限制了它的可利用范围,我们希望能够人为的控制它的长度。本文采取两种方法进行病毒颗粒的调控：(1)尝试利用起始组装位点来引导DNA的组装。DNA分子在自然界分布广泛,相比于RNA分子,DNA分子更稳定,也更容易得到任意长度的核酸链。我们利用T4 RNA连接酶将RNA片段和DNA片段连接在一起,构建了153个核苷酸的杂合链,并检测了它们被TMV壳蛋白包裹的能力。(2)通过控制体外重组的RNA的长度来实现精确控制病毒颗粒的粒度。我们通过PCR得到不同长度的DNA分子,利用体外转录的方法得到其对应的RNA片段,这些片段都含有起始组装位点序列,进一步与壳蛋白进行体外组装,形成具有均一长度的纳米颗粒,实现对颗粒粒度的精确调控。
四、烟草花叶病毒壳蛋白的体外表达。TMV的表面修饰手段多种多样,但是无论通过酶法还是化学法都很难实现定点修饰。我们考虑在大肠杆菌中对烟草花叶病毒的壳蛋白进行体外表达。利用表达出来的壳蛋白进行组装,能够实现多方面,多位点的修饰,这对于TMV组装机制的研究有极大的促进作用。我们成功的在大肠杆菌中表达了TMV壳蛋白,并检测了它组装核酸的能力。
研究Antofine与烟草花叶病毒的作用模式,对病毒进行表面修饰和粒度的精确控制以及实现壳蛋白的体外表达,开拓了开发抗病毒药物的思路,加深了对其特性的认识,丰富了调控它的手段。总而言之,病毒防治是医药和农药研发领域中极其重要的课题,对Antofine抑制TMV组装靶点的寻找、对烟草花叶病毒组装机制的了解以及对于TMV表面修饰和粒度调控的深入研究和广泛利用能够促进多个科学和技术领域的发展。
Research on tobacco mosaic virus (TMV) has played a leading role in the development of virology for more than a century. TMV is one of the most harmful plant virus found worldwide, meanwhile, also the most deeply studied on the configuration, structure, chemical composition, assembly, subunit, DNA replication, protein translation, and cell to cell movement, et al. TMV exhibits most of its popularity as a model virus to the investigation on regular assembly mode and nano-dimension character. Studies on TMV have been last for a long period, and its prominent position in both fundamental and applied research will still continue to occupy. Our study interests focused on two major aspects:one, prevention and inhibition of TMV, which is a hot subject with practical significance in the field of research and development of new pesticides. Based on our previous work, we wondered the exact interaction model between TMV and Antofine; another, regulation of TMV. We hope to increase the understanding of the character and application of TMV, by means of its modification and length control.
This article is mainly focus on the following four parts:
First:Antofine is reported to have shown remarkable inhibition on TMV, and its analogs have pronounced activities including cytotoxicity, antitumor activity et al, which attracts many attentions. Our group has reported that high order of molecular recognition to bulged hairpin DNA afforded by Antofine, also got some deduction on Antofine's basic mode of its interaction with DNA by means of fluorescence and UV-Vis spectroscopy. On the basis of these work, herein, we designed and synthesized a series of bulged DNA containing much more subtle differences in comparison with HT3AGT which has the best affinity with Antofine in previous study. We ascertained the exact interaction mode between Antofine and bulged hairpin DNA.
Antofine is a well-known inhibitor for TMV, but its target is still unknown. Dr. Ruoyu Zhang has found the strong affinity between Antofine and TMV RNA. Herein, we determined the Kd value of Antofine and TMV CP by equilibrium dialysis. Combined with the determination of affinity with TMV RNA and assembly inhibition ability of Antofine analogs, we found that the activities of antofine and its analogs to inhibit TMV assembly may correlate with their binding affinity to TMV RNA. So we deduced antofine analogs inhibit TMV assembly mostly by virtue of interacting with TMV RNA.
Second:OriRNA plays a dominate role in TMV lifecycle and total assembly inhibition, thus, our group using SELEX, constructed a library of-109 different RNA sequences with 16 random sites. We sequenced all the members in the final library after 7 cycles'selection, and conclusions could be drawn from the analysis of the mutations:results from the statistical point of view, it is not obvious of the feature that the apex contains the specific trinucleotide 'NNG', but N prefer A and G, while C is dislike; G in the second 'NNG' of the apex maybe important to the assembly ability; the melting ability of the base pair closed to the apex is crucial to the assembly; G-U wobble pair may play a certain role in the recognition between OriRNA and TMV CP. From the view of the abundance of sequence, we found that wild-type OriRNA has the maximum frequency of its appearance, which indicated that both artificial evolution and natural selection got the same result.
Third:TMV has a hollow cylindrical structure with a high aspect ratio and formed through the periodical self-assembly of the TMV CP and TMV RNA. Because of its well-characterized nanosacle structure, TMV has been utilized as a template for functionalization with inorganic and organic molecules both in the inner cavity and on the exterior surface. TMV has also been used in the biotechnological sphere:as the source of transgenic sequences conferring virus resistance, in vaccines consisting of TMV particles genetically and in systems for expressing foreign genes. In order to better understanding these applications of TMV, we need to get much more information on its assembly mechanism while the character of TMV surface. We described the application of photochemical crosslinking of coat protein of TMV particle and its effect on infectivity and stability of TMV. Compared to native TMV, the crosslinked TMV showed lower thermostability and resistance to dilute alkaline, though it remains physical integrity; crosslinked TMV nearly lost its infectivity on tobacco leaves. On the other hand, Alkylsulfonium salts (ASS) have been reported as powerful alkylation agents. We use a tandem method of sulfonium alkylation and "click" chemistry (CuAAC) for TMV modification. This facile modification should be useful in bionanoscience.
Although TMV has such promising features for its application to nanoscale materials, the length of wild-type TMV rod which is limited to 300nm restricts its further application. We may replace the rod structure by other different lengths of RNA or DNA using suitable methods to realize length control and functional reconstruction. We adopted two methods as follow:first, we wondered whether the OriRNA can lead the assembly of DNA. If it works, we can be free to control the rod length, so we constructed a 153nt RNA-DNA hybrid in which the RNA part comprised the OriRNA of TMV, then determined the assembly ability of this hybrid; second, using PCR and transcription in vitro to construct different lengths of TMV RNA strands, during assembly procedure with TMV CP, we may get different lengths of virus rod evenly, to realize precise controlling of nano-scale particles of TMV.
Finally:people try many methods to achieve the modification of TMV, but neither by enzyme nor by chemistry can realize site-directed modification. So we considered to express TMV coat protein in E.coli, then assemble reconstituted or modified CP with TMV RNA into particles. Herein we successfully expressed the TMV CP in E. coli and checked its assembly ability at the same time.
Research on the interaction mode of Antofine and tobacco mosaic virus has opened up our thinking about the development of new antiviral strategies. Modification of TMV surface has deepened our understanding of its properties. Precise control of nano-scale particles of TMV has laid the foundation for TMV as a drug carrier. In vitro expression of TMV CP has enriched our means to control it. Virus infection is a severe public health problem related to serious personal, social, and economical consequences, herein, we ascertained the target of Antofine, developed some methods to modify TMV surface, which can be beneficial to the anti-viral research and application of TMV.
引文
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