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题名	宿主与病原微生物共进化的分子机制探讨
作者	程东强
学位类别	博士
答辩日期	2014-05
授予单位	中国科学院研究生院
授予地点	北京
导师	黄京飞
关键词	分子进化 甲型流感病毒 分子动力学模型
其他题名	Studies on the Molecular Mechanism of Host and Pathogen Co-evolution
学位专业	细胞生物学
中文摘要	灵长类α-/θ-防御素多基因家族编码一类多功能的、内源的、带正电荷并且两亲性的短肽，这些短肽具有广谱的抵抗细菌、真菌和病毒的活性。早期的研究曾报道过α-/θ-防御素基因（DEFA/DEFT）的进化符合生灭演化（birth-and-death evolution）模型，存在频繁的基因重复和快速的进化。但是关于灵长类DEFA/DEFT基因的进化仍然存在许多有待解决的问题，包括它们的系统发育关系，抗菌谱的形成及其在近缘物种中相似的遗传基础，以及θ-防御素环肽在旧大陆猴中产生又迅速地在人、黑猩猩、大猩猩中丢失相关的进化过程。本研究收集了灵长类和树鼩全部DEFA/DEFT基因，对其进行了详细的系统发育、序列和结构、选择压力以及比较基因组学分析。系统发育分析的结果显示所有树鼩、原猴亚目和猿猴亚目的DEFA/DEFT基因被划分成两大枝，并且在猿猴亚目这两大枝分别是组织特异表达的肠系和髓系防御素。猿猴亚目肠系和髓系防御素进一步分为序列分化，结构差异，功能约束改变及选择压力不同的六个功能聚类，所有这些结果表明在近缘物种中存在相似的抗菌谱。猿猴亚目某些功能聚类中存在物种特异的基因重复和假基因化表明这一抗菌谱是动态变化的，提示周围的病原微生物环境可能也是不断变化的。我们的结果表明DEFT基因起源于髓系的DEFA8基因。此外，在θ-防御素的前片段区检测到了与成熟肽区新蛋白折叠共进化的适应性改变，这一结果也符合先前报道的前片段区在成熟肽的正确折叠中起重要作用的结论。最后，我们提出了less-is-hitchhiking假说来解释人和黑猩猩中假基因DEFTP的扩增及功能基因DEFT的丢失。less-is-hitchhiking假说认为在多基因家族生灭演化的过程中，搭车基因的扩增或者丢失受到它邻近的驱动基因的影响。 流感病毒血球凝集素HA的不同亚型与宿主细胞膜上α2,3或α2,6糖苷键多糖分子的结合差异影响流感病毒的跨宿主传播及同宿主传播的传播性及致病性。尽管一些与寡糖结合的HA蛋白结构已经被解析出来，但是可感染人的不同亚型HA在其配体结合口袋区的序列差异，与配体结合动态过程的结合差异，及潜在的共进化位点还没有系统的比较分析过。我们通过序列分析生成不同HA（可感染人的不同突变亚型H1、H3或H5）与配体（α2,3或α2,6糖苷键寡糖）结合时结合口袋位点的序列标识，进行分子动力学模拟，并计算结合能量差异、结合时物理因素（用配体的θ角来衡量配体结合时空间位阻）及化学因素（用分子间紧密接触原子的距离来衡量氢键频率或范德华相互作用）差异。研究结果表明不同亚型或感染不同宿主的HA其结合口袋序列标识具有显著差异性或专一性；能感染人的突变亚型H1、H3和H5与α2,3或α2,6糖苷键寡糖结合时，结合能量、配体结合空间位阻及分子间氢键频率都检测到相应的差异；与结合口袋共进化位点的序列标识也具有不同亚型不同宿主的显著差异性或专一性。结合口袋和与其共进化位点的序列标识展示出的差异可能影响流感病毒跨宿主传播和同宿主传播的传播性及致病性，因此该研究为流感流行病学的监控提供了帮助。 分析和监控流感病毒的演化动态有助于我们理解流感病毒流行病学特征的遗传基础，并为控制和预防提供指导信息。我们构建了InFlu网页服务器（http://www.influ.org），提供对流感病毒的整合分析，包括基于位点频率对占主导传播的病毒单倍型的鉴定，主导单倍型的时空分布的汇报，以及显著固定下来的突变鉴定。InFlu界面友好，提供计算结果的图形输出，可以作为研究和监控全球流感病毒的有用工具。
英文摘要	The primate α-/θ-defensin multigene family encodes versatile endogenous cationic and amphipathic peptides that have broad-spectrum antibacterial, antifungal and antiviral activity. Although previous studies have reported that α-/θ-defensin (DEFA/DEFT) genes are under birth-and-death evolution with frequent duplication and rapid evolution, the phylogenetic relationships of the primate DEFA/DEFT genes; the genetic bases for the existence of similar antimicrobial spectra among closely related species; and the evolutionary processes involved in the emergence of cyclic θ-defensins in Old World monkeys and their subsequent loss of function in humans, chimpanzees and gorillas require further investigation. In this study, the DEFA/DEFT gene repertoires from primate and treeshrew were collected, followed by detailed phylogenetic, sequence and structure, selection pressure and comparative genomics analyses. All treeshrew, prosimian and simian DEFA/DEFT genes are grouped into two major clades, which are tissue-specific for enteric and myeloid defensins in simians. The simian enteric and myeloid α-defensins are classified into six functional gene clusters with diverged sequences, variable structures, altered functional constraints and different selection pressures, which likely reflect the antimicrobial spectra among closely related species. Species-specific duplication or pseudogenization within each simian cluster implies that the antimicrobial spectrum is ever-shifting, most likely challenged by the ever-changing pathogen environment. The DEFT evolved from the myeloid DEFA8. The prosegment of θ-defensin is detected with adaptive changes coevolving with the new protein fold of mature peptide, coincident with the importance of the prosegment for the correct folding of the mature peptide. Lastly, a less-is-hitchhiking hypothesis was proposed as a possible explanation for the expansion of pseudogene DEFTP and the loss of functional DEFT, where the gain or loss of the hitchhiker is determined by its adjacent driver gene during the birth-and-death evolutionary process. The binding abilities of different influenza hemagglutinins (HA) to the α2,3-glycan or α2,6-glycan on the host membrane affect their cross-species transmission, as well as transmissibility and pathogenicity within a species. Although the crystal structures of HA in complex with α2,3- or α2,6-glycan have been available, many questions remain unsolved. The sequence difference in binding pocket among different human-infecting HA types, the binding dynamics difference with α2,3- or α2,6-glycan as well as the potential sites that co-evoleved with binding pocket lack systematical analyses. In this study, we generated the sequence logo for the binding pocket from different HA types, and performed molecular dynamics simulation for different HAs (human-infecting H1, H3 and H5) binding with α2,3- or α2,6-glycans. Based on the simulation results, we analyzed their binding energetics, biophysical (the θ-angle of ligand for steric hindrance) and biochemical characteristics (atomic distances for the hydrogen bond frequency and Van der Waals interaction). Our results show that the binding pockets of different HA types from different hosts have remarkably different sequence profile, with each type from the same host being specific. The binding of human-infecting H1, H3 and H5 with the ligand α2,3- or α2,6-glycan show difference in binding energetics, binding steric hindrance and hydrogen bond frequency. The co-evolved sites with the binding pocket also show specificity for each human-infecting HA type, which probably also affect the cross-species transmission as well as transmissibility and pathogenicity within a species. Our results might provide some useful insight for the surveillance of epidemics or pandemics. Analyzing and monitoring the evolutionary dynamics of influenza viruses assists our understanding of the genetic determination of viral epidemiological properties and
语种	中文
公开日期	2014-06-04
内容类型	学位论文
源URL	[http://159.226.149.42:8088/handle/152453/7882]
专题	昆明动物研究所_结构生物信息学
推荐引用方式 GB/T 7714	程东强. 宿主与病原微生物共进化的分子机制探讨[D]. 北京. 中国科学院研究生院. 2014.

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