德克拉酵母有氧酵解途径的适应性进化研究
文献类型：学位论文
| 作者 | 张琳 |
| 学位类别 | 硕士 |
| 答辩日期 | 2015-04 |
| 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 | 有氧酵解 基因组分析 正选择 顺式作用元件 |
| 其他题名 | The adaptive evolution of aerobic fermentation in Dekkera yeast |
| 学位专业 | 生物工程 |
| 中文摘要 | 在有氧气存在的情况下，一般酵母会将葡萄糖等糖类经过三羧酸循环、氧化磷酸化等途径经过一系列化学反应，最终把葡萄糖分解成为水和二氧化碳，并释放大量能量，支持有机体的生命活动。相反的，尽管是在氧气存在的环境中，酿酒酵母也不会通过氧化磷酸化等途径为有机体提供能量，而是在细胞质中，不需要氧气参与的情况下直接把糖类降解成为二碳物质，尤其是乙醇。 这种途径叫做有氧酵解，也称为反巴斯的效应，是酿酒酵母在一亿年前经过全基因组重复之后出现的新表型。氧酵解的功能使酿酒酵母在生存进化中可以战胜其他生物成为胜利者。 然而，从两亿年前独立进化出来的德克拉酵母属的某些物种也具有有氧酵解表型，与该属进化上十分相近的酒香酵母属却不具有。更值得注意的是，德克拉酵母并没有发生全基因组重复事件，是独立于酿酒酵母的分枝进化出的有氧酵解表型。德克拉酵母属可以获得有氧酵解的功能而酒香酵母属却不能获得的原因至今尚未研究清楚。本篇研究希望通过对两个酵母属的四个物种进行从头测序，在基因组层次上研究分析德克拉酵母属和酒香酵母属在有氧酵解表型上差异的原因。 首先，AAAATT基序在与快速生长相关的基因中大量存在，通过生物信息学方法分析AAAATT基序在四个测序物种中的存在情况，以INPARANOID软件找出测序物种直系同源基因，并找到正选择相关基因，分析四个物种相关基因的AAAATT基序含量区别。其次，两个在进化上十分相近的属具有不同的表型，基因进化也会存在不同。根据PAML软件分析四个测序物种的全部基因组，通过branch-model分析物种间基因是否放松选择的情况，通过branch-site model分析物种间基因正选择位点的情况。经研究发现：A.具有有氧酵解功能Dekkera属的两个物种与呼吸作用相关基因的顺式作用调控原件AAAATT基序在线粒体功能相关基因内有大量缺失，相反的，在不具有有氧酵解Brettanomyces属的两个物种相应的区域却没有缺失现象；B.在Dekkera属中，与有氧酵解途径相关的基因有正选择位点，并且有正选择位点的基因大多编码化学反应通路中限速步骤的酶，限速步骤的酶对有氧酵解速率有很重要的调控作用，其中丙酮酸激酶的正选择位点对该酶的结构和活性有一定影响，反之，在Brettanomyces属相应的位置却没有发生正选择；C.在不能有氧酵解的Brettanomyces属物种中，糖酵解通路某些基因在进化上发生了放松选择，该进化不利于有氧酵解表型的获得，在可以有氧酵解的Dekkera属物种中糖酵解通路中没有发现放松选择的基因，为有氧酵解功能的获得提供了有利条件。经过深入的研究分析较合理的解释有氧酵解表型的适应性进化。 |
| 英文摘要 | In a general way, a major process to generate cellular energy in eukaryotic organisms is respiration, which requires oxygen. According to this, yeasts will degrade sugars to waters, carbon dioxide and ATP components though tricarboxylic acid cycle and oxidative phosphorylation. However, even in the presence of excess oxygen, saccharomyces cerevisiae still not generate ATP for the life of organic entity. Alternatively, saccharomyces yeasts degrade sugars to two-carbon components at cytoplasm, in particular ethanol, which occurs aerobically. This phenotype is called the aerobic fermentation. This characteristic is called the Crabtree effect and is the background for the ' make accumulate consume' life strategy. This brand-new phenotype emerges about 100 million years ago after the whole genome duplication event. It is because of aerobic fermentation that saccharomyces yeasts can out-compete other microorganisms and become a winner. However, Dekkera yeasts that evolved independently of saccharomyces cerevisiae have the brand-new phenotype, yet Brettanomyces yeasts do not have. What is more, Dekkera yeasts do not go through the whole genome duplication event. The reasons why Dekkera yeasts and Brettanomyces yeasts are quite different even they are close to each other on the evolutionary tree are still not clear. Hence, in this research, we hope to understand and explain the reasons why they are so different. Firstly, the AAAATT motif, rapid growth element (RGE), has been studied profoundly before, which found that it responds to fast organism growth, so we analyzed the presence in these four sequenced species. We found homologous genes by INPARANOID software and finally found the rapid growth-associated genes. Secondly, we analyzed the evolution of genes though PAML software. We use branch-model to study whether genes undergone the relaxation of selection or not and branch-site-model to study the rapid evolution of gene sites. Consequently, first of all, we found that the AAAATT motif claimed to be a massive loss in the respiration-associated genes at the fixed position of Dekkera yeasts which can ferment even in the presence of oxygen. On the contrary, the AAAATT motif of Brettanomyces yeasts abounds in relevant position. Next, at Dekkera yeasts, the rapid evolution of gene sites is found in some important genes which are relevant to glycolytic pathway. Finally, at Brettanomyces yeasts, the genes that associate with glycolytic pathway go though the relaxation of selection, which is not beneficial to the acquisition of aerobic ferment. Ultimately we can explain the reasons why the two categories have various characteristic by these researches. |
| 语种 | 中文 |
| 源URL | [http://159.226.149.26:8080/handle/152453/10201]  |
| 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 | 张琳. 德克拉酵母有氧酵解途径的适应性进化研究[D]. 北京. 中国科学院研究生院. 2015. |
入库方式： OAI收割
来源：昆明动物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。