国际基因工程机器大赛中的生物资源宝库

国际基因工程机器大赛（international Genetically Engineered Machine competition, iGEM）是面向世界范围的大学生科技赛事,该比赛旨在推广合成生物学,各个参赛队伍通过使用原始元件和自己设计的新元件来构建新的生物系统,并在活细胞中表达,令其行使某种既定功能。每年的参赛队伍会设计许多新的生物元件（biological part）,其长期积累为生物系统的构建提供了便利与创新,其本质上也是生物资源不断丰富的体现。本文从生物资源的角度,重点阐述iGEM比赛生物元件库的发展、分类与特点,让更多人了解生物元件的特征,并在基因工程操作中参考使用,推动元件库的扩充与发展。     

动态规划算法对GenoCAD设计结果的优化

GenoCAD(www.genocad.com)是一种基于Web的免费合成生物学设计软件,用它可以进行表达载体及人工基因网络设计。持续点击代表各种合成生物学标准“零件”的图标,以一种语法进行设计,最后就可以得到由数十个功能片段组成的复杂质粒载体。但是在GenoCAD中,每一类的合成生物学标准“零件”数量众多。随着这些标准“零件”的不断开发,其数量也在进一步增加,目前选择合适的“零件”组装成功能性的质粒载体费时费力并且容易发生错误。在进行载体设计的最后阶段,从众多的“零件”中选择合适的往往比较困难。为解决这一问题,本文采用了自然语言处理的统计语言模型,它最初用于自然语言识别,用来估算一组词串成为一个正确语句的概率的大小。本文最后以该模型为基础应用动态规划算法优化质粒载体设计,从众多的选项中找出最优者。利用这一方法可以减少进行生物学实验的冗余操作,从而减少载体构建过程中的花费。     

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

This work puts forward a toolkit that enables the conversion of alkanes by Escherichia coli and presents a proof of principle of its applicability. The toolkit consists of multiple standard interchangeable parts (BioBricks)⁹ addressing the conversion of alkanes, regulation of gene expression and survival in toxic hydrocarbon-rich environments.A three-step pathway for alkane degradation was implemented in E. coli to enable the conversion of medium- and long-chain alkanes to their respective alkanols, alkanals and ultimately alkanoic-acids. The latter were metabolized via the native β-oxidation pathway. To facilitate the oxidation of medium-chain alkanes (C5-C13) and cycloalkanes (C5-C8), four genes (alkB2, rubA3, rubA4and rubB) of the alkane hydroxylase system from Gordonia sp. TF6^8,21 were transformed into E. coli. For the conversion of long-chain alkanes (C15-C36), theladA gene from Geobacillus thermodenitrificans was implemented. For the required further steps of the degradation process, ADH and ALDH (originating from G. thermodenitrificans) were introduced^10,11. The activity was measured by resting cell assays. For each oxidative step, enzyme activity was observed.To optimize the process efficiency, the expression was only induced under low glucose conditions: a substrate-regulated promoter, pCaiF, was used. pCaiF is present in E. coli K12 and regulates the expression of the genes involved in the degradation of non-glucose carbon sources.The last part of the toolkit - targeting survival - was implemented using solvent tolerance genes, PhPFDα and β, both from Pyrococcus horikoshii OT3. Organic solvents can induce cell stress and decreased survivability by negatively affecting protein folding. As chaperones, PhPFDα and β improve the protein folding process e.g. under the presence of alkanes. The expression of these genes led to an improved hydrocarbon tolerance shown by an increased growth rate (up to 50%) in the presences of 10% n-hexane in the culture medium were observed.Summarizing, the results indicate that the toolkit enables E. coli to convert and tolerate hydrocarbons in aqueous environments. As such, it represents an initial step towards a sustainable solution for oil-remediation using a synthetic biology approach.