Fate of foreign genes in experimental evolution

环境中细菌之间的DNA转移具有重要的后果。当DNA以一种不涉及父母向其后代提供遗传物质的方式从一个有机体传递到另一个有机体时，这个过程被称为水平基因转移(HGT)。这种类型的遗传对人类健康、生物技术和进化的基本机制做出了重大贡献。例如，HGT突出了细菌对抗生素耐药的严重问题。HGT的有益方面包括细菌对污染物的解毒能力。HGT还具有令人兴奋的前景，使细菌能够产生有用的化合物，包括燃料。这个项目关注的是外来DNA被转移到新的细菌宿主后的命运。一个新的实验系统将促进对HGT的研究，以提高对遗传物质如何在不同环境中发挥作用和适应的理解。这些研究将用于开发和改进加速生物技术应用成功的技术。研究人员有在各级培训学生以及在科学界加强多样性和包容性方面的成功历史，包括对残疾学生的培训。该项目将用于加强此类活动。此外，该项目还涉及与国家可再生能源实验室的研究人员合作，开发在生物能源生产中的应用。培训机会将使学生能够参观这个国家实验室并进行研究。将使用一种加速实验进化的方法来跟踪外来基因插入土壤细菌贝利不动杆菌染色体后的命运。这些基因将在串联阵列中被扩增，以使重复片段(扩增子)的拷贝数自发增加或减少。这种扩张和收缩的过程允许对新获得的基因表达的基本控制的进化。这个实验系统模拟了HGT和基因扩增之间的自然相互作用。基因剂量可以增加外源DNA提供的微弱但有益的功能。当扩增片段发生突变时，不太适合的基因拷贝将会丢失，而更适合的等位基因可能会通过选择而增加。该项目利用基因扩增来加速进化过程，从而使基因发散成为实验研究的重点。其他研究将改变外来DNA的遗传含量，改变同义密码子的使用、GC含量和染色体位置。然后就可以测试这些改变如何影响基因的改善和保留。菌株将在受控环境中连续培养生长。将分析拷贝数、mRNA、蛋白质和DNA序列的变化。

The transfer of DNA between bacteria in the environment has important consequences. When DNA is passed from one organism to another in a fashion that does not involve a parent providing genetic material to its offspring, the process is called horizontal gene transfer (HGT). This type of inheritance contributes significantly to human health, biotechnology, and fundamental mechanisms of evolution. For example, HGT underlies the serious problem of bacterial resistance to antibiotics. Beneficial aspects of HGT include the ability of bacteria to detoxify pollutants. HGT also holds exciting promise for applications that enable bacteria to produce useful compounds, including fuels. This project focuses on the fate of foreign DNA after it has been transferred to a new bacterial host. A novel experimental system will facilitate investigations of HGT to improve understanding of how genetic material functions and adapts in diverse contexts. These studies will be used to develop and improve techniques that accelerate the success of biotechnology applications. The researchers have a successful history of training students at all levels and in enhancing diversity and inclusiveness in the scientific community, including training of students with disabilities. This project will be used to augment such activities. Furthermore, this project involves collaborations with researchers at the National Renewable Energy Lab to develop applications in bioenergy production. Training opportunities will enable students to visit and conduct research at this national laboratory.An accelerated approach to experimental evolution will be used to follow the fate of foreign genes after their insertion into the chromosome of a soil bacterium, Acinetobacter baylyi. These genes will be amplified in a tandem array to enable copy number of the repeated segment (amplicon) to increase or decrease spontaneously. This process of expansion and contraction allows evolution of rudimentary control of the expression of newly acquired genes. This experimental system mimics the natural interplay between HGT and gene amplification. Gene dosage can increase a weak but beneficial function provided by foreign DNA. As mutations accrue within the amplicons, gene copies that are less fit will be lost and alleles that are more fit may increase via selection. This project exploits gene amplification to accelerate the evolutionary process so that gene divergence can be the focus of experimental study. Additional studies will alter the genetic content of the foreign DNA, changing synonymous codon usage, G+C content and chromosomal location. It will then be possible to test how these alterations affect the amelioration and retention of the genes. Strains will be grown under continuous culture in controlled environments. Copy number, mRNA, protein and DNA sequence changes will be analyzed.