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从一个生物体传递到另一个生物体时，不需要亲本向其后代提供遗传物质，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有重大贡献。例如，HGT是细菌对抗生素耐药这一严重问题的根源。HGT的有益方面包括细菌解毒污染物的能力。HGT在使细菌产生包括燃料在内的有用化合物的应用方面也有着令人兴奋的前景。这个项目的重点是外源DNA转移到新的细菌宿主后的命运。一个新的实验系统将促进HGT的研究，以提高对遗传物质如何在不同环境下起作用和适应的理解。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。这组科学家在培训各级学生以及加强科学界的多样性和包容性（包括培训残疾学生）方面有着成功的历史。这个项目将用于加强这些活动。此外，该项目还包括与国家可再生能源实验室的研究人员合作，开发生物能源生产中的应用。培训机会将使学生能够参观并在这个国家实验室进行研究。一种加速实验进化的方法将被用来追踪外源基因插入一种土壤细菌——贝氏不动杆菌（Acinetobacter baylyi）的染色体后的命运。这些基因将在串联阵列中扩增，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提供的一种微弱但有益的功能。当突变在扩增子内累积时，不太适合的基因拷贝将丢失，而更适合的等位基因可能通过选择而增加。本项目利用基因扩增加速进化过程，使基因分化成为实验研究的重点。进一步的研究将改变外源DNA的遗传含量，改变同义密码子的使用，G+C含量和染色体位置。这样就有可能测试这些改变是如何影响基因的改良和保留的。菌株将在受控环境下连续培养。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.