EAGER: Exploratory Research in Accordion-Style Genome Dynamics

智力价值在所有生物体中，都会发生动态的遗传变化，即染色体的片段相对于周围区域的复制增加或减少。基因组的这种扩张和收缩被称为“手风琴式的动力”，可以在适应和进化中发挥关键作用。尽管这一过程具有许多重要的生物学意义，但很难进行研究。识别特定基因改变的困难源于染色体改变的瞬时性和随机性，以及发生在种群不同细胞中的事件的变异性。这个项目将利用一种土壤细菌--贝利不动杆菌ADP1的特殊特性，以促进实验研究。这种细菌自然转化和重组的高效率使设计和工程菌株成为可能，在这些菌株中，大多数细胞的同一染色体片段的多个拷贝以高拷贝串联阵列排列在彼此相邻的位置。然后，这些工程菌株可以作为实验室模型，研究拷贝数变化对适应和进化的贡献的分子细节。首先，特定的基因将从基因组中删除。下一步，其他基因将被正确定位，以便如果基因组扩张将它们放置在串联阵列中，它们可以取代缺失的基因。在重组后的细菌群体中，具有相同“扩展”版本的染色体的大量细胞增加了进化过程的机会，以优化新的遗传和酶活性。重组后的细菌群体还放大了在实验过程中可以检测到的信号，这样就可以更容易地观察到特定的基因变化。这项研究将包括测试特定的基因组，以证明基因组扩张如预测的那样发生。建立串联阵列后，将有可能改变细菌的生长条件，以便以高度敏感和可重复的方式监测和测试遗传进化。开发一种进行定向遗传扩展的系统的优势还包括促进细菌生产用于生物技术的重要化合物，并产生具有有用活性的新酶。广泛影响染色体重排的操作和分析将有助于科学界利用大规模DNA序列数据的努力。此外，佐治亚大学正在进行的项目将与这一项目相衔接，以帮助扩大参与和增加多样性。这样的项目包括NSF支持的本科生研究经验(REU)原核生物学站点项目。对土壤细菌贝氏不动杆菌ADP1的研究也被纳入一门本科实验室课程，该课程使用真实的研究项目，让学生参与主动学习和科学参与。高中生、本科生和研究生将参加这个项目，他们将接受遗传学、生物化学和生物信息学的多学科培训。

Intellectual MeritIn all organisms dynamic genetic changes can occur in which segments of the chromosome increase or decrease in copy relative to surrounding regions. Such expansion and contraction of the genome, termed "accordion-style dynamics," can play a critical role in adaptation and evolution. Although the process has many important biological implications, it is difficult to study. The difficulty in identifying specific genetic alteration stems from the transient and stochastic nature of the chromosomal changes and the variability of the events that occur in different cells of the population. This project will exploit special features of a soil bacterium, Acinetobacter baylyi ADP1, to facilitate experimental investigation. The high efficiency of natural transformation and recombination in this bacterium make it possible to design and engineer strains in which most cells of the population have multiple copies of the same segment of the chromosome arranged adjacent to each other in a high copy tandem array. These engineered strains can then serve as laboratory models to investigate the molecular details of the contribution of copy number change in adaptation and evolution. First, specific genes will be deleted from the genome. Next, other genes will be properly positioned such that they can substitute for the missing genes if the genome expands to place them in tandem arrays. In the restructured bacterial population, the large number of cells that have the same "expanded" version of the chromosome increase the opportunity for evolutionary processes to optimize new genetic and enzymatic activities. The restructured bacterial population also amplifies the signals that can be detected during experimentation such that the specific genetic changes can be much more readily observed. This research will involve testing specific gene sets to demonstrate that genomic expansion occurs as predicted. Having established the tandem arrays, it will be possible to vary the growth conditions for the bacteria to allow genetic evolution to be monitored and tested in a highly sensitive and reproducible manner. The advantages of developing a system that undergoes directed genetic expansion also include facilitating the bacterial production of important compounds for biotechnology and generating new enzymes with useful activities.Broader ImpactsThe manipulation and analysis of chromosomal rearrangements will contribute to efforts in the scientific community to take advantage of large scale DNA sequence data. In addition, ongoing programs at the University of Georgia will dovetail with this project to help broaden participation and increase diversity. Such programs include an NSF-supported Research Experiences for Undergraduate (REU) site program in prokaryotic biology. Research on the soil bacterium Acinetobacter baylyi ADP1 is also being integrated into an undergraduate lab course that uses authentic research projects to involve students in active learning and scientific engagement. High school students, undergraduates, and graduate students will participate in this project, and they will receive multidisciplinary training in genetics, biochemistry, and bioinformatics.