SG: Origin and Evolutionary History of Gene Transfer Agents in Marine Bacteria

基因交换是一个重要的进化过程，在微生物种群中频繁发生，使它们能够快速适应不断变化的环境条件。在细菌中获得对抗生素的抗药性是这种基因交换影响社会的众多方式之一。由于对它们的生存有潜在的巨大好处，细菌已经开发了大量的基因交易机制。一种神秘的基因交换机制涉及穿梭包装在类似细菌病毒的颗粒(所谓的基因转移剂)中的基因。这引发了许多关于这一机制的起源和功能的问题。以这种方式交换基因有多大好处？基因转移剂是否代表被细菌“驯化”的前病毒？细菌病毒是地球上数量最多的生物。这些病毒中有很多真的是基因转移剂吗？对这些问题的回答将促进我们对基因交换如何有助于细菌适应的理解。由于越来越多的证据表明，基因转移剂对整个微生物种群而不是对单个细胞有用，该项目还将促进我们对合作的起源和维持的了解，这是进化生物学的一个长期谜团。由于细菌和病毒是包括人体在内的所有地球环境中的关键参与者，该项目将使科学界和更广泛的社会受益。达特茅斯学院的研究人员将通过对海洋细菌的遗传信息进行计算分析来研究上述问题。这些细菌是地球营养循环和海洋宜居性的关键参与者。编码基因转移剂(GTA)的基因将从细菌基因组和海洋元基因组中识别和提取。然后，这些GTA将被严格地与细菌病毒的相似基因进行比较。这种比较将评估GTA与病毒的进化关系，以及细菌宿主对它们的基因施加的选择压力。鉴于最近发现的GTA系统及其与实际病毒的相似之处，现有基因组序列中的许多真实GTA可能被错误地注释为整合细菌病毒。为了解决这一重要问题，研究人员将开发一种新的生物信息学方法，旨在成功地区分基因转移剂和病毒转移剂。最终，这一跨学科项目将有助于更好地了解海洋和全球元素循环，以及推动海洋和其他环境中细菌种群的适应性进化过程。该项目中产生的数据集和计算机程序将与科学界共享。

Exchange of genes is an important evolutionary process that occurs at high frequency within microbial populations, allowing them to adapt quickly to changing environmental conditions. Acquisition of resistance to antibiotics in bacteria is one of the many ways in which such gene swapping impacts society. Because of the potentially tremendous benefit to their survival, bacteria have developed a large arsenal of mechanisms for gene trade. One enigmatic gene exchange mechanism involves shuttling genes packaged in particles (so-called Gene Transfer Agents) that resemble bacterial viruses. This raises many questions about the origin and functionality of this mechanism. How beneficial is it to exchange genes this way? Do Gene Transfer Agents represent former viruses that were "domesticated" by bacteria? Bacterial viruses are numerically the most abundant organisms on Earth. Could many of these viruses in fact be Gene Transfer Agents? Answers to these questions will advance our understanding of how gene exchange contributes to bacterial adaptation. Because of accumulating evidence that Gene Transfer Agents are of use to a microbial population as a whole rather than to an individual cell, this project will also advance our knowledge on the origin and maintenance of cooperation, a long-standing mystery of evolutionary biology. Since bacteria and viruses are key players in all Earth environments, including human bodies, the project will benefit both the scientific community and broader society. Researchers at Dartmouth College will investigate the above questions via computational analyses of genetic information from marine bacteria. Those bacteria are key players in Earth's nutrient cycling and ocean habitability. Genes encoding Gene Transfer Agents (GTAs) will be identified and extracted from bacterial genomes and oceanic metagenomes. These GTAs will then be rigorously compared to similar genes from bacterial viruses. The comparison will assess the GTA's evolutionary relationship to viruses and the selective pressure exerted on their genes by bacterial hosts. Given the recent discovery of the GTA system and its resemblance to actual viruses, many true GTAs in available genomic sequences could be mistakenly annotated as integrated bacterial viruses. To address this important issue, the researchers will develop a novel bioinformatic method that aims to successfully distinguish Gene Transfer Agents from their viral counterparts. Ultimately, this cross-disciplinary project will contribute to better understanding of oceanic and global elemental cycles and of adaptive evolutionary processes that drive bacterial populations in marine and other environments. The data sets and computer programs generated in this project will be shared with scientific community.