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

SG：海洋细菌基因转移剂的起源和进化史

• 批准号: 1551674
• 负责人: Olga Zhaxybayeva
• 金额: $ 15万
• 依托单位: Dartmouth College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2019-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1551674&HistoricalAwards=false
• 关键词: SG; Origin; Evolutionary; History; Gene

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.

基因的交换是一个重要的进化过程，它在微生物种群内的高频出现，使它们能够迅速适应不断变化的环境条件。获得细菌中对抗生素的抗药性是这种基因交换会影响社会的众多方式之一。由于可能对其生存具有巨大的好处，细菌已经开发了大量的基因贸易机制。一种神秘的基因交换机制涉及包装在类似细菌病毒的颗粒（所谓基因转移剂）中的穿梭基因。这就引发了许多有关该机制的起源和功能的问题。以这种方式交换基因有多有益？基因转移剂是否代表了被细菌“驯化”的以前的病毒？ 细菌病毒在数值上是地球上最丰富的生物。这些病毒中的许多实际上可以是基因转移剂吗？这些问题的答案将提高我们对基因交换如何有助于细菌适应的理解。由于积累的证据表明，基因转移剂全部用于微生物种群而不是单个细胞，因此该项目还将提高我们对合作起源和维持合作的了解，这是进化生物学的长期之谜。由于细菌和病毒是包括人体在内的所有地球环境中的主要参与者，因此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调查上述问题。这些细菌是地球营养循环和海洋可居住性的关键参与者。编码基因转移剂（GTA）的基因将从细菌基因组和海洋宏基因组中鉴定并提取。然后，这些GTA将与细菌病毒的类似基因进行严格的比较。该比较将评估GTA与病毒的进化关系以及细菌宿主对其基因施加的选择性压力。 鉴于GTA系统的最新发现及其与实际病毒的相似之处，可以将许多真实的基因组序列中的许多真正的GTA误认为是集成的细菌病毒。为了解决这一重要问题，研究人员将开发一种新型的生物信息学方法，旨在成功区分基因转移剂与病毒对应物。最终，这个跨学科项目将有助于更好地了解海洋和全球元素周期以及适应性进化过程，这些过程驱动海洋和其他环境中的细菌种群。该项目中生成的数据集和计算机程序将与科学界共享。