Genomic Interactions between Psyllids and Their Obligately Intracellular Bacteria

描述(申请人提供)：只在其他生物的细胞内生长和繁殖的细菌表现出一致的基因组减少模式。在某些情况下，还原过程是如此极端，以至于细菌缺乏许多被认为对细胞生命至关重要的基因。尽管通常认为这些细菌以某种方式依赖于宿主细胞的遗传机制来抵消其退化基因组的限制，但原核和真核基因组之间这种密切关系的实际机制基础仍不清楚。拟议的研究将利用高通量DNA测序技术的最新进展来表征木虱(昆虫纲：半翅目)与其营养共生体Carsonella之间的基因组相互作用，这是迄今发现的最极端的细菌基因组减少和退化案例之一。这项研究的主要目标是确定宿主基因组在使细菌共生体能够生存和繁殖方面的作用，尽管它们的基因含量严重减少。将对7个Carsonella谱系和一个相关的外群物种的基因组进行测序和分析，以全面确定这些细菌保留的功能能力。此外，还将使用高通量的cDNA测序对宿主基因的表达进行全基因组分析。细菌被限制在昆虫宿主中特定器官的细胞内。因此，宿主基因在含细菌细胞中的表达将与身体其他部位的表达模式进行比较，以确定与卡氏杆菌相关的特异性上调的宿主基因。功能注释和分析将用于评估已识别的宿主基因是否能够取代共生菌基因组中不再编码的关键途径。此外，系统发育分析将确定宿主基因的来源，以确定它们是从先前存在的宿主功能中增选出来的，还是从外来来源(如卡森氏菌或其他细菌谱系)获得的。这项工作将使我们了解细菌进化的极限(即“最小细胞”)，并确定与真核基因组的相互作用如何使细胞内的细菌突破这些极限。这项研究的结果也将与理解作为人类病原体的大量细胞内细菌的基因组功能相关。

DESCRIPTION (provided by applicant): Bacteria that grow and reproduce solely inside the cells of other organisms exhibit a consistent pattern of genome reduction. In some cases, the reductive process is so extreme that the bacteria lack many genes thought to be essential for cellular life. Although it is generally assumed that these bacteria somehow rely on the genetic machinery of their host cell to offset the limitations of their degenerated genomes, the actual mechanistic basis for these intimate relationships between prokaryotic and eukaryotic genomes remains unclear. The proposed research will take advantage of recent advances in high throughput DNA sequencing technology to characterize the genomic interactions between psyllids (Insecta: Hemiptera) and their nutritional symbiont Carsonella, which exhibits one of the most extreme cases of bacterial genome reduction and degradation ever identified. The primary goal of this research is to determine the role of the host genome in enabling the bacterial symbionts to survive and reproduce in spite of their severely reduced gene content. The genomes from 7 Carsonella lineages and a related outgroup species will be sequenced and analyzed to comprehensively determine the functional capabilities retained by these bacteria. In addition, high throughput cDNA sequencing will be used to perform a genome-wide analysis of host gene expression. The bacteria are restricted to the cells of a specific organ in the insect host. Therefore, host gene expression in bacteria-containing cells will be compared to expression patterns in the rest of the body to identify host genes that are specifically upregulated in association with Carsonella. Functional annotation and analysis will be used to assess whether the identified host genes are capable of replacing key pathways that are no longer encoded within the symbiont genome. Furthermore, phylogenetic analysis will identify the origin of the host genes to determine whether they were co-opted from pre-existing host functions or acquired from a foreign source such as Carsonella or another bacterial lineage. This work will inform our understanding of the limits of bacterial evolution (i.e., "the minimal cell") and determine how interactions with eukaryotic genomes may allow intracellular bacteria to break through these limits. The results of this study will also be relevant to understanding the genomic function of the large number of intracellular bacteria that act as human pathogens.