Plasmid Biology of Rhizobium leguminosarum

根瘤菌是一种在豆科植物（如豌豆、黄豆、扁豆和苜蓿）根部形成固氮根瘤的能力显著的细菌。它们能够使这些植物在不添加含氮合成肥料的情况下生长，而含氮合成肥料的生产和施用在化石燃料消耗和温室气体排放方面成本很高，这使得它们在可持续农业中极其重要。生产更有效和更具竞争力的根瘤菌菌株作为豆科植物的接种剂是生物技术的主要目标。然而，引入的根瘤菌菌株之间的相互作用，以及菌株之间在环境中遗传转移的可能性，还没有得到很好的了解。根瘤菌在细菌中相对不常见，因为它们具有大而复杂的基因组，通常由一条染色体和几个非常大的染色体外遗传元件（称为质粒）组成。质粒往往非常稳定，其中一些表现出介于质粒和染色体之间的特性。本课题将重点研究豆科根瘤菌VF39菌株的质粒，该菌株是豌豆、扁豆、蚕豆、豌豆和各种豆科植物的共生体。重点将放在决定细菌菌株之间通过接合转移的机制和后果的基因，以及质粒编码基因在细菌在土壤、根际和根瘤环境中生存和茁壮成长的能力中的其他作用。这项研究建立在先前实验室研究大型质粒的专业知识，以及细菌基因组序列和感染它的多种噬菌体的可用性的基础上。主要的主题将是：1)详细分析编码在质粒pRleVF39b和pRleVF39a上的新型质粒转移和IV型分泌系统；2)鉴定调节质粒转移基因的因子；3)鉴定质粒转移中涉及的蛋白-蛋白相互作用；4)继续探索质粒编码的分解代谢基因在根瘤菌生态成功中的作用。5)鉴定与限制噬菌体感染有关的质粒编码位点。根瘤菌水平基因转移的信息对于理解未来任何优化菌株（包括基因增强菌株）作为豆科植物接种剂释放的后果至关重要。了解这些属性，包括噬菌体抗性和分解代谢能力，使单个菌株能够在土壤中持续存在，成功定殖根区，并与其他菌株竞争，对于选择和设计更好的接种菌株非常重要。

Rhizobia are bacteria that are notable for their ability to form nitrogen-fixing nodules on the roots of legume plants, such as peas, beans, lentils and alfalfa. Their ability to allow these plants to grow without addition of synthetic nitrogen-containing fertilizers, whose production and application has a high cost in fossil fuel consumption and greenhouse gas emissions, makes them extremely important in sustainable agriculture. Production of more efficient and more competitive rhizobial strains for use as legume inoculants is a major goal in biotechnology. However, the interactions of introduced rhizobial strains, and the potential for genetic transfer between strains in the environment, are not well understood. Rhizobia are relatively unusual among bacteria in that they have large and complex genomes that usually consist of one chromosome and several very large extrachromosomal genetic elements known as plasmids. The plasmids tend to be very stable, and some of them exhibit properties intermediate between those expected of a plasmid and those of a chromosome. This proposal will focus on the plasmids of Rhizobium leguminosarum biovar viciae strain VF39, a symbiont of peas, lentils, faba beans, vetches, and various Lathyrus species. The emphasis will be on the genes that determine the mechanisms and consequences of transfer by conjugation between bacterial strains, and other roles of plasmid-encoded genes in the ability of the bacterium to survive and thrive in the soil, rhizosphere, and nodule environments. The research builds on previous expertise in the lab studying large plasmids, and the availability of genome sequences of the bacterium and multiple bacteriophages that infect it. The main themes will be 1) detailed analysis of the novel plasmid transfer and type IV secretion systems encoded on plasmids pRleVF39b and pRleVF39a and 2) identification of factors regulating plasmid transfer genes 3) identification of the protein-protein interactions involved in plasmid transfer 4) continued exploration of the role of plasmid-encoded catabolic genes in the ecological success of rhizobia, and 5) identification of plasmid-encoded loci that are involved in limiting phage infections. Information on horizontal gene transfer in rhizobia is vital to understanding the consequences of release of any future optimized strains (included genetically enhanced strains) as legume inoculants. Understanding the attributes, including phage resistance and catabolic capacity, that allow individual strains to persist in soil, successfully colonize the root region, and compete with other strains, is of great importance in selecting and designing better inoculant strains.