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。根瘤菌在细菌中是不寻常的，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和3841菌株的质粒，这两种菌株都有6个质粒，可以在豌豆、扁豆、蚕豆、豌豆和各种豆科植物上形成根瘤。重点将放在决定细菌菌株之间结合转移的机制和后果的基因，以及质粒编码基因在碳分解代谢和根际竞争中的作用。这项研究建立在实验室以前研究大型质粒的专业知识和两种菌株的基因组序列的可用性的基础上。两个主要主题将是1)详细分析pRleVF39b、pRleVF39a和pRL7JI质粒上编码的新型质粒转移和IV型分泌系统；2)分析两种菌株基因组中存在的两种不同的、交替的、质粒编码的利比醇运输和分解代谢系统。主题1将确定质粒转移所需的所有基因，并确定调节质粒转移的途径。主题2将研究利比醇分解代谢在根际定植和根瘤感染中的作用，并确定两种降解途径在利比醇代谢中的作用。本文将研究两条平行路径存在的可能原因。这项研究将为了解农业上重要细菌的多样性、生存和竞争以及水平基因转移提供重要信息。这些信息对设计和应用优质豆科植物接种菌株，实现作物可持续生产具有重要的参考价值。***************

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, 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 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 strains VF39 and 3841, both of which have six plasmids and can form nodules on 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 on the role of plasmid-encoded genes in carbon catabolism and rhizosphere competition. The research builds on previous expertise in the lab studying large plasmids, and the availability of genome sequences for both strains. The two main themes will be 1) detailed analysis of the novel plasmid transfer and type IV secretion systems encoded on plasmids pRleVF39b, pRleVF39a and pRL7JI and 2) analysis of the two distinct, alternate, plasmid-encoded systems for ribitol transport and catabolism that are present in the genomes of both strains. Theme 1 will identify all genes required for transfer of the plasmids, and identify the pathways regulating plasmid transfer. Theme 2 will study the role of ribitol catabolism in rhizosphere colonization and nodule infection, and will determine the contributions each of the two degradation pathways makes in ribitol metabolism. The possible reasons for the existence of two parallel pathways will be investigated.This research should provide important information about diversity, survival and competition, and horizontal gene transfer in an agriculturally important bacterium. This information could be very valuable for the design and application of superior legume inoculant strains for use in sustainable crop production. ***************