Host of environmental interactions of members of the rhizobiales order of alphaproteobacteria

在过去的十年里，细菌基因组全序列的测定从根本上改变了微生物学的研究。现在很多工作都集中在识别新发现的基因和转录调控途径的功能上。具有良好特性的紫花苜蓿中华根瘤菌是这类研究的领先模式系统。它形成了紫花苜蓿根瘤，在根瘤中，大气中的氮被转化为氨，对植物有利，从而减轻了对氮肥的需求。紫花苜蓿细胞使用各种碳基质进行生长；这种杂食性动物可能有助于在土壤和植物根部附近生存。在被称为短链脱氢酶/还原酶(SDR)的78个成员的蛋白质家族中，发现了几个对分解能力有贡献的候选蛋白质。在以前的工作中，我们已经对紫花苜蓿基因组中所有编码SDR的基因进行了突变，并通过随后的表型分析确定了其中几个实际上是利用特定碳源和与紫花苜蓿有效共生所必需的。我们现在将重点分析每个SDR编码基因周围的基因突变，试图了解其中涉及的机制。我们还在研究一个关键的转录调控系统，该系统是有效共生所必需的，并在与植物、动物和人类形成共生或致病相互作用的相关细菌中保守。我们开发了一种新的、简单的DNA结合TRAP分析来确定潜在的转录因子结合位点。我们将利用这个实验来确定这个转录调控系统的靶点，然后继续研究这些靶基因的功能，并评估它们参与共生的情况。最后，我们正在开发另一种细菌，人的Ochrobactrum，作为宿主病原体相互作用的模式系统。虽然这种生物与人类病原体布鲁氏菌关系密切，本身就是一种投机的人类病原体，但它似乎也能够在土壤和根际环境中拥有更多样的生活方式。使用比较基因组分析，然后是实验分析，我们将研究共享机制。

In the past decade, the determination of the complete sequences of bacterial genomes has radically altered microbiological research. Much effort is now directed towards the identification of the functions of newly discovered genes and transcriptional regulation pathways. The well-characterized bacterium Sinorhizobium meliloti is a leading model system for this type of research. It forms alfalfa root nodules in which atmospheric nitrogen is converted to ammonia for the benefit of the plant, relieving the need for nitrogen fertilizers. S. meliloti cells use a variety of carbon substrates for growth; this omnivory probably contributes to ability to survive in the soil and near the plant roots. Several candidates for contribution to the catabolic capacity are found within the 78-member family of proteins called short chain dehydrogenases / reductases (SDR). In previous work, we have made mutations in all SDR-encoding genes in the S. meliloti genome, and through subsequent phenotypic analysis determined that several of them are in fact required for utilization of specific carbon sources, and for effective symbiosis with alfalfa. We will now focus on mutational analysis of genes surrounding each of the SDR-encoding genes, in an attempt to understand the mechanisms involved. We are also studying a key transcriptional regulatory system that is required for effective symbiosis, and is conserved in related bacteria that form symbiotic or pathogenic interactions with plants, animals and humans. We have developed a novel and simple DNA binding trap assay to identify potential transcriptional factor binding sites. We will use this assay to identify the targets for this transcriptional regulatory system, and then go on to study the functions of the target genes and evaluate their involvement in symbiosis. Finally, we are developing another bacterium, Ochrobactrum anthropi, as a model system for host pathogen interaction. Although this organism is quite closely related to the human pathogen Brucella, and is itself an opportunistic human pathogen, it also appears to be capable of a more versatile lifestyle in the soil and rhizosphere. Using comparative genomic analysis, followed by experimental analysis, we will investigate shared mechanisms.