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

在过去的十年中，细菌基因组完整序列的确定从根本上改变了微生物学研究。现在很多的努力都是针对鉴定新发现的基因和转录调控途径的功能。具有良好特征的梅利洛蒂Sinorhizobium meliloti细菌是这类研究的主要模型系统。它形成苜蓿根瘤，在根瘤中，大气中的氮转化为氨，对植物有益，减轻了对氮肥的需求。S. meliloti细胞利用多种碳基质进行生长；这种杂食性可能有助于它们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）的蛋白质家族中发现了几个对分解代谢能力有贡献的候选蛋白。在之前的工作中，我们在S. meliloti基因组中对所有sdr编码基因进行了突变，并通过随后的表型分析确定其中几个基因实际上是利用特定碳源和与苜蓿有效共生所必需的。我们现在将重点放在对每个sdr编码基因周围基因的突变分析上，试图了解其中的机制。我们还在研究有效共生所需的关键转录调控系统，该系统在与植物、动物和人类形成共生或致病相互作用的相关细菌中保守。我们已经开发了一种新的和简单的DNA结合陷阱测定，以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目标，然后继续研究目标基因的功能，并评估它们在共生中的作用。最后，我们正在开发另一种细菌，人类Ochrobactrum anthropi，作为宿主病原体相互作用的模型系统。虽然这种生物与人类病原体布鲁氏菌非常密切相关，并且本身是一种机会性人类病原体，但它似乎也能够在土壤和根际中以更多样化的方式生活。通过比较基因组分析和实验分析，我们将探讨共同机制。

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.