Elucidating novel pathways and regulation of nitrogen assimilation in alpha proteobacteria exemplified by the soil organism Paracoccus denitrificans

氮是地球上所有形式的生物生命所必需的关键元素之一，因为它是DNA和蛋白质的基石。因此，所有生物生命形式都必须具有从环境中捕获氮并将其纳入重要细胞成分的机制。这个过程被称为氮同化。处于食物链顶端的生命形式，如人类，从他们摄入和消化的植物和动物中提取的有机氮源中吸收氮。然而，在食物链中较低的一些生命形式，如细菌，可以从简单的无机形式（如氮气、硝酸盐或铵）以及简单的有机形式（如氨基酸）中吸收氮。许多农业土壤含有丰富的硝酸盐，因为农民使用这些土壤来促进高产作物的生产，而土壤的径流反过来又使河流、湖泊和海洋富含硝酸盐。这就提供了一个氮源，可以导致细菌的增殖，细菌可以利用硝酸盐作为氮源进行同化。在农业领域，将硝酸盐转移到土壤微生物的“食物来源”，而不是转移到作物上，这在经济上是浪费的。然而，一些估计表明，这种情况可能正在大规模发生。因此，及时寻求一个学术知识库，从而有可能制定减少这些损失的战略。这需要了解土壤细菌在硝酸盐同化过程中将硝酸盐中的氮转化为细胞氮的分子机制，以及当存在其他氮源时该过程被调节的方法。然而，在某些条件下，细菌对土壤中硝酸盐的代谢具有额外的复杂性。如果土壤变得厌氧，例如通过积水，一些土壤细菌可以开始“呼吸”硝酸盐。从本质上讲，这种硝酸盐呼吸过程是氧呼吸的替代方法，使细菌能够维持生长所需的能量产生。它还消耗了添加到土壤中的昂贵肥料。如果细菌既能吸收硝酸盐又能呼吸硝酸盐呢？许多种类的土壤反硝化细菌确实可以做到这一点，因此为作物提供硝酸盐的可用性提供了双重打击。目前尚不清楚的是，许多土壤反硝化细菌是如何调节硝酸盐同化过程的。参与硝酸盐同化的分子系统与参与硝酸盐呼吸的分子系统在多大程度上重叠。在这个研究项目中，我们将使用一种叫做反硝化副球菌的土壤细菌来解决这些问题。多年来，这种细菌一直是研究硝酸盐呼吸作用的模式生物，它是反硝化过程的一部分，在反硝化过程中，可溶性土壤硝酸盐转化为氮气，然后消失在大气中。这种物种作为一种模式生物的重要性促使美国能源部提供资金，以使其基因组的DNA测序成为可能。这使我们能够识别编码硝酸盐同化系统的基因，我们称之为Nas系统。该Nas系统的研究是本课题研究的重点。

Nitrogen is one of the critical elements that is required for all forms of biological life on Earth because it is a building block for DNA and proteins. All biological life forms must therefore have mechanisms by which they can capture nitrogen from the environment and incorporate it into important cellular components. This process is called NITROGEN ASSIMILATION. Life forms at the top of the food chain, such as Humans, assimilate nitrogen from organic nitrogen sources extracted from the plants and animals that they ingest and digest. However, some life forms lower down in the food chain, such as bacteria, can assimilate nitrogen from simple inorganic forms such as nitrogen gas, nitrate or ammonium as well as from simple organic forms such as amino acids. Many agricultural soils are rich in nitrates as they are applied by farmers to encourage high yielding plant crop production and water run-off from soils is in turn enriching rivers, lakes and oceans in nitrate. This then provides a source of nitrogen that can lead to proliferation of the bacteria that can utilise nitrate as a nitrogen-source for assimilation. In agricultural fields the diversion of nitrate towards a 'food source' for soil microbes, rather than the crops for which it was intended, is economically wasteful. However, some estimates suggest that this may be happening on a large scale. It is then timely to seek an academic knowledge base from which it might be possible to develop strategies to lessen these losses. This requires an understanding of the molecular machinery with which soil bacteria incorporate nitrogen from nitrate into cellular nitrogen in the process of NITRATE ASSIMILATION and also the means by which this process is regulated when other sources of nitrogen are present. However, under certain conditions the metabolism of nitrate in soils by bacteria takes on an added complication. If a soil becomes anaerobic, for example through water logging, some species of soil bacteria can begin to 'breathe' nitrate. Essentially, this NITRATE RESPIRATION process is an alternative to oxygen-respiration enabling the bacteria to sustain energy generation for growth. It also consumes the costly fertilisers added to soils. What then if the bacterium can do both NITRATE ASSIMILATION and NITRATE RESPIRATION? Many species of soil denitrifying bacterium can indeed do just this and so provide what amounts to a double whammy for the availability of nitrate to crops. What is not yet clear many species of soil denitrifying bacteria is how the NITRATE ASSIMILATION process is regulated and.to what extent the molecular systems involved in NITRATE ASSIMILATION overlap with those involved in NITRATE RESPIRATION. In this research programme we will address these questions using a soil bacterium called Paracoccus denitrificans. For many years this species of bacterium has been a model organism for the study of the nitrate respiration as part of a process called denitrification in which the soluble soil nitrate is converted to nitrogen gas and so lost to the atmosphere. The importance of this species as a model organism led to the United States Department of Energy providing the funds to enable the sequencing of the DNA of it's genome. This has allowed us to identify the genes that encode a nitrate assimilation system, which we term the Nas system. The study of this Nas system provides the focus for this research programme.