sRNAs: Critical yet overlooked regulators of bacterial denitrification

面对环境中氧气的短缺，许多细菌物种能够转而使用硝酸盐，而不是氧气来维持生命。反硝化作用允许细菌将硝酸盐转化为气态产物、一氧化氮(NO)、一氧化二氮(N2O)，最后转化为可释放到大气中的氮素(N2)。这种反硝化过程可以在农业土壤中进行，在那里添加富氮化肥来刺激植物生长也可以刺激细菌生命。然而，这种细菌生存策略具有重大的环境后果，因为有时N2O-一种会破坏臭氧层的强有力的温室气体-被释放到大气中，而不是无害的N2。当讨论温室气体排放时，普通公众敏锐地意识到二氧化碳和甲烷带来的问题。然而，N2O的排放也应该引起公众和政治的关注。N2O可能最为人所知的是牙科麻醉剂“笑气”。在过去的100年里，大气中的N2O增加了20%以上，而且这种大气负荷每年都在增加。由于人口增长以及对食品、动物饲料和能源的需求，以及工业过程和废水处理来源的增加，N2O排放量预计将继续同比增加。尽管大气中N2O的水平只是二氧化碳的一小部分，但N2O的全球变暖潜力是二氧化碳的300倍。由于它的大气寿命超过100年，今天产生的N2O将影响我们的曾孙所经历的气候，因此，现在就制定战略来减缓这些排放是很重要的。反硝化细菌从硝酸盐产生N2O或N2的途径是从分子水平上了解的，将硝酸盐转化为亚硝酸盐(硝酸盐还原酶)和亚硝酸盐转化为一氧化氮(亚硝酸盐还原酶)的蛋白质的结构是已知的。将N2O分解为惰性氮气的酶是一种名为一氧化二氮还原酶或NOZ的蛋白质。它是地球上主要的酶，负责破坏强大的N2O温室气体。如果没有NOZ，大气中的N2O水平甚至会比现在更高。然而，由于有时环境中的N2O是由反硝化细菌排放的，所以没有产生NOZ，我们想知道为什么。对于这些反硝化蛋白在环境中如何开启/关闭的理解还不是很清楚，我们的团队一直专注于解决这一重要的全球挑战。这需要对模型生物进行基础研究，因为它允许我们在受控的实验室环境中操纵它们，解决环境因素和遗传开关调节模型反硝化细菌中N2O排放的机制。我们的模式生物是细菌Paracoccus denitriicans，它存在于海洋和陆地环境中，在生物化学和遗传上都很容易驯化，在实验室的反硝化条件下生长良好。特别是，这项研究将集中在sRNA调控的新途径上。SRNA是细菌产生的小开关，使它们能够对环境的变化做出快速反应，并打开/关闭基因。我们的团队最近发现sRNA对控制反硝化和N2O排放至关重要，并描述了其中一种sRNA的工作机制。我们现在需要了解其他调节N2O生产和消费的sRNA如何使用我们已有的技术来发挥作用，这将使我们能够解析控制细菌N2O排放的核心sRNA。这些信息随后可以用来通过操纵这些开关来控制环境中的N2O，可能是通过向土壤施加的化肥的成分。

Faced with a shortage of oxygen in their environment many bacterial species are capable of switching to using nitrate, rather than oxygen to support life. Denitrification, allows bacteria to convert nitrate to gaseous products, nitric oxide (NO), nitrous oxide (N2O) and finally to dinitrogen (N2) that can be released into the atmosphere. This denitrification process can takes place in agricultural soils where nitrogen-rich fertilisers added to stimulate plant growth can also stimulate bacterial life. However, this bacterial survival strategy has significant environmental consequences as sometimes N2O a potent greenhouse gas that can damage the ozone layer is released into the atmosphere rather than harmless N2.When discussing greenhouse gas emissions, the general public are acutely aware of the problems posed by carbon dioxide and methane. However, emissions of N2O, perhaps best known as the dental anaesthetic "laughing gas", should also be a cause for public and political concern. Over the last 100 years, N2O in the atmosphere has increased by more than 20% and this atmospheric loading is increasing each year. N2O emissions are expected to continue to increase year on year as a result of the growing population and demand for food, animal feed, and energy, as well as an increase in sources from industrial processes and wastewater treatment. Although the atmospheric levels of N2O are only a fraction of that of CO2, N2O has a 300-fold greater global warming potential. Since it has an atmospheric lifetime of more than 100 years the N2O produced today will influence the climate experienced by our great-great grandchildren therefore it is important to devise strategies to mitigate these releases now. The pathways by which denitrifying bacteria produce N2O or N2 from nitrate are understood from a molecular level with structures of the proteins that convert nitrate to nitrite (nitrate reductases) and nitrite to nitric oxide (nitrite reductases) being known. The enzyme that breaks down N2O to inert N2 is a protein called nitrous oxide reductase or NosZ. It is the major enzyme on the planet that is responsible for the destruction of the potent N2O greenhouse gas. Without NosZ the atmospheric levels of N2O would be even greater than they currently are. However, as sometimes in the environment N2O is being emitted by denitrifying bacteria, NosZ is not being produced and we want to know why. The understanding of how these denitrification proteins are switched on/off in the environment is not well understood and our team have been focusing on addressing this important global challenge. This requires fundamental studies on model organisms as it allows us to manipulate them in controlled laboratory environments, addressing the mechanisms by which environmental factors and genetic switches regulate N2O emissions in model denitrifying bacteria. Our model organism is the bacteria Paracoccus denitrificans, which is found in marine and terrestrial environments, is biochemically and genetically tractable and grows well under denitrifying conditions in the laboratory. In particular, this study will focus on new pathways of regulation by sRNA. sRNAs are small switches produced by bacteria that allow them to quickly respond to changes in their environments and switch genes on/off. Our team have recently discovered sRNAs are critical for controlling denitrification and N2O emissions and have characterised the mechanism of how one of these sRNA work. We now need to understand how other sRNAs that regulate production and consumption of N2O function using our established techniques which will allow us to resolve the core sRNAs that control bacterial N2O emissions. This information can then subsequently be used to control N2O in the environment through manipulation of these switches, perhaps through the composition of fertilizers applied to soils.