sRNAs: Critical yet overlooked regulators of bacterial denitrification

面对环境中氧气的短缺，许多细菌物种能够切换到使用硝酸盐，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），最后转化为可以释放到大气中的二氮（N2）。这种反硝化过程可以发生在农业土壤中，在那里，为了刺激植物生长而添加的富氮肥料也可以刺激细菌的生命。然而，这种细菌生存策略具有显著的环境后果，因为有时N2O（一种可以破坏臭氧层的强效温室气体）而不是无害的N2被释放到大气中。当讨论温室气体排放时，公众敏锐地意识到二氧化碳和甲烷所带来的问题。然而，N2O的排放，也许最为人所知的是牙科麻醉剂的“笑气”，也应该引起公众和政治关注。在过去的100年里，大气中的N2O增加了20%以上，并且每年都在增加。由于人口和对食品、动物饲料和能源的需求不断增长，以及工业过程和废水处理来源的增加，N2O排放量预计将继续逐年增加。虽然大气中N2O的含量只是CO2的一小部分，但N2O的全球变暖潜能值要高出300倍。由于它在大气中的寿命超过100年，今天产生的N2O将影响我们的曾曾孙经历的气候，因此现在制定战略来减少这些排放是很重要的。从分子水平理解硝化细菌从硝酸盐产生N2O或N2的途径，其中已知将硝酸盐转化为亚硝酸盐（硝酸盐还原酶）和将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。将N2O分解为惰性N2的酶是一种称为一氧化二氮还原酶或NosZ的蛋白质。它是地球上负责破坏强效N2O温室气体的主要酶。如果没有NosZ，大气中的N2 O水平将比目前更高。然而，由于环境中有时N2O是由细菌释放的，NosZ并没有产生，我们想知道为什么。对这些反硝化蛋白在环境中如何打开/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。这需要对模式生物进行基础研究，因为它使我们能够在受控的实验室环境中操纵它们，解决环境因素和基因开关调节模式细菌中N2O排放的机制。我们的模式生物是海洋和陆地环境中发现的细菌Paracoccus peculficans，在生化和遗传上易于处理，在实验室的冷冻条件下生长良好。特别是，这项研究将重点关注sRNA调控的新途径。sRNA是细菌产生的小开关，使它们能够快速响应环境的变化并打开/关闭基因。我们的团队最近发现sRNA对于控制反硝化和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产生和消耗的sRNA是如何使用我们已建立的技术发挥作用的，这将使我们能够解决控制细菌N2O排放的核心sRNA。这些信息随后可用于通过操纵这些开关来控制环境中的N2O，也许是通过施用到土壤中的肥料的组成。

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.