Characterization of an anaerobic Escherichia coli K-12 cyclic-di-GMP phosphodiesterase

细菌是地球上适应性最强的生物。它们适应不同条件的能力的根本是为特定环境选择和表达最佳基因组合的能力。这通常是由称为转录因子的蛋白质实现的，这些转录因子感知信号分子，然后作用于打开或关闭特定基因。有时，转录因子并不直接感知信号，而是与充当信使的小分子相互作用。在这些情况下，信号对改变细菌细胞中信使分子浓度的代谢过程有影响，然后由转录因子感知。最近在许多细菌中发现了一种称为cyclic-di-GMP的信使分子。循环二GMP信号与细菌的许多重要特性相关，包括移动能力和形成生物膜（附着在表面的细菌群落）的能力。然而，尽管广泛发生的循环二GMP信号通路很少知道他们的工作方式。在这个项目中，我们想更多地了解一种名为YfgF的蛋白质。我们之前的工作已经表明，YfgF是由大肠杆菌在缺氧时产生的。我们还发现，YfgF具有分解环状二GMP的能力，因此应该对由该分子控制的过程（例如运动性和生物膜形成）具有影响。由于对cyclic-di-GMP信号通路知之甚少，我们希望使用YfgF，这得到了关于E.大肠杆菌作为模型细菌，以了解更多关于cyclic-di-GMP如何改变基因表达模式。我们的方法将是分离YfgF蛋白，并研究其催化活性以及这些活性在不同条件下如何变化。我们还将发现哪些基因受到YfgF存在或不存在的影响，然后试图填补感知信号，YfgF活性变化和受调控基因之间的缺失环节。通过这种方式，我们将更多地了解YfgF的工作原理，并了解其他与cyclic-di-GMP相互作用的蛋白质的工作原理。这可能具有重要的意义，因为许多细菌感染都与缺氧生物膜有关。

Bacteria are the most adaptable organisms on the planet. At the root of their ability to adapt to different conditions is the ability to select and express optimal combinations of genes for particular environments. This is generally achieved by proteins known as transcription factors which sense signal molecules and then act to turn specific genes on or off. Sometimes the transcription factor does not sense the signal directly but rather interacts with a small molecule that acts as a messenger. In these cases the signal has an effect on a metabolic process that changes the concentration of the messenger molecule in the bacterial cell, which is then sensed by the transcription factor. Recently a messenger molecule called cyclic-di-GMP has been identified in many bacteria. Cyclic-di-GMP signalling is associated with many important properties of bacteria, including the ability to move and the ability to form biofilms (communities of bacteria attached to surfaces). However, despite the widespread occurrence of cyclic-di-GMP signalling pathways little is known about the way they work. In this project we want to learn more about a protein called YfgF. Our previous work has shown us that YfgF is made by the bacterium Escherichia coli when it is starved of oxygen. We have also discovered that YfgF has the ability to breakdown cyclic-di-GMP and so should have an effect on processes controlled by this molecule, e.g. motility and biofilm formation. Because so little is known about cyclic-di-GMP signalling pathways we want to use YfgF, supported by the enormous amount of information that is known about E. coli as a model bacterium, to learn more about how cyclic-di-GMP alters patterns of gene expression. Our approach will be to isolate the YfgF protein and characterise its catalytic activities and how these change under different conditions. We will also discover which genes are influenced by the presence or absence of YfgF and then attempt to fill in the missing links between the signal perceived, the change in YfgF activity and the genes that are regulated. In this way we will learn more about how YfgF works and also learn some general lessons on how other proteins that interact with cyclic-di-GMP work. This could have important implications because bacteria because many infections are associated with oxygen-starved biofilms.