Department of Biotechnology, Delft University of Technology Delft, Netherlands.
Front Microbiol. 2012 Oct 18;3:370. doi: 10.3389/fmicb.2012.00370. eCollection 2012.
A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled. The metabolic model was used to test hypotheses that were formulated based on the experimental results and offers a structured look on the processes that occur in the cell during transition in respiration. The main phenomena that were modeled are the inhibition of the cytochrome c oxidase by nitric oxide (NO) and the (indirect) inhibition of oxygen on the denitrification enzymes. The activation of transcription of nitrite reductase and NO reductase by their respective substrates were hypothesized. The general assumption that nitrite and NO reduction are controlled interdependently to prevent NO accumulation does not hold for A. tumefaciens. The metabolic network model was demonstrated to be a useful tool for unraveling the different factors involved in the complex response of A. tumefaciens to highly dynamic environmental conditions.
基于根癌农杆菌的实验数据，建立了兼性反硝化的代谢网络模型。该模型包括酶水平的动力学调控和酶合成水平的转录调控。本工作的目的是研究调控反硝化途径代谢响应从好氧呼吸向缺氧呼吸转变的关键因素，并找到所建模型中生物过程的参数值。代谢模型用于检验基于实验结果提出的假设，并为细胞在呼吸转变过程中发生的过程提供了结构化的认识。所建模的主要现象是一氧化氮（NO）抑制细胞色素 c 氧化酶和氧气对反硝化酶的（间接）抑制。假设亚硝酸盐还原酶和一氧化氮还原酶的转录分别由各自的底物激活。一般假设亚硝酸盐和 NO 的还原受相互制约以防止 NO 积累，但这对于根癌农杆菌并不成立。代谢网络模型被证明是一种有用的工具，可用于揭示根癌农杆菌对高度动态环境条件的复杂响应中涉及的不同因素。
