Construction of a genome scale metabolic model of Mycobacterium tuberculosis to investigate growth-regulated modulation of metabolism.

构建结核分枝杆菌基因组规模的代谢模型，以研究代谢的生长调节。

• 批准号: BB/D007208/1
• 负责人: Johnjoe McFadden
• 金额: $ 55.53万
• 依托单位: University of Surrey
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FD007208%2F1
• 关键词: Construction; genome; scale; metabolic; model

The TB bacillus is an important pathogen of man and animals that kills about three million people each year. This proposal is to develop a virtual model of the BCG vaccine strain of the TB bacillus in a computer. The model will provide important insight into how this pathogen grows and replicates. The model may also be used to perform virtual experiments that would be very hard or impossible to perform in the real world. For instance, it is difficult to study the behaviour of the TB bacillus when it is growing inside patient's lungs. But if we can identify the metabolic pathways that are active then we can perform easily virtual experiments that will, for instance, investigate how the bacillus will respond to a new antibiotic whilst it is living in the patient's lungs. The virtual TB may also be used to screen new compounds for activity against the TB bacillus: the effect of various antibiotics can be tested in the virtual TB cell far more quickly than with live cells (and with no possibility of the experimenter catching TB). But probably most importantly, the virtual TB cell can be used to invent new antibiotics, by identifying pathways, or groups of pathways, that are essential for growth. This model will first be built using DNA sequence data from the genome. However, to make the virtual cell more realistic, we must incorporate biological data. We will therefore grow the real life organism (actually the vaccine strain of the TB bacillus) in highly defined conditions in the laboratory and perform chemical analysis of what goes in and what comes out of the cell. A remarkable mathematical technique, known as metabolic flux analysis, can then be used to estimate the flux of metabolites through each central metabolism pathway inside the cell. This information will be incorporated into the virtual cell to make its behaviour correspond more closely with the biological organism. The next stage of the project is testing our virtual cell. To do this we will identify which pathways are essential in the virtual cell and then inactivate those pathways in living cells. We will then see if the growth (or absence of growth) of the real life cells matches the predictions of the model. These tests will be used to refine and improve the model that may thereafter be used in drug development.

结核杆菌是人类和动物的一种重要病原体，每年造成约300万人死亡。本课题拟在计算机上建立结核杆菌卡介苗株的虚拟模型。该模型将为了解这种病原体如何生长和复制提供重要的见解。该模型还可用于执行在现实世界中很难或不可能执行的虚拟实验。例如，很难研究结核杆菌在患者肺部生长时的行为。但是，如果我们能够识别活跃的代谢途径，那么我们就可以轻松地进行虚拟实验，例如，研究细菌在患者肺部生活时对新抗生素的反应。虚拟结核也可用于筛选抗结核杆菌活性的新化合物：在虚拟结核细胞中测试各种抗生素的效果比在活细胞中测试要快得多（而且实验人员不可能感染结核）。但可能最重要的是，虚拟结核细胞可以通过识别对生长至关重要的途径或途径组来发明新的抗生素。该模型将首先使用基因组的DNA序列数据建立。然而，为了使虚拟细胞更加真实，我们必须结合生物数据。因此，我们将在实验室严格规定的条件下培养真正的生物体（实际上是结核杆菌的疫苗菌株），并对细胞的进出进行化学分析。一种非凡的数学技术，被称为代谢通量分析，可以用来估计代谢物通过细胞内每个中心代谢途径的通量。这些信息将被整合到虚拟细胞中，使其行为更接近生物有机体。该项目的下一阶段是测试我们的虚拟单元。为此，我们将确定虚拟细胞中哪些通路是必需的，然后在活细胞中使这些通路失活。然后，我们将看到真实生命细胞的生长（或不生长）是否与模型的预测相匹配。这些测试将用于完善和改进模型，以后可能用于药物开发。

项目成果

¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation.

• DOI: 10.1371/journal.ppat.1002091
• 发表时间: 2011-07
• 期刊: PLoS pathogens
• 影响因子: 6.7
• 作者: Beste DJ;Bonde B;Hawkins N;Ward JL;Beale MH;Noack S;Nöh K;Kruger NJ;Ratcliffe RG;McFadden J
• 通讯作者: McFadden J

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism.

• DOI: 10.1186/gb-2007-8-5-r89
• 发表时间: 2007
• 期刊: GENOME BIOLOGY
• 影响因子: 12.3
• 作者: Beste, Dany J V;Hooper, Tracy;Stewart, Graham;Bonde, Bhushan;Avignone-Rossa, Claudio;Bushell, Michael E;Wheeler, Paul;Klamt, Steffen;Kierzek, Andrzej M;McFadden, Johnjoe
• 通讯作者: McFadden, Johnjoe

The genetic requirements for fast and slow growth in mycobacteria.

• DOI: 10.1371/journal.pone.0005349
• 发表时间: 2009-04-28
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Beste DJ;Espasa M;Bonde B;Kierzek AM;Stewart GR;McFadden J
• 通讯作者: McFadden J

Differential producibility analysis (DPA) of transcriptomic data with metabolic networks: deconstructing the metabolic response of M. tuberculosis.

• DOI: 10.1371/journal.pcbi.1002060
• 发表时间: 2011-06
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Bonde BK;Beste DJ;Laing E;Kierzek AM;McFadden J
• 通讯作者: McFadden J

Metabolic flux partitioning between the TCA cycle and glyoxylate shunt combined with a reversible methyl citrate cycle provide nutritional flexibility for Mycobacterium tuberculosis

TCA 循环和乙醛酸分流之间的代谢通量分配与可逆柠檬酸甲酯循环相结合，为结核分枝杆菌提供了营养灵活性

• DOI: 10.1101/2021.01.29.428863
• 发表时间: 2021
• 作者: Borah K