Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast.
Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast.
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DOI：
10.1186/gb-2005-6-6-r49
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发表时间：
2005
期刊：
影响因子：
12.3
通讯作者：
Sauer U
中科院分区：
文献类型：
--
作者：
Blank LM;Kuepfer L;Sauer U
在酿酒酵母中进行的基因组规模的13C -通量分析表明，具有代谢功能的基因敲除突变体表面上的可有可无性可通过特定条件下的基因不活跃、通过重复基因导致的网络冗余或替代途径来解释。
通过13C -示踪实验对细胞内代谢物通量进行定量分析正逐渐成为一种常规的高通量分析方法。现在的问题是应该分析哪些突变体。在此，我们利用酿酒酵母代谢的基因组规模模型，在系统生物学方法中确定了关键实验，从而减少了实验性网络分析和功能基因组学的工作量。
基因组规模的13C通量分析表明，在葡萄糖上生长期间，745个生化反应中约有一半是活跃的，但仅有51个具有显著通量的基因编码反应存在替代途径。这些通过计算机模拟确定的灵活反应是实验性通量分析的关键目标，并且我们给出了酵母的第一批大规模代谢通量数据，涵盖了在葡萄糖上生长期间这些突变体的一半。代谢损伤常常通过通量重定向来抵消，但如在adh1、ald6、cox5A、fum1、mdh1、pda1和zwf1突变中，辅因子依赖反应的敲除会在网络更远处引起通量反应。通过整合计算分析、通量数据以及所有活跃反应突变体的生理表型，我们量化了通过替代途径实现的“遗传缓冲”以及通过重复基因实现的网络冗余对网络遗传稳健性的相对重要性。
具有代谢功能的基因敲除突变体表面上的可有可无性在约一半的情况下是由特定条件下的基因不活跃所解释。对于其余207个活跃反应的存活突变体，通过重复基因实现的网络冗余是酿酒酵母遗传网络稳健性的主要（75%）分子机制，而替代途径是次要（25%）分子机制。
Genome-scale 13C-flux analysis in Saccharomyces cerevisiae revealed that the apparent dispensability of knockout mutants with metabolic function can be explained by gene inactivity under a particular condition, by network redundancy through duplicated genes or by alternative pathways. Quantification of intracellular metabolite fluxes by 13C-tracer experiments is maturing into a routine higher-throughput analysis. The question now arises as to which mutants should be analyzed. Here we identify key experiments in a systems biology approach with a genome-scale model of Saccharomyces cerevisiae metabolism, thereby reducing the workload for experimental network analyses and functional genomics. Genome-scale 13C flux analysis revealed that about half of the 745 biochemical reactions were active during growth on glucose, but that alternative pathways exist for only 51 gene-encoded reactions with significant flux. These flexible reactions identified in silico are key targets for experimental flux analysis, and we present the first large-scale metabolic flux data for yeast, covering half of these mutants during growth on glucose. The metabolic lesions were often counteracted by flux rerouting, but knockout of cofactor-dependent reactions, as in the adh1, ald6, cox5A, fum1, mdh1, pda1, and zwf1 mutations, caused flux responses in more distant parts of the network. By integrating computational analyses, flux data, and physiological phenotypes of all mutants in active reactions, we quantified the relative importance of 'genetic buffering' through alternative pathways and network redundancy through duplicate genes for genetic robustness of the network. The apparent dispensability of knockout mutants with metabolic function is explained by gene inactivity under a particular condition in about half of the cases. For the remaining 207 viable mutants of active reactions, network redundancy through duplicate genes was the major (75%) and alternative pathways the minor (25%) molecular mechanism of genetic network robustness in S. cerevisiae.
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影响因子：
7
作者：
Förster, J;Famili, I;Nielsen, J
通讯作者：
Nielsen, J
影响因子：
3.2
作者：
Gombert, AK;dos Santos, MM;Nielsen, J
通讯作者：
Nielsen, J
影响因子：
46.9
作者：
Allen, J;Davey, HM;Kell, DB
通讯作者：
Kell, DB
影响因子：
--
作者：
dos Santos, MM;Gombert, AK;Nielsen, J
通讯作者：
Nielsen, J
DOI：
10.1046/j.1432-1327.2001.02126.x
发表时间：
2001-04-01
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
Maaheimo, H;Fiaux, J;Szyperski, T
通讯作者：
Szyperski, T