An evaluation of minimal cellular functions to sustain a bacterial cell
An evaluation of minimal cellular functions to sustain a bacterial cell
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DOI：
10.1186/1752-0509-3-111
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发表时间：
2009-11-28
影响因子：
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通讯作者：
Ota, Motonori
中科院分区：
文献类型：
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作者：
Azuma, Yusuke;Ota, Motonori
背景：计算和实验方法都被用来确定维持细菌细胞所需的最小基因集。这类研究提供了生命所需的最小细胞功能集的线索。我们直接评估最小细胞功能集，而不是基因组集。结果：基于比较基因组学和代谢网络分析，我们估计了KEGG路径图作为细胞功能实体的重要性。前者通过同源搜索来检验每个路径图的进化保守性，并检测到“保守路径图”。后者确定了为保守的路径图提供所需化合物的“生物体特定路径图”。我们将这两种路径图定义为“自主路径图”。在一组自主路径图中，一组能够合成所有生物量成分(大肠杆菌/枯草芽孢杆菌细胞成分的基本成分)，并且由最少数量的路径图组成的图，被确定为对大肠杆菌和枯草芽孢杆菌的每个都是“最小路径图”。我们认为它们对应于最小元胞函数集。最小路径图的网络由20个保守的路径图和21个生物特异性的大肠杆菌路径图组成，从碳水化合物代谢开始一系列分解代谢过程。分解后的化合物被用于合成代谢，从而为细胞成分和遗传信息处理创造材料。结论：我们对这些路径图的分析表明，那些在“遗传信息处理”中发挥作用的化合物可能是保守的，而那些分解代谢的化合物则不是，反映了细胞功能的进化方面。将最小路径图与系统基因敲除实验、其他计算结果和寄生基因组进行比较，结果显示定性一致，但由于实验条件或计算方法的差异，有一些合理的例外。我们的方法为探索最小细胞函数集提供了另一种方法。
Background: Both computational and experimental approaches have been used to determine the minimal gene set required to sustain a bacterial cell. Such studies have provided clues to the minimal cellular-function set needed for life. We evaluate a minimal cellular-function set directly, instead of a geneset.Results: We estimated the essentialities of KEGG pathway maps as the entities of cellular functions, based on comparative genomics and metabolic network analyses. The former examined the evolutionary conservation of each pathway map by homology searches, and detected "conserved pathway maps". The latter identified "organism-specific pathway maps" that supply compounds required for the conserved pathway maps. We defined both pathway maps as "autonomous pathway maps". Among the set of autonomous pathway maps, the one that could synthesize all of the biomass components (the essential constituents for the cellular component of Escherichia coli/Bacillus subtilis), and that was composed of a minimal number of pathway maps, was determined for each of E. coli and B. subtilis, as "minimal pathway maps". We consider that they correspond to a minimal cellular-function set. The network of minimal pathway maps, composed of 20 conserved pathway maps and 21 organism-specific pathway maps for E. coli, starts a sequence of catabolic processes from carbohydrate metabolism. The catabolized compounds are used for anabolism, thus creating materials for cell components and for genetic information processing.Conclusion: Our analyses of these pathway maps revealed that those functioning in "genetic information processing" are likely to be conserved, but those for catabolism are not, reflecting an evolutionary aspect of cellular functions. Minimal pathway maps were compared with a systematic gene knockout experiment, other computational results and parasitic genomes, and showed qualitative agreement, with some reasonable exceptions due to the experimental conditions or differences of computational methods. Our method provides an alternative way to explore the minimal cellular function set.