Protein complexes in bacteria.
Protein complexes in bacteria.
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DOI：
10.1371/journal.pcbi.1004107
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发表时间：
2015-02
影响因子：
4.3
通讯作者：
Uetz P
中科院分区：
文献类型：
--
作者：
Caufield JH;Abreu M;Wimble C;Uetz P
对蛋白质复合物的大规模分析近期已可用于大肠杆菌和肺炎支原体，分别产生了443个和116个异源多聚体可溶性蛋白质复合物。我们将这些经质谱鉴定的蛋白质复合物的结果与EcoCyc鉴定的285个“金标准”蛋白质复合物相结合。与基因直系同源、保守性和必需性数据库进行比较，确定了在其他物种的复合物中保守或缺失的蛋白质。例如，在大肠杆菌的285个“金标准”蛋白质复合物中，在7个远缘相关的细菌“模式”物种中完全保守的不到10%。复合物的保守性遵循三种模式之一：高度保守的复合物、具有保守核心的复合物以及具有部分保守性但无保守核心的复合物。将比较范围扩大到894个不同的细菌基因组，说明了部分保守性以及蛋白质复合物各组分间共同保守的限度：在285个模式蛋白质复合物中，只有14个在所用的95%的基因组中完全保守，但我们预测超过180个可能在至少一半的基因组中部分保守。未观察到基因必需性与蛋白质复合物保守性之间存在明确的关系，因为即使是保守性较差的复合物也包含大量必需蛋白质。最后，我们确定了183个含有高度保守组分和未表征蛋白质的复合物，这些复合物将是未来实验研究的有趣目标。
尽管针对一些研究较为深入的细菌物种已经公布了两万多种二元蛋白质 - 蛋白质相互作用，但这些结果很少能涵盖蛋白质参与复合物的全部程度。在此，我们利用来自大肠杆菌或肺炎支原体的实验观测到的蛋白质复合物以及基因直系同源性，来预测多种细菌的蛋白质复合物。令人惊讶的是，大多数蛋白质复合物并不保守，这显示出一种意想不到的进化灵活性。我们还观察到蛋白质复合物保守性方面更广泛的趋势，特别是在具有最少蛋白质复合物集合的基因组精简物种中。
Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. Though more than 20,000 binary protein-protein interactions have been published for a few well-studied bacterial species, the results rarely capture the full extent to which proteins take part in complexes. Here, we use experimentally-observed protein complexes from E. coli or Mycoplasma pneumoniae, as well as gene orthology, to predict protein complexes across many species of bacteria. Surprisingly, the majority of protein complexes is not conserved, demonstrating an unexpected evolutionary flexibility. We also observe broader trends within protein complex conservation, especially in genome-reduced species with minimal sets of protein complexes.
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