By their genes ye shall know them: genomic signatures of predatory bacteria
By their genes ye shall know them: genomic signatures of predatory bacteria
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DOI：
10.1038/ismej.2012.149
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发表时间：
2013-04-01
期刊：
影响因子：
11
通讯作者：
Jurkevitch, Edouard
中科院分区：
文献类型：
--
作者：
Pasternak, Zohar;Pietrokovski, Shmuel;Jurkevitch, Edouard
捕食性细菌在分类上是不同的，表现出不同的捕食策略，并广泛分布在不同的环境中。到目前为止，它们的捕食性表型还不能从基因组序列数据中辨别出来，从而限制了我们对细菌捕食及其在自然界中的影响的理解。这里，我们定义了捕食组，即反映捕食性细菌表型的一组蛋白质家族。对11个测序的捕食性细菌和19个非捕食性细菌的蛋白质组进行了比较。对区分两组的蛋白质家族进行了鉴定和量化，表明捕食性和非捕食性细菌的蛋白质组差异很大和显著。正如我们从基因组数据中确认了一种被忽视的细菌捕食者所显示的那样，这种分析使得预测成为可能。捕食者在核黄素和氨基酸的生物合成方面表现出缺陷，这表明捕食者从猎物那里获得核黄素和氨基酸。相比之下，这些基因组高度富含粘附素、蛋白酶和特定的代谢蛋白，分别用于结合、加工和消费猎物。引人注目的是，捕食者和非捕食者在类异戊二烯的生物合成上存在差异：捕食者使用甲戊酸途径，而非捕食者像几乎所有细菌一样，使用DOXP途径。通过定义细菌基因组中的捕食性特征，可以发现它们编码的捕食性潜力，填补了衡量自然界中细菌捕食性的一个重要空白。此外，我们认为全基因组蛋白质组学比较也适用于微生物之间的其他生态相互作用，为细菌的功能分类提供了一个方便而合理的工具。《ISME期刊》(2013年)7756-769；doi：10.1038/ismej.2012.149；2012年11月29日在线出版
Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the 'predatome,' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that fullgenome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria. The ISME Journal (2013) 7, 756-769; doi:10.1038/ismej.2012.149; published online 29 November 2012