Evidence of a large novel gene pool associated with prokaryotic genomic islands.
Evidence of a large novel gene pool associated with prokaryotic genomic islands.
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DOI：
10.1371/journal.pgen.0010062
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发表时间：
2005-11
期刊：
影响因子：
4.5
通讯作者：
Brinkman FS
中科院分区：
文献类型：
--
作者：
Hsiao WW;Ung K;Aeschliman D;Bryan J;Finlay BB;Brinkman FS
微生物基因“新颖”（在其他物种中没有可检测到的同系物）已经变得越来越有趣，因为环境采样表明，在尚未培养的微生物中有更多这样的新基因。通过分析已知的微生物基因组岛和噬菌体，我们在63个原核生物基因组中建立了系统鉴定假定基因组岛（原核生物基因组中可能水平起源的基因簇）的标准，然后表征了新基因的分布和其他特征。除了少数基因组外，所有被检测的基因组在其预测的基因组岛中包含的新基因比例明显高于其他基因组（配对t检验= 4.43E-14至1.27E-18，取决于方法）。此外，相反的观察结果（即，岛屿以外的新基因比例更高）在任何被检查的生物体中从未达到统计显著性。我们表明，在预测的基因组岛中，新基因的比例较高并不是因为基因组岛区域的基因预测不准确，而可能反映了这些区域中细菌和古细菌的新基因的真正增加。这代表了对原核基因组岛中新基因的第一次全面分析，并提供了有关新基因起源的线索。我们的集体结果表明，最近水平传播的基因组区域与主要垂直遗传的基因组区域存在不同的基因库。此外，基因库中还有更多与基因组岛相关的新基因。由于基因组岛通常与特定的微生物适应有关，如抗生素耐药性、病原体毒力或金属耐药性，这表明微生物可能有比以前认为的更大的适应新基因“武器库”。迄今为止，已有超过250个微生物基因组被测序。这些基因组中有很大一部分基因与已知基因没有明显的相似性，它们的功能是未知的（即，它们似乎是新的）。随着测序基因组数量的增加，这些新基因的数量也在继续增加。在这篇论文中，作者们现在通过对多种原核生物基因组的分析表明，新基因在被称为基因组岛的地区更为普遍。基因组岛是基因组中显示水平起源证据的基因簇。这项研究是值得注意的，因为基因组岛不成比例地包含许多具有医学、农业和环境重要性的基因（例如，动植物病原体毒力因子、抗生素抗性基因、酚类降解基因等）。高比例的新基因也定位于基因组岛的观察表明，微生物可能比以前认为的有更大的新基因“武器库”来进行重要的适应。这些结果还表明，最近水平传播的基因组区域与主要垂直遗传的基因组区域存在不同的基因库。作者建议，需要进行进一步的研究，包括大规模的环境基因组采样，以帮助描述这一未被充分研究的基因库。
Microbial genes that are “novel” (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examined contained significantly higher proportions of novel genes in their predicted genomic islands compared with the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of novel genes in predicted genomic islands is not due to less accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regions for both bacteria and archaea. This represents the first comprehensive analysis of novel genes in prokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequently associated with a particular microbial adaptation, such as antibiotic resistance, pathogen virulence, or metal resistance, this suggests that microbes may have access to a larger “arsenal” of novel genes for adaptation than previously thought. More than 250 microbial genomes have been sequenced to date. A significant proportion of the genes in these genomes have no apparent similarity to known genes and their functions are unknown (i.e., they appear to be novel). As the number of sequenced genomes increases, the number of these novel genes continues to increase. In this paper, the authors now show, through an analysis of a diverse range of prokaryotic genomes, that novel genes are more prevalent in regions called genomic islands. Genomic islands are clusters of genes in genomes that show evidence of horizontal origins. This study is notable since genomic islands disproportionately contain many genes of medical, agricultural, and environmental importance (e.g., animal and plant pathogen virulence factors, antibiotic resistance genes, phenolic degradation genes, etc.). The observation that high proportions of novel genes are also localized to genomic islands suggests that microbes may have access to a larger “arsenal” of novel genes for important adaptations than previously thought. These results also imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. The authors suggest that further studies involving large-scale environmental genomic sampling are required to help characterize this understudied gene pool.
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