Diversification of bacterial genome content through distinct mechanisms over different timescales.
Diversification of bacterial genome content through distinct mechanisms over different timescales.
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通过不同时间尺度的不同机制使细菌基因组含量的多样化。
DOI：
10.1038/ncomms6471
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发表时间：
2014-11-19
影响因子：
16.6
通讯作者：
Hanage WP
中科院分区：
文献类型：
--
作者：
Croucher NJ;Coupland PG;Stevenson AE;Callendrello A;Bentley SD;Hanage WP
细菌种群通常由多个共循环谱系组成。确定这种种群结构是如何产生的，需要了解是什么推动了细菌的多样化。利用616个系统采样的基因组，我们发现肺炎链球菌谱系典型的特征是不频繁转移的稳定基因组岛的组合：那些主要通过转化移动的，以及整合和接合元件以及与噬菌体相关的染色体岛。唯一包含广泛独特序列的谱系对应于一组可能代表不同物种的非典型未被包裹的分离物。然而，即使在谱系中，噬菌体的含量也是高度可变的，这表明频繁的水平传播将需要迅速多样化的抗噬菌体机制，以防止这些病毒在人群中席卷。相应地，编码I型限制性内切酶修饰系统的两个基因座能够通过基因组内重组在短时间内改变它们的特异性，在整个集合中无处不在。因此，肺炎球菌的短期变异以噬菌体的移动和基因组内重排为特征，稳定的基因座区别谱系的转移较慢。致病细菌肺炎链球菌的种群由不同的共循环谱系组成。在这里，作者表明，谱系的特征是稳定的基因组岛的特殊组合，而原噬菌体和限制性内切酶修饰系统在短时间尺度上有所不同。
Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages. Populations of the pathogenic bacterium Streptococcus pneumoniae consist of distinct co-circulating lineages. Here, the authors show lineages are characterized by particular combinations of stable genomic islands, whereas prophage and restriction-modification systems vary over short timescales.