Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation
Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation
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DOI：
10.1101/381442
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发表时间：
2018-08
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影响因子：
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通讯作者：
Alexander Esin;T. Ellis;Tobias Warnecke
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文献类型：
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作者：
Alexander Esin;T. Ellis;Tobias Warnecke
细菌中的水平基因转移（HGT）发生在适应性基因组结构的背景下。因此，某些染色体邻近区域可能比其他区域更容易发生HGT。在这里，我们调查的染色体拓扑结构的水平基因流到一个分支的芽孢杆菌科，包括土芽孢杆菌。重建HGT模式，再加上基于模型的和解系统发育的方法，我们发现三个大的连续染色体区的HGT富集。这些区域包含并连接经典定义的基因组岛。分析拓扑和链偏差的最近和较旧的转移事件，我们表明，进入的限制是迅速执行的选择和限制和许可区已经存在于其当前位置的长期演变。最大的区域集中在末端，其特征是代谢基因的高流入。另外两个区域位于复制起点周围的一个狭窄的非允许区域的侧面，并延伸到染色体的前三分之一-在早期孢子形成期间限制在前孢子中的染色体部分。水平转移到这一领域偏向于功能，经典控制的前孢子特异性西格玛因子σF：信号转导，转录，特别是膜生物发生。类似的富集模式存在于产芽孢杆菌中，但不存在于非产芽孢杆菌中。我们的研究结果表明，HGT的拓扑结构在土芽孢杆菌，芽孢杆菌更普遍，反映了染色体组织的快速和孢子形成的限制，作为不对称的染色体截留在孢子形成早期限制HGT驱动的孢子形成的创新可以发生在前孢子。
Horizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillus spp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment. These zones encompass and connect classically defined genomic islands. Analyzing topological and strand biases of recent and older transfer events, we show that restrictions on entry are rapidly enforced by selection and that restrictive and permissive zones have existed in their current locations for long periods of evolution. The largest zone, characterized by a high influx of metabolic genes, is centred on the terminus. The other two zones flank a narrow non-permissive zone around the origin of replication and extend to delimit the first third of the chromosome – the part of the chromosome that is confined to the forespore during early spore formation. Horizontal transfers into this area are biased towards functions classically controlled by the forespore-specific sigma factor σF: signal transduction, transcription, and particularly membrane biogenesis. Similar enrichment patterns are present in spore-forming but absent in non-spore-forming Bacilli. Our results suggest that the topology of HGT in Geobacillus, and Bacilli more generally, reflects constraints imposed by chromosomal organization for fast and sporulation, as asymmetric chromosomal entrapment in the forespore during early spore formation restricts where HGT-driven innovation in sporulation can occur.