Biosciences and Biotechnology Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
Mol Biol Evol. 2024 Oct 4;41(10). doi: 10.1093/molbev/msae206.
Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them-an important step in the translation of synthetic strains into natural contexts. Toxin-antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.
细菌通过水平基因转移（HGT）进行进化，反映了它们的群落相互作用。通过这种方式，HGT 网络非常适合映射群落相互作用，但对控制它们的作用不大——这是将合成菌株转化为自然环境的重要步骤。毒素-抗毒素（TA）系统是普遍存在且多样化的选择剂；然而，由于它们在宿主中的分布不稳定，其用途受到限制。在这里，我们研究了 TA 系统的异质分布，因为它们的可移动性。通过系统地在 10000 个质粒网络上绘制 TA 系统，我们发现 HGT 群落具有独特且可预测的 TA 特征。我们提出这些 TA 特征是由质粒竞争产生的，并且有可能进一步表明质粒、宿主和噬菌体相互作用的程度。为了强调这些关系，我们仅基于 TA 相似性构建了一个 HGT 网络，将特定的选择标记置于细菌群落的更广泛背景下。这项工作不仅阐明了 TA 系统的进化，而且还为通过 TA 兼容性操纵群落相互作用提供了一个通用框架。
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