School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
Appl Environ Microbiol. 2019 Jan 9;85(2). doi: 10.1128/AEM.02153-18. Print 2019 Jan 15.
Members of the genus , which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in spp. The results showed that the evolutionary history of metal resistance genes in spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in spp. were acquired by early HGT events from species that shared habitats with spp., such as , , , and species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing , , and and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of spp. to adapt to harsh environments. Altogether, the results suggested that spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in spp. Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of spp.
属中的成员能够适应极高浓度的重金属，普遍存在于酸性矿山排水（AMD）点。在这里，我们对属中的 37 株进行了比较基因组分析，以回答关于 spp.金属抗性基因的机制和进化历史的未解决问题。结果表明， spp.金属抗性基因的进化历史涉及基因获得和丧失、水平基因转移（HGT）和基因复制的组合。系统发育分析表明， spp.中的金属抗性基因是通过早期 HGT 事件从与 spp.共享栖息地的物种中获得的，例如 、 、 、 和 物种。涉及铜解毒的多铜氧化酶基因在铁氧化的 、 、 和 中丢失，并在进化过程中被铁锈素基因取代。此外，广泛的纯化选择和预测的高表达水平强调了金属抗性基因在 spp.适应恶劣环境的能力中的不可或缺作用。总的来说，这些结果表明， spp.通过 HGT、基因复制和纯化选择，在适应挑战性环境的过程中招募并整合了额外的新功能。本研究揭示了 spp.中金属抗性基因的分布、组织、功能和复杂进化历史。水平基因转移（HGT）、自然选择和基因复制是驱动微生物基因组适应性进化的三个主要引擎。先前的研究表明，HGT 是嗜酸菌应对富含重金属环境的主要适应机制。然而，关于 spp.对富含挑战性金属环境的 HGT 证据以及金属抗性基因起源和进化的机制在 中仍然缺乏。本研究的发现揭示了一种有趣的跨门 HGT 现象，表明 spp.通过 HGT、基因复制和纯化选择，在适应挑战性环境的过程中招募并整合了额外的新功能。总的来说，本研究的结果提高了我们对 spp.金属抗性策略的理解。
