Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus.
Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus.
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DOI：
10.1186/s12864-023-09372-8
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发表时间：
2023-05-25
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
酸性硫杆菌属因其在酸性矿山废水(AMD)中具有良好的生存和氧化能力而受到广泛关注。然而，插入序列对它们的生物进化和环境适应的贡献是非常有限的。ISS是最简单的可移动遗传元件(MGE)，能够通过转座活动来阻断基因、操纵子或调节基因的表达。ISS可以分为不同的家族，有自己的成员，拥有不同的副本。本研究对36个酸性硫杆菌基因组中ISS的分布和进化以及ISS周围基因的功能进行了分析。结果表明，在目标基因组中共鉴定出248个成员，分属23个IS家族，共10,652个拷贝。不同种间的IS家族和拷贝数差异显著，说明酸杆菌IS的分布不均匀。氧化亚铁杆菌有166个IS成员，与其他酸性硫杆菌相比，可能开发出更多的基因转座策略。更重要的是，A.thiooxans拥有最多的IS拷贝，这表明他们的ISS是最活跃的，也更有可能转置。ISS与寄主基因组的进化趋势大体不同，在系统发育树上大致按科聚类。由此可见，酸性硫杆菌ISS的近期活性不仅与其遗传特性有关，而且与环境压力有关。此外，在As/Hg/Cu/Co/Zn/Cd转位和硫氧化的区域周围插入了许多ISS，特别是Tn3和IS110家族，这表明ISS可以通过提高酸杆菌对重金属的抗性和对硫的利用来提高其对极端酸性环境的适应能力。本研究为IS在嗜酸性硫杆菌的进化和适应中的贡献提供了基因组证据，为研究这些嗜酸菌的基因组可塑性开辟了新的视角。网上版载有补充材料，可在10.1186/s12864-023-09372-8查阅。
The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What’s more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles. The online version contains supplementary material available at 10.1186/s12864-023-09372-8.
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