Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus

• Published in: BMC genomics 2023-05, Vol.24 (1), p.282-282, Article 282
• Main Authors: Huang, Shanshan, Li, Huiying, Ma, Liyuan, Liu, Rui, Li, Yiran, Wang, Hongmei, Lu, Xiaolu, Huang, Xinping, Wu, Xinhong, Liu, Xueduan
• Format: Article
• Language: English
• Subjects: Acid mine drainage; Acidithiobacillus; Adaptation; Adaptation (Biology); Algorithms; Amino acids; Bacteria; Biological evolution; Cadmium; Copper; DNA Transposable Elements - genetics; Environmental adaptation; Evolution; Evolution & development; Evolutionary genetics; Gene expression; Genes; Genetic aspects; Genome; Genomes; Genomics; Heavy metals; Humans; Insertion; Insertion sequence; Metabolism; Metals, Heavy; Microbiological research; Microorganisms; Natural history; Operons; Oxidation; Phylogenetics; Phylogeny; Physiological aspects; Proteobacteria; Sulfur; Sulfur - metabolism; Sulfur oxidation; Translocation; Transposition
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09372-8

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.