Supplementary Material for: ICE<b><i>Afe</i></b>1, an Actively Excising Genetic Element from the Biomining Bacterium <b><i>Acidithiobacillus ferrooxidans</i></b>

Integrative conjugative elements (ICEs) are self-transferred mobile genetic elements that contribute to horizontal gene transfer. An ICE (ICE<i>Afe</i>1) was identified in the genome of <i>Acidithiobacillus ferrooxidans</i> ATCC 23270. Excision of the element and expression of relevant genes under normal and DNA-damaging growth conditions was analyzed. Bioinformatic tools and DNA amplification methods were used to identify and to assess the excision and expression of genes related to the mobility of the element. Both basal and mitomycin C-inducible excision as well as expression and induction of the genes for integration/excision are demonstrated, suggesting that ICE<i>Afe</i>1 is an actively excising SOS-regulated mobile genetic element. The presence of a complete set of genes encoding self-transfer functions that are induced in response to DNA damage caused by mitomycin C additionally suggests that this element is capable of conjugative transfer to suitable recipient strains. Transfer of ICE<i>Afe</i>1 may provide selective advantages to other acidophiles in this ecological niche through dissemination of gene clusters expressing transfer RNAs, CRISPRs, and exopolysaccharide biosynthesis enzymes, probably by modification of translation efficiency, resistance to bacteriophage infection and biofilm formation, respectively. These data open novel avenues of research on conjugative transformation of biotechnologically relevant microorganisms recalcitrant to genetic manipulation.

整合接合元件（Integrative conjugative elements, ICEs）是一类可自主转移的可移动遗传元件，参与介导水平基因转移过程。研究者在氧化亚铁硫杆菌（Acidithiobacillus ferrooxidans）ATCC 23270的基因组中鉴定得到一株整合接合元件ICE<Afe>1。本研究分析了该元件在正常培养与DNA损伤培养条件下的切离过程及相关基因的表达情况，通过生物信息学工具与DNA扩增方法，对该元件移动相关基因的切离与表达特征进行鉴定与评估。实验结果显示，该元件既存在基础水平的切离，也可被丝裂霉素C（mitomycin C）诱导切离；同时整合与切离相关基因的表达也被显著诱导，表明ICE<Afe>1是一类可被SOS通路调控的、可主动切离的可移动遗传元件。此外，该元件携带一套完整的自主转移功能基因，且这些基因可响应丝裂霉素C引发的DNA损伤而被诱导表达，进一步提示该元件可通过接合转移进入合适的受体菌株。ICE<Afe>1可通过传播携带转运RNA、成簇规律间隔短回文重复序列（CRISPRs）以及胞外多糖合成酶编码基因的基因簇，分别通过调控翻译效率、抵抗噬菌体感染以及形成生物膜，为该生态位中的其他嗜酸菌提供选择优势。本研究的数据为解析难以进行遗传操作的、具有生物技术应用价值的微生物的接合转化机制开辟了全新的研究方向。