Laboratory of Bacterial Communication, Department of Biology, Faculty of Sciences, University of Chile, Santiago 780-0024, Chile.
Int J Mol Sci. 2013 Aug 16;14(8):16901-16. doi: 10.3390/ijms140816901.
The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS), we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME) to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase) might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process.
生物浸矿细菌嗜酸氧化亚铁硫杆菌氧化硫化矿并促进金属溶解。该过程的效率取决于细胞对表面的附着，这一过程在许多革兰氏阴性菌中受到群体感应（QS）细胞间信号的调节。嗜酸氧化亚铁硫杆菌具有功能性 QS 系统，AHLs 的存在增强了其对黄铁矿的附着。然而，QS 转录因子 AfeR 的直接靶标仍然未知。在这项研究中，基于 AfeR 结合位点的特殊回文特征，使用生物信息学方法推断可能的 AfeR 直接靶标。一组旨在维持回文区域并改变非回文区域的隐马尔可夫模型被用于筛选可能的结合位点。通过注释每个预测结合位点（PBS）的上下文，我们根据它们相对于其他可能的基因组结构（如起始密码子、RNA 聚合酶启动子元件和基因间区域）的位置一致性对它们进行分类。我们进一步使用 motif elicitation for multiple EM (MEME) 算法进一步筛选出低同源性的 PBS。总之，鉴定了 75 个靶基因，其中 34 个具有更高的置信度。在所鉴定的基因中，我们发现了自身的 afeR、zwf 基因、编码糖基转移酶活性的基因、金属-β内酰胺酶和主动运输相关蛋白。糖基转移酶和 Zwf（葡萄糖 6-磷酸-1-脱氢酶）可能直接参与多糖生物合成以及嗜酸氧化亚铁硫杆菌细胞在生物浸矿过程中对矿物的附着。
