Global transcriptional analysis of Geobacter sulfurreducens under palladium reducing

Geobacter sulfurreducens is capable of reducing Pd(II) to Pd(0) using pyruvate as an electron donor; however, the biochemical and genetic mechanisms involved in this process have not been described. In this work, we carried out transcriptome profiling analyes to identify genes involved in Pd(II) reduction in this bacteria. Our results showed that 254 genes were upregulated while 142 were downregulated during Pd(II) reduction. Among the upregulated genes, 12 were related to energy metabolism and electron transport; 50 were classified as involved in protein synthesis; 42 were associated with regulatory functions and transcription, and 47 have no homologs with known function. RT-qPCR data confirmed upregulation during Pd(II) reduction of genes encoding PilA, the structural protein for the electrically conductive pili, and c-type cytochromes GSU1062, GSU2513, GSU2808, GSU2934, GSU3107, OmcH, OmcM, PpcA, PpcD. ΔpilA and ΔpilR mutant strains showed 20% and 40%, decrease in the Pd(II) reduction respectively, compared to the wild type strain, indicating the central role of the pili in this process. RT-qPCR data also confirmed downregulation during Pd(II) reduction of the omcB, omcC, omcZ, and omcS genes, which have been shown to be involved in Fe(III) reduction and electrodes. Based on these results, we propose mechanisms involved in Pd(II) reduction by G. sulfurreducens. mRNA profiles of Geobacter sulfurreducens in Pd(II) reduction or NBAF medium, in duplicate, using Illumina Genome Analyzer Iix

还原硫地杆菌（Geobacter sulfurreducens）能够以丙酮酸作为电子供体，将Pd(II)还原为Pd(0)，但该过程所涉及的生化与遗传机制尚未被阐明。本研究通过转录组分析筛选该菌中参与Pd(II)还原的相关基因。研究结果显示，在Pd(II)还原过程中，共有254个基因表达上调、142个基因表达下调。其中上调基因里，12个与能量代谢及电子传递相关，50个参与蛋白质合成过程，42个与调控功能及转录过程相关，另有47个基因未发现具有已知功能的同源基因。实时定量聚合酶链式反应（RT-qPCR）数据证实，Pd(II)还原过程中，编码PilA（导电菌毛结构蛋白）的基因以及c型细胞色素（c-type cytochromes）GSU1062、GSU2513、GSU2808、GSU2934、GSU3107、OmcH、OmcM、PpcA、PpcD的表达均出现上调。与野生型菌株相比，pilA基因缺失突变株（ΔpilA）与pilR基因缺失突变株（ΔpilR）的Pd(II)还原能力分别下降20%和40%，这表明菌毛在该过程中发挥核心作用。实时定量聚合酶链式反应（RT-qPCR）数据还证实，Pd(II)还原过程中omcB、omcC、omcZ及omcS基因表达下调，上述基因此前已被证实参与Fe(III)还原及电极相关过程。基于上述结果，本研究提出了还原硫地杆菌（Geobacter sulfurreducens）介导Pd(II)还原的潜在机制。本数据集包含采用Illumina Genome Analyzer Iix测序平台获得的还原硫地杆菌（Geobacter sulfurreducens）在Pd(II)还原体系与NBAF培养基中的转录组mRNA图谱，共设置2次生物学重复。