Response and Mechanism of Iron-Reducing Bacterium Shewanella oneidensis MR-1 to Perturbance of H2O2
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摘要: 铁还原菌参与的铁循环是地表系统中物质循环的重要驱动力，自然生成和人工注入地下环境的H2O2可能通过氧化胁迫影响铁还原菌的活性和功能，但铁还原菌在H2O2扰动下的响应及机制仍不清楚.以铁还原模式菌株Shewanella oneidensis MR-1作为研究对象，结合批实验和转录组测序研究了不同浓度水平H2O2扰动下MR-1活性和功能的变化及其调控机制.结果表明，MR-1能够有效抵御H2O2的胁迫，且H2O2扰动使MR-1的铁还原能力增强.转录组测序表明，H2O2使MR-1处于抗应激状态，通过积极氧化有机物供能、促进过氧化氢酶的合成抵御H2O2的负面影响.Abstract: Iron cycling mediated by iron-reducing bacteria is an important factor driving material cycle in the surface system of earth. H2O2 naturally generated and artificially injected into the subsurface environment may affect the activity and function of iron-reducing bacteria through oxidative stress, but the response and mechanism of iron-reducing bacteria to H2O2 disturbance is still unclear. In this study, Shewanella oneidensis MR-1 was chosen as a representative iron-reducing bacterium. In combination with batch experiments and RNA-seq analysis, the changes of MR-1 activity and function under different concentrations of H2O2 and its regulatory mechanism were investigated. Results show that MR-1 could resist H2O2 stress effectively, and H2O2 enhanced the Fe(Ⅲ)-reducing ability of MR-1. RNA-seq results show that MR-1 maintained in an anti-stress state infacing to H2O2 disturbance, which could resist the negative effects of H2O2 by actively oxidizing organic matter to provide energy and promoting the synthesis of catalase.
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图 1 不同浓度H2O2扰动下MR-1的生长曲线
Fig. 1. Effects of different concentrations of H2O2 on the viability of MR-1
图 2 有菌和无菌体系中H2O2浓度变化
Fig. 2. Variations of H2O2 concentration in the presence and absence of MR-1
图 4 H2O2对MR-1铁还原能力的影响
与空白组相比，***P < 0.001，****P < 0.000 1
Fig. 4. Effect of H2O2 on Fe(Ⅲ) reduction capacity of MR-1
表 1 差异基因表达情况
Table 1. Differential gene expression results
基因ID log2(变化倍数) P值 描述 SO_RS10090 -5.67 4.44×10-93 海洋变形菌分选酶靶蛋白 SO_RS10085 -6.46 7.06×10-81 分选酶相关ompa样蛋白PdsO SO_RS10095 -3.96 1.36×10-58 GN分选酶 SO_RS03930 -3.77 8.98×10-54 OXA-48家族水解酶 SO_RS06920 3.39 1.25×10-45 苏氨酸脱氢酶基因 SO_RS07720 3.10 7.72×10-37 外膜蛋白OmpW SO_RS15335 3.00 1.64×10-35 细胞色素d泛醇氧化酶亚基Ⅱ SO_RS17985 3.92 6.21×10-33 钼酸盐ABC转运蛋白底物结合蛋白 SO_RS15340 2.82 6.21×10-33 细胞色素泛醇氧化酶亚基Ⅰ SO_RS10080 -3.28 4.57×10-28 变形菌分选酶系统反应调节器 SO_RS18135 2.50 8.75×10-28 孔蛋白 SO_RS13090 2.25 1.56×10-18 碳饥饿蛋白A SO_RS06640 2.20 1.34×10-17 钼喋呤支撑的氧化还原酶 SO_RS09405 1.97 2.17×10-17 蛋白-蛋氨酸-亚砜还原酶催化亚基MsrP SO_RS01505 3.27 6.67×10-17 鸟氨酸脱羧酶 SO_RS14360 2.08 2.56×10-15 Sigma70家族RNA聚合酶因子 SO_RS21580 2.04 2.98×10-15 H家族蛋白 SO_RS19750 -2.79 4.06×10-15 ISSod4家族转座酶 SO_RS03335 1.89 4.38×10-15 分子伴侣GroEL SO_RS10010 2.51 5.15×10-15 细胞色素C氧化酶 SO_RS10075 -2.83 1.57×10-14 变形杆菌专用分选酶系统组氨酸激酶 SO_RS20140 -2.92 2.08×10-14 细胞包膜完整性蛋白CreD SO_RS04535 -1.76 2.08×10-14 ISSod2家族转座酶 SO_RS09350 -1.76 2.08×10-14 ISSod2家族转座酶 SO_RS09940 -1.76 2.08×10-14 ISSod2家族转座酶 SO_RS19795 -1.76 2.08×10-14 ISSod2家族转座酶 SO_RS21600 1.75 1.49×10-12 含有DUF3300结构域的蛋白 SO_RS08155 1.63 3.25×10-12 OmcA/MtrC家族血红素c型细胞色素 SO_RS14365 1.80 6.92×10-12 含有DUF3379结构域的蛋白 SO_RS07745 1.70 1.60×10-11 辅酶a酰化甲基丙二酸半醛脱氢酶 
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表 2 GO富集分析结果
Table 2. GO enrichment analysis results
GO ID 描述 P值 分类 差异基因数量 GO: 1901606 α-氨基酸分解代谢过程 6.13×10-5 BP 8 GO: 0009063 细胞氨基酸分解代谢过程 1.18×10-4 BP 8 GO: 0016054 有机酸分解代谢过程 1.11×10-3 BP 8 GO: 0046395 羧酸分解代谢过程 1.11×10-3 BP 8 GO: 0055114 氧化还原过程 3.00×10-3 BP 25 GO: 0006091 前体代谢产物和能量的产生 3.36×10-3 BP 14 GO: 0044282 小分子分解代谢过程 3.51×10-3 BP 8 GO: 1901565 有机氮化合物分解代谢过程 3.56×10-3 BP 8 GO: 0016491 氧化还原酶 8.02×10-3 MF 24 GO: 0006536 谷氨酸代谢过程 1.15×10-2 BP 4 GO: 0009056 分解代谢过程 1.27×10-2 BP 11 GO: 0044248 细胞分解代谢过程 1.94×10-2 BP 9 GO: 0022900 电子传递链 1.94×10-2 BP 10 GO: 0006574 缬氨酸分解代谢过程 2.60×10-2 BP 2 GO: 1901575 有机物分解代谢过程 2.60×10-2 BP 10 GO: 0015980 由有机化合物氧化产生的能量 2.74×10-2 BP 6 GO: 0045333 细胞呼吸 3.34×10-2 BP 5 GO: 0009259 核糖核苷酸代谢过程 3.34×10-2 BP 7 GO: 0009156 磷酸核糖核苷生物合成过程 3.34×10-2 BP 5 GO: 1901564 有机氮化合物代谢过程 3.34×10-2 BP 33
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