Supplementary Material for: Substrate-Dependent Regulation of Carbon Catabolism in Marine Sulfate-Reducing <i>Desulfobacterium autotrophicum</i> HRM2

<i>Desulfobacterium autotrophicum</i> HRM2 is a metabolically versatile sulfate-reducing bacterium, capable of heterotrophic (e.g. with organic acids and alcohols) and chemolithoautotrophic growth (with H₂/CO₂). It employs the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO₂ and for CO₂ fixation. Here, we investigated substrate-dependent regulation at different levels of anaerobic carbon catabolism in this bacterium. (a) Whole-cell adaptation studies indicated an inducibleutilization of short-chained alcohols, agreeing with a substrate-specific abundance increase (up to 40-fold) of alcohol dehydrogenase Adh4. Simultaneous utilization of lactate and 1-propanol was paralleled by <i>adh4</i> expression and Adh4 formation, respectively. (b) Degradation of propionate generally involves methylmalonyl-CoA mutase (Sbm). Expression of <i>sbm</i> was upregulated during growth with 1-propanol, but not with a mixture of lactate and 1-propanol. Correspondingly, propionate was excreted during growth with this substrate mixture. (c) CO dehydrogenase, the key enzyme of the Wood-Ljungdahl pathway, is encoded by several genes <i>(cdhC</i>, <i>cdh1</i> and <i>cdh2)</i> located at different genomic positions. Expression of all of these genes during heterotrophic and autotrophic growth points to a reversible operation of the Wood-Ljungdahl pathway. In summary, the different regulatory patterns displayed by <i>Db. autotrophicum</i> HRM2 at the tested metabolic levels point to a multi-layered regulatory network.

自养脱硫杆菌（Desulfobacterium autotrophicum）HRM2是一株代谢多样的硫酸盐还原菌，能够通过异养（如以有机酸、醇类为碳源）与化能自养（以H₂/CO₂为碳源）方式生长。该菌株借助伍德-隆德哈尔途径（Wood-Ljungdahl pathway）完成乙酰辅酶A的完全氧化生成CO₂，以及CO₂的固定。本研究针对该菌株厌氧碳分解代谢不同层级的底物依赖型调控机制展开探究。
（a）全细胞适应性研究显示，短链醇类的利用可被诱导，这与醇脱氢酶Adh4的底物特异性丰度提升（最高可达40倍）结果一致。乳酸与1-丙醇的共利用分别伴随adh4基因的表达与Adh4蛋白的合成。
（b）丙酸盐的降解通常依赖甲基丙二酰辅酶A变位酶（methylmalonyl-CoA mutase, Sbm）。在以1-丙醇为单一碳源生长时，sbm基因的表达会上调，但在乳酸与1-丙醇的混合碳源培养时则无此现象。相应地，在该混合碳源培养条件下，菌株会分泌丙酸盐。
（c）作为伍德-隆德哈尔途径的关键酶，一氧化碳脱氢酶由分布于基因组不同位置的多个基因（cdhC、cdh1和cdh2）编码。在异养与自养生长条件下，这些基因均有表达，表明伍德-隆德哈尔途径可双向运行。
综上，D. autotrophicum HRM2在本次检测的代谢层级中所展现出的多样化调控模式，表明其存在多层级调控网络。