Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis

Methanococcus maripaludis utilizes selenocysteine-(Sec-) containing proteins (selenoproteins), mostly active in the organism’s primary energy metabolism, methanogenesis. Under selenium depletion, M. maripaludis employs a set of enzymes containing cysteine (Cys) instead of Sec. The genes coding for these Sec-/Cys-containing isoforms are the only genes known expression of which is influenced by the selenium status of the cell. Using quantitative proteomics and transcriptomics approx. 7% and 12%, respectively, of all genes/proteins were differentially expressed/synthesized in response to the selenium supply. Some of the genes identified involve methanogenesis, nitrogenase functions, and putative transporters. An increase of transcript abundance for putative transporters under selenium-depleted conditions indicated the organism’s effort to tap into alternative sources of selenium. Selenium sources M. maripaludis is known to utilize are selenite and dimethylselenide. To expand this list, a selenium responsive reporter strain was assessed with nine other, environmentally relevant selenium species. While some had a similar biological window as selenite, others were effectively utilized at lower concentrations. Conversely, selenate and seleno-amino acids were only utilized at unphysiologically high concentrations and two compounds were not utilized at all. To address the role of the selenium-regulated putative transporters in selenium transport, M. maripaludis mutant strains lacking one or two of the putative transporters were tested for the capability to utilize the different selenium species. Of the five putative transporters analyzed by loss-of-function mutagenesis, none appeared to be absolutely required for utilizing any of the selenium species tested, indicating they have redundant and/or overlapping specificities, or are not dedicated selenium transporters.

马氏甲烷球菌（Methanococcus maripaludis）可合成含硒半胱氨酸（selenocysteine, Sec）的蛋白质（即硒蛋白），这类蛋白大多参与该菌体的核心能量代谢过程——甲烷生成作用。在硒匮乏条件下，马氏甲烷球菌会启用一组以半胱氨酸（cysteine, Cys）替代硒半胱氨酸的同工酶。目前已知，编码这类含Sec/Cys同工酶的基因是唯一一类表达水平受菌体硒营养状态调控的基因。研究人员通过定量蛋白质组学与转录组学分析发现，分别有约7%和12%的全部基因/蛋白在硒供应改变时发生了差异表达/合成。已鉴定的相关基因涉及甲烷生成、固氮酶功能以及推定转运蛋白编码基因。硒匮乏条件下推定转运蛋白的转录本丰度上升，这表明该菌会主动尝试获取替代性硒源。已知马氏甲烷球菌可利用的硒源包括亚硒酸盐与二甲基硒化物。为拓展已知可利用硒源的范围，研究人员构建了硒响应报告菌株，并对另外9种环境相关的硒化合物进行了测试。部分化合物的生物活性窗口与亚硒酸盐相近，另有部分可在更低浓度下被有效利用；与之相反，硒酸盐与硒代氨基酸仅能在非生理高浓度下被利用，另有两种化合物完全无法被该菌利用。为探究硒调控的推定转运蛋白在硒转运中的作用，研究人员构建了缺失一种或多种推定转运蛋白的马氏甲烷球菌突变菌株，测试其利用不同硒化合物的能力。通过功能丧失诱变分析的5种推定转运蛋白中，未发现任何一种是利用任一测试硒化合物的绝对必需因子，这表明这些转运蛋白存在功能冗余和/或底物特异性重叠，或者并非专门的硒转运蛋白。