Proteomics of candidate Desulfatiglans TRIP_1 and identification of enzymes involved in anaerobic degradation of phenanthrene

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As in saturated PAH-contaminated sites oxygen is rapidly depleted, microorganisms able to use these compounds as a carbon source in the absence of molecular oxygen are crucial for their consumption. Here, we described the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of deltaproteobacteria. Proteogenome analysis revealed that the metabolic capacity of this bacterium includes the key enzymes for dissimilatory sulfate reduction, the Embden-Meyerhof-Parnas pathway, a complete tricarboxylic acid cycle as well as the key elements of the Wood-Ljungdahl pathway. Genes encoding enzymes potentially involved in the degradation of phenanthrene were identified in the genome of this bacterium. Two gene clusters were identified encoding a carboxylase enzyme involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses and provide the first metabolic pathway for anaerobic degradation of three-rings PAHs.

多环芳烃（Polycyclic aromatic hydrocarbons, PAHs）是一类分布广泛的污染物。在饱和的多环芳烃污染场地中，氧气会被快速耗尽，因此能够在无分子氧条件下以这类化合物为碳源的微生物，对于此类污染物的降解去除至关重要。本研究从一处天然沥青湖中富集得到硫酸盐还原富集培养物TRIP，本文阐述了该培养物厌氧降解菲的代谢通路。该培养物中的优势菌隶属于δ-变形菌纲（Deltaproteobacteria）的脱硫杆菌科（Desulfobacteraceae）。蛋白质基因组学分析显示，该菌的代谢能力涵盖异化硫酸盐还原关键酶、Embden-Meyerhof-Parnas途径、完整的三羧酸循环以及Wood-Ljungdahl途径的核心元件。研究人员在该菌的基因组中鉴定出了潜在参与菲降解过程的酶编码基因。同时鉴定到两个基因簇，分别编码参与菲活化过程的羧化酶，以及潜在参与后续苯环脱芳构化与还原步骤的还原酶编码基因。通过转录组与蛋白质组学分析验证了所预测的代谢通路，该研究首次阐明了三环多环芳烃的厌氧降解代谢通路。