Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus
Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus
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DOI：
10.1016/j.ymben.2018.06.009
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发表时间：
2018-09-01
影响因子：
8.4
通讯作者：
Dantas, Gautam
中科院分区：
文献类型：
--
作者：
Henson, William R.;Campbell, Tayte;Dantas, Gautam
木质素利用率已被确定为生物炼制盈利能力的关键因素。然而，木质素解聚产生多相芳香族混合物，其抑制微生物生长和木质纤维素向生物化学品的转化。不透明红球菌是一种很有前途的芳香分解代谢，产油细菌，但其芳香耐受性和利用机制仍不清楚。为了更好地理解这些机制，我们自适应地进化了R。opacus用于改进不同芳香族化合物的32种组合的利用。进化河与野生型菌株相比，Opacus突变体在苯酚、愈创木酚、4-羟基苯甲酸酯、香草酸酯和苯甲酸酯的利用方面表现出高达1900%的生长改善。全基因组测序揭示了几个氧化还原相关基因，其突变在多个适应突变体中共享。PVHG 6是在多种芳香化合物的混合物上生长最快的突变体，其超氧化物歧化酶活性比野生型菌株低56%，表明氧化还原反应对芳香耐受性和利用率很重要。比较转录组学揭示了副产品解毒途径和五个芳香族funtening途径，上调响应特定的芳香族化合物。基因敲除实验证实了五种芳香族化合物的β-酮己二酸途径的两种降解途径。这些结果为芳香族化合物的生物转化提供了更好的理解，并促进了R。opacus作为生物精炼厂的宿主
Lignin utilization has been identified as a key factor in biorefinery profitability. However, lignin depolymerization generates heterogeneous aromatic mixtures that inhibit microbial growth and the conversion of lignocellulose to biochemicals. Rhodococcus opacus is a promising aromatic-catabolizing, oleaginous bacterium, but mechanisms for its aromatic tolerance and utilization remain undercharacterized. To better understand these mechanisms, we adaptively evolved R. opacus for improved utilization of 32 combinations of diverse aromatic compounds. Evolved R. opacus mutants showed up to 1900% growth improvement in the utilization of phenol, guaiacol, 4-hydroxybenzoate, vanillate, and benzoate compared to the wild-type strain. Whole genome sequencing revealed several redox-related genes with mutations shared across multiple adapted mutants. PVHG6, the mutant with the most improved growth on a mixture of multiple aromatic compounds, showed 56% lower superoxide dismutase activity than the wild-type strain, suggesting that redox reactions are important for aromatic tolerance and utilization. Comparative transcriptomics revealed by-product detoxification pathways and five aromatic funneling pathways that were upregulated in response to specific aromatic compounds. Gene knockout experiments confirmed the two degradation routes of the beta-ketoadipate pathway for five aromatic compounds. These results provide an improved understanding of aromatic bioconversion and facilitate development of R. opacus as a biorefinery host.