Polyomic elucidation of the 9,10-anthraquinone biodegradation pathway by a newly isolated oxy-PAH degrading specialist from PAH-contaminated soil

We report the isolation of the first bacterial strain, Sphingobium sp. AntQ-1, with the ability to grow on the oxy-PAH anthraquinone as sole carbon and energy source. We combine genomic, transcriptomic and metabolomic analysis to comprehensively elucidate the anthraquinone metabolic pathway and to identify key degradative genes. For the transcriptomic analysis, we performed a comparative RNA-seq experiment comparing the expression of cultures of Sphingobium sp. AntQ-1 grown either with anthraquinone or with acetate as control condition. Cells were grown in liquid mineral medium supplemented with vitamin B12 containing either anthraquinone or acetate as sole carbon sources. At the mid-exponential phase, cells were harvested for total RNA extraction. For each growth condition, RNA-seq analysis was done on three biological replicates of distinct rRNA-depleted RNA preparations.