Catabolic Mechanism of 17β-Estradiol in Rhodococcus erythropolis KB1: Insights from Metabolomics, Genomics, and Transcriptomics

The release and prolonged retention of steroid hormones pose significant risks to both human health and the environment. Research on efficient-degrading bacteria at higher concentrations and their degradation pathways, genes, and enzymes is limited. In this study, Rhodococcus erythropolis KB1 efficiently degraded 96.75% of 50 mg/L 17β-estradiol (E2) within nine days. Including the 4,5- and 9,10-seco pathways, five putative degradation pathways were identified based on the analysis of metabolic intermediates and products using high-performance liquid chromatography–quadrupole–time-of-flight–mass spectrometry (HPLC-Q-TOF-MS). Under the proposed aerobic pathways, E2 undergoes hydroxylation or cleavage at ring A or B. The resultant products are subsequently converted into a common steroid metabolite, 3aα-H-4α(3′-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP), via β-oxidation. HIP is further degraded through a central pathway and ultimately assimilated into the tricarboxylic acid (TCA) cycle. Whole-genome sequencing predicted a steroid degradation-related gene cluster on contig NZ_CP050127.1 . Transcriptomic analysis demonstrated that the expression of the short-chain dehydrogenase (SDR) gene and three cyp genes in this gene cluster were significantly induced by E2. Additionally, the global response of E2 in strain KB1 was analyzed using transcriptome analysis. Various genes involved ATP-binding cassette (ABC) transport system, electron transfer and energetic metabolism, and stress response—were significantly increased in mRNA levels in response to strain KB1 that can use E2 as the single carbon source. These findings highlight strain KB1 as a promising candidate for E2 biodegradation, offer novel insights into the microbial mechanisms of E2 catabolism, and establish a theoretical basis for future applications.