The degradation mechanisms of Rhodopseudomonas palustris toward hexabromocyclododecane by time-course transcriptome analysis

•The transcriptome revealed that HBCD triggered the expression of 126 transcripts.•The increased expression of regulators and working enzymes was confirmed by qRT-PCR.•HBCD signal transferred from memebrane to LysR and then to downstream enzymes.•The systematic transcriptomics discover and elucidate the microbial metabolisms. Hexabromocyclododecane (HBCD) is one of the most frequently used brominated flame retardants (BFRs). However, the HBCD degradation method's development has become vital because it readily bioaccumulates and is persistent in the environment. A previous study showed Rhodopseudomonas palustris degrades HBCD through several possible metabolic pathways based on transcriptomic analysis of compared samples. This study introduces multiple time-course transcriptomic analysis approaches to identify the specific HBCD metabolic pathway in R. palustris inbubated at different temperatures. The transcriptome profiles revealed that the addition of HBCD triggered 126 transcripts in cells at 25°C and 35°C. Further KEGG analysis showed several HBCD induced metabolic pathways, including ABC transporter, butanoate metabolism, dephosphorylation, lipid glycosylation pathways, etc. The principal component analysis further provides evidence of genes directly affected by HBCD. The increased expression level of transcriptional regulator LysR, two-component system regulators, HBCD degradation enzymes, including haloacid dehalogenases, glutathione-S-transferase, cytochrome p450, hydrolases, and dioxygenases in R. palustris were confirmed by qRT-PCR analysis. Combining the transcriptomic profiles and gene expression level analysis, we proposed the HBCD metabolic pathway in R. palustris. Briefly, HBCD signal transferred from cell membrane to transcriptional regulator LysR, then further to downstream degradation working enzymes. Overall, our results highlight the value of systematic transcriptomic approaches to discover and elucidate the intrinsic microbial metabolisms for HBCD degradation in R. palustris. The results of this study provide a novel perspective on the degradation of persistent organic pollutants (POPs) such as HBCD using a bio-omics approach.