TY - JOUR
T1 - The degradation mechanisms of Rhodopseudomonas palustris toward hexabromocyclododecane by time-course transcriptome analysis
AU - Li, Yi Jie
AU - Wang, Reuben
AU - Lin, Chung Yen
AU - Chen, Shu Hwa
AU - Chuang, Chia Hsien
AU - Chou, Tzu Ho
AU - Ko, Chi Fang
AU - Chou, Pei Hsin
AU - Liu, Chi Te
AU - Shih, Yang hsin
N1 - Funding Information:
Research grants from Taiwan's Ministry of Science and Technology (No. 106-2221-E-002 -043 -MY3 ) and the joint program of National Taiwan University and Academia Sinica, Taiwan (NTU-AS-109L104312 and NTU-AS-110L104312) support this work. We also thank the High Throughput Sequencing Core hosted in the Biodiversity Research Center at Academia Sinica for performing the NGS experiments.
Publisher Copyright:
© 2021 Elsevier B.V.
PY - 2021/12/1
Y1 - 2021/12/1
N2 - 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.
AB - 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.
KW - Biodegradation
KW - Hexabromocyclododecane
KW - Metabolic pathway
KW - Rhodopseudomonas palustris
KW - Transcriptome
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U2 - 10.1016/j.cej.2021.130489
DO - 10.1016/j.cej.2021.130489
M3 - Article
AN - SCOPUS:85111058276
SN - 1385-8947
VL - 425
JO - Chemical Engineering Journal
JF - Chemical Engineering Journal
M1 - 130489
ER -