Genomic and transcriptomic analyses reveal insights into cadmium resistance mechanisms of Cupriavidus nantongensis strain E324

• Published in: The Science of the total environment 2024-11, Vol.952, p.175915, Article 175915
• Main Authors: Kerdsomboon, Kittikhun, Techo, Todsapol, Mhuantong, Wuttichai, Limcharoensuk, Tossapol, Luangkamchorn, Supinda Tatip, Laoburin, Patcharee, Auesukaree, Choowong
• Format: Article
• Language: English
• Subjects: Biodegradation, Environmental; Cadmium; Cadmium - toxicity; Cupriavidus - drug effects; Cupriavidus - genetics; Cupriavidus - metabolism; Cupriavidus nantongensis; Gene Expression Profiling; Genomics; Oxidative Stress; Resistance mechanism; Transcriptome; Transcriptome - drug effects; Whole-genome sequencing; Zinc
• ISSN: 0048-9697; 1879-1026; 1879-1026
• DOI: 10.1016/j.scitotenv.2024.175915

The cadmium-resistant Cupriavidus sp. strain E324 has been previously shown to have a high potential for use in cadmium (Cd) remediation, due to its high capacity for cadmium bioaccumulation. According to the comparative genomic analysis, the strain E324 was most closely related to C. nantongensis X1T, indicating that the strain E324 should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of C. nantongensis strain E324, the transcriptional response of this strain to acute Cd exposure was assessed using RNA-seq-based transcriptome analysis, followed by validation through qRT-PCR. The results showed that the upregulated Differentially Expressed Genes (DEGs) were significantly enriched in categories related to metal binding and transport, phosphate transport, and oxidative stress response. Consistently, we observed significant increases in both the cell wall and intracellular contents of certain essential metals (Cu, Fe, Mn, and Zn) upon Cd exposure. Among these, only the Zn pretreatment resulting in high Zn accumulation in the cell walls could enhance bacterial growth under Cd stress conditions through its role in inhibiting Cd accumulation. Additionally, the promotion of catalase activity and glutathione metabolism upon Cd exposure to cope with Cd-induced oxidative stress was demonstrated. Meanwhile, the upregulation of phosphate transport-related genes upon Cd treatment seems to be the bacterial response to Cd-induced phosphate depletion. Altogether, our findings suggest that these adaptive responses are critical mechanisms contributing to increased Cd tolerance in C. nantongensis strain E324 via the enhancement of metal-chelating and antioxidant capacities of the cells. [Display omitted] •The cadmium-resistant strain E324 was re-identified as Cupriavidus nantongensis.•Increased Zn levels in the cell walls by Zn pretreatment suppress Cd accumulation.•Catalase is a major antioxidant enzyme involved in coping with prolonged Cd stress.•The upregulation of glutathione genes helps maintain the GSH pool during Cd stress.•The upregulation of Pi transport genes is a response to Cd-induced Pi depletion.