Transcriptome analysis of copper resistance in Lysobacter soli strian RCu6

Copper is a trace element that has essential functions in many cellular enzymes; however, excessive copper levels can be toxic. Bacteria have evolved several copper resistance strategies, but the underlying mechanisms are not yet fully understood. Elucidating the mechanisms of copper resistance in bacteria is important for developing microbe-based techniques for mitigation of heavy metal pollution. In this study, a highly copper-resistant (resistant to copper concentrations up to 3.2 mmol∙L⁻¹) bacterial strain RCu6 was isolated. The genomic characteristics of RCu6 were studied using whole-genome sequencing, and copper resistance mechanisms were analyzed using transcriptome analysis. Whole-genome sequencing of strain RCu6 indicated that it belonged to Lysobacter soli. Compared to other strains in the same genus, this strain has a unique DNA fragment encompassing cop, cus, czc, and other homologous copper resistance genes. Transcriptome analysis showed that 315 (239 up-regulated and 76 down-regulated) and 839 (449 up-regulated and 390 down-regulated) genes were differentially expressed under 0.8 mmol∙L⁻¹ and 1.6 mmol∙L⁻¹ copper concentrations, respectively. The differential gene expression was mainly associated with copper homeostasis, histidine metabolism, sulfur metabolism, and iron-sulfur cluster assembly metabolism, indicating that these processes may play important roles in copper resistance of RCu6. The results of the transcriptome analysis were further verified using qPCR. The expression levels of 12 randomly selected genes associated with copper resistance showed significant correlations between qPCR and RNA-Seq data (R²=0.84 for GAPDH gene and R²=0.98 for 16S rRNA gene as internal reference genes). Therefore, the genomic and transcriptome results suggest that copper resistance in the strain Lysobacter soli RCu6 is an intracellular multi-system collaborative process. This study provides new information for understanding the complex regulatory network of copper homeostasis in prokaryotes. It also provides bacterial resources and a theoretical basis for the remediation of heavy metals in farmland soil.