Transcriptome analysis of copper resistance in Lysobacter soli strian RCu6

Copper is a trace element essential for the functions of many cellular enzymes; however, excessive level of copper could be toxic. Bacteria have evolved a number of 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 heavy metal pollution. In this study, a highly copper-resistant (resistant to copper concentration up to 3.2 mmol∙L −1 ) bacterial strain RCu6 was isolated. The genomic characteristics of RCu6 were studied by whole-genome sequencing, and the copper resistance mechanisms were analyzed by transcriptome analysis. Whole genome sequencing of strain RCu6 indicated that the strain belonged to Lysobacter soli. Compared with other strains in the same genus, this strain has a unique DNA fragment encompassing cop, cus, czc and other copper resistance homologous 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 an important role for the copper resistance of RCu6. The results of 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 (R 2 = 0.84 for GAPDH gene and R 2 = 0.98 for 16S rRNA gene as internal reference genes). Taken together, genomic and transcriptome results suggested that copper resistance in strain Lysobacter soli RCu6 is an intracellular multi-system collaborative process. This study provided new information for understanding the complex regulatory network of copper homeostasis in prokaryotes. It also provides bacterial resources and theoretical basis for remediation of heavy metals in farmland soils.