Analysis of the transcriptome in a multi-drug resistant uropathogenic Escherichia coli strain treated with water decoction of rhizoma coptidis by using RNA-seq

Objective To investigate the molecular mechanism of the inhibitory effects of rhizoma coptidis on multi-drug resistant uropathogenic Escherichia coli. Methods High-throughput RNA sequencing (RNA-seq) was performed to investigate the transcriptome in a multi-drug resistant uropathogenic Escherichia coli strain (NB8) treated with water decoction of rhizoma coptidis. Agar dilution test was used to determine the minimal inhibitory concentration (MIC) of water decoction of rhizoma coptidis against the NB8 strain. A growth curve was drawn to evaluate the effects of water decoction of rhizoma coptidis on the growth of NB8 strain. Total RNAs were extracted from the NB8 strain after treated with the water decoction of rhizoma coptidis for 30 minutes and then synthetized to cDNA by reverse transcription after screening out the rRNAs. The HiSeq 2000 sequencing system was used for transcriptome sequencing. The TopHat software was used to map and analyze the RNA-Seq reads, and then Cufflinks was run to assemble transcripts and estimate their abundances. The differential expression, GO enrichment and KEGG metabolic pathway were further analyzed. The NB8 strain dealt with normal saline was used as negative control. Results The MIC of water decoction of rhizoma coptidis to NB8 strain was 12.5 mg/ml. There were 3665 genes expressed in NB8 strain treated with water decoction of rhizoma coptidis and 3430 genes expressed in NB8 strain treated with normal saline. The number of differentially expressed genes was 1428 including 921 up-regulated genes and 507 down-regulated genes. Those differentially expressed genes mainly enriched in the modules of binding and catalysis. The genes concerning cell adhesion, apoptosis and multicellular process were up-regulated, while those concerning the regulation of enzyme activities were down-regulated. Results of the KEGG metabolic pathway enrichment analysis showed that the genes concerning synthetic pathway of LPS were significantly up-regulated as well as those encoding the repair polymerase Ⅲ that was involved in DNA replication. However, the genes concerning fatty acid metabolism, histidine metabolism, thiamine metabolism, folate metabolism and iron carrier in ribosome synthesis showed overall down-regulation. Conclusion The transcriptome in uropathogenic Escherichia coli strain treated with rhizoma coptidis was profiled. The main molecular mechanism of the inhibitory effects of rhizoma coptidis on uropathogenic Escherichia coli was to destroy the cell wall of Escherichia coli, affect the replication of DNA and regulate the transcription and translation of proteins. This study illustrated that the inhibitory effects of rhizoma coptidis on uropathogenic Escherichia coli were achieved in multiple levels. Key words: Escherichia coli; Transcriptome; Water decoction of rhizoma coptidis; RNA-seq; Differentially expressed genes; Functional enrichment