Modulation of transcriptomic response of Streptomyces coelicolor towards ciprofloxacin with altered nutrient composition
Minal Patkari, Sarika Mehra*
Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai-400076
Antibiotic resistance is a major concern in the field of medicine as bacteria in the environment can come in close contact with one another and spread the resistance to many of the clinically important antibiotics. Some non-pathogenic bacteria harbour genes for intrinsic resistance, which are likely to transfer to pathogens. Study of intrinsic resistance mechanisms in non-pathogenic organism is, therefore, as important as a similar study in pathogens. Understanding the multiple ways in which bacteria develop resistance is important to devise effective solutions and to develop novel antimicrobials. Study of intrinsic resistance mechanisms in non-pathogenic organism is, therefore, as important as a similar study in pathogens. An extensive study on transcriptomics of S. coelicolor showed altered gene expression in presence of ciprofloxacin in Supplemented Minimal Medium (SMM) (Patkari & Mehra, 2013). The susceptibility for ciprofloxacin is decreased by four fold in a nutrient rich medium referred to as R5. This indicates that the growth conditions may also determine the response of bacteria towards particular antibiotic. Therefore, susceptibility of a bacterium to an antibiotic is dependent on the expression of various genes responsible for protection against stress conditions. This study aims to analyse the transcriptomic response of Streptomyces coelicolor towards ciprofloxacin treatment in rich medium as compared to minimal medium. A detailed transcriptomic study is performed at sub-inhibitory and inhibitory concentrations of ciprofloxacin to understand the mechanisms underlying the elevated resistance. The intracellular drug levels in the two media are also compared.
The response at sub-inhibitory concentration is mainly a stress response showing activation of most of anti-oxidant genes and few genes from nucleotide biosynthesis pathway. However, when the cells were exposed to a higher concentration of drug (MIC), upregulation of additional genes involved in protection against the stress and DNA damage were observed. The up-regulated genes belong to a variety of functional classes. Many genes from the DNA repair pathways and nucleic acid and protein metabolism are differentially regulated in both rich R5 medium and in supplemented minimal medium. Thus, the concentration of ciprofloxacin to induce SOS response is almost 8-folds higher in cells grown in richer R5 medium. We compared the basal expression of drug transporters which was found to be higher in rich medium cells as compared to cells grown in minimal medium. This data justifies the lower intracellular drug levels in rich medium cells which was almost 12 fold less in cells grown in minimal medium at ciprofloxacin 80 µg/ml. When exposed to inhibitory concentration of drug, cell attempts to survive by activating various mechanisms that assist in damage control. Thus, in this work we have compared the global response of S. coelicolor towards ciprofloxacin to establish the role of gene expression modulation with the nutrient supplements in resistance.
Keywords: S. coelicolor, ciprofloxacin, gene expression, antibiotic resistance