Streptomyces tsukubaensis: transcriptomic response to tacrolimus repressing carbon sources

In this work, we identified glucose and glycerol as tacrolimus repressing carbon sources in the important species Streptomyces tsukubaensis. A genome-wide analysis of the transcriptomic response to glucose and glycerol additions was performed using microarray technology. The transcriptional time series obtained allowed us to compare the transcriptomic profiling of S. tsukubaensis growing under tacrolimus producing and non-producing conditions. The analysis revealed important and different metabolic changes after the additions and a lack of transcriptional activation of the fkb cluster. In addition, we detected important differences in the transcriptional response to glucose between S. tsukubaensis and the model species Streptomyces coelicolor. A number of genes encoding key players of morphological and biochemical differentiation were strongly and permanently downregulated by the carbon sources. Finally, we identified several genes showing transcriptional profiles highly correlated to that of the tacrolimus biosynthetic pathway regulator FkbN that might be potential candidates for the improvement of tacrolimus production The transcriptomic experiment is composed of 54 samples from three time series named glucose, glycerol and maltose. Streptomyces tsukubaensis spores (10e9) were inoculated into 0.5-L flasks containing 100 mL of MGm-2.5 medium (PMID 22990582) and cultivated at 28 ºC, 220 rpm. Samples for RNA extraction were taken from flask cultures at 70 h, immediately before carbon source addition; then, glucose, glycerol or maltose were added and more samples were taken at 70.7 h, 72 h, 76 h, 80 h, 89 h, 92 h, 100 h, 124 h and 148 h. The final concentrations of glucose and glycerol were established at the same molarity (0.22 M; 2 % w/v and 4 % w/v for glucose and glycerol, respectively). The final concentration of maltose was 0.11 M (3 % w/v) in order to equalize the number of glucose molecules available after maltose incorporation. Each time series is composed of 2 biological replicates for 8 the first timepoints (70 h - 100 h) and 1 biological replicate for the rest of the culture time; i.e., only one culture was sampled at 124 h and 148 h. In summary, (8 timepoints × 2 replicates × 3 carbon sources) = 48 samples; (2 timepoints × 1 replicates × 3 carbon sources) = 6 samples; 48 + 6 = 54 samples in total.