Complete Gene Expression Profiling of Saccharopolyspora erythraea NRRL 2338

A DNA microarray was designed and constructed using the genome sequence of Saccharopolyspora erythraea strain NRRL 2338. Following growth in liquid medium, we analysed the expression of 6494 ORFs along the time course. The results indicated that the 404 genes, whose expression significatively correlated with the time course, identify three distinct growth phases: a rapid growth until 32 h (phase A); a growth slowdown until 52 h (phase B); another rapid growth phase from 56 h to 72 h (phase C) before entering the stationary phase. We experimentally determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, but also strand specific patterns of expression, and the behavior of major functional classes. Temporal expression of all the gene clusters for secondary metabolism was analyzed, confirming ery cluster up-regulation during the first growth phase, and finding out six secondary metabolism clusters that are clearly regulated during growth. The use of a DNA microarray, specifically designed on the Sac. erythraea genome sequence, improved specificity and sensitivity of gene expression analysis, giving a global and at the same time detailed picture of how Sac. erythraea genes are modulated. Keywords: time course Overall design: Spores of S. erythraea strain NRRL2338 were inoculated into SCM liquid medium. Samples were withdrawn at different time points: after 12h, 16h, 20h, 32h, 36h, 40h, 52h, 56h, 60h and 72h from the initial inoculum. Erythromycin production and wet cell weight were determined. RNA samples were extracted from two independent cultures, processed and hybridized to custom made GeneChips containing DNA oligonucleotide probes corresponding to 6494 predicted Sac. erythaea ORFs.