Time Course of Thio-Phosphate Induced Metabolic Changes in E coli

Thio-phosphate (TP) results in profound metabolic consequences when added to culture media leading to increases in biosynthetic pathways in E coli. Analysis of total RNA after one hour of growth in TP containing media reveals a massive increase in mRNA (non-ribosomal RNA) on the order of 25-30% detected directly in Agilent RNA gels. By 5 hrs this increase is reduced ~50%, and stays that way reaching an apparent steady state relative to controls. RNA seq analysis at 1 hr confirms an average increase of 8X fold in transcripts relative to controls. Even at this early-stage, signs of transcriptional control are evident. While most gene transcripts detected are enhanced, ~17% are reduced relative to controls. The massive increase in non-ribosomal RNA makes it difficult to detect many gene transcripts in treated samples via RNA seq and the results clearly favor those transcripts already expressed at high levels. Nevertheless, the results indicate an early increase in amino acid synthesis, carbohydrates, the TCA cycle, exterior membrane proteins, and fermentation pathways. This is followed by later significant increases in lipid, isoprenoid, cofactor, and respiration pathways. A potential key regulator is identified, YegI, a ser/thr kinase that is induced 190X fold by 1 hr and not detected later.