Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli

Abstract

Transcription networks consist of hundreds of transcription factors with thousands of often overlapping target genes. While we can reliably measure gene expression changes, we still understand relatively little why expression changes the way it does. How does a coordinated response emerge in such complex networks and how many input signals are necessary to achieve it? Here, we unravel the regulatory program of gene expression in Escherichia coli central carbon metabolism with more than 30 known transcription factors. Using a library of fluorescent transcriptional reporters, we comprehensively quantify the activity of central metabolic promoters in 26 environmental conditions. The expression patterns were dominated by growth rate‐dependent global regulation for most central metabolic promoters in concert with highly condition‐specific activation for only few promoters. Using an approximate mathematical description of promoter activity, we dissect the contribution of global and specific transcriptional regulation. About 70% of the total variance in promoter activity across conditions was explained by global transcriptional regulation. Correlating the remaining specific transcriptional regulation of each promoter with the cell's metabolome response across the same conditions identified potential regulatory metabolites. Remarkably, cyclic AMP, fructose‐1,6‐bisphosphate, and fructose‐1‐phosphate alone explained most of the specific transcriptional regulation through their interaction with the two major transcription factors Crp and Cra. Thus, a surprisingly simple regulatory program that relies on global transcriptional regulation and input from few intracellular metabolites appears to be sufficient to coordinate E. coli central metabolism and explain about 90% of the experimentally observed transcription changes in 100 genes.

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

“…To apply the notion of saturation to our data, we obtained previously published metabolite concentrations in exponentially growing E. coli cultures on 13 different carbon sources (Kochanowski et al, 2017). For each unique binding constant/metabolite concentration pair, we calculated the saturation level (332 enzyme-inhibitor-condition triplets and 798 enzyme-substrate-condition triplets, Figure 4e).…”

“…Middle diagram indicates reactions which are indirectly regulated by metabolites via transcription: in each case, the reaction is regulated by transcription factors that are recipients of metabolic signals (i.e. Cra-FDP, Crp-cAMP), as reported in (Kochanowski et al, 2017). Some reactions, e.g.…”

Drug persistence – From antibiotics to cancer therapies

“…Lessons from bacterial research may provide some inspiration. For example, recent works have shown that the global coordination of protein expression in bacteria heavily depends on the growth rate [61–65] and can be described by few so-called ‘growth laws’ [66]. It is tempting to speculate that in cancer cells similar mechanisms could potentially induce an EMT-type transcriptional program if growth is impaired.…”

The imbroglio of the physiological Cra effector clarified at last

“…However, Bledig et al () suggested also the possibility that the high levels of FBP that occur during glycolysis in vivo could be enough to allosterically regulate Cra in cells. Following this somewhat speculative statement, many subsequent articles took for granted that FBP was a real effector of Cra (Hardiman et al, ; Kotte et al, ; Kochanowski et al, ; ; Wei et al, ; Zhu et al, ; Kim et al, ). This assumption was not devoid of logic, as FBP has been recognized as a flux‐signaling metabolite that correlates with the flow of carbon through glycolysis in Bacillus subtilis and E. coli (Litsios et al, ).…”