The Escherichia coli FadR transcription factor: Too much of a good thing?

Abstract

Escherichia coli FadR is a transcription factor regulated by acyl-CoA thioester binding that optimizes fatty acid (FA) metabolism in response to environmental FAs. FadR represses the fad genes of FA degradation (β-oxidation) and activates the fab genes of FA synthesis thereby allowing E. coli to have its cake (acyl chains for phospholipid synthesis) and eat it (degrade acyl chains to acetyl-CoA). Acyl-CoA binding of FadR derepresses the transcription of the fad genes and cancels fab gene transcriptional activation. Activation of fab genes was thought restricted to the fabA and fabB genes of unsaturated FA synthesis, but FadR overproduction markedly increases yields of all FA acyl chains. Subsequently, almost all of the remaining fab genes were shown to be transcriptionally activated by FadR binding, but binding was very weak. Why are the low-affinity sites retained? What effects on cell physiology would result from their conversion to high-affinity sites (thereby mimicking FadR overproduction)? Investigations of E. coli cell size determinants showed that FA synthesis primarily determines E. coli cell size. Upon modest induction of FadR, cell size increases, but at the cost of growth rate and accumulation of intracellular membranes. Greater induction resulted in further growth rate decreases and abnormal cells. Hence, too much FadR is bad. FadR is extraordinarily conserved in γ-proteobacteria but has migrated. Mycobacterium tuberculosis encodes FadR orthologs one of which is functional in E. coli. Strikingly, the FadR theme of acyl-CoA-dependent transcriptional regulation is found in a different transcription factor family where two Bacillus species plus bacterial and archaeal thermophiles contain related proteins of similar function.

Keywords: FadR; Fatty acid synthesis; acyl-CoA; binding sites; thioesterase.

FIGURE 1

Fad R Regulates Two Opposing Pathways in E. coli. Fad R is a repressor of the fad genes and an activator of the fab genes. When present, environmental long-chain fatty acids are converted to their acyl-CoA thioesters after entering the cytosol. The acyl-CoAs (red dots) bind to FadR (blue ovals) resulting in the formation of a helix piston that spreads the N-terminal FadR DNA binding domains thereby eliminating the ability to cooperatively bind to the operator sites of the genes. In the absence of exogenous fatty acids (hence no acyl-CoAs) FadR is bound to the operators of both then fad and fab genes. The strongly regulated genes (+ and − denote positive and negative regulation, respectively) are those regulated by wild-type levels of FadR whereas the weakly related genes fall into two classes. The fatty acid uptake genes (fadD and fadL) are weakly negatively regulated by wild-type FadR whereas the fab, acc, and acpP genes show positive regulation only when FadR is overexpressed. Note that the genes of the anaerobic fatty acid degradation pathway are not under FadR regulation (Campbell et al., 2003)