Mechanisms of Nutrient Sensing and Gene Regulation by the E. Coli Leucine-responsive Regulatory Protein, a Global Feast-Famine Transcriptional Regulator

Abstract

The E. coli Leucine-responsive Regulatory Protein (Lrp) belongs to an ancient and highly conserved class of transcription factors called the Feast/Famine Response Proteins (FFRPs), which are present in nearly half of all sequenced bacteria and almost all archaea. As the name suggests, these proteins can sense the environmental nutrient status by binding to one or more effector molecules (usually an amino acid) under “feast” conditions, and subsequently regulate relevant gene expression to optimize fitness of the host organism in that environment. Most FFRPs serve as local transcription factors that alter expression of one or two operons in response to an effector molecule. E. coli Lrp, on the other hand, serves a dual role as both a general nucleoid-associated protein that compacts and organizes the chromosome, and also as a global transcriptional regulator that specifically controls the expression of up to one-third of the genes in E. coli in response to environmental nutrient availability. However, despite over 50 years of research, little is known about the precise mechanisms by which Lrp senses the environmental nutrient status or how it subsequently regulates its target genes.

To address these two major questions, we utilized a combination of high-throughput experiments, follow-up case studies at a handful of regions where Lrp is known to regulate gene expression, analysis of various Lrp mutants, and careful biochemical and structural studies. We determined that Lrp bridges DNA under starvation conditions to regulate gene expression, and that leucine (which is abundant in “feast” conditions) causes drastic global Lrp-mediated changes in gene expression by inhibiting Lrp bridging and reducing Lrp binding to DNA across the genome. Furthermore, we also re-characterized two previously identified “octamer-only” Lrp mutants as a leucine insensitive Lrp mutant (L136R) and a hyper-bridging Lrp variant (D114E). With respect to environmental nutrient sensing, we show that Lrp responds to a variety of metabolites aside from leucine, the most notable of which is 3,4-dihydroxyphenylglycol (DHPG), a breakdown product of norepinephrine, which is a neurotransmitter that is highly abundant in the human gut. Unlike leucine, DHPG modulates Lrp activity by reducing the oligomerization state of Lrp from an octamer/hexadecamer to a dimer, which alters DNA binding. Collectively, these findings shed light on how E. coli Lrp regulates expression of its target genes in response to nutrient availability, while also expanding upon the known set of molecules through which Lrp senses its environment.