Abstract
Lipid A is a highly conserved component of lipopolysaccharide (LPS), itself a major component of the outer membrane of Gram-negative bacteria. Lipid A is essential to cells and elicits a strong immune response from humans and other animals. We developed a quantitative model of the nine enzyme-catalyzed steps of Escherichia coli lipid A biosynthesis, drawing parameters from the experimental literature. This model accounts for biosynthesis regulation, which occurs through regulated degradation of the LpxC and WaaA (also called KdtA) enzymes. The LpxC degradation signal appears to arise from the lipid A disaccharide concentration, which we deduced from prior results, model results, and new LpxK overexpression results. The model agrees reasonably well with many experimental findings, including the lipid A production rate, the behaviors of mutants with defective LpxA enzymes, correlations between LpxC half-lives and cell generation times, and the effects of LpxK overexpression on LpxC concentrations. Its predictions also differ from some experimental results, which suggest modifications to the current understanding of the lipid A pathway, such as the possibility that LpxD can replace LpxA and that there may be metabolic channeling between LpxH and LpxB. The model shows that WaaA regulation may serve to regulate the lipid A production rate when the 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) concentration is low and/or to control the number of KDO residues that get attached to lipid A. Computation of flux control coefficients showed that LpxC is the rate-limiting enzyme if pathway regulation is ignored, but that LpxK is the rate-limiting enzyme if pathway regulation is present, as it is in real cells. Control also shifts to other enzymes if the pathway substrate concentrations are not in excess. Based on these results, we suggest that LpxK may be a much better drug target than LpxC, which has been pursued most often.
Highlights
Lipopolysaccharide (LPS) is a glycolipid that forms the major component of the outer leaflet of the outer membrane of most Gram-negative bacteria
The LpxC product still accumulated in cells without FtsH due to the higher metabolite flux through the LpxC step and the lack of product inhibition at this step. This Ki value caused the steady-state lipid X concentration to be about 22,000 molecules, in either wild-type or FtsH mutant cells, which is much larger than the 2000 that were observed experimentally [77]. We found that this difference cannot be eliminated by adjusting enzyme kinetic parameters without creating large metabolite accumulations, which suggests that this region of the biosynthesis pathway includes dynamics that are not in our model
We constructed a model of the E. coli lipid A biosynthesis pathway, including its regulation, using parameters derived from published experimental data
Summary
Lipopolysaccharide (LPS) is a glycolipid that forms the major component of the outer leaflet of the outer membrane of most Gram-negative bacteria. It occurs with roughly 1 million copies in Escherichia coli cells, covering about 75% of the cell surface area [1],[2],[3]. A Model for Lipid A Biosynthesis in E. coli doi:10.1371/journal.pone.0121216.g001 surfaces [4] It elicits a strong immune response in humans and other animals (and is a main contributor to Gram-negative septic shock), getting detected at picomolar levels by the innate immune system’s TLR4 protein [5]. These attributes have made the study of LPS important to the fields of immunology, bacteriology, and drug discovery [1],[2],[5],[6],[7],[8]
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