Metabolic characterization of Escherichia coli adapted to growth on lactate

Qiang Hua, Andrew R. Joyce, Bernhard . Palsson^*, and Stephen S. Fong

Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412; Bioinformatics Program, University of San Diego, La Jolla, California

^* To whom correspondence should be addressed. Email: palsson{at}ucsd.edu.

	Abstract

In comparison with intensive studies of genetic mechanisms related to biological evolutionary systems, much less analysis has been conducted on metabolic network responses to adaptive evolution that are directly associated with evolved metabolic phenotypes. Metabolic mechanisms involved in laboratory evolution of Escherichia coli on gluconeogenic carbon source such as lactate were studied based on intracellular flux states determined from ¹³C tracer experiments and ¹³C-constrained flux analysis. At the endpoint of laboratory evolution, strains exhibited a more than doubling in average growth rate and a 50% increase in average biomass yield. Despite different evolutionary trajectories among parallel evolved populations, most improvements were obtained within the first 250 generations of evolution and were generally characterized by a significant increase in pathway capacity. Partitioning between gluconeogenic and pyruvate catabolic flux at the pyruvate node remained almost unchanged, while flux distributions around the key metabolites phosphoenolpyruvate, oxaloacetate, and acetyl-CoA were relatively flexible over the course of evolution on lactate to meet energetic and anabolic demands during rapid growth on this gluconeogenic carbon substrate. There were no clear qualitative correlations between most transcriptional expression and metabolic flux changes, suggesting complex regulatory mechanisms at multiple levels of genetics and molecular biology. Moreover, higher fitness gains for cell growth on both evolutionary and alternative carbon sources were found in strains adaptively evolved on gluconeogenic carbon sources compared to those evolved on glucose. These results provide a novel systematic view of the mechanisms underlying the microbial adaptation to growth on a gluconeogenic substrate.