Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

Authors

Pep Charusanti, University of California San Diego
Tom M. Conrad, University of California - San Diego
Eric M. Knight, University of California San Diego
Karthik Venkataraman, University of California San Diego
Nicole L. Fong, University of California San Diego
Bin Xie, Virginia Commonwealth University
Yuan Gao, Virginia Commonwealth University
Bemhard O. Palsson, University of California San Diego

Document Type

Article

Original Publication Date

2010

Journal/Book/Conference Title

PLOS Genet

Volume

6

DOI of Original Publication

10.1371/journal.pgen.1001186

Comments

Originally Published at http://dx.doi.org/10.1371/journal.pgen.1001186

Date of Submission

November 2014

Abstract

Bacterial survival requires adaptation to different environmental perturbations such as exposure to antibiotics, changes in temperature or oxygen levels, DNA damage, and alternative nutrient sources. During adaptation, bacteria often develop beneficial mutations that confer increased fitness in the new environment. Adaptation to the loss of a major non-essential gene product that cripples growth, however, has not been studied at the whole-genome level. We investigated the ability of Escherichia coli K-12 MG1655 to overcome the loss of phosphoglucose isomerase (pgi) by adaptively evolving ten replicates of E. coli lackingpgi for 50 days in glucose M9 minimal medium and by characterizing endpoint clones through whole-genome re-sequencing and phenotype profiling. We found that 1) the growth rates for all ten endpoint clones increased approximately 3-fold over the 50-day period; 2) two to five mutations arose during adaptation, most frequently in the NADH/NADPH transhydrogenasesudhA and pntAB and in the stress-associated sigma factor rpoS; and 3) despite similar growth rates, at least three distinct endpoint phenotypes developed as defined by different rates of acetate and formate secretion. These results demonstrate that E. coli can adapt to the loss of a major metabolic gene product with only a handful of mutations and that adaptation can result in multiple, alternative phenotypes.

Rights

Copyright: © 2010 Charusanti et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Is Part Of

VCU Study of Biological Complexity Publications