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Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models

Nathan E Lewis, Kim K Hixson, Tom M Conrad, Joshua A Lerman, Pep Charusanti, Ashoka D Polpitiya, Joshua N Adkins, Gunnar Schramm, Samuel O Purvine, Daniel Lopez‐Ferrer, Karl K Weitz, Roland Eils, Rainer König, Richard D Smith, Bernhard Ø Palsson

Author Affiliations

  1. Nathan E Lewis1,
  2. Kim K Hixson2,
  3. Tom M Conrad3,
  4. Joshua A Lerman4,
  5. Pep Charusanti1,
  6. Ashoka D Polpitiya2,
  7. Joshua N Adkins2,
  8. Gunnar Schramm5,6,
  9. Samuel O Purvine2,
  10. Daniel Lopez‐Ferrer2,
  11. Karl K Weitz2,
  12. Roland Eils5,6,
  13. Rainer König5,6,
  14. Richard D Smith2 and
  15. Bernhard Ø Palsson*,1
  1. 1 Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
  2. 2 Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
  3. 3 Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
  4. 4 Systems Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
  5. 5 Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, and Bioquant, University of Heidelberg, Heidelberg, Germany
  6. 6 Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
  1. *Corresponding author. Department of Bioengineering, University of California San Diego, 417 Powell‐Focht Bioengineering Hall, 9500 Gilman Drive, La Jolla, CA 92093‐0412, USA. Tel.: +1 858 534 5668; Fax: +1 858 822 3120; E-mail: palsson{at}ucsd.edu
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Abstract

After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild‐type and evolved strains. Here, we report that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the evolved strains upregulate genes within the optimal growth predictions, and downregulate genes outside of the optimal growth solutions. In addition, bottlenecks from dosage limitations of computationally predicted essential genes are overcome in the evolved strains. We also identify regulatory processes that may contribute to the development of the optimal growth phenotype in the evolved strains, such as the downregulation of known regulons and stringent response suppression. Thus, differential gene and protein expression from wild‐type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM‐computed optimal growth states.

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Synopsis

When prokaryotes are maintained at early‐ to mid‐log phase growth through serial passaging for hundreds of generations, the strains improve fitness and evolve a higher growth rate (Lenski and Travisano, 1994; Ibarra et al, 2002). This increased growth rate is the result of the appearance of a few causal mutations (Herring et al, 2006; Conrad et al, 2009). In Escherichia coli, these altered growth phenotypes are consistent with predictions from genome‐scale models of metabolism (GEMs) (Ibarra et al, 2002; Fong and Palsson, 2004). However, it is still not known (1) whether absolute gene and protein expression levels and expression changes are consistent with optimal growth predictions from in silico GEMs or (2) whether measured expression changes can be linked to physiological changes that are based on known mechanisms or pathways. In this study, we begin to address these questions using constraint‐based modeling of E. coli K‐12 metabolism (Feist and Palsson, 2008) to analyze omic data that document the expression changes in E. coli under adaptive evolution in three different growth conditions.

Mapping high‐throughput data to a network can be useful for interpretation. However, it does not account for upstream and downstream effects of gene and protein expression changes. The analysis of data in the context of GEMs can suggest if predicted activity is consistent with the data. For this work, we used a variant of flux balance analysis (FBA), called Parsimonious enzyme usage FBA (pFBA) (Figure 1), to classify all genes according to whether they are used in the optimal growth solutions. Results from these models were compared with the data to assess whether the data were consistent with genes and proteins within the predicted optimal solutions, and whether the expression changes were consistent with measured physiology. Through this analysis, we find that the data provide a high coverage of genes that contribute to the optimal growth solutions (Figure 1B). In fact, the union of the proteomic and transcriptomic data for non‐essential genes provides support for 97.7% of all non‐essential gene‐associated reactions within the optimal growth predictions. Thus, the spectrum of expressed genes and proteins is consistent with the pathway utilization that is predicted for these optimal growth phenotypes.

Laboratory‐evolved strains attain a higher growth rate. This higher growth rate is usually associated with an increased substrate uptake rate (Ibarra et al, 2002; Fong et al, 2005) and in some cases more efficient metabolism (Ibarra et al, 2002). Both of these properties are also witnessed in the strains studied here. It has been reported that in most cases, evolved strain growth phenotype is consistent with GEM predictions (Ibarra et al, 2002; Teusink et al, 2009). Here, we evaluate whether the laboratory‐evolved strains adjust the gene and protein expression levels in accordance with pathway usage in the optimal growth predictions. Essential and non‐essential genes and proteins within the optimal growth solutions are significantly upregulated (Figure 1B). This suggests that these proteins may be acting as bottlenecks that are relieved through the adaptive process, thereby allowing for a higher substrate uptake rate and growth rate. However, genes and proteins associated with reactions that cannot carry a flux in the given growth conditions are downregulated in the evolved strains (Figure 1B). Furthermore, there is downregulation of genes associated with less efficient pathways (Figure 5C). Thus, the omic data support the emergence of the predicted optimal growth states, consistent with the increased substrate uptake upstream and the increased biomass production downstream of these internal pathways.

Regulatory mechanisms, both known and unknown, are responsible for the changes seen here. Across all data sets, several metabolic regulons are significantly downregulated. However, no known regulons were enriched among upregulated genes or proteins for all but one data set. Aside from just regulating the metabolic pathways directly, these mechanisms lead to additional physiological changes. For example, in the minimal media growth conditions used here, the stringent response normally represses growth while upregulating amino‐acid biosynthetic processes. However, evolved strain gene expression shows a suppression of the stringent response, as evolved strain gene expression shows either no expression change or changes opposite to the normal stringent response.

The implications of this work are as follows: (1) genome‐scale gene and protein expression data are consistent with FBA computed optimal growth states, and evolved strains reinforce these optimal states; (2) genome‐scale models will have an important function bridging the gap between genotype and phenotype; and (3) the development of additional genome‐scale models of other growth‐related processes such as transcription and translation (Thiele et al, 2009) will have an important function in elucidating the mechanisms that contribute the most to altered phenotypes (Lewis et al, 2009a). In addition, reconstruction of the transcriptional regulation network will aid in identifying the control of expression changes seen in the other systems.

  • Proteomic and transcriptomic data from wild‐type and laboratory‐evolved strains of Escherichia coli are consistent with predicted pathway usage from optimal growth rate solutions.

  • In laboratory‐evolved strains, there is an upregulation of the pathways in the computed optimal growth states, and downregulation of non‐functional pathways.

  • Known regulatory mechanisms are only partially responsible for altered metabolic pathway activity.

Mol Syst Biol. 6: 390

  • Received March 18, 2010.
  • Accepted June 1, 2010.

This is an open‐access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.

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