Exploring the Proteome of E. coli Following Adaptation to Environmental and Genetic Perturbation
EMSL Project ID
25660
Abstract
Microorganisms rapidly adapt to changes in the environment which ensures their survival under suboptimal conditions. It is well known that microorganisms display genomic plasticity that enables rapid evolution, but little information is available regarding specific links between the evolved genotype and phenotype. We have employed laboratory evolution, long used to investigate adaptive processes, with Escherichia coli as a model system for the comprehensive investigation of genotype-phenotype relationships. Whole genome resequencing and other post-genomic technology-driven studies of strains evolved in the laboratory are emerging, but proteomic analyses to date have been limited. This proposal sets forth a plan to utilize the novel proteomic strategies at PNNL to investigate three sets of E. coli K-12 MG1655 derived strains adapted to environmental and genetic perturbations. Two sets of strains were adapted to growth on M9 minimal medium supplemented with the non-preferred substrates glycerol (six strains) and lactate (five strains). The third set of ten strains harbor a deletion in the phosphoglucose isomerase (pgi) gene, essentially re-routing glycolytic carbon flux through the pentose phosphate pathway. The adaptation of these single gene deletion strains to growth on glucose-supplemented M9 minimal medium represent examples of how E. coli overcomes a genetic perturbation. Each of these 21 strains exhibited dramatic fitness gains as measured by at least a doubling of growth rate at the endpoint of experimental evolution (600-1000 generations) when compared to the respective progenitor strains. In conjunction with the Biological Interactions and Dynamics imitative at the Environmental Molecular Sciences Laboratory, we aim to obtain high-throughput quantitative proteomics data for these 21 adapted E. coli strains. This data will identify both local and system-wide changes in the proteome which can be linked to increased fitness on non-preferred carbon sources glycerol and lactate, as well as increased fitness following adaptation to a single gene deletion (pgi). We also plan to perform integrative analyses using the resulting proteomics data in conjunction with existing high throughput data for these strains to gain a deeper understanding of the systemic changes that underlie the observed fitness gains. Furthermore, this experimental program presents a unique opportunity to assess the ability of the PNNL proteomic technologies to directly identify potentially important changes in individual proteins in biological systems. The ability to detect amino acid changes directly in this proteomic data would represent a significant advance and could serve as a more cost-effective proxy to identifying causal adaptive changes than whole genome resequencing. Our multidisciplinary team, including Dr.'s Richard Smith at PNNL and Pavel Pevzner at UCSD as collaborators, is eager to explore the role of the proteome in adaptive processes through the approaches available at the EMSL. By addressing this important topic of genome plasticity, the proposed work has broad potential implications for fundamental biological understanding, industrial strain engineering and renewable energy applications, and studies of infectious disease.Project Details
Project type
Large-Scale EMSL Research
Start Date
2007-06-05
End Date
2010-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Related Publications
Cho BK, K Zengler, Y Qiu, YS Park, EM Knight, C Barrett, Y Gao, and BO Palsson. 2009. "The Transcription Unit Architecture of the Escherichia Coli Genome." Nature Biotechnology 27(11):1043-1051.
Lewis NE, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R Konig, RD Smith, and BO Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390. doi:10.1038/msb.2010.47
Qiu Y, BK Cho, YS Park, DR Lovley, BO Palsson, and K Zengler. 2010. "Structural and Operational Complexity of the Geobacter Sulfurreducens Genome." Genome Research 20:1304-1311. doi:10.1101/gr.107540.110