|
| Status |
Public on May 14, 2018 |
| Title |
Enzyme promiscuity shapes evolutionary innovation and optimization |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
A computational model of underground metabolism and laboratory evolution experiments were employed to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in E. coli K-12 MG1655. After as few as 20 generations, the evolving populations repeatedly acquired the capacity to grow on five predicted novel substrates--D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate--none of which could support growth in wild-type cells. Promiscuous enzyme activities played key roles in multiple phases of adaptation. Potential mechanisms for optimizing growth on the non-native carbon sources were explored by analyzing the transcriptomes of initial and endpoint populations.
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| |
|
| Overall design |
RNAseq was performed on various evolved populations grown on four different carbon sources: D-lyxose, D-2-deoxyribose, D-arabinose, and m-tartrate. Differentially expressed genes were examined comparing endpoint (optimized) samples to initial (innovation) samples.
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| |
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| Contributor(s) |
Guzman GI, Feist AM |
| Citation(s) |
30962359 |
| |
| Submission date |
May 11, 2018 |
| Last update date |
Apr 23, 2019 |
| Contact name |
Adam M Feist |
| E-mail(s) |
afeist@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Bioengineering
|
| Lab |
Palsson Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18956 |
Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655) |
|
| Samples (22)
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| Relations |
| BioProject |
PRJNA471071 |
| SRA |
SRP145496 |
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