Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome
Adaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, new insights into the systemic function of a gene product. Two E. coli knockout strains were constructed: one that blocked the Pentose Phosphate Pathway (gnd KO...
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| Format: | Article |
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Frontiers Media S.A.
2018-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.01793/full |
| _version_ | 1818651987839811584 |
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| author | Douglas McCloskey Douglas McCloskey Sibei Xu Troy E. Sandberg Elizabeth Brunk Ying Hefner Richard Szubin Adam M. Feist Adam M. Feist Bernhard O. Palsson Bernhard O. Palsson |
| author_facet | Douglas McCloskey Douglas McCloskey Sibei Xu Troy E. Sandberg Elizabeth Brunk Ying Hefner Richard Szubin Adam M. Feist Adam M. Feist Bernhard O. Palsson Bernhard O. Palsson |
| author_sort | Douglas McCloskey |
| collection | DOAJ |
| description | Adaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, new insights into the systemic function of a gene product. Two E. coli knockout strains were constructed: one that blocked the Pentose Phosphate Pathway (gnd KO) and one that decoupled the TCA cycle from electron transport (sdhCDAB KO). Despite major perturbations in central metabolism, minimal growth rate changes were found in the two knockout strains. More surprisingly, many similarities were found in their initial transcriptomic states that could be traced to similarly perturbed metabolites despite the differences in the network location of the gene perturbations and concomitant re-routing of pathway fluxes around these perturbations. However, following ALE, distinct metabolomic and transcriptomic states were realized. These included divergent flux and gene expression profiles in the gnd and sdhCDAB KOs to overcome imbalances in NADPH production and nitrogen/sulfur assimilation, respectively, that were not obvious limitations of growth in the unevolved knockouts. Therefore, this work demonstrates that ALE provides a productive approach to reveal novel insights of gene function at a systems level that cannot be found by observing the fresh knockout alone. |
| first_indexed | 2024-12-17T02:14:51Z |
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| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-17T02:14:51Z |
| publishDate | 2018-08-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-d974948cf11c42d2b9f388f9aa44dbd02022-12-21T22:07:27ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-08-01910.3389/fmicb.2018.01793398699Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the TranscriptomeDouglas McCloskey0Douglas McCloskey1Sibei Xu2Troy E. Sandberg3Elizabeth Brunk4Ying Hefner5Richard Szubin6Adam M. Feist7Adam M. Feist8Bernhard O. Palsson9Bernhard O. Palsson10Department of Bioengineering, University of California, San Diego, San Diego, CA, United StatesNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DenmarkDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DenmarkDepartment of Bioengineering, University of California, San Diego, San Diego, CA, United StatesNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DenmarkAdaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, new insights into the systemic function of a gene product. Two E. coli knockout strains were constructed: one that blocked the Pentose Phosphate Pathway (gnd KO) and one that decoupled the TCA cycle from electron transport (sdhCDAB KO). Despite major perturbations in central metabolism, minimal growth rate changes were found in the two knockout strains. More surprisingly, many similarities were found in their initial transcriptomic states that could be traced to similarly perturbed metabolites despite the differences in the network location of the gene perturbations and concomitant re-routing of pathway fluxes around these perturbations. However, following ALE, distinct metabolomic and transcriptomic states were realized. These included divergent flux and gene expression profiles in the gnd and sdhCDAB KOs to overcome imbalances in NADPH production and nitrogen/sulfur assimilation, respectively, that were not obvious limitations of growth in the unevolved knockouts. Therefore, this work demonstrates that ALE provides a productive approach to reveal novel insights of gene function at a systems level that cannot be found by observing the fresh knockout alone.https://www.frontiersin.org/article/10.3389/fmicb.2018.01793/fulladaptive laboratory evolutionsdhD gene knockoutssystems biologycasual mutationsgndsdhA |
| spellingShingle | Douglas McCloskey Douglas McCloskey Sibei Xu Troy E. Sandberg Elizabeth Brunk Ying Hefner Richard Szubin Adam M. Feist Adam M. Feist Bernhard O. Palsson Bernhard O. Palsson Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome Frontiers in Microbiology adaptive laboratory evolution sdhD gene knockouts systems biology casual mutations gnd sdhA |
| title | Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome |
| title_full | Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome |
| title_fullStr | Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome |
| title_full_unstemmed | Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome |
| title_short | Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome |
| title_sort | growth adaptation of gnd and sdhcb escherichia coli deletion strains diverges from a similar initial perturbation of the transcriptome |
| topic | adaptive laboratory evolution sdhD gene knockouts systems biology casual mutations gnd sdhA |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.01793/full |
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