Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures
<p>Abstract</p> <p>Background</p> <p>It is important to understand the cellular responses emanating from environmental perturbations to redesign the networks for practical applications. In particular, the carbon (C) metabolism, nitrogen (N) assimilation, and energy gene...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2011-01-01
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| Series: | Microbial Cell Factories |
| Online Access: | http://www.microbialcellfactories.com/content/10/1/3 |
| _version_ | 1818806767021195264 |
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| author | Kumar Rahul Shimizu Kazuyuki |
| author_facet | Kumar Rahul Shimizu Kazuyuki |
| author_sort | Kumar Rahul |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>It is important to understand the cellular responses emanating from environmental perturbations to redesign the networks for practical applications. In particular, the carbon (C) metabolism, nitrogen (N) assimilation, and energy generation are by far important, where those are interconnected and integrated to maintain cellular integrity. In our previous study, we investigated the effect of C/N ratio on the metabolic regulation of <it>gdhA, glnL, glt B,D </it>mutants as well as wild type <it>Escherichia coli </it>(Kumar and Shimizu, MCF, 1-17, <b>9</b>:8,2010), where it was shown that the transcript levels of <it>cyoA </it>and <it>cydB </it>which encode the terminal oxidases, <it>fnr </it>and <it>fur </it>which encode global regulators were significantly up-regulated under N-limited condition as compared to C-limited condition. In the present study, therefore, the effects of such single-gene knockout on the metabolic regulation were investigated to clarify the roles of those genes in the aerobic continuous culture at the dilution rate of 0.2 h<sup>-1</sup>.</p> <p>Results</p> <p>The specific glucose consumption rates and the specific CO<sub>2 </sub>production rates of <it>cyoA, cydB, fnr</it>, and <it>fur </it>mutants were all increased as compared to the wild type under both C-limited and N-limited conditions. The former phenomenon was consistent with the up-regulations of the transcript levels of <it>ptsG </it>and <it>ptsH</it>, which are consistent with down-regulations of <it>crp </it>and <it>mlc </it>genes. Moreover, the increase in the specific glucose consumption rate was also caused by up-regulations of the transcript levels of <it>pfkA</it>, <it>pykF </it>and possibly <it>zwf</it>, where those are consistent with the down regulations of <it>cra, crp </it>and <it>mlc </it>genes. Moreover, the transcript levels of <it>rpoN </it>together with <it>glnK, glnB, glnE </it>were up-regulated, and thus the transcript levels of <it>glnA,L,G</it>, and <it>gltB,D </it>as well as <it>nac </it>were up-regulated, while <it>gdhA </it>was down-regulated. This implies the interconnection between cAMP-Crp and P<sub>II</sub>-Ntr systems. Moreover, <it>cyoA</it>, <it>cydB</it>, <it>fnr </it>and <it>fur </it>gene deletions up-regulated the transcript levels of respiration (<it>nuoA, ndh, cyoA, cydB</it>, and <it>atpA</it>) and the oxidative stress related genes such as <it>soxR</it>, <it>S </it>and <it>sodA</it>, where this was further enhanced under N-limitation. In the cases of <it>cyoA </it>and <it>cydB </it>mutants, <it>arcA, fnr, fur, cydB </it>(for <it>cyoA </it>mutant), and <it>cyoA </it>(for <it>cydB </it>mutant) genes were up-regulated, which may be due to incomplete oxidation of quinol. It was also shown that <it>fur </it>gene transcript level was up-regulated in accordance with the activation of respiratory chain genes. It was shown that the deletion of <it>fur </it>gene activated the enterobactin pathway.</p> <p>Conclusion</p> <p>The present result demonstrated how the fermentation characteristics could be explained by the transcript levels of metabolic pathway genes as well as global regulators in relation to the knockout of such single genes as <it>cyoA, cydB, fnr</it>, and <it>fur</it>, and clarified the complex gene network regulation in relation to glycolysis, TCA cycle, respiration, and N-regulated pathways. The present result is quite important in understanding the metabolic regulation for metabolic engineering. Moreover, the present result may be useful in improving the specific glucose consumption rate and activation of the TCA cycle by modulating the respiratory chain genes and the related global regulators. The result obtained under N-limited condition may be useful for the heterologous protein production under N-limitation.</p> |
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| institution | Directory Open Access Journal |
| issn | 1475-2859 |
| language | English |
| last_indexed | 2024-12-18T19:15:00Z |
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| series | Microbial Cell Factories |
| spelling | doaj.art-d610856305834b518104bec1b86100ac2022-12-21T20:56:09ZengBMCMicrobial Cell Factories1475-28592011-01-01101310.1186/1475-2859-10-3Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous culturesKumar RahulShimizu Kazuyuki<p>Abstract</p> <p>Background</p> <p>It is important to understand the cellular responses emanating from environmental perturbations to redesign the networks for practical applications. In particular, the carbon (C) metabolism, nitrogen (N) assimilation, and energy generation are by far important, where those are interconnected and integrated to maintain cellular integrity. In our previous study, we investigated the effect of C/N ratio on the metabolic regulation of <it>gdhA, glnL, glt B,D </it>mutants as well as wild type <it>Escherichia coli </it>(Kumar and Shimizu, MCF, 1-17, <b>9</b>:8,2010), where it was shown that the transcript levels of <it>cyoA </it>and <it>cydB </it>which encode the terminal oxidases, <it>fnr </it>and <it>fur </it>which encode global regulators were significantly up-regulated under N-limited condition as compared to C-limited condition. In the present study, therefore, the effects of such single-gene knockout on the metabolic regulation were investigated to clarify the roles of those genes in the aerobic continuous culture at the dilution rate of 0.2 h<sup>-1</sup>.</p> <p>Results</p> <p>The specific glucose consumption rates and the specific CO<sub>2 </sub>production rates of <it>cyoA, cydB, fnr</it>, and <it>fur </it>mutants were all increased as compared to the wild type under both C-limited and N-limited conditions. The former phenomenon was consistent with the up-regulations of the transcript levels of <it>ptsG </it>and <it>ptsH</it>, which are consistent with down-regulations of <it>crp </it>and <it>mlc </it>genes. Moreover, the increase in the specific glucose consumption rate was also caused by up-regulations of the transcript levels of <it>pfkA</it>, <it>pykF </it>and possibly <it>zwf</it>, where those are consistent with the down regulations of <it>cra, crp </it>and <it>mlc </it>genes. Moreover, the transcript levels of <it>rpoN </it>together with <it>glnK, glnB, glnE </it>were up-regulated, and thus the transcript levels of <it>glnA,L,G</it>, and <it>gltB,D </it>as well as <it>nac </it>were up-regulated, while <it>gdhA </it>was down-regulated. This implies the interconnection between cAMP-Crp and P<sub>II</sub>-Ntr systems. Moreover, <it>cyoA</it>, <it>cydB</it>, <it>fnr </it>and <it>fur </it>gene deletions up-regulated the transcript levels of respiration (<it>nuoA, ndh, cyoA, cydB</it>, and <it>atpA</it>) and the oxidative stress related genes such as <it>soxR</it>, <it>S </it>and <it>sodA</it>, where this was further enhanced under N-limitation. In the cases of <it>cyoA </it>and <it>cydB </it>mutants, <it>arcA, fnr, fur, cydB </it>(for <it>cyoA </it>mutant), and <it>cyoA </it>(for <it>cydB </it>mutant) genes were up-regulated, which may be due to incomplete oxidation of quinol. It was also shown that <it>fur </it>gene transcript level was up-regulated in accordance with the activation of respiratory chain genes. It was shown that the deletion of <it>fur </it>gene activated the enterobactin pathway.</p> <p>Conclusion</p> <p>The present result demonstrated how the fermentation characteristics could be explained by the transcript levels of metabolic pathway genes as well as global regulators in relation to the knockout of such single genes as <it>cyoA, cydB, fnr</it>, and <it>fur</it>, and clarified the complex gene network regulation in relation to glycolysis, TCA cycle, respiration, and N-regulated pathways. The present result is quite important in understanding the metabolic regulation for metabolic engineering. Moreover, the present result may be useful in improving the specific glucose consumption rate and activation of the TCA cycle by modulating the respiratory chain genes and the related global regulators. The result obtained under N-limited condition may be useful for the heterologous protein production under N-limitation.</p>http://www.microbialcellfactories.com/content/10/1/3 |
| spellingShingle | Kumar Rahul Shimizu Kazuyuki Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures Microbial Cell Factories |
| title | Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures |
| title_full | Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures |
| title_fullStr | Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures |
| title_full_unstemmed | Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures |
| title_short | Transcriptional regulation of main metabolic pathways of <it>cyoA</it>, <it>cydB</it>, <it>fnr</it>, and <it>fur </it>gene knockout <it>Escherichia coli </it>in C-limited and N-limited aerobic continuous cultures |
| title_sort | transcriptional regulation of main metabolic pathways of it cyoa it it cydb it it fnr it and it fur it gene knockout it escherichia coli it in c limited and n limited aerobic continuous cultures |
| url | http://www.microbialcellfactories.com/content/10/1/3 |
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