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Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase YeaG.

Figueira R, Brown DR, Ferreira D, Eldridge MJ, Burchell L, Pan Z, Helaine S, Wigneshweraraj S - Sci Rep (2015)

Bottom Line: The mechanism by which yeaG acts, involves the transcriptional repression of two toxin/antitoxin modules, mqsR/mqsA and dinJ/yafQ.This, consequently, has a positive effect on the expression of rpoS, the master regulator of the general bacterial stress response.Overall, results indicate that yeaG is required to fully execute the rpoS-dependent gene expression program to allow E. coli to adapt to sustained N starvation and unravels a novel facet to the regulatory basis that underpins adaptive response to N stress.

View Article: PubMed Central - PubMed

Affiliation: MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK.

ABSTRACT
The Escherichia coli eukaryote-like serine/threonine kinase, encoded by yeaG, is expressed in response to diverse stresses, including nitrogen (N) starvation. A role for yeaG in bacterial stress response is unknown. Here we reveal for the first time that wild-type E. coli displays metabolic heterogeneity following sustained periods of N starvation, with the metabolically active population displaying compromised viability. In contrast, such heterogeneity in metabolic activity is not observed in an E. coli ∆yeaG mutant, which continues to exist as a single and metabolically active population and thus displays an overall compromised ability to survive sustained periods of N starvation. The mechanism by which yeaG acts, involves the transcriptional repression of two toxin/antitoxin modules, mqsR/mqsA and dinJ/yafQ. This, consequently, has a positive effect on the expression of rpoS, the master regulator of the general bacterial stress response. Overall, results indicate that yeaG is required to fully execute the rpoS-dependent gene expression program to allow E. coli to adapt to sustained N starvation and unravels a novel facet to the regulatory basis that underpins adaptive response to N stress.

No MeSH data available.


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A proposed a role for yeaG in ensuring sustained adaptation to sustained N stress in E. coli (see text for details).
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f7: A proposed a role for yeaG in ensuring sustained adaptation to sustained N stress in E. coli (see text for details).

Mentions: It is well established that rpoS is not expressed in exponentially growing bacteria and the regulation of its expression is tightly controlled at the transcription, translation and protein stability and activity levels as it impacts multiple physiological properties of the cell that affect growth. Therefore, managing transcription and translation of rpoS is an essential aspect of the bacterial stress response. Our results suggest that yeaG acts upstream of rpoS in the regulatory cascade that allows adaptation to sustained N starvation. In the scenario proposed in Fig. 7, in response to sustained N starvation, YeaG represses the transcription of mqsR/mqsA and dinJ/yafQ TA genes. This positively impacts rpoS transcription and translation, which as a consequence will result in the execution of the rpoS-dependent gene expression programme, needed to fully implement the adaptive response to sustained N stress. Conversely, in the absence of yeaG, our results show that the transcription of mqsR/mqsA and dinJ/yafQ TA genes become de-repressed in response to sustained N starvation. This negatively impacts rpoS at the transcriptional and translational levels and collectively results in an incomplete execution of the rpoS-dependent adaptive response to sustained N stress. Interestingly, a ΔrpoS mutant grows poorly compared to the wild-type and ∆yeaG strains in the recovery growth experiment (Figure S2), We thus propose that the correct intracellular levels of rpoS is important to instigate the appropriate adaptive response to sustained N starvation, whereas the absence of rpoS is likely to have significant pleiotropic effects on how E. coli adapts to N stress. This observation further underscores the view that yeaG, acting upstream of rpoS, ensures that intracellular levels of rpoS in E. coli exposed to sustained N starvation are maintained to allow the appropriate adaptive response to be executed. The mechanistic basis by which the YeaG mediated repression of mqsR/mqsA and dinJ/yafQ transcription occurs remains elusive and will be the subject of future studies. However, since MqsR, MqsA, DinJ or YafQ are not phosphorylated in a global phosphoproteome analysis of E. coli cells from stationary phase batch cultures grown in minimal media23, it is unlikely that they serve as substrates for YeaG. It is well established that a variety of regulatory mechanisms (anti-adaptor proteins, small RNAs) contribute to increasing σ38 levels (via either increased rpoS translation and decreased σ38 degradation) in response to suboptimal growth conditions24252627 including nutrient deprivation, and thus we cannot exclude an effect of YeaG on these mechanisms. Nevertheless, we previously reported that NtrC couples the Ntr stress response and the stringent response via the activation of relA transcription14. The new results now indicate that the full coupling of these two major bacterial stress responses to N stress adaptation may also involve YeaG. Further, the results also highlight the requirement for the three major E. coli σ factors for implementing the full Ntr response: σ54 (for the NtrC-mediated activation of Ntr genes, including yeaG), σ70 (for nitrogen assimilation control protein (Nac)-mediated regulation of Ntr response genes) and σ38 (for the general stress response).


Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase YeaG.

Figueira R, Brown DR, Ferreira D, Eldridge MJ, Burchell L, Pan Z, Helaine S, Wigneshweraraj S - Sci Rep (2015)

A proposed a role for yeaG in ensuring sustained adaptation to sustained N stress in E. coli (see text for details).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664914&req=5

f7: A proposed a role for yeaG in ensuring sustained adaptation to sustained N stress in E. coli (see text for details).
Mentions: It is well established that rpoS is not expressed in exponentially growing bacteria and the regulation of its expression is tightly controlled at the transcription, translation and protein stability and activity levels as it impacts multiple physiological properties of the cell that affect growth. Therefore, managing transcription and translation of rpoS is an essential aspect of the bacterial stress response. Our results suggest that yeaG acts upstream of rpoS in the regulatory cascade that allows adaptation to sustained N starvation. In the scenario proposed in Fig. 7, in response to sustained N starvation, YeaG represses the transcription of mqsR/mqsA and dinJ/yafQ TA genes. This positively impacts rpoS transcription and translation, which as a consequence will result in the execution of the rpoS-dependent gene expression programme, needed to fully implement the adaptive response to sustained N stress. Conversely, in the absence of yeaG, our results show that the transcription of mqsR/mqsA and dinJ/yafQ TA genes become de-repressed in response to sustained N starvation. This negatively impacts rpoS at the transcriptional and translational levels and collectively results in an incomplete execution of the rpoS-dependent adaptive response to sustained N stress. Interestingly, a ΔrpoS mutant grows poorly compared to the wild-type and ∆yeaG strains in the recovery growth experiment (Figure S2), We thus propose that the correct intracellular levels of rpoS is important to instigate the appropriate adaptive response to sustained N starvation, whereas the absence of rpoS is likely to have significant pleiotropic effects on how E. coli adapts to N stress. This observation further underscores the view that yeaG, acting upstream of rpoS, ensures that intracellular levels of rpoS in E. coli exposed to sustained N starvation are maintained to allow the appropriate adaptive response to be executed. The mechanistic basis by which the YeaG mediated repression of mqsR/mqsA and dinJ/yafQ transcription occurs remains elusive and will be the subject of future studies. However, since MqsR, MqsA, DinJ or YafQ are not phosphorylated in a global phosphoproteome analysis of E. coli cells from stationary phase batch cultures grown in minimal media23, it is unlikely that they serve as substrates for YeaG. It is well established that a variety of regulatory mechanisms (anti-adaptor proteins, small RNAs) contribute to increasing σ38 levels (via either increased rpoS translation and decreased σ38 degradation) in response to suboptimal growth conditions24252627 including nutrient deprivation, and thus we cannot exclude an effect of YeaG on these mechanisms. Nevertheless, we previously reported that NtrC couples the Ntr stress response and the stringent response via the activation of relA transcription14. The new results now indicate that the full coupling of these two major bacterial stress responses to N stress adaptation may also involve YeaG. Further, the results also highlight the requirement for the three major E. coli σ factors for implementing the full Ntr response: σ54 (for the NtrC-mediated activation of Ntr genes, including yeaG), σ70 (for nitrogen assimilation control protein (Nac)-mediated regulation of Ntr response genes) and σ38 (for the general stress response).

Bottom Line: The mechanism by which yeaG acts, involves the transcriptional repression of two toxin/antitoxin modules, mqsR/mqsA and dinJ/yafQ.This, consequently, has a positive effect on the expression of rpoS, the master regulator of the general bacterial stress response.Overall, results indicate that yeaG is required to fully execute the rpoS-dependent gene expression program to allow E. coli to adapt to sustained N starvation and unravels a novel facet to the regulatory basis that underpins adaptive response to N stress.

View Article: PubMed Central - PubMed

Affiliation: MRC Centre for Molecular Microbiology and Infection, Imperial College London, UK.

ABSTRACT
The Escherichia coli eukaryote-like serine/threonine kinase, encoded by yeaG, is expressed in response to diverse stresses, including nitrogen (N) starvation. A role for yeaG in bacterial stress response is unknown. Here we reveal for the first time that wild-type E. coli displays metabolic heterogeneity following sustained periods of N starvation, with the metabolically active population displaying compromised viability. In contrast, such heterogeneity in metabolic activity is not observed in an E. coli ∆yeaG mutant, which continues to exist as a single and metabolically active population and thus displays an overall compromised ability to survive sustained periods of N starvation. The mechanism by which yeaG acts, involves the transcriptional repression of two toxin/antitoxin modules, mqsR/mqsA and dinJ/yafQ. This, consequently, has a positive effect on the expression of rpoS, the master regulator of the general bacterial stress response. Overall, results indicate that yeaG is required to fully execute the rpoS-dependent gene expression program to allow E. coli to adapt to sustained N starvation and unravels a novel facet to the regulatory basis that underpins adaptive response to N stress.

No MeSH data available.


Related in: MedlinePlus