Metabolomic and transcriptomic stress response of <i>Escherichia coli</i>

Józefczuk, Szymon; Klie, Sebastian; Catchpole, Gareth; Szymański, Jędrzej; Cuadros-Inostroza, Álvaro; Steinhauser, Dirk; Selbig, Joachim; Willmitzer, Lothar

doi:10.1038/msb.2010.18

Cited by 438 publications

(412 citation statements)

References 51 publications

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“…The measurement of time-course b-galactosidase activity at 37, 42, and 48°C (Fig. S4) indicates that transcription of yrhB seems to be regulated by r 70 -dependent promoter, which also corresponds to the following previous results [18][19][20][21]: the transcription level of yrhB was not increased by the overexpression of rpoH [18,19] and was not upregulated by heat shock [20,21]. Consequently, it seems that YrhB cannot be defined as a traditional heat shock protein.…”

Section: -Dependent Promotersupporting

confidence: 87%

YrhB is a highly stable small protein with unique chaperone‐like activity in Escherichia coli BL21(DE3)

et al. 2012

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Edited by Miguel De la RosaKeywords: YrhB BL21(DE3) Chaperone-like protein Heat shock a b s t r a c t Escherichia coli YrhB (10.6 kDa) from strain BL21(DE3) that is commonly used for protein overexpression is a stable chaperone-like protein and indispensable for supporting the growth of BL21(DE3) at 48°C but not defined as conventional heat shock protein (HSP). YrhB effectively prevented heat-induced aggregation of ribonucleotide synthetase (PurK). Without ATP, YrhB alone promoted in vitro refolding of uridine phosphorylase (UDP) and protected thermal denaturation of the refolded UDP. As a cis-acting fusion partner, YrhB also significantly reduced inclusion body formation of nine aggregation-prone heterologous proteins in BL21(DE3). Unlike conventional small HSPs, YrhB remained monomer under heat shock condition.

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Section: -Dependent Promotersupporting

confidence: 87%

YrhB is a highly stable small protein with unique chaperone‐like activity in Escherichia coli BL21(DE3)

et al. 2012

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“…Dissolved and free amino acids have also been previously identified in viral lysates (Middelboe and Jorgensen, 2006), but the contribution of individual amino acids was not reported. Of the extracellular amino acids detected here, several of those with the largest increases in concentration for the phage-infected cultures are also part of the normal cellular stress response (for example, asparagine, cysteine, homoserine and methionine; Jozefczuk et al, 2010). Acyl-CoAs may not be efficiently transported and assimilated because of their large size and/or low concentrations in nature, potentially explaining their relative increase in infected culture filtrates.…”

Section: Discussionmentioning

confidence: 89%

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

Ankrah

May²,

Middleton³

et al. 2013

The ISME Journal

134

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Viruses contribute to the mortality of marine microbes, consequentially altering biological species composition and system biogeochemistry. Although it is well established that host cells provide metabolic resources for virus replication, the extent to which infection reshapes host metabolism at a global level and the effect of this alteration on the cellular material released following viral lysis is less understood. To address this knowledge gap, the growth dynamics, metabolism and extracellular lysate of roseophage-infected Sulfitobacter sp. 2047 was studied using a variety of techniques, including liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. Quantitative estimates of the total amount of carbon and nitrogen sequestered into particulate biomass indicate that phage infection redirects B75% of nutrients into virions. Intracellular concentrations for 82 metabolites were measured at seven time points over the infection cycle. By the end of this period, 71% of the detected metabolites were significantly elevated in infected populations, and stable isotope-based flux measurements showed that these cells had elevated metabolic activity. In contrast to simple hypothetical models that assume that extracellular compounds increase because of lysis, a profile of metabolites from infected cultures showed that 470% of the 56 quantified compounds had decreased concentrations in the lysate relative to uninfected controls, suggesting that these small, labile nutrients were being utilized by surviving cells. These results indicate that virus-infected cells are physiologically distinct from their uninfected counterparts, which has implications for microbial community ecology and biogeochemistry.

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“…Relies on multivariate statistical methods such as canonical correlation analysis (CCA) (Jozefczuk et al 2010) and orthogonal partial least squares discriminant analysis (OPLS-DA) (Boccard and Rutledge 2013) to calculate relationship between different levels of -omics data R package mixOmics González et al…”

Section: Resultsmentioning

confidence: 99%

Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes

et al. 2015

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Worldwide population is aging, and a large part of the growing burden associated with age-related conditions can be prevented or delayed by promoting healthy lifestyle and normalizing metabolic risk factors. However, a better understanding of the pleiotropic effects of available nutritional interventions and their influence on the multiple processes affected by aging is needed to select and implement the most promising actions. New methods of analysis are required to tackle the complexity of the interplay between nutritional interventions and aging, and to make sense of a growing amount of -omics data being produced for this purpose. In this paper, we review how various systems biology-inspired methods of analysis can be applied to the study of the molecular basis of nutritional interventions promoting healthy aging, notably caloric restriction and polyphenol supplementation. We specifically focus on the role that different versions of network analysis, molecular signature identification and multiomics data integration are playing in elucidating the complex mechanisms underlying nutrition, and provide some examples on how to extend the application of these methods using available microarray data.

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Metabolomic and transcriptomic stress response of Escherichia coli

Cited by 438 publications

References 51 publications

YrhB is a highly stable small protein with unique chaperone‐like activity in Escherichia coli BL21(DE3)

YrhB is a highly stable small protein with unique chaperone‐like activity in Escherichia coli BL21(DE3)

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes

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