PMID:21299642

Citation	Traxler, MF, Zacharia, VM, Marquardt, S, Summers, SM, Nguyen, HT, Stark, SE and Conway, T (2011) Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Mol. Microbiol. 79:830-45
Abstract	Bacteria comprehensively reorganize their global gene expression when faced with starvation. The alarmone ppGpp facilitates this massive response by co-ordinating the downregulation of genes of the translation apparatus, and the induction of biosynthetic genes and the general stress response. Such a large reorientation requires the activities of multiple regulators, yet the regulatory network downstream of ppGpp remains poorly defined. Transcription profiling during isoleucine depletion, which leads to gradual starvation (over > 100 min), allowed us to identify genes that required ppGpp, Lrp and RpoS for their induction and to deduce the regulon response times. Although the Lrp and RpoS regulons required ppGpp for their activation, they were not induced simultaneously. The data suggest that metabolic genes, i.e. those of the Lrp regulon, require only a low level of ppGpp for their induction. In contrast, the RpoS regulon was induced only when high levels of ppGpp accumulated. We tested several predictions of a model that explains how bacteria allocate transcriptional resources between metabolism and stress response by discretely tuning two regulatory circuits to different levels of ppGpp. The emergent regulatory structure insures that stress survival circuits are only triggered if homeostatic metabolic networks fail to compensate for environmental deficiencies.
Links	PubMed PMC3073637 Online version:10.1111/j.1365-2958.2010.07498.x
Keywords	Bacterial Proteins/metabolism; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli/physiology; Escherichia coli Proteins/metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Guanosine Tetraphosphate/biosynthesis; Guanosine Tetraphosphate/genetics; Guanosine Tetraphosphate/metabolism; Isoleucine/metabolism; Leucine-Responsive Regulatory Protein/metabolism; Metabolic Networks and Pathways; Oligonucleotide Array Sequence Analysis; Promoter Regions, Genetic; Regulon; Sigma Factor/metabolism; Stress, Physiological
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Significance

Comments from Journal Club:

1.There are 2 levels of regulation : one under normal growth balance situation and the other, alarm situation. They are addressing the extremes here.

2.Page 831: "The primary synthase of ppGpp is RelA, which catalyses the production of ppGpp in response to amino acid starvation". This is This is not true for normal (balanced) growth, where SpoT is the sole source. RelA only kicks in during AA starvation.

3.Page 831: "However, more recent work has shown that elevating the levels of s70- bound RNAP actually results in enhanced transcription of genes of the translation apparatus, rather than enhanced transcription of stress and metabolic genes". The concentration of free RNA polymerase increases with increasing nutritional value of the growth medium due to increased RNA polymerase synthesis and increased repression of mRNA genes by exogenous amino acids and/or other nutrients. However, even when the rrn promoters are most active during fast growth in nutrient-rich media (like LB medium), they are not yet fully saturated with polymerase. One reason for this is the large number of rrn operons present in the cell. E. coli has seven rrn operons per genome and, as a result of chromosome branching during replication,the rrn gene dosage increases with increasing growth rate to about 38 rrn operons per average cell at 3.0 doublings/h. All of these copies contribute equally to the total rRNA synthesis rate.

4.Page 832: Fig.1 The ppGpp' strain has its sample taken at a different time and OD than the other three.

5.Page 834: Fig.2 Does the "two fold" mean one fold increase or twice as high? Is just the two fold increase really significant?

6.Page 836: Fig.3 Some genes are being switched on and off i.e. their levels of expression are going up and down as time progresses. What are these genes involved in?

7.Page 837: Fig.4 Need for error bars.100 pmol/OD = approx. 100 uM internal concentration in cell. Normal ppGpp is in 30 nM range (i.e, 1000 x lower). So actually ppGpp increases very dramatically in first minute, then gradually increases for a long time after that.

8. Fig.5: Panel B, It would be more appropriate to say aminoacid depletion rather than starvation.

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References

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