<i>Escherichia coli</i>
            Ribosome-Associated Protein SRA, Whose Copy Number Increases during Stationary Phase

Izutsu, Kaori; Wada, Chieko; Komine, Yuriko; Sako, Tomoyuki; Ueguchi, Chiharu; Nakura, Satomi; Wada, Akira

doi:10.1128/jb.183.9.2765-2773.2001

Cited by 72 publications

(72 citation statements)

References 49 publications

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“…b1481) that directly maps at 33.5 min on the E. coli genetic map between osmC and rpsV. rpsV, which encodes a small ribosomal protein, has recently been described as stationary phase inducible and is partly under the control of S and the integration host factor (35). Under our test conditions, the expression of rpsV was unchanged.…”

Section: Northern Blot Measurementsmentioning

confidence: 82%

Profiling Early Osmostress-Dependent Gene Expression in Escherichia coli Using DNA Macroarrays

2002

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DNA macroarray technology was used to monitor early transcriptional alterations of Escherichia coli in response to an osmotic upshift imposed by the addition of 0.4 M NaCl. Altered mRNA levels of 152 genes were detected; 45 genes showed increased expression while the expression of the remaining 107 genes was reduced. Northern blot analysis of several selected genes differing in their relative expression values confirmed the results obtained by the array technology.Mechanisms of adaptation to environments of high osmolality have been investigated by genetic, physiological, and biochemical methods (for reviews, see references 17 and 18). Sudden exposure of Escherichia coli to an environment of high osmolality causes rapid loss of water (plasmolysis), loss of turgor, and shrinkage of the cell. Within the first minutes, respiration ceases (46), whereas both the intracellular ATP concentration (51) and the cytoplasmic pH increase (20). Among the first adaptive responses to a hyperosmotic upshift there is a large increase in the rate of uptake and the amount of cytosolic K ϩ (20,23,47,53). A number of secondary adaptive mechanisms occur after the onset of increased accumulation of K ϩ , including the accumulation of glutamate (44), the synthesis of trehalose (12, 57), and the release of putrescine (56). A number of so-called osmoprotectants (e.g., betaine and proline) are taken up by E. coli when available externally. These solutes are able to increase the internal osmotic pressure without interfering with vital cellular protein functions (18,(24)(25)(26)48).There are a few studies in which the general response of E. coli to osmotic upshift has been investigated (14,29). The analysis of two-dimensional gel electrophoresis patterns of radiolabeled total cellular proteins (9, 34) as well as the analysis of global transcription patterns (13) indicated that an increase in osmolality has a global effect on gene expression. It has been shown that in response to osmotic stress, E. coli expresses a broad set of normally stationary phase-specific genes whose expression depends widely on RpoS ( S ), an alternative transcription factor (31,34,49).DNA macroarray measurements. DNA macroarrays were used to profile early osmostress-dependent gene expression. E. coli MC4100 (11) was grown at 37°C in phosphate-buffered minimal medium supplemented with 0.4% (wt/vol) glucose (22) containing 10 mM K ϩ until the mid-logarithmic phase. Cells were then transferred in fresh prewarmed medium (control cells) or in medium containing 0.4 M NaCl (stressed cells) (37), and after 9 min, total RNA was isolated according to the method of Aiba et al. (1). The obtained RNA samples were treated with RNase-free DNase I (Qiagen).33 P-labeled cDNA was synthesized by using open reading frame (ORF)-specific E. coli primers and hybridized to DNA macroarrays (Sigma-Genosys) according to the manufacturer's instructions. Exposed PhosphorImager screens were scanned on a PhosphorImager SI (Molecular Dynamics), and quantification of all 4,290 PCRamplified ORFs of t...

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Section: Northern Blot Measurementsmentioning

confidence: 82%

Profiling Early Osmostress-Dependent Gene Expression in Escherichia coli Using DNA Macroarrays

2002

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“…This gene possesses a single promoter that is partly dependent on S . Transcription from this promoter is decreased in mutants lacking S , FIS (factor for inversion stimulation), HNS (histone-like nucleoid structuring protein), cAMP, and ppGpp (37).…”

Section: Resultsmentioning

confidence: 99%

Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli

et al. 2005

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In Escherichia coli, the ferric uptake regulator (Fur) controls expression of the iron regulon in response to iron availability while the cyclic AMP receptor protein (Crp) regulates expression of the carbon regulon in response to carbon availability. We here identify genes subject to significant changes in expression level in response to the loss of both Fur and Crp. Many iron transport genes and several carbon metabolic genes are subject to dual control, being repressed by the loss of Crp and activated by the loss of Fur. However, the sodB gene, encoding superoxide dismutase, and the aceBAK operon, encoding the glyoxalate shunt enzymes, show the opposite responses, being activated by the loss of Crp and repressed by the loss of Fur. Several other genes including the sdhA-D, sucA-D, and fumA genes, encoding key constituents of the Krebs cycle, proved to be repressed by the loss of both transcription factors. Finally, the loss of both Crp and Fur activated a heterogeneous group of genes under S control encoding, for example, the cyclopropane fatty acid synthase, Cfa, the glycogen synthesis protein, GlgS, the 30S ribosomal protein, S22, and the mechanosensitive channel protein, YggB. Many genes appeared to be regulated by the two transcription factors in an apparently additive fashion, but apparent positive or negative cooperativity characterized several putative Crp/Fur interactions. Relevant published data were evaluated, putative Crp and Fur binding sites were identified, and representative results were confirmed by real-time PCR. Molecular explanations for some, but not all, of these effects are provided.Processes that alter the rates of transcriptional initiation, elongation and termination, mRNA degradation, and mRNA translation control gene expression in all living organisms. Of these, regulation of transcriptional initiation is of greatest physiological importance in bacteria (34). About one-fourth of all Escherichia coli proteins interact functionally with nucleic acids, and about one-fourth of these are pleiotropic transcriptional regulators that control expression of multioperon regulons, primarily by influencing the transcriptional initiation step (57, 72). In fact, each regulon is defined by the activity of a transcription factor that coordinately controls expression of the operons included within that regulon (28). The global regulator, responsive to select cellular stimuli, binds to specific sites in the control regions of these operons. Examples of such pleiotropic transcription factors in E. coli include Crp, a primary sensor of carbon availability (8,15,23,65), NtrBC, a sensor of nitrogen availability (32, 63, 77), CysB, the sensor of sulfur availability (38,39,41,42), and Fur, a dominant sensor of iron availability (30,31,50,71). Crp when complexed with cyclic AMP (cAMP) binds to a consensus sequence in the DNA and activates transcription of many genes while repressing transcription of a few others. Some genes are subject to both positive and negative regulation by the cAMP-Crp complex due to th...

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“…It also lays the foundation for forthcoming studies with a more detailed analysis of ribosomal distributions during the exponential phase (55), stationary phase (56)(57)(58), and during cold shock (59).…”

Section: Discussionmentioning

confidence: 99%

Single-molecule investigations of the stringent response machinery in living bacterial cells

English

Hauryliuk

Sanamrad

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

260

294

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The RelA-mediated stringent response is at the heart of bacterial adaptation to starvation and stress, playing a major role in the bacterial cell cycle and virulence. RelA integrates several environmental cues and synthesizes the alarmone ppGpp, which globally reprograms transcription, translation, and replication. We have developed and implemented novel single-molecule tracking methodology to characterize the intracellular catalytic cycle of RelA. Our single-molecule experiments show that RelA is on the ribosome under nonstarved conditions and that the individual enzyme molecule stays off the ribosome for an extended period of time after activation. This suggests that the catalytically active part of the RelA cycle is performed off, rather than on, the ribosome, and that rebinding to the ribosome is not necessary to trigger each ppGpp synthesis event. Furthermore, we find fast activation of RelA in response to heat stress followed by RelA rapidly being reset to its inactive state, which makes the system sensitive to new environmental cues and hints at an underlying excitable response mechanism. cytosolic diffusion | single particle tracking | photoactivated localization microscopy | stroboscopic illumination

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Escherichia coli Ribosome-Associated Protein SRA, Whose Copy Number Increases during Stationary Phase

Cited by 72 publications

References 49 publications

Profiling Early Osmostress-Dependent Gene Expression in Escherichia coli Using DNA Macroarrays

Profiling Early Osmostress-Dependent Gene Expression in Escherichia coli Using DNA Macroarrays

Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli

Single-molecule investigations of the stringent response machinery in living bacterial cells

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