Control of rRNA Expression by Small Molecules Is Dynamic and Nonredundant

Murray, Heath; Schneider, David A.; Gourse, Richard L.

doi:10.1016/s1097-2765(03)00266-1

Cited by 189 publications

(293 citation statements)

References 54 publications

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“…Our measurements of relative levels of all four NTPs (ATP Ͼ GTP Ͼ UTP Ͼ CTP) during logarithmic growth phase were roughly comparable with those reported in previous studies in which NTP pools were measured during limited periods of cell growth (31,(61)(62)(63). Measurements recently made during the first 10 min of outgrowth from stationary phase indicate that it is possible to detect an increase in NTP levels as early as 1 min of outgrowth from stationary phase (58,64). Our measurements, which extend throughout the entire logarithmic growth phase and early stationary phase, indicate that the NTP levels continue to rise during the early logarithmic growth phase to peak after about 80 min of growth in our experimental conditions.…”

Section: Discussionsupporting

confidence: 88%

The Escherichia coli fis Promoter Is Regulated by Changes in the Levels of Its Transcription Initiation Nucleotide CTP

Walker

Mallik

Pratt

et al. 2004

Journal of Biological Chemistry

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Expression of the Escherichia coli nucleoid-associated protein Fis (factor for inversion stimulation) is controlled at the transcriptional level in accordance with the nutritional availability. It is highly expressed during early logarithmic growth phase in cells growing in rich medium but poorly expressed in late logarithmic and stationary phase. However, fis mRNA expression is prolonged at high levels throughout the logarithmic and early stationary phase when the preferred transcription initiation site (؉1C) is replaced with A or G, indicating that initiation with CTP is a required component of the regulation pattern. We show that RNA polymerase-fis promoter complexes are short lived and that transcription is stimulated over 20-fold from linear or supercoiled DNA if CTP is present during formation of initiation complexes, which serves to stabilize these complexes. Use of fis promoter fusions to lacZ indicated that fis promoter transcription is sensitive to the intracellular pool of the predominant initiating NTP. Growth conditions resulting in increases in CTP pools also result in corresponding increases in fis mRNA levels. Measurements of NTP pools performed throughout the growth of the bacterial culture in rich medium revealed a dramatic increase in all four NTP levels during the transition from stationary to logarithmic growth phase, followed by reproducible oscillations in their levels during logarithmic growth, which later decrease during the transition from logarithmic to stationary phase. In particular, CTP pools fluctuate in a manner consistent with a role in regulating fis expression. These observations support a model whereby fis expression is subject to regulation by the availability of its initiating NTP.Diverse cellular functions have been ascribed to the Escherichia coli Fis (factor for inversion stimulation). In addition to mediating specialized site-specific DNA recombination events (1), this nucleoid-associated protein regulates transcription of ribosomal and tRNAs (2, 3) and a growing number of structural genes (4 -16). Fis levels are transcriptionally regulated according to the nutritional conditions and the growth phase (17-19). A dramatic burst in fis mRNA levels is observed when stationary phase cells are outgrown in rich medium, which reach a peak during early logarithmic growth phase, decrease to much lower levels during late logarithmic growth phase, and become undetectable during stationary phase (17, 18), an expression pattern that is closely followed at the protein level (17,19). The fis mRNA half-life is short (about 2 min) and does not vary appreciably throughout the period of growth phase-dependent expression, indicating that the fis mRNA expression pattern is not attributed to changes in mRNA turnover rates but is primarily attributed to transcriptional control (20). Such drastic changes in intracellular Fis levels are likely to influence its role as a global gene regulator. Prolonged Fis expression well into stationary phase is detrimental to cell viability (21). Hence, cells m...

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Section: Discussionsupporting

confidence: 88%

The Escherichia coli fis Promoter Is Regulated by Changes in the Levels of Its Transcription Initiation Nucleotide CTP

Walker

Mallik

Pratt

et al. 2004

Journal of Biological Chemistry

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“…rRNA promoter activity was very weak in stationary phase (Murray et al 2003), but the separation between the two rRNA operons was essentially the same as in exponentially growing cells (105 nm in Fig. 4G vs. 120 nm in log phase in Fig.…”

Section: (C) Oric Rrnc (Rlg11999) (D) Rrnb Oric (Rlg7440) (E) λAtmentioning

confidence: 65%

“…rRNA synthesis rates are coordinated with the cell's translational capacity following nutritional shifts such as amino acid starvation. The primary signal molecules responsible for adjusting ribosome synthesis rates to changing nutritional conditions are ppGpp, an "alarmone" whose synthesis is induced by uncharged transfer RNAs (tRNAs) in the ribosomal A site (Paul et al 2004;Potrykus and Cashel 2008;Ross et al 2016), and the concentration of the initial NTP responsible for forming the rRNA transcript (Murray et al 2003).…”

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confidence: 99%

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

et al. 2016

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The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180°on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.

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“…As expected because of the action of adenylate kinase and consistent with ref. 23, the fall in ATP occurs relatively late in carbon starvation. ATP levels are not provided for S. cerevisiae, because our methanol/water procedure did not effectively extract triphosphates from filter-grown yeast.…”

Section: Resultsmentioning

confidence: 99%

Conservation of the metabolomic response to starvation across two divergent microbes

Brauer

Yuan

Bennett

et al. 2006

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

244

209

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We followed 68 cellular metabolites after carbon or nitrogen starvation of Escherichia coli and Saccharomyces cerevisiae, using a filter-culture methodology that allows exponential growth, nondisruptive nutrient removal, and fast quenching of metabolism. Dynamic concentration changes were measured by liquid chromatography-tandem mass spectrometry and viewed in clustered heat-map format. The major metabolic responses anticipated from metabolite-specific experiments in the literature were observed as well as a number of novel responses. When the data were analyzed by singular value decomposition, two dominant characteristic vectors were found, one corresponding to a generic starvation response and another to a nutrient-specific starvation response that is similar in both organisms. Together these captured a remarkable 72% of the metabolite concentration changes in the full data set. The responses described by the generic starvation response vector (42%) included, for example, depletion of most biosynthetic intermediates. The nutrient-specific vector (30%) included key responses such as increased phosphoenolpyruvate signaling glucose deprivation and increased ␣-ketoglutarate signaling ammonia deprivation. Metabolic similarity across organisms extends from the covalent reaction network of metabolism to include many elements of metabolome response to nutrient deprivation as well.Escherichia coli ͉ metabolomics ͉ nitrogen/carbon metabolism ͉ Saccharomyces cerevisiae ͉ starvation response T he pathways of cellular metabolism are close to identical across widely divergent organisms (1). The prokaryote Escherichia coli and the eukaryote Saccharomyces cerevisiae share essentially the same metabolic network (2) despite radically different compartmentation. The concentrations and fluxes of metabolites depend on the interactions among this conserved network structure, the cellular environment, and species-specific factors, such as the location, activities, and regulation of metabolic enzymes. Except for a few classic examples, e.g., central carbon metabolism in E. coli and yeast (3-5) and nitrogen assimilation in bacteria (6-8) the effect of environmental nutrient perturbations on the cellular metabolome have not been directly measured.We explored exponentially growing E. coli and S. cerevisiae cultures suddenly deprived of their carbon or nitrogen sources. Metabolic composition can change in as little as a few seconds (9, 10). To get accurate snapshots of the metabolome, we devised a method of growing cells directly on filters to avoid time-consuming procedures (e.g., centrifugation or filtration) before quenching of biochemical activity (11). Transfer of a filter from a plate containing growth medium into cold organic solvent quickly quenches metabolism; transfer to a plate with a different medium composition allows a quick change of the nutrient environment (Fig. 1).For measurement of a number of metabolites simultaneously, we used a liquid chromatography-electrospray ionization-triple quadrupole mass spectrometry (LC-MS/...

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Control of rRNA Expression by Small Molecules Is Dynamic and Nonredundant

Cited by 189 publications

References 54 publications

The Escherichia coli fis Promoter Is Regulated by Changes in the Levels of Its Transcription Initiation Nucleotide CTP

The Escherichia coli fis Promoter Is Regulated by Changes in the Levels of Its Transcription Initiation Nucleotide CTP

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

Conservation of the metabolomic response to starvation across two divergent microbes

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