Growth Phase-Dependent Regulation and Stringent Control of
 fis
 Are Conserved Processes in Enteric Bacteria and Involve a Single Promoter (
 fis
 P) in
 Escherichia coli

Mallik, Prabhat; Pratt, Timothy S.; Beach, Michael B.; Bradley, Meranda D.; Undamatla, Jayanthi; Osuna, Robert

doi:10.1128/jb.186.1.122-135.2004

Cited by 54 publications

(71 citation statements)

References 52 publications

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“…Chemicals, Enzymes, and Growth Media-Chemicals, enzymes, and growth media were as described (23). Polyethyleneimine-cellulose plates were from Aldrich.…”

Section: Methodsmentioning

confidence: 99%

“…The regulation of fis mRNA expression represents an important step in controlling the intracellular Fis levels. Its importance is emphasized by the strict conservation of this expression pattern in other bacterial species (21)(22)(23).…”

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confidence: 99%

“…However, fis P is unusual in its preferential use of CTP to initiate transcription, which occurs from a site located 8 nucleotides downstream of the Ϫ10 promoter region (23,24,27). Replacement of ϩ1C with either A or G resulted in prolonged high level expression throughout logarithmic growth phase and early stationary phase (24), indicating that the tight GPDR pattern of fis is strongly linked to a predominant use of CTP at ϩ1C as the transcription initiation nucleotide.…”

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confidence: 99%

“…A single promoter (fis P) 1 is responsible for the transcription and regulation of the fis operon in E. coli (17,18,23). It is negatively regulated by Fis (17, 18) and by stringent control (18,23,24) and stimulated by integration host factor (20).…”

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confidence: 99%

“…It is negatively regulated by Fis (17, 18) and by stringent control (18,23,24) and stimulated by integration host factor (20). Nevertheless, growth phase-dependent regulation (GPDR) 1 continues to be observed at the mRNA level in the absence of Fis, integration host factor, or stringent control (17,21,24).…”

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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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“…Chemicals, Enzymes, and Growth Media-Chemicals, enzymes, and growth media were as described (23). Polyethyleneimine-cellulose plates were from Aldrich.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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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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Evolution of global regulatory networks during a long‐term experiment withEscherichia coli

Philippe¹,

Crozat²,

Lenski³

et al. 2007

BioEssays

141

107

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Evolution has shaped all living organisms on Earth, although many details of this process are shrouded in time. However, it is possible to see, with one's own eyes, evolution as it happens by performing experiments in defined laboratory conditions with microbes that have suitably fast generations. The longest-running microbial evolution experiment was started in 1988, at which time twelve populations were founded by the same strain of Escherichia coli. Since then, the populations have been serially propagated and have evolved for tens of thousands of generations in the same environment. The populations show numerous parallel phenotypic changes, and such parallelism is a hallmark of adaptive evolution. Many genetic targets of natural selection have been identified, revealing a high level of genetic parallelism as well. Beneficial mutations affect all levels of gene regulation in the cells including individual genes and operons all the way to global regulatory networks. Of particular interest, two highly interconnected networks -- governing DNA superhelicity and the stringent response -- have been demonstrated to be deeply involved in the phenotypic and genetic adaptation of these experimental populations.

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The role of the local environment of engineered Tyr to Trp substitutions for probing the denaturation mechanism of FIS

et al. 2011

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Factor for inversion stimulation (FIS), a 98-residue homodimeric protein, does not contain tryptophan (Trp) residues but has four tyrosine (Tyr) residues located at positions 38, 51, 69, and 95. The equilibrium denaturation of a P61A mutant of FIS appears to occur via a three-state (N 2 I 2 2U) process involving a dimeric intermediate (I 2 ). Although it was suggested that this intermediate had a denatured C-terminus, direct evidence was lacking. Therefore, three FIS double mutants, P61A/Y38W, P61A/Y69W, and P61A/Y95W were made, and their denaturation was monitored by circular dichroism and Trp fluorescence. Surprisingly, the P61A/Y38W mutant best monitored the N 2 I 2 transition, even though Trp38 is buried within the dimer removed from the C-terminus. In addition, although Trp69 is located on the protein surface, the P61A/Y69W FIS mutant exhibited clearly biphasic denaturation curves. In contrast, P61A/Y95W FIS was the least effective in decoupling the two transitions, exhibiting a monophasic fluorescence transition with modest concentration-dependence. When considering the local environment of the Trp residues and the effect of each mutation on protein stability, these results not only confirm that P61A FIS denatures via a dimeric intermediate involving a disrupted C-terminus but also suggest the occurrence of conformational changes near Tyr38. Thus, the P61A mutation appears to compromise the denaturation cooperativity of FIS by failing to propagate stability to those regions involved mostly in intramolecular interactions. Furthermore, our results highlight the challenge of anticipating the optimal location to engineer a Trp residue for investigating the denaturation mechanism of even small proteins.

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Growth Phase-Dependent Regulation and Stringent Control of fis Are Conserved Processes in Enteric Bacteria and Involve a Single Promoter ( fis P) in Escherichia coli

Cited by 54 publications

References 52 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

Evolution of global regulatory networks during a long‐term experiment withEscherichia coli

The role of the local environment of engineered Tyr to Trp substitutions for probing the denaturation mechanism of FIS

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