The Design Involved in PapI and Lrp Regulation of the pap Operon

Kawamura, Tetsuya; Vartanian, Armand S.; Zhou, Hongjun; Dahlquist, Frederick W.

doi:10.1016/j.jmb.2011.01.058

Cited by 13 publications

(18 citation statements)

References 40 publications

(105 reference statements)

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“…3B). The affinity of PapI/ Lrp for hemimethylated pap sites 4 -6 is significantly higher than for the fully methylated DNA (52,56). If PapI/Lrp binds to site 5 before Dam methylates the daughter strand, cooperative binding of Lrp/PapI to sites 4 -6 will occur to initiate transition to the phase on state.…”

Section: Phase Variation Via Dna Methylation Patternsmentioning

confidence: 99%

“…PapI increases the affinity of Lrp for pap sites 2 and 5 via an ACGATC sequence present in each site (52,56,62). PapB, the product of the first gene of the pap operon, binds near the papI promoter and activates papI transcription, forming a positive feedback loop (Fig.…”

Section: Phase Variation Via Dna Methylation Patternsmentioning

confidence: 99%

“…If PapI/Lrp binds to site 5 before Dam methylates the daughter strand, cooperative binding of Lrp/PapI to sites 4 -6 will occur to initiate transition to the phase on state. Evidence indicates that a dimer of Lrp and a monomer of PapI bind to pap site 5 (56). This transition is also dependent on dissociation of Lrp from sites 1-3 and methylation of GATC prox : increasing the off rate (k dis ) of Lrp at sites 1-3 increases the off-to-on rate (64).…”

Section: Phase Variation Via Dna Methylation Patternsmentioning

confidence: 99%

See 2 more Smart Citations

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Casadesús

Low

2013

Journal of Biological Chemistry

199

183

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Contrary to the traditional view that bacterial populations are clonal, single-cell analysis reveals that phenotypic heterogeneity is common in bacteria. Formation of distinct bacterial lineages appears to be frequent during adaptation to harsh environments, including the colonization of animals by bacterial pathogens. Formation of bacterial subpopulations is often controlled by epigenetic mechanisms that generate inheritable phenotypic diversity without altering the DNA sequence. Such mechanisms are diverse, ranging from relatively simple feedback loops to complex self-perpetuating DNA methylation patterns.

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Section: Phase Variation Via Dna Methylation Patternsmentioning

confidence: 99%

Section: Phase Variation Via Dna Methylation Patternsmentioning

confidence: 99%

Section: Phase Variation Via Dna Methylation Patternsmentioning

confidence: 99%

See 1 more Smart Citation

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Casadesús

Low

2013

Journal of Biological Chemistry

199

183

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show abstract

“…3I and J). PapI is a nonspecific DNAbinding protein (16,36,37), and it can directly interact with Lrp. We and others have previously shown that a low concentration of FooI and PapI significantly increases the binding and stability of Lrp at both sites in the repressor and activator regions (16,29,35).…”

Section: Discussionmentioning

confidence: 99%

Monitoring F165 ₁ P-Like Fimbria Expression at the Single-Cell Level Reveals a Highly Heterogeneous Phenotype

et al. 2015

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A dherence to host cells relies on the synthesis of specialized molecules that play an important role in multiple steps during the infectious process. Adhesins contribute to virulence by promoting the attachment and bacterial colonization on the host cell surface. Escherichia coli possesses a wide variety of adhesins, which all differ in structure and in functions. Moreover, a single strain can present more than one adhesin. This implies a complex regulatory network to produce exclusively one adhesin or to simultaneously express more than one.Phase variation of P fimbriae is a stochastic and reversible switch between an on phenotype and an off phenotype, "all-ornothing" (ON/OFF), each capable of responding to a specific condition. After cell division, the majority of daughter cells retain the expression phase of the parent; a minority switches to the opposite expression phase. F165 1 fimbriae, encoded by the foo gene cluster, are members of the type P fimbria family of Escherichia coli (1-4). The regulatory region of foo shares more than 96% identity with that of the pyelonephritis-associated pili (pap) gene. Previous work showed that F165 1 fimbriae are essential for virulence and survival during systemic stages of infection in young pigs (5-8). F165 1 fimbriae are principally found in infections caused by opportunistic E. coli in animals, while Pap fimbriae are found in human clinical cases of urinary tract infections. The phase variation of F165 1 fimbriae shares similar features with that of the wellcharacterized Pap fimbriae (9-11). This includes an ϳ400-bp intergenic region surrounded by two divergently transcribed genes (papI and papB for Pap, fooI and fooB for F165 1 ). It also includes six leucine-responsive regulatory protein (Lrp) binding sites, of which two are GATC sites (referred to as GATC prox and GATC dist , respectively), spaced 102 bp apart. In pap and foo, phase variation occurs because of methylation-controlled modifications within the regulatory region of the fimbrial operon. This regulation is epigenetic since it does not involve any changes in DNA sequence (12). The differential methylation status of these sequences determines the binding of Lrp. Indeed, the switch from one phenotype to the other arises from the competition between the binding of Lrp at its distal or proximal binding sites and methylation by the Dam methyltransferase at the opposite GATC site (for reviews, see references 9, 10, and 11). When GATC dist is fully methylated, Lrp cooperatively binds to sites 1 to 3, maintaining the cells in the OFF state; when GATC prox is fully methylated, Lrp binds to sites 4 to 6, maintaining the ON state (Fig. 1). Control of pap expression also requires the action of PapI, a positive regulator that increases the affinity of Lrp for sites 4 to 6 in vivo (11,13). PapB, the second specific regulator of the pap operon, plays an important role by coordinating the expression of the pBA and pI promoters (11). All together, the combined actions of Lrp, Dam methyltransferase, PapI, and PapB result...

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“…34 One-hundred µl volumes of protein samples maintained at 3 mg/mL in a solution containing 50 mM HEPES (pH 7.5), 100 mM NaCl, 20 mM KCl, 10 mM MgCl 2 , and 5 mM DTT were first separated on a Wyatt WTC-030S5 size-exclusion column at a flow rate of 0.50 mL/min using a Waters 600 HPLC, and were then analyzed in-line by a UV/Vis spectrophotometer, a Wyatt miniDAWN TREOS light-scattering detector, and a Wyatt Optilab T-rEX refractive index detector. Prior to the experiments, the column running buffer, comprised of 50 mM HEPES (pH 7.5), 100 mM NaCl, 20 mM KCl, 10 mM MgCl 2 , and 5 mM DTT was sterile-filtered (0.20 µm) and degassed for 10 min.…”

Section: Methodsmentioning

confidence: 99%

Linking Energy Production and Protein Synthesis in Hydrogenotrophic Methanogens

Oza

Sowers

Perona³

2012

Biochemistry

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Hydrogenotrophic methanogens possessing the hydrogen-dependent dehydrogenase Hmd also encode paralogs of this protein whose function is poorly understood. Here we present biochemical evidence that the two inactive Hmd paralogs of Methanocaldococcus jannaschii, HmdII and HmdIII, form binary and ternary complexes with several components of the protein translation apparatus. HmdII and HmdIII, but not the active dehydrogenase Hmd, bind with micromolar binding affinities to a number of tRNAs, and form ternary complexes with tRNAPro and prolyl-tRNA synthetase (ProRS). Fluorescence spectroscopy experiments also suggest that binding of HmdII and ProRS involves distinct binding determinants on the tRNA. These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions.

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The Design Involved in PapI and Lrp Regulation of the pap Operon

Cited by 13 publications

References 40 publications

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Monitoring F165 ₁ P-Like Fimbria Expression at the Single-Cell Level Reveals a Highly Heterogeneous Phenotype

Linking Energy Production and Protein Synthesis in Hydrogenotrophic Methanogens

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The Design Involved in PapI and Lrp Regulation of the pap Operon

Cited by 13 publications

References 40 publications

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Monitoring F165 1 P-Like Fimbria Expression at the Single-Cell Level Reveals a Highly Heterogeneous Phenotype

Linking Energy Production and Protein Synthesis in Hydrogenotrophic Methanogens

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Product

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Monitoring F165 ₁ P-Like Fimbria Expression at the Single-Cell Level Reveals a Highly Heterogeneous Phenotype