Monovalent Cations Regulate DNA Sequence Recognition by 434 Repressor

Mauro, Steven A.

doi:10.1016/s0022-2836(04)00528-5

Cited by 5 publications

(11 citation statements)

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“…Our previous findings showed that in vitro, the affinity of 434 repressor for its specific binding sites depends not only on the concentration, but also the type, of monovalent cation (32). These results also indicated that changing the type of divalent cation had little effect on repressor-DNA complex stability.…”

Section: Resultsmentioning

confidence: 88%

“…Our in vitro results demonstrating that changing the monovalent cation type and concentration differentially affects 434 repressor binding to its various operator sites (32,33) suggested to us that an increased internal salt concentration might affect the interaction of the repressor with DNA, at least transiently. This hypothesis predicted that changing the external salt concentration would influence the stability of imm434 lysogens stabilized by the DNA binding activity of 434 repressor.…”

mentioning

confidence: 74%

“…Changing the type and/or concentration of monovalent cations differentially alters the affinities of 434 repressor for its various binding sites (32,33) in vitro. We wished to determine whether changing the salt type and concentration affected the gene-regulatory activities of bacteriophage 434 repressor in vivo.…”

Section: Resultsmentioning

confidence: 99%

“…In large measure, the sensitivities of these complexes to changes in the salt concentration derive from the contributions of charge-charge interactions between the protein and DNA. In addition, the binding of cations to DNA and/or protein-DNA complexes can influence complex stability by modulating the overall structure of the protein-DNA interface (4,5,32). The demonstrated importance of ionic conditions for protein-DNA complex formation in vitro suggests that the intracellular ionic environment may also influence protein-DNA interactions in vivo.…”

mentioning

confidence: 99%

“…However, the salt concentration dependence of 434 repressor's affinity for DNA also varies with the sequence of the binding site (2,3). Changing the type of monovalent cation markedly affects the affinity of 434 repressor for O R 1 but has no effect on the affinity of the repressor for O R 3 (32). Since the repressor's ability to direct the lysis-lysogeny decision depends on its overall affinity for DNA and its relative affinities for O R 1 and O R 3, these findings suggest that the cytosolic cation type and concentration may play important roles in regulating the lysis-lysogen decisions of bacteriophage 434.…”

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confidence: 99%

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Effect of Salt Shock on Stability of λ ^imm434 Lysogens

Shkilnyj

Koudelka

2007

J Bacteriol

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The affinities of the bacteriophage 434 repressor for its various binding sites depend on the type and/or concentration of monovalent cations. The ability of bacteriophage 434 repressor to govern the lysis-lysogeny decision depends on the DNA binding activities of the phage's cI repressor protein. We wished to determine whether changes in the intracellular ionic environment influence the lysis-lysogeny decision of the bacteriophage imm434 . Our findings show that the ionic composition within bacterial cells varies with the cation concentration in the growth media. When imm434 lysogens were grown to mid-log or stationary phase and subsequently incubated in media with increasing monovalent salt concentrations, we observed a salt concentration-dependent increase in the frequency of bacteriophage spontaneous induction. We also found that the frequency of spontaneous induction varied with the type of monovalent cation in the medium. The saltdependent increase in phage production was unaffected by a recA mutation. These findings indicate that the salt-dependent increase in phage production is not caused by activation of the SOS pathway. Instead, our evidence suggests that salt stress induces this lysogenic bacteriophage by interfering with 434 repressor-DNA interactions. We speculate that the salt-dependent increase in spontaneous induction is due to a direct effect on the repressor's affinity for DNA. Regardless of the precise mechanism, our findings demonstrate that salt stress can regulate the phage lysis-lysogeny switch.In vitro studies show that the stability and specificity of protein-DNA complexes are remarkably dependent on the type and concentration of ions present in the solvent milieu (for a review, see reference 43). In large measure, the sensitivities of these complexes to changes in the salt concentration derive from the contributions of charge-charge interactions between the protein and DNA. In addition, the binding of cations to DNA and/or protein-DNA complexes can influence complex stability by modulating the overall structure of the protein-DNA interface (4,5,32). The demonstrated importance of ionic conditions for protein-DNA complex formation in vitro suggests that the intracellular ionic environment may also influence protein-DNA interactions in vivo.We were interested in knowing whether changes in the intracellular ionic environment influence the lysis-lysogeny decision of lambdoid bacteriophages, in particular, bacteriophage 434 that infects Escherichia coli. Similar to bacteriophage , imm434 is a temperate phage whose life cycle alternates between the lysogenic and lytic developmental pathways (11,38). In a lysogen, the phage's genome is integrated into the chromosome of its host and is replicated along with the host chromosome. The lysogen is a metastable developmental state; all lysogenized phage can undergo lytic development (40). In lytic growth, phage DNA is not integrated into the chromosome; rather, its intracellular replication, assembly into phage particles, and subsequent host cell ly...

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Section: Resultsmentioning

confidence: 88%

mentioning

confidence: 74%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Effect of Salt Shock on Stability of λ ^imm434 Lysogens

Shkilnyj

Koudelka

2007

J Bacteriol

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Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical DNA

Srinivasan

Sauers

Fenley³

et al. 2009

Biophys Rev

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The nucleic-acid bases carry structural and energetic signatures that contribute to the unique features of genetic sequences. Here we review the connection between the chemical structure of the constituent nucleotides and the polymeric properties of DNA. The sequence-dependent accumulation of charge on the major- and minor-groove edges of the Watson-Crick base pairs, obtained from ab initio calculations, presents unique motifs for direct sequence recognition. The optimization of base interactions generates a propellering of base-pair planes of the same handedness as that found in high-resolution double-helical structures. The optimized base pairs also deform along conformational pathways, i.e., normal modes, of the same type induced by the binding of proteins. Empirical energy computations that incorporate the properties of the base pairs account satisfactorily for general features of the next level of double-helical structure, but miss key sequence-dependent differences in dimeric structure and deformability. The latter discrepancies appear to reflect factors other than intrinsic base-pair structure.

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