Coupled energetics of λ cro repressor self-assembly and site-specific DNA operator binding II: cooperative interactions of cro dimers

Darling, Paul J.; Holt, Jo M.; Ackers, Gary K.

doi:10.1006/jmbi.2000.4050

Cited by 76 publications

(125 citation statements)

References 49 publications

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“…Dimerization free energies are taken to be Ϫ11 kcal/mol for CI (36,37) and Ϫ8.7 kcal/mol for Cro (38). The association reaction is again assumed to be diffusion-limited.…”

Section: The Modelmentioning

confidence: 99%

DNA looping provides stability and robustness to the bacteriophage λ switch

Morelli

Wolde

Allen

2009

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

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The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage λ presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of the extreme stability of the lysogenic state remains unclear. We have constructed a stochastic model for this switch. Using Forward Flux Sampling simulations, we show that this model predicts an extremely low rate of spontaneous prophage induction in a recA mutant, in agreement with experimental observations. In our model, the DNA loop formed by octamerization of CI bound to the O L and O R operator regions is crucial for stability, allowing the lysogenic state to remain stable even when a large fraction of the total CI is depleted by nonspecific binding to genomic DNA. DNA looping also ensures that the switch is robust to mutations in the order of the O R binding sites. Our results suggest that DNA looping can provide a mechanism to maintain a stable lysogenic state in the face of a range of challenges including noisy gene expression, nonspecific DNA binding, and operator site mutations.

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“…Dimerization free energies are taken to be Ϫ11 kcal/mol for CI (36,37) and Ϫ8.7 kcal/mol for Cro (38). The association reaction is again assumed to be diffusion-limited.…”

Section: The Modelmentioning

confidence: 99%

DNA looping provides stability and robustness to the bacteriophage λ switch

Morelli

Wolde

Allen

2009

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

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“…These values allow us to determine the hydrodynamic radius, R s , of a protein [19,20]. The bed and the void volumes were determined by using riboflavin and blue-dextran, yielding 23.65 and 7.01 ml, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…(e) Gel filtration measurements: In the absence of the ion, SmelDhp eluted at 10.96 ml at pH 7.0, which yields a R s of 47.5 Å [19,20] (Fig. 5 A).…”

Section: +mentioning

confidence: 99%

Metal-triggered changes in the stability and secondary structure of a tetrameric dihydropyrimidinase: A biophysical characterization

Martínez‐Rodríguez

Encinar

Hurtado-Gómez

et al. 2009

Biophysical Chemistry

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 3 ABSTRACTDihydropyrimidinase is involved in the reductive pathway of pyrimidine degradation, catalysing the reversible hydrolysis of the cyclic amide bond (-CO-NH-) of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N-carbamoyl-β-amino acids. This enzyme is an attractive candidate for commercial production of D-amino acids, which are used in the production of semisynthetic β-lactams, antiviral agents, artificial sweeteners, peptide hormones and pesticides. We have obtained the crystal structure of the dihydropyrimidinase from Sinorhizobium meliloti (SmelDhp) in the presence of zinc ions, but we have not been able to obtain good diffracting crystals in its absence. Then, the role of the ion in the structure of the protein, and in its stability, remains to be elucidated. In this work, the stability and the structure of SmelDhp have been studied in the absence and in the presence of zinc. In its absence, the protein acquired a tetrameric functional structure at pH ~6.0, which is stable up to pH ~9.0, as concluded from fluorescence and CD.Chemical-denaturation occurred via a monomeric intermediate with non-native structure. The addition of zinc caused: (i) an increase of the helical structure, and changes in the environment of aromatic residues; and, (ii) a higher thermal stability. However, chemical-denaturation still occurred through a monomeric intermediate. This is the first hydantoinase whose changes in the stability and in the secondary structure upon addition of zinc are described and explained, and one of the few examples where the zinc exclusively alters the secondary helical structure and the environment of some aromatic residues in the protein, leaving unchanged the quaternary structure.

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“…It is well known that repressor binds cooperatively to neighboring operator sites (20). Similarly, Cro dimers also bind cooperatively, although to a lesser extent (21). These cooperativities are fully incorporated in our model (see SI Appendix for details).…”

Section: Probability Landscape Of Phage Lambda In Lysogenic and Lyticmentioning

confidence: 99%

Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda

Cao

Liang

2010

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

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Computational studies of biological networks can help to identify components and wirings responsible for observed phenotypes. However, studying stochastic networks controlling many biological processes is challenging. Similar to Schrödinger's equation in quantum mechanics, the chemical master equation (CME) provides a basic framework for understanding stochastic networks. However, except for simple problems, the CME cannot be solved analytically. Here we use a method called discrete chemical master equation (dCME) to compute directly the full steady-state probability landscape of the lysogeny maintenance network in phage lambda from its CME. Results show that wild-type phage lambda can maintain a constant level of repressor over a wide range of repressor degradation rate and is stable against UV irradiation, ensuring heritability of the lysogenic state. Furthermore, it can switch efficiently to the lytic state once repressor degradation increases past a high threshold by a small amount. We find that beyond bistability and nonlinear dimerization, cooperativity between repressors bound to O R 1 and O R 2 is required for stable and heritable epigenetic state of lysogeny that can switch efficiently. Mutants of phage lambda lack stability and do not possess a high threshold. Instead, they are leaky and respond to gradual changes in degradation rate. Our computation faithfully reproduces the hair triggers for UVinduced lysis observed in mutants and the limitation in robustness against mutations. The landscape approach computed from dCME is general and can be applied to study broad issues in systems biology.B acteriophage lambda is a virus that infects Escherichia coli cells. It has served as a model system for studying regulatory networks and for engineering gene circuits (1-5). Of central importance is the molecular circuitry that controls phage lambda to choose between two productive modes of development, namely, the lysogenic state and the lytic state (Fig 1A). In the lysogenic state, phage lambda represses its developmental function, integrates its DNA into the chromosome of the host E. coli bacterium, and is replicated in cell cycles for potentially many generations. When threatening DNA damage occurs, phage lambda switches from the epigenetic state of lysogeny to the lytic state and undergoes massive replications in a single cell cycle, releases 50-100 progeny phages upon lysis of the E. coli cell. This switching process is called prophage induction (5).The molecular network that controls the choice between these two different physiological states has been studied extensively during the past 40 y (5-9). All of the major molecular components of the network have been identified, binding constants and reaction rates characterized, and there is a good experimental understanding of the general mechanism of the molecular switch (5). Theoretical studies have also contributed to the illumination of the central role of stochasticity (3) and the stability of lysogen against spontaneous switching (4, 10). With the advent o...

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Coupled energetics of λ cro repressor self-assembly and site-specific DNA operator binding II: cooperative interactions of cro dimers

Cited by 76 publications

References 49 publications

DNA looping provides stability and robustness to the bacteriophage λ switch

DNA looping provides stability and robustness to the bacteriophage λ switch

Metal-triggered changes in the stability and secondary structure of a tetrameric dihydropyrimidinase: A biophysical characterization

Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda

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