Literature DB >> 14695249

Sensitivity of OR in phage lambda.

Audun Bakk1, Ralf Metzler, Kim Sneppen.   

Abstract

We investigate the sensitivity of the right operator in bacteriophage lambda. In particular, the system is probed in the three different regulatory protein concentration-regimes: 1), lysogen (CI dominates); 2), during induction (CI and Cro at comparable concentrations); and 3), after induction (Cro dominates). Systematic perturbations of the protein-operator binding energies show in a lysogen that the activity (production rate) at promoter PRM is robust to variations, in contrast to PR, where the sensitivity is high. Both promoters, however, show large sensitivity in regimes 2 and 3. In all regimes we identify several suppressors, meaning that for a given large perturbation (+/-2 kcal/mol) of one binding energy, there exist compensating perturbation(s) that restore the wild-type activity.

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Year:  2004        PMID: 14695249      PMCID: PMC1303827          DOI: 10.1016/S0006-3495(04)74083-7

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  24 in total

1.  Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny.

Authors:  I B Dodd; A J Perkins; D Tsemitsidis; J B Egan
Journal:  Genes Dev       Date:  2001-11-15       Impact factor: 11.361

2.  Epigenetics as a first exit problem.

Authors:  E Aurell; K Sneppen
Journal:  Phys Rev Lett       Date:  2002-01-08       Impact factor: 9.161

3.  Stability puzzles in phage lambda.

Authors:  Erik Aurell; Stanley Brown; Johan Johanson; Kim Sneppen
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-05-16

4.  Thermodynamics of Cro protein-DNA interactions.

Authors:  Y Takeda; P D Ross; C P Mudd
Journal:  Proc Natl Acad Sci U S A       Date:  1992-09-01       Impact factor: 11.205

5.  The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation.

Authors:  M A Shea; G K Ackers
Journal:  J Mol Biol       Date:  1985-01-20       Impact factor: 5.469

6.  Rate-limiting steps in RNA chain initiation.

Authors:  W R McClure
Journal:  Proc Natl Acad Sci U S A       Date:  1980-10       Impact factor: 11.205

Review 7.  lambda Repressor and cro--components of an efficient molecular switch.

Authors:  A D Johnson; A R Poteete; G Lauer; R T Sauer; G K Ackers; M Ptashne
Journal:  Nature       Date:  1981-11-19       Impact factor: 49.962

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

Authors:  P J Darling; J M Holt; G K Ackers
Journal:  J Mol Biol       Date:  2000-09-22       Impact factor: 5.469

9.  Quantitative model for gene regulation by lambda phage repressor.

Authors:  G K Ackers; A D Johnson; M A Shea
Journal:  Proc Natl Acad Sci U S A       Date:  1982-02       Impact factor: 11.205

10.  Interactions between DNA-bound repressors govern regulation by the lambda phage repressor.

Authors:  A D Johnson; B J Meyer; M Ptashne
Journal:  Proc Natl Acad Sci U S A       Date:  1979-10       Impact factor: 11.205

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  8 in total

1.  Target search of N sliding proteins on a DNA.

Authors:  Igor M Sokolov; Ralf Metzler; Kiran Pant; Mark C Williams
Journal:  Biophys J       Date:  2005-05-20       Impact factor: 4.033

2.  A quantitative study of lambda-phage SWITCH and its components.

Authors:  Chunbo Lou; Xiaojing Yang; Xili Liu; Bin He; Qi Ouyang
Journal:  Biophys J       Date:  2007-01-26       Impact factor: 4.033

Review 3.  Transcriptional regulation by the numbers: models.

Authors:  Lacramioara Bintu; Nicolas E Buchler; Hernan G Garcia; Ulrich Gerland; Terence Hwa; Jané Kondev; Rob Phillips
Journal:  Curr Opin Genet Dev       Date:  2005-04       Impact factor: 5.578

4.  Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility.

Authors:  Elizabeth Eck; Jonathan Liu; Maryam Kazemzadeh-Atoufi; Sydney Ghoreishi; Shelby A Blythe; Hernan G Garcia
Journal:  Elife       Date:  2020-10-19       Impact factor: 8.140

Review 5.  Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.

Authors:  Rob Phillips; Nathan M Belliveau; Griffin Chure; Hernan G Garcia; Manuel Razo-Mejia; Clarissa Scholes
Journal:  Annu Rev Biophys       Date:  2019-05-06       Impact factor: 12.981

6.  Effect of transcription factor resource sharing on gene expression noise.

Authors:  Dipjyoti Das; Supravat Dey; Robert C Brewster; Sandeep Choubey
Journal:  PLoS Comput Biol       Date:  2017-04-17       Impact factor: 4.475

7.  Elements in the λ immunity region regulate phage development: beyond the 'Genetic Switch'.

Authors:  Lynn C Thomason; Kathleen Morrill; Gillian Murray; Carolyn Court; Brenda Shafer; Thomas D Schneider; Donald L Court
Journal:  Mol Microbiol       Date:  2019-10-08       Impact factor: 3.979

8.  General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

Authors:  Vladimir B Teif
Journal:  Nucleic Acids Res       Date:  2007-05-25       Impact factor: 16.971

  8 in total

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