Abstract
The lambda (λ) bacteriophage epigenetic switch is a molecular mechanism that permits the quiescent (lysogenic) state of the bacteriophage to irreversibly switch to the virulent (lytic) state. After infection of its host, E. coli, λ, a temperate phage, most often grows lysogenically. The phage DNA integrates in the bacterial chromosome and is replicated along with it and transmitted to the bacterial progeny as a prophage. Lysogeny is very stable and yet, the switch to lysis is very efficient. Upon switching to lysis, the viral DNA is excised from the bacterial chromosome and the host machinery is used to produce viral progeny that is then released upon bursting of the host. The pathway to lysis is triggered in response to threats such as starvation, poisoning, or DNA damage.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Anderson L, Yang H (2008) A simplified model for lysogenic regulation through DNA looping. Conf Proc IEEE Eng Med Biol Soc 2008:607–610
Anderson LM, Yang H (2008) DNA looping can enhance lysogenic CI transcription in phage lambda. Proc Natl Acad Sci U S A 105(15):5827–5832
Atsumi S, Little JW (2006) Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach. Proc Natl Acad Sci USA 103(12):4558–4563
Bakk A, Metzler R (2004) Nonspecific binding of the O-R repressors CI and Cro of bacteriophage lambda. J Theor Biol 231(4):525–533
Beausang JF, Zurla C, Finzi L, Sullivan L, Nelson PC (2007) Elementary simulation of tethered Brownian motion. Am J Phys 75:520–523
Beausang JF, Zurla C, Manzo C, Dunlap D, Finzi L, Nelson PC (2007) DNA looping kinetics analyzed using diffusive hidden Markov model. Biophys J 92(8):L64–L66
Bell CE, Frescura P, Hochschild A, Lewis M (2000) Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. Cell 101(7):801–811
Colquhoun D, Sigworth FJ (1983) Fitting and statistical analysis of single channel recording. Plenum, New York
Dodd IB, Perkins AJ, Tsemitsidis D, Egan JB (2001) Octamerization of lambda CI repressor is needed for effective repression of P-RM and efficient switching from lysogeny. Genes Dev 15(22):3013–3022
Dodd IB, Shearwin KE, Egan JB (2005) Revisited gene regulation in bacteriophage lambda. Curr Opin Genet Dev 15(2):145–152
Dodd IB, Shearwin KE, Perkins AJ, Burr T, Hochschild A, Egan JB (2004) Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev 18(3):344–354
Finzi L, Gelles J (1995) Measurement of lactose repressor-mediated loop formation and breakdown in single DNA-molecules. Science 267(5196):378–380
Frantsuzov P, Kuno M, Janko B, Marcus RA (2008) Universal emission intermittency in quantum dots, nanorods and nanowires. Nat Phys 4(5):519–522 [10.1038/nphys1001]
Guerra RF, Imperadori L, Mantovani R, Dunlap DD, Finzi L (2007) DNA compaction by the nuclear factor-Y. Biophys J 93(1):176–182
Hochschild A, Ptashne M (1988) Interaction at a distance between lambda-repressors disrupts gene activation. Nature 336(6197):353–357
Jain D, Nickels BE, Sun L, Hochschild A, Darst SA (2004) Structure of a ternary transcription activation complex. Mol Cell 13(1):45–53
Koblan KS, Ackers GK (1992) Site-specific enthalpic regulation of DNA-transcription at bacteriophage-lambda OR. Biochemistry 31(1):57–65
Leiderman P, Huppert D, Agmon N (2006) Transition in the temperature-dependence of gfp fluorescence: from proton wires to proton exit. Biophys J 90(3):1009–1018. doi:10.1529/biophysj.105.069393
Leiderman P, Huppert D, Remington SJ, Tolbert LM, Solntsev KM (2008) The effect of pressure on the excited-state proton transfer in the wild-type green fluorescent protein. Chem Phys Lett 455(4–6):303–306. doi:10.1016/j.cplett.2008.02.079
Liebovitch LS (1989) Analysis of fractal ion channel gating kinetics – kinetic rates, energy-levels, and activation-energies. Math Biosci 93(1):97–115
Liebovitch LS (1989) Testing fractal and Markov-models of ion channel kinetics. Biophys J 55(2):373–377
Liebovitch LS, Fischbarg J, Koniarek JP (1987) Ion channel kinetics – a model based on fractal scaling rather than multistate Markov-processes. Math Biosci 84(1):37–68
Liebovitch LS, Fischbarg J, Koniarek JP, Todorova I, Wang M (1987) Fractal model of ion-channel kinetics. Biochim Biophys Acta 896(2):173–180
Liebovitch LS, Sullivan JM (1987) Fractal analysis of a voltage-dependent potassium channel from cultured mouse hippocampal-neurons. Biophys J 52(6):979–988
Liebovitch LS, Toth TI (1991) Distributions of activation-energy barriers that produce stretched exponential probability-distributions for the time spent in each state of the 2 state reaction a-reversible-B. Bull Math Biol 53(3):443–455
Maniatis T, Ptashne M (1973) Multiple repressor binding at operators in bacteriophage-lambda – (nuclease protection polynucleotide sizing pyrimidine tracts supercoils E. coli). Proc Natl Acad Sci U S A 70(5):1531–1535
Manzo C, Finzi L (2010) Quantitative analysis of DNA looping kinetics from tethered particle motion experiments in Methods in Enzymology, volume 475 “Molecule Tools, Part B: Super-Resolution, Particle Tracking, Multiparameter, and Force Based Methods”, Ed. Nils G. Walter, pp 199–220.
Matthews KS (1992) DNA looping. Microbiol Rev 56(1):123–136
Maurer R, Meyer BJ, Ptashne M (1980) Gene-regulation at the right operator (Or) of bacteriophage-lambda.1. Or3 and autogenous negative control by repressor. J Mol Biol 139(2):147–161
Meyer BJ, Maurer R, Ptashne M (1980) Gene-regulation at the right operator (Or) of bacteriophage-lambda.2. Or1, Or2, and Or3 – their roles in mediating the effects of repressor and Cro. J Mol Biol 139(2):163–194
Nelson PC, Zurla C, Brogioli D, Beausang JF, Finzi L, Dunlap D (2006) Tethered particle motion as a diagnostic of DNA tether length. J Phys Chem B 110(34):17260–17267
Nickels BE, Dove SL, Murakami KS, Darst SA, Hochschild A (2002) Protein–protein and protein–DNA interactions of sigma(70) region 4 involved in transcription activation by lambda cl. J Mol Biol 324(1):17–34
Oppenheim AB, Kobiler O, Stavans J, Court DL, Adhya S (2005) Switches in bacteriophage lambda development. Annu Rev Genet 39:409–429
Ptashne M (2004) A genetic switch: phage lambda revisited, vol 3, 3rd edn. Cold Spring Harbor Laboratory, New York
Ptashne M, Gann A (2002) Genes and signals. Cold Spring Harbor Laboratory, New York
Qian H (2000) A mathematical analysis for the Brownian dynamics of a DNA tether. J Math Biol 41(4):331–340
Revet B, von Wilcken-Bergmann B, Bessert H, Barker A, Muller-Hill B (1999) Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances. Curr Biol 9(3):151–154
Senear DF, Brenowitz M, Shea MA, Ackers GK (1986) Energetics of cooperative protein–DNA interactions – comparison between quantitative deoxyribonuclease footprint titration and filter binding. Biochemistry 25(23):7344–7354
Stayrook S, Jaru-Ampornpan P, Ni J, Hochschild A, Lewis M (2008) Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding. Nature 452(7190):1022–1025
van den Broek B, Vanzi F, Normanno D, Pavone FS, Wuite GJL (2006) Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res 34(1):167–174
Vanzi F, Broggio C, Sacconi L, Pavone FS (2006) Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion. Nucleic Acids Res 34(12):3409–3420
Vilar JMG, Saiz L (2005) DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr Opin Genet Dev 15(2):136–144
Wang H, Finzi L, Lewis D, Dunlap D (2009) AFM studies of the CI oligomers that secure DNA loops. J Pharm Biotechnol 10:494–501
Wang Y, Guo L, Golding I, Cox EC, Ong NP (2009) Quantitative transcription factor binding kinetics at the single-molecule level. Biophys J 96:609–620
Watkins LP, Yang H (2005) Detection of intensity change points in time-resolved single-molecule measurements. J Phys Chem B 109(1):617–628
Zhang HY, Marko JF (2008) Maxwell relations for single-DNA experiments: monitoring protein binding and double-helix torque with force-extension measurements. Phys Rev E 77(3):031916.1–031916.9
Zurla C, Franzini A, Galli G, Dunlap DD, Lewis DEA, Adhya S et al (2006) Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda. J Phys Condens Matter 18(14):S225–S234
Zurla C, Manzo C, Dunlap DD, Lewis DEA, Adhya S, Finzi L (2009) Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Res 37:2789–2795
Zurla C, Samuely T, Bertoni G, Valle F, Dietler G, Finzi L et al (2007) Integration host factor alters LacI-induced DNA looping. Biophys Chem 128(2–3):245–252
Liebesny P, Goyal S, Dunlap D, Fereydoon family, Finz L, Fereydoon Family, Determination of the Number of Proteins Bound non-Specifically to DNA. JPCM (in press)
Acknowledgments
We would like to thank previous and current members of our groups whose research has facilitated these studies. We are also grateful to Haw Yang, who has provided reagents, analytical tools, and advice. The work described in this chapter was supported by the Italian Funding of Basic Research to LF and DDD, by the HFSP(RGP0050/2002-C) to L.F. and S.A., by the Intramural Research Program of the National Institutes of Health, National Cancer Institute and the Center for Cancer Research to S.A., by the Emory University Research Council and the NIH (RGM084070A) to LF.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Finzi, L. et al. (2010). DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy. In: Williams, M., Maher, L. (eds) Biophysics of DNA-Protein Interactions. Biological and Medical Physics, Biomedical Engineering. Springer, New York, NY. https://doi.org/10.1007/978-0-387-92808-1_9
Download citation
DOI: https://doi.org/10.1007/978-0-387-92808-1_9
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-92807-4
Online ISBN: 978-0-387-92808-1
eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)