Stepwise Bending of DNA by a Single TATA-Box Binding Protein

Nørrelykke, Simon F.; Rasmussen, Mette B.; Pavone, Francesco S.; Berg-Sørensen, Kirstine; Oddershede, Lene B.

doi:10.1529/biophysj.105.074856

Cited by 50 publications

(47 citation statements)

References 52 publications

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“…The excursions of the bead were analyzed by a principal component analysis as detailed in ref. 25 and in SI Text. Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Inspired by the literature (25,27) and the results from Fig. S3, we imposed the following selection criteria to minimize the occurrence of unspecific tethers in the analyzed datasets: (i) Results from beads that probably were attached directly to the surface, or by unspecific tethers, and hence had a small RMSD were discarded, and (ii) if the positions visited by the bead displayed a low degree of symmetry (s) as defined in SI Text, the bead might be attached to the surface by more than one DNA tether and the time series was discarded.…”

Section: Resultsmentioning

confidence: 99%

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DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

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Andersson

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et al. 2013

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

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Bacteriophage λ stably maintains its dormant prophage state but efficiently enters lytic development in response to DNA damage. The mediator of these processes is the λ repressor protein, CI, and its interactions with λ operator DNA. This λ switch is a model on the basis of which epigenetic switch regulation is understood. Using single molecule analysis, we directly examined the stability of the CI-operator structure in its natural, supercoiled state. We marked positions adjacent to the λ operators with peptide nucleic acids and monitored their movement by tethered particle tracking. Compared with relaxed DNA, the presence of supercoils greatly enhances juxtaposition probability. Also, the efficiency and cooperativity of the λ switch is significantly increased in the supercoiled system compared with a linear assay, increasing the Hill coefficient. The decision between the dormant state (the lysogenic state) and the vegetative state (the lytic state) made by bacteriophage λ upon infection of an Escherichia coli was the first epigenetic switch to be deciphered (1) and continues to provide insights into biological processes (2, 3). Once the lysogenic state is established, it is exceptionally stable and departure in the absence of the DNA damage sensing system is nearly always caused by mutation (4-6). Maintenance of lysogeny is mediated by the λ repressor protein, CI, and its formation of a complex with phage DNA. The CI protein binds at two regulatory regions called operator right (OR) and operator left (OL), located about 2.3 kbp apart on the phage genome. Each operator is a constellation of three adjacent subsites that each bind dimers of CI in a hierarchical manner (1, 7). In a lysogenic cell, CI prevents lytic growth by directly repressing the lytic promoters pR and pL. This repression is enhanced by longrange cooperative interactions between CI dimers bound to the OL1-OL2 and OR1-OR2 regions, thus looping the DNA that lies between them (8) (Fig. 1 A and B). CI-mediated DNA looping brings OR3 in proximity to OL3. This juxtaposition allows a CI dimer bound to the strong OL3 to facilitate another CI dimer to bind to the intrinsically weak OR3, thus reducing the concentration of CI necessary to occupy OR3. In this manner CI can autoregulate its own expression by binding to OR2 (activation) or by binding to OR3 (repression). This autoregulation is crucial for the phage to maintain repression while preventing excessive accumulation of CI. When DNA in the lysogen is damaged, the bacterial DNA-damage-sensing system is triggered, leading to CI inactivation by self-cleavage (9) and to an efficient switch to the lytic state, eventually leading to production of progeny phage and cell death (1).The switch from the lysogenic to the lytic state must be decisive. Partial entry into vegetative growth may kill the host without producing a full burst of progeny phage. Because the in vivo state of DNA is supercoiled (10), we sought to examine protein-mediated DNA looping on native, supercoiled DNA. In vitro single molecule exper...

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“…The excursions of the bead were analyzed by a principal component analysis as detailed in ref. 25 and in SI Text. Fig.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

Nørregaard

Andersson

Sneppen

et al. 2013

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

Self Cite

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show abstract

“…5). The calculation of the scattering amplitudes has been slightly modified from its application of analyzing Brownian motion of DNAtethered beads (Tolic-Norrelykke et al, 2006). For a twodimensional image, the tensor of inertia I is given by the following matrix ͒ / 2 (standard deviation around the center of mass) for the individual channels as well as the ratio S = S red / S green .…”

Section: Appendix: Quantitative Image Analysismentioning

confidence: 99%

Quantitative differences in tissue surface tension influence zebrafish germ layer positioning

et al. 2008

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“…Despite the high sequence identity and structural conservation of TBP in the archaeal-eukaryotic lineage we found that TBP from the euryarchaeal organism M. jannaschii (Mj) and from the crenarchaeal organism Sulfolobus acidocaldarius (Sa) do not follow a common DNA bending mechanisms and deviate significantly from the bending pathway observed for the eukaryotic TBP-TF(II)B-DNA interaction [12,78,79]. Interestingly, unlike all other TBP-DNA-promoter DNA interactions described so far, TBP from S. acidocaldarius was not able to induce DNA bending by itself but strictly required TFB to evoke the conformational change in the DNA.…”

Section: Early Steps Of Initiationmentioning

confidence: 99%