共查询到20条相似文献,搜索用时 46 毫秒
1.
K S Matthews 《Microbiological reviews》1992,56(1):123-136
2.
3.
4.
Nicole A. Becker Justin P. Peters Troy A. Lionberger L. James Maher III 《Nucleic acids research》2013,41(1):156-166
The Escherichia coli lactose (lac) operon encodes the first genetic switch to be discovered, and lac remains a paradigm for studying negative and positive control of gene expression. Negative control is believed to involve competition of RNA polymerase and Lac repressor for overlapping binding sites. Contributions to the local Lac repressor concentration come from free repressor and repressor delivered to the operator from remote auxiliary operators by DNA looping. Long-standing questions persist concerning the actual role of DNA looping in the mechanism of promoter repression. Here, we use experiments in living bacteria to resolve four of these questions. We show that the distance dependence of repression enhancement is comparable for upstream and downstream auxiliary operators, confirming the hypothesis that repressor concentration increase is the principal mechanism of repression loops. We find that as few as four turns of DNA can be constrained in a stable loop by Lac repressor. We show that RNA polymerase is not trapped at repressed promoters. Finally, we show that constraining a promoter in a tight DNA loop is sufficient for repression even when promoter and operator do not overlap. 相似文献
5.
6.
7.
8.
9.
10.
11.
12.
The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information. 相似文献
13.
14.
15.
16.
17.
Chiara Zurla Carlo Manzo David Dunlap Dale E. A. Lewis Sankar Adhya Laura Finzi 《Nucleic acids research》2009,37(9):2789-2795
Recently, it was proposed that DNA looping by the λ repressor (CI protein) strengthens repression of lytic genes during lysogeny and simultaneously ensures efficient switching to lysis. To investigate this hypothesis, tethered particle motion experiments were performed and dynamic CI-mediated looping of single DNA molecules containing the λ repressor binding sites separated by 2317 bp (the wild-type distance) was quantitatively analyzed. DNA containing all three intact operators or with mutated o3 operators were compared. Modeling the thermodynamic data established the free energy of CI octamer-mediated loop formation as 1.7 kcal/mol, which decreased to –0.7 kcal/mol when supplemented by a tetramer (octamer+tetramer-mediated loop). These results support the idea that loops secured by an octamer of CI bound at oL1, oL2, oR1 and oR2 operators must be augmented by a tetramer of CI bound at the oL3 and oR3 to be spontaneous and stable. Thus the o3 sites are critical for loops secured by the CI protein that attenuate cI expression. 相似文献
18.
Cherstvy AG 《European biophysics journal : EBJ》2011,40(1):69-80
We analyze looping of thin charged elastic filaments under applied torques and end forces, using the solution of linear elasticity
theory equations. In application to DNA, we account for its polyelectrolyte character and charge renormalization, calculating
electrostatic energies stored in the loops. We argue that the standard theory of electrostatic persistence is only valid when
the loop’s radius of curvature and close-contact distance are much larger than the Debye screening length. We predict that
larger twist rates are required to trigger looping of charged rods as compared with neutral ones. We then analyze loop shapes
formed on charged filaments of finite length, mimicking DNA looping by proteins with two DNA-binding domains. We find optimal
loop shapes at different salt amounts, minimizing the sum of DNA elastic, DNA electrostatic, and protein elastic energies.
We implement a simple model where intercharge repulsions do not affect the loop shape directly but can choose the energy-optimized
shape from the allowed loop types. At low salt concentrations more open loops are favored due to enhanced repulsion of DNA
charges, consistent with the results of computer simulations on formation of DNA loops by lac repressor. Then, we model the
precise geometry of DNA binding by the lac tetramer and explore loop shapes, varying the confined DNA length and protein opening
angle. The characteristics of complexes obtained, such as the total loop energy, stretching forces required to maintain its
shape, and the reduction of electrostatic energy with increment of salt, are in good agreement with the outcomes of more elaborate
numerical calculations for lac-repressor-induced DNA looping. 相似文献
19.