Modulation of DNA Binding by Gene-Specific Transcription Factors

Schleif, Robert

doi:10.1021/bi400968e

Cited by 17 publications

(11 citation statements)

References 59 publications

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“…It is unlikely that arabinose‐dependent adventitious interactions between the conjugated IAEDANS and some part of the protein generated anomalous results. An interaction that altered the allosteric response of the protein would, of thermodynamic necessity, have altered the affinity of arabinose binding. Conjugated IAEDANS, however, did not detectably alter the affinity of arabinose binding.…”

Section: Discussionmentioning

confidence: 99%

“…How then can information about the status of the ligand binding site be transmitted to a DNA binding domain(s) to change the DNA binding affinity of the protein? In the three proteins that have been studied most extensively, AraC, LacI, and CAP, DNA binding affinity has been found to be modulated by controlling the relative positions and/or orientations of the DNA binding domains . In the cases of LacI and CAP, the binding or release of a small molecule ligand controls a helix‐coil transition of a portion of the protein, and it is the rigidity‐flexibility or structural integrity of this portion of the protein that plays a major role in controlling the positioning of the protein's DNA binding domains.…”

Section: Discussionmentioning

confidence: 99%

“…In the three proteins that have been studied most extensively, AraC, LacI, and CAP, DNA binding affinity has been found to be modulated by controlling the relative positions and/or orientations of the DNA binding domains. 57,58 In the cases of LacI and CAP, the binding or release of a small molecule ligand controls a helix-coil transition of a portion of the protein, 38-41 and it is the rigidity-flexibility or structural integrity of this portion of the protein that plays a major role in controlling the positioning of the protein's DNA binding domains. Helix-coil transitions also appear to play a role in controlling the binding of TetR, the tet repressor.…”

Section: Discussionmentioning

confidence: 99%

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A genetic and physical study of the interdomain linker ofE. ColiAraC protein-atrans-subunit communication pathway

et al. 2016

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Genetic experiments with full length AraC and biophysical experiments with its dimerization domain plus linker suggest that arabinose binding to the dimerization domain changes the properties of the inter-domain linker which connects the dimerization domain to the DNA binding domain via interactions that do not depend on the DNA binding domain. Normal AraC function was found to tolerate considerable linker sequence alteration excepting proline substitutions. The proline substitutions partially activate transcription even in the absence of arabinose and hint that a structural shift between helix and coil may be involved. To permit fluorescence anisotropy measurements that could detect arabinose-dependent dynamic differences in the linkers, IAEDANS was conjugated to a cysteine residue substituted at the end of the linker of dimerization domain. Arabinose, but not other sugars, decreased the steady-state anisotropy, indicating either an increase in mobility and/or an increase in the fluorescence lifetime of the IAEDANS. Time-resolved fluorescence measurements showed that the arabinose-induced anisotropy decrease did not result from an increase in the excited-state lifetime. Hence arabinose-induced decreases in anisotropy appear to result from increased tumbling of the fluorophore. Arabinose did not decrease the anisotropy in mutants incapable of binding arabinose nor did it alter the anisotropy when IAEDANS was conjugated elsewhere in the dimerization domain. Experiments with heterodimers of the dimerization domain showed that the binding of arabinose to one subunit of the dimer decreases the fluorescence anisotropy of only a fluorophore on the linker of the other subunit.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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A genetic and physical study of the interdomain linker ofE. ColiAraC protein-atrans-subunit communication pathway

et al. 2016

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“…The literature is replete with examples of regulatory proteins that control transcription initiation and the history of the field is dominated by examples of proteindependent control mechanisms, such as those controlling the life cycle of bacteriophage lambda or the expression of the lac operon (Lewis 2011;Oppenheim et al 2005;Wilson et al 2007). Research that has focused intensively on protein regulators for more than five decades has pushed the regulatory role of DNA into the background where, at best, it is regarded as contributing to gene control by providing cis-acting sites for the binding of regulatory proteins or through its possession of a structural flexibility that facilitates interactions between bound proteins via DNA looping (Schleif 2013;Semsey et al 2005). This regulatory model, where DNA plays largely a passive role, is incomplete because it omits the active contribution that is made by DNA itself through its topological dynamism.…”

Section: Introductionmentioning

confidence: 99%

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

Dorman

2016

Biophys Rev

107

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Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.

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“…The level of repression has to be determined by comparison with an identical strain which lacks the repressor, instead of the inducer. Modulation of DNA binding by gene-specific transcription factors is a crucial element and some aspects still have to be cleared (Schleif, 2013). Replacing the weak operators by the strong one has qualitatively the same effect (high level of repression) as replacing the repressor by a mutant superrepressor which binds tightly DNA (Willson et al, 1964; Bourgeois and Jobe, 1970).…”

Section: Further Developmentsmentioning

confidence: 99%

From adjacent activation in Escherichia coli and DNA cyclization to eukaryotic enhancers: the elements of a puzzle

Amouyal¹

2014

Front. Genet.

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Deoxyribonucleic acid cyclization, Escherichia coli lac repressor binding to two spaced lac operators and repression enhancement can be successfully used for a better understanding of the conditions required for interaction between eukaryotic enhancers and the machinery of transcription initiation. Chronologically, the DNA looping model has first accounted for the properties initially defining enhancers, i.e., independence of action with distance or orientation with respect to the start of transcription. It has also predicted enhancer activity or its disruption at short distance (site orientation, alignment between promoter and enhancer sites), with high-order complexes of protein, or with transcription factor concentrations close or different from the wild-type situation. In another step, histones have been introduced into the model to further adapt it to eukaryotes. They in fact favor DNA cyclization in vitro. The resulting DNA compaction might explain the difference counted in base pairs in the distance of action between eukaryotic transcription enhancers and prokaryotic repression enhancers. The lac looping system provides a potential tool for analysis of this discrepancy and of chromatin state directly in situ. Furthermore, as predicted by the model, the contribution of operators O2 and O3 to repression of the lac operon clearly depends on the lac repressor level in the cell and is prevented in strains overproducing lac repressor. By extension, gene regulation especially that linked to cell fate, should also depend on transcription factor levels, providing a potential tool for cellular therapy. In parallel, a new function of the O1–O3 loop completes the picture of lac repression. The O1–O3 loop would at the same time ensure high efficiency of repression, inducibility through the low-affinity sites and limitation of the level of repressor through self-repression of the lac repressor. Last, the DNA looping model can be successfully adapted to the enhancer auxiliary elements known as insulators.

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Modulation of DNA Binding by Gene-Specific Transcription Factors

Cited by 17 publications

References 59 publications

A genetic and physical study of the interdomain linker ofE. ColiAraC protein-atrans-subunit communication pathway

A genetic and physical study of the interdomain linker ofE. ColiAraC protein-atrans-subunit communication pathway

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

From adjacent activation in Escherichia coli and DNA cyclization to eukaryotic enhancers: the elements of a puzzle

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