Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins

Bondos, Sarah E.; Swint-Kruse, Liskin; Matthews, Kathleen S.

doi:10.1074/jbc.r115.685032

Cited by 19 publications

(23 citation statements)

References 102 publications

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“…(C) Electrophoretic mobility shift assays. Varying concentrations of His 6 ‐LacI‐51 and 10 −7 M LacI were each mixed with [P]‐labeled 40 bp O1 DNA (≤10 −11 M ) and equilibrated, followed by rapid loading onto a polyacrylamide gel. Note the loss of free DNA and detection of bound bands for His 6 ‐LacI‐51 at 10 −5 M protein; the lowest bound band exhibits slightly higher mobility compared to wild‐type LacI, as expected for this smaller tetramer.…”

Section: Resultsmentioning

confidence: 99%

“…Later studies produced crystallographic and NMR structures of LacI and other members of the LacI/GalR family of regulatory proteins that illuminated the role of the hinge helix in bending the central region of the DNA target sequence to align the flanking sequences for HtH binding . Within the LacI/GalR family, specific DNA binding and regulatory responses for each protein are generated by variations in shared structural motifs . Structural homology is evident from detailed sequence analysis and crystallographic structures that include LacI, PurR, and CcpA .…”

Section: Discussionmentioning

confidence: 99%

“…Within the LacI/GalR family, specific DNA binding and regulatory responses for each protein are generated by variations in shared structural motifs . Structural homology is evident from detailed sequence analysis and crystallographic structures that include LacI, PurR, and CcpA . Insertion of the hinge helix into the minor groove is a common feature of these structures, enabling high affinity binding by the HtH to flanking sequences .…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, comparison of LacI and PurR structures has indicated that these proteins utilize different contacts between the hinge region and flanking sequences and the core regulatory domain . Within this small subset of LacI/GalR proteins with known structure, the variety of ways that similar folds can be utilized to regulate DNA is impressive, and the hinge domain that links the DNA‐ and effector‐binding domains plays a critical functional role . Although no structural data are available for the CytR protein, which interacts with cAMP receptor protein to regulate transcription, flexibility of the hinge domain and flanking linker region has been shown to be essential to its regulatory function …”

Section: Discussionmentioning

confidence: 99%

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Lactose repressor hinge domain independently binds DNA

Hewitt

Gulati

et al. 2018

Protein Science

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The short 8–10 amino acid “hinge” sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer‐binding domains. Structural studies of full‐length or truncated LacI‐operator DNA complexes demonstrate insertion of the dimeric helical “hinge” structure at the center of the operator sequence. This association bends the DNA ∼40° and aligns flanking semi‐symmetric DNA sites for optimal contact by the N‐terminal helix‐turn‐helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences. To determine ability of the hinge helix alone to mediate DNA binding, we examined (i) binding of LacI variants with deletion of residues 1–50 to remove the HtH DNA binding domain or residues 1–58 to remove both HtH and hinge domains and (ii) binding of a synthetic peptide corresponding to the hinge sequence with a Val52Cys substitution that allows reversible dimer formation via a disulfide linkage. Binding affinity for DNA is orders of magnitude lower in the absence of the helix‐turn‐helix domain with its highly positive charge. LacI missing residues 1–50 binds to DNA with ∼4‐fold greater affinity for operator than for nonspecific sequences with minimal impact of inducer presence; in contrast, LacI missing residues 1–58 exhibits no detectable affinity for DNA. In oxidized form, the dimeric hinge peptide alone binds to O1 and nonspecific DNA with similarly small difference in affinity; reduction to monomer diminished binding to both O1 and nonspecific targets. These results comport with recent reports regarding LacI hinge interaction with DNA sequences.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Lactose repressor hinge domain independently binds DNA

Hewitt

Gulati

et al. 2018

Protein Science

Self Cite

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“…Rather, TFs appear to use a rapid search model that uses two phases of binding to DNA, weak and potentially non-specific binding, followed by migration, either by rapid cycles of dissociation and reassociation, intersegmental transfer, or sliding and subsequent high affinity binding to a high affinity site, as reviewed in [27 ]. For example, molecular dynamics simulations of HoxD9, Antp, and NK-2 homeodomains indicate that after initial low affinity binding by the core helical homeodomain, the disordered N-terminal tail of these domains aids in scanning DNA for a high affinity binding site [28], apparently though sequence specific charge-charge interactions [29].…”

Section: Multiple Dna-binding Events Facilitate Target Site Bindingmentioning

confidence: 99%

Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors

Smith

Matthews

2016

Current Opinion in Structural Biology

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Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction

et al. 2017

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How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox-PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity.

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Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins

Cited by 19 publications

References 102 publications

Lactose repressor hinge domain independently binds DNA

Lactose repressor hinge domain independently binds DNA

Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors

Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction

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