Btcd, a mouse protein that binds to curved DNA, can substitute in Escherichia coli for H-NS, a bacterial nucleoid protein.

Timchenko, Tatiana; Bailone, Adriana; Devoret, Raymond

doi:10.1002/j.1460-2075.1996.tb00772.x

Cited by 46 publications

(31 citation statements)

References 46 publications

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“…H-NS has been shown to bind preferentially to AT-rich/ curved DNA sequences (Yamada et al, 1990;OwenHughes et al, 1992). The region implicated in H-NS binding by our deletion analysis, which contains short A and T tracts in a periodic arrangement, shows a retarded mobility in a two-dimensional gel, indicative of the presence of an intrinsic curvature in the sequence (Timchenko et al, 1996). Moreover, though direct binding of H-NS to this region was not demonstrated, the authors have shown that the mouse nuclear protein Btcd, a functional analogue of H-NS, binds tightly to this sequence.…”

Section: Discussionmentioning

confidence: 87%

Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H‐NS, and CRP–cAMP in regulation

Mukerji

Mahadevan

1997

Molecular Microbiology

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SummaryThe bgl operon of Escherichia coli is rendered cryptic and uninducible in wild-type cells by the presence of DNA structural elements that negatively regulate transcription. We have carried out a detailed analysis of the sequences implicated in negative regulation. Finestructure deletion analysis of the upstream sequences showed the presence of at least two elements involved in silencing the promoter. Chemical probing of genomic DNA in vivo showed that a region of dyad symmetry, present upstream of the promoter, is hypersensitive to KMnO 4 . The hypersensitive region detected corresponds to the potential cruciform structure implicated earlier in negative regulation. Enhancement of transcription from the wild-type promoter, observed in the presence of the gyrase inhibitor novobiocin, was absent in a mutant that carried point mutations in the inverted repeat. This observation suggests that the activation seen in a gyrase mutant is mediated by destabilization of the cruciform because of reduced supercoiling. Deletion of sequences downstream of the potential cruciform also resulted in an increase in transcription, indicating the presence of a second regulatory element. Measurement of transcription from the bgl promoter carrying the deletion, in a strain that has a mutation in the hns gene, indicated that this region is likely to be involved in binding to H-NS or a protein regulated by H-NS, which acts as a non-specific repressor. We also provide evidence which suggests that transcriptional activation by mutations at the cAMP receptor protein (CRP)-binding site is mediated partly by antagonization of the negative effect of H-NS by CRP-cAMP as a result of its increased affinity for the mutant site.

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Section: Discussionmentioning

confidence: 87%

Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H‐NS, and CRP–cAMP in regulation

Mukerji

Mahadevan

1997

Molecular Microbiology

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“…This result, in light of the correlation between GapR ChIP-seq enrichment and local AT richness, suggests that the association of GapR with DNA is specified by local AT content rather than by an explicit consensus binding sequence. Indeed, DNA-associated proteins with generic affinity for AT-rich sequences have been described in various prokaryotic and eukaryotic organisms, including mammals (26)(27)(28)(29)(30)(31)(32).…”

Section: Gapr Is Essential For Normal Growth and Cell Division In Caumentioning

confidence: 99%

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

Ricci

Melfi

Lasker

et al. 2016

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

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Faithful cell cycle progression in the dimorphic bacterium Caulobacter crescentus requires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required for Caulobacter growth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter. The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed in E. coli, suggesting that GapR and H-NS have distinct functions. We propose that Caulobacter has co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.

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“…We used a gel retardation assay to characterize the ability of modified H-NS proteins to recognize specific DNA fragments (30,34,35). Digestion of a pBR322 plasmid using TaqI and SspI enzymes yields, in particular, a fragment carrying the bla promoter, which is known to contain curved sequences (36).…”

Section: Different Binding Modes Of the Modified H-ns Proteins To Thementioning

confidence: 99%

The Degree of Oligomerization of the H-NS Nucleoid Structuring Protein Is Related to Specific Binding to DNA

Badaut

Williams

Arluison

et al. 2002

Journal of Biological Chemistry

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At several E. coli promoters, initiation of transcription is repressed by a tight nucleoprotein complex formed by the assembly of the H-NS protein. In order to characterize the relationship between the structure of H-NS oligomers in solution and on relevant DNA fragments, we have compared wild-type H-NS and several transdominant H-NS mutants using gel shift assays, DNase I footprinting, analytical ultracentrifugation, and reactivity toward a cross-linking reagent. In solution, oligomerization occurs through two protein interfaces, one necessary to construct a dimeric core (and involving residues 1-64) and the other required for subsequent assembly of these dimers. We show that, as well as region 64 -95, residues present in the NH 2 -terminal coiled coil domain also participate in this second interface. Our results support the view that the same interacting interfaces are also involved on the DNA. We propose that the dimeric core recognizes specific motifs, with the second interface being critical for their correct head to tail assembly. The COOH-terminal domain of the protein contains the DNA binding motif essential for the discrimination of this specific functional assembly over competitive nonspecific H-NS polymers.

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Btcd, a mouse protein that binds to curved DNA, can substitute in Escherichia coli for H-NS, a bacterial nucleoid protein.

Cited by 46 publications

References 46 publications

Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H‐NS, and CRP–cAMP in regulation

Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H‐NS, and CRP–cAMP in regulation

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

The Degree of Oligomerization of the H-NS Nucleoid Structuring Protein Is Related to Specific Binding to DNA

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