On the Connection Between Inherent DNA Flexure and Preferred Binding of Hydroxymethyluracil- containing DNA by the Type II DNA-binding Protein TF1

Grove, Anne; Galeone, Aldo; Mayol, Luciano; Geiduschek, Peter

doi:10.1006/jmbi.1996.0392

Cited by 39 publications

(97 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The HMG domain is followed by a region that has basic sequences similar to the C-terminal domain of histone H1 and a short C-terminal acidic stretch also seen in HMGB proteins. The NMR structure of the HMG domain from HMG-D is very similar to the previously determined structure of the B domain of HMG1, which revealed the characteristic L-shaped fold formed by three ␣-helices (17-21).High mobility group proteins of the HMGB family bind DNA with little sequence specificity but recognize structural features in DNA (22-24), including cruciforms, kinks, DNA bulges, and bends (22,23,(25)(26)(27)(28). DNA footprint analysis and mutagenesis experiments suggest that HMG domain proteins bind in the minor groove (29).…”

supporting

confidence: 67%

See 1 more Smart Citation

HMG-D and Histone H1 Interplay during Chromatin Assembly and Early Embryogenesis

Ner¹,

Blank²,

Pérez‐Parallé³

et al. 2001

Journal of Biological Chemistry

View full text Add to dashboard Cite

HMG-D is an abundant chromosomal protein associated with condensed chromatin during the first nuclear cleavage cycles of the developing Drosophila embryo. We previously suggested that HMG-D might substitute for the linker histone H1 in the preblastoderm embryo and that this substitution might result in the characteristic less compacted chromatin. We have now studied the association of HMG-D with chromatin using a cellfree system for chromatin reconstitution derived from The vertebrate high mobility group proteins of the HMGB class (formerly termed HMG1/2) (1) are relatively abundant nuclear DNA-binding proteins that bend DNA substantially and appear to act primarily as architectural facilitators in the assembly of nucleoprotein complexes (recently reviewed in Refs. 2-4). There is direct evidence that these proteins facilitate the binding of transcription factors to their cognate sites both in vitro and in vivo, but any involvement in the assembly of histone-DNA complexes is less well documented. Circumstantial evidence indicates that certain functions of the vertebrate HMGB proteins (5-7) may parallel those of the linker histone H1 (8). Both have been shown to bind to linker DNA sequences (7, 9, 10), and both stabilize and bind to four-way junctions (11)(12)(13)(14). HMG-D is one of two Drosophila proteins closely related to the vertebrate HMGB proteins but in contrast to these proteins contains only a single HMG DNA-binding domain (6,15,16). The HMG domain is followed by a region that has basic sequences similar to the C-terminal domain of histone H1 and a short C-terminal acidic stretch also seen in HMGB proteins. The NMR structure of the HMG domain from HMG-D is very similar to the previously determined structure of the B domain of HMG1, which revealed the characteristic L-shaped fold formed by three ␣-helices (17-21).High mobility group proteins of the HMGB family bind DNA with little sequence specificity but recognize structural features in DNA (22-24), including cruciforms, kinks, DNA bulges, and bends (22,23,(25)(26)(27)(28). DNA footprint analysis and mutagenesis experiments suggest that HMG domain proteins bind in the minor groove (29). In addition, both crystallization and NMR studies show that HMG-D bending is achieved by the intercalation of hydrophobic residues at two different base steps (21, 30).The addition of histone H1 protein to an extended array of nucleosome core particles promotes its folding into a fiber with an approximate width of 30 nm (31-33). During early Drosophila development, histone H1 is not detectable (34 -36) until nuclear cycles 7/8 (37). Therefore, H1 is not involved in chromatin condensation in these earliest phases of Drosophila development characterized by rapid condensation-decondensation cycles. We have previously suggested that HMG-D could function as a linker protein in the absence of histone H1 in Drosophila (37). In support of this hypothesis, Wolffe and colleagues (10, 38) have postulated a similar role for the Xenopus HMG B1 protein. Thus, as the maternal pool of H...

show abstract

supporting

confidence: 67%

“…High mobility group proteins of the HMGB family bind DNA with little sequence specificity but recognize structural features in DNA (22-24), including cruciforms, kinks, DNA bulges, and bends (22,23,(25)(26)(27)(28). DNA footprint analysis and mutagenesis experiments suggest that HMG domain proteins bind in the minor groove (29).…”

mentioning

confidence: 99%

HMG-D and Histone H1 Interplay during Chromatin Assembly and Early Embryogenesis

Ner¹,

Blank²,

Pérez‐Parallé³

et al. 2001

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…TF1 was overexpressed in Escherichia coli DL39 (6) and purified as described (5). Oligonucleotides with hmU content were synthesized as described (7) and purified by high pressure liquid chromatography.…”

Section: Methodsmentioning

confidence: 99%

“…Electrophoretic mobility shift experiments were carried out as described (5). Experiments with perfect duplex hmU-or hybrid T/hmU-DNA were done at room temperature unless noted otherwise.…”

Section: Methodsmentioning

confidence: 99%

“…We recently showed that the affinity of TF1 for hmU-DNA is matched in T-containing DNA constructs that contain sets of two consecutive mismatches separated by 9 bp of duplex, indicating that hmUcontent and appropriately placed flexible loops contribute similarly to complex formation. We proposed, therefore, that DNA in a complex with TF1 is distorted at two sites that are separated by 9 bp of duplex DNA, sites corresponding to two hmU-A base pair steps, and that TF1 identifies its target sites through recognition of sequence-dependent DNA flexibility (5). Here we examine the requirement for hmU residues across a 37-mer DNA duplex representing a preferred binding site within the phage genome (4) and specifically evaluate sequence requirements at the two inferred sites of DNA distortion.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Twin Hydroxymethyluracil-A Base Pair Steps Define the Binding Site for the DNA-bending Protein TF1

Grove

Figueiredo

Galeone

et al. 1997

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The DNA-bending protein TF1 is the Bacillus subtilis bacteriophage SPO1-encoded homolog of the bacterial HU proteins and the Escherichia coli integration host factor. We recently proposed that TF1, which binds with high affinity (K d was ϳ3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility. Here, we show that two hmU-A base pair steps coinciding with two previously proposed sites of DNA distortion are critical for complex formation. The affinity of TF1 is reduced 10-fold when both of these hmU-A base pair steps are replaced with A-hmU, G-C, or C-G steps; only modest changes in affinity result when substitutions are made at other base pairs of the TF1 binding site. Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA. T-DNA constructs with 3-base bulges spaced apart by 9 base pairs of duplex also generate nM affinity of TF1. We suggest that twin hmU-A base pair steps located at the proposed sites of distortion are key to target site selection by TF1 and that recognition is based largely, if not entirely, on sequence-dependent DNA flexibility.The genome of the Bacillus subtilis bacteriophage SPO1 contains 5-hydroxymethyluracil (hmU) 1 in place of thymine, and discrimination between T-and hmU-containing DNA is important during phage multiplication (1, 2). For one phageencoded protein, the DNA-binding and -bending protein TF1, this discrimination is essentially absolute: the high affinity of TF1 (K d order of magnitude nM) for preferred sites within the hmU-containing phage genome is greatly reduced for the corresponding T-containing DNA (3, 4). We recently showed that the affinity of TF1 for hmU-DNA is matched in T-containing DNA constructs that contain sets of two consecutive mismatches separated by 9 bp of duplex, indicating that hmUcontent and appropriately placed flexible loops contribute similarly to complex formation. We proposed, therefore, that DNA in a complex with TF1 is distorted at two sites that are separated by 9 bp of duplex DNA, sites corresponding to two hmU-A base pair steps, and that TF1 identifies its target sites through recognition of sequence-dependent DNA flexibility (5). Here we examine the requirement for hmU residues across a 37-mer DNA duplex representing a preferred binding site within the phage genome (4) and specifically evaluate sequence requirements at the two inferred sites of DNA distortion. EXPERIMENTAL PROCEDURESTF1 was overexpressed in Escherichia coli DL39 (6) and purified as described (5). Oligonucleotides with hmU content were synthesized as described (7) and purified by high pressure liquid chromatography. T-containing oligonucleotides were purchased and purified by denaturing polyacrylamide gel electrophoresis. The top strand (shared among bulge constructs...

show abstract

Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: Structural insights

Pasternack

Kearns

1999

Biopolymers

View full text Add to dashboard Cite

The genomic materials from some Bacillus subtilis bacteriophages are found to contain 5‐(hydroxymethyl)‐2'‐deoxyuridine in place of thymine. Phage‐encoded proteins such as transcription factor 1 specifically and preferentially bind to the minor grooves of these hmU‐containing DNA but not to thymine‐containing DNA. Data from electrophoretic mobility shift assays suggest that the inherent, localized flexibility of hmU‐DNA, which is sequence‐specific, is responsible for its discriminative binding. We discuss here, from the NMR‐derived structural point of view, how differential DNA flexibility can contribute to specific binding of TF1 to hmU‐DNA. © 2000 John Wiley & Sons, Inc. Biopoly 52: 57–63, 1999

show abstract

On the Connection Between Inherent DNA Flexure and Preferred Binding of Hydroxymethyluracil- containing DNA by the Type II DNA-binding Protein TF1

Cited by 39 publications

References 39 publications

HMG-D and Histone H1 Interplay during Chromatin Assembly and Early Embryogenesis

HMG-D and Histone H1 Interplay during Chromatin Assembly and Early Embryogenesis

Twin Hydroxymethyluracil-A Base Pair Steps Define the Binding Site for the DNA-bending Protein TF1

Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: Structural insights

Contact Info

Product

Resources

About