Dual architectural roles of HU: Formation of flexible hinges and rigid filaments

Noort, John van; Verbrugge, Sander; Goosen, Nora; Dekker, Cees; Dame, Remus T.

doi:10.1073/pnas.0308230101

Cited by 285 publications

(400 citation statements)

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“…This indicates that the protein-DNA complexes are flexible; the bending may be eliminated by force, while the proteins remain bound. For HU, this observation is consistent with previous structural studies (14) and with recent results of van Noort et al (24). Our experiments with HMGB1 and NHP6A indicate that these proteins also form flexibly bent DNA-protein complexes.…”

Section: Discussionsupporting

confidence: 93%

“…For HU, the onset of stabilization coincides with a switch from a DNA compaction to a DNA stiffening mode of binding. Our data support the qualitative picture discussed by Dame and Goosen on the basis of SFM visualization of HU-DNA complexes (9) and are in good quantitative accord with single-DNA experiments with HU reported very recently by van Noort et al (24). The striking change of mechanical properties of long DNA molecules as a function of HU concentration helps to explain previously reported and sometimes conflicting properties of HU-DNA complexes in vitro (9).…”

supporting

confidence: 92%

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Micromechanical Analysis of the Binding of DNA-Bending Proteins HMGB1, NHP6A, and HU Reveals Their Ability To Form Highly Stable DNA−Protein Complexes

et al. 2004

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The mechanical response generated by binding of the nonspecific DNA-bending proteins HMGB1, NHP6A, and HU to single tethered 48.5 kb λ-DNA molecules is investigated using DNA micromanipulation. As protein concentration is increased, the force needed to extend the DNA molecule increases, due to its compaction by protein-generated bending. Most significantly, we find that for each of HMGB1, NHP6A, and HU there is a well-defined protein concentration, not far above the binding threshold, above which the proteins do not spontaneously dissociate. In this regime, the amount of protein bound to the DNA, as assayed by the degree to which the DNA is compacted, is unperturbed either by replacing the surrounding protein solution with protein-free buffer or by straightening of the molecule by applied force. Thus, the stability of the protein-DNA complexes formed is dependent on the protein concentration during the binding. HU is distinguished by a switch to a DNA-stiffening function at the protein concentration where the formation of highly stable complexes occurs. Finally, introduction of competitor DNA fragments into the surrounding solution disassembles the stable DNA complexes with HMGB1, NHP6A, and HU within seconds. Since spontaneous dissociation of protein does not occur on a time scale of hours, we conclude that this rapid protein exchange in the presence of competitor DNA must occur only via "direct" DNA-DNA contact. We therefore observe that protein transport along DNA by direct transfers occurs even for proteins such as NHP6A and HU that have only one DNA-binding domain.Non-histone DNA-bending proteins are associated with chromosomes of prokaryotic and eukaryotic cells. Prominent among these in eukaryotes are the nonspecifically binding class of HMGB 1 proteins, present in the nucleus at micromolar concentrations (1-3). HMGB proteins possess a ∼75 amino acid residue DNA-minor-groove-binding domain, which induces a bend of about 90°. Charged residues within extended peptide segments at the N-or C-termini of the HMGB domain can strongly modulate DNA binding affinities of these proteins. Saccharomyces cereVisiae NHP6A contains one HMGB domain but binds DNA with considerably higher affinity than mammalian HMGB1, which contains two domains (4). HMGB proteins function in a variety of localized DNA transactions including assembly of transcription and recombination complexes and chromatin remodeling (1-3). A general role for HMGB proteins in modulating global DNA organization in eukaryotes is not yet established, but yeast HMGB proteins have been shown to condense chromosomal DNA in prokaryotic models (4,5).

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Section: Discussionsupporting

confidence: 93%

supporting

confidence: 92%

Micromechanical Analysis of the Binding of DNA-Bending Proteins HMGB1, NHP6A, and HU Reveals Their Ability To Form Highly Stable DNA−Protein Complexes

et al. 2004

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“…Filaments were stiff and likely to be poor substrates for DNA ligase. A similar binding mode has been observed for HU protein [42]. …”

supporting

confidence: 80%

“…HMGB proteins share some features with bacterial IHF [43] and X-ray structures of complexes of the similar HU protein with DNA suggest that a range of induced DNA bend angles are possible [44]. Results from atomic force microscopy for DNA/ HU complexes also suggest a range of protein-induced bend angles rather than a fixed geometry [42]. HMGB protein overview and materials.…”

Section: Hmgb Mechanismsmentioning

confidence: 99%

Transient HMGB protein interactions with B-DNA duplexes and complexes

Zimmerman

Maher

2008

Biochemical and Biophysical Research Communications

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HMGB proteins are abundant, non-histone proteins in eukaryotic chromatin. HMGB proteins contain one or two conserved "HMG boxes" and can be sequence specific or nonspecific in their DNA binding. HMGB proteins cause strong DNA bending and bind preferentially to deformed DNAs. We wish to understand how HMGB proteins increase the apparent flexibility of non-distorted B-form DNA. We test the hypothesis that HMGB proteins bind transiently, creating an ensemble of distorted DNAs with rapidly-interconverting conformations. We show that binding of B-form DNA by HMGB proteins is both weak and transient under conditions where DNA cyclization is strongly enhanced. We also detect novel complexes in which HMGB proteins simultaneously bind more than one DNA duplex.Double-stranded DNA is among the least flexible biopolymers. The local stiffness of DNA is reflected in its persistence length, P, (~150 bp) [1]. The global flexibility of naked DNA in solution is insufficient to allow the degree of compaction required for packaging within cells, or for deformed structures involved in DNA replication, recombination, and transcriptional control. While some controversy exists concerning the accuracy of predictive models for DNA flexibility over short lengths [2;3;4], it is clear that short lengths of DNA require proteins to induce strongly bent and looped conformations.The apparent physical properties of DNA may differ in vitro and in vivo [5;6]. Activation over short distances in assays of eukaryotic transcription activation in vitro raised the possibility of apparent DNA flexibility enhancement by nuclear factors [7]. Indeed, heat-resistant HMGB proteins in nuclear extracts were found to dramatically enhance the cyclization of short DNA restriction fragments by DNA ligase [8].Eukaryotic HMGB proteins are abundant small non-histone chromosomal proteins [9;10;11; 12] that share one or two copies of an ~80-amino acid HMG box domain. Fig. 1A shows the amino acid alignment of HMG box domains, illustrating the partial conservation of intercalating residues [13]. As shown in Fig. 1B, this domain specifies three α-helices (red) whose L-shaped fold engages one face of DNA while delivering one or two intercalating residues into the minor groove [14;15;16]. Biophysical studies have provided some insights into the thermodynamic basis of DNA binding [17;18;19;20]. HMGB proteins to induce DNA kinking or bending of 22;23;24;25], and bind preferentially to distorted DNA structures [16;21;26]. HMGB proteins may stabilize DNA bending either by *To whom correspondence should be addressed at maher@mayo.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all l...

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“…At low concentrations, HU moderately compacts DNA by inducing flexible bends and negative writhe [Swinger et al, 2003;Sagi et al, 2004;van Noort et al, 2004]. Increased protein levels, however, trigger polymerization of HU into rigid, helical filaments without inducing significant condensation [Sagi et al, 2004;Skoko et al, 2004;van Noort et al, 2004]. Formation of such nucleoprotein complexes could locally reverse H-NS-induced DNA condensation [Dame, 2005].…”

Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 99%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

122

101

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Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.

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Dual architectural roles of HU: Formation of flexible hinges and rigid filaments

Cited by 285 publications

References 38 publications

Micromechanical Analysis of the Binding of DNA-Bending Proteins HMGB1, NHP6A, and HU Reveals Their Ability To Form Highly Stable DNA−Protein Complexes

Micromechanical Analysis of the Binding of DNA-Bending Proteins HMGB1, NHP6A, and HU Reveals Their Ability To Form Highly Stable DNA−Protein Complexes

Transient HMGB protein interactions with B-DNA duplexes and complexes

The bacterial nucleoid: A highly organized and dynamic structure

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