Article

Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA

State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
Molecular Microbiology (Impact Factor: 5.03). 03/2010; 76(3):749-59. DOI: 10.1111/j.1365-2958.2010.07136.x
Source: PubMed

ABSTRACT Cren7, a newly found chromatin protein, is highly conserved in the Crenarchaeota. The protein shows higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils in vitro and is associated with genomic DNA in vivo. Here we report the crystal structures of the Cren7 protein from Sulfolobus solfataricus in complex with two DNA sequences. Cren7 binds in the minor groove of DNA and causes a single-step sharp kink in DNA (approximately 53 degrees) through the intercalation of the hydrophobic side chain of Leu28. Loop beta 3-beta 4 of Cren7 undergoes a significant conformational change upon binding of the protein to DNA, suggesting its critical role in the stabilization of the protein-DNA complex. The roles of DNA-contacting amino acid residues in stabilizing the Cren7-DNA interaction were examined by mutational analysis. Structural comparison of Cren7-DNA complexes with Sac7d-DNA complexes reveals significant differences between the two proteins in DNA binding surface, suggesting that Cren7 and Sul7d serve distinct functions in chromosomal organization.

Download full-text

Full-text

Available from: Tao Jiang, Sep 03, 2015
0 Followers
 · 
143 Views
 · 
66 Downloads
  • Source
    • "Our experimental results converge to a protein/DNA model, in which the monomeric protein MC1 interacts on the concave side of a strongly bent DNA: 1) MC1 bears structural similarities to the small basic architectural proteins Sul7d and Cren7, belonging to the Sulfolobus strains of the Crenarchaea subdomain [37], [38], and interacts with the DNA minor groove. However, the later proteins bind on the convex side of the DNA curvature (Figure 6); and 2) Protein interactions with the concave side of DNA curvature have only been observed so far for dimeric proteins, such as histone-like HU or IHF, bound to U-shape DNA [39] (Figure 6). "
    [Show abstract] [Hide abstract]
    ABSTRACT: In Archaea the two major modes of DNA packaging are wrapping by histone proteins or bending by architectural non-histone proteins. To supplement our knowledge about the binding mode of the different DNA-bending proteins observed across the three domains of life, we present here the first model of a complex in which the monomeric Methanogen Chromosomal protein 1 (MC1) from Euryarchaea binds to the concave side of a strongly bent DNA. In laboratory growth conditions MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55. Like most proteins that strongly bend DNA, MC1 is known to bind in the minor groove. Interaction areas for MC1 and DNA were mapped by Nuclear Magnetic Resonance (NMR) data. The polarity of protein binding was determined using paramagnetic probes attached to the DNA. The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry. Residues essential to DNA-binding and -bending were highlighted and confirmed by site-directed mutagenesis. It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.
    PLoS ONE 02/2014; 9(2):e88809. DOI:10.1371/journal.pone.0088809 · 3.23 Impact Factor
  • Source
    • "Cren7 has a larger binding size (8 bp) and constrains negative supercoils more efficiently than Sul7d (26). Structural comparison also reveals differences between Cren7 and Sul7d in DNA binding surface and binding pattern, suggesting that the two proteins serve different roles in chromosomal organization (27,37). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Strand displacement by a DNA polymerase serves a key role in Okazaki fragment maturation, which involves displacement of the RNA primer of the preexisting Okazaki fragment into a flap structure, and subsequent flap removal and fragment ligation. We investigated the role of Sulfolobus chromatin proteins Sso7d and Cren7 in strand displacement by DNA polymerase B1 (PolB1) from the hyperthermophilic archaeon Sulfolobus solfataricus. PolB1 showed a robust strand displacement activity and was capable of synthesizing thousands of nucleotides on a DNA-primed 72-nt single-stranded circular DNA template. This activity was inhibited by both Sso7d and Cren7, which limited the flap length to 3-4 nt at saturating concentrations. However, neither protein inhibited RNA displacement on an RNA-primed single-stranded DNA minicircle by PolB1. Strand displacement remained sensitive to modulation by the chromatin proteins when PolB1 was in association with proliferating cell nuclear antigen. Inhibition of DNA instead of RNA strand displacement by the chromatin proteins is consistent with the finding that double-stranded DNA was more efficiently bound and stabilized than an RNA:DNA duplex by these proteins. Our results suggest that Sulfolobus chromatin proteins modulate strand displacement by PolB1, permitting efficient removal of the RNA primer while inhibiting excessive displacement of the newly synthesized DNA strand during Okazaki fragment maturation.
    Nucleic Acids Research 07/2013; 41(17). DOI:10.1093/nar/gkt588 · 9.11 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The interaction of insulin with calf thymus deoxyribonucleic acid (ctDNA) leads to a complex that displays remarkably enhanced resonance Rayleigh scattering (RRS). The complex and its formation were investigated by atomic force microscopy and by absorption, fluorescence and circular dichroism spectroscopies. We show that the Tyr B16, Tyr B26 and Phe B24 amino acids near the active center (Phe B25) were influenced by the interaction, whereas Tyr A14, Tyr A19 and Phe B1 (which are located far away from the active center) were less influenced. The interaction provide a way in the quantitation of both ctDNA and insulin with high sensitivity. When ctDNA is used as a probe to quantify insulin, the detection limit (3σ) is 6.0 ng mL-1. If, inversely, insulin is used as a probe to quantify ctDNA, the detection limit (3σ) is 7.2 ng mL-1. The analysis of synthetic DNA samples and an insulin infection sample provided satisfactory results. Figure The interaction of insulin with calf thymus deoxyribonucleic acid (ctDNA) leads to a complex that displays remarkable enhanced resonance Rayleigh scattering (RRS). The complex and its formation were investigated by atomic force microscopy and by absorption, fluorescence and circular dichroism spectroscopies. A sensitive RRS method for determination of insulin and DNA were established.
    Microchimica Acta 11/2012; 179(3-4). DOI:10.1007/s00604-012-0891-5 · 3.72 Impact Factor
Show more