Architectural roles of Cren7 in folding crenarchaeal chromatin filament

Abstract

Summary Archaea have evolved various strategies in chromosomal organization. While histone homologues exist in most archaeal phyla, Cren7 is a chromatin protein conserved in the Crenarchaeota. Here, we show that Cren7 preferentially binds DNA with AT‐rich sequences over that with GC‐rich sequences with a binding size of 6~7 bp. Structural studies of Cren7 in complex with either an 18‐bp or a 20‐bp double‐stranded DNA fragment reveal that Cren7 binds to the minor groove of DNA as monomers in a head‐to‐tail manner. The neighboring Cren7 monomers are located on the opposite sides of the DNA duplex, with each introducing a single‐step sharp kink by intercalation of the hydrophobic side chain of Leu28, bending the DNA into an S‐shape conformation. A structural model for the chromatin fiber folded by Cren7 was established and verified by the analysis of cross‐linked Cren7‐DNA complexes by atomic force microscopy. Our results suggest that Cren7 differs significantly from Sul7, another chromatin protein conserved among Sulfolobus species, in both DNA binding and deformation. These data shed significant light on the strategy of chromosomal DNA organization in crenarchaea.

Archaeal Chromatin Proteins Cren7 and Sul7d Compact DNA by Bending and Bridging

“…This finding agrees with the previous observations made by using magnetic tweezers that Cren7 and Sul7d reduced the length of DNA by ∼50% at an extension force of 0.5 pN ( 20 ). The crystal structures of DNA bound by multiple Cren7 molecules revealed no changes in DNA length ( 21 ). However, it was shown previously that DNA bending induced by Cren7 and Sul7d reduced the persistence length of DNA in solution ( 20 ), presumably allowing DNA retraction at low extension forces.…”

“…4B and C ). Modeling of these sites on the structures of the Cren7-DNA complex, derived from the crystal structure of Cren7 in complex with 18-bp DNA ( 21 ), and of the Sis7d-DNA complex, derived from the solution structure of Sso7d in complex with a 12-bp DNA ( 23 ), revealed that these sites were not involved in the lateral interaction between two neighboring Cren7 or Sis7d molecules bound to the same DNA duplex, given the distance between the same residues from the two protein ( Fig. 4B and C ).…”

“…However, the proteins appear to introduce more conformational changes than bending in DNA as suggested by their ability to constrain DNA in negative supercoils ( 5 ). The roles of the two proteins in DNA organization were further complicated by the recent finding that Cren7 and Sso7d induced opposite changes in the writhe of the axis of the bound DNA, presumably forming protein-DNA filaments in different patterns ( 21 ). Furthermore, Sso7d bound more strongly to GC-rich DNA sequences than to AT-rich sequences ( 22 , 23 ), whereas Cren7 showed the opposite binding preference ( 21 ).…”

“…The roles of the two proteins in DNA organization were further complicated by the recent finding that Cren7 and Sso7d induced opposite changes in the writhe of the axis of the bound DNA, presumably forming protein-DNA filaments in different patterns ( 21 ). Furthermore, Sso7d bound more strongly to GC-rich DNA sequences than to AT-rich sequences ( 22 , 23 ), whereas Cren7 showed the opposite binding preference ( 21 ). Therefore, it is of interest to determine if and how Cren7 and Sul7d serve distinct roles in chromosomal organization.…”

Conservation of an Ancient Oxidation Response That Controls Archaeal Epigenetic Traits Through Chromatin Protein Networks

“…Each protein also exhibited unique gene associations. Cren7 was highly abundant at CRISPR array loci amounting to 47% of its total genome binding and may form a chromatin fiber (34). In contrast, Sso7D was abundant at the rDNA locus, but only in SARC at pH 1, amounting to 4% of its total genome binding while Cren7 was absent at this locus (Fig.…”