Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends

Abstract

Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.

A Prototypic Lysine Methyltransferase 4 from Archaea with Degenerate Sequence Specificity Methylates Chromatin Proteins Sul7d and Cren7 in Different Patterns

“…Intriguingly, methylation of sul7d-5A protein was significantly inhibited in the presence of DNA (Fig. 7, A-C), suggesting that in vitro methylation of sul7d-5A alone resulted from the extra exposed sites, most likely Lys-28 and other lysines (Table 1) located near the protein-DNA interface (Val-26 and Met-29) (49). These results suggest that although aKMT4 has very low sequence bias, its specificity can nevertheless be influenced by the local structure of the target residues.…”

Genomic Looping: A Key Principle of Chromatin Organization

“…Instead, they express proteins that are functionally analogous to the HU, IHF and FIS proteins found in bacteria. Proteins, such as Sul7 and Cren7 bind and deform DNA [Baumann et al, 1994;Guo et al, 2008], resulting in compaction [Driessen et al, 2013]. To date, it is unclear whether the archaeal genome is organized into DNA loops in vivo.…”

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

“…acidocaldarius ), which are hyperthermophilic crenarchaeal organisms, encode a variety of small, abundant and basic proteins ranging in molecular weight from 7 to 10 kDa that modulate their genome. Five classes of architectural proteins have been characterized and classified as histone-like proteins according to their physical properties: Alba (acetylation lowers binding affinity, also known as the Sso10b [24–26]/Sac10b [27] family), Sso10a [28]/Sac10a [29], Sul7d (Sso7d/Sac7d) [30–32], Cren7 [33,34] and Sso7c4 [35,36]. As observed in atomic force microscopy (AFM) images, Alba proteins form dimers in solution and exhibit two different binding modes by bridging DNA or forming stiff filaments along DNA, depending on the dimer concentration and composition [26].…”

“…Cren7 is the only NAP known to be conserved at the kingdom level in crenarchaea. Cren7 is a structural homologue of Sul7d, and the biochemical properties and structures of both Cren7 and its DNA complex are similar to the properties and structures of Sul7d [33,34]. …”