Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization

Abstract

Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA. The architectural properties of Sso10a proteins suggest that these proteins fulfil generic roles in chromatin organization and compaction. As these proteins exhibit different binding behaviour depending on their DNA binding stoichiometry, altered levels of expression in the cell can be exploited to drive changes in local genome folding, which may operate to modulate transcription.

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

“…At increased wild-type Sso7c4-DNA ratios (0.5 bp/dimer), more bridged complexes were observed (98%, n = 86), of which some of the DNA molecules were completely bridged (15%, n = 86) (Fig 4C, right). These wild-type Sso7c4-DNA complexes are similar to the bridged protein-DNA complexes observed for the bacterial H-NS [17], the archaeal Sso10a1 [28] and Alba1 (Sso10b1) at low protein concentrations [26]. In contrast, the addition of comparable concentrations of C-terminally truncated Sso7c4 induced the formation of complexes that were distinctly different from the complexes observed with the wild-type protein.…”

“…At higher protein:DNA ratios (1:0.5 dimer:bp), a considerable number of C-terminally truncated Sso7c4-DNA complexes were observed to form a more open circular shape (67%, n = 109) (Fig 4E), suggesting that the C-terminally truncated proteins induced DNA stiffening. The round and open shape of the DNA molecules is a signature of DNA stiffening, as shown in previous studies on bacterial HU [12], archaeal Sac10a2 [28] and Alba1 proteins at high protein concentrations [26]. …”

“…In Sulfolobus species, NAPs predominantly organize the genome by bridging or bending DNA. The Sso10b and Sso10a proteins have been shown to bridge or rigidify DNA in EM [52] and AFM studies [26,28], whereas Sac7d/Sso7d [30–32] and Cren7 [33,34] were shown to bend DNA in their complex 3D structures. In our study, Sso7c4 exhibits DNA-binding activity and alters the trajectory of the DNA through bending and bridging.…”

“…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].…”

“…In contrast, Sso10a also exists as a dimer in solution via antiparallel coiled-coil interactions. Sso10a1 bridges DNA duplexes, but Sso10a2 forms filaments along DNA [28]. Sul7d non-cooperatively binds to dsDNA as a monomer with micromolar affinity and introduces a sharp kink into the DNA duplex via the intercalation of hydrophobic side chains into the minor groove [30–32].…”