Swi2/Snf2 remodelers: hybrid views on hybrid molecular machines

Abstract

Swi2/Snf2 (switch/sucrose non-fermentable) enzymes form a large and diverse class of proteins and multiprotein assemblies that remodel nucleic acid:protein complexes, using the energy of ATP hydrolysis. The core Swi2/Snf2 type ATPase domain belongs to the 'helicase and NTP driven nucleic acid translocase' superfamily 2 (SF2). It serves as a motor that functionally and structurally interacts with different targeting domains and functional modules to drive a plethora of remodeling activities in chromatin structure and dynamics, transcription regulation and DNA repair. Recent progress on the interaction of Swi2/Snf2 enzymes and multiprotein assemblies with their substrate nucleic acids and proteins, using hybrid structural biology methods, illuminates mechanisms for complex chemo-mechanical remodeling reactions. For Mot1, a hybrid mechanism of remodeler and chaperone emerged.

Fig. 1

Swi2/Snf2 ATPases. (a) Domain organization of selected Swi2/Snf2 ATPases. (b) The Swi2/Snf2 ATPase domain consists of a DExx (RecA like 1) and a HELICc (RecA like 2) domain that together have at least 12 characteristic sequence motifs with roles in nucleic acid and/or nucleotide binding or hydrolysis. (c) Selected structures of adjunct domains in Swi2/Snf2 ATPases in complex with their substrates. (d) Functions of respective domains present in various remodelers.

Fig. 2

Swi2/Snf2 enzyme architecture and model for nucleosome spacing by ISWI. (a) Crystal structure of E. coli RapA, the only full length Swi2/Snf2 enzyme structure [10]. The positions of the ATPase lobes 1A and 1B (DExx domain) as well as 2A and 2B (HELICc) are indicated. (b) Crystal structures of S. cerevisiae Chd1 domains. Left: SANT (dark green) and SLIDE (light green) domains bound to DNA (brown) [39]. Right: The tandem chromodomains (pink) block the DNA binding site on the Swi2/Snf2 ATPase domain. (c) Crystal structure of yeast Isw1a(ΔATPase) in complex with DNA (brown) [37]. According to the proposed dinucleosome model of remodeling (cf. (d)) the two DNA duplexes bound by the yIoc3 subunit (yellow) and the SANT (dark green) and SLIDE (light green) domains of yIsw1, represent external- and internal-linker DNA, respectively. (d) Dinucleosome model of remodeling by yeast Isw1a [37]. Nucleosome spacing by Isw1a is proposed to occur by one of the two schematically represented alternative mechanisms with either flexible linker DNA or flexible protein linker between Isw1`s ATPase domain and the HSS (HAND-SAND-SLIDE) assembly. In both scenarios, the Swi2/Snf2 domain slides the mobile nucleosome and pulls together the dinucleosome until the HSS-HL (HSS – helical linker) module between the two nucleosomes prevents further movements.

Fig. 3

Hybrid remodeler - chaperone. (a) Crystal structure of the HEAT domain of Encephalitozoon cuniculi Mot1 (yellow) in complex with its substrate TBP (grey). Loops of the HEAT domain and the latch are highlighted in pink. (b) Highly conserved acidic loops of Mot1 are important for recognition of TBP`s convex surface. (c) Chaperone activities by the Mot1 latch, which blocks the hydrophobic site on TPB that binds DNA or another TBP molecule in forming dimers. (d) A hybrid methods approach. The principle is to combine information from different structural methods, typically X-ray crystallography, homology modeling and electron microscopy. Interactions constraints provided by e.g. crosslinking studies and mass spectrometry can help put together the individual pieces of high resolution structures in the EM 3D reconstruction.

Fig. 4

Comparative multistep remodeling models. (a) Mot1. (I) TBP surface recognition of Mot1 by HEAT repeat loops (I) activates the ATPase activity of the enzyme and DNA binding by TBP (II). Groove tracking of the ATPase domain generates torque that weakens TBP:DNA interactions, leading to TBP displacement from the DNA (III). The Mot1 latch acts as a chaperone to prevent TBP from binding to DNA and from dimer formation (IV). (b) Isw1a and Chd1. (I) Nucleosomal linker-DNA duplexes are bound by the yIoc3 subunit and by the SANT domain of yIsw1. (II) Yeast Chd1`s chromodomains regulate the DNA binding site [9]. (III) Remodeling by yeast Isw1a by the dinucleosome spacing model (see Fig. 2d for details). (IV) Nucleosome remodelers may have intrinsic chaperone functions similar to Mot1, however there is a dedicated chaperone network for histones to maintain correct delivery to sites of remodeling and chromatin formation.