Structural comparisons reveal diverse binding modes between nucleosome assembly proteins and histones

Abstract

Nucleosome assembly proteins (NAPs) are histone chaperones that play a central role in facilitating chromatin assembly/disassembly which is of fundamental importance for DNA replication, gene expression regulation, and progression through the cell cycle. In vitro, NAPs bind to the core histones H2A, H2B, H3, H4 and possibly to H1. The NAP family contains well-characterized and dedicated histone chaperone domain called the NAP domain, and the NAP-histone interactions are key to deciphering chromatin assembly. Our comparative structural analysis of the three three-dimensional structures of NAPs from S. cerevisiae, C. elegans, and A. thaliana in complex with the histone H2A-H2B dimer reveals distinct and diverse binding of NAPs with histones. The three NAPs employ distinct surfaces for recognizing the H2A-H2B dimer and vice versa. Though histones are highly conserved across species they display diverse footprints on NAPs. Our analysis indicates that understanding of NAPs and their interaction with histone H2A-H2B remains sparse. Due to divergent knowledge from the current structures analyzed here, investigations into the dynamic nature of NAP-histone interactions are warranted.

Keywords: Histone chaperone; NAP; Nucleosome assembly protein; Structural analysis.

Fig. 1

The three-dimensional apo structure of nucleosome assembly protein (NAP) from S. cerevisiae (ScNAP1) (PDB ID: 2Z2R). All NAP proteins, including ScNAP1, have the overall NAP fold consisting of a domain I, which is a long dimerization helix (colored brown) and domain II, an “earmuff” NAP domain (colored tan). The other monomer is colored pink. The secondary structure details are collated from PDBSUM (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html)

Fig. 2

Structural depiction of the histone H2A–H2B dimer interacting residues of ScNAP1, CeNAP1 and AtNRP1. NAP dimer is shown as ribbon and monomers are colored pink and tan. Histones H2A and histone H2B are shown as cyan and green ribbon. The interacting residues of NAPs and histones are shown as violet and blue sticks, respectively. The binding site of histones on each NAP is marked with red boxes. A ScNAP1 dimer interacting with H2A–H2B dimer (PDB ID: 5G2E). HBR1, HBR2 and the corresponding interacting residues of ScNAP1 are highlighted. B CeNAP1 dimer interacting with H2B 1-H2A fusion protein  (PDB ID: 6K00). Regions I, II, III and the corresponding interacting residues of CeNAP1 are highlighted. C AtNRP1 dimer interacting with H2A–H2B dimer (PDB ID: 7C7X). The dimerization domain I and the interacting residues of AtNRP1 are highlighted. Interacting residues are collated from PDBSUM (www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/) and all structural depictions are made using Pymol (www.pymol.org)

Fig. 3

Sequence alignment of NAPs and histones. A Alignment of ScNAP1, CeNAP1 and AtNRP1. NES and NLS are colored cyan and green, respectively. The residues of CTAD are underlined. Histone-binding residues are colored red. B Alignment of histone H2A and H2B from X. laevis (ScNAP1 complex), C. elegans and A. thaliana. NAP-binding residues of these histones are colored red. Sequences are taken from Protein Data Bank (www.rcsb.org) and sequence alignments are done using Clustal Omega (www.ebi.ac.uk/Tools/msa/clustalo/)

Fig. 4

Structural superposition of the three NAP–histone complexes - ScNAP1, CeNAP1 and AtNRP1. Only ScNAP1 dimer is shown as surface in two orientations for simplicity. The monomers are colored pink and tan. Histone H2A–H2B dimer that binds to ScNAP1 is shown as purple ribbon. The histone H2B 1–H2A fusion protein bound at CeNAP1–histone binding region is shown as orange ribbon. Similarly, two H2A–H2B dimers bound at AtNRP1 binding region are shown as blue and green ribbon

Fig. 5

Histone H2A–H2B dimer interaction interfaces (IF) on NAPs. NAP dimers are shown as transparent surface with monomers as pink and tan ribbons. Histone H2A and H2B are shown in cyan and green, respectively. The three interaction interfaces (IF1, IF2 and IF3) of histones are marked with red spheres and the interacting residues of histones that lie in each interface are colored red. A ScNAP1-(H2A–H2B) complex. B CeNAP1-(H2B 1-H2A) complex. C AtNRP1-(H2A–H2B) complex. Only one H2A–H2B dimer is shown for simplicity