The unique presence of long positively charged tails in eukaryotic nucleosomal histones appears to have provided the selective pressure for evolution of a panoply of histone chaperones.1
This diverse group of proteins escorts histones right from the point of their synthesis, through their entry into the nucleus, to their repeated deposition on DNA during chromatin assembly and remodeling.1–3
The functions performed by different histone chaperones include histone storage (nucleoplasmin), shuttling of histone to the nucleus (NAP-1), and deposition of nucleosomes in conjunction with specific chromatin remodeling complexes (various nuclear histone chaperones).1,2,4–15
This latter group includes complexes with specific temporal roles, such as the CAF-1 complex required for histone deposition during replication, the FACT complex required for histone disassembly and reassembly during transcription elongation and the Hir complex that appears to be active throughout the cell cycle.1,2,10,16–21
Also included in this group are complexes specific to certain histone variants such as Swr1–Chz1 system involved in the incorporation of H2AZ and Scm3 required for cenH3 assembly.1,3,22–26
Of the characterized histone chaperones, Asf1 is required for both replication-dependent and independent nucleosome assembly via
direct binding of the H3–H4 dimer.2,19,20,27
In these two distinct processes it, respectively, associates with either of two paralogous WD40 repeat proteins, Cac2p and HirA (Hir1p and Hir2p in Saccharomyces cerevisiae
) to form two distinct chaperone complexes namely CAF-1 and Hir.20,28–31
Biochemical studies in S. cerevisiae
have shown that the complete Hir complex comprises 4 proteins (Hir1p, Hir2p, Hir3p and Hpc2p), which also show functional interactions with a wide range of chromatin associated complexes, such as the FACT, CAF-1, PAF1 and Swi2–Snf2 complexes.19,21,32–36
Additionally, genetic studies also imply that the Hir complex might function independently of Asf1 in maintenance of kinetochore chromatin structure.32,33,36,37
Taken together the evidence suggests that the Hir complex and Asf1p are important generalized histone chaperones providing functional backup for a number of functionally specialized complexes involved in nucleosome deposition and remodeling.
Evolutionary comparisons have shown that Asf1p is highly conserved throughout eukaryotes—it is present even in organisms with highly reduced functional systems, such as microsporidians, the nucleomorph of Guillardia theta
This suggests that Asf1 is indeed the key generalized histone chaperone that was already present in the last common ancestor of extant eukaryotes. The evolutionary history of its functional partners in generalized histone deposition, i.e.
the components of the Hir complex, and the differentiation of the replication-linked Caf-1 complex are less understood. The core WD40 subunits of these complexes HirA and Cac2 are known to be widely conserved in various lineages of the eukaryotic crown group (fungi, animals and plants), with comparable functions and interactions.1
But the exact role and evolutionary pattern of the other subunits, Hir3p and Hpc2p, are unclear. We were specifically interested in understanding the origins of these less-studied Hir complex components and potentially uncovering previously uncharacterized features of their role in nucleosome assembly and deposition. Utilizing several distinct computational approaches we show that Hpc2p contains an ancient conserved domain that is likely to have a key pan-eukaryotic role in the nucleosome assembly mediated by the Hir–Asf1 complex. We also show that Hir3p is a rapidly diverging member of the complex that has possibly undergone extensive functional differentiation in the eukaryotic crown group.