Basic surface features of nuclear FKBPs facilitate chromatin binding

Andrew Leung,Cameron D Mackereth,Christopher J Nelson,Francy-Pesek Jardim,Rodrigo González-Romero,Geoff Gudavicius,Jose M Eirin-Lopez,Till Bartke,Juan Ausió,Yoan R Monneau,Neda Savic

doi:10.1038/s41598-017-04194-7

Abstract

The nucleoplasmin family of histone chaperones is identified by a pentamer-forming domain and multiple acidic tracts that mediate histone binding and chaperone activity. Within this family, a novel domain organization was recently discovered that consists of an N-terminal nucleoplasmin-like (NPL) domain and a C-terminal FKBP peptidyl-proline isomerase domain. Saccharomyces cerevisiae Fpr4 is one such protein. Here we report that in addition to its known histone prolyl isomerase activities, the Fpr4 FKBP domain binds to nucleosomes and nucleosome arrays in vitro. This ability is mediated by a collection of basic patches that enable the enzyme to stably associate with linker DNA. The interaction of the Fpr4 FKBP with recombinant chromatin complexes condenses nucleosome arrays independently of its catalytic activity. Based on phylogenetic comparisons we propose that the chromatin binding ability of ‘basic’ FKBPs is shared amongst related orthologues present in fungi, plants, and insects. Thus, a subclass of FKBP prolyl isomerase enzymes is recruited to linker regions of chromatin.

Highlights

The assembly and disassembly of nucleosomes is mediated by ATP-dependent and independent histone chaperones
We focused our efforts on the known important sequence features of this enzyme including the NPL domain, the highly-charged regions (A1/B1 and A2) and the C-terminal FKBP domain
Amino acids 1–59 and 116–169 form the classical nucleoplasmin core but are separated by a highly-charged acidic/basic loop (A1/B1 loop) that is predicted to protrude from the nucleoplasmin fold (Fig. 1A)

Summary

Introduction

The assembly and disassembly of nucleosomes is mediated by ATP-dependent and independent histone chaperones. While nucleoplasmin proteins do not contain additional domains, a nucleoplasmin-like (NPL) domain was recently found in several yeast, insect, and plant chromatin regulatory proteins[5] Included in this group is the NPL-FKBP sub-family that has a unique pairing of pentamer-forming NPL and FK506-binding (FKBP) peptidyl-prolyl isomerase domains. The NPL domain of fly FKBP39 can be crosslinked to histones in vitro[5], and the NPL of yeast Fpr[4] is located within the minimal histone binding[6] and nucleosome chaperoning[7, 8] region of the protein. We identify evolutionarily-conserved basic features of the FKBP fold that enable direct binding to linker regions between nucleosomes These basic surface patches are conserved in NPL-FKBP proteins in yeasts, insects and plants, implying an important function for this FKBP subclass. Together our results support a model where separate domains of NPL-FKBPs permit chromatin association and the chaperoning of nucleosomes

Methods

Results

Conclusion