Mechanical and structural properties of archaeal hypernucleosomes

Abstract

Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone–DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of DNA wrapped around an ‘endless’ histone-protein core. However, if and how such a hypernucleosome structure assembles on a long DNA substrate and which interactions provide for its stability, remains unclear. Here, we describe micromanipulation studies of complexes of the histones HMfA and HMfB with DNA. Our experiments show hypernucleosome assembly which results from cooperative binding of histones to DNA, facilitated by weak stacking interactions between neighboring histone dimers. Furthermore, rotational force spectroscopy demonstrates that the HMfB–DNA complex has a left-handed chirality, but that torque can drive it in a right-handed conformation. The structure of the hypernucleosome thus depends on stacking interactions, torque, and force. In vivo, such modulation of the archaeal hypernucleosome structure may play an important role in transcription regulation in response to environmental changes.

Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis

“…Discrete DNA fragments >90 bp were absent, demonstrating histone:DNA interactions occurred to allow initial DNA wrapping but that continued polymerization to form extended AHCPs was not possible. The observed digestion pattern is consistent with previous (Mattiroli et al, 2017) digestions of chromatin from variant HTkA G17encoding strains, suggesting histone dimers form tetramers, protecting ∼60 bp of DNA, and an additional dimer interacts to form a hexamer, protecting ∼90 bp of DNA, but that larger associations of histone dimers are restricted due to clashes between adjacent gyres of AHCPs and loss of potential electrostatic interactions across the adjacent gyres (Henneman et al, 2018;Henneman et al, 2020;Bowerman et al, 2021). Thus, across the entire genome, the single HTkA G17D variant encoded in TS620 disrupts the L1-L1 interface within AHCPs, preventing continued polymerization of histone dimers that normally provides a route to extended AHCP formation.…”

“…(B) A loci diagram of the annotated T. kodakarensis viral region 2 (TKVR2: TK0381-TK0421) that highlights the observed region of excision (∼TK0389 -∼TK0412) superimposed over a genome alignment plot derived from PacBio long read sequencing of TS620. (Bhattacharyya et al, 2018;Sanders et al, 2019b;Henneman et al, 2020;Stevens et al, 2020;Bowerman et al, 2021;Laursen et al, 2021).…”

“…The polymerization of histone dimers in Archaea does not resemble the nucleosome-nucleosome interactions observed in eukaryotes (Luger et al, 1997;Mattiroli et al, 2017;Sanders et al, 2019b;Henneman et al, 2020;Stevens et al, 2020;Bowerman et al, 2021). Alignments and analyses of unique archaeal histone sequences reveals the vast majority of archaeal histone proteins retain only the residues comprising the core eukaryotic histone-fold and that many amino acids are highly conserved in positions that form the histone-fold or mediate DNA interactions (Mattiroli et al, 2017;Nishida and Oshima, 2017;Zaremba-Niedzwiedzka et al, 2017;Henneman et al, 2020;Stevens et al, 2020). The core histone fold, common to eukaryotic and archaeal histones, consists of three alpha helices (α1, α2, and α3) connected through two flexible loops (L1 and L2).…”

“…While dynamic changes in AHCPs are expected, particularly in species with multiple histone isoforms (Henneman et al, 2020;Stevens et al, 2020), it is also likely that specific DNA sequences and loci are more likely to retain extended AHCPs that are important for regulating gene expression (Čuboňová et al, 2012;Nalabothula et al, 2013;Dulmage et al, 2015). Although the presence of several histone isoforms in many Archaea suggests the potential for variation in superhelix composition and length (Mattiroli et al, 2017;Bhattacharyya et al, 2018;Henneman et al, 2018;Sanders et al, 2019b;Henneman et al, 2020;Stevens et al, 2020;Bowerman et al, 2021), the viability of strains with only a single histone demonstrate that even homopolymers permit formation of AHCPs in vivo Reeve, 2001, 2006;Santangelo et al, 2009;Čuboňová et al, 2012;Dulmage et al, 2015). The biological importance of AHCPs is supported by the evolutionary retention of the AGA motif in L1 which permits close association of adjacent superhelical gyres.…”

“…Most Archaea encode histone proteins to organize their DNA into a protein:DNA complex known as chromatin ( Sandman and Reeve, 2000 , 2001 , 2006 ; Peeters et al, 2015 ; Mattiroli et al, 2017 ; Bhattacharyya et al, 2018 ; Henneman et al, 2018 ; Sanders et al, 2019b ; Henneman et al, 2020 ; Stevens et al, 2020 ; Bowerman et al, 2021 ; Laursen et al, 2021 ). The organization and tractability of chromatin structure is essential to regulate adaptive gene expression ( Wilkinson et al, 2010 ; Nalabothula et al, 2013 ; Mattiroli et al, 2017 ).…”