Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways

Abstract

Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that continuously wind between 60 - 500 base pairs of DNA ('archaeasomes'), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90o out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.

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).…”

“…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 ).…”

“…In most cases, however, the extensions or tails common to eukaryotic histones are not present in archaeal histone isoforms ( Peeters et al, 2015 ; Mattiroli et al, 2017 ; Nishida and Oshima, 2017 ; Bhattacharyya et al, 2018 ; Henneman et al, 2018 ; Henneman et al, 2020 ; Sanders et al, 2019b ; Stevens et al, 2020 ). Unlike their eukaryotic counterparts, archaeal histones can homodimerize and spontaneously oligomerize to form chromatin with a single protein ( Decanniere et al, 2000 ; Mattiroli et al, 2017 ; Bhattacharyya et al, 2018 ; Henneman et al, 2020 ; Stevens et al, 2020 ; Bowerman et al, 2021 ; Laursen et al, 2021 ), and thus unlike their eukaryotic counterparts ( Luger et al, 1997 ), archaeal chromatin structures are not defined in size. Continued polymerization of archaeal histone proteins produces a symmetrical superstructure composed of increasing lengths of DNA wrapped around a core of polymerized histone dimers ( Mattiroli et al, 2017 ).…”