DNA-bridging by an archaeal histone variant via a unique tetramerisation interface

Abstract

In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into ‘hypernucleosome’ particles of varying sizes with each dimer wrapping 30 bp of DNA. These are composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension enabling MJ1647 homotetramerisation. The 1.9 Å X-ray structure of a dimeric MJ1647 species, structural modelling of the tetramer, and site-directed mutagenesis reveal that the C-terminal tetramerization module consists of two alpha helices in a handshake arrangement. Unlike canonical histones like M. jannaschii A3, MJ1647 tetramers can bridge two DNA molecules in vitro. Using single-molecule tethered particle motion and DNA binding assays, we show that MJ1647 tetramers bind ~60 bp DNA and compacts DNA in a highly cooperative manner. We furthermore show that MJ1647 effectively competes with the transcription machinery to block access to the promoter in vitro. Our results reveal MJ1647 as the first histone with DNA bridging properties, which has important implications for genome structure and gene expression in archaea.

The chromatin landscape of the euryarchaeon Haloferax volcanii

“…Despite the relevance of archaeal chromatin to understanding the deep evolution of chromatin organization, up until now, the structure of archaeal chromatin has received little direct experimental investigation using modern genomic tools, with the exception of early MNase-seq studies nearly a decade ago that mapped nucleosomal positioning in the euryarchaeotes Haloferax volcanii [ 28 ] and Methanothermobacter thermautotrophicus and Thermococcus kodakarensis [ 29 ], and more recent MNAse-seq studies in Methanothermus fervidus [ 30 ], Thermoplasma acidophilum [ 31 ], and Methanocaldococcus jannaschii [ 32 ]. Furthermore, very little is known about the relationship between chromatin structure and the regulation of gene expression in these organisms.…”

The landscape of the histone-organized chromatin of Bdellovibrionota bacteria

“…However, two observations complicate such an interpretation. First, we do not observe a protection signature in the ATAC-seq fragment length distribution analogous to what is seen in eukaryotes and also in some archaea with histone-based chromatin 86 ; it is thus not entirely clear how exactly Bacteriovorax histones physically protect DNA and bind to it (somewhat different models have been proposed in the past year 26,27 ). Second, in starved cells we observe loss of ATAC-seq enrichment over promoters but not of actively transcribing polymerases.…”

Novel histones and histone variant families in prokaryotes

“…The Methanococcales (Mc) histones are exclusively found in the Methanococcales order and contain a tetramerisation domain on the C-terminus which facilitates DNA bridging. The DNA bridging ability of Mc histone MJ1647 from Methanocaldococcus jannaschii has been confirmed experimentally [17]. The coiled-coil (CC) histones are more widely distributed throughout archaea, being found in Aenigmatarchaeota, Altiarchaeota, B1Sed10-29, EX4484-52, Iainarchaeota, Methanobacteriota( B), Micrarchaeota, Nanoarchaeota, Nanohaloarchaeota, and Undinarchaeota (Fig.…”

“…Histones have, until recently, been considered to only wrap DNA. However, histone MJ1647 from Methanocaldococcus jannaschii diverges from conventional histones in that it bridges DNA [17]. MJ1647's bridging ability facilitates long-range DNA-interactions, a feature not found in any other histone.…”