A giant virus genome is densely packaged by stable nucleosomes within virions

Abstract

The doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap DNA to form remarkably similar nucleosomes. By releasing Marseillevirus chromatin from virions into solution and performing genome-wide nuclease digestion and chemical cleavage assays, we find that the higher-order organization of Marseillevirus chromatin differs greatly from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions, without linker DNA or phasing along genes. Likewise, we observe that most nucleosomes reconstituted onto 3-copy tandem repeats of a nucleosome positioning sequence are tightly packed and fully wrapped. We also document repeat generation and instability during viral passage in amoeboid culture. Dense promiscuous packing of fully wrapped nucleosomes rather than 'beads-on-a-string' with genic punctuation suggests a viral genome protection function for doublet histones.

Viral histones: pickpocket’s prize or primordial progenitor?

“…To assess whether viral nucleosomes assemble on marseillevirus DNA in virions, capsids from marseillevirus T19 and a more recent isolate marseillevirus G648 were opened and permeabilized [ 86 ]. The chromatin was digested with micrococcal nuclease (MNase), revealing densely packed ~ 121 bp particles resistant to internal cleavage and lacking linker DNA, with dinucleosome and trinucleosome sizes of ~ 270 and ~ 390 bp, in contrast to Drosophila nucleosomes with mono-, di-, and trinucleosome sizes of 150, 330, and 540 bp.…”

“…These viral nucleosomes were not phased over genes, as is typical in eukaryotes. Cleavage with methidiumpropyl-EDTA-Fe(II), or MPE [ 87 ], gave similar mono- and dinucleosome size fragments for Drosophila , but gave a broad distribution of fragment sizes with a peak at 147 bp for marseillevirus chromatin, and no di- or tri-nucleosome peaks, suggesting packaging is too tight for MPE to cleave effectively between nucleosomes [ 86 ]. The endonucleolytic activity of MPE may generate random cleavages and then trim them to the most common size of 147 bp DNA that can be protected by the marseillevirus nucleosome, while the exo-endonuclease activity of MNase more frequently cuts between nucleosomes and nibbles loose ends to the minimally protected 121 bp particle.…”

“…A role in packaging does not necessarily preclude other roles, such as protecting the DNA from host mechanisms that sense or restrict invading viral DNA. Although the dense packing and lack of genic phasing argue against a role in gene regulation, it is possible that the Hζ–Hε doublet could have a role in initiating transcription by replacing Hβ–Hα, similar to the H2A.Z variants of eukaryotes that replace H2A [ 86 ]. Heterotrimeric nucleosome-like structures lacking one Hβ–Hα unit were also recovered in cryo-EM, suggesting a possible diversity of nucleosome-like particles [ 34 ].…”

Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses

“…Their results indicated that virus histones are essential for viral infectivity and are mostly associated with viral DNA packaging in the capsid. Bryson et al assessed whether viral nucleosomes assemble on Marseillevirus DNA in virions [ 109 ]. They reported that after permeabilization of Marseillevirus virions, the viral genome was digested with micrococcal nuclease, which predominantly produced 121 base pair DNA fragments [ 109 ].…”

“…Bryson et al assessed whether viral nucleosomes assemble on Marseillevirus DNA in virions [ 109 ]. They reported that after permeabilization of Marseillevirus virions, the viral genome was digested with micrococcal nuclease, which predominantly produced 121 base pair DNA fragments [ 109 ]. Based on these results, viral histone doublets assemble their genomic DNA into chromatin in virions [ 105 , 109 ].…”