Linear adenovirus DNA is organized into supercoiled domains in virus particles

Abstract

Electron microscopic analysis of bis-psoralen crosslinked adenovirus type 5 virion DNA revealed supercoiled domains in an otherwise linear DNA. The existence of supercoiled arrangement in all the virion DNA was demonstrated by the sensitivity of Ad5 DNA in pentonless virus particles to the supercoiling-dependent endonucleolytic activity of Bal31 and S1 nucleases. These nucleases were found to cleave Ad5 virion DNA at specific sites. The observation of stable cleavage sites in the limit digestion of virion DNA by Bal31 suggests that cleavage sites represent boundaries of core proteins which impede the exonuclease activity of Bal31. These data suggest that specific arrangement of core proteins on Ad5 virion DNA. Based on this analysis we determined positions of core proteins in viral genome using indirect end labeling technique. The size of supercoiled domains of virion DNA was estimated by electron microscopy and also by boundaries of mutually exclusive Bal31 cleavage sites at limit digestion condition. Our data suggest each supercoiled domain is equal to about 12% of Ad5 genome length and about 8 loops can be accommodated in Ad5 virion. However sequences at two extreme ends of the viral genome were found to be outside of supercoiled domains. An interesting correlation between supercoiled domains and gene domains of Ad5 genome was noticed.

Differential Effect of DNA Supercoiling on Transcription of Adenovirus Genes in vitro

“…The three genes we tested reside within the first loop (2 to 14 map units) of twelve intertwined domains that are supercoiled in virion genomes (Wong & Hsu, 1989). DNA supercoiling induces S1 nuclease-sensitive secondary structures within the control elements of fl-globin genes (Schon et al, 1983) and SV40 DNA (Iacono-Connors & Kowalski, 1986).…”

“…The formation of such structures could involve distinct topological changes during infection and such changes might affect transcription. Indeed, a recent report shows that adenovirus DNA is folded into multiple loops with torsional constraints that can be relieved by topoisomerase I (Wong & Hsu, 1989). Moreover, genomic organization of the penton-less virion can undergo structural transitions during infection.…”

Adenovirus Protein VII Condenses DNA, Represses Transcription, and Associates with Transcriptional Activator E1A

“…DNA within the capsid is in a highly compact configuration, and electron microscopy studies of purified viral core reveal structures reminiscent of beads on a string, or higherorder chromatin compaction, depending on the method of preparation (8,18,45,49,50,60,63). Nuclease digestion of core preparations results in discrete populations of protected DNA fragments, suggesting a chromatin-like configuration but without a characteristic ladder of repeating units (15,45,58,60).…”

Sequences regulating temporal poly(A) site switching in the adenovirus major late transcription unit.

“…This could entail either or both of two possibilities: a change in the physical nature of the viral chromosome, resulting in a change in the dynamics of transcription and how the nascent RNA is recognized by the processing machinery, or a change in subnuclear localization of the chromosome, resulting in a different environment of trans-acting factors. Indeed, electron microscopy and sedimentation analyses have revealed structural and topological changes in the adenovirus template during infection (45). Furthermore, during infection, there is stable attachment of the adenovirus chromosome to the nuclear matrix (5,33,46), which could serve to compartmentalize the DNA.…”