Replication Compartments of Eukaryotic and Bacterial DNA Viruses: Common Themes Between Different Domains of Host Cells

Abstract

Subcellular organization is essential for life. Cells organize their functions into organelles to concentrate their machinery and supplies for optimal efficiency. Likewise, viruses organize their replication machinery into compartments or factories within their host cells for optimal replicative efficiency. In this review, we discuss how DNA viruses that infect both eukaryotic cells and bacteria assemble replication compartments for synthesis of progeny viral DNA and transcription of the viral genome. Eukaryotic DNA viruses assemble replication compartments in the nucleus of the host cell while DNA bacteriophages assemble compartments called phage nuclei in the bacterial cytoplasm. Thus, DNA viruses infecting host cells from different domains of life share common replication strategies.

Keywords: DNA virus; bacteriophage; infection; phage nucleus; viral replication compartment.

Figure 1.

HSV RCs in the nuclei of infected cells. Shown are Vero cells infected with HSV-1 virus and fixed at 7 hpi and stained with anti-ICP8 antibody (green) to mark RCs and antilamin B1 antibody (red) to mark the nuclear lamina and define the boundaries of the nucleus. The punctate structures containing ICP8 within the larger globular RCs colocalize with sites of viral DNA synthesis. Abbreviations: hpi, hours post infection; HSV, herpes simplex virus; ICP, infected cell protein; RC, replication compartment. Copyright Lynne Chang and David Knipe.

Figure 2.

Heterochromatin is excluded from HSV replication compartments. Immunofluorescence images of human Hep-2 cells infected with HSV-1, fixed at the indicated hpi, and stained with anti-H3K9me3-specific antibody (red) and anti-ICP8 DNA-binding protein antibody (green). Abbreviations: hpi, hours post infection; HSV, herpes simplex virus; ICP, infected cell protein. Copyright Lindsey Silva and David Knipe.

Figure 3.

Images of Pseudomonas infected with nucleus-forming jumbo phage, illustrating the subcellular localization imposed by formation of a nucleus-like replication compartment. Membranes are stained with FM4-64 (red), and DNA is stained with DAPI (blue). (a) Shell protein tagged with GFP (green) surrounds replicating phage φPA3 DNA in Pseudomonas aeruginosa. (b,c) Phage 201φ2-1 proteins tagged with GFP in Pseudomonas chlororaphis involved in DNA processes such as gp237 (recombination-related protein UvsX) colocalize with phage DNA (b) while metabolic enzymes such as gp287 (TMK) (c) are excluded. (d) An example of a host Cas9 enzyme tagged with GFP in the cytoplasm of P. aeruginosa being excluded by the φPA3 phage nucleus. The scale bar is 1 micron. (e) Segmented cryo-electron tomogram of focused ion beam-milled phage 201φ2-1 infected P. chlororaphis showing chimallin protein (blue), ribosomes (yellow), phage tails (cyan), inner membrane (pink), outer membrane (red), and capsids (green). (f) Cryo-electron tomogram of P. chlororaphis cell infected by 201φ2-1 jumbo phage. The scale bar is 250 nm. (g) In situ subtomogram average (EMD-25221) of the native 201φ2-1 ChmA lattice derived from cellular tomograms like the one presented in panel f. (h) In vitro single-particle cryo-electron microscopy structure of purified, recombinant ChmA assembled as a cubic 24-mer (PDB-7SQQ, EMD-25390). The coordinate model is depicted as an illustration and the map as a transparent surface. The structure is depicted along the fourfold axis. An individual ChmA protomer is rainbow colored from the N to C termini, and the extended N-terminal and C-terminal segments are depicted as spheres. Unresolved loops connecting the terminal segments are modeled for visualization purposes. (i) ChmA lattice model derived from combining the in situ map (transparent surface) and in vitro coordinate model (illustration) shown from the cytosolic face. An individual protomer is colored sequentially as in panel h with the extended terminal segments depicted as spheres. Abbreviations: GFP, green fluorescent protein; TMK, thymidylate kinase. Panels a and d copyright 2022 Amy Prichard and Joe Pogliano; panels b and c copyright 2022 Vorrapon Chaikeeratisak and Joe Pogliano; panels e and f copyright 2022 Thomas Laughlin and Elizabeth Villa; panels g, h, and i copyright 2022 Thomas Laughlin, Kevin Corbett, and Elizabeth Villa.

Figure 4.

Comparison of RCs formed in herpes simplex virus–infected cells (a) and a phage nucleus and associated structures formed in nucleus-forming jumbo phage–infected Pseudomonas (b). Abbreviation: RC, replication compartment. Panel a copyright Surendra Sharma and David Knipe; panel b copyright 2022 Amy Prichard and Joe Pogliano.