Interactions between adenoviruses and PML NBs
The family
Adenoviridae comprises medium size, non-enveloped viruses with linear, double-stranded DNA (dsDNA) genomes ranging from 25 to 48 kbp in length. Their genomes are packed into an icosahedral capsid that has a diameter of approximately 95 nm and fibers protruding from its vertices. Adenoviruses (AdVs) have been isolated from a variety of vertebrate hosts, reviewed in [
101]. Although AdV infections in humans are mostly subclinical, some types are associated with pathologies, such as acute respiratory infections or acute gastroenteritis. After internalization by the cell, AdVs use the endosomal pathway for trafficking to the nucleus, where the viral core is delivered after uncoating, and also where viral transcription, replication, and assembly take place. AdV proteins are denoted as early (E), intermediate (I), or late (L), depending on the phase of infection in which they are produced.
AdV infection results in the remodeling of spherical PML NBs into fibrous structures, a process that requires the viral protein E4-ORF3, which directly interacts with PML isoform II (PML-II) [
102‐
104]. E4-ORF3 can form dimers that assemble into linear and branched oligomer threads
via the exchange of their C-terminal tails. E4-ORF3 oligomers form a 3D network in the nucleus around viral replication domains, resulting in avidity-driven interactions with PML [
105]. Moreover, emergent E4-ORF3 oligomers serve as a binding interface for MRE11/RAD50/NBS1 (MRN) DNA repair complexes. The sequestration of this complex during infection prevents its activity, which leads to the formation of AdV genome concatemers during replication. In addition, it has been shown that AdVs avert genome concatemerization by targeting the MRN complex not only through E4-ORF3 but also
via the viral proteins E4-ORF6 and E1B-55 K [
106,
107].
Several studies have provided insight into the molecular details underlying how MRN is inactivated during infection. Initially, during infection, MRE11 and other cellular proteins, such as p53, are subjected to proteasomal degradation by a multiprotein complex with E3 ubiquitin ligase activity. This complex is formed by the viral proteins E4-ORF6 and E1B-55 K and the host cell proteins elongin B/C, CUL5, and RBX1 [
108,
109]. Subsequently, MRN complexes are exported from the nucleus to the cytoplasm and sequestered in aggresomes composed of E1B-55 K [
110]. It was proposed that, initially, E4-ORF3 and MRN are localized to the nucleus bound to PML NBs of altered morphology. Following the recruitment of E1B-55 K to the PML NBs, the proteins traffic to the cytoplasm, where E1B-55 K forms aggresomes that sequester MRN, thereby inhibiting its function and accelerating the ubiquitination-dependent proteasomal degradation of MRE11 [
110].
It has been reported the MRE11 and Nbs1 are transiently SUMOylated during AdV type 5 infection. This modification was observed following E4-OFR3-mediated MRN translocation and was proposed to facilitate the degradation of the MRN complex [
111]. E4-ORF3 can also function as a viral SUMO E3 ligase and E4 elongase [
112], while E4-OFR3 complexes can sequester the host cell E3 SUMO ligase PIAS3 [
113].
Importantly, Ullman and Hearing showed that in the absence of functional E4-ORF3, an antiviral state induced in the cell by IFN-α or IFN-γ leads to significant inhibition of AdV genome replication, effects that can be reversed by PML protein downregulation [
114]. This suggests that the E4-ORF3-mediated disruption of PML NB integrity likely represents a viral defense mechanism against the antiviral activities of the NBs. This function of E4-OFR3 is conserved among AdV serotypes [
115].
Schreiner et al. [
116] showed that the Daxx protein negatively regulates AdV type 5 replication and that, during infection, Daxx undergoes proteasomal degradation in an E1B-55 K-, but not E4-OFR6-, dependent manner. Later, it was shown that upon infection, E1B-55 K co-localizes with RING finger protein 4 (RNF4), a cellular SUMO-targeted E3 ubiquitin ligase, in specific insoluble aggregates in the nucleus, which mediates the interaction between Daxx and RNF4, leading to Daxx degradation [
117]. Also, it has been demonstrated that ATRX can suppress AdV replication. The ATRX/Daxx complex localizes to the promoter regions of the AdV genome during infection. As Daxx does not possess a DNA-binding domain, ATRX likely links the complex to chromatin. The repressive function of Daxx and ATRX is then mediated
via the recruitment of histone deacetylases (HDACs). In the absence of ATRX/Daxx, reduced genome condensation enables a more efficient expression of AdV genes. Unlike for Daxx alone, but like for the MRN complex, the degradation of the ATRX/Daxx complex is mediated by the E1B-55 K/E4-ORF6 E3 ubiquitin ligase complex [
118]. Moreover, adenoviral capsid protein VI also suppresses Daxx activity. A subpopulation of capsid protein VI molecules is targeted to the nucleus, localizes in the vicinity of PML NBs, interacts with Daxx, and may be involved in its translocation to the cytoplasm [
119]. Meanwhile, Daxx is responsible for the repression of the immediate early E1A promoter, which functions as the key regulator of viral transcription and replication, reviewed in [
120].
AdV transactivating protein E1A-13 S is essential for activating viral transcription in the early phase of infection. During infection, the protein is localized to PML NBs and interacts with PML-II. Such interaction positively regulates the transcription of viral genes. Interestingly, mutation of the SIM motif of PML-II increased its viral gene transactivating activity. This suggested that, as the PML SIM has been shown to mediate noncovalent interactions with other SUMOylated proteins as well as other PML isoforms, the coactivator properties of PML-II do not depend on its localization to PML bodies [
121].
During AdV infection, only the Sp100A isoform of Sp100, but not isoforms Sp100B, Sp100C, or Sp100-HMG, is localized to PML NBs of altered morphology. A significant number of remodeled PML NBs containing Sp100A are found in association with the outer rim of viral replication centers (RCs), whereas other Sp100 isoforms accumulate exclusively within RCs. The C-terminal domains of these longer Sp100 isoforms are likely responsible for this differential localization. Newly synthesized viral RNA is also localized to the outer parts of adenoviral RCs. In addition, Sp100A binding to heterochromatin protein 1 alpha (HP1α) is reduced during infection. It has been proposed that the Sp100-HP1α complex functions as a repressor of viral replication
via a chromatin condensation-based mechanism and that AdV counteracts the repressive function of the complex by disrupting its integrity[
121]. In detail, Berscheminski et al. found that Sp100A alone can act positively on adenoviral promoters when located in disrupted PML NBs, possibly by recruiting histone acetylases (HATs) and thus creating a transcriptionally favorable environment. The authors suggested that Sp100A is retained within disrupted PML NBs surrounding RCs, that is, at sites of active viral transcription, whereas Sp100B, Sp100C, and Sp100-HMG are displaced from these regions and cannot suppress transcription. AdVs, therefore, not only counteract mechanisms of innate immunity but also hijack PML NB components. Fewer interactions between Sp100 and HP1α might also result from decreased SUMOylation of Sp100. Current evidence supports a model whereby AdVs induce the deSUMOylation of specific components of PML NBs, which prevents the localization of viral transcriptional repressors, such as HP1, Daxx, and ATRX, to disrupted PML NBs [
122].
Adenoviral DNA-binding protein E2A is SUMOylated during infection and likely connects viral RCs with disrupted PML NBs. The post-translational modification of E2A does not affect its ability to bind to the viral genome. E2A binds Sp100A, which, in turn, increases the number of E2A molecules in the vicinity of transcriptionally active sites and positively affects viral gene expression [
123]. This association has been observed 4 h post-infection, once the E2A protein has been synthesized [
124].
In summary, during AdV infection, PML NBs components are targeted by the virus as they mostly represent a barrier to viral infection. However, Sp100A promotes viral transcription and PML-II can either restrict or promote infection by interacting with different viral proteins.
Box 1. Highlights of the interplay between adenoviruses and PML NBs
1.
E4-ORF3 binds to PML-II and induces PML NB remodeling -“disruption”.
2.
E4-ORF3, E4-ORF6, and E1B-55K target/remodel PML to (a) promote the degradation of MRE11, thus preventing genome concatemerization; and (b) promote the degradation of ATRX/Daxx, thereby preventing repression of replication.
3.
Protein VI interacts with Daxx thereby inhibiting its repressive activity.
4.
PML-II binds to the viral transactivator protein E1A-13S, which promotes its activity.
5.
SP100A localizes to the outer part of viral replication centres and promotes the transcription of the viral genome.
Interactions between papillomaviruses and PML NB components
Papillomaviruses (PVs) are small DNA tumor viruses with non-enveloped icosahedral capsids of approximately 52–55 nm in diameter. PVs have circular dsDNA genomes (approximately 8 kbp) packaged as a minichromosome with cellular histones. This group of viruses infects a wide range of vertebrates, from birds to mammals. To date, at least 450 human papillomavirus (HPV) genotypes have been identified [
125]. Although infection by some PVs leads to the production of benign warts, other PVs can induce cancer [
126,
127]. PVs infect basal keratinocytes
via skin microlesions, and these cells serve as reservoirs for infection. The infected keratinocytes contain only a few copies of the viral genome, which are present as episomes. The full life cycle of PVs relies on the terminal differentiation of these cells [
128,
129]. Owing to the complexity of the PV life cycle, PV propagation in tissue culture is challenging. Consequently, most related studies have employed models simulating different phases of infection, such as the overexpression of individual viral proteins, pseudovirus infection, or PV genome transfection.
PV genomes are composed of E and L coding regions separated by control region sequences. The E region encodes up to eight proteins (E1 to E8), depending on the virus type. E1 and E2 are important for genome replication and transcription, while E6 and E7 are viral oncoproteins. The L region encodes the capsid proteins L1 and L2 [
130].The infection of basal epithelial cells by the virus is followed by the initial amplification of the genome. In this process, the PV genome is replicated until an optimal copy number is reached, followed by a maintenance phase in which a constant PV genome copy number is maintained. Later, a massive amplification of the viral genome and virion assembly occurs in terminally differentiated cells [
128,
131,
132].
PVs traffic to the nucleus within endocytic vesicles in the endosomal pathway. The virions undergo remodeling in which the L2 protein is arranged in a transmembrane configuration. Until recently, the remodeled subparticle was thought to be composed of L2 protein and viral DNA with histones [
133], reviewed in [
134]. However, it has since been demonstrated that L1 proteins, likely in capsomer form, are also components of the subviral particle (L2-L1/vDNA complex) [
135]. After endosomal sorting, the L2-L1/vDNA complex travels to the
trans-Golgi network (TGN) by retrograde transport [
136,
137]. The nuclear import of the complex depends on mitotic nuclear envelope breakdown [
138]. It was recently found that viral subparticles in transport vesicles enter the nucleus and remain “covered” for a short time after the completion of mitosis [
135,
139].
The association of viral proteins with PML NB components was observed in studies where viral proteins were overexpressed. First, the minor capsid protein L2 of bovine PV (BPV) was shown to be essential for attracting the major structural protein L1 and the non-structural protein E2 to PML NBs [
133]. Subsequently, Florin et al. found that the HPV L2 protein induced PML NB reorganization [
140]. Specifically, the authors reported that Sp100 was excluded from the PML NBs, as well as the massive recruitment of Daxx protein, while the spot-like shape of the bodies was preserved. Further studies showed that the L2 protein binds to Daxx
via its C-terminal region [
141,
142]. Finally, it was found that, when overexpressed in human keratinocytes, the E4 protein forms inclusions that are surrounded by PML protein [
143].
Next, several experiments using pseudoviruses or even viruses provided clear evidence that interactions between viral proteins and PML NBs are required during the early stages of infection. Using BPV pseudovirions, Day et al. demonstrated that after cell entry, remodeled pseudovirions that were transported to the nucleus co-localized with PML NBs [
144]. Furthermore, it was shown that the expression of the gene that was packaged in the pseudovirions was decreased in infected PML knockout cells. The positive role of PML NBs in the life cycle of the virus was confirmed by experiments using BPVs isolated from bovine warts [
144]. Additionally, Bienkowska-Haba et al. demonstrated that PML NBs confer a protective environment for the HPV pseudogenome [
145]. Specifically, the authors found that the amount of EdU-labelled DNA delivered by HPV16 particles was greatly reduced in PML knockdown HaCaT cells compared with that in the parental cell line.
Details regarding the interaction between PML NB components and PVs have gradually emerged. Bund et al. [
146] identified a SIM motif at position 286–289 of the L2 capsid protein that is responsible for the localization of L2 in PML NBs. In agreement with this, when the L2 SIM motif was mutated, neither entry nor sorting of pseudoviruses was affected; in contrast, L2-L1/vDNA complexes did not accumulate in the PML NBs. The authors concluded that L2 interaction with SUMO-2 proteins is required for the localization of the viral L2-L1/vDNA complex with PML NBs. The importance of this motif was later also independently corroborated [
147]. Next, Kivipold et al. [
148] to understand the role of Daxx in the PV life cycle, transfected U2OS cells with HPV genomes and investigated the localization of the RCs relative to that of PML and Daxx. They found that RCs are localized near PML NBs. Furthermore, Daxx downregulation negatively affected the expression of early genes and, consequently, viral genome replication. Finally, Schweiger et al. [
149] recently showed that the autophagy receptor p62 binds to subviral particles in endosomes and accompanies them to the nucleus, where hybrid p62-subviral particle-PML assemblies are detected. The authors suggested that the interaction between subviral particles and p62 exerts a protective effect on the viral genome. p62 depletion resulted in the degradation of L2 and a decrease in the expression of the reporter gene carried by the pseudovirions [
149].
Notably, despite the overall beneficial effect of the association between PVs and PML NBs for the virus, it has also been demonstrated that Sp100, a PML NB component, plays a negative role in the early and late phases of the viral life cycle. First, it was shown that the transfection of Sp100-depleted immortalized primary human keratinocytes with the PV genome resulted in enhanced viral transcription and replication and increased the immortalization of keratinocytes [
150]. Further studies showed that Sp100 not only associated with the replication foci formed upon differentiation in a HPV-containing cervical cell line (derived from a HPV31-positive cervical biopsy) but also mediated the repression of late HPV31 transcription and reduced viral replication in the differentiated cells. Chromatin immunoprecipitation studies showed that Sp100 binds at multiple sites in the viral genomes, implying that Sp100 binding is sequence-independent [
151].
Recently, Guion et al. used high-resolution microscopy in combination with methods for differential membrane permeabilization to understand the dynamics of the interactions between PML NB components and HPV pseudovirions. They followed the co-localization of membrane-associated or naked subviral particles with PML, SUMO-1, and Sp100 at early and late interphase. In early interphase, large cytosolic PML protein aggregates could be seen; however, the pseudovirions only co-localized with PML in the nucleus when PML was recruited back to the nucleus after mitosis, and this association with PML continued throughout interphase. Moreover, the genomes, still enclosed in transport vesicles, co-localized with PML and SUMO-1 in the nucleus, while Sp100 was recruited to the pseudogenomes only after they had shed their transport vesicles, which occurred during late interphase [
147].
In conclusion, for PVs, it has been demonstrated that PML NB components mostly promote viral infection via several mechanisms. Nevertheless, one PML NB component, Sp100, has been shown to restrict viral transcription and replication in the later stages of infection.
Box 2. Highlights of the interplay between papillomaviruses and PML NBs
1.
The viral capsid protein L2 interacts with PML via its SIM motif.
2.
PML and SUMO-1 are recruited to transport vesicles containing subviral particles, thus conferring protection to the viral genome in the nucleus.
3.
Daxx positively regulates viral gene expression.
4.
In the nucleus, once the subviral particles are released from transport vesicles, they interact with Sp100. This interaction negatively influences viral genome transcription and replication.
Interactions between polyomaviruses and PML NB components
Polyomaviruses (PyVs) are small, non-enveloped icosahedral viruses (~ 45 nm in diameter) with circular dsDNA genomes (~ 5 kbps) packaged as a minichromosome with cellular histones. The viral genomes encode early, so-called tumorigenic T antigens—multifunctional proteins that play a role in the regulation of gene expression as well as in the modulation of the host cell immune response and tumorigenesis—and late gene products, namely, the capsid proteins VP1, VP2, and VP3 [
152‐
154]. Primate PyVs encode an additional late protein, a helper phosphoprotein called agnoprotein, the function of which is incompletely understood [
155].
PyVs are widespread in nature. They primarily infect mammals and birds, causing predominantly persistent, asymptomatic infections. The most studied PyVs are model viruses—mouse polyomavirus (MPyV), simian virus 40 (SV40), and human BK (BKPyV) [
156], JC (JCPyV) [
157], and Merkel cell (MCPyV) [
158] polyomaviruses. Immunodeficiency or immunosuppression allows the reactivation of these viruses. When this happens, BKPyV causes an opportunistic infection of the kidneys, which may result in nephropathy. JCPyV can cause the brain disease progressive multifocal leukoencephalopathy, while MCPyV is associated with a rare type of skin cancer called Merkel cell carcinoma.
PyVs enter cells by receptor-mediated endocytosis and travel in endosomes to the endoplasmic reticulum. They are subsequently released into the cytosol, from where they translocate to the nucleus through nucleopores, reviewed in [
159]. In the nucleus, they use host cell functions for early and late gene transcription, alternative splicing, and genome replication. However, the role of PML NBs in PyVs propagation remains poorly understood.
In the early stage of SV40 infection, viral DNA and large T antigen (LT) were observed in close proximity to PML NBs [
8,
102,
160]. Although individually expressed SV40 LT antigens have been found to co-localize with PML NBs [
102,
161], active replication of viral DNA is required for the localization of viral DNA close to PML NBs [
160,
162]. Thus, although SV40 replicates its genomic DNA close to PML NBs, no alterations or modifications of the NBs during infection have been detected [
8]. Interestingly, similarly to AdV E4-ORF6 and E1B-55 K of adenovirus, the SV40 large T antigen targets the MRN complex and disturbs the formation of nuclear foci containing MRE11 [
163,
164]. Whether PML NBs play a role in this process is unknown.
In contrast, infection with other PyVs was shown to result in significant alterations and modifications to PML NBs during infection. BKPyV alters the number and size of PML NBs during infection. In BKPyV-infected cells, there are fewer but larger PML NBs compared with that seen in non-infected cells [
165]. Moreover, LT antigen was found to co-localize with PML NB structures, whereas viral DNA was observed juxtaposed to PML NBs [
160,
165]. In addition to number and size, BKPyV infection also influences the composition of PML NBs. For instance, PML and SUMO-1 were reported to be associated with PML NBs during the whole course of infection, whereas Sp100 and Daxx dissociated from NBs in the late phase of infection [
165]. Although active replication of viral DNA is indispensable for PML NB reorganization and viral DNA association with PML NBs, intact PML NBs are not required for virus replication. PML protein knockdown leads to the complete disruption of PML NB structures without affecting viral titer or viral protein levels [
165]. Similar effects have been observed in cells infected with other PyVs. Specifically, PML NBs are larger in MPyV infected cells than in non-infected cells. Furthermore, whereas LT antigen localizes close to PML NBs, MPyV DNA localizes adjacent to and in NBs. As with BKPyV infection, PML NBs are not required for MPyV replication [
166]. Enlarged, sphere-shaped PML NBs were also detected in cells transfected with a replication-competent MCPyV genome [
167]. In MCPyV-infected cells, LT antigen was detected in proximity to PML NBs, and an increase in the number and size of the NBs was also observed. Moreover, no Sp100 signal was detected in approximately 30% of the NBs evaluated, indicative of PML NB reorganization. Although the knockdown of PML had little effect on the efficiency of viral genome replication, Sp100 knockdown resulted in increased replication of MCPyV genomes, suggesting that Sp100 plays a restrictive role of in virus replication [
167].
The most prominent reorganization of PML NBs was seen in JCPyV-infected cells. PML NBs were found to be larger in the late phase of JCPyV infection both in vitro and in oligodendrocytes obtained from patients with progressive multifocal leukoencephalopathy [
168‐
170]. Viral DNA replication was detected in close proximity to PML NBs [
169], as were virus particles [
171]. Meanwhile, the structural proteins VP1, VP2, and VP3 were reported to accumulate in PML NBs in JCPyV-infected cells [
170], and the viral late gene product, the non-structural agnoprotein, participates in this association. In the presence of agnoprotein, the ectopic expression of structural proteins led to the formation of virus-like particles on the surface of PML NBs; however, in its absence, the virus-like particles were predominantly located under the inner nuclear membrane [
171]. Thus, it seems that PML NBs provide a scaffold for JCPyV replication and progeny formation. The accumulation of structural proteins inside PML NBs results in the enlargement of the latter [
168,
170] and, in the very late phase of infection, their final disruption [
168,
169].
Interestingly, an increased number of PML NBs was detected in JCPyV-infected cells early after infection [
172]. The authors suggested that in this case, the change in PML NBs number was rather a cellular response to the increased level of interferon induced by the infection than a direct consequence of viral replication.
Altogether, these data suggest that PML NBs may play several roles in PyV infection. Although the absence of PML NBs does not influence viral genome replication, the bodies may still act as scaffolds for virion assembly. Since PML NBs are often re-organized following infection, it is possible that PyVs induce remodeling of the bodies, in order to affect their functionality (e.g., to avoid activation of the innate immune response). Nevertheless, more studies are required to fully understand the complex role of PML NBs and their components in PyV infection.
Box 3. Highlights of the interplay between polyomaviruses and PML NBs
1.
The replication of PyV genomes occurs in close proximity to PML NBs.
2.
During infection, PML NBs increase in size and number and their composition changes.
3.
In MCPyV infection, Sp100 was found to negatively influence viral transcription.
4.
In JCPyV infection, particle formation was detected at the surface of PML NBs.
Interactions between PML-NB components and hepatitis B virus
Hepadnaviruses are enveloped, small DNA viruses, approximately 42 nm in diameter, with an icosahedral capsid. Compared to all the already mentioned DNA viruses, members of the Hepadnaviridae family are unique in that their DNA genomes are not replicated in the nucleus. Instead, once their genomic DNA has been transcribed in the nucleus, the longest transcript, pregenomic RNA (pgRNA), is encapsidated in the cytoplasm and, at the same time, reverse transcribed into viral DNA, reviewed in [
173].
Hepatitis B virus (HBV) has a relaxed circular (rc) dsDNA genome approximately 3.2 kbp in length. Unlike the (−) strand, the (+) strand is not complete. The HBV genome encodes a DNA polymerase (Pol) that has reverse transcriptase activity and is covalently attached to the 5′ end of the (−) strand. The (+) strand has a 5′ short RNA primer. Other proteins encoded by the HBV genome include a capsid protein (also called core protein C or HBcAg), a non-structural secreted.
protein (E; HBeAg), a multifunctional regulatory X protein (HBx), and three surface glycoproteins (HBsAgs) of differing size (small, medium, and large S protein) derived from the same sequence. After transport into the nucleus, HBV rcDNA is converted into covalently closed circular DNA (cccDNA) by host enzymes, and during this process, the above-mentioned 5′ end structure is removed. Transcription of the viral genomic DNA is performed by host RNA Pol II. The template for reverse transcription, pgRNA, also serves for HBcAg and Pol translation. During the early stages of infection, cccDNA can also be amplified in such a way that the newly formed nucleocapsids are, in turn, targeted to the nucleus, where the released genomes are further transcribed, summarized in [
46,
173,
174].
Members of the Hepadnaviridae family comprise five genera. They infect mammals (e.g., humans, woodchucks, and ground squirrels), birds (e.g., ducks, geese, and wild herons ), teleost fish, reptiles, and frogs [
173,
175]. Human HBV is the prototype and the most-studied member of the Hepadnaviridae family. HBV attacks the liver and can cause both acute and chronic disease, which may result in cirrhosis or even hepatocellular carcinoma (HCC). The World Health Organisation (WHO) estimates that 296 million people were living with chronic hepatitis B infection in 2019, while approximately 830 000 people died, mostly from cirrhosis or HCC [
174].
The involvement of PML protein in the early stage of hepatocarcinogenesis and HBV infection and the possible association of HBV infection with PML overexpression or changes in PML NB morphology was revealed by the analysis of human HCC, liver cirrhosis, and chronic hepatitis samples [
176]. Meanwhile, Chung and Tsai found an association between HBV genome and PML NBs when studied the progression of HBV-induced HCC [
177]. Specifically, the authors reported that chemotherapy and irradiation-induced DNA repair signaling resulted in an increase in PML protein expression as well as the number and size of PML NBs. Moreover, following radiotherapy and chemotherapy, extensive interactions were observed among PML, HDAC1, phosphorylated histone H2AX (γ-H2AX, a marker of dsDNA damage), and breast cancer susceptibility protein type 1 (BRCA1), important for homologous recombination-mediated DNA repair. Additionally, HBcAg and viral DNA were detected in newly formed PML NBs. The authors proposed a model for the feedback loop involving PML, HDAC1, and HBcAg where, in the absence of a stress stimulus, HDAC1 in PML NBs inhibits the basal core promoter of HBV. However, following DNA damage and subsequent repair signaling activation, the expression of pgRNA is enhanced, yielding HBcAg. HBcAg targets PML and disrupts the interaction between HDAC1 and PML, thereby reducing HDAC1 activity and further enhancing viral transcription [
177].
S100A10 protein recruits HBV polymerase to PML NBs
A yeast two-hybrid screen for cellular protein interacting partners of HBV reverse transcriptase (HBV Pol) led to the identification of S100 calcium-binding protein A10 (S100A10, also known as p11) [
45]. The interaction led to the inhibition of DNA Pol activity. Moreover, it was found that S100A10 recruited HBV Pol to the nucleus, where the complex co-localized with PML NBs in an intracellular calcium ion (Ca
2+)-dependent manner. However, the significance of this interaction is unknown. Whether the S100A10-mediated transport of HBV Pol to PML NBs inhibits viral replication or initiates genome transcription is not clear [
45].
The FOXO4 transcription factor inhibits transcription from the HBV core promoter
Another relationship between HBV transcription and PML NBs was identified very recently. The transcription of cccDNA from the HBV core promoter can be inhibited by the transcription factor forkhead box O4 (FOXO4) through the FOXO4-mediated downregulation of the expression of another transcription factor, hepatocyte nuclear factor 4 alpha (HNF4α) [
178]. The same research group showed that FOXO4 could induce the epigenetic silencing of cccDNA by promoting its heterochromatinization [
179]. FOXO4 binds cccDNA and its overexpression decreases the recruitment of euchromatin to cccDNA while increasing that of heterochromatin markers. Interestingly, the authors found that FOXO4 co-localizes with PML NBs and interacts with PML protein. This interaction was shown to be essential for FOXO4-mediated cccDNA epigenetic modification. PML knockdown reversed the FOXO4-mediated epigenetic suppression of cccDNA transcription and, consequently, HBV replication, but did not affect the expression level of HNF4α. These results indicated that the FOXO4-mediated epigenetic suppression of HBV cccDNA transcription and the inhibition of transcription from the core promoter
via the downregulation of HNF4α are independent processes.
The molecular basis of the role of PML and PML NBs in FOXO4-mediated epigenetic silencing of cccDNA awaits clarification. The same study also revealed that FOXO4 is downregulated in HBV infected primary human hepatocytes and liver biopsy specimens of patients with HBV-positive chronic hepatitis B by an as-yet unidentified mechanism [
179].
In the next section, we describe the interactions between the HBV HBx protein and PML NB-associated proteins such as the chromatin remodelers SUZ12 and ZNF198, Sp110, or SMC5/6, which affect the progression of HBV infection.
Initially, it was shown that HBx mediates the degradation of the PML NB components polycomb protein SUZ12 and zinc finger protein 198 (ZNF198), proteins that have a role in chromatin remodeling. HBx has been found to mediate the activation of the host serine/threonine kinase polo-like kinase 1 (PLK1), which may be associated with cell transformation [
180]. SUZ12 and ZNF198 can serve as PLK1 substrates [
181]. SUZ12, together with histone-lysine
N-methyltransferase EZH2 (EZH2) and polycomb protein EED (EED), is a component of polycomb repressive complex 2 (PRC2). The function of this complex is to methylate lysine 27 of histone 3 [H3K27me3], which is associated with the repression of transcription. The ZNF198 protein plays a key role in stabilizing the CoREST complex comprising lysine demethylase 1 (LSD1), REST corepressor 1 (RCOR1), and HDAC1. This large complex is important for its ability to remove activation modifications from chromatin [reviewed in [
46]]. The absence of SUZ12 and ZNF198 was observed to lead to defects in DNA repair as well as p53-mediated apoptosis. Interestingly, during HBx-mediated cellular transformation, the level of these proteins decreases, which correlates with an increase in PLK1 levels. Based on these observations, it was proposed that the degradation of SUZ12 and ZNF198 may be related to PLK1 activity [
182]. Later, this kinase was shown to phosphorylate SUZ12 and ZNF198, which disrupts their association with the respective complexes, and leads to their ubiquitination-dependent proteasomal degradation [
181].
It is important to also mention the long non-coding RNA (lncRNA) HOX antisense intergenic RNA (HOTAIR). Interestingly, this lncRNA functions as a platform for protein ubiquitination through its association with E3 ubiquitin ligases Dzip3 and Mex3b [
183]. HOTAIR is thought to facilitate the ubiquitination of phosphorylated SUZ12 and ZFN198 by acting as a bridge between PRC2 and the CoREST complex. The degradation of these complexes may result in the re-expression of some silenced genes, such as epithelial cell adhesion molecule (EpCAM), which may be associated with tumor development. Indeed, the expression of EpCAM is upregulated in some types of HCC [
181]. Despite the importance of these findings, further studies are needed to accurately reveal the functional significance of the above-described phenomena.