Palmitoylation of viral proteins enhances their interaction with the plasma membrane, thereby promoting fusion between the viral and host cell membranes and increasing infection efficiency. Studies have shown that ZDHHC5 and GOLGA7 can bind to SARS-CoV-2 spike (S) protein and promote its palmitoylation process (Wu et al., 2021; Zeng et al., 2021). Several cysteine residues within the S protein—particularly Cys15 and those located in the C-terminal cytoplasmic tail—have been identified as critical palmitoylation sites. This modification is essential for S protein-mediated syncytia formation (Li D. et al., 2022; Mesquita et al., 2021). Furthermore, palmitoylation also promotes the proper trafficking of the mature S protein to the Golgi apparatus and plasma membrane (Tien et al., 2022), thereby triggering the fusion of virus and host cell membrane.

Beyond viral entry, palmitoylation also contributes to viral assembly and particle maturation. The SARS-CoV-2 E protein is palmitoylated at residues C40, C43, and C44 by zDHHC3, 6, 12, 15, and 20. This modification is essential for the production of virus-like particles (VLPs) and for maintaining normal viral particle density (Wang et al., 2024), highlighting the role of palmitoylation in late structural stages of the viral life cycle.

Palmitoylation can further modulate viral protein stability, abundance, and functional activity. In hepatitis C virus (HCV), palmitoylation of the NS2 protein at residue C113 facilitates RNA replication by promoting NS2–NS3 autolytic cleavage and recruiting the E2 protein to membrane microdomains (Wu et al., 2019). In Japanese encephalitis virus (JEV), palmitoylation of the NS2A protein at the C221 enhances protein stability, thereby increasing viral replication efficiency and virulence (Ma et al., 2023). In contrast, palmitoylation can also exert restrictive effects. ZDHHC11 interacts with ZIKV E protein and acts as the main catalytic enzyme for its palmitoylation. Overexpression of ZDHHC11 significantly reduces the level of ZIKV infection, whereas its knockdown enhances viral infectivity (Hu et al., 2023). The functional outcome of palmitoylation varies with the specific viral protein and host enzyme involved.

In nearly all picornaviruses, the capsid protein VP4 undergoes N-terminal myristoylation mediated by NMT within the host cell (Corbic Ramljak et al., 2018). For example, in enterovirus 71 (EV71), the N-terminus of VP4 is myristoylated, and although loss of this modification does not affect viral protein expression or virion morphology, it markedly reduces viral infectivity, underscoring its functional importance in early stages of infection. In retroviruses, myristoylation is typically highly conserved. With few exceptions, nearly all retroviral Gag proteins undergo co-translational myristoylation at the N-terminal glycine residue within the matrix (MA) domain (Wang et al., 2021). During human immunodeficiency virus type 1 (HIV-1) infection, myristoylated Gag and Nef proteins significantly enhanced viral replication and infectivity (Seaton and Smith, 2008). Collectively, these findings indicate that myristoylation promotes efficient viral entry and early replication by enabling dynamic membrane association and spatial organization of viral structural proteins across distinct virus families.

Beyond viral entry, myristoylation plays a critical role in viral assembly and particle maturation. In mammalian viruses, the Z matrix protein and the stable signal peptide of the GP1/2 envelope glycoprotein are two of the four encoded proteins that undergo myristoylation (Carnec et al., 2024). The Z protein of Mopeia virus (MOPV) interacts with both N-myristoyltransferase 1 (NMT1) and 2 (NMT2), with NMT1 identified as the virus-dependent isoform that plays a dominant role in the production of infectious viral particles (Carnec et al., 2024). Consistent with this requirement, myristoyltransferase inhibitors such as DDD85646 block viral assembly and budding by inhibiting the myristoylation of the arenavirus Z protein and SSP. They also interfere with GP-mediated membrane fusion events (Witwit et al., 2024). These findings suggest that NMT-dependent myristoylation represents a potential broad-spectrum antiviral target against mammalian arenavirus infections.

In retroviruses, beyond myristoylation established role in promoting Gag multimerization and membrane association via the myristoyl switch in the HIV-1 MA domain, it may also regulate the ordered cleavage of Gag proteins in immature Mason–Pfizer monkey virus particles, thereby influencing viral maturation and infectivity (Castoralova et al., 2024). N-myristoylation of the Gag polyprotein is essential for its co-transport to late endosomes and lysosomes. Research has shown that inhibiting N-myristoylation of the Gag polyprotein significantly impairs HIV-1 assembly in macrophages and suppresses the formation of virus-containing compartments (VCCs) (Guajardo-Contreras et al., 2024). Furthermore, myristoylated Gag proteins form trimeric cores within membrane models and selectively bind dimeric RNA harboring packaging signals, providing a crucial structural basis for the initial assembly of the HIV-1 capsid (Zhou et al., 2023).

Glycosylation frequently acts at early stages of infection, yet the degree of dependence on specific glycan sites varies markedly across virus families and even among viral variants. In SARS-CoV-2, removal of N-linked glycans at the N61 and N122 sites of the spike protein markedly reduces pseudovirus infectivity, indicating a general requirement for glycosylation at these positions (Zhang F. et al., 2024). By contrast, the contribution of glycosylation at other sites depends on the viral genetic background, as illustrated by differential effects of N717 and N801 glycan loss across SARS-CoV-2 variants (Watanabe et al., 2020). Loss of glycosylation at these sites nearly abolishes infectivity in the Omicron BA.1 variant, whereas the D614G variant remains largely unaffected under the same conditions (Lusvarghi et al., 2023). These findings illustrate that glycosylation can be reshaped during viral evolution to accommodate structural changes in surface proteins.

IAV has two main surface glycoproteins, haemagglutinin (HA) and neuraminidase (NA). NA functions during the late stages of viral replication by catalyzing the cleavage of the linkage between sialic acid and HA, thereby facilitating the release of progeny virions. The N-glycosylation modification of NA protein regulates the budding, replication ability and virulence of the virus. The N-glycosylation site at position 219 is particularly critical, and its mutation can significantly reduce the virulence of the virus and can be used to develop attenuated vaccines (Bao et al., 2021; Ostbye et al., 2020).

For many enveloped viruses, glycosylation of surface proteins plays a critical role in shaping receptor usage and attachment efficiency. Severe fever with thrombocytopenia syndrome virus (SFTSV) exploits N-linked glycosylation on its glycoprotein (GP) to mediate specific interactions with host C-type lectins, thereby facilitating viral attachment and promoting infection (Shimojima et al., 2024). Similarly, the glycoprotein of EBOV contains multiple complex N- and O-linked glycosylation sites, among which N-linked glycans at positions N257 and N563 are critical for DC-SIGN-mediated viral attachment (Peng et al., 2022; Bagdonaite et al., 2024).

In SARS-CoV-2, glycosylation of the S protein critically shapes receptor engagement. Glycosylation at N165 and N234 stabilizes the conformation of the receptor-binding domain (RBD), thereby directly regulating its interaction with the host ACE2 receptor and influencing viral infectivity. Additionally, the N-linked glycan at N343 has been implicated in facilitating the transition of the RBD from a “closed” to an “open” conformation, a prerequisite for receptor engagement (Sztain et al., 2021). These examples illustrate how glycosylation modulates viral entry not merely by shielding epitopes, but by actively shaping protein conformations that enable receptor engagement.

Beyond entry, glycosylation is essential for maintaining the structural integrity of viral proteins and ensuring efficient virion assembly and release. In rotavirus (RV), defects in glycosylation result in aberrant intracellular localization of the nonstructural protein NSP4, thereby disrupting calcium ion homeostasis, impairing viroplasm formation, and reducing viral replication efficiency. These effects vary across different cell types, with only mild inhibition of replication observed in MA104 cells, but a marked impairment of viral assembly in HT29 cells. Animal studies further demonstrated that viruses lacking NSP4 glycosylation exhibit attenuated virulence in mice, highlighting the essential regulatory role of NSP4 glycosylation in viral pathogenicity (Nurdin et al., 2023). In addition, deglycosylation of the WNV envelope protein similarly results in reduced release of mature viral particles (Hanna et al., 2005).

Glycosylation can promote viral immune evasion through the formation of a “glycan shield” that masks neutralizing epitopes on the viral surface. The glycoprotein complex (GPC) of LASV contains 11 N-glycosylation sites, among which N99, N119, N167, N365, and N373 are believed to conceal epitopes on GPC and suppress host immune responses (Zhu et al., 2021). In arenaviruses, the removal of glycans at N83 and N166 on the GPC protein disrupts the glycan shielding effect, thereby enhancing viral immunogenicity and increasing sensitivity to neutralizing antibodies, ultimately weakening viral pathogenicity (Koma et al., 2021). Moreover, for SARS-CoV-2, glycosylation of the ORF8 protein reduces its binding capacity to immune cells, demonstrating that glycosylation is involved in immune evasion (Wu et al., 2023). In contrast, the S protein of human coronavirus NL63 (HCoV-NL63) exhibits dense oligomannose-type glycosylation, forming a more effective glycan shield and further enhancing its capacity to evade immune detection (Chmielewski et al., 2023). Such glycan-based masking strategies allow viruses to modulate immune visibility without altering underlying protein sequences, providing a flexible means of immune evasion across diverse host environments.

Efficient viral genome replication depends on finely coordinated, reversible phosphorylation of viral polymerase components and their cofactors, allowing different functional states to operate at distinct stages of the replication cycle. The L protein of RVFV is regulated through a dynamic phosphorylation–dephosphorylation cycle mediated by CK1α kinase and PP1α phosphatase; inhibition of either enzyme leads to a marked reduction in viral genomic RNA levels, highlighting the requirement for balanced phosphorylation states during replication (Bracci et al., 2024). In human metapneumovirus (HMPV), the multifunctional regulatory role of phosphorylation on the polymerase cofactor P protein has also been established (Thompson et al., 2023). This study demonstrated that several phosphorylation sites of the P protein are located within intrinsically disordered regions (IDRs). Either phosphomimetic substitution or dephosphorylation mutations at specific sites (e.g., S268 and S271) significantly impair viral RNA synthesis, inclusion body (IB) formation, and viral rescue efficiency. The inability of some phosphomimetic P mutants to restore minireplicon activity suggests a requirement for multiple P protein populations existing in distinct phosphorylation states to coordinate efficient RNA synthesis throughout the viral replication cycle.

Phosphorylation at the S181 site of IAV PB2 negatively regulates IAV replication and pathogenicity. The phosphorylation-mimetic mutation (S181E) results in reduced polymerase activity, restricted viral replication, attenuated virulence, and diminished expression of immune-related factors, suggesting that dynamic phosphorylation at this site is required to maintain the proper function of PB2 (Hu et al., 2024). The degree and timing of phosphorylation may directly influence the balance of the viral life cycle, with hyperphosphorylation impairing efficient replication and transmission. Phosphorylation at residues Y393 and S395 of the IAV PA subunit also suppresses polymerase activity by weakening its binding affinity to vRNA and cRNA, thereby reducing viral replication efficiency (Liu et al., 2023a). The replication of IAV is also dependent on phosphorylation at the T108 residue of the M1 protein. Loss of phosphorylation at this site prevents M1 from entering the nucleus and impairs its ability to mediate nuclear export of vRNPs (Liu et al., 2023b). Phosphorylation of NS1 at S205 further modulates viral replication by promoting its interaction with the host restriction factor DDX21, thereby enhancing polymerase activity (Patil et al., 2021).

Phosphorylation also serves as a key regulatory switch in viral transcription by controlling the activity of viral transcription factors. The transcription process of EBOV is tightly regulated through dynamic phosphorylation of the viral transcription factor VP30 by host phosphatases, with the phosphorylation status of VP30 and NP playing a critical role in this regulation. The N-terminal domain of VP30 harbors a dynamically phosphorylated site that directly modulates its interaction with viral RNA and NP (Biedenkopf et al., 2016). Studies have demonstrated a dual role of VP30 phosphorylation: phosphorylated VP30 exhibits reduced binding affinity to viral RNA and NP, thereby inhibiting the initiation of viral transcription and virion packaging, whereas dephosphorylation of VP30 is essential for viral genome transcription (Modrof et al., 2002). Concurrently, the phosphorylation status of NP itself—particularly the dynamic phosphorylation at residue T603—serves as an important regulatory element in viral transcription. Dephosphorylation at NP-T603 promotes transcription initiation, while its phosphorylated state may exert an inhibitory effect (Kamper et al., 2025). A similar transcriptional regulation mechanism has been also observed in MARV, wherein NP recruits PP2A to efficiently promote VP30 dephosphorylation. Induction of VP30 hyperphosphorylation markedly impairs viral transcription and propagation, underscoring the importance of phosphatase-mediated regulation in filovirus transcriptional control (von Creytz et al., 2024).

During ZIKV infection, the expression of PIM1 kinase is significantly upregulated in host cells and mediates the phosphorylation of the prM protein. This modification disrupts the interaction between prM and the E3 ubiquitin ligase AMFR, thereby preventing AMFR-mediated ubiquitination and degradation of prM and promoting virion maturation (Ren Y. et al., 2024). The N protein of SARS-CoV-2 is extensively phosphorylated and displays distinct functional roles at different stages of infection. Lower levels of N phosphorylation favor viral particle assembly, whereas higher phosphorylation levels enhance viral genome replication (Syed et al., 2024). Phosphorylation of the serine-rich (SR) region interferes with RNA binding by disrupting intramolecular interactions and introducing electrostatic repulsion between phosphorylated residues and the RNA-binding domain (Adly et al., 2023). This dual role highlights an intrinsic regulatory mechanism during infection, wherein the virus balances efficient genome replication with effective virion assembly to maximize transmissibility and adaptability.

In addition to directly modifying viral proteins, phosphorylation modifications can also facilitate viral infection by modulating host proteins. In enteroviruses, phosphorylation of the highly conserved Ser/Thr125 residue of 2A^pro activates its proteolytic activity against the eukaryotic initiation factor 4GI, thereby enhancing the adaptability of enteroviruses to the host and ensuring viral proliferation (Wang et al., 2023). HIV-1 phosphorylates the Vif protein via the Tat-activated AKT signaling pathway, which increases Vif stability and enables more efficient targeting and degradation of the host antiviral factor APOBEC3G, thereby attenuating its potent antiviral activity (Raja et al., 2022). Similarly, phosphorylation of the SARS-CoV-2 nucleocapsid protein at Ser79 promotes its interaction with the host protein Pin1, and this interaction enhances the infectivity of viral particles (Ino et al., 2022).

Acetylation has emerged as an important regulatory layer in IAV infection, reshaping how the nucleoprotein (NP) engages viral RNA (vRNA) and how genome segments are coordinated, with direct consequences for viral replication output. Several proteins within the IAV ribonucleoprotein (RNP) complex are subject to acetylation, which in turn modulates viral transcription and replication. Acetylation at lysine 229 (K229) of NP is associated with efficient production of infectious viral particles (Giese et al., 2017). Moreover, the coordinated packaging of the IAV genome depends on the specific interaction between the RNA-binding groove of NP and the vRNA packaging signals—an interaction regulated by the acetylation of lysine residues (Ciminski et al., 2024).

Acetylation directly modulates the function of key IAV proteins, influencing viral particle production and pathogenicity. The K187 residue of the PB2 subunit in the IAV polymerase undergoes acetylation. This site is located on the surface of the PB2 protein and is highly conserved. Acetylation at K187 stabilizes the PB2 subunit and enhances the pathogenicity of the virus (Hu et al., 2024). On the other hand, N-terminal acetylation of the PA-X protein is essential for IAV-mediated host shutoff (Oishi et al., 2018). Subsequent research has identified two acetylation sites within PA-X. While acetylation at either site is sufficient to ensure proper nuclear localization, only acetylation at the initiating methionine is critical for the full execution of its host shutoff function (Daly et al., 2026). This separation between localization competence and effector potency highlights how acetylation can partition viral protein functions across infection stages.

Acetylation can significantly impact the enzymatic activity of viral proteins, and its functional direction can vary with both residue context and host enzyme identity. The flavivirus NS3 protein, a highly conserved multifunctional enzyme, possesses serine protease activity at its N-terminus and SF2-family helicase activity at its C-terminus—both of which are indispensable for viral replication. The host acetyltransferase KAT5γ acetylates NS3 to modulate its helicase function, thereby facilitating efficient viral replication (Serman et al., 2023).

In IAV, NP acetylation involves multiple host acetyltransferases, and perturbing these enzymes can produce distinct effects on viral polymerase activity. Silencing the histone acetyltransferases PCAF via RNA interference enhances viral polymerase activity, whereas silencing GCN5 reduces polymerase activity and suppressing viral replication (Hatakeyama et al., 2018). Similarly, acetylation at the K19 site of the PA subunit enhances the activity of the viral endonuclease and RNA polymerase (Hatakeyama et al., 2022). These observations suggest that “acetylation status” alone is insufficient to predict functional impact—enzyme context and the specific acetylation site are often key determinants that shape the infection outcome.

Acetylation can enhance the interactions of viral proteins with host factors or viral RNA, thereby supporting efficient viral infection. The E protein of SARS-CoV-2 interacts with BET proteins (particularly the second bromodomain of BRD4) via acetylation, leading to the suppression of the host antiviral response (Chen et al., 2022). In vitro studies have identified 12 acetylated lysine residues on the SARS-CoV-2 N protein. Among them, acetylation at K61 was shown to modulate the binding affinity between the N protein and viral RNA (Hatakeyama et al., 2021).

Following entry and uncoating, RNA viruses must rapidly establish efficient genome replication and transcription to gain a replicative advantage within the host cell. During the early phase of infection, ubiquitination often acts in a non-degradative capacity, shaping viral replication complex formation and supporting replication-associated activities. Influenza A virus (IAV) provides a representative example, all components of the ribonucleoprotein complex (RNP) are subject to ubiquitination (Kirui et al., 2016). During IAV infection, the E3 ubiquitin ligase CRL4 mediates non-degradative ubiquitination at lysine 29 (K29) of the PB2 subunit, markedly enhancing viral replication efficiency and infectivity (Karim et al., 2020). Furthermore, nucleoprotein (NP) undergoes CNOT4-mediated monoubiquitination at multiple sites, which facilitates viral RNA replication (Lin et al., 2017). Specific ubiquitination of the PB1 subunit at lysine 578 (K578) promotes polymerase dimerization and NP binding, thereby augmenting the activity of the viral polymerase complex (Gunl et al., 2023). These studies illustrate how IAV employs precise, non-degradative ubiquitination to optimize polymerase function and replication.

A similar regulatory paradigm is observed in other RNA viruses. VP35 serves as a key cofactor of the EBOV polymerase complex (Basler et al., 2003; Cardenas et al., 2006). It has been demonstrated that VP35 interacts with the host E3 ubiquitin ligase TRIM6, undergoing site-specific ubiquitination. TRIM6 not only modulates VP35 function but also enhances its polymerase activity, thereby increasing viral replication efficiency (Bharaj et al., 2017). In SARS-CoV-2, the nucleocapsid (N) protein is modified by K29-linked polyubiquitination at lysine residues K102, K347, and K361. This modification strengthens NP binding to the viral genome, facilitating viral proliferation (Zhang F. et al., 2024). Together, these studies illustrate how viruses employ precise, non-degradative ubiquitination to rapidly assemble functional replication complexes and initiate robust genome replication and transcription.

As viral replication progresses, host antiviral defenses such as innate immune signaling, autophagy, and apoptosis are activated to restrict viral spread. At this stage, viruses increasingly exploit ubiquitination-dependent pathways to modulate host antiviral mechanisms and maintain a cellular environment permissive for continued replication (Chen et al., 2023). ZIKV non-structural protein NS2A is ubiquitinated through K48 chain mediated by E3 ubiquitin ligase AMFR and subsequently binds to ER autophagy receptor FAM134B, promoting its degradation. This process suppresses ER-phagy, induces ER stress, and ultimately enhances viral infectivity and pathogenicity (Zhang et al., 2024b).

During SARS-CoV-2 infection, lysine residue 119 of ORF7a protein is ubiquitinated, which subsequently inhibits STAT2 phosphorylation and suppresses the interferon-α signaling pathway, facilitating viral evasion of host immune surveillance (Cao et al., 2021). Beyond immune suppression, ubiquitination of ORF7a also contributes to fine-tuning host cell fate. ORF7a recruits the anti-apoptotic protein BclXL to the endoplasmic reticulum, thereby activating the PERK-eIF2α-CHOP pathway, inducing ER stress-mediated apoptosis. However, ubiquitination of ORF7a disrupts its interaction with BclXL, reducing its accumulation in the endoplasmic reticulum, which lowers ER stress levels and partially mitigates apoptosis. This dynamic modulation of ORF7a ubiquitination illustrates how viruses balance immune suppression and host cell survival to sustain productive infection (Liu Z. et al., 2022). Through these mechanisms, ubiquitination emerges as an important means by which viruses attenuate host antiviral barriers to sustain productive infection.

At later stages of infection, precise control of viral protein abundance becomes essential to coordinate replication, assembly, and egress. Ubiquitination and deubiquitination jointly regulate the stability of viral proteins, shaping their fate at different stages of infection. Numerous studies have demonstrated that host E3 ubiquitin ligases specifically mediate the ubiquitination of viral proteins, triggering their degradation. For instance, WWP2 targets lysine residues Lys265 and Lys284 on the ZIKV NS1 protein, mediating K63- and K48-linked ubiquitination respectively, which leads to NS1 degradation and consequently inhibits ZIKV infection (Huang et al., 2024). Similarly, in IAV, the E3 ligase TRIM21 recognizes the M1 protein at residue R95, induces ubiquitination at lysine 242 (K242), and promotes its proteasomal degradation, thereby attenuating viral replication and pathogenicity (Lin et al., 2023).

In coronaviruses, ubiquitin-mediated degradation of viral proteins constitutes an important antiviral mechanism, which viruses actively counteract to preserve essential factors. In SARS-CoV-2, the viral proteins NSP5 and ORF6 are targeted by distinct host E3 ligases for ubiquitin-mediated degradation, thereby impairing their anti-interferon functions (Zhou et al., 2024b; Zhang et al., 2024a). Conversely, SARS-CoV-2 exploits deubiquitination to stabilize key viral proteins. The ORF9b protein undergoes ubiquitination and proteasomal degradation; however, the deubiquitinating enzyme USP29 removes ubiquitin chains from ORF9b, preventing its degradation and enhancing protein stability (Gao et al., 2022; Yu et al., 2024). At the same time, ORF9b is subject to K48-linked polyubiquitination at lysine 67 (K67) mediated by CUL5, which restricts viral replication (Zhou et al., 2024a). This restriction is counteracted by the binding of HSP90α to ORF9b, forming a CUL5–TOM70–HSP90α regulatory complex that preserves ORF9b function during infection.

Ubiquitin-dependent control of viral protein abundance can also vary across different stages of infection. Studies have revealed that the expression level of IAV NS2 protein exerts a dual effect on the viral life cycle: during the early phase of infection, low abundance of NS2 facilitates viral transcription, whereas elevated levels of NS2 inhibit transcription while simultaneously promoting viral RNA synthesis (Guillon et al., 2022). Furthermore, NS2 undergoes polyubiquitination at lysine residues K64 and K88, targeting it for proteasomal degradation. Nonetheless, this ubiquitination process does not impair NS2-mediated viral ribonucleoprotein (vRNP) nuclear export. The host deubiquitinating enzyme OTUB1 removes the polyubiquitin chains conjugated to NS2, markedly enhancing its stability and promoting its accumulation during the late stages of viral infection. This indicates that the virus prolongs NS2’s half-life by modulating host deubiquitinase activity to fulfill stage-specific functional requirements (Li et al., 2024). Through this dynamic regulation of ubiquitination and deubiquitination, NS2 protein levels are adjusted to meet stage-specific functional demands, illustrating how protein degradation and stabilization together shape antiviral restriction while allowing selected viral factors to persist when required.

Small ubiquitin-like modifiers (SUMOs) represent a crucial class of protein post-translational modification molecules. The covalent attachment of a SUMO protein to lysine residues on target proteins is referred to as SUMOylation (Martin et al., 2007). Many SUMOylated proteins also harbor SUMO interaction motifs (SIMs), which mediate non-covalent interactions with free SUMO or SUMOylated proteins, thereby broadening their functional regulatory scope.

SUMOylation plays a crucial role in facilitating viral replication and modulating host immune defenses (Figure 3 and Table 1). The envelope and precursor membrane (prM) proteins of DENV are identified as potential SUMOylation substrates. Their SUMOylation facilitates viral replication and transmission in Aedes aegypti (Weng and Shiao, 2022). SARS-CoV-2 N protein regulates nuclear translocation and viral particle assembly through SUMO modification (Madahar et al., 2023). Interfering with N protein SUMOylation can significantly reduce the efficiency of viral replication, reflecting its potential as a therapeutic target (Ren J. et al., 2024). Additionally, VP24 of EBOV is a well-characterized SUMOylation target. This modification maintains the protein’s stability and enhances its capacity to suppress type I interferon signaling and block STAT1 nuclear translocation. Loss of SUMOylation results in reduced VP24 stability and diminished binding affinity to the nuclear import receptor KPNA5, thereby impairing its immune antagonistic function (Vidal et al., 2019).

Notably, SUMOylation does not uniformly favor viral infection. In certain contexts, SUMO modification can restrain viral replication by dampening the activity of key viral proteins. SUMOylation of the IAV NS1 protein attenuates its capacity to inhibit interferon signaling (Santos et al., 2013), while SUMOylation of the PB2 subunit compromises the activity of the viral RNP complex, thereby reducing viral replication efficiency and virulence (Wang G. et al., 2022).

Ubiquitination and SUMOylation frequently converge on the same viral proteins and operate in a coordinated or sequential manner to regulate viral protein localization, stability, and activity. In IAV, a representative example of such interplay is observed in the matrix protein M1. During infection, M1 can undergo both ubiquitination and SUMOylation at overlapping lysine residues, and host factors facilitate a functional shift from ubiquitination to SUMOylation, promoting efficient nuclear export of viral ribonucleoproteins and supporting productive replication (Gao et al., 2015). Beyond direct modification switching, parallel regulation by ubiquitination and SUMOylation has also been documented for viral proteins involved in genome replication. The NP of IAV is subject to both SUMOylation and ubiquitination during infection, with these modifications contributing to RNP activity and viral RNA synthesis (Liao et al., 2010). Although these modifications do not necessarily compete for the same residues, their convergence on shared viral factors facilitates transitions between nuclear trafficking, genome replication, and particle assembly across the viral life cycle.

NEDDylation is a ubiquitin-like post-translational modification in which the neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) is covalently conjugated to lysine residues of substrate protein. Owing to its substantial sequence similarity to ubiquitin, NEDDylation follows an enzymatic cascade analogous to ubiquitination and often targets lysine residues that are also subject to other post-translational modifications, thereby allowing potential competition or coordination among distinct regulatory pathways. NEDD8 is typically conjugated to lysine residues, which are also potential targets for other modifications, indicating possible competition or crosstalk among different post-translational modifications.

Several viral proteins have been reported as targets of neddylation (Figure 3 and Table 1). The VP2 protein of EV71 undergoes neddylation at lysine 69 (K69), a modification that facilitates the degradation of viral proteins and consequently suppresses EV71 proliferation (Wang H. et al., 2022). The PB2 and M1 proteins of IAV are subject to neddylation, which reduces protein stability and leads to diminished viral replication capacity (Zhang et al., 2017; Li et al., 2020).

ISG15 is a 17-kDa ubiquitin-like protein that is robustly induced in response to viral infection. Conjugation of ISG15 to target proteins, termed ISGylation, occurs through an enzymatic cascade that parallels ubiquitination and results in the covalent attachment of ISG15 to specific lysine residues on substrate proteins (Mustachio et al., 2018). ISGylation serves as a host antiviral mechanism by impairing the function of viral proteins and restricting viral replication (Figure 3 and Table 1). In IAV, ISGylation of the NS1A protein leads to its functional loss, thereby suppressing viral replication (Hsiang et al., 2009; Zhao et al., 2010; Tang et al., 2010). In SARS-CoV-2, ISGylation of the N protein inhibits its oligomerization and reduces viral RNA synthesis (Rhamadianti et al., 2024).

To overcome ISGylation-mediated antiviral restriction, some viruses have evolved strategies to remove or neutralize ISG15 modifications, thereby restoring viral protein function and promoting replication. SARS-CoV-2 encodes the papain-like protease (PLpro), which specifically cleaves ISG15 from the N protein, relieving its functional inhibition, facilitating immune evasion, and enhancing viral replication (Zhu et al., 2024; Bang et al., 2024). Additionally, in recombinant IBV, although the NS1B protein does not directly inhibit the ISGylation process, it binds to and sequesters ISGylated NP protein, thereby blocking its antiviral function and indirectly alleviating ISGylation-mediated suppression of viral replication (Zhao et al., 2016). These examples illustrate how viruses can neutralize ISGylation without globally suppressing the host interferon response.

Notably, ISGylation does not universally restrict viral infection and can, in specific contexts, be repurposed to support viral replication. In HCV, the NS5A protein undergoes ISGylation at multiple lysine residues (K20, K26, K44, K139, and K166), a modification that promotes viral RNA replication (Bawono et al., 2021). Further studies using luciferase reporter replicon assays demonstrated that lysine 308 (K308) is critical for HCV replication (Abe et al., 2020). In this setting, ISGylation of NS5A functions as a proviral modification by recruiting the host factor cyclophilin A (CypA), thereby enhancing viral RNA replication.