biomolecules Review Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection Maria Grazia Masucci Department of Cell and Molecular Biology, Karolinska Institutet, S-17177 Stockholm, Sweden; [email protected] Received: 13 July 2020; Accepted: 31 July 2020; Published: 1 August 2020 Abstract: Posttranslational modifications of cellular proteins by covalent conjugation of ubiquitin and ubiquitin-like polypeptides regulate numerous cellular processes that are captured by viruses to promote infection, replication, and spreading. The importance of these protein modifications for the viral life cycle is underscored by the discovery that many viruses encode deconjugases that reverse their functions. The structural and functional characterization of these viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infections and the host’s antiviral defense. Given the growing body of evidence demonstrating their key contribution to pathogenesis, the viral deconjugases are now recognized as attractive targets for the design of novel antiviral therapeutics. Keywords: ubiquitin-like deconjugase; herpesvirus; coronavirus; virus cycle; innate immunity; type I IFN 1. UbL Signaling Networks Viruses have shaped the fate of human societies throughout history. Understanding how these potentially life-threatening pathogens establish infection and how they interact with their hosts is our best strategy for acquiring the means to control the diseases they cause. Being obligatory intracellular parasites, viruses face a double challenge. On one side, they need to commandeer the molecular machinery of the host cell to support the production of new virus particles, while on the other side, they must hold back the multifaceted cellular and organismal defenses that are triggered by infection. These challenges are met by the expression of specialized viral products that hijack or manipulate critical cellular functions. Many of these viral pathogenicity factors are multifunctional proteins that mimic the activity of cellular counterparts whose activity controls key aspects of normal cell physiology. Virtually all cellular processes are regulated by posttranslational modifications that dictate the function, subcellular localization, and interactions of effector proteins. Among those, the covalent attachment of small polypeptides of the ubiquitin family (henceforth collectively referred to as ubiquitin-like polypeptides, UbLs) provides a flexible means to control the activity and fate of the modified substrate. Cell functions that orchestrate the outcome of infection such as the cell cycle, cell survival and programmed cell death, gene expression, protein trafficking and degradation, autophagy, and the immune response are all dependent on UbL modifications [1]. It is therefore not surprising that viruses have evolved means to interfere with the UbL signaling networks in order to secure a cellular environment conducive to their own replication and spread. The UbLs are a family of structurally related small polypeptides that share a β-grasp fold organization consisting of a mixed β-sheet structure with a central α-helix [2]. To date, seventeen human UbLs have been reported to be conjugated to other molecules. In addition to ubiquitin (Ub), the UbLs include the small ubiquitin-related modifier (SUMO)-1, -2, and -3; NEDD8 (neural precursor cell expressed, developmentally downreagulated-8); ISG15 (interferon stimulated gene-15); UFM1 (ubiquitin-fold modifier-1); URM1 (ubiquitin-related modifier-1); FAT10 (HLA-F adjacent transcript Biomolecules 2020, 10, 1137; doi:10.3390/biom10081137 www.mdpi.com/journal/biomolecules Biomolecules 2020, 10, 1137 2 of 24 Biomoleculescell expressed,2020, 10 developmentally, 1137 downreagulated-8); ISG15 (interferon stimulated gene-15); UFM12 of 24 (ubiquitin-fold modifier-1); URM1 (ubiquitin-related modifier-1); FAT10 (HLA-F adjacent transcript 10); MNSFβ (monoclonal nonspecific suppressor factor β); and the LC3 (microtubule-associated light 10);chain-3) MNSF andβ (monoclonal GABARAP nonspecific(γ-aminobutyric suppressor acid receptor factor β );associated and the LC3 protein) (microtubule-associated family of modifiers light [3]. chain-3)The attachment and GABARAP of UbLs to (γ their-aminobutyric protein or, acidin th receptore case of associatedthe LC3/GABARAP protein) familyfamily, of lipid modifiers substrates [3]. Theis mediated attachment by an of UbLsenzymatic to their cascade protein that or, starts in the wi caseth ofprocessing the LC3/ GABARAPof the UbL family,precursor lipid by substrates a specific isprotease, mediated which by an generates enzymatic a cascadeC-terminal that Gly starts residue with processing required for of theconjugation. UbL precursor The bymature a specific UbL protease,becomes whichthe substrate generates of an a C-terminal activating Glyenzyme residue (E1) required that forms for a conjugation. high-energy The thiolester mature bond UbL becomeswith the theC-terminal substrate Gly of anand activating then loads enzyme the activated (E1) that UbL forms on the a high-energy catalytic Cys thiolester residue bond of a conjugating with the C-terminal enzyme Gly(E2). and The then E2 transfers loads the the activated UbL to UbL the substrate on the catalytic with th Cyse help residue of a ligase of a conjugating (E3) that promotes enzyme (E2). the transfer The E2 transfers[4,5] (Figure the UbL1). As to a the rule, substrate each UbL with conjugation the help of syst a ligaseem involves (E3) that distinct promotes sets the of transfer dedicated [4,5 E1,] (Figure E2, and1). AsE3, aenzymes rule, each but UbL enzyme conjugation sharing system is not uncommon involves distinct and E3 sets ligases of dedicated with mixed E1, specificity E2, and E3, for enzymes Ub and butISG15, enzyme e.g., sharingTRIM25 is(Tripartite not uncommon motif-25) and [6]; E3 ligasesubiquitin with and mixed NEDD8, specificity e.g., MDM2 for Ub and(Mouse ISG15, double e.g., TRIM25minie-2) (Tripartite[7]; or Ub motif-25)and SUMO, [6]; e.g., ubiquitin TOPORS and (T NEDD8,OP1 binding e.g., MDM2 Arginine/Serin (Mouse doublee rich protein), minie-2) TRAF7 [7]; or Ub(TNF and receptor SUMO, associated e.g., TOPORS factor-7), (TOP1 UHRF2 binding (Ubiquitin Arginine like/Serine with rich PHD protein), and RING TRAF7 finger (TNF domain-2), receptor associatedand TRIM27 factor-7), [8–11] have UHRF2 been (Ubiquitin described. like with PHD and RING finger domain-2), and TRIM27 [8–11] have been described. Figure 1. Schematic illustration of the UbL activation, conjugation and deconjugation cycle. The covalent attachmentFigure 1. Schematic of UbLs to theirillustration substrates of the involves UbL sequentialactivation catalytic, conjugation reactions and that deconjugation initiate with processingcycle. The ofcovalent the UbL attachment precursor byof aUbLs specific to their UbL protease.substrates The involves mature sequential UbL is activated catalytic by reactions an activating that enzymeinitiate (E1)with and processing then transferred of the UbL to aprecursor conjugating by a enzyme specific (E2) UbL that, protease. with the The help mature of a substrate-specific UbL is activated ligaseby an (E3),activating transfer enzyme the activated (E1) and UbL then to transferred the "-amino to residuea conjugating of a Lys enzyme on the target(E2) that, protein with via the a help covalent of a isopeptidesubstrate-specific bond. ligase Additional (E3), tr UbLsansfer can the be activated linked to UbL the to previous the ε-amino one toresidue form chains.of a Lys UbL-specificon the target proteasesprotein via can a reversecovalent the isopeptide modification, bond. supplementing Additional UbLs the cellularcan be linked pools of to free the UbLs.previous The one attachment to form ofchains. a Ub UbL-specific moiety to the proteases N-terminal can Met1reverse or the to anmodi internalfication, Lys supplementing residue of the the previous cellularUb pools (K6, of K11,free k27,K29,K33,K48UbLs. The attachment or K63) of resultsa Ub moiety in the formation to the N-term of topologicallyinal Met1 or di fftoerent an internal poly-Ub Lys chains residue that, of upon the recognitionprevious Ub by (K6, signal K11, transducers k27,K29,K33,K48 contain or dedicated K63) results binding in the domains, formation target of topologically the substrates different various fatespoly-Ub and chains cellular that, functions upon recognition by signal transducers contain dedicated binding domains, target the substrates various fates and cellular functions Ubiquitin is the first recognized and best-known member of the family. The covalent attachment of Ub, ubiquitination,Ubiquitin is the is first mediated recognized by specific and best-known combinations member of E2s and of the E3s family. that promote The covalent the formation attachment of a peptideof Ub, ubiquitination, bond between is the mediated C-terminal by Glyspecific and thecomb N-terminalinations of Met E2s or and the E3s"-amino that promote group of the a Lys formation residue inof thea peptide substrate. bond In between addition the to theC-terminal attachment Gly ofand a singlethe N-terminal Ub to one Met (mono-Ub) or the ε-amino or several group (multi-Ub) of a Lys Lysresidue residues, in the poly-Ub substrate. chains In additi can beon formed to the uponattachment attachment of a single of a new Ub Ub to moietyone (mono-Ub) to Met1 or or Lys6, several 11, 27, 29, 33, 48, or 63 of the first conjugated Ub. In the poly-Ub chain, Ub is usually attached to the same Biomolecules 2020, 10, 1137 3 of 24 (multi-Ub) Lys residues, poly-Ub chains can be formed upon attachment of a new Ub moiety to Met1 Biomolecules 2020, 10, 1137 3 of 24 or Lys6, 11, 27, 29, 33, 48, or 63 of the first conjugated Ub. In the poly-Ub chain, Ub is usually attached to the same Lys residue on each Ub in the chain but mixed-linkage and branched poly-Ub chains may beLys more residue common on each than Ub originally in the chain thought but mixed-linkage[12] (Figure 1). and The branched attachment poly-Ub of Ub chainsor poly-Ub may bechains more generatescommon new than interaction originally thoughtsurfaces [ 12in ]the (Figure modified1).