Assessing ubiquitination of viral proteins: Lessons from flavivirus NS5

Abstract

Ubiquitin (Ub) conjugation to a substrate protein is a widely used cellular mechanism for control of protein stability and function, modulation of signal transduction pathways and antiviral responses. Identification and characterization of ubiquitinated viral proteins is an important step in understanding novel mechanisms of viral protein regulation as well as elucidating cellular antiviral strategies. Here we describe a protocol to easily detect and characterize the ubiquitination status of a viral substrate protein expressed either during infection or ectopically expressed as a fusion with a biotinylatable epitope tag. This tag provides advantages over current immunoprecipitation techniques by making use of the extremely tight biotin–streptavidin interaction. We provide an example of this protocol using the nonstructural protein 5 (NS5) from Langat virus (LGTV), a member of the tick-borne encephalitis virus (TBEV) serocomplex within the Flavivirus genus. Using the protocols outlined here, we describe some of the pitfalls inherent in determination of Ub linkage and demonstrate that NS5 is modified by at least two distinct ubiquitination types, multiubiquitination and K48-linked polyubiquitin chains.

Introduction

The limited size of many virus genomes necessitates efficient strategies to encode and express proteins that perform multiple functions in the viral replication cycle, from genome replication to immune evasion. Viruses achieve this through various mechanisms including utilizing ambisense transcription, transcriptional editing, and encoding for overlapping open reading frames. Following expression, viral proteins can bestow multiple biological functions, in part through the use of reversible post-translational modifications (PTMs). The covalent attachment of the 76 amino acid polypeptide ubiquitin (Ub) is one such PTM that can markedly affect the function, cellular localization, protein–protein interactions or stability of the target protein. Indeed, ubiquitination is involved in most cellular processes ranging from protein degradation and receptor trafficking to innate immunity [1], [2], [3], [4], [5]. Not surprisingly, viruses have evolved strategies to use host processes of ubiquitination to regulate viral proteins for the benefit of viral replication [6], [7], [8], [9], [10], [11]. Conversely, ubiquitination is also used by host antiviral effector molecules as part of innate defenses to accelerate degradation of key viral proteins as a means to restrict viral replication [12], [13]. Increasing evidence suggests viruses have evolved evasion strategies that specifically use or disable Ub-dependent responses through expression of viral Ub-like molecules, Ub ligases, and deubiquitinases (DUBs) [12], [14], [15]. Thus, identifying the Ub conjugation status of viral proteins is an important step in understanding the broader roles of these proteins in virus–host cell interactions.

The impact of Ub on a target protein is determined by the Ub conjugation status. Ub can be attached as a monomer at one (monoubiquitination) or more (multiubiquitination) sites. Ligation usually occurs at internal lysine residues within the substrate, though cysteine, serine, threonine, and terminal amino groups may serve as Ub acceptor residues. These noncanonical acceptor sites are commonly found in viral proteins or are ubiquitinated by viral E3 Ub ligases [15], [16], [17], [18], [19], [20]. Alternatively, a single Ub molecule can act as a substrate for additional molecules to form polyubiquitin chains. The three-dimensional structure of the chain is determined by the linkage of Ub; the carboxy-terminal glycine is linked to one of seven lysine residues integral to Ub (K6, K11, K27, K29, K33, K48, and K63) or to the amino-terminal methionine (M1; termed linear chains) [1], [21]. Both the configuration of Ub conjugation and the selection of the target protein are mediated by E3 Ub ligases that coordinate with E2 Ub conjugation enzymes to transfer activated Ub molecules (Fig. 1A). This process results in the reversible covalent linkage of the 8.5 kDa Ub moiety onto a target protein. As this PTM is of considerable size relative to a phosphorylation or acetylation event, ubiquitination can have dramatic steric and functional effects on target proteins. Like many biological systems, it is getting more difficult to generalize the roles of monoubiquitination or specific polyubiquitin chain formation in determining the fate of the targeted protein [1], [22]. The most commonly associated modification types and associated functions are represented graphically in Fig. 1B. Generally, K48-linked polyubiquitin chains facilitate protein degradation via the proteasome [23], [24] whereas K63-linked chains enable signal transduction by recruiting multi-protein signaling complexes [2], [5], [25]. Monoubiquitination can regulate a wide variety of cellular processes by facilitating protein–protein interactions, altering cellular localization or directing membrane protein endocytosis [26].

The nonstructural protein 5 (NS5) of flaviviruses, including dengue virus, tick-borne encephalitis virus (TBEV) and West Nile virus, is of utmost importance to virus replication owing to the fact that it encodes the viral methyltransferase and RNA-dependent RNA polymerase [27]. It also encodes the major antagonist of type I interferon (IFN) signaling and, in the case of TBEV, is known to interact with at least two pathways associated with degradation, the proteasome and the lysosome [28], [29]. In addition IFN antagonism by dengue virus NS5 is dependent upon the ubiquitin–proteasome system [30]. However, little is known about the precise PTMs that contribute to these processes and almost nothing is known about the ubiquitination status of flavivirus NS5. Therefore, we used NS5 derived from Langat virus (LGTV), a member of the TBEV serogroup, as an example of a multifunctional viral protein to examine its conjugation to Ub and highlight some of the complexities in assessing this critical PTM.