Interplay of the ubiquitin proteasome system and the innate immune response is essential for the replication of infectious bronchitis virus

Abstract

Infectious bronchitis virus (IBV) is the only coronavirus known to infect poultry. The replication and pathogenesis of IBV are poorly understood, mainly because of the unavailability of a robust cell culture system. Here, we report that an active ubiquitin proteasome system (UPS) is necessary for efficient replication of IBV in Vero cells. Synthesis of IBV-specific RNA as well as viral protein is hampered in the presence of chemical inhibitors specific for the UPS. Like other coronaviruses, IBV encodes a papain-like protease (PLpro) that exhibits in vitro deubiquitinase activity in addition to proteolytically processing the replicase polyprotein. Our results show that the IBV PLpro enzyme inhibits the synthesis of interferon beta (IFNβ) in infected chicken embryonic fibroblast (DF-1) cells and that this activity is enhanced in the presence of melanoma differentiation-associated protein 5 (MDA5) and TANK binding kinase 1 (TBK1). IBV PLpro, when overexpressed in DF-1 cells, deubiquitinates MDA5 and TBK1. Both of these proteins, along with other adapter molecules such as MAVS, IKKε, and IRF3, form a signaling cascade for the synthesis of IFNβ. Ubiquitination of MDA5 and TBK1 is essential for their activation, and their deubiquitination by IBV PLpro renders them unable to participate in antiviral signaling. This study shows for the first time that there is cross-talk between the UPS and the innate immune response during IBV infection and that the deubiquitinase activity of IBV PLpro is involved in its activity as an IFN antagonist. This insight will be useful for designing better antivirals targeting the catalytic activity of the IBV PLpro enzyme.

Myricetin exerts its antiviral activity against infectious bronchitis virus by inhibiting the deubiquitinating activity of papain-like protease

“…The RIG-I-like receptors mainly consists of 2 members, retinoic-acid-inducible gene I ( RIG-I ) and melanoma differentiation-associated antigen 5 ( MDA5 ), which can recognize the double-stranded RNA structure of viruses during cytoplasmic replication. Due to the lack of RIG-I in chicken RLRs receptors, therefore, MDA5 becomes the only model receptor for intracytoplasmic virus recognition in chicken cells ( Kong et al, 2015 ; Ojha et al, 2021 ; Zhang et al, 2021 ).…”

“…After MDA5 recognizing the viral RNA structure, the signal will be transmitted to MAVS, and then the expression of type I interferon and pro-inflammatory cytokines will be initiated through IRF7 and NF-κB, respectively ( Nanduri et al, 2013 ; Ojha et al, 2021 ). PLpro, as a crucial protease which is translated in the early stage of IBV infection, can remove the ubiquitin modification of proteins in antiviral signaling pathway through its deubiquitinating activity in the early stage of virus infection, thus blocking the innate immune response of cells ( Nanduri et al, 2013 ; Yu et al, 2017 ; Ojha et al, 2021 ).…”

“…Papain-like protease ( PLpro ) is encoded by the open reading frame 1a, comprising the catalytic domain of nonstructural protein 3 ( nsp3 ) ( Yu et al, 2017 ). IBV PLpro can not only process the polyproteins to play a key role in the process of viral replication, but also act as a deubiquitinating enzyme to block the host innate immune response pathways ( Yu et al, 2017 ; Hartenian et al, 2020 ; Ojha et al, 2021 ). In vitro characterization of PLpro enzyme activity showed that it can recognize and hydrolyze the ubiquitin and ubiquitin-like protein interferon-stimulated gene 15 ( ISG15 ), which both carry the LXGG recognition motif at the C-terminal ( Lim and Liu, 1998 ; Lim et al, 2000 ).…”

“…Due to the dual activities in viral replication and blocking host immune response, PLpro is considered as a potential target for developing antiviral agents against IBV ( Kong et al, 2015 ; Ojha et al, 2021 ). In fact, IBV used to be a virus that was difficult to culture in vitro.…”

Construction, Identification and Analysis of the Interaction Network of African Swine Fever Virus MGF360-9L with Host Proteins

“…Interestingly, most of the target proteins are involved in proteasome, ribosome, spliceosome, Epstein-Barr virus infection, RNA degradation, and the carbon metabolism pathway. The proteasome pathway is closely related to virus infection, for example, an active ubiquitin proteasome system is necessary for efficient replication of infectious bronchitis virus in Vero cells [ 35 , 36 ]. TRIM21 inhibits porcine epidemic diarrhea virus proliferation by proteasomal degradation of the nucleocapsid protein [ 36 ].…”