Differential and convergent utilization of autophagy components by positive-strand RNA viruses

Abstract

Many viruses interface with the autophagy pathway, a highly conserved process for recycling cellular components. For three viral infections in which autophagy constituents are proviral (poliovirus, dengue, and Zika), we developed a panel of knockouts (KOs) of autophagy-related genes to test which components of the canonical pathway are utilized. We discovered that each virus uses a distinct set of initiation components; however, all three viruses utilize autophagy-related gene 9 (ATG9), a lipid scavenging protein, and LC3 (light-chain 3), which is involved in membrane curvature. These results show that viruses use noncanonical routes for membrane sculpting and LC3 recruitment. By measuring viral RNA abundance, we also found that poliovirus utilizes these autophagy components for intracellular growth, while dengue and Zika virus only use autophagy components for post-RNA replication processes. Comparing how RNA viruses manipulate the autophagy pathway reveals new noncanonical autophagy routes, explains the exacerbation of disease by starvation, and uncovers common targets for antiviral drugs.

Manipulation of autophagy by (+) RNA viruses

“…However, among the 30 odd autophagy-related genes, the functional contribution of the individual components in virus infection is far from clear. A recent targeted CRISPR/Cas9 screen uncovered a fairly diverse range of involvement among autophagic components in three +RNA RNA virus infections -PV, DENV and ZIKV [29]. The authors reported that all three viruses employed multiple proteins of the autophagy pathway while bypassing others, and each virus used a unique set of initiation components.…”

The viral replication organelles within cells studied by electron microscopy

“…Due to their complex composition and functions, virus factories could be contemplated as the living state of viruses . Two main pathways have been identified so far as being responsible for viral factory biogenesis: aggresome formation for DNA viruses and autophagy for RNA viruses (Abernathy et al, 2019;Jackson et al, 2005;Kajitani et al, 2013;Wileman, 2007). Fig.…”

The interplay of autophagy and enterovirus

“…Moreover, they found that SQSTM1 was cleaved and digested in a non-canonical manner in poliovirus infected cells [97], similar to the aforementioned CVB3 infected cells [94]. However, Abernathy et al recently reported that depletion of autophagy-related protein 9 (ATG9), ULK1, FIP200 and LC3B undermined poliovirus replication, while knockout of VPS34, Beclin-1 and ATG5 did not affect viral production [99]. They further demonstrated that poliovirus recruited the non-lipid-bound form of LC3 to the remodeled membranes in GFP-LC3-G120A expressing cells, indicating that the canonical PE-linked LC3, an essential form in autophagosome formation, is not required for poliovirus replication [99].…”

“…Poliovirus has been reported to benefit from virus induced autophagy according to several research [5,[96][97][98][99]. Double-membrane autophagy-like vesicles can be observed in poliovirus infected COS-1 cells under electron microscopy [96].…”

“…However, Abernathy et al recently reported that depletion of autophagy-related protein 9 (ATG9), ULK1, FIP200 and LC3B undermined poliovirus replication, while knockout of VPS34, Beclin-1 and ATG5 did not affect viral production [99]. They further demonstrated that poliovirus recruited the non-lipid-bound form of LC3 to the remodeled membranes in GFP-LC3-G120A expressing cells, indicating that the canonical PE-linked LC3, an essential form in autophagosome formation, is not required for poliovirus replication [99]. Although the detailed mechanism of how poliovirus utilizes autophagy network reported from different research teams is not be perfectly consistent, these data do suggest that poliovirus manipulates a noncanonical autophagy pathway to facilitate its propagation, and poliovirus-induced reorganized membranes might not be originated from the autophagosomes.…”