Table 1.

Protein–protein interaction (PPI) found between autophagy proteins and viral proteins from seven data sets (Coyaud et al., 2018; Scaturro et al., 2018; Shah et al., 2018; Li et al., 2019; Golubeva et al., 2020; Zeng et al., 2020).

Autophagy protein	Autophagy related role	Viral proteins
ACBD5	Pexophagy receptor	NS4A1
AMBRA1	Key regulator of autophagy by modulating the BECN1-PIK3C3 complex	NS17, NS2B7
ATG9A	Supplies membrane for the growing autophagosome	Env7
BNIP3 (NIP3)	Mitophagy receptor	NS51,2
EI24 (EPG4)	Regulates formation of degradative autolysosomes	NS12, NS4B3
LGALS8	Restricts infection by initiating autophagy via interaction with CALCOCO2/NDP52	NS36
MTOR	Key regulator of autophagy through phosphorylation of ULK1, DAP, AMBRA1, and RUBCNL	NS4A1,2
PHB2	Mitophagy receptor	NS2B33, NS4B3
SQSTM1 (p62)	Multiple cargo receptor	NS4B2
STX17	Regulates autophagosome fusion with lysosomes	NS2A7
VCP	Essential for the maturation of ubiquitin-containing autophagosomes and the clearance of ubiquitinated protein by autophagy	NS2B35
WAC	Regulator of autophagy	NS2B6
AUP1	Lipophagy regulator	NS2A4, NS4B3,4
FAM134C	Reticulophagy receptor	NS4A1, NS4B3
RTN3	Reticulophagy receptor	NS4A1
SEC62	Reticulophagy receptor	NS4A2
CALCOCO1	Reticulophagy receptor	NS55
NBR1	Aggrephagy, pexophagy, and xenophagy receptor	NS2A4
VMP1	Required for autophagosome biogenesis	NS4A4
TMEM41B	Required for autophagosome biogenesis	NS4B3

¹Shah et al. (2018) (ZIKV).

²Shah et al. (2018) (DENV).

³Scaturro et al. (2018) (ZIKV),

⁴Coyaud et al. (2018) (ZIKV).

⁵Li et al. (2019) (WNV).

⁶Golubeva et al. (2020) (ZIKV).

⁷Zeng et al. (2020) (ZIKV).

PPI that were found significant by the authors were considered for the search. Approximately, 100 autophagy proteins were probed for interactions based on a list of proteins mentioned in these studies (Galluzzi et al., 2017; Gatica et al., 2018; Gubas and Dikic, 2021).