Hepatitis D virus (HDV) encodes two proteins, the 24-kDa small delta antigen (S-HDAg) and 27-kDa large delta antigen (L-HDAg) in its single open reading frame. Both of them had been identified as nuclear phosphoproteins. Moreover, the phosphorylated form of S-HDAg was shown to be important for HDV replication. However, the kinase responsible for S-HDAg phosphorylation remains unknown. Therefore, we employed an ingel kinase assay to search candidate kinases and indeed identified a kinase with a molecular mass of about 68 kDa. Much evidence demonstrated this kinase to be the double-stranded RNA-activated kinase, PKR. The immunoprecipitated endogenous PKR was sufficient to catalyze S-HDAg phosphorylation, and the kinase activity disappeared in the PKR-depleted cell lysate. The S-HDAg and PKR could be co-immunoprecipitated together, and both of them co-located in the nucleolus. The LC/MS/MS analysis revealed that the serine 177, serine 180, and threonine 182 of S-HDAg were phosphorylated by PKR in vitro. This result was consistent with previous phosphoamino acid analysis indicating that serine and threonine were phosphorylation targets in S-HDAg. Furthermore, serine 177 was also shown to be the predominant phosphorylation site for S-HDAg purified the from cell line. In dominant negative PKR-transfected cells, the level of phosphorylated S-HDAg was suppressed, but replication of HDV was enhanced. Other than human immunodeficiency virus type 1 trans-activating protein (Tat), S-HDAg is another viral protein phosphorylated by PKR that may regulates HDV replication and viral response to interferon therapy.Hepatitis delta virus (HDV) 1 is the satellite virus of hepatitis B virus (1, 2), since it requires the hepatitis B virus envelope surface antigen (HBsAg) for viral particle assembly (3-5). Upon superinfection or co-infection with hepatitis B virus, HDV may cause fulminant hepatitis and progressive chronic liver disease (6, 7). The genome of HDV is a circular, single-stranded RNA that resembles the structure of plant viroid (8, 9). HDV contains the ribozyme domains for self-cleavage and self-ligation in both genomic and antigenomic strands of RNA (10, 11). Similar to viroid replication, HDV undergoes a double rolling circle scheme. However, different from viroids, HDV encodes two proteins translated from the same mRNA, small delta antigen (S-HDAg) and large delta antigen (L-HDAg) (12, 13). This viral mRNA is responsible for S-HDAg production. LHDAg is translated from the same open reading frame through a specific RNA editing process by which the UAG amber termination codon of S-HDAg was converted to UGG tryptophan codon and an additional 19 amino acids were made (14,15). This adenosine-to-inosine RNA editing is catalyzed by doublestranded RNA adenosine deaminase (15, 16). Although both forms of delta antigens (HDAg) share an identical N-terminal 194 amino acids, their functions are quite different. The SHDAg is essential for viral replication, whereas L-HDAg inhibits replication and is required for viral assembly (17-19...