Structural insight into African swine fever virus I73R protein reveals it as a Z‐DNA binding protein

Abstract

African Swine Fever (ASF) is a highly contagious viral haemorrhagic disease of swine, leading to enormous economic losses in the swine industry. However, vaccines and drugs to treat ASF have yet to be developed. African swine fever virus (ASFV) encodes more than 150 proteins, but 50% of them have unknown functions. Here, we present the crystal structure of the ASFV I73R protein at a resolution of 2.0 Å. Similar search tools based solely on amino acid sequence shows that it has no relationships to any proteins of known function. Interestingly, the overall structure of the I73R protein shares a winged helix‐turn‐helix fold, structural similarity with the Z‐DNA binding domain (Zα). In accordance with this result, the I73R is capable of binding to a CpG repeats DNA duplex, which has a high propensity for forming Z‐DNA during the DNA binding assays. In addition, the I73R protein was shown to be expressed at both early and late stages of ASFV post‐infection in PAM cells as an 8.9 kDa protein. Immunofluorescence studies revealed that the I73R protein is expressed in the nucleus at early times post‐infection and gradually translocated from the nucleus to the cytoplasm. Taken together, these data indicate that the I73R could be a member of Zα family that is important in host–pathogen interaction, which paves the way for the design of inhibitors to target this severe pathogen. Further exploring the biological role of I73R during ASFV infection in vitro and in vivo will provide new clues for development of new antiviral strategies.

Structure and function of African swine fever virus proteins: Current understanding

“…Key residues of I73R protein are highly conserved in other Zα domain proteins, and behave similarly to those of other Zα domain-containing proteins such as ADAR1, PKZ, and DAI (Ha et al, 2008(Ha et al, , 2009de Rosa et al, 2013). As a member of the Zα family with the ability to bind Z-DNA, I73R protein may be involved in the process of immune evasion (Sun et al, 2022). I73R protein has also been shown to inhibit host gene expression and to play an important role in host-pathogen interactions and nuclear organization during the initial phase of ASFV replication (Sun et al, 2022).…”

“…This protein has no homology with any known or other functionally identified protein sequence. I73R protein has a classical α/β architecture wherein three α-helices form the core of the domain, and helices 2 and 3 form the helix-turn-helix unit (Sun et al, 2022). I73R protein shares structural similarity with Z-DNA-binding domains (Zα), which are specific for the left-handed conformation of nucleic acid duplexes of DNA, DNA/RNA hybrids, and RNA (Lee et al, 2016).…”

Z-RNA and the Flipside of the SARS Nsp13 Helicase: Is There a Role for Flipons in Coronavirus-Induced Pathology?

“…Z-DNA and Z-RNA are recognized in a conformation specific manner by proteins containing the Za domain, which was first discovered in the dsRNA editing enzyme ADAR1 (17). The Za domain is also found in many other proteins, including ZBP1 and virally encoded proteins like vaccinia virus E3 (18) and African swine fever virus (19). Interaction between Za proteins regulates cell death pathways (20,21) (Figure 1B).…”

Z-RNA and the flipside of the SARS Nsp13 helicase

“…Z-DNA and Z-RNA are recognized in a conformation specific manner by proteins containing the Zα domain, which was first discovered in the dsRNA editing enzyme ADAR1 [17]. The Zα domain is also found in many other proteins, including ZBP1 and virally encoded proteins like vaccinia virus E3 [18] and African swine fever virus [19]. Interaction between Zα proteins regulates cell death pathways [20; 21] (Figure 1B).…”

“…The Zα domain is also found in many other proteins, including ZBP1 and virally encoded proteins like vaccinia virus E3 [18] and African swine fever virus [19]. Interaction between Zα proteins regulates cell death pathways [20; 21] (Figure 1B).…”