A unique DNA-binding mode of African swine fever virus AP endonuclease

Yiqing Chen,Jianhua Gan,Qiyao Wang,Xi Chen,Yijun Gu,Yangyang Li,Qi Huang,Yong-Zhen Zhang,Jinbiao Ma,Hehua Liu,Jixi Li,Yanqing Gao,Zhiwei Shao,Chun Yang

doi:10.1038/s41421-020-0146-2

Abstract

African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. ASFV is primarily replicated in the cytoplasm of pig macrophages, which is oxidative and caused constant damage to ASFV genome. ASFV AP endonuclease (AsfvAP) catalyzes DNA cleavage reaction at the abasic site and is a key enzyme of ASFV base excision repair (BER) system. Although it plays an essential role in ASFV survival in host cells, the basis underlying substrate binding and cleavage by AsfvAP remains unclear. Here, we reported the structural and functional studies of AsfvAP, showing that AsfvAP adopts a novel DNA-binding mode distinct from other APs. AsfvAP possesses many unique structural features, including one narrower nucleotide-binding pocket at the active site, the C16–C20 disulfide bond-containing region, and histidine-rich loop. As indicated by our mutagenesis, in vitro binding and cleavage assays, these features are important for AsfvAP to suit the acidic and oxidative environment. Owing to their functional importance, these unique features could serve as targets for designing small molecule inhibitors that could disrupt the repair process of ASFV genome and help fight against this deadly virus in the future.

Highlights

African swine fever virus (ASFV) is a large doublestranded DNA virus, and the only member of the Asfarviridae family
Different from ASFV AP endonuclease (AsfvAP), the cleavage assay results suggested that E. Coli Nfo (EcNfo) prefers basic condition for its AP endonuclease activity
ASFV has caused a substantial loss in agricultural industry in the world over the past century, no vaccine or other useful treatment against this virus has been developed so far

Summary

Introduction

African swine fever virus (ASFV) is a large doublestranded DNA (dsDNA) virus, and the only member of the Asfarviridae family. ASFV is highly contagious[1] and can cause lethal disease in pigs[2]. ASFV has been found in many countries of the world and has caused a substantial loss in agricultural industry since its first report in Kenya in 19213. To prevent a nationwide epidemic, more than 500,000 pigs were killed in Cuba in 1971, which was labeled the “most alarming event” of 1971 by the United Nations Food and Agricultural Organization[4]. In 2011, the virus killed over 300,000 pigs in the Russian Federation region. Since the first report in August 20185, ASFV has been reported in over 30 provinces in China, caused huge economic losses, as well as immediate pork shortage. Due to its serious threat to the agricultural industry, ASFV has attracted tremendous attention from governments and scientists in the past decade in the world. No vaccine or other useful treatment against this virus has been developed so far[6]

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Conclusion