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Nucleolin Is Essential for Rabbit Hemorrhagic Disease Virus Replication By bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.094185; this version posted May 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 Nucleolin is essential for rabbit hemorrhagic disease virus replication by 3 providing a physical link in replication complex formation 4 5 Jie Zhu1, Qiuhong Miao1, 2, Hongyuan Guo1, Ruibin Qi1, Aoxing Tang1, Dandan Dong1, 6 Jingyu Tang1, Guangzhi Tong1*, Guangqing Liu1* 7 8 1 Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 9 Shanghai, 200241, China; 10 2 Laboratory of Virology, Wageningen University and Research, Wageningen, 6708 PB, The 11 Netherlands; 12 13 *Corresponding author 14 E-mail: [email protected] (GL); [email protected] (GT) 15 16 17 18 19 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.094185; this version posted May 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 22 Abstract 23 Rabbit hemorrhagic disease virus (RHDV) is an important member of the Caliciviridae 24 family and cannot be propagated in vitro, which has greatly impeded progress of 25 investigating its replication mechanism. Construction of an RHDV replicon system has 26 recently provided a platform for exploring RHDV replication in host cells. Here, aided by this 27 replicon system and using two-step affinity purification, we purified the RHDV replicase and 28 identified its associated host factors. We identified rabbit nucleolin (NCL) as a physical link 29 required for the formation of RHDV replication complexes (RCs), by mediating the 30 interaction between other host proteins and the viral RNA replicase, RNA-dependent RNA 31 polymerase (RdRp). We found that RHDV RdRp uses an amino acid (aa) region spanning 32 residues 448–478 to directly interact with NCL’s RNA-recognition motif 2. We also found 33 that the viral p16 protein uses a highly conserved region (35Cys–Ile–Arg–Ala38 or CIRA 34 motif) to specifically bind the N-terminal region of NCL (aa 1–110) and that RHDV p23 uses 35 a specific domain (aa 90–145) to bind NCL’s RNA-recognition motif 1. Disrupting these 36 protein–protein interactions severely weakened viral replication. Furthermore, NCL 37 overexpression or knockdown significantly increased or severely impaired, respectively, 38 RHDV replication. Collectively, these results indicate that the host protein NCL is essential 39 for RHDV replication and plays a key role in the formation of RHDV RCs. The mechanisms 40 by which NCL promotes viral replicase assembly reported here shed light on viral RC 41 biogenesis and may inform antiviral therapies. 42 43 44 45 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.094185; this version posted May 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. NCL is essential for RHDV replication 46 Author summary 47 Rabbit hemorrhagic disease virus (RHDV) is the causative agent of highly contagious 48 and lethal hemorrhagic disease in the European rabbit, but the host factors involved in RHDV 49 replication remain poorly understood. In the present study, we isolated RHDV replication 50 complex (RC) for the first time and identified its main components. We found that nucleolin 51 (NCL) plays a key role in the formation of the RHDV RC. NCL not only interacts with viral 52 replicase (RdRp), it also specifically binds to other important host factors. In addition, we 53 proved that NCL is necessary for RHDV replication because the level of RHDV replication is 54 significantly affected by knocking down the NCL gene in cells. Together, our data suggest 55 that RHDV completes its replication by hijacking NCL to recruit other viral proteins and host 56 factors, thereby assembling the RC of RHDV. 57 Introduction 58 Rabbit hemorrhagic disease virus (RHDV) is the causative agent of rabbit hemorrhagic 59 disease (RHD), which primarily infects the wild and domestic European rabbit (Orcytolagus 60 cuniculus) [1] and is characterized by liver degeneration, diffuse hemorrhaging and high 61 mortality [2,3]. However, the molecular mechanisms responsible for RHDV replication 62 remain poorly understood, mainly due to the lack of a robust cell culture system for 63 propagation of the virus. 64 RHDV is a nonenveloped positive-sense single-stranded RNA virus, which belongs to the 65 family Caliciviridae, genus Lagovirus. RHDV virions contain the genomic RNA (gRNA) and 66 an additional 2.2 kb of subgenomic RNA (sgRNA), which is collinear with the 3′ end of the 67 gRNA [1]. The gRNA of RHDV consists of a positive-sense single-stranded molecule of 68 7,437 nucleotides with a virus-encoded protein, VPg, which is covalently attached to its 5′ 69 end [4,5]. The gRNA also contains two slightly overlapping open reading frames (ORFs) of 7 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.094185; this version posted May 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. NCL is essential for RHDV replication 70 kb (ORF1) and 351 nucleotides (ORF2). ORF1 is translated into a large polyprotein that is 71 cleaved into the major structural protein VP60, the capsid protein, and seven nonstructural 72 proteins: p16, p23, helicase, p29, VPg, protease, and RNA-dependent RNA polymerase 73 (RdRp). ORF2 encodes the minor structural protein VP10 [6-8]. The sgRNA, which only 74 encodes VP60 and VP10, usually contributes to the production of high levels of products 75 required during intermediate and late stages of infection [9]. Flanking the coding regions of 76 RHDV is a 5′ terminal noncoding region of nine nucleotides and a 3′ terminal noncoding 77 region of 59 nucleotides [8]. 78 The function of some of the nonstructural proteins encoded by the genome of 79 caliciviruses has been identified and/or predicted by relying on previous knowledge gathered 80 from members of the closely related Picornaviridae family. For RHDV, two nonstructural 81 proteins might be involved in the replication of viral RNA, a helicase and an RdRp, and a 82 protease is involved in the autoproteolytic processing of the large viral polyprotein encoded 83 by ORF1 [7,10,11]. The genome-binding protein VPg is covalently linked to both genomic 84 and subgenomic RHDV RNAs at the 5’ end. Our previous study suggested that the VPg 85 protein serves as a novel cap substitute during the initiation of RHDV translation [5]; 86 however, the precise function of the RHDV nonstructural proteins (p16, p23, and p29) 87 remains unclear. 88 Following attachment of RHDV to the cell surface, internalization and desencapsidation 89 occur, leading to release of the viral genome into the cytoplasm of the host cell. The virus life 90 cycle then proceeds to translation of the polyprotein precursor encoded by the viral genome 91 through interaction with the host cellular machinery. The gRNA and the sgRNA covalently- 92 linked VPg use the cellular translation machinery, positioning the ribosome at the start codon 93 AUG without ribosome scanning and initiating translation. Posttranslational proteolytic 94 processing by the viral gRNA encoded protease cleaves the polyprotein precursor into the 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.094185; this version posted May 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. NCL is essential for RHDV replication 95 mature nonstructural proteins and, in RHDV, into the capsid protein VP60. The nonstructural 96 proteins, helicase and RdRp, then form a replication complex (RC), synthesizing 97 complementary negative-sense RNA from the gRNA, which is used as a template for the 98 synthesis of gRNA and sgRNA. 99 The positive-strand RNA viruses share a conserved replication mechanism in which viral 100 proteins induce host cell membrane modification to assemble membrane-associated viral RC 101 [12]. Viruses hijack host factors to facilitate this energy-consuming process [13]. However, 102 understanding the detailed molecular mechanism of how viral proteins hijack host factors for 103 RC assembly has been hampered by the lack of a suitable in vitro culture system for RHDV. 104 Identification of replicase-associated host factors and dissection of their roles in RC assembly 105 will shed light on the molecular mechanism of RHDV replication. In 2013, we developed an 106 RHDV replicon system, which has the ability to automatically replicate in RK-13 cells [14]. 107 Construction of this RHDV replicon system has provided a platform for exploring RHDV 108 replication in host cells. In 2017, we successfully constructed mutant RHDV (mRHDV) in 109 RK-13 cells in vitro, which has a specific receptor-recognition motif (Arg-Gly-Asp) on the 110 surface of the capsid protein that is characterized by two aa substitutions. mRHDV is 111 recognized by the intrinsic membrane receptor (integrin ɑ3β1) of RK-13 cells, by which 112 mRHDV gains entry, replicates, and imparts apparent cytopathic effects [15].
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