Archives of Virology (2020) 165:355–366 https://doi.org/10.1007/s00705-019-04490-9 ORIGINAL ARTICLE Structural basis for hijacking of the host ACBD3 protein by bovine and porcine enteroviruses and kobuviruses Miroslav Smola1 · Vladimira Horova1 · Evzen Boura1 · Martin Klima1 Received: 6 August 2019 / Accepted: 31 October 2019 / Published online: 16 December 2019 © Springer-Verlag GmbH Austria, part of Springer Nature 2019 Abstract Picornaviruses infect a wide range of mammals including livestock such as cattle and swine. As with other picornavirus genera such as Aphthovirus, there is emerging evidence of a signifcant economic impact of livestock infections caused by members of the genera Enterovirus and Kobuvirus. While the human-infecting enteroviruses and kobuviruses have been intensively studied during the past decades in great detail, research on livestock-infecting viruses has been mostly limited to the genomic characterization of the viral strains identifed worldwide. Here, we extend our previous studies of the structure and function of the complexes composed of the non-structural 3A proteins of human-infecting enteroviruses and kobuvi- ruses and the host ACBD3 protein and present a structural and functional characterization of the complexes of the following livestock-infecting picornaviruses: bovine enteroviruses EV-E and EV-F, porcine enterovirus EV-G, and porcine kobuvirus AiV-C. We present a series of crystal structures of these complexes and demonstrate the role of these complexes in facilita- tion of viral replication. Introduction The bovine enteroviruses EV-E and EV-F are endemic in cattle populations worldwide. They have been isolated Enteroviruses and kobuviruses are small non-enveloped from cattle with a wide range of clinical signs including positive-sense single-stranded RNA viruses that belong gastrointestinal and respiratory diseases, reproductive dis- to the family Picornaviridae of the order Picornavirales. orders, and infertility [2–4]. The porcine enterovirus EV-G They can infect a wide range of mammals including humans has been isolated from swine faecal samples in Europe, Asia, and livestock such as cattle and swine. Currently, the genus and North America, as well as from wild boars. Their infec- Enterovirus consists of 15 species, Enterovirus A-L and tions may be asymptomatic; however, an association with Rhinovirus A-C, while the genus Kobuvirus consists of six diarrhoea, dermal lesions, pyrexia, or faccid paralysis has species, Aichivirus A-F [1]. In this study, we focus on the occasionally been observed [5–7]. The porcine kobuvirus livestock-infecting enteroviruses and kobuviruses, namely AiV-C has been reported in several European, Asian, and two bovine enteroviruses, enterovirus E (EV-E) and entero- American countries among domestic pigs and wild boars [8, virus F (EV-F), the porcine enterovirus EV-G, and porcine 9]. Infections with this virus have been reported to correlate kobuvirus aichivirus C (AiV-C). with diarrhoea in pigs [10]. Enterovirus and kobuvirus genomes are approximately 7.4 kb and 8.3 kb in length, respectively, and encode single polyproteins. Their open reading frames are fanked by 5’ Handling Editor: Diego G. Diel. and 3’ untranslated regions (5’- and 3’-UTRs). The 5’-UTR contains a cloverleaf-like structure that is indispensable for Miroslav Smola and Vladimira Horova contributed equally. viral replication and an internal ribosome entry site that is * Evzen Boura crucial for viral cap-independent translation. After transla- [email protected] tion, viral polyproteins are cleaved by viral proteases, gener- * Martin Klima ating both structural (VP1–VP4) and non-structural (2A–2C [email protected] and 3A–3D) proteins. In addition, kobuviruses encode a leader protein (Lpro), which is located at the N-terminus of 1 Institute of Organic Chemistry and Biochemistry, Czech the kobuviral polyprotein but is absent in enteroviruses. In Academy of Sciences, Prague, Czech Republic Vol.:(0123456789)1 3 356 M. Smola et al. this study, we focus on the small non-structural 3A protein, these synthetically constructed genes under the control of a which is a critical component of the viral replication com- T7 promoter and inserting the gene encoding the mCherry plex and is responsible for the recruitment of one or more fuorescent protein [21] at the position of the capsid-pro- host factors to the site of viral replication. tein-encoding region by Gibson assembly [22]. Mutations Acyl-CoA-binding domain-containing protein-3 were generated by site-directed mutagenesis using Phusion (ACBD3) is a well-described host protein that is recruited Flash High-Fidelity PCR Master Mix (Thermo Scientifc). to the viral replication site by a direct protein-protein inter- For expression of the EGFP-fused full-length 3A protein action with the viral 3A protein. It is a multifunctional, of enterovirus F2 and its mutants in mammalian cells, the multidomain, Golgi-resident protein [11] that facilitates respective wild-type and mutant 3A-protein-encoding genes replication of all enteroviruses and kobuviruses studied so were recloned into the pEGFP-C1 vector (Clontech) using far [12–18]. The interaction between the viral 3A protein PCR and restriction endonuclease recognition site cloning. and the host ACBD3 protein is mediated by the N-terminal For bacterial expression of the cytoplasmic domains of cytoplasmic domain of the 3A protein and the C-terminal various enteroviral and kobuviral 3A proteins, the respec- Golgi-dynamics domain (GOLD) of ACBD3. In our recent tive 3A-protein-encoding genes were generated directly from studies, we analyzed the structure and function of the com- synthetic oligonucleotides (Sigma) by PCR and subcloned plexes composed of the ACBD3 GOLD domain and the 3A into the pRSFD vector (Novagen) with an N-terminal 6xHis proteins of enteroviruses EV-A to EV-D and kobuviruses tag followed by a GB1 solubility tag and a TEV protease AiV-A and AiV-B [19, 20]. Here, we extend our previous cleavage site using PCR and restriction endonuclease recog- work to the analysis of the complexes formed by the GOLD nition site cloning. For bacterial expression of the GOLD/3A domain of bovine and porcine ACBD3 and the bovine and complexes used for the crystallographic experiments, the porcine enteroviruses EV-E to EV-G and the porcine kobu- respective ACBD3 GOLD-domain-encoding regions were virus AiV-C. subcloned into the second multiple cloning site of this plas- mid using PCR and restriction endonuclease recognition site cloning. Materials and methods All DNA constructs were verifed by sequencing. Plasmids Protein expression and purifcation A human ACBD3-encoding plasmid was kindly provided All recombinant proteins used in this study were bacterially by Carolyn Machamer. To generate plasmids encoding the expressed as fusion proteins with an N-terminal 6x histidine bovine and porcine ACBD3 GOLD domains (correspond- (His6) purifcation tag followed by a GB1 solubility tag and a ing to GenBank accession numbers NP_001178112.1 and TEV protease cleavage site. For the structural analysis of the NP_001009581.1, respectively), the human ACBD3-encod- GOLD/3A complexes, the cytoplasmic domains of the 3A ing plasmid was used as a template. Mutations correspond- proteins, which were N-terminally fused to His 6-GB1-TEV ing to the respective substitutions of the amino acid residues were directly co-expressed with the untagged ACBD3 were introduced by site-directed mutagenesis using Phusion GOLD domains. The proteins were expressed in the E. coli Flash High-Fidelity PCR Master Mix (Thermo Scientifc). BL21 DE3 NiCo bacterial strain (New England Biolabs) in For expression in Escherichia coli, the bovine and porcine autoinduction ZY medium. Bacterial cells were harvested ACBD3 GOLD-domain-encoding regions were cloned into by centrifugation at 5,000 g for 8 min and lysed using a a pRSFD vector (Novagen) with an N-terminal 6xHis tag French press cell disruptor instrument (Thermo) at 1,000 followed by a GB1 solubility tag and a TEV protease cleav- psi in lysis bufer (50 mM Tris-HCl, pH 8, 300 mM NaCl, age site using PCR and restriction endonuclease recognition 3 mM β-mercaptoethanol, 30 mM imidazole, and 10% site cloning. For bacterial expression of the EGFP-GOLD glycerol). The lysate was incubated with HisPur Ni-NTA fusion proteins, the EGFP-encoding sequence was inserted Superfow agarose (Thermo Fisher Scientifc) for 30 min, between the TEV cleavage site and the GOLD-domain- and the agarose beads were then extensively washed with encoding regions. wash bufer (50 mM Tris-HCl pH 8, 300 mM NaCl, 1 mM The genomes of enterovirus F2 (corresponding to Gen- β-mercaptoethanol, and 20 mM imidazole). The proteins of Bank accession no. DQ092795) and enterovirus G1 (corre- interest were eluted with elution bufer (50 mM Tris-HCl, sponding to GenBank accession no. AF363453) lacking the pH 8, 200 mM NaCl, 3 mM β-mercaptoethanol, and 300 mM capsid-protein-encoding regions were generated syntheti- imidazole). cally by GeneArt synthesis (Thermo Scientifc). The pT7- For biochemical analysis of the 3A proteins by micro- EVF2/mCherry and pT7-EVG1/mCherry plasmids for viral scale thermophoresis, the N-terminal His 6-GB1 tags subgenomic replicon assays were generated by subcloning were preserved to increase protein solubility and to avoid 1 3 Complexes of picornaviral 3A proteins with host ACBD3 357 aggregation at the required concentrations. For the crystal- Crystallization and crystallographic analysis lographic analysis of the GOLD/3A complexes, the N-termi- nal His6-GB1 tags were removed using TEV protease. Next, Protein crystals were obtained at 291 K in sitting drops, the proteins were purifed using size-exclusion chromatog- using the vapor difusion method. They were cryoprotected, raphy on a HiLoad 16/60 Superdex 75 prep grade column fash frozen in liquid nitrogen, and analyzed by X-ray crys- (GE Healthcare) in storage bufer (10 mM Tris-HCl, pH tallography. The datasets were collected from single frozen 8, 200 mM NaCl, and 3 mM β-mercaptoethanol).