Virology Journal | |
Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus | |
Mark J. van Raaij3  Mária Benkő1  Balázs Harrach1  Abhimanyu K. Singh2  Marta Sanz-Gaitero4  Mónika Z. Ballmann1  Márton Z. Vidovszky1  Thanh H. Nguyen3  | |
[1] Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary;Current address: School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom;Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), calle Darwin 3, Madrid, 28049, Spain;Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland | |
关键词: Ruminants; Isomorphous replacement; Host-cell recognition; Fibre protein; Crystallography; Beta-sandwich; Atadenovirus; Anomalous dispersion; | |
Others : 1224933 DOI : 10.1186/s12985-015-0309-1 |
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received in 2015-03-02, accepted in 2015-05-11, 发布年份 2015 | |
【 摘 要 】
Background
In adenoviruses, primary host cell recognition is generally performed by the head domains of their homo-trimeric fibre proteins. This first interaction is reversible. A secondary, irreversible interaction subsequently takes place via other adenovirus capsid proteins and leads to a productive infection. Although many fibre head structures are known for human mastadenoviruses, not many animal adenovirus fibre head structures have been determined, especially not from those belonging to adenovirus genera other than Mastadenovirus.
Methods
We constructed an expression vector for the fibre head domain from a ruminant atadenovirus, bovine adenovirus 4 (BAdV-4), consisting of amino acids 414–535, expressed the protein in Escherichia coli, purified it by metal affinity and cation exchange chromatography and crystallized it. The structure was solved using single isomorphous replacement plus anomalous dispersion of a mercury derivative and refined against native data that extended to 1.2 Å resolution.
Results
Like in other adenoviruses, the BAdV-4 fibre head monomer contains a beta-sandwich consisting of ABCJ and GHID sheets. The topology is identical to the fibre head of the other studied atadenovirus, snake adenovirus 1 (SnAdV-1), including the alpha-helix in the DG-loop, despite of them having a sequence identity of only 15 %. There are also differences which may have implications for ligand binding. Beta-strands G and H are longer and differences in several surface-loops and surface charge are observed.
Conclusions
Chimeric adenovirus fibres have been used to retarget adenovirus-based anti-cancer and gene therapy vectors. Ovine adenovirus 7 (OAdV-7), another ruminant atadenovirus, is intensively tested as a basis for such a vector. Here, we present the high-resolution atomic structure of the BAdV-4 fibre head domain, the second atadenovirus fibre head structure known and the first of an atadenovirus that infects a mammalian host. Future research should focus on the receptor-binding properties of these fibre head domains.
【 授权许可】
2015 Nguyen et al.; licensee BioMed Central.
【 预 览 】
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20150915140153774.pdf | 2973KB | download | |
Fig. 5. | 179KB | Image | download |
Fig. 4. | 62KB | Image | download |
Fig. 3. | 211KB | Image | download |
Fig. 2. | 26KB | Image | download |
Fig. 1. | 27KB | Image | download |
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【 参考文献 】
- [1]Davison AJ, Benkő M, Harrach B. Genetic content and evolution of adenoviruses. J Gen Virol. 2003; 84(Pt 11):2895-2908.
- [2]Harrach B, Benkő M, Both GW, Brown M, Davison AJ, Echavarría M et al.. Family Adenoviridae. In: Virus taxonomy: classification and nomenclature of viruses. Ninth report of the international committee on taxonomy of viruses. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. Elsevier, New York; 2011: p.125-141.
- [3]Harrach B. Adenoviruses: general features. In Reference Module in Biomedical Sciences. Elsevier (2014), doi:10.1016/B978-0-12-801238-3.02523-X.
- [4]Harrach B. Available adenovirus sequences. http://www.vmri.hu/~harrach/ADENOSEQ.HTM. Accessed 25 Feb 2015.
- [5]Wold WS, Horwitz MS. Adenoviruses. In: Fields virology. 5th edition. Fields BN, Knipe DM, Howley PM, editors. Wolters Kluwer Health/Lippincott Williams & Wilkins, Philadelphia; 2007: p.2395-2436.
- [6]Benkő M. Adenoviruses: pathogenesis. In: Encyclopedia of virology, 5 vols. Third edition, vol.1. Mahy BWJ, Regenmortel MHV, editors. Elsevier, Oxford; 2008: p.24-29.
- [7]San Martin C. Latest insights on adenovirus structure and assembly. Viruses. 2012; 4(5):847-877.
- [8]Pénzes JJ, Menendez-Conejero R, Condezo GN, Ball I, Papp T, Doszpoly A et al.. Molecular characterization of a lizard adenovirus reveals the first atadenovirus with two fiber genes and the first adenovirus with either one short or three long fibers per penton. J Virol. 2014; 88(19):11304-11314.
- [9]Sharma A, Li X, Bangari DS, Mittal SK. Adenovirus receptors and their implications in gene delivery. Virus Res. 2009; 143(2):184-194.
- [10]Wolfrum N, Greber UF. Adenovirus signalling in entry. Cell Microbiol. 2013; 15(1):53-62.
- [11]Ariza L, Giménez-Llort L, Cubizolle A, Pagès G, García-Lareu B, Serratrice N et al.. Central nervous system delivery of helper-dependent canine adenovirus corrects neuropathology and behavior in mucopolysaccharidosis type VII mice. Hum Gene Ther. 2014; 25(3):199-211.
- [12]Arnberg N. Adenovirus receptors: implications for tropism, treatment and targeting. Rev Med Virol. 2009; 19(3):165-178.
- [13]Bachtarzi H, Stevenson M, Fisher K. Cancer gene therapy with targeted adenoviruses. Expert Opin Drug Del. 2008; 5(11):1231-1240.
- [14]Both GW, Cameron F, Collins A, Lockett LJ, Shaw J. Production and release testing of ovine atadenovirus vectors. Methods Mol Med. 2007; 130:69-90.
- [15]Nicklin SA, Wu E, Nemerow GR, Baker AH. The influence of adenovirus fiber structure and function on vector development for gene therapy. Mol Ther. 2005; 12:384-393.
- [16]Tang R, Li K, Wilson M, Both GW, Taylor JA, Young SL. Potent anti-tumor immunity in mice induced by vaccination with an ovine atadenovirus vector. J Immunother. 2012; 35(1):32-41.
- [17]Thacker EE, Timares L, Matthews QL. Strategies to overcome host immunity to adenovirus vectors in vaccine development. Expert Rev Vaccines. 2009; 8(6):761-777.
- [18]Lopez-Gordo E, Podgorski II, Downes N, Alemany R. Circumventing antivector immunity: potential use of nonhuman adenoviral vectors. Hum Gene Ther. 2014; 25(4):285-300.
- [19]Seiradake E, Lortat-Jacob H, Billet O, Kremer EJ, Cusack S. Structural and mutational analysis of human Ad37 and canine adenovirus 2 fiber heads in complex with the D1 domain of coxsackie and adenovirus receptor. J Biol Chem. 2006; 281(44):33704-33716.
- [20]Guardado-Calvo P, Llamas-Saiz AL, Fox GC, Langlois P, van Raaij MJ. Structure of the C-terminal head domain of the fowl adenovirus type 1 long fibre. J Gen Virol. 2007; 88(Pt 9):2407-2416.
- [21]El Bakkouri M, Seiradake E, Cusack S, Ruigrok RW, Schoehn G. Structure of the C-terminal head domain of the fowl adenovirus type 1 short fibre. Virology. 2008; 378(1):169-176.
- [22]Guardado-Calvo P, Muñoz EM, Llamas-Saiz AL, Fox GC, Kahn R, Curiel DT et al.. Crystallographic structure of porcine adenovirus type 4 fiber head and galectin domains. J Virol. 2010; 84(20):10558-10568.
- [23]Singh AK, Menéndez-Conejero R, San Martín C, van Raaij MJ. Crystal structure of the fibre head domain of the atadenovirus snake adenovirus 1. PLoS One. 2014; 9(12):e114373.
- [24]Singh AK, Ballmann MZ, Benkő M, Harrach B, van Raaij MJ. Crystallization of the C-terminal head domain of the fibre protein from a siadenovirus, turkey adenovirus 3. Acta Cryst F. 2013; 69(10):1135-1139.
- [25]Benkő M, Harrach B. A proposal for establishing a new (third) genus within the Adenoviridae family. Arch Virol. 1998; 143:829-837.
- [26]Farkas SL, Benkő M, Élő P, Ursu K, Dán A, Ahne W et al.. Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus. J Gen Virol. 2002; 83(Pt 10):2403-2410.
- [27]Pantelic RS, Lockett LJ, Rothnagel R, Hankamer B, Both GW. Cryoelectron microscopy map of Atadenovirus reveals cross-genus structural differences from human adenovirus. J Virol. 2008; 82(15):7346-7356.
- [28]Ascher JM, Geneva AJ, Ng J, Wyatt JD, Glor RE. Phylogenetic analyses of novel squamate adenovirus sequences in wild-caught Anolis lizards. PLoS One. 2013; 8(4):e60977.
- [29]Ball I, Behncke H, Schmidt V, Geflügel FT, Papp T, Stöhr AC et al.. Partial characterization of new adenoviruses found in lizards. J Zoo Wildl Med. 2014; 45(2):287-297.
- [30]Harrach B, Meehan BM, Benkő M, Adair BM, Todd D. Close phylogenetic relationship between egg drop syndrome virus, bovine adenovirus serotype 7, and ovine adenovirus strain 287. Virology. 1997; 229(1):302-306.
- [31]Harrach B. Reptile adenoviruses in cattle? Acta Vet Hung. 2000; 48(4):485-490.
- [32]Papp T, Fledelius B, Schmidt V, Kaján GL, Marschang RE. PCR-sequence characterization of new adenoviruses found in reptiles and the first successful isolation of a lizard adenovirus. Vet Microbiol. 2009; 134(3–4):233-240.
- [33]Thomson D, Meers J, Harrach B. Molecular confirmation of an adenovirus in brushtail possums (Trichosurus vulpecula). Virus Res. 2002; 83(1–2):189-195.
- [34]To KK, Tse H, Chan WM, Choi GK, Zhang AJ, Sridhar S et al.. A novel psittacine adenovirus identified during an outbreak of avian chlamydiosis and human psittacosis: zoonosis associated with virus-bacterium coinfection in birds. PLoS Negl Trop Dis. 2014; 8(12):e3318.
- [35]Wellehan JFX, Johnson AJ, Harrach B, Benkő M, Pessier AP, Johnson CM et al.. Detection and analysis of six lizard adenoviruses by consensus primer PCR provides further evidence of a reptilian origin for the atadenoviruses. J Virol. 2004; 78(23):13366-13369.
- [36]International Committee on Taxonomy of Viruses. http://www.ictvonline.org. Accessed 25 Feb 2015.
- [37]Evans PS, Benkő M, Harrach B, Letchworth GJ. Sequence, transcriptional analysis, and deletion of the bovine adenovirus type 1 E3 region. Virology. 1998; 244(1):173-185.
- [38]Ursu K, Harrach B, Matiz K, Benkő M. DNA sequencing and analysis of the right-hand part of the genome of the unique bovine adenovirus type 10. J Gen Virol. 2004; 85(Pt 3):593-601.
- [39]Bartha A, Áldásy P. Further two serotypes of bovine adenovirus (serotype 4 and 5). Acta Vet Hung Acad Sci. 1966; 16(1):107-108.
- [40]Élő P, Farkas SL, Dán AL, Kovács GM. The p32K structural protein of the atadenovirus might have bacterial relatives. J Mol Evol. 2003; 56(2):175-180.
- [41]Dán ÁL, Ruzsics ZS, Russell WC, Benkő M, Harrach B. Analysis of the hexon gene sequence of bovine adenovirus type 4 provides further support for a new adenovirus genus (Atadenovirus). J Gen Virol. 1998; 79(6):1453-1460.
- [42]Dán ÁL, Élő P, Harrach B, Zádori Z, Benkő M. Four new inverted terminal repeat sequences from bovine adenoviruses reveal striking differences in the length and content of the ITRs. Virus Genes. 2001; 22(2):175-179.
- [43]Chroboczek J, Ruigrok RW, Cusack S. Adenovirus fiber. Curr Top Microbiol Immunol. 1995; 199(Pt 1):163-200.
- [44]van Raaij MJ, Mitraki A, Lavigne G, Cusack S. A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein. Nature. 1999; 401(6756):935-938.
- [45]Renaut L, Colin M, Leite JP, Benkő M, D’Halluin JC. Abolition of hCAR-dependent cell tropism using fiber knobs of Atadenovirus serotypes. Virology. 2004; 321(2):189-204.
- [46]Geoghegan KF, Dixon HB, Rosner PJ, Hoth LR, Lanzetti AJ, Borzilleri KA et al.. Spontaneous α-N-6-phosphogluconoylation of a “His Tag” in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem. 1999; 267(1):169-184.
- [47]Van Raaij MJ, Louis N, Chroboczek J, Cusack S. Structure of the human adenovirus serotype 2 fibre head domain at 1.5 Å resolution. Virology. 1999; 262(2):333-343.
- [48]Matthews BW. Solvent content of protein crystals. J Mol Biol. 1968; 33(2):491-497.
- [49]Xia D, Henry LJ, Gerard RD, Deisenhofer J. Crystal structure of the receptor-binding domain of adenovirus type 5 fibre protein at 1.7 Å resolution. Structure. 1994; 2(12):1259-1270.
- [50]Chappell JD, Prota AE, Dermody TS, Stehle T. Crystal structure of reovirus attachment protein sigma1 reveals evolutionary relationship to adenovirus fiber. EMBO J. 2002; 21(1–2):1-11.
- [51]Guardado Calvo P, Fox GC, Hermo Parrado XL, Llamas-Saiz AL, Costas C, Martinez-Costas J et al.. Structure of the carboxy-terminal receptor-binding domain of avian reovirus fibre sigmaC. J Mol Biol. 2005; 354(1):137-149.
- [52]Merckel MC, Huiskonen JT, Bamford DH, Goldman A, Tuma R. The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture. Mol Cell. 2005; 18(2):161-170.
- [53]Spinelli S, Campanacci V, Blangy S, Moineau S, Tegoni M, Cambillau C. Modular structure of the receptor binding proteins of Lactococcus lactis phages. The RBP structure of the temperate phage TP901-1. J Biol Chem. 2006; 281(20):14256-14262.
- [54]Spinelli S, Desmyter A, Verrips CT, Dehaard HJ, Moineau S, Cambillau C. Lactococcal bacteriophage p2 receptor-binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses. Nat Struct Mol Biol. 2006; 13(1):85-89.
- [55]Benkő M, Harrach B. Molecular evolution of adenoviruses. Curr Top Microbiol Immunol. 2003; 272:3-35.
- [56]Guardado-Calvo P, Llamas-Saiz AL, Langlois P, van Raaij MJ. Crystallization of the C-terminal head domain of the avian adenovirus CELO long fibre. Acta Cryst F. 2006; 62(5):449-452.
- [57]Singh AK, Menéndez-Conejero R, San Martín C, van Raaij MJ. Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus. Acta Cryst F. 2013; 69(12):1374-1379.
- [58]Dán A, Benkő M, Harrach B. Analysis of the complete DNA sequence of bovine adenovirus type 4 confirms the genome organization characteristic of the proposed new genus atadenovirus. Abstracts of the XII. International Congress of Virology, Paris; 2002.
- [59]Lavinder JJ, Hari SB, Sullivan BJ, Magliery TJ. High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering. J Am Chem Soc. 2009; 131(11):3794-3795.
- [60]Juanhuix J, Gil-Ortiz F, Cuni G, Colldelram C, Nicolas J, Lidon J et al.. Developments in optics and performance at BL13-XALOC, the macromolecular crystallography beamline at the Alba Synchrotron. J Synchrotron Rad. 2014; 21(Pt 4):679-689.
- [61]de Sanctis D, Beteva A, Caserotto H, Dobias F, Gabadinho J, Giraud T et al.. ID29: a high-intensity highly automated ESRF beamline for macromolecular crystallography experiments exploiting anomalous scattering. J Synchrotron Radiat. 2012; 19(Pt 3):455-461.
- [62]Battye TG, Kontogiannis L, Johnson O, Powell H, Leslie AG. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Cryst D. 2011; 67(Pt 4):271-281.
- [63]Evans PR. An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr D Biol Crystallogr. 2011; 67(Pt 4):282-292.
- [64]Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR et al.. Overview of the CCP4 suite and current developments. Acta Cryst D. 2011; 67(Pt 4):235-242.
- [65]Kabsch W. XDS. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 2):125-132.
- [66]Kabsch W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 2):133-144.
- [67]Vagin A, Teplyakov A. Molecular replacement with MOLREP. Acta Cryst D. 2010; 66(Pt 1):22-25.
- [68]Vonrhein C, Blanc E, Roversi P, Bricogne G. Automated structure solution with autoSHARP. Meth Mol Biol. 2007; 364:215-230.
- [69]Sheldrick GM. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Cryst D. 2010; 66(Pt 4):479-485.
- [70]de la Fortelle E, Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Meth Enzymol. 1997; 276:472-494.
- [71]Abrahams JP, Leslie AG. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst D. 1996; 52(Pt 1):30-42.
- [72]Brunger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 1992; 355(6359):472-475.
- [73]Langer G, Cohen SX, Lamzin VS, Perrakis A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc. 2008; 3(7):1171-1179.
- [74]Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501.
- [75]Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA et al.. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2011; 67(Pt 4):355-367.
- [76]Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ et al.. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Cryst D. 2010; 66(Pt 1):12-21.
- [77]Holm L, Rosenstrom P. Dali server: conservation mapping in 3D. Nucl Acids Res. 2010; 38(Web Server issue):W545-W549.
- [78]Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007; 372:774-797.
- [79]Tina KG, Bhadra R, Srinivasan N. PIC: protein interactions calculator. Nucl Acids Res. 2007; 35(Web Server issue):W473-W476.