Convergent evolution in the mechanisms of ACBD3 recruitment to picornavirus replication sites
Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
31381608
PubMed Central
PMC6695192
DOI
10.1371/journal.ppat.1007962
PII: PPATHOGENS-D-19-00266
Knihovny.cz E-zdroje
- MeSH
- adaptorové proteiny signální transdukční chemie genetika metabolismus MeSH
- fosfotransferasy s alkoholovou skupinou jako akceptorem genetika metabolismus MeSH
- HEK293 buňky MeSH
- interakce hostitele a patogenu * MeSH
- konformace proteinů MeSH
- krystalizace MeSH
- krystalografie rentgenová MeSH
- lidé MeSH
- membránové proteiny chemie genetika metabolismus MeSH
- molekulární modely MeSH
- mutace MeSH
- Picornaviridae fyziologie MeSH
- replikace viru * MeSH
- sekvence aminokyselin MeSH
- sekvenční homologie MeSH
- vazba proteinů MeSH
- virové proteiny chemie genetika metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- ACBD3 protein, human MeSH Prohlížeč
- adaptorové proteiny signální transdukční MeSH
- fosfotransferasy s alkoholovou skupinou jako akceptorem MeSH
- membránové proteiny MeSH
- virové proteiny MeSH
Enteroviruses, members of the family of picornaviruses, are the most common viral infectious agents in humans causing a broad spectrum of diseases ranging from mild respiratory illnesses to life-threatening infections. To efficiently replicate within the host cell, enteroviruses hijack several host factors, such as ACBD3. ACBD3 facilitates replication of various enterovirus species, however, structural determinants of ACBD3 recruitment to the viral replication sites are poorly understood. Here, we present a structural characterization of the interaction between ACBD3 and the non-structural 3A proteins of four representative enteroviruses (poliovirus, enterovirus A71, enterovirus D68, and rhinovirus B14). In addition, we describe the details of the 3A-3A interaction causing the assembly of the ACBD3-3A heterotetramers and the interaction between the ACBD3-3A complex and the lipid bilayer. Using structure-guided identification of the point mutations disrupting these interactions, we demonstrate their roles in the intracellular localization of these proteins, recruitment of downstream effectors of ACBD3, and facilitation of enterovirus replication. These structures uncovered a striking convergence in the mechanisms of how enteroviruses and kobuviruses, members of a distinct group of picornaviruses that also rely on ACBD3, recruit ACBD3 and its downstream effectors to the sites of viral replication.
Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague Czech Republic
Institute of Physics Polish Academy of Sciences Warsaw Poland
Zobrazit více v PubMed
Tapparel C, Siegrist F, Petty TJ, Kaiser L. Picornavirus and enterovirus diversity with associated human diseases. Infect Genet Evol. 2013;14:282–93. 10.1016/j.meegid.2012.10.016 PubMed DOI
Wessels E, Duijsings D, Niu T-K, Neumann S, Oorschot VM, de Lange F, et al. A viral protein that blocks Arf1-mediated COP-I assembly by inhibiting the guanine nucleotide exchange factor GBF1. Dev Cell. 2006;11:191–201. 10.1016/j.devcel.2006.06.005 PubMed DOI
Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. J Virol. 2012;86:3605–16. 10.1128/JVI.06778-11 PubMed DOI PMC
Liao J, Guan Y, Chen W, Shi C, Yao D, Wang F, et al. ACBD3 is required for FAPP2 transferring glucosylceramide through maintaining the Golgi integrity. J Mol Cell Biol. 2018. 10.1093/jmcb/mjy030 PubMed DOI PMC
Sohda M, Misumi Y, Yamamoto A, Yano A, Nakamura N, Ikehara Y. Identification and characterization of a novel Golgi protein, GCP60, that interacts with the integral membrane protein giantin. J Biol Chem. 2001;276:45298–306. 10.1074/jbc.M108961200 PubMed DOI
Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding. mBio. 2013;4:e00098–13. 10.1128/mBio.00098-13 PubMed DOI PMC
Klima M, Tóth DJ, Hexnerova R, Baumlova A, Chalupska D, Tykvart J, et al. Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein. Sci Rep. 2016;6:23641 10.1038/srep23641 PubMed DOI PMC
Lei X, Xiao X, Zhang Z, Ma Y, Qi J, Wu C, et al. The Golgi protein ACBD3 facilitates Enterovirus 71 replication by interacting with 3A. Sci Rep. 2017;7:44592 10.1038/srep44592 PubMed DOI PMC
Hsu N-Y, Ilnytska O, Belov G, Santiana M, Chen Y-H, Takvorian PM, et al. Viral reorganization of the secretory pathway generates distinct organelles for RNA replication. Cell. 2010;141:799–811. 10.1016/j.cell.2010.03.050 PubMed DOI PMC
Mejdrova I, Chalupska D, Plackova P, Mueller C, Sala M, Klima M, et al. Rational design of novel highly potent and selective phosphatidylinositol 4-kinase III beta (PI4KB) inhibitors as broad-spectrum antiviral agents and tools for chemical biology. J Med Chem. 2017;60(1):100–18. 10.1021/acs.jmedchem.6b01465 PubMed DOI
Xiao X, Lei X, Zhang Z, Ma Y, Qi J, Wu C, et al. Enterovirus 3A facilitates viral replication by promoting PI4KB-ACBD3 interaction. J Virol. 2017. 10.1128/JVI.00791-17 PubMed DOI PMC
Arita M. Phosphatidylinositol-4 kinase III beta and oxysterol-binding protein accumulate unesterified cholesterol on poliovirus-induced membrane structure. Microbiol Immunol. 2014;58:239–56. 10.1111/1348-0421.12144 PubMed DOI
Banerjee S, Aponte-Diaz D, Yeager C, Sharma SD, Ning G, Oh HS, et al. Hijacking of multiple phospholipid biosynthetic pathways and induction of membrane biogenesis by a picornaviral 3CD protein. PLoS Pathog. 2018;14(5):e1007086 10.1371/journal.ppat.1007086 PubMed DOI PMC
Sasaki J, Ishikawa K, Arita M, Taniguchi K. ACBD3-mediated recruitment of PI4KB to picornavirus RNA replication sites. EMBO J. 2012;31:754–66. 10.1038/emboj.2011.429 PubMed DOI PMC
Ishikawa-Sasaki K, Sasaki J, Taniguchi K. A complex comprising phosphatidylinositol 4-kinase IIIβ, ACBD3, and Aichi virus proteins enhances phosphatidylinositol 4-phosphate synthesis and is critical for formation of the viral replication complex. J Virol. 2014;88:6586–98. 10.1128/JVI.00208-14 PubMed DOI PMC
McPhail JA, Ottosen EH, Jenkins ML, Burke JE. The molecular basis of Aichi virus 3A protein activation of phosphatidylinositol 4 kinase IIIbeta, PI4KB, through ACBD3. Structure. 2017;25(1):121–31. 10.1016/j.str.2016.11.016 PubMed DOI
Dubankova A, Humpolickova J, Klima M, Boura E. Negative charge and membrane-tethered viral 3B cooperate to recruit viral RNA dependent RNA polymerase 3Dpol. Sci Rep. 2017;7(1):17309 10.1038/s41598-017-17621-6 PubMed DOI PMC
Mesmin B, Bigay J, Moser von Filseck J, Lacas-Gervais S, Drin G, Antonny B. A four-step cycle driven by PI(4)P hydrolysis directs sterol/PI(4)P exchange by the ER-Golgi tether OSBP. Cell. 2013;155:830–43. 10.1016/j.cell.2013.09.056 PubMed DOI
Chung J, Torta F, Masai K, Lucast L, Czapla H, Tanner LB, et al. PI4P/phosphatidylserine countertransport at ORP5- and ORP8-mediated ER-plasma membrane contacts. Science. 2015;349:428–32. 10.1126/science.aab1370 PubMed DOI PMC
Roulin PS, Lötzerich M, Torta F, Tanner LB, van Kuppeveld FJM, Wenk MR, et al. Rhinovirus uses a phosphatidylinositol 4-phosphate/cholesterol counter-current for the formation of replication compartments at the ER-Golgi interface. Cell Host Microbe. 2014;16:677–90. 10.1016/j.chom.2014.10.003 PubMed DOI
Lyoo H, van der Schaar HM, Dorobantu CM, Rabouw HH, Strating JRPM, van Kuppeveld FJM. ACBD3 is an essential pan-enterovirus host factor that mediates the interaction between viral 3A protein and cellular protein PI4KB. mBio. 2019;10(1):e02742–18. 10.1128/mBio.02742-18 PubMed DOI PMC
Strauss DM, Glustrom LW, Wuttke DS. Towards an understanding of the poliovirus replication complex: the solution structure of the soluble domain of the poliovirus 3A protein. J Mol Biol. 2003;330:225–34. 10.1016/s0022-2836(03)00577-1 PubMed DOI
Klima M, Chalupska D, Rozycki B, Humpolickova J, Rezabkova L, Silhan J, et al. Kobuviral non-structural 3A proteins act as molecular harnesses to hijack the host ACBD3 protein. Structure. 2017;25(2):219–30. 10.1016/j.str.2016.11.021 PubMed DOI
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. The FoldX web server: an online force field. Nucleic Acids Res. 2005;33:W382–8. 10.1093/nar/gki387 PubMed DOI PMC
Wessels E, Notebaart RA, Duijsings D, Lanke K, Vergeer B, Melchers WJ, et al. Structure-function analysis of the coxsackievirus protein 3A: identification of residues important for dimerization, viral RNA replication, and transport inhibition. J Biol Chem. 2006;281(38):28232–43. 10.1074/jbc.M601122200 PubMed DOI
Dorobantu CM, van der Schaar HM, Ford LA, Strating JRPM, Ulferts R, Fang Y, et al. Recruitment of PI4KIIIβ to coxsackievirus B3 replication organelles is independent of ACBD3, GBF1, and Arf1. J Virol. 2014;88:2725–36. 10.1128/JVI.03650-13 PubMed DOI PMC
Dorobantu CM, Ford-Siltz LA, Sittig SP, Lanke KHW, Belov GA, van Kuppeveld FJM, et al. GBF1- and ACBD3-independent recruitment of PI4KIIIβ to replication sites by rhinovirus 3A proteins. J Virol. 2015;89:1913–8. 10.1128/JVI.02830-14 PubMed DOI PMC
Esser-Nobis K, Harak C, Schult P, Kusov Y, Lohmann V. Novel perspectives for hepatitis A virus therapy revealed by comparative analysis of hepatitis C virus and hepatitis A virus RNA replication. Hepatology. 2015;62(2):397–408. 10.1002/hep.27847 PubMed DOI PMC
Berryman S, Moffat K, Harak C, Lohmann V, Jackson T. Foot-and-mouth disease virus replicates independently of phosphatidylinositol 4-phosphate and type III phosphatidylinositol 4-kinases. J Gen Virol. 2016;97(8):1841–52. 10.1099/jgv.0.000485 PubMed DOI PMC
Dorobantu CM, Albulescu L, Harak C, Feng Q, van Kampen M, Strating JRPM, et al. Modulation of the host lipid landscape to promote RNA virus replication: the picornavirus encephalomyocarditis virus converges on the pathway used by hepatitis C virus. PLoS Pathog. 2015;11:e1005185 10.1371/journal.ppat.1005185 PubMed DOI PMC
Heinz BA, Vance LM. The antiviral compound enviroxime targets the 3A coding region of rhinovirus and poliovirus. J Virol. 1995;69(7):4189–97. PubMed PMC
De Palma AM, Thibaut HJ, van der Linden L, Lanke K, Heggermont W, Ireland S, et al. Mutations in the nonstructural protein 3A confer resistance to the novel enterovirus replication inhibitor TTP-8307. Antimicrob Agents Chemother. 2009;53(5):1850–7. 10.1128/AAC.00934-08 PubMed DOI PMC
Arita M, Wakita T, Shimizu H. Cellular kinase inhibitors that suppress enterovirus replication have a conserved target in viral protein 3A similar to that of enviroxime. J Gen Virol. 2009;90(Pt 8):1869–79. 10.1099/vir.0.012096-0 PubMed DOI
Arita M, Bigay J. Poliovirus evolution towards independence from the phosphatidylinositol-4 kinase III beta/oxysterol-binding protein family I pathway. ACS Infect Dis. 2019. 10.1021/acsinfecdis.9b00038 PubMed DOI
Greninger AL. Picornavirus—host interactions to construct viral secretory membranes. Prog Mol Biol Transl. 2015;129:189–212. 10.1016/bs.pmbts.2014.10.007 PubMed DOI
Ai HW, Hazelwood KL, Davidson MW, Campbell RE. Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors. Nat Methods. 2008;5(5):401–3. 10.1038/nmeth.1207 PubMed DOI
Kremers GJ, Hazelwood KL, Murphy CS, Davidson MW, Piston DW. Photoconversion in orange and red fluorescent proteins. Nat Methods. 2009;6(5):355–8. 10.1038/nmeth.1319 PubMed DOI PMC
Cole NB, Smith CL, Sciaky N, Terasaki M, Edidin M, Lippincott-Schwartz J. Diffusional mobility of Golgi proteins in membranes of living cells. Science. 1996;273(5276):797–801. 10.1126/science.273.5276.797 PubMed DOI
Mueller U, Darowski N, Fuchs MR, Förster R, Hellmig M, Paithankar KS, et al. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J Synchrotron Radiat. 2012;19:442–9. 10.1107/S0909049512006395 PubMed DOI PMC
Kabsch W. XDS. Acta Crystallogr D. 2010;66:125–32. 10.1107/S0907444909047337 PubMed DOI PMC
Krug M, Weiss MS, Heinemann U, Mueller U. XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS. J Appl Crystallogr. 2012;45:568–72. 10.1107/S0021889812011715 DOI
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr. 2007;40:658–74. 10.1107/S0021889807021206 PubMed DOI PMC
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D. 2010;66:213–21. 10.1107/S0907444909052925 PubMed DOI PMC
Cowtan K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D. 2006;62:1002–11. 10.1107/S0907444906022116 PubMed DOI
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D. 2011;67:235–42. 10.1107/S0907444910045749 PubMed DOI PMC
Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D. 2012;68:352–67. 10.1107/S0907444912001308 PubMed DOI PMC
Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D. 2004;60:2126–32. 10.1107/S0907444904019158 PubMed DOI
The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.
Lanke KH, van der Schaar HM, Belov GA, Feng Q, Duijsings D, Jackson CL, et al. GBF1, a guanine nucleotide exchange factor for Arf, is crucial for coxsackievirus B3 RNA replication. J Virol. 2009;83(22):11940–9. 10.1128/JVI.01244-09 PubMed DOI PMC
Kim YC, Hummer G. Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol. 2008;375(5):1416–33. 10.1016/j.jmb.2007.11.063 PubMed DOI PMC
Rozycki B, Kim YC, Hummer G. SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure. 2011;19(1):109–16. 10.1016/j.str.2010.10.006 PubMed DOI PMC
Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI. OPM: orientations of proteins in membranes database. Bioinformatics. 2006;22(5):623–5. 10.1093/bioinformatics/btk023 PubMed DOI
Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graphics. 1996;14:33–8, 27–8. PubMed
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–802. 10.1002/jcc.20289 PubMed DOI PMC
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998;102:3586–616. 10.1021/jp973084f PubMed DOI
Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B. 2010;114:7830–43. 10.1021/jp101759q PubMed DOI PMC
MacKerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem. 2004;25:1400–15. 10.1002/jcc.20065 PubMed DOI
Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12(1):7–8. 10.1038/nmeth.3213 PubMed DOI PMC
The Present and Future of Virology in the Czech Republic-A New Phoenix Made of Ashes?
Precursors of Viral Proteases as Distinct Drug Targets
Localization of SARS-CoV-2 Capping Enzymes Revealed by an Antibody against the nsp10 Subunit