Abstract
Acanthamoeba polyphaga mimivirus (APMV) is a member of the family of giant viruses, harboring a 1,200 kbp genome within its 700 nm-diameter viral particle. The R214 gene of the APMV genome was recently shown to encode a homologue of the Rab GTPases, molecular switch proteins known to play a pivotal role in the regulation of membrane trafficking that were considered to exist only in eukaryotes. Herein, we report the first crystal structures of GDP- and GTP-bound forms of APMV Rab GTPase, both of which were determined at high resolution. An in-depth structural comparison of APMV Rab with each other and with mammalian Rab homologues led to an atomic-level elucidation of the inactive–active conformational change upon GDP/GTP exchange. APMV Rab GTPase exhibited considerable structural similarity to human Rab5, as previously predicted based on its amino acid sequence. However, it also contains unique structural features differentiating it from mammalian homologues, such as the functional substitution of a phenylalanine residue for the stabilization of the nucleotide’s guanine base.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D (2003) A giant virus in amoebae. Science 299:2033
Ghigo E, Kartenbeck J, Lien P, Pelkmans L, Capo C, Mege JL, Raoult D (2008) Ameobal pathogen mimivirus infects macrophages through phagocytosis. PLoS Pathog 4:e1000087
Khan M, La Scola B, Lepidi H, Raoult D (2007) Pneumonia in mice inoculated experimentally with Acanthamoeba polyphaga mimivirus. Microb Pathog 42:56–61
Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE (2006) Mimivirus and the emerging concept of “giant” virus. Virus Res 117:133–144
Abrahao JS, Dornas FP, Silva LC, Almeida GM, Boratto PV, Colson P, La Scola B, Kroon EG (2014) Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries. Virol J 11:120
Xiao C, Chipman PR, Battisti AJ, Bowman VD, Renesto P, Raoult D, Rossmann MG (2005) Cryo-electron microscopy of the giant Mimivirus. J Mol Biol 353:493–496
Xiao C, Kuznetsov YG, Sun S, Hafenstein SL, Kostyuchenko VA, Chipman PR, Suzan-Monti M, Raoult D, McPherson A, Rossmann MG (2009) Structural studies of the giant mimivirus. PLoS Biol 7:e92
Mutsafi Y, Shimoni E, Shimon A, Minsky A (2013) Membrane assembly during the infection cycle of the giant Mimivirus. PLoS Pathog 9:e1003367
Legendre M, Santini S, Rico A, Abergel C, Claverie JM (2011) Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing. Virol J 8:99
Zade A, Sengupta M, Kondabagil K (2015) Extensive in silico analysis of Mimivirus coded Rab GTPase homolog suggests a possible role in virion membrane biogenesis. Front Microbiol 6:929
Stenmark H (2009) Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol 10:513–525
Bhuin T, Roy JK (2014) Rab proteins: the key regulators of intracellular vesicle transport. Exp Cell Res 328:1–19
Lazar T, Gotte M, Gallwitz D (1997) Vesicular transport: how many Ypt/Rab-GTPases make a eukaryotic cell? Trends Biochem Sci 22:468–472
Zerial M, McBride H (2001) Rab proteins as membrane organizers. Nat Rev Mol Cell Biol 2:107–117
Stroupe C, Brunger AT (2000) Crystal structures of a Rab protein in its inactive and active conformations. J Mol Biol 304:585–598
Schoebel S, Cichy AL, Goody RS, Itzen A (2011) Protein LidA from Legionella is a Rab GTPase supereffector. Proc Natl Acad Sci U S A 108:17945–17950
Murata T, Delprato A, Ingmundson A, Toomre DK, Lambright DG, Roy CR (2006) The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotide-exchange factor. Nat Cell Biol 8:971–977
Tan Y, Arnold RJ, Luo ZQ (2011) Legionella pneumophila regulates the small GTPase Rab1 activity by reversible phosphorylcholination. Proc Natl Acad Sci USA 108:21212–21217
Ku B, Lee KH, Park WS, Yang CS, Ge J, Lee SG, Cha SS, Shao F, Heo WD, Jung JU, Oh BH (2012) VipD of Legionella pneumophila targets activated Rab5 and Rab22 to interfere with endosomal trafficking in macrophages. PLoS Pathog 8:e1003082
Spano S, Gao X, Hannemann S, Lara-Tejero M, Galan JE (2016) A bacterial pathogen targets a host Rab-family GTPase defense pathway with a GAP. Cell Host Microbe 19:216–226
Spano S, Liu X, Galan JE (2011) Proteolytic targeting of Rab29 by an effector protein distinguishes the intracellular compartments of human-adapted and broad-host Salmonella. Proc Natl Acad Sci USA 108:18418–18423
Brumell JH, Scidmore MA (2007) Manipulation of rab GTPase function by intracellular bacterial pathogens. Microbiol Mol Biol Rev 71:636–652
Stein MP, Muller MP, Wandinger-Ness A (2012) Bacterial pathogens commandeer Rab GTPases to establish intracellular niches. Traffic 13:1565–1588
Bucci C, Parton RG, Mather IH, Stunnenberg H, Simons K, Hoflack B, Zerial M (1992) The small GTPase rab5 functions as a regulatory factor in the early endocytic pathway. Cell 70:715–728
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674
Zhu G, Zhai P, Liu J, Terzyan S, Li G, Zhang XC (2004) Structural basis of Rab5-Rabaptin5 interaction in endocytosis. Nat Struct Mol Biol 11:975–983
Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221
Stenmark H, Olkkonen VM (2001) The Rab GTPase family. Genome Biol 2:reviews3007.3001–3007.3007
Khosravi-Far R, Lutz RJ, Cox AD, Conroy L, Bourne JR, Sinensky M, Balch WE, Buss JE, Der CJ (1991) Isoprenoid modification of rab proteins terminating in CC or CXC motifs. Proc Natl Acad Sci USA 88:6264–6268
Hutagalung AH, Novick PJ (2011) Role of Rab GTPases in membrane traffic and cell physiology. Physiol Rev 91:119–149
Mishra A, Eathiraj S, Corvera S, Lambright DG (2010) Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1). Proc Natl Acad Sci USA 107:10866–10871
Wu M, Wang T, Loh E, Hong W, Song H (2005) Structural basis for recruitment of RILP by small GTPase Rab7. EMBO J 24:1491–1501
Hou X, Hagemann N, Schoebel S, Blankenfeldt W, Goody RS, Erdmann KS, Itzen A (2011) A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1. EMBO J 30:1659–1670
Shiba T, Koga H, Shin HW, Kawasaki M, Kato R, Nakayama K, Wakatsuki S (2006) Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1. Proc Natl Acad Sci USA 103:15416–15421
Acknowledgements
We are grateful for the use of the 5C and 7A beamlines at the Pohang Accelerator Laboratory in Korea. This work was supported by the BioNano Health-Guard Research Center funded by the Ministry of Science, ICT, and Future Planning of Korea (MSIP) as the Global Frontier Project (Grant number H-GUARD_2016M3A6B2941317) and supported by the National Research Foundation of Korea funded by the MSIP (Grant number 2015M3A9B5030308). This work was also supported by the Korea Research Institute of Bioscience and Biotechnology Research Initiative Programs for Creative Research and for Disease Target Structural Research.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
On behalf of all authors, the corresponding authors state that there is no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ku, B., You, J.A., Oh, KJ. et al. Crystal structures of two forms of the Acanthamoeba polyphaga mimivirus Rab GTPase. Arch Virol 162, 3407–3416 (2017). https://doi.org/10.1007/s00705-017-3510-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-017-3510-2