Structure of the Virulence Factor, SidC Reveals a Unique PI(4)P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome
Legionnaires’ disease is caused by the intracellular bacterial pathogen Legionella pneumophila. Successful infection by this bacterium requires a special secretion system that injects nearly 300 effector proteins into the cytoplasm of host cells. The effector SidC and its paralog SdcA anchor on the Legionella-containing vacuole (LCV) and are important for the recruitment of ER proteins to the LCV. Recent data demonstrated that SidC and SdcA are ubiquitin E3 ligases and that their activity is required for the enrichment of ER proteins and ubiquitin conjugates on the LCV. Here we present the crystal structure of SidC revealing the architecture of a novel PI(4)P-binding module. Our biochemical and cell biological studies highlight key determinants involved in PI(4)P-binding and membrane insertion. Characterization of this novel PI(4)P binding module opens a potential avenue for the development of an accurate in vivo PI(4)P probe. Our data also reveals a distinct regulatory mechanism of the ubiquitin E3 ligase activity of SidC, which is activated by the lipid molecule, PI(4)P. Furthermore, our results suggest that proper spatial localization of SidC to the cytoplasmic surface of the bacterial phagosome through the binding with PI(4)P is crucial to its function.
Vyšlo v časopise:
Structure of the Virulence Factor, SidC Reveals a Unique PI(4)P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome. PLoS Pathog 11(6): e32767. doi:10.1371/journal.ppat.1004965
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1004965
Souhrn
Legionnaires’ disease is caused by the intracellular bacterial pathogen Legionella pneumophila. Successful infection by this bacterium requires a special secretion system that injects nearly 300 effector proteins into the cytoplasm of host cells. The effector SidC and its paralog SdcA anchor on the Legionella-containing vacuole (LCV) and are important for the recruitment of ER proteins to the LCV. Recent data demonstrated that SidC and SdcA are ubiquitin E3 ligases and that their activity is required for the enrichment of ER proteins and ubiquitin conjugates on the LCV. Here we present the crystal structure of SidC revealing the architecture of a novel PI(4)P-binding module. Our biochemical and cell biological studies highlight key determinants involved in PI(4)P-binding and membrane insertion. Characterization of this novel PI(4)P binding module opens a potential avenue for the development of an accurate in vivo PI(4)P probe. Our data also reveals a distinct regulatory mechanism of the ubiquitin E3 ligase activity of SidC, which is activated by the lipid molecule, PI(4)P. Furthermore, our results suggest that proper spatial localization of SidC to the cytoplasmic surface of the bacterial phagosome through the binding with PI(4)P is crucial to its function.
Zdroje
1. Fields BS, Benson RF, Besser RE (2002) Legionella and Legionnaires' disease: 25 years of investigation. Clin Microbiol Rev 15: 506–526. 12097254
2. Nash TW, Libby DM, Horwitz MA (1984) Interaction between the legionnaires' disease bacterium (Legionella pneumophila) and human alveolar macrophages. Influence of antibody, lymphokines, and hydrocortisone. J Clin Invest 74: 771–782. 6470140
3. Zhu W, Banga S, Tan Y, Zheng C, Stephenson R, et al. (2011) Comprehensive identification of protein substrates of the Dot/Icm type IV transporter of Legionella pneumophila. PLoS One 6: e17638. doi: 10.1371/journal.pone.0017638 21408005
4. Segal G, Purcell M, Shuman HA (1998) Host cell killing and bacterial conjugation require overlapping sets of genes within a 22-kb region of the Legionella pneumophila genome. Proc Natl Acad Sci U S A 95: 1669–1674. 9465074
5. Vogel JP, Andrews HL, Wong SK, Isberg RR (1998) Conjugative transfer by the virulence system of Legionella pneumophila. Science 279: 873–876. 9452389
6. Asrat S, de Jesus DA, Hempstead AD, Ramabhadran V, Isberg RR (2014) Bacterial Pathogen Manipulation of Host Membrane Trafficking. Annu Rev Cell Dev Biol.
7. Tilney LG, Harb OS, Connelly PS, Robinson CG, Roy CR (2001) How the parasitic bacterium Legionella pneumophila modifies its phagosome and transforms it into rough ER: implications for conversion of plasma membrane to the ER membrane. J Cell Sci 114: 4637–4650. 11792828
8. Swanson MS, Isberg RR (1995) Association of Legionella pneumophila with the macrophage endoplasmic reticulum. Infect Immun 63: 3609–3620. 7642298
9. Kagan JC, Roy CR (2002) Legionella phagosomes intercept vesicular traffic from endoplasmic reticulum exit sites. Nat Cell Biol 4: 945–954. 12447391
10. Horwitz MA (1983) Formation of a novel phagosome by the Legionnaires' disease bacterium (Legionella pneumophila) in human monocytes. J Exp Med 158: 1319–1331. 6619736
11. Isberg RR, O'Connor TJ, Heidtman M (2009) The Legionella pneumophila replication vacuole: making a cosy niche inside host cells. Nat Rev Microbiol 7: 13–24. doi: 10.1038/nrmicro1967 19011659
12. Stenmark H (2009) Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol 10: 513–525. doi: 10.1038/nrm2728 19603039
13. Machner MP, Isberg RR (2006) Targeting of host Rab GTPase function by the intravacuolar pathogen Legionella pneumophila. Dev Cell 11: 47–56. 16824952
14. Murata T, Delprato A, Ingmundson A, Toomre DK, Lambright DG, et al. (2006) The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotide-exchange factor. Nat Cell Biol 8: 971–977. 16906144
15. Muller MP, Peters H, Blumer J, Blankenfeldt W, Goody RS, et al. (2010) The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b. Science 329: 946–949. doi: 10.1126/science.1192276 20651120
16. Mukherjee S, Liu X, Arasaki K, McDonough J, Galan JE, et al. (2011) Modulation of Rab GTPase function by a protein phosphocholine transferase. Nature 477: 103–106. doi: 10.1038/nature10335 21822290
17. Neunuebel MR, Chen Y, Gaspar AH, Backlund PS Jr., Yergey A, et al. (2011) De-AMPylation of the small GTPase Rab1 by the pathogen Legionella pneumophila. Science 333: 453–456. doi: 10.1126/science.1207193 21680813
18. Tan Y, Luo ZQ (2011) Legionella pneumophila SidD is a deAMPylase that modifies Rab1. Nature 475: 506–509. doi: 10.1038/nature10307 21734656
19. Tan Y, Arnold RJ, Luo ZQ (2011) Legionella pneumophila regulates the small GTPase Rab1 activity by reversible phosphorylcholination. Proc Natl Acad Sci U S A 108: 21212–21217. doi: 10.1073/pnas.1114023109 22158903
20. Ingmundson A, Delprato A, Lambright DG, Roy CR (2007) Legionella pneumophila proteins that regulate Rab1 membrane cycling. Nature 450: 365–369. 17952054
21. Sherwood RK, Roy CR (2013) A Rab-centric perspective of bacterial pathogen-occupied vacuoles. Cell Host Microbe 14: 256–268. doi: 10.1016/j.chom.2013.08.010 24034612
22. Weber S, Wagner M, Hilbi H (2014) Live-cell imaging of phosphoinositide dynamics and membrane architecture during Legionella infection. MBio 5: e00839–00813. doi: 10.1128/mBio.00839-13 24473127
23. Di Paolo G, De Camilli P (2006) Phosphoinositides in cell regulation and membrane dynamics. Nature 443: 651–657. 17035995
24. Weber SS, Ragaz C, Reus K, Nyfeler Y, Hilbi H (2006) Legionella pneumophila exploits PI(4)P to anchor secreted effector proteins to the replicative vacuole. PLoS Pathog 2: e46. 16710455
25. Hsu F, Zhu W, Brennan L, Tao L, Luo ZQ, et al. (2012) Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase. Proc Natl Acad Sci U S A 109: 13567–13572. doi: 10.1073/pnas.1207903109 22872863
26. Toulabi L, Wu X, Cheng Y, Mao Y (2013) Identification and structural characterization of a Legionella phosphoinositide phosphatase. J Biol Chem 288: 24518–24527. doi: 10.1074/jbc.M113.474239 23843460
27. Weber SS, Ragaz C, Hilbi H (2009) The inositol polyphosphate 5-phosphatase OCRL1 restricts intracellular growth of Legionella, localizes to the replicative vacuole and binds to the bacterial effector LpnE. Cell Microbiol 11: 442–460. doi: 10.1111/j.1462-5822.2008.01266.x 19021631
28. Brombacher E, Urwyler S, Ragaz C, Weber SS, Kami K, et al. (2009) Rab1 guanine nucleotide exchange factor SidM is a major phosphatidylinositol 4-phosphate-binding effector protein of Legionella pneumophila. J Biol Chem 284: 4846–4856. doi: 10.1074/jbc.M807505200 19095644
29. Hubber A, Arasaki K, Nakatsu F, Hardiman C, Lambright D, et al. (2014) The machinery at endoplasmic reticulum-plasma membrane contact sites contributes to spatial regulation of multiple Legionella effector proteins. PLoS Pathog 10: e1004222. doi: 10.1371/journal.ppat.1004222 24992562
30. Schoebel S, Blankenfeldt W, Goody RS, Itzen A (2010) High-affinity binding of phosphatidylinositol 4-phosphate by Legionella pneumophila DrrA. EMBO Rep 11: 598–604. doi: 10.1038/embor.2010.97 20616805
31. Del Campo CM, Mishra AK, Wang YH, Roy CR, Janmey PA, et al. (2014) Structural basis for PI(4)P-specific membrane recruitment of the Legionella pneumophila effector DrrA/SidM. Structure 22: 397–408. doi: 10.1016/j.str.2013.12.018 24530282
32. Ragaz C, Pietsch H, Urwyler S, Tiaden A, Weber SS, et al. (2008) The Legionella pneumophila phosphatidylinositol-4 phosphate-binding type IV substrate SidC recruits endoplasmic reticulum vesicles to a replication-permissive vacuole. Cell Microbiol 10: 2416–2433. doi: 10.1111/j.1462-5822.2008.01219.x 18673369
33. Horenkamp FA, Mukherjee S, Alix E, Schauder CM, Hubber AM, et al. (2014) Legionella pneumophila Subversion of Host Vesicular Transport by SidC Effector Proteins. Traffic.
34. Hsu F, Luo X, Qiu J, Teng YB, Jin J, et al. (2014) The Legionella effector SidC defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling. Proc Natl Acad Sci U S A 111: 10538–10543. doi: 10.1073/pnas.1402605111 25006264
35. Gazdag EM, Schobel S, Shkumatov AV, Goody RS, Itzen A (2014) The structure of the N-terminal domain of the Legionella protein SidC. J Struct Biol.
36. Luo ZQ, Isberg RR (2004) Multiple substrates of the Legionella pneumophila Dot/Icm system identified by interbacterial protein transfer. Proc Natl Acad Sci U S A 101: 841–846. 14715899
37. Lin DY, Diao J, Chen J (2012) Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions. Proc Natl Acad Sci U S A 109: 1925–1930. doi: 10.1073/pnas.1115025109 22308380
38. Verdecia MA, Joazeiro CA, Wells NJ, Ferrer JL, Bowman ME, et al. (2003) Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase. Mol Cell 11: 249–259. 12535537
39. Horenkamp FA, Mukherjee S, Alix E, Schauder CM, Hubber AM, et al. (2014) Legionella pneumophila subversion of host vesicular transport by SidC effector proteins. Traffic 15: 488–499. doi: 10.1111/tra.12158 24483784
40. Kamadurai HB, Souphron J, Scott DC, Duda DM, Miller DJ, et al. (2009) Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Mol Cell 36: 1095–1102. doi: 10.1016/j.molcel.2009.11.010 20064473
41. Matsuoka K, Schekman R (2000) The use of liposomes to study COPII- and COPI-coated vesicle formation and membrane protein sorting. Methods 20: 417–428. 10720463
42. Cho W, Stahelin RV (2005) Membrane-protein interactions in cell signaling and membrane trafficking. Annu Rev Biophys Biomol Struct 34: 119–151. 15869386
43. Moravcevic K, Oxley CL, Lemmon MA (2012) Conditional peripheral membrane proteins: facing up to limited specificity. Structure 20: 15–27. doi: 10.1016/j.str.2011.11.012 22193136
44. Balla A, Tuymetova G, Tsiomenko A, Varnai P, Balla T (2005) A plasma membrane pool of phosphatidylinositol 4-phosphate is generated by phosphatidylinositol 4-kinase type-III alpha: studies with the PH domains of the oxysterol binding protein and FAPP1. Mol Biol Cell 16: 1282–1295. 15635101
45. Dowler S, Currie RA, Campbell DG, Deak M, Kular G, et al. (2000) Identification of pleckstrin-homology-domain-containing proteins with novel phosphoinositide-binding specificities. Biochem J 351: 19–31. 11001876
46. Hammond GR, Machner MP, Balla T (2014) A novel probe for phosphatidylinositol 4-phosphate reveals multiple pools beyond the Golgi. J Cell Biol 205: 113–126. doi: 10.1083/jcb.201312072 24711504
47. Yagisawa H, Hirata M, Kanematsu T, Watanabe Y, Ozaki S, et al. (1994) Expression and characterization of an inositol 1,4,5-trisphosphate binding domain of phosphatidylinositol-specific phospholipase C-delta 1. J Biol Chem 269: 20179–20188. 8051106
48. Watzele G, Bachofner R, Berger EG (1991) Immunocytochemical localization of the Golgi apparatus using protein-specific antibodies to galactosyltransferase. Eur J Cell Biol 56: 451–458. 1724963
49. VanRheenen SM, Luo ZQ, O'Connor T, Isberg RR (2006) Members of a Legionella pneumophila family of proteins with ExoU (phospholipase A) active sites are translocated to target cells. Infect Immun 74: 3597–3606. 16714592
50. Dorer MS, Kirton D, Bader JS, Isberg RR (2006) RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics. PLoS Pathog 2: e34. 16652170
51. Liu Y, Luo ZQ (2007) The Legionella pneumophila effector SidJ is required for efficient recruitment of endoplasmic reticulum proteins to the bacterial phagosome. Infect Immun 75: 592–603. 17101649
52. Singer AU, Rohde JR, Lam R, Skarina T, Kagan O, et al. (2008) Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases. Nat Struct Mol Biol 15: 1293–1301. doi: 10.1038/nsmb.1511 18997778
53. Graham TR, Burd CG (2011) Coordination of Golgi functions by phosphatidylinositol 4-kinases. Trends Cell Biol 21: 113–121. doi: 10.1016/j.tcb.2010.10.002 21282087
54. D'Angelo G, Vicinanza M, Di Campli A, De Matteis MA (2008) The multiple roles of PtdIns(4)P—not just the precursor of PtdIns(4,5)P2. J Cell Sci 121: 1955–1963. doi: 10.1242/jcs.023630 18525025
55. Roy A, Levine TP (2004) Multiple pools of phosphatidylinositol 4-phosphate detected using the pleckstrin homology domain of Osh2p. J Biol Chem 279: 44683–44689. 15271978
56. Godi A, Di Campli A, Konstantakopoulos A, Di Tullio G, Alessi DR, et al. (2004) FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns(4)P. Nat Cell Biol 6: 393–404. 15107860
57. He J, Scott JL, Heroux A, Roy S, Lenoir M, et al. (2011) Molecular basis of phosphatidylinositol 4-phosphate and ARF1 GTPase recognition by the FAPP1 pleckstrin homology (PH) domain. J Biol Chem 286: 18650–18657. doi: 10.1074/jbc.M111.233015 21454700
58. Levine TP, Munro S (2002) Targeting of Golgi-specific pleckstrin homology domains involves both PtdIns 4-kinase-dependent and-independent components. Curr Biol 12: 695–704. 12007412
59. Rameh LE, Arvidsson A, Carraway KL 3rd, Couvillon AD, Rathbun G, et al. (1997) A comparative analysis of the phosphoinositide binding specificity of pleckstrin homology domains. J Biol Chem 272: 22059–22066. 9268346
60. Zhu Y, Hu L, Zhou Y, Yao Q, Liu L, et al. (2010) Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA. Proc Natl Acad Sci U S A 107: 4699–4704. doi: 10.1073/pnas.0914231107 20176951
61. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307–326.
62. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33: 491–497. 5700707
63. Trapani S, Navaza J (2008) AMoRe: classical and modern. Acta Crystallogr D Biol Crystallogr 64: 11–16. 18094462
64. Collaborative Computational Project N (1994) The CCP4 suite: programs for protein crystallography. Acta Cryst D: 760–763.
65. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132. 15572765
66. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240–255. 15299926
67. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283–291.
68. Berger KH, Isberg RR (1993) Two distinct defects in intracellular growth complemented by a single genetic locus in Legionella pneumophila. Mol Microbiol 7: 7–19. 8382332
69. Conover GM, Derre I, Vogel JP, Isberg RR (2003) The Legionella pneumophila LidA protein: a translocated substrate of the Dot/Icm system associated with maintenance of bacterial integrity. Mol Microbiol 48: 305–321. 12675793
70. Xu L, Shen X, Bryan A, Banga S, Swanson MS, et al. (2010) Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector. PLoS Pathog 6: e1000822. doi: 10.1371/journal.ppat.1000822 20333253
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2015 Číslo 6
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- HIV Latency Is Established Directly and Early in Both Resting and Activated Primary CD4 T Cells
- A 21st Century Perspective of Poliovirus Replication
- Battling Phages: How Bacteria Defend against Viral Attack
- Adenovirus Tales: From the Cell Surface to the Nuclear Pore Complex