A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins

English version České info

Type IV secretion systems (T4SS) are used by Gram-negative bacteria to translocate protein and DNA substrates across the cell envelope and into target cells. Translocation across the outer membrane is achieved via a ringed tetradecameric outer membrane complex made up of a small VirB7 lipoprotein (normally 30 to 45 residues in the mature form) and the C-terminal domains of the VirB9 and VirB10 subunits. Several species from the genera of Xanthomonas phytopathogens possess an uncharacterized type IV secretion system with some distinguishing features, one of which is an unusually large VirB7 subunit (118 residues in the mature form). Here, we report the NMR and 1.0 Å X-ray structures of the VirB7 subunit from Xanthomonas citri subsp. citri (VirB7_XAC2622) and its interaction with VirB9. NMR solution studies show that residues 27–41 of the disordered flexible N-terminal region of VirB7_XAC2622 interact specifically with the VirB9 C-terminal domain, resulting in a significant reduction in the conformational freedom of both regions. VirB7_XAC2622 has a unique C-terminal domain whose topology is strikingly similar to that of N0 domains found in proteins from different systems involved in transport across the bacterial outer membrane. We show that VirB7_XAC2622 oligomerizes through interactions involving conserved residues in the N0 domain and residues 42–49 within the flexible N-terminal region and that these homotropic interactions can persist in the presence of heterotropic interactions with VirB9. Finally, we propose that VirB7_XAC2622 oligomerization is compatible with the core complex structure in a manner such that the N0 domains form an extra layer on the perimeter of the tetradecameric ring.

Vyšlo v časopise: A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins. PLoS Pathog 7(5): e32767. doi:10.1371/journal.ppat.1002031
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1002031

Souhrn

Zdroje

1. TsengTTTylerBMSetubalJC 2009 Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol 9 Suppl 1 S2

2. EconomouAChristiePJFernandezRCPalmerTPlanoGV 2006 Secretion by numbers: Protein traffic in prokaryotes. Mol Microbiol 62 308 319

3. JuhasMCrookDWHoodDW 2008 Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence. Cell Microbiol 10 2377 2386

4. BackertSMeyerTF 2006 Type IV secretion systems and their effectors in bacterial pathogenesis. Curr Opin Microbiol 9 207 217

5. NinioSRoyCR 2007 Effector proteins translocated by Legionella pneumophila: strength in numbers. Trends Microbiol 15 372 380

6. ShrivastavaRMillerJF 2009 Virulence factor secretion and translocation by Bordetella species. Curr Opin Microbiol 12 88 93

7. VothDEHeinzenRA 2009 Coxiella type IV secretion and cellular microbiology. Curr Opin Microbiol 12 74 80

8. DehioC 2008 Infection-associated type IV secretion systems of Bartonella and their diverse roles in host cell interaction. Cell Microbiol 10 1591 1598

9. CelliJ 2006 Surviving inside a macrophage: the many ways of Brucella. Res Microbiol 157 93 98

10. BackertSSelbachM 2008 Role of type IV secretion in Helicobacter pylori pathogenesis. Cell Microbiol 10 1573 1581

11. McCullenCABinnsAN 2006 Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer. Annu Rev Cell Dev Biol 22 101 127

12. ChristiePJAtmakuriKKrishnamoorthyVJakubowskiSCascalesE 2005 Biogenesis, architecture, and function of bacterial type IV secretion systems. Annu Rev Microbiol 59 451 485

13. BruningsAMGabrielDW 2003 Xanthomonas citri: breaking the surface. Mol Plant Pathol 4 141 157

14. da SilvaACFerroJAReinachFCFarahCSFurlanLR 2002 Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417 459 463

15. AlegriaMCSouzaDPAndradeMODocenaCKhaterL 2005 Identification of new protein-protein interactions involving the products of the chromosome- and plasmid-encoded type IV secretion loci of the phytopathogen Xanthomonas axonopodis pv. citri. J Bacteriol 187 2315 2325

16. QianWJiaYRenSXHeYQFengJX 2005 Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res 15 757 767

17. VorholterFJSchneikerSGoesmannAKrauseLBekelT 2008 The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J Biotechnol 134 33 45

18. PierettiIRoyerMBarbeVCarrereSKoebnikR 2009 The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics 10 616

19. StudholmeDJKemenEMacleanDSchornackSArituaV 2010 Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt. FEMS Microbiol Lett 310 182 192

20. CrossmanLCGouldVCDowJMVernikosGSOkazakiA 2008 The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol 9 R74

21. RoccoFDe GregorioEColonnaBDi NoceraPP 2009 Stenotrophomonas maltophilia genomes: a start-up comparison. Int J Med Microbiol 299 535 546

22. ThiemeFKoebnikRBekelTBergerCBochJ 2005 Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 187 7254 7266

23. LeeBMParkYJParkDSKangHWKimJG 2005 The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res 33 577 586

24. OchiaiHInoueVTakeyaMSasakiAKakuH 2005 Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Jpn Agric Res Q 39 275 287

25. SalzbergSLSommerDDSchatzMCPhillippyAMRabinowiczPD 2008 Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 9 204

26. MoreiraLMAlmeidaNFJrPotnisNDigiampietriLAAdiSS 2010 Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. BMC Genomics 11 238

27. El YacoubiBBruningsAMYuanQShankarSGabrielDW 2007 In planta horizontal transfer of a major pathogenicity effector gene. Appl Environ Microbiol 73 1612 1621

28. FernandezDDangTASpudichGMZhouXRBergerBR 1996 The Agrobacterium tumefaciens virB7 gene product, a proposed component of the T-complex transport apparatus, is a membrane-associated lipoprotein exposed at the periplasmic surface. J Bacteriol 178 3156 3167

29. SchroderGLankaE 2005 The mating pair formation system of conjugative plasmids-A versatile secretion machinery for transfer of proteins and DNA. Plasmid 54 1 25

30. SpudichGMFernandezDZhouXRChristiePJ 1996 Intermolecular disulfide bonds stabilize VirB7 homodimers and VirB7/VirB9 heterodimers during biogenesis of the Agrobacterium tumefaciens T-complex transport apparatus. Proc Natl Acad Sci U S A 93 7512 7517

31. DasAAndersonLBXieYH 1997 Delineation of the interaction domains of Agrobacterium tumefaciens VirB7 and VirB9 by use of the yeast two-hybrid assay. J Bacteriol 179 3404 3409

32. WardDVDraperOZupanJRZambryskiPC 2002 Peptide linkage mapping of the Agrobacterium tumefaciens vir-encoded type IV secretion system reveals protein subassemblies. Proc Natl Acad Sci U S A 99 11493 11500

33. FronzesRSchaferEWangLSaibilHROrlovaEV 2009 Structure of a type IV secretion system core complex. Science 323 266 268

34. ChandranVFronzesRDuquerroySCroninNNavazaJ 2009 Structure of the outer membrane complex of a type IV secretion system. Nature 462 1011 1015

35. BaylissRHarrisRCoutteLMonierAFronzesR 2007 NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system. Proc Natl Acad Sci U S A 104 1673 1678

36. CaoTBSaierMHJr 2001 Conjugal type IV macromolecular transfer systems of Gram-negative bacteria: organismal distribution, structural constraints and evolutionary conclusions. Microbiology 147 3201 3214

37. HerrmannTGuntertPWuthrichK 2002 Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319 209 227

38. BaxA 2003 Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 12 1 16

39. CornilescuGMarquardtJLOttigerMBaxA 1998 Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120 6836 6837

40. BaxAGrishaevA 2005 Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr Opin Struct Biol 15 563 570

41. DominguezCBoelensRBonvinAM 2003 HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125 1731 1737

42. FernandezDSpudichGMZhouXRChristiePJ 1996 The Agrobacterium tumefaciens VirB7 lipoprotein is required for stabilization of VirB proteins during assembly of the T-complex transport apparatus. J Bacteriol 178 3168 3176

43. HeYQZhangLJiangBLZhangZCXuRQ 2007 Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris. Genome Biol 8 R218

44. HolmLSanderC 1996 Mapping the protein universe. Science 273 595 603

45. FergusonADAmezcuaCAHalabiNMChelliahYRosenMK 2007 Signal transduction pathway of TonB-dependent transporters. Proc Natl Acad Sci U S A 104 513 518

46. Garcia-HerreroAVogelHJ 2005 Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli. Mol Microbiol 58 1226 1237

47. KorotkovKVPardonESteyaertJHolWG 2009 Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody. Structure 17 255 265

48. SpreterTYipCKSanowarSAndreIKimbroughTG 2009 A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nat Struct Mol Biol 16 468 476

49. KanamaruSLeimanPGKostyuchenkoVAChipmanPRMesyanzhinovVV 2002 Structure of the cell-puncturing device of bacteriophage T4. Nature 415 553 557

50. KondouYKitazawaDTakedaSTsuchiyaYYamashitaE 2005 Structure of the central hub of bacteriophage Mu baseplate determined by X-ray crystallography of gp44. J Mol Biol 352 976 985

51. LeimanPGBaslerMRamagopalUABonannoJBSauderJM 2009 Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. Proc Natl Acad Sci U S A 106 4154 4159

52. SpagnuoloJOpalkaNWenWXGagicDChabaudE 2010 Identification of the gate regions in the primary structure of the secretin pIV. Mol Microbiol 76 133 150

53. NakanoNKuboriTKinoshitaMImadaKNagaiH 2010 Crystal Structure of Legionella DotD: Insights into the Relationship between Type IVB and Type II/III Secretion Systems. PLoS Pathog 6 e1001129

54. ChristiePJVogelJP 2000 Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells. Trends Microbiol 8 354 360

55. SattlerMSchleucherJGriesingerC 1999 Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog NMR Spectrosc 34 93 158

56. TjandraNGrzesiekSBaxA 1996 Magnetic field dependence of nitrogen-proton J splittings in N-15-enriched human ubiquitin resulting from relaxation interference and residual dipolar coupling. J Am Chem Soc 118 6264 6272

57. RuckertMOttingG 2000 Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J Am Chem Soc 122 7793 7797

58. ZweckstetterMBaxA 2000 Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J Am Chem Soc 122 3791 3792

59. DossetPHusJCMarionDBlackledgeM 2001 A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings. J Biomol NMR 20 223 231

60. DelaglioFGrzesiekSVuisterGWZhuGPfeiferJ 1995 NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6 277 293

61. VrankenWFBoucherWStevensTJFoghRHPajonA 2005 The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59 687 696

62. CornilescuGDelaglioFBaxA 1999 Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13 289 302

63. LaskowskiRARullmannnJAMacArthurMWKapteinRThorntonJM 1996 AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8 477 486

64. BhattacharyaATejeroRMontelioneGT 2007 Evaluating protein structures determined by structural genomics consortia. Proteins 66 778 795

65. KoradiRBilleterMWuthrichK 1996 MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14 51 55, 29–32

66. DossetPHusJCBlackledgeMMarionD 2000 Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 16 23 28

67. FarrowNAMuhandiramRSingerAUPascalSMKayCM 1994 Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33 5984 6003

68. RossiPSwapnaGVHuangYJAraminiJMAnklinC 2010 A microscale protein NMR sample screening pipeline. J Biomol NMR 46 11 22

69. MulderFASchipperDBottRBoelensR 1999 Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins. J Mol Biol 292 111 123

70. JorgensenWLMaxwellDSTirado-RivesJ 1996 Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118 11225 11236

71. RouxBSimonsonT 1999 Implicit solvent models. Biophys Chem 78 1 20

72. HessBKutznerCvan der SpoelDLindahlE 2008 Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4 435 447

73. OtwinowskiZMinorW 1997 Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276 307 326

74. McCoyAJGrosse-KunstleveRWAdamsPDWinnMDStoroniLC 2007 Phaser crystallographic software. J Appl Crystallogr 40 658 674

75. EmsleyPCowtanK 2004 Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60 2126 2132

76. MurshudovGNVaginAADodsonEJ 1997 Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53 240 255

77. Collaborative Computational Project Number 4 1994 The CCP4 Suite - Programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50 760 763

78. LaskowskiRAMacarthurMWMossDSThorntonJM 1993 Procheck - a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26 283 291

79. LovellSCDavisIWArendallWB3rdde BakkerPIWordJM 2003 Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50 437 450

80. DavisIWLeaver-FayAChenVBBlockJNKapralGJ 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35 W375 383

81. CorreaFSalinasRKBonvinAMFarahCS 2008 Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex. Proteins 73 902 917

82. CorreaFFarahCS 2007 Different effects of trifluoroethanol and glycerol on the stability of tropomyosin helices and the head-to-tail complex. Biophys J 92 2463 2475

83. SchaggerH 2006 Tricine-SDS-PAGE. Nat Protoc 1 16 22

84. GuzzoCRSalinasRKAndradeMOFarahCS 2009 PILZ protein structure and interactions with PILB and the FIMX EAL domain: implications for control of type IV pilus biogenesis. J Mol Biol 393 848 866

85. De FeyterRYangYGabrielDW 1993 Gene-for-genes interactions between cotton R genes and Xanthomonas campestris pv. malvacearum avr genes. Mol Plant Microbe Interact 6 225 237

86. WengelnikKMarieCRusselMBonasU 1996 Expression and localization of HrpA1, a protein of Xanthomonas campestris pv. vesicatoria essential for pathogenicity and induction of the hypersensitive reaction. J Bacteriol 178 1061 1069

87. CascalesEChristiePJ 2004 Agrobacterium VirB10, an ATP energy sensor required for type IV secretion. Proc Natl Acad Sci U S A 101 17228 17233

88. LivakKJSchmittgenTD 2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) Method. Methods 25 402 408

89. MoseleyHNSahotaGMontelioneGT 2004 Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 28 341 355