Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Resistance Gene

English version České info

Hyaloperonospora arabidopsidis (Hpa) is an obligate biotroph oomycete pathogen of the model plant Arabidopsis thaliana and contains a large set of effector proteins that are translocated to the host to exert virulence functions or trigger immune responses. These effectors are characterized by conserved amino-terminal translocation sequences and highly divergent carboxyl-terminal functional domains. The availability of the Hpa genome sequence allowed the computational prediction of effectors and the development of effector delivery systems enabled validation of the predicted effectors in Arabidopsis. In this study, we identified a novel effector ATR39-1 by computational methods, which was found to trigger a resistance response in the Arabidopsis ecotype Weiningen (Wei-0). The allelic variant of this effector, ATR39-2, is not recognized, and two amino acid residues were identified and shown to be critical for this loss of recognition. The resistance protein responsible for recognition of the ATR39-1 effector in Arabidopsis is RPP39 and was identified by map-based cloning. RPP39 is a member of the CC-NBS-LRR family of resistance proteins and requires the signaling gene NDR1 for full activity. Recognition of ATR39-1 in Wei-0 does not inhibit growth of Hpa strains expressing the effector, suggesting complex mechanisms of pathogen evasion of recognition, and is similar to what has been shown in several other cases of plant-oomycete interactions. Identification of this resistance gene/effector pair adds to our knowledge of plant resistance mechanisms and provides the basis for further functional analyses.

Vyšlo v časopise: Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Resistance Gene. PLoS Genet 8(2): e32767. doi:10.1371/journal.pgen.1002502
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002502

Souhrn

Zdroje

1. NishimuraMTDanglJL 2010 Arabidopsis and the plant immune system. Plant J 61 1053 1066

2. SchornackSHuitemaECanoLMBozkurtTOOlivaR 2009 Ten things to know about oomycete effectors. Mol Plant Pathol 10 795 803

3. ChisholmSTCoakerGDayBStaskawiczBJ 2006 Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124 803 814

4. Hammond-KosackKEJonesJD 1996 Resistance gene-dependent plant defense responses. Plant Cell 8 1773 1791

5. RehmanyAPGordonARoseLEAllenRLArmstrongMR 2005 Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. Plant Cell 17 1839 1850

6. ShanWCaoMLeungDTylerBM 2004 The Avr1b locus of Phytophthora sojae encodes an elicitor and a regulator required for avirulence on soybean plants carrying resistance gene Rps1b. Mol Plant Microbe Interact 17 394 403

7. AllenRLBittner-EddyPDGrenville-BriggsLJMeitzJCRehmanyAP 2004 Host-parasite coevolutionary conflict between Arabidopsis and downy mildew. Science 306 1957 1960

8. BaileyKCevikVHoltonNByrne-RichardsonJSohnKH 2011 Molecular cloning of ATR5(Emoy2) from Hyaloperonospora arabidopsidis, an avirulence determinant that triggers RPP5-mediated defense in Arabidopsis. Mol Plant Microbe Interact 24 827 838

9. ArmstrongMRWhissonSCPritchardLBosJIVenterE 2005 An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A 102 7766 7771

10. ChouSKrasilevaKVHoltonJMSteinbrennerADAlberT Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces. Proc Natl Acad Sci U S A 108 13323 13328

11. BoutemyLSKingSRWinJHughesRKClarkeTA 2011 Structures of Phytophthora RXLR effector proteins: a conserved but adaptable fold underpins functional diversity. J Biol Chem 286 35834 35842

12. YaenoTLiHChaparro-GarciaASchornackSKoshibaS 2011 Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity. Proc Natl Acad Sci U S A 108 14682 14687

13. WinJKrasilevaKVKamounSShirasuKStaskawiczBJ 2011 Sequence divergent RXLR effectors share a structural fold conserved across plant pathogenic oomycete species. PLoS Pathog in press

14. BhattacharjeeSHillerNLLioliosKWinJKannegantiTD 2006 The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathog 2 e50

15. GrouffaudSvan WestPAvrovaAOBirchPRWhissonSC 2008 Plasmodium falciparum and Hyaloperonospora parasitica effector translocation motifs are functional in Phytophthora infestans. Microbiology 154 3743 3751

16. HaasBJKamounSZodyMCJiangRHHandsakerRE 2009 Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461 393 398

17. BaxterLTripathySIshaqueNBootNCabralA 2010 Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 330 1549 1551

18. TylerBMTripathySZhangXDehalPJiangRH 2006 Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313 1261 1266

19. CunnacSLindebergMCollmerA 2009 Pseudomonas syringae type III secretion system effectors: repertoires in search of functions. Curr Opin Microbiol 12 53 60

20. JiangRHTripathySGoversFTylerBM 2008 RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc Natl Acad Sci U S A 105 4874 4879

21. WinJMorganWBosJKrasilevaKVCanoLM 2007 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell 19 2349 2369

22. SchornackSvan DammeMBozkurtTOCanoLMSmokerM 2010 Ancient class of translocated oomycete effectors targets the host nucleus. Proc Natl Acad Sci U S A 107 17421 17426

23. CaillaudMCPiquerezSJFabroGSteinbrennerJIshaqueN 2011 Subcellular localization of the Hpa RxLR effector repertoire identifies the extrahaustorial membrane-localized HaRxL17 that confers enhanced plant susceptibility. Plant J DOI:10.1111/j.1365-313X.2011.04787.x

24. CabralAStassenJHSeidlMFBautorJParkerJE 2011 Identification of Hyaloperonospora arabidopsidis transcript sequences expressed during infection reveals isolate-specific effectors. PLoS One 6 e19328

25. VleeshouwersVGRietmanHKrenekPChampouretNYoungC 2008 Effector genomics accelerates discovery and functional profiling of potato disease resistance and Phytophthora infestans avirulence genes. PLoS One 3 e2875

26. OhSKYoungCLeeMOlivaRBozkurtTO 2009 In planta expression screens of Phytophthora infestans RXLR effectors reveal diverse phenotypes, including activation of the Solanum bulbocastanum disease resistance protein Rpi-blb2. Plant Cell 21 2928 2947

27. HolubEBBroseETorMClayCCruteIR 1995 Phenotypic and genotypic variation in the interaction between Arabidopsis thaliana and Albugo candida. Mol Plant Microbe Interact 8 916 928

28. SlusarenkoAJSchlaichNL 2003 Downy mildew of Arabidopsis thaliana caused by Hyaloperonospora parasitica (formerly Peronospora parasitica). Mol Plant Pathol 4 159 170

29. MeyersBCKozikAGriegoAKuangHMichelmoreRW 2003 Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15 809 834

30. BombliesKLempeJEpplePWarthmannNLanzC 2007 Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol 5 e236

31. KrasilevaKVDahlbeckDStaskawiczBJ 2010 Activation of an Arabidopsis resistance protein is specified by the in planta association of its leucine-rich repeat domain with the cognate oomycete effector. Plant Cell 22 2444 2458

32. Bittner-EddyPDBeynonJL 2001 The Arabidopsis downy mildew resistance gene, RPP13-Nd, functions independently of NDR1 and EDS1 and does not require the accumulation of salicylic acid. Mol Plant Microbe Interact 14 416 421

33. FinnRDTateJMistryJCoggillPCSammutSJ 2008 The Pfam protein families database. Nucleic Acids Res 36 D281 288

34. KaleSDTylerBM 2011 Assaying effector function in planta using double-barreled particle bombardment. Methods Mol Biol 712 153 172

35. RentelMCLeonelliLDahlbeckDZhaoBStaskawiczBJ 2008 Recognition of the Hyaloperonospora parasitica effector ATR13 triggers resistance against oomycete, bacterial, and viral pathogens. Proc Natl Acad Sci U S A 105 1091 1096

36. SohnKHLeiRNemriAJonesJD 2007 The downy mildew effector proteins ATR1 and ATR13 promote disease susceptibility in Arabidopsis thaliana. Plant Cell 19 4077 4090

37. ThomasWJThireaultCAKimbrelJAChangJH 2009 Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. Plant J 60 919 928

38. AranzanaMJKimSZhaoKBakkerEHortonM 2005 Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1 e60

39. AllenRLMeitzJCBaumberREHallSALeeSC 2008 Natural variation reveals key amino acids in a downy mildew effector that alters recognition specificity by an Arabidopsis resistance gene. Mol Plant Pathol 9 511 523

40. KochESlusarenkoA 1990 Arabidopsis is susceptible to infection by a downy mildew fungus. Plant Cell 2 437 445

41. KrasilevaKZhengCLeonelliLGoritschnigSDahlbeckD 2011 Global analysis of Arabidopsis/downy mildew interactions reveals prevalence of incomplete resistance and rapid evolution of pathogen recognition. PLoS One 6 e28765

42. AartsNMetzMHolubEStaskawiczBJDanielsMJ 1998 Different requirements for EDS1 and NDR1 by disease resistance genes define at least two R gene-mediated signaling pathways in Arabidopsis. Proc Natl Acad Sci U S A 95 10306 10311

43. ShapiroADZhangC 2001 The role of NDR1 in avirulence gene-directed signaling and control of programmed cell death in Arabidopsis. Plant Physiol 127 1089 1101

44. CoatesMEBeynonJL 2010 Hyaloperonospora arabidopsidis as a pathogen model. Annu Rev Phytopathol 48 329 345

45. HallSAAllenRLBaumberREBaxterLAFisherK 2009 Maintenance of genetic variation in plants and pathogens involves complex networks of gene-for-gene interactions. Mol Plant Pathol 10 449 457

46. HaltermanDAChenYSopeeJBerduo-SandovalJSanchez-PerezA 2010 Competition between Phytophthora infestans effectors leads to increased aggressiveness on plants containing broad-spectrum late blight resistance. PLoS One 5 e10536

47. IgariKEndoSHibaraKAidaMSakakibaraH 2008 Constitutive activation of a CC-NB-LRR protein alters morphogenesis through the cytokinin pathway in Arabidopsis. Plant J 55 14 27

48. ZhangYGoritschnigSDongXLiX 2003 A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of npr1-1, constitutive 1. Plant Cell 15 2636 2646

49. EdgarRC 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32 1792 1797

50. EarleyKWHaagJRPontesOOpperKJuehneT 2006 Gateway-compatible vectors for plant functional genomics and proteomics. Plant J 45 616 629

51. DayBDahlbeckDStaskawiczBJ 2006 NDR1 interaction with RIN4 mediates the differential activation of multiple disease resistance pathways in Arabidopsis. Plant Cell 18 2782 2791

52. CloughSJBentAF 1998 Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16 735 743