#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to


Fusarium oxysporum is a fungal pathogen that represents a species complex, with members that infect numerous crops. In spite of its importance to agriculture, very little is known about roles of small RNAs in plant immunity against F. oxysporum. In this study, we set up a screen for tomato microRNAs (miRNAs) that correlate with resistance to F. oxysporum f.sp. lycopersici by performing deep sequencing of small RNAs from a resistant and susceptible tomato cultivar. We focused on two miRNAs that are uniquely down-regulated in the resistant cultivar during fungal infection. All predicted targets of these miRNAs encode proteins with NB domains, a motif associated with pathogen resistance in plants. Using a heterologous system, we validated that the miRNAs could regulate expression of four targets. Silencing of the target genes in tomato resulted in decreased immunity to F. oxysporum in the normally resistant cultivar. The finding that none of our targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Our results suggest that the potential resistance of the susceptible cultivar is insufficiently expressed due to the action of miRNAs.


Vyšlo v časopise: MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to. PLoS Pathog 10(10): e32767. doi:10.1371/journal.ppat.1004464
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004464

Souhrn

Fusarium oxysporum is a fungal pathogen that represents a species complex, with members that infect numerous crops. In spite of its importance to agriculture, very little is known about roles of small RNAs in plant immunity against F. oxysporum. In this study, we set up a screen for tomato microRNAs (miRNAs) that correlate with resistance to F. oxysporum f.sp. lycopersici by performing deep sequencing of small RNAs from a resistant and susceptible tomato cultivar. We focused on two miRNAs that are uniquely down-regulated in the resistant cultivar during fungal infection. All predicted targets of these miRNAs encode proteins with NB domains, a motif associated with pathogen resistance in plants. Using a heterologous system, we validated that the miRNAs could regulate expression of four targets. Silencing of the target genes in tomato resulted in decreased immunity to F. oxysporum in the normally resistant cultivar. The finding that none of our targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Our results suggest that the potential resistance of the susceptible cultivar is insufficiently expressed due to the action of miRNAs.


Zdroje

1. LlaveC, KasschauKD, RectorMA, CarringtonJC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14: 1605–1619.

2. ReinhartBJ, SlackFJ, BassonM, PasquinelliAE, BettingerJC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901–906.

3. ParkW, LiJ, SongR, MessingJ, ChenX (2002) CARPEL FACTORY, a dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current biology: CB 12: 1484–1495.

4. AukermanMJ, SakaiH (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 2730–2741.

5. BartelDP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.

6. PadmanabhanC, ZhangX, JinH (2009) Host small RNAs are big contributors to plant innate immunity. Curr Opin Plant Biol 12: 465–472.

7. PalatnikJF, AllenE, WuX, SchommerC, SchwabR, et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257–263.

8. Rubio-SomozaI, CuperusJT, WeigelD, CarringtonJC (2009) Regulation and functional specialization of small RNA-target nodes during plant development. Curr Opin Plant Biol 12: 622–627.

9. SunkarR, ChinnusamyV, ZhuJ, ZhuJK (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12: 301–309.

10. SunkarR, KapoorA, ZhuJK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051–2065.

11. SunkarR, ZhuJK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001–2019.

12. FabianMR, SonenbergN, FilipowiczW (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351–379.

13. FukayaT, TomariY (2012) MicroRNAs mediate gene silencing via multiple different pathways in Drosophila. Mol Cell 48: 825–836.

14. LiS, LiuL, ZhuangX, YuY, LiuX, et al. (2013) MicroRNAs inhibit the translation of target mRNAs on the Endoplasmic Reticulum in Arabidopsis. Cell 153: 562–574.

15. BollerT, FelixG (2009) A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol 60: 379–406.

16. JonesJD, DanglJL (2006) The plant immune system. Nature 444: 323–329.

17. PumplinN, VoinnetO (2013) RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 11: 745–760.

18. NaqviAR, HaqQM, MukherjeeSK (2010) MicroRNA profiling of tomato leaf curl New Delhi virus (tolcndv) infected tomato leaves indicates that deregulation of mir159/319 and mir172 might be linked with leaf curl disease. Virol J 7: 281.

19. FahlgrenN, HowellMD, KasschauKD, ChapmanEJ, SullivanCM, et al. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2: e219.

20. ZhangW, GaoS, ZhouX, ChellappanP, ChenZ, et al. (2011) Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol 75: 93–105.

21. NavarroL, DunoyerP, JayF, ArnoldB, DharmasiriN, et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436–439.

22. LiF, PignattaD, BendixC, BrunkardJO, CohnMM, et al. (2012) MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci U S A 109: 1790–1795.

23. ShivaprasadPV, ChenHM, PatelK, BondDM, SantosBA, et al. (2012) A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell 24: 859–874.

24. MohorianuI, SchwachF, JingR, Lopez-GomollonS, MoxonS, et al. (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J 67: 232–246.

25. KarlovaR, van HaarstJC, MaliepaardC, van de GeestH, BovyAG, et al. (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot 64: 1863–1878.

26. Di PietroA, MadridMP, CaracuelZ, Delgado-JaranaJ, RonceroMIG (2003) Fusarium oxysporum: exploring the molecular arsenal of a vascular wilt fungus. Molecular Plant Pathology 4: 315–325.

27. Leslie JF, Summerell BA (2006) The Fusarium Laboratory Manual. Ames, IA: Blackwell Publishing. 388 pages p.

28. SimonsG, GroenendijkJ, WijbrandiJ, ReijansM, GroenenJ, et al. (1998) Dissection of the fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. Plant Cell 10: 1055–1068.

29. HoutermanPM, MaL, van OoijenG, de VroomenMJ, CornelissenBJ, et al. (2009) The effector protein Avr2 of the xylem-colonizing fungus Fusarium oxysporum activates the tomato resistance protein I-2 intracellularly. Plant J 58: 970–978.

30. de IlarduyaOM, MooreAE, KaloshianI (2001) The tomato Rme1 locus is required for Mi-1-mediated resistance to root-knot nematodes and the potato aphid. Plant J 27: 417–425.

31. Di PietroA, RonceroMI (1998) Cloning, expression, and role in pathogenicity of pg1 encoding the major extracellular endopolygalacturonase of the vascular wilt pathogen Fusarium oxysporum. Mol Plant Microbe Interact 11: 91–98.

32. YuSC, ZouYM (2008) A co-dominant molecular marker of Fusarium wilt resistance gene I-2 derived from gene sequence in tomato. Yi Chuan 30: 926–932.

33. ManavellaPA, KoenigD, WeigelD (2012) Plant secondary siRNA production determined by microRNA-duplex structure. Proc Natl Acad Sci U S A 109: 2461–2466.

34. MiS, CaiT, HuY, ChenY, HodgesE, et al. (2008) Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide. Cell 133: 116–127.

35. MontgomeryTA, HowellMD, CuperusJT, LiD, HansenJE, et al. (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133: 128–141.

36. HarveyJJ, LewseyMG, PatelK, WestwoodJ, HeimstadtS, et al. (2011) An antiviral defense role of AGO2 in plants. PLoS One 6: e14639.

37. XuW, MengY, WiseRP (2013) Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. New Phytol 201: 1396–412 doi: 10.1111/nph.12598

38. Abdel-GhanySE, PilonM (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. Journal of Biological Chemistry 283: 15932–15945.

39. AxtellMJ, BartelDP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 1658–1673.

40. ChiouTJ, AungK, LinSI, WuCC, ChiangSF, et al. (2006) Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell 18: 412–421.

41. LiuHH, TianX, LiYJ, WuCA, ZhengCC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14: 836–843.

42. SunkarR (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21: 805–811.

43. ZhaoB, GeL, LiangR, LiW, RuanK, et al. (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10: 29.

44. ZhaoB, LiangR, GeL, LiW, XiaoH, et al. (2007) Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 354: 585–590.

45. CuperusJT, CarbonellA, FahlgrenN, Garcia-RuizH, BurkeRT, et al. (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol 17: 997–1003.

46. FelippesFF, SchneebergerK, DezulianT, HusonDH, WeigelD (2008) Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14: 2455–2459.

47. MeyersBC, AxtellMJ, BartelB, BartelDP, BaulcombeD, et al. (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20: 3186–3190.

48. JohnsonC, KasprzewskaA, TennessenK, FernandesJ, NanGL, et al. (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 19: 1429–1440.

49. VoinnetO (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669–687.

50. DaiX, ZhaoPX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: W155–159.

51. CoggillP, FinnRD, BatemanA (2008) Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics Chapter 2: Unit 2 5.

52. LanfermeijerFC, DijkhuisJ, SturreMJ, de HaanP, HilleJ (2003) Cloning and characterization of the durable tomato mosaic virus resistance gene Tm-2(2) from Lycopersicon esculentum. Plant Mol Biol 52: 1037–1049.

53. LanfermeijerFC, WarminkJ, HilleJ (2005) The products of the broken Tm-2 and the durable Tm-2(2) resistance genes from tomato differ in four amino acids. J Exp Bot 56: 2925–2933.

54. KasschauKD, XieZ, AllenE, LlaveC, ChapmanEJ, et al. (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev Cell 4: 205–217.

55. LlaveC, XieZ, KasschauKD, CarringtonJC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053–2056.

56. TangG, ReinhartBJ, BartelDP, ZamorePD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17: 49–63.

57. MantelinS, PengHC, LiB, AtamianHS, TakkenFL, et al. (2011) The receptor-like kinase SlSERK1 is required for Mi-1-mediated resistance to potato aphids in tomato. Plant J 67: 459–471.

58. ValidovSZ, KamilovaFD, LugtenbergBJ (2011) Monitoring of pathogenic and non-pathogenic Fusarium oxysporum strains during tomato plant infection. Microb Biotechnol 4: 82–88.

59. ConsortiumTG (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641.

60. PilcherRL, MoxonS, PaksereshtN, MoultonV, ManningK, et al. (2007) Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 226: 709–717.

61. WangY, ItayaA, ZhongX, WuY, ZhangJ, et al. (2011) Function and evolution of a microRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell 23: 3185–3203.

62. FerracinM, VeroneseA, NegriniM (2010) Micromarkers: miRNAs in cancer diagnosis and prognosis. Expert Rev Mol Diagn 10: 297–308.

63. Katiyar-AgarwalS, JinH (2010) Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 48: 225–246.

64. MaC, LuY, BaiS, ZhangW, DuanX, et al. (2013) Cloning and characterization of miRNAs and their targets, including a novel miRNA-targeted NBS-LRR protein class gene in apple (golden delicious). Mol Plant

65. MukhtarMS (2013) Engineering NLR immune receptors for broad-spectrum disease resistance. Trends Plant Sci 18: 469–472.

66. TaiHH, GoyerC, Bud PlattHW, De KoeyerD, MurphyA, et al. (2013) Decreased defense gene expression in tolerance versus resistance to Verticillium dahliae in potato. Funct Integr Genomics 13: 367–378.

67. CaiG, RestrepoS, MyersK, ZuluagaP, DaniesG, et al. (2013) Gene profiling in partially resistant and susceptible near-isogenic tomatoes in response to late blight in the field. Mol Plant Pathol 14: 171–184.

68. LeeSK, SongMY, SeoYS, KimHK, KoS, et al. (2009) Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes. Genetics 181: 1627–1638.

69. LoutreC, WickerT, TravellaS, GalliP, ScofieldS, et al. (2009) Two different CC-NBS-LRR genes are required for Lr10-mediated leaf rust resistance in tetraploid and hexaploid wheat. Plant J 60: 1043–1054.

70. NarusakaM, ShirasuK, NoutoshiY, KuboY, ShiraishiT, et al. (2009) RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens. Plant J 60: 218–226.

71. OkuyamaY, KanzakiH, AbeA, YoshidaK, TamiruM, et al. (2011) A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes. Plant J 66: 467–479.

72. PeartJR, MestreP, LuR, MalcuitI, BaulcombeDC (2005) NRG1, a CC-NB-LRR protein, together with N, a TIR-NB-LRR protein, mediates resistance against tobacco mosaic virus. Curr Biol 15: 968–973.

73. SinapidouE, WilliamsK, NottL, BahktS, TorM, et al. (2004) Two TIR:NB:LRR genes are required to specify resistance to Peronospora parasitica isolate Cala2 in Arabidopsis. Plant J 38: 898–909.

74. ChenX (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022–2025.

75. GandikotaM, BirkenbihlRP, HohmannS, CardonGH, SaedlerH, et al. (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49: 683–693.

76. AllenE, XieZ, GustafsonAM, CarringtonJC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207–221.

77. ChenHM, ChenLT, PatelK, LiYH, BaulcombeDC, et al. (2010) 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 107: 15269–15274.

78. ZhaiJ, JeongDH, De PaoliE, ParkS, RosenBD, et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev 25: 2540–2553.

79. ChomczynskiP, SacchiN (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156–159.

80. ParkG, BorkovichKA (2012) Small RNA isolation and library construction for expression profiling of small RNAs from Neurospora and Fusarium using illumina high-throughput deep sequencing. Methods Mol Biol 883: 155–164.

81. KevilCG, WalshL, LarouxFS, KalogerisT, GrishamMB, et al. (1997) An improved, rapid Northern protocol. Biochem Biophys Res Commun 238: 277–279.

82. QiaoY, LiuL, XiongQ, FloresC, WongJ, et al. (2013) Oomycete pathogens encode RNA silencing suppressors. Nat Genet 45: 330–333.

83. KockenCH, JansenJ, KaanAM, BeckersPJ, PonnuduraiT, et al. (1993) Cloning and expression of the gene coding for the transmission blocking target antigen Pfs48/45 of Plasmodium falciparum. Mol Biochem Parasitol 61: 59–68.

84. LiuY, SchiffM, Dinesh-KumarSP (2002) Virus-induced gene silencing in tomato. Plant J 31: 777–786.

85. EkengrenSK, LiuY, SchiffM, Dinesh-KumarSP, MartinGB (2003) Two MAPK cascades, NPR1, and TGA transcription factors play a role in Pto-mediated disease resistance in tomato. Plant J 36: 905–917.

86. PengHC, KaloshianI (2014) The tomato leucine-rich repeat receptor-like kinases SlSERK3A and SlSERK3B have overlapping functions in bacterial and nematode innate immunity. PLoS One 9: e93302.

87. Abd-ElsalamKA, Asran-AmalA, SchniederF, MigheliQ, VetreetJA (2006) Molecular detection ofFusarium oxysporum f. sp vasinfectum in cotton roots by PCR and real-time PCR assay. J Plant Dis Prot 113: 14–19.

88. WestphalA, LiC, XingL, McKayA, MalvickD (2014) Contributions of Fusarium virguliforme and Heterodera glycines to the Disease Complex of Sudden Death Syndrome of Soybean. PLoS One 9: e99529.

89. LaterrotHS (1993) Revised list of near isogenic tomato lines in Moneymaker type with different genes for disease resistances. Report of the Tomato Genetics Cooperative 43: 79–80.

90. TamuraK, PetersonD, PetersonN, StecherG, NeiM, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 28: 2731–2739.

Štítky
Hygiena a epidemiológia Infekčné lekárstvo Laboratórium

Článok vyšiel v časopise

PLOS Pathogens


2014 Číslo 10
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#