1887

Abstract

is the cause of late blight, a devastating and re-emerging disease of potato. Significant advances have been made in understanding the biology of , and in the development of molecular tools to study this oomycete. Nevertheless, little is known about the molecular bases of the establishment or development of disease in this hemibiotrophic pathogen. Suppression subtractive hybridization (SSH) was used to generate cDNA enriched for sequences upregulated during potato infection. To identify pathogen-derived cDNAs, and eliminate host sequences from further study, SSH cDNA was hybridized to a bacterial artificial chromosome library. A new gene family was identified called 1, comprising more than 400 members arranged in clusters of up to nine copies throughout the draft genome sequence. Real-time RT-PCR was used to quantify the expression of five classes of transcript within the family, relative to the constitutively expressed A gene, and it revealed them to be significantly upregulated from 12 to 33 h post-inoculation, a period defining the biotrophic phase of infection. Computational analysis of sequences suggested that transcripts were non-protein coding, and this was confirmed by transient expression of FLAG-tagged ORFs in .

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2007-03-01
2020-04-02
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References

  1. Ah Fong A. M. V., Judelson H. S.. 2004; The hAT -like DNA transposon DodoPi resides in a cluster of retro- and DNA transposons in the stramenopile Phytophthora infestans . Mol Genet Genom271:577–585[CrossRef]
    [Google Scholar]
  2. Andersen A. A., Panning B.. 2003; Epigenetic gene regulation by noncoding RNAs. Curr Opin Cell Biol15:281–289[CrossRef]
    [Google Scholar]
  3. Armstrong M. R., Whisson S. C., Pritchard L., Bos J. I. B., Venter E., Avrova A. O., Rehmany A. P., Böhme, U., Brooks K.. other authors 2005; An ancestral oomycete locus contains late blight avirulence gene Avr3a , encoding a protein that is recognised in the host cytoplasm. Proc Natl Acad Sci U S A102:7766–7771[CrossRef]
    [Google Scholar]
  4. Avrova A. O., Stewart H. E., De Jong W., Heilbronn J., Lyon G. D., Birch P. R. J.. 1999; A cysteine protease gene is expressed early in resistant potato interactions with Phytophthora infestans . Mol Plant Microbe Interact12:1114–1119[CrossRef]
    [Google Scholar]
  5. Avrova A. O., Venter E., Birch P. R. J., Whisson S. C.. 2003; Profiling and quantifying differential gene transcription in Phytophthora infestans prior to and during the early stages of potato infection. Fungal Genet Biol40:4–14[CrossRef]
    [Google Scholar]
  6. Avrova A. O., Taleb N., Rokka V. M., Heilbronn J., Hein I., Gilroy E. M., Cardle L., Stewart H. S., Loake G.. other authors 2004; Potato oxysterol binding protein and cathepsin B are rapidly upregulated in independent defence pathways that distinguish R gene-mediated and field resistances to Phytophthora infestans . Mol Plant Pathol5:45–56[CrossRef]
    [Google Scholar]
  7. Baldauf S. L.. 2003; The deep roots of eukaryotes. Science300:1703–1706[CrossRef]
    [Google Scholar]
  8. Bartel D. P.. 2004; MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116:281–297[CrossRef]
    [Google Scholar]
  9. Bell K. S., Avrova A. O., Holeva M. C., Cardle L., Morris W., De Jong W., Toth I. K., Waugh R., Bryan G. J., Birch P. R. J.. 2002; Sample sequencing of a selected region of the genome of Erwinia carotovora subsp. atroseptica reveals candidate phytopathogenicity genes and allows comparison with Escherichia coli . Microbiology148:1367–1378
    [Google Scholar]
  10. Bendtsen J. D., Nielsen H., von Heijne G., Brunak S.. 2004; Improved prediction of signal peptides: SignalP 3.0. J Mol Biol340:783–795[CrossRef]
    [Google Scholar]
  11. Beyer K., Binder A., Boller T., Collinge M.. 2001; Identification of potato genes induced during colonization by Phytophthora infestans . Mol Plant Pathol2:125–135[CrossRef]
    [Google Scholar]
  12. Beyer K., Jimenez Jimenez S., Randall T. A., Lam S., Binder A., Boller T., Collinge M.. 2002; Characterisation of Phytophthora infestans genes regulated during the interaction with potato. Mol Plant Pathol3:473–485[CrossRef]
    [Google Scholar]
  13. Bhattacharjee S., Hiller N. L., Liolios K., Win J., Kanneganti T.-D., Young C., Kamoun S., Haldar K.. 2006; The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathog2:e50 doi: 10.1371/journal.ppat.0020050[CrossRef]
    [Google Scholar]
  14. Birch P. R. J., Whisson S. C.. 2001; Phytophthora infestans enters the genomics era. Mol Plant Pathol2:257–263[CrossRef]
    [Google Scholar]
  15. Birch P. R. J., Avrova A. O., Duncan J. M., Lyon G. D., Toth R. L.. 1999; Isolation of potato genes that are induced during an early stage of the hypersensitive response to Phytophthora infestans . Mol Plant Microbe Interact12:356–361[CrossRef]
    [Google Scholar]
  16. Birch P. R. J., Avrova A. O., Armstrong M., Venter E., Taleb N., Gilroy E. M., Phillips M. S., Whisson S. C.. 2003; The potato– Phytophthora infestans interaction transcriptome. Can J Plant Pathol25:226–231[CrossRef]
    [Google Scholar]
  17. Birch P. R. J., Rehmany A. P., Pritchard L., Kamoun S., Beynon J. L.. 2006; Trafficking arms: Oomycete effectors enter host plant cells. Trends Microbiol14:8–11[CrossRef]
    [Google Scholar]
  18. Bittner-Eddy P. D., Allen R. L., Rehmany A. P., Birch P. R. J., Beynon J. L.. 2003; Use of suppression subtractive hybridization to identify downy mildew genes expressed during infection of Arabidopsis thaliana . Mol Plant Pathol4:501–508[CrossRef]
    [Google Scholar]
  19. Blanco F. A., Judelson H. S.. 2005; A bZIP transcription factor from Phytophthora interacts with a protein kinase and is required for zoospore motility and plant infection. Mol Microbiol56:638–648[CrossRef]
    [Google Scholar]
  20. Cawley S., Bekiranov S., Ng S. S., Kapranov P., Sekinger E. A., Kampa D., Piccolboni A., Sementchenko V., Cheng J.. other authors 2004; Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell116:499–509[CrossRef]
    [Google Scholar]
  21. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., Long J., Stern D., Tammana H.. other authors 2005; Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science308:1149–1154[CrossRef]
    [Google Scholar]
  22. Claverie J. M.. 2005; Fewer genes, more noncoding RNA. Science309:1529–1530[CrossRef]
    [Google Scholar]
  23. Cook P. R.. 2003; Nongenic transcription, gene regulation and action at a distance. J Cell Sci116:4483–4491[CrossRef]
    [Google Scholar]
  24. Cvitanich C., Judelson H. S.. 2003; Stable transformation of the oomycete, Phytophthora infestans , using microprojectile bombardment. Curr Genet42:228–235
    [Google Scholar]
  25. Dekker J., Rippe K., Dekker M., Kleckner N.. 2002; Capturing chromosome conformation. Science295:1306–1311[CrossRef]
    [Google Scholar]
  26. Duncan J. M.. 1999; Phytophthora – an abiding threat to our crops. Microbiol Today26:114–116
    [Google Scholar]
  27. Fickett J. W.. 1982; Recognition of protein coding regions in DNA sequences. Nucleic Acids Res10:5303–5318[CrossRef]
    [Google Scholar]
  28. Goodrich J. A., Kugel J. F.. 2006; Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol7:612–616[CrossRef]
    [Google Scholar]
  29. Grenville-Briggs L. J., Avrova A. O., Bruce C. R., Williams A., Whisson S. C., Birch P. R. J., van West P.. 2005; Elevated amino acid biosynthesis in Phytophthora infestans during appressorium formation and potato infection. Fungal Genet Biol42:244–256[CrossRef]
    [Google Scholar]
  30. Hall T. A.. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser41:95–98
    [Google Scholar]
  31. Hirsch J., Lefort V., Vankersschaver M., Boualem A., Lucas A., Thermes C., d'Aubenton-Carafa Y., Crespi M.. 2006; Characterization of 43 non-protein-coding mRNA genes in Arabidopsis , including the MIR162a -derived transcripts. Plant Physiol140:1192–1204[CrossRef]
    [Google Scholar]
  32. Hopp T. P., Prickett K. S., Price V. L., Libby R. T., March C. J., Cerretti D. P., Urdal D. L., Conlon P. J.. 1988; A short polypeptide marker sequence useful for recombinant protein identification and purification. Bio/Technology6:1204–1210[CrossRef]
    [Google Scholar]
  33. Huang X., Madan A.. 1999; cap3: a DNA sequence assembly program. Genome Research9:868–877[CrossRef]
    [Google Scholar]
  34. Jiang R. H., Dawe A. L., Weide R., van Staveren M., Peters S., Nuss D. L., Govers F.. 2005; Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements. Mol Genet Genom273:20–32[CrossRef]
    [Google Scholar]
  35. Judelson H. S.. 2002; Sequence variation and genomic amplification of a family of Gypsy -like elements in the oomycete genus Phytophthora . Mol Biol Evol19:1313–1322[CrossRef]
    [Google Scholar]
  36. Judelson H. S., Randall T. A.. 1998; Families of repeated DNA in the oomycete Phytophthora infestans and their distribution within the genus. Genome41:605–615[CrossRef]
    [Google Scholar]
  37. Kamoun S.. 2003; Molecular genetics of pathogenic oomycetes. Eukaryot Cell2:191–199[CrossRef]
    [Google Scholar]
  38. Kamoun S.. 2006; A Catalogue of the effector secretome of plant pathogenic oomycetes. Annu Rev Phytopathol44:41–60[CrossRef]
    [Google Scholar]
  39. Latijnhouwers M., Ligterink W., Vleeshouwers V. G. A. A., Van West P., Govers F.. 2004; A G α subunit controls zoospore motility and virulence in the potato late blight pathogen Phytophthora infestans . Mol Microbiol51:925–936[CrossRef]
    [Google Scholar]
  40. Ling J., Baibakov B., Pi W., Emerson B. M., Tuan D.. 2005; The HS2 enhancer of the β -globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis -linked globin promoter. J Mol Biol350:883–896[CrossRef]
    [Google Scholar]
  41. Llave C., Kasschau K. D., Rector M. A., Carrington J. C.. 2002; Endogenous and silencing-associated small RNAs in plants. Plant Cell14:1605–1619[CrossRef]
    [Google Scholar]
  42. Mallory A. C., Vaucheret H.. 2006; Functions of microRNAs and related small RNAs in plants. Nat Genet38:SupplS31–S36[CrossRef]
    [Google Scholar]
  43. Mattick J. S.. 2003; Challenging the dogma: the hidden layers of non-protein-coding RNAs in complex organisms. BioEssays25:930–939[CrossRef]
    [Google Scholar]
  44. Morey C., Avner P.. 2004; Employment opportunities for non-coding RNAs. FEBS Lett567:27–34[CrossRef]
    [Google Scholar]
  45. Okazaki Y., Furuno M., Kasukawa T., Adachi J., Bono H., Kondo S., Nikaido I., Osato N., Saito R.. other authors 2002; Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature420:563–573[CrossRef]
    [Google Scholar]
  46. Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H.. other authors 2004; Complete sequencing and characterization of 21 243 full-length human cDNAs. Nat Genet36:40–45[CrossRef]
    [Google Scholar]
  47. Pollard K. S., Salama S. R., Lambert N., Lambot M.-A., Coppens S., Pedersen J., Katzman S., King B., Onodera C.. other authors 2006; An RNA gene expressed during cortical development evolved rapidly in humans. Nature443:167–172[CrossRef]
    [Google Scholar]
  48. Pritchard L., White J. A., Birch P. R. J., Toth I. K.. 2006; GenomeDiagram: a Python package for the visualisation of large-scale genomic data. Bioinformatics22:616–617[CrossRef]
    [Google Scholar]
  49. Randall T. A., Dwyer R. A., Huitema E., Beyer K., Cvitanich C., Kelkar H., Ah Fong A., Gates K., Roberts S.. other authors 2005; Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Mol Plant Microbe Interact18:229–243[CrossRef]
    [Google Scholar]
  50. Rehmany A. P., Gordon A., Rose L. E., Allen R. L., Armstrong M. R., Whisson S. C., Kamoun S., Tyler B. M., Birch P. R. J., Beynon J. L.. 2005; Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. Plant Cell17:1839–1850[CrossRef]
    [Google Scholar]
  51. Saha S., Murthy S., Rangarajan P. N.. 2006; Identification and characterization of a virus-inducible non-coding RNA in mouse brain. J Gen Virol87:1991–1995[CrossRef]
    [Google Scholar]
  52. Srikantan V., Zou Z., Petrovics G., Zu L., Augustus M., Davis L., Livezey J. R., Connell T., Sesterhenn I. A.. other authors 2000; PCGEM1 , a prostate-specific gene, is overexpressed in prostate cancer. Proc Natl Acad Sci U S A97:12216–12221[CrossRef]
    [Google Scholar]
  53. Tooley P. W., Garfinkel D. G.. 1996; Presence of Ty1-copia group retrotransposon sequences in the potato late blight pathogen Phytophthora infestans . Mol Plant Microbe Interact9:305–309[CrossRef]
    [Google Scholar]
  54. Torto T. A., Li S., Styer A., Huitema E., Testa A., Gow N. A., van West P., Kamoun S.. 2003; EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora . Genome Res13:1675–1685[CrossRef]
    [Google Scholar]
  55. van West P., de Jong A. J., Judelson H. S., Emons A. M. C., Govers F.. 1998; The ipiO gene of Phytophthora infestans is highly expressed in invading hyphae during infection. Fungal Genet Biol23:126–138[CrossRef]
    [Google Scholar]
  56. Vleeshouwers V. G., van Dooijeweert W., Govers F., Kamoun S., Colon L. T.. 2000; The hypersensitive response is associated with host and nonhost resistance to Phytophthora infestans . Planta210:853–864[CrossRef]
    [Google Scholar]
  57. Wassenegger M.. 2000; RNA-directed DNA methylation. Plant Mol Biol43:203–220[CrossRef]
    [Google Scholar]
  58. Whisson S. C., van der Lee T., Bryan G., Waugh R., Govers F., Birch P. R. J.. 2001; Physical mapping across an avirulence locus of Phytophthora infestans using a highly representative, large-insert bacterial artificial chromosome library. Mol Genet Genomics266:289–295[CrossRef]
    [Google Scholar]
  59. Whisson S. C., Avrova A. O., Lavrova O., Pritchard L.. 2005; Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans . Fungal Genet Biol4:351–365
    [Google Scholar]
  60. Zhang B., Pan X., Cobb G. P., Anderson T. A.. 2006; Plant microRNA: a small regulatory molecule with big impact. Dev Biol289:3–16[CrossRef]
    [Google Scholar]
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