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April 2006

PHI-base. Kim Hammond-Kosack Wheat Pathogenesis Programme Jacob Koehler Bioinformatics and Biomaths Division. April 2006. PHI-base@Rothamsted. A database containing expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions.

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April 2006

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  1. PHI-base Kim Hammond-Kosack Wheat Pathogenesis Programme Jacob Koehler Bioinformatics and Biomaths Division April 2006

  2. PHI-base@Rothamsted A database containing expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions http://www.phi-base.org Winnenburg, Baldwin et al., (2006) Nucleic Acids Research 34: 459 – 465 Balwin, Winnenburg et al., (2006) Mol. Plant Microbe Interact (accepted)

  3. Definition of a pathogen An organism that, to complete a part or all of its life cycle, grows inside another organism and in so doing has a detrimental effect on its host.

  4. Identification of pathogenicity, virulence and effector genes Pathogenicity factor Life cycle on host completed = DISEASE Effector = activate / suppress plant disease resistance Methods: Forward and Reverse Genetics Pathogen transformation involving protoplast or Agrobacterium mediated Gene disruption, replacement or silencing Purification of secreted proteins Map based cloning

  5. Searching for Pathogenicity Genes • Keyword search of the Web of Science and PubMed • (fung* or yeast) and (gene or factor) and (pathogenicity or virulen* or avirulence gene*) PubMed 2677 Web of Science 2803 1277 1390 1413

  6. f, g d,e b a c Pathogenicity gene publication rate is rising Papers / year Cumulative genes a Saccharomyces cerevisiae genome sequenced d Ashbya gossypii genome sequenced b First Magnaporthe grisea EST deposited in GenBank e First version of COGEME made available online c Candida albicans genome sequenced f Neurospora crassa genome sequenced g Magnaporthe grisea genome sequenced

  7. Candida albicans Candida glabrata Why PHI-base? Rice blast • Comparative genomics • Gene and protein • function studies S. cerevisiae (sequenced genome) Fusarium ear blight

  8. Saprophytes Pathogens What is the cause of pathogenicity ? Novel genes Gene loss Selective gene regulation Plant pathogens Animal pathogens

  9. Human pathogens Plant pathogens Healthy plants To finish Immuno-compromised humans

  10. http://www.phibase.org

  11. PHI:125 – Candida albicans SAP4

  12. PHI:44 Fusarium graminearumTRI5 gene codes for trichodiene synthase

  13. Gene name Disease name Pathogen species Vegetative spores Experimental host Sexual spores Function In vitro growth Phenotype of mutant Spore germination Mating defect prior to penetration Essential gene (Lethal knockout) Pre - penetrationdefect Inducer Penetration defect Host response Post - penetrationdefect Experimental evidence PHI - base accession Entered by: EMBL accession Manual (M) or textmining (T) Linkout accession Literature ID Database Literature source Host NCBI Taxonomy ID Full citation Pathogen NCBI Taxonomy ID Author email Monocot/Dicot plant Comments Pathway Database Headings No effect

  14. PHI-base@Rothamsted Version 2.1 (Jan 06) 405 entries for genes from plant, fungal and animal attacking fungi and Oomycetes Version 2.2 (April 06) – 481 entries includes 40 where the gene deletion fails to affect the phenotype

  15. The top 10 species in PHI-Base peer-reviewed publications only

  16. Where do you publish ? PUBMED covers 4,800 journals, WOS 8,700 journals 52% of PHI-base entries were recovered from 5 journals Molecular Plant-Microbe Interactions Molecular Microbiology Infection and Immunity The Plant Cell Eukaryotic Cell The remaining 48% of entries were obtained from an additional 45 journals

  17. MIPS categories in PHI-base No unknown function category !!!

  18. Common gene functions required by fungi and Oomycetes which infect plant or animal hosts Plant Pathogens* Animal Pathogens* * Number of distinct species

  19. Specific gene functions required by either plant or animal infecting fungi and Oomycetes “possibly just a snap shot in time” Plant Pathogens* Animal Pathogens* Plant specific Animal specific * Number of distinct species

  20. Candida albicans – Secreted Aspartyl Proteinases

  21. The Fusarium oxysporum multihost model:isolate 4287 infects tomato plants and immunodepressed mice 2 x 107 conidia 20 mm 20 mm Survival Lung Heart 100 80 conidia wt wt heat-killed 60 Survival (%) 40 20 0 0 2 4 6 8 10 12 14 Time after infection (days) Ortoneda et al. (2004) Infect. Immun. 72:1760-1766

  22. Role of Fusarium oxysporum genes in virulence on plant and mammalian hosts Required on plants Required on mammals Gene Description Biological function fmk1 MAP kinase Signal transduction Yes No fgb1 Gb subunit Signal transduction Yes No fmk1+fgb1 Signal transduction Yes Yes pacC Transcription factor Ambient pH response No Yes fpr1 PR-1 protein family Unknown No Yes Antonio de Pietro’s group at the University of Cordoba, Spain Josep Guarro's group at the University Rovira y Virgili, Spain

  23. Future versions of PHI-base • Text-mining • Semi-automated literature searching and database curation (pilot test – 70% recall, 40% precision) • BLAST search facility • Sequence similarity comparisons with all the pathogenicity genes • Other pathogen-host data • Plant resistance and defence signalling genes • Fungicide targets • Other invader types e.g. bacteria, nematodes Interactive pathway and network maps

  24. Species experts Plant Pathogenic fungi and Oomycetes 21 experts covering 17 species Animal Pathogenic fungi 4 experts covering 3 species Plant resistance / defence genes 16 experts covering 15 interaction types Plant bacterial effector genes 3 experts

  25. Existing and future links

  26. ~ 50% entries have functions in cellular communication/ signal transduction or metabolism Comparative genomics Medical and agricultural scientists, evolutionary biologists and bioinformaticians Pathogen Host Interactions database (PHI-base) Contains expertly curated molecular and biological information on genes proven to affect the interaction outcome 405 gene entries – 169 animal, 176 plant, 3 fungi 54 pathogenic species, fungi and Oomyctes

  27. Many thanks to Bioinformatics and Text mining Wheat Pathogenesis Thomas Baldwin* Martin Urban Kim Hammond-Kosack Rainer Winnenburg Jacob Koehler Chris Rawlings John Antoniw John Keon John Lucas Jason Rudd Other beta testers Darren Soanes Nick Talbot *

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