April 2006

Kim Hammond-KosackWheat Pathogenesis Programme

Jacob Koehler Bioinformatics and Biomaths Division

PHI-base

PHI-base@Rothamsted

A database containing expertly curated molecularand biological information on genes proven toaffect the outcome of pathogen-host interactions

Winnenburg, Baldwin et al., (2006) Nucleic Acids Research 34: 459 – 465Balwin, Winnenburg et al., (2006) Mol. Plant Microbe Interact (accepted)

http://www.phi-base.org

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.

Definition of a pathogen

Identification of pathogenicity, virulence and effector genes

Methods: Forward and Reverse Genetics Pathogen transformation involving protoplast or Agrobacterium mediated Gene disruption, replacement or silencing Purification of secreted proteins Map based cloning

Life cycle on host

completed

Pathogenicity factor

DISEASE=

Effector = activate / suppress plant disease resistance

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*)

1277 1390 1413

PubMed

2677

Web of Science

2803

0

50

100

150

200

250

300

350

400

450

500

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005

Year

Pa

pe

rs

0

25

50

75

100

125

150

175

200

225

250

Ge

ne

s

WOS

Pubmed

Cumulative Total of Plant Pathogen Genes

Cumulative Total of Animal Pathogen Genesf, g

ba

d,e

c

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

Pathogenicity gene publication rate is rising

Papers /year Cumulative

genes

Why PHI-base?

S. cerevisiae(sequenced genome)

Rice blast Comparative genomics Gene and protein function studies

Candida albicans Candida glabrata Fusarium ear blight

What is the cause of pathogenicity ?

Novel genes

Gene loss

Selective gene regulation

Saprophytes Pathogens

Plantpathogens

Animal pathogens

Immuno-compromisedhumans

Plant pathogens Human pathogens

To finish Healthy plants

http://www.phibase.org

PHI:125 – Candida albicans SAP4

PHI:44 Fusarium graminearum TRI5 gene codes for trichodiene synthase

Database Headings

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-penetration defect Inducer Penetration defect Host response Post-penetration defect 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

No effect

PHI-base@Rothamsted

405 entries for genes from plant, fungal and animal attacking fungi and Oomycetes

Version 2.1 (Jan 06)

Host Pathogen Species

Host Species

Pathogenicity Genes

Virulence Genes

Effector genes

Animal 10 5 40 129 0Plant 42 32 66 110 13Fungal 2 3 0 3 0

Version 2.2 (April 06) – 481 entries includes 40 where the gene deletion fails to affect the phenotype

The top 10 species in PHI-Base

Species Name Host Taxonomy Number of genes

Candida albicans Animal Ascomycota 102

Cryptococcus neoformans Animal Basidiomycota 50

Magnaporthe grisea Plant Ascomycota 44

Ustilago maydis Plant Basidiomycota 29

Aspergillus fumigatus Animal Ascomycota 13

Botrytis cinerea Plant Ascomycota 12

Fusarium graminearum Plant Ascomycota 12

Fusarium oxysporum Plant Ascomycota 12

Colletotrichum lagenarium Plant Ascomycota 10

peer-reviewed publications only

Where do you publish ?

52% of PHI-base entries were recovered from 5 journals

Molecular Plant-Microbe InteractionsMolecular MicrobiologyInfection and ImmunityThe Plant CellEukaryotic Cell

PUBMED covers 4,800 journals, WOS 8,700 journals

The remaining 48% of entries were obtained from an additional 45 journals

MIPS categories in PHI-base

No unknown function category !!!

Common gene functions required by fungi and Oomyceteswhich infect plant or animal hosts

Plant Pathogens*

* Number of distinct species

Animal Pathogens*

MAP kinase 12 2

G protein subunit 10 2

ABC transporter 5 1

Adenylate cyclase 4 2

Chitin Synthase 3 2

PKA catalytic subunit 3 2

Polyketide synthase 3 2

MAP kinase kinase kinase 3 2

MAP kinase kinase 3 1

Cyclophilin 2 1

Isocitrate lyase 2 1

Fatty acid synthetase 1 1

Methionine synthase 1 1

Trehalose-6-phosphate synthase 1 1

Superoxide dismutase 1 3

Adenylate forming enzymes 3 0

Tetraspanin 3 0

Endopolygalacturonase 3 0

Pectate lyase 2 0

PKA regulatory subunit 2 0

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

Aspartyl proteinase 0 1

Phospholipase B 0 2

Candida albicans – Secreted Aspartyl Proteinases

Ortoneda et al. (2004) Infect. Immun. 72:1760-1766

2 x 107 conidia

The Fusarium oxysporum multihost model:isolate 4287 infects tomato plants and immunodepressed mice

20 mm 20 mm

Lung Heart

conidia

Time after infection (days)0 2 4 6 8 10 12 14

Su

rviv

al (

%)

0

20

40

60

80

100

wt wt heat-killed

Survival

Role of Fusarium oxysporum genes in virulence on plant and mammalian hosts

Biological functionGene Description

Signal transductionfmk1 MAP kinase

Signal transductionfgb1 G subunit

Ambient pH responsepacC Transcription factor

Unknownfpr1 PR-1 protein family

fmk1+fgb1

Yes

No

No

Yes

Yes

Requiredon plants

No

Yes

Yes

No

Yes

Requiredon mammals

Signal transduction

Antonio de Pietro’s group at the University of Cordoba, Spain Josep Guarro's group at the University Rovira y Virgili, Spain

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

Species experts

Plant Pathogenic fungi and Oomycetes

21 experts covering 17 species

Animal Pathogenic fungi

Plant resistance / defence genes

16 experts covering 15 interaction types

Plant bacterial effector genes3 experts

4 experts covering 3 species

Existing and future links

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

~ 50% entries have functions in cellular communication/ signal transduction or metabolism

Comparative genomics

Medical and agricultural scientists, evolutionarybiologists and bioinformaticians

Thomas Baldwin*Martin UrbanKim Hammond-Kosack

Many thanks to

John AntoniwJohn KeonJohn LucasJason Rudd

Rainer WinnenburgJacob KoehlerChris Rawlings

*

Other beta testersDarren SoanesNick Talbot

Wheat Pathogenesis Bioinformatics and Text mining