This database contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries.

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PHI-base includes the following fields:

Column name Description

PHI-base accession

Stable accession number for each database entry to aid curation

Protein ID

Link-out to Protein ID

Gene Locus ID

Link-out to Gene Locus ID

Gene name

Name of the fungal gene that was disrupted in the published study

Genome location

Chromosome number where gene is located or name of pathogenicity island

Amino acid sequence

Amino acid sequence of the gene product

Nucleotide sequence

Nucleotide sequence of the gene

Multiple mutation

PHI-base accessions of other genes in case multiple gene mutations were tested in one strain

Pathogen NCBI Taxonomy ID

NCBI taxonomy ID of the pathogenic species

Pathogen species

Systematic name of the pathogenic species

Strain

Strain, in which gene function was tested

Disease name

Name of the disease caused by the pathogen host interaction

Monocot / Dicot plant

Number of cotyledons, if the host is a plant

Host NCBI Taxonomy ID

NCBI taxonomy ID of the host organism

Experimental host

Common name of the host organism

GO annotation

Gene ontology annotation that describes gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner (http://www.geneontology.org).

Pathway

Name of the pathway the disrupted gene is involved in

Phenotype of mutant

Definition of phenotypes:

  • Loss of pathogenicity - the transgenic strain fails to cause disease
  • Reduced virulence - the transgenic strain still causes some disease formation but this is less than the wild-type strain (ie. a quantitative effect). Synonymous with the term reduced aggressiveness.
  • Unaffected pathogenicity - the transgenic strain which expresses no or reduced levels of a specific gene product(s) has wild-type disease causing ability
  • Increased virulence (Hypervirulence) - the transgenic strain causes higher levels of disease than the wild-type strain
  • Effector (plant avirulence determinant) - currently a plant pathogen specific term which was previously known as an avirulence gene. An effector gene is required for the direct or indirect recognition of a pathogen only in resistant host genotypes which possess the corresponding disease resistance gene. Positive recognition leads to activation of plant defences and the pathogen fails to cause disease. Note some effector genes are required to cause disease on susceptible hosts but most are not.
  • Lethal - the transgenic strain which expresses no or reduced levels of a specific gene product(s) is not viable. The gene product is essential for life.
  • Enhanced antagonism - the transgenetic strain of a endophyte which shows no asymptomatic colonisation, but is gaining the upperhand of the pathogen-host-interaction.
  • Wild-type mutualism - the transgenetic strain of a endophyte which shows no difference in the pathogen-host-interaction comparing to the wild-type

Mating defect

Yes/No If the gene disruption causes a mating defect affecting pathogenicity

Pre-penetration defect

Yes/No If the gene disruption causes a block in the disease process before penetration e.g. Formation of appressoria

Penetration defect

Yes/No If the gene disruption causes a block in the disease process at penetration

Post-penetration defect

Yes/No If the gene disruption causes a block in the disease process after penetration

Vegetative spores

Defects in asexual sporulation caused by the gene disruption e.g reduced sporulation

Sexual spores

Defects in sexual sporulation caused by the gene disruption e.g reduced sporulation

In vitro growth

Growth defects in culture caused by the gene disruption e.g. reduced growth

Spore germination

Defects in spore germination caused by the gene disruption

Essential gene

Lethal effect from gene disruption

Inducer

For cases where a particular compound is needed to induce gene expression e.g. Pectin

Host response

Details any difference in the host defence response to a pathogen with a disrupted gene

Experimental evidence

  • Gene disruption
  • Gene disruption; gene mutation
  • Gene disruption; gene mutation; characterised
  • Gene disruption; gene deletion; complementation
  • Gene disruption; gene deletion
  • Gene disruption; complementation
  • Gene disruption; complementation; other evidence
  • Gene disruption; altered gene expression / gene regulation: overexpression
  • Gene disruption; altered gene expression / gene regulation: overexpression; complementation
  • Gene deletion
  • Gene deletion; altered gene expression / gene regulation: overexpression
  • Gene deletion; complementation
  • Gene deletion; complementation; biochemical evidence
  • Cluster gene deletion
  • Altered gene expression / gene regulation
  • Altered gene expression / gene regulation: downregulation
  • Altered gene expression / gene regulation: overexpression
  • Altered gene expression / gene regulation: silencing
  • Altered gene expression / gene regulation: down- and upregulation
  • Altered gene expression / gene regulation; complementation
  • Biochemical analysis
  • Biochemical analysis; mutation: characterised
  • Biochemical analysis; mutation: characterised; complementation
  • Functional test in host
  • Functional test in host: direct injection
  • Functional test in host: transient expression
  • Mutation
  • Mutation: characterised
  • Mutation: characterised; complementation
  • Complementation
  • Sequence analysis of sensitive and resistant strains
  • Sexual cross, sequencing of resistance conferring allele
  • Other evidence

Species Expert

Research scientist outside Rothamsted with excellent knowledge on specific pathogen species, who contributes to databaseby suggesting new entries and by revising existing entries

Entered by

Name of the curator who entered the interaction to the database

Reference

Related literature to the database entry, linked to PubMed or via DOI to the full publication where possible; Fulltext reference is given, if the article is not available online.

Comments

Field provided for any further free text information

CAS

CAS Registry Number (often referred to as a CAS Number)

Anti-infective (Chemical)

Chemical name

Compound

Accepted (or proposed) common name for an individual active ingredient expected to appear on the product label as definition of the product.

Target site

Target Site of Action: The biochemical mode of action is given.

Group name

The Group names listed are widely accepted in literature. They are based on different sources (mode of action, first important representative, chemical group).

Chemical group

Sub-grouping due to chemical considerations.

Mode in planta

Describes how chemical protects plant against pathogen attack, i. e.systemic - taken up by the plant's leaves or roots and spread throughout the plant's system.

FRAC CODE

Numbers and letters are used to distinguish the anti-infective according to their cross resistance behaviour (see www.frac.info).

Comments

Field provided for any further free text information for anti-infective information


Version: 4.2 Last revision: 03/10/2016

PHI-base is being developed and maintained by scientists at Rothamsted Research and funded by the Biotechnology and Biological Sciences Research Council (BBSRC, UK).

PHI-base is one of the ELIXIR-UK node resources.
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