Platforms, resources and approaches

A wide range of tools and hosts are used to study effector function.

Solanaceous model host and effector-target bioassays

Nicotiana benthamiana is the Solanaceous model plant used to study effector functions and to investigate the roles effector targets play in the plant immune system. Read more on host plants and assays here [1].

Computational Biology 

Computational biology in the Effector Group [2] encompasses identification and classification of effectors themselves, and the interactions of effectors with their hosts.

Cell Biology

Cell biology [3] is used to study effector delivery, effector and target co-localisations in infected and uninfected plants, and to verify effector-target interactions.

Protein-protein interactions

A number of yeast-2-hybrid and split-ubiquitin libraries, and pull-down assays are available for use across the effector consortium. These resources and approaches provide the principle means by which effector targets are identified and verified. Read more on protein-protein interactions [4].

Genomics and transcriptomics

The genome sequences of all of the pathogens we work on have been sequenced. Moreover, the crop host plants potato, tomato and barley are sequenced. This allows us to study transcriptional changes in both host and pathogen (wild-type and mutant forms) during their interactions, using microarrays. In addition, RNAseq is being used to investigate detailed transcriptional changes in many of the pathogens we study. These studies are often run through The James Hutton Institute Genome Technology facility.

Pathogen Biodiversity

Studies of effector gene sequence diversity are vital to inform us about the co-evolution of these virulence factors with their target proteins and with resistance proteins in the host. The James Hutton Institute houses pathogen collections providing a wealth of biodiversity for sequence studies, epidemiology and population biology.