Fungal immunity: how do NLR genes allow fungi to navigate the microbial world?

Secondary Supervisor(s): Dr Lisa Lamberte

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Microbiology, Plant Science)

Project Outline

The ability of an organism to distinguish between self and non-self and to mount an effective response is the foundation of a functional immune system. The immune systems of animals and plants have been well characterised. However, the nature of the fungal immune system, how it works and how it allows fungi to effectively interact with other organisms in their environment is unknown.

Nucleotide-binding domain and leucine-rich repeat (NLR) genes play important roles as the sensors/receptors of non-self molecules and in activation of immune responses such as transcriptional reprogramming and cell death. The role of NLR genes in these processes has been thoroughly described for plants and animals, but how they contribute to the fungal immune system is unexplored. Fungal NLR genes also show hugely increased diversity of N- and C-terminal domains in comparison to their plant and animal counterparts, suggesting that fungal NLRs may have interesting and unique functions or modes of action not previously described. In this project, we will investigate the roles of NLR genes in the fungal immune system. Our overall objective is to understand how NLR genes contribute to self/non-self recognition and to interactions with potential pathogens.

To achieve this objective, we will use the genetically tractable model fungus Zymoseptoria tritici. This fungus also causes Septoria tritici blotch (STB) disease of wheat and is one of the world’s major agricultural pathogens. Z. tritici has a complement of 20 NLR genes, a comparatively small number compared to other ascomycete fungi. This makes it an appealing system to study how this gene family contributes to diverse processes such as fungal-bacterial interactions, self-incompatibility and host plant interactions.

In addressing our objective, this project will provide the student with training in diverse techniques related to molecular and cellular biology, bioinformatics and protein biochemistry. A key activity in this project will be the use of targeted reverse genetics to make fungal gene knockout strains for subsequent characterisation. In addition, high-throughput screens of microbial collections will be used to identify antagonistic interactions between specific fungal or bacterial species. RNAseq profiling of the fungal transcriptome during interactions with other microbes will be used to identify gene networks important for a coordinated immune response. Confocal fluorescence microscopy will be employed for direct visualisation of microbe-microbe interactions using labelled reporter strains. Finally, proximity labelling techniques such as TurboID will be used to identify key protein-protein interactions during fungal immune responses.

Prior experience of working with bacteria/fungi, or in any of the techniques listed above would be desirable but not essential, as full training will be provided. For informal enquiries, please contact Dr Graeme Kettles at g.j.kettles@bham.ac.uk.

References

Uehling et al. PLoS Pathogens. 2017;13(10):e1006578. doi:10.1371/journal.ppat.1006578.

Daskalov A. iScience. 2023;26(6):106793. doi:10.1016/j.isci.2023.106793.