Fungi-plant intergenomic relationships

Small RNAs are critical for transcriptional and post-transcriptional gene silencing. Recently, scientists discovered their role in plant pathogenesis.

Scientists now hypothesise that small RNAs and effector proteins such as the Argonaute (AGO) protein family move and function across the plant-pathogen interface. Researchers within the EU-funded SMALLRNATRANSFER (Intergenomic relationships during plant-pathogen interactions) project tested this theory.

As the interaction of the fungus Colletotrichum higginsianum with the Arabidopsis thaliana plant is well characterised, researchers used this model for testing. They utilised high-throughput sequencing technology to identify C. higginsianum-specific small RNAs associated with Arabidopsis AGO proteins.

After obtaining small RNA libraries from Arabidopsis plants infected with C. higginsianum, researchers performed deep sequencing. As they could not confirm that most of the fungal reads were bona fide, they generated small RNA libraries from C. higginsianum mycelia. During this process, they identified important components of the RNA silencing machinery, namely two AGOs, two DICERs and three RNA-dependent RNA polymerases.

To characterise small RNA profiles of C. higginsianum, project members generated several gene silencing-defective fungal strains as well as epitope-tagged fungal AGO1 and AGO2 proteins. Some of the gene silencing-defective fungal strains such as Δdcl1 and Δago1 caused defects in conidiation and conidia morphology. Conidiation refers to asexual reproduction from spores.

Through transcriptomic analysis, researchers demonstrated that a particular C. higginsianum strain has a resident virus. This is a key finding as this fungus uses RNA interference (RNAi) machinery to control virus proliferation and prevent defective conidiation. Results are intriguing as they indicate that there is no connection between plant immunity suppression and virus-induced decrease in pathogenesis.

The knowledge and tools developed during this project are invaluable for basic and applied research on plant-pathogen interactions. Future research activities could explore the impact of viral small RNAs and mutualistic virus/fungus associations on disease incidence and severity in plants.

Applications include pest control and development of disease-resistant plant strains. This in turn should help enhance food security and quality.