Interkingdom communication via small RNAs: Parasitic nematodes and their plant hosts

Supervisors: Mark Blaxter, Peter Cock

Project description:

Plant parasitic nematodes remain a devastating threat to global agriculture, even in the face of naturally resistant crop cultivars and anti-nematode treatments. Sedentary plant parasitic nematodes manipulate their hosts, avoiding induction of immune systems while establishing a permanent feeding site. Feeding sites are characterised by transformed cell types that channel nutrients to the nematode to the detriment of the host. The nematodes secrete many different proteins and peptides into these feeding sites during establishment, and continuously during maintenance. Secreted products thus play roles in site induction as well as in digestion and nutrient uptake. The secreted products include plant hormone mimics, carbohydrate-active enzymes acquired by horizontal gene transfer, and proteins of unknown function.

This project will explore a possible novel axis of nematode manipulation of the host plant through small RNAs. In animal parasitic nematodes it is now clear that many species secrete specific small RNAs, including microRNAs, into their hosts, and in gut parasites it has been shown that these small RNAs affect the anti-nematode immune system. The small RNAs are carried by an argonaute protein that has been shown, in model species, to play roles in small RNA trafficking between cells.
In the commercially important potato cyst nematode (Globodera species) - potato system (where the nematodes do ~£80 M of damage annually in the UK) we know that specific argonaute genes, components of the small RNA system, are upregulated in the stages that establish the feeding site. Why is this? Which small RNA cargoes do these argonautes carry, and what endogenous (nematode) and host (potato) genes do they target?

Using both laboratory (greenhouse and growth chamber controlled infections; small RNA sequencing) and computational biology (small RNA classification, target gene identification, gene regulatory network analyses) the student will identify the small RNAs expressed by the nematode and the host in the root system. Small RNAs secreted by the nematode into roots will be identified, and the effects of these small RNAs on host small RNA and protein-coding gene expression networks identified. The genomes of the potato host and the potato cyst nematodes have been sequenced.

The project will be based jointly in the James Hutton Institute (Dundee), a world-leading agricultural research centre leading genomic work on Globodera, and in the Institute of Evolutionary Biology (University of Edinburgh), which has expertise in nematode genome analysis and small RNAs. To support the project, Blaxter and Cock have close collaborations with Amy Buck (Edinburgh; nematode smRNA-host transfer), John Jones (JHI; nematode parasitism of plants) and Runxuan Zhang (JHI; potato smRNAs).

References:

1. Buck, A.H., et al., Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat Commun, 2014. 5: 5488.
2. Eves-van den Akker, S., et al., The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biol, 2016. 17:124.
3. Buck, A.H. and M. Blaxter, Functional diversification of Argonautes in nematodes: an expanding universe. Biochemical Society transactions, 2013. 41:881-6.

 

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