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Reprogramming of small RNA function in plant-pathogen interactions

Periodic Reporting for period 3 - PATHORISC (Reprogramming of small RNA function in plant-pathogen interactions)

Reporting period: 2020-05-01 to 2021-10-31

This project investigates how a particular mode of gene regulation - repression of gene activity via small non-coding RNA molecules - is employed by plants in their defense against pathogens, and, conversely, how some pathogens may take advantage of this system to promote virulence. The research has broad societal relevance in at least a couple of ways. First, it adds new knowledge on an important aspect of interactions between plants on the one side and pathogens as different as viruses and fungi on the other. Given the impact on plant disease for food and fiber production world wide, it is of great society to learn more about plant disease to be able to take efficient measures against crop destruction in the future. Second, it tries to define exactly how plants tell the difference between their own and foreign (e.g. viral) RNA. This is a fundamental problem facing all cellular life, and it is possible that its solutions in plants extend beyond the plant kingdom in relevance, possibly even to human biology.

The precise objectives of the project are
1) to figure out how recognition of foreign RNA is coupled to a specific positive feedback module in small RNA-guided gene repression that allows exponential amplification of repression specifically against foreign RNA.
2) to find out how the abundance of the central factor in small RNA-guided gene regulation - ARGONAUTE - is controlled, and how this control relates to susceptibility towards fungi that use small non-coding RNA injected into the plant as virulence factors.
3) to find out how gene regulation via a specific type of covalent mRNA modification - N6-methyladenosine - relates to small RNA-guided gene regulation, in particular in cells undergoing activation of innate immunity.
We have started our investigation of this problem by turning the question around: Instead of asking directly "what is it about foreign RNA that allows positive feedback", we have asked "what is it about endogenous RNA that leads to restriction of positive feedback". This turns out to have been a fruitful way of attacking the problem: We now have a good understanding of molecular systems that must be in place to keep positive feedback from happening on endogenous mRNAs. Armed with this knowledge, we can now investigate precisely how these systems get overridden in the face of viral RNAs.

We have focused on ARGONAUTE1 and tried to identify properties of this protein that allow its abundance to be tightly controlled via regulated proteolysis. Our work in the project until this point has allowed the identification of a precise site in the ARGONAUTE1 protein that is responsible for interaction with several regulatory factors and that plays a role for regulated degradation - but not activity per se - in vivo. We have yet to find out how ARGONAUTE1 variants in this site behave in pathogen interactions, an important set of experiments for the second half of the project.

We have been laying the groundwork here. We now have a clear idea of processes for which the N6-methyladenosine modification system is important, and we have mapped mRNAs that are under dual control by small non-coding RNAs and by N6-methyladenosine. This is the prerequisite for figuring out if and how mechanistic links exist between the two important modes of post-transcriptional gene control.
The progress beyond the state of the art has been briefly summarized together with the outline of the work done above.

With the progress made thus far, and a full second half of the project ahead of us, we expect to be able to deliver clear answers to the questions raised in the three project objectives outlines in the preceding sections. Exactly what these answers will be is a bit early to say, but we feel confident that we have made enough progress to deliver answers by the end of the project period.