Nabila El Arbi sheds light on plant RNA regulation

You did your PhD in Markus Schmid's research group at Umeå Plant Science Centre. What motivated you to move to Umeå and join Markus’ group?

Nabila El Arbi: Well, to be completely honest – I was not actively looking for a PhD. I was in the final weeks of wrapping up my master’s thesis project and was confronted with the simple yet scary question: “What do you want to do now?”.  By chance, somebody at a festival told another person, who then told me, about a “really good plant science centre” in northern Sweden. That is how I found UPSC and the open PhD position in Markus’ group. When I read the project description, I thought this was really tailored to me, building up on what I focussed on during my Bachelor’s and Master’s projects. I immediately had a head full of ideas. At the time, Markus had two PhD positions available and offered me and the other candidates to visit UPSC and meet people from his group. We got along well, and this gave me an additional motivation boost for the project.

During your PhD, you explored “the role of RNA metabolism in the context of plant development under temperature stress”. Why is it important to study this?

Nabila El Arbi: For me as a researcher, I want to know more about things that are not known or poorly understood. Very little is still known about how RNA metabolism is regulated in plants. When genes are activated, their DNA sequence is transcribed into RNA, which then serve as a protein template. This sounds very simple, but the process is much more complicated. Which gene is activated when and why and how is the transcript processed? We still lack a lot of information to answer these questions that are central to the regulation of RNA metabolism and plant development and adaptation in general. Just minor changes in the RNA machinery might have big effects. This can provide us with incredibly powerful tools to create more resilient plants, but it is really important that we first understand everything properly.

One gene can contain information for different protein variants

You focussed mainly on alternative splicing. What is that and why is it relevant for plant development under temperature stress?

Nabila El Arbi: It is not so easy to describe what alternative splicing is, but one can maybe explain it a bit by comparing it to one of these super awesome functional hiking trousers that contain a lot of zippers. You do not need several trousers but can only take one pair and by removing or adding parts you can adjust it to your needs. It is still the same pair of trousers, but it can be short or long, it can have several pockets or just a few. With alternative splicing, it is a bit similar. All information is stored in the DNA but the way how it is transcribed into RNA can vary. One gene can contain information for different protein variants depending on how the various parts of the gene are put together when transcribed into RNA. The fruit fly Drosophila has one gene that has about 38 000 different splice variants, meaning different RNA sequences that are produced based on the information of this one gene. At least 19 000 of them have a function. I think this is absolutely mind-blowing, especially when considering that Drosophila just has about 15 000 genes. This example illustrates the variety that can be produced by alternative splicing. Plants use this mechanism a lot to flexibly adjust their growth and development to their environment, especially when adjusting to cold or heat.  

What do you consider as the major outcome of your thesis?

Nabila El Arbi: When I started my PhD, there were only two papers published about the splicing mutant that I focussed on. It is called porcupine because of its “spiky” look. This mutant grows completely normal under ambient temperature but develops severe defects under low temperature stress. The PORCUPINE gene contains information for a protein that is part of the splicing machinery but becomes more active under low temperature stress. We compared it with other splicing mutants that show similar behaviours and investigated how they are regulated at different temperatures. They all appear to be controlled at least partially by overlapping pathways, but they are still quite different from each other. It is very complex. The good thing is that we now have more data and knowledge about alternative splicing and temperature, and that helps us to formulate the questions more precisely. It is a very good starting point for people who will follow up on these projects. For me, this is one of the biggest outcomes.

We know now much more, but all our results opened up many more questions.

You summarise your thesis with “It is really complicated”. Did you expect this complexity when you started your PhD?

Nabila El Arbi: No, not at all. When I started, I was very optimistic, but I was very quickly confronted with the fact that nothing worked as expected. The porcupine mutant was very interesting but also not very confined. The mutation affected everything from root growth to shoot growth, from flower development to leaf development – like the magic box where you take out a tissue that never ends. When we did an experiment to answer one question, the answer was often neither yes nor no. We even started to collaborate with a group in Germany and were sure that from these joint experiments, we would get a clear answer about how the PORCUPINE protein regulates alternative splicing, but the results are only clear in the sense that they are unclear. We know now much more about alternative splicing and temperature than when I started my PhD, but all our results opened up many more questions. It is really complicated.

What kind of challenges did you have to overcome during your PhD?

Nabila El Arbi: During my bachelor’s and master's projects, I was very protected. My supervisor was very well organised and gave me very clearly structured projects, which was great. When starting my PhD, I had to learn that the responsibility was now on me even though I was of course supported by Markus and his group. I had to plan the experiments, do the experiments and deal with troubleshooting. At one point, I was the person who knew most about the project. It is normal during the PhD; I just did not anticipate this in the beginning.

In plants, the mechanisms seem to work completely differently.

Then, I had to deal of course with the frustration that things did not work as expected. We were working with models that were based on results from humans and yeast, but in plants, the mechanisms seem to work completely differently. It was challenging not to get lost in the project and just accept that we might not get a clear answer even if I would repeat the experiment another time. I had to learn to let go of some projects even though they were interesting, choose what was safe and focus on succeeding with my PhD.  

What are you planning to do now?

Nabila El Arbi: Ah, the scary question again. I do not know, honestly. Frankly, I just want to breathe for a moment. I have always put so much pressure on myself to not take a break, to keep moving and to start the next project right after another has ended – I do not feel like I want to do that anymore. I will take some time off now to see what possibilities are out there and then choose something that I really feel passionate about. I have applied for a position at the European Space Agency because I would really like to work in the space sector, maybe even go to space if possible. They were looking more for engineers and not for biologists, but I thought I just give it a try. Otherwise, I think I would like to take a break from academia and to try how it is to work in industry. But first, I will visit my family and some friends that I have not seen for a long time.