Caroline Dean: Winter is coming

Caroline Dean, Image Courtesy of Caroline Dean

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As a teenager, Caroline Dean was more into marine life than plant life, having been inspired by the great undersea explorer Jacques Cousteau, and she initially went to university to study marine biology. But a few plant-based practical lessons persuaded her that the green stuff was worth another look, and she became hooked on plant sciences. Fast forward a couple of years, and another chance encounter set her on the path to the scientific question that would come to dominate her research career. 

Caroline: I liked growing plants and I went to California as a postdoc and bought some tulip bulbs. And the person in the shop said to me, "Put them in the fridge for six weeks before you plant them in the soil." And that intrigued me, and so then I went and read a lot about this, and of course some plants need winter before they will flower and that's a way of making sure they align their flowering, which is a very sensitive developmental phase, with much better environmental conditions.

Caroline: Different plant species use different strategies to maximise their reproduction, basically. And in different parts of the world different strategies work, some work better than others. There are two major seasonal cues: photoperiod, the day length change, different times of the year; and cold temperature. Exposure to prolonged cold has been observed many, many years ago as a very important cue for flowering.

Caroline: And many plants overwinter before they flower, or they actually don't even germinate until the spring and then they flower very rapidly in the summer. Plants in the desert monitor water, and so, depending on where plants are growing, they'll use different environmental cues, basically to judge when is the right time, when is the best time to flower.

Kat: I love that a chance encounter with some tulips has basically set you on your entire research career to find out how do plants know when winter's coming, how do they deal with it, and what do they do afterwards.

Caroline: Yeah, I think a lot of people tend to follow on something they've started in their postdoc period, but for me, I think it was fantastic to have this just brand new question and it really has sustained me for 35 years.

Caroline: And it's taken us from a very plant specific question into mechanism, which has taken us into how genes are regulated in different environments, not just for plants, but for everything. What gene expression is monitoring in terms of environmental inputs? Is it an average, for example, for temperature? Everyone assumed it was an average temperature that was driving changes, but we've ended up finding it's the fluctuations, the daily fluctuations. that are important as well.

Caroline: But it's also taken us into memory mechanisms because of course if you have to decide, "Have I had the whole of winter," if you're a plant, it's not how am I feeling now but also what was the temperature last week and the week before and the week before that. You have to register temperature over a prolonged period, and that involves memory mechanisms, which has taken us into these memory mechanisms that are important in the human body as well. How our DNA is packaged in our cells, it's the same overall mechanism, it's absolutely remarkable. We can study it in plants and really see the same mechanisms happening in the human body.

Kat: I really want to dig into this because when we talk about memory, we think about having a brain or a calendar or something like that, but plants don't have brains in the same way that animals do.

Kat: So let's dig into a bit more about what you're studying because there's a lot of plants in the world, but you're really just focusing on one. Tell me about that one.

Caroline: When I started, which was a long time ago, as I say, 35 years, when you looked at plant biology, people worked on many different species because they studied that particular process and that particular species was the best one to study that in, but we couldn't then compare what we are understanding between species very well.

Caroline: And just as I was setting up my lab, the whole Arabidopsis initiative emerged, this multinational initiative, where actually plant biologists decided that we needed a reference plant. A plant where we could not only compare between labs because they'd chosen to work on the same species, but also one where we could affect by mutation, a process that we knew nothing about, and go from a phenotype, how that mutation changes the behaviour of the plant, to clone the gene.

Caroline: It was what was called a molecular genetic approach. You could actually clone the gene based on no understanding except how it changed the plant behaviour. And the multinational community decided to pick Arabidopsis and to set up resources so that we could easily clone genes that way. And so in 2000, the first eukaryotic plant genome, which was the Arabidopsis genome, was published through this effort of this multinational community.

Caroline: And that has really transformed plant biology. So we can now go in, look at the DNA sequence, understand which genes are controlling which different traits and processes, and compare that widely across all of the many thousands of plant biologists across the world who are using Arabidopsis.

Kat: And so Arabidopsis has this response to winter. It knows when winter's come, it knows when winter's been. What do we know about how it's doing that? What are the key players, the genetic players in this plant? How are they working?

Caroline: Well, let me just start with one thing. I mean, actually Arabidopsis was picked because the types of Arabidopsis that most people use didn't need cold because it was a rapid cycler; the advantage was you could do your genetics very quickly.

Caroline: But actually, when I went and searched the literature, it was clear that there were many types of Arabidopsis that did need the cold. And there had been a lot of genetics on that in the 50s by a group of Arabidopsis researchers that had worked on the genetics of a whole series of processes but using Arabidopsis.

Caroline: So I went over to Germany and met some of these researchers who gave me all their seed. They were just retiring and they were very delighted this young person was going to come and carry on their research. What was clear was that when we looked at the different inputs for flowering, whether it be photoperiod or ambient temperature or this long period of cold requirement or fertilisation, actually all of those pathways converged on a common set of genes.

Caroline: So, that was quite a eureka moment in the field, because before that, everyone had assumed there were very different mechanisms for plants; whether they needed water in the desert or whether they needed cold, that there's going to be an entirely different molecular mechanism underlying that. But the initial work in Arabidopsis quite quickly took us into the realisation that there are many inputs, but they all converge on the same targets.

Caroline: And so that you can see now how evolution would have then picked a different input and that could have evolved from the same mechanism to give very different responses in different plant species. So that was a really exciting time.

Caroline: Now we and others then carried on with looking at the winter. And the need for winter and the ability to respond to this winter cold all turned out to be immediately through the regulation of one gene.

Caroline: And this gene makes a protein that basically stops the plant flowering. It's a gene called flowering locus C. And you can sort of visualise it as a brake in the car: if the brake's on, the plant won't flower. So if the plant needs winter, when it germinates, it makes a lot of this protein and the plant will not flower.

Caroline: Then slowly, slowly, over the long period of winter, that gene is switched off. So then in spring, there's no protein, there's no break. The plants can flower when the day lengths get long and the afternoons get warm, and all of the other factors that promote flowering can then actually cause flowering to occur.

Caroline: And so as we got into this mechanism and it was very interesting - that it was one gene made our life much simpler - we could really do a deep dive into the mechanism of how that worked. And so that's taken us into the world of epigenetics. In that cold switches the gene off quite quickly. But then what happens is there's a second switch, which is a low probability switch, so it takes a long time for that to occur throughout the whole plant. So the plant then has to go through the whole of winter before it understands, "Yes, spring has come."

Kat: So this stops your plants getting confused by a really unusually warm day in February. They don't all suddenly go, "Woohoo lads, it's time to come out."

Caroline: Absolutely right. You know if it was just a transcriptional shutdown, then any sort of perturbation in February or whenever, they would get horribly confused. This is a lockdown to prevent the gene reactivating, and if you look at the whole plant, it's halfway through winter, it's a mosaic. In some cells it's off and in some cells it's on, and it takes the whole of winter for all of the cells to have the gene switched off.

Kat: Because this was going to be my question because last winter, I'm sure we all remember that it was a big, big deep freeze. I don't remember a winter that cold for many, many years. And then last summer was a very, very hot summer. So this presumably gets some kind of smoothing out of the noise of all these temperatures going up and down throughout the winter and then the summer.

Caroline: What our current work is looking at actually is how the plant is dealing with all these fluctuations, and also, as you say, winter is not the same each year. How is it smoothing it out?

Caroline: What we've found is that actually the plant is monitoring many, many aspects of the temperature. And that was a change from thinking, because people imagined there would be some accumulation of some protein that was accumulating at a certain temperature and accumulate it slowly. And so you could imagine then there will be a threshold over a certain period of time; once enough had accumulated, the plants would be allowed to flower or repressed in our case.

Caroline: But in fact as we go in and look at what is going on, the plant is using every facet of that fluctuating temperature.

Caroline: And so all of those facets converge to regulate this gene FLC. So it's smoothing but it's also been very clever in that some years there'll be very cold nights, so the cold nights will drive mostly what's going on. Other years there'll be fluctuations in warm afternoon temperatures and that will prevent it silencing too quickly.

Caroline: So the plant is really using many aspects of that temperature profile to make sure it's really understanding what's going on out there. It's much smarter than we realised.

Kat: I'm finding it incredible thinking about my garden and all the different plants. So is it the same genes and the same mechanisms in all these plants just set to go at different times of the year as well?

Caroline: I would say, do you remember I described how the different species converge to regulate a common set of targets? Those common targets will be the same in all of the plant species. As we look at the different inputs, the environmental inputs, you can see evolution's used the same sort of mechanism, but often chosen different players to do that with.

Caroline: So that's still an ongoing process, I would say, but a lot of those plants won't be monitoring winter, they'll be monitoring day length, and then it will input those slightly differently. They'll also be monitoring the ambient temperature.

Caroline: And there's a whole series of work going on in many labs trying to understand how plants are really integrating all this information, because of course it's hugely important as we're getting such fluctuating climates, plants that have adapted to a certain climate are getting confused. And we've really got to understand the plasticity and yet the robustness to actually be able to, for our major crops, make sure the yield doesn't drop too much and to really understand what's going on and the implications of changing climate.

Kat: Yeah, and that, I think, is the really big question. You're talking at a Genetics Society meeting in November, which is all about the genetics of future food production, the green revolution.

Kat: So where are the really big challenges in our understanding, particularly relating to your field of understanding how the environment, how seasons are talking to our plants. What do we really need to understand?

Caroline: Well, I think the major concepts underlying the mechanism are not what we expected.

Caroline: So if we can really understand the actual temperature inputs, I like to call them antennae of the plant. They've lots of antennae looking at different facets and how they actually converge to regulate this one gene, in our case FLC, but it'll be what the targets are in other plants, especially crops. How those fit together so that in different years are they going to be flexible to give us the same silencing or do we perhaps need to breed for particular types which could cope better?

Caroline: We also need to understand really, just how conserved the switching mechanism is in different plant species, because, we might want to be tweaking by breeding the kind of requirements for cold and photoperiod to actually make sure in our crops, for example, we have a nice production throughout the year.

Caroline: Because what's happened recently, and there's one example, you mentioned a deep freeze, for a lot of our vegetables - all the brassicas, the cauliflowers - these are very closely related to Arabidopsis, so you can go quite quickly and look at the same mechanism.

Caroline: When there's a deep freeze, actually they all vernalise too fast. And so what happens is that the growers have sown them all in August and then they plant different varieties so that they have a nice sequential harvest so we can have them in our supermarkets all year round. But of course if there's a deep freeze and suddenly all of that changes and they all flower rather similarly, so there's a glut for a month and then there's two months where there's no availability.

Caroline: We saw that with tomatoes and peppers this year from Spain. So somehow we have to understand how different varieties, by integrating these different signals in different ways, how they've adapted to their different climates, and then incorporate that in our production chain so that we have good food supply.

Caroline: And I think understanding the mechanism will really allow shortcuts to actually do that.

Kat: I guess now we've got some interesting genetic tools as well. I'm thinking about things like CRISPR. You can actually go in and make really specific changes to genes or switch in a gene from one closely related species to another that just tweaks this response to the environment. Is that a possibility?

Caroline: That's absolutely a possibility and for FLC, the joy of Arabidopsis is that it is adapted to environments from right at the Arctic Circle all the way to the equator. And when we look at what's the basis of that adaptation for vernalisation, it's often single nucleotide changes within the FLC gene.

Caroline: So that then absolutely opens up gene editing to create now variation, which will influence the response to cold and what we know in Arabidopsis translates exactly to all the vegetables. So if we know what the targets are in wheat, then absolutely gene editing would be a very straightforward thing to do.

Caroline: And of course, around the world, it's very safe technology. So there are new tools and going forward, we hopefully will have the understanding to be able to tweak whatever the plant species is in whatever way we want.

Kat: I think it's very exciting now we're in a world of really precision gene editing because a lot of the old GM techniques were about putting things in, adding whole genes and other bits and bobs of DNA, whereas we're talking now about making very, very specific changes that don't change anything else in the rest of the plants.

Kat: We're not adding anything artificial and hopefully people will understand that that is very safe and it is tantamount to a natural process of mutational change.

Caroline: Absolutely. That's what we can do with the gene editing. But I think if you look at the variation between different varieties of plants, many genes move around, many genes have been added.

Caroline: So I think we shouldn't convey the idea of, "If we add something it's dangerous." It's really not, and there's a lot of understanding there. So I think I would just argue that we shouldn't be too anxious about GM. Gene editing has now been allowed and absolutely it's precise and it's exactly the same mutation event as in many cases in different genes and natural variants.

Kat: And we shouldn't, of course, forget that my heroine, Barbara McClintock, was the first person to discover that genes can jump around in a plant, in maize.

Caroline: Absolutely. I think one of the interesting things is how fast plants can adapt to different situations. Her thesis was always that stress would induce the transposons to jump, which would then change gene expression all over the genome, and give that plant an advantage to survive the stress.

Caroline: She proposed this many, many years ago, but actually, when you get to the molecular level, that's exactly right. The molecular understanding now is now endorsing all of the ideas that she had way before any of this molecular data came out. She was remarkable in terms of the imagination of just what was going on at the DNA level.

Kat: Yeah, and I'd recommend that our listeners do go and check out our previous episodes about Barbara McClintock and what she did. But just to wrap up, I do want to ask you, are you a keen gardener outside the lab? And when you look at your garden, do you think about the genes and the molecules or do you just enjoy the plants?

Caroline: We have a big garden. I look at it every breakfast. I stare out there because one of the very first things that happens in this silencing after a frost is we have induction of a non coding piece of RNA at this gene and we called it COOLAIR. And the first night there's a frost, COOLAIR peaks enormously.

Caroline: So every time there's a frost, I go out and look at all these plants and think, I wonder what's been induced. So absolutely. I love thinking about it. I think by looking at the plant, it kind of tells you the questions to go and pursue, like my tulip moment, you know? I think there is so much to understand them about how plants change in response to the environment.

Caroline: They're amazingly plastic, so actually looking at them is really good.

Thanks to Caroline Dean, from the John Innes Centre in Norwich.