Priya Crosby: Tick tock - how can genes tell the time?
Dr Priya Crosby, image courtesy of Priya Crosby
"Click here to listen to the full podcast episode"
I sat down with Dr Priya Crosby who is a molecular biologist at UC Santa Cruz. She’s interested in how circadian rhythms work at the cellular level, and how molecules can tell the time. But before we go any further, what exactly are circadian rhythms?
Priya: Circadian rhythms are an intrinsic biological oscillation with a period - a repeating unit - of around 24 hours. And they occur across biological kingdoms; fungi, humans, plants, fish, some bacteria. And at all levels of biological scale; so you can have a circadian rhythm in whole ecosystems, but you can also have a circadian rhythm at the level of the single cell, so single cells keep time. So they're these really broad biological oscillations.
Sally: When you say it's an intrinsic oscillating mechanism, that immediately makes me think of quartz watches, because I'll be honest, I find it magical that devices can tell the time, let alone biological living things. And if I'm right, quartz clocks tell the time because the crystal inside - a literal crystal of quartz - wobbles about a certain frequency and they're like, "Ah, after you've done a certain thousand wobbles, that's a second."
Sally: Do we have tiny, little, wobbling crystals inside our bodies that tell the time?
Priya: Not quite, so it's not quite as directly physical or perhaps as simple as that. But it is intrinsic in the same way, and if you think about your quartz watch, it doesn't require any external information to know how long a day is.
Priya: It doesn't necessarily know what the time is, you will have to reset your watch to the exact time, but it will know how long a day is left to its own devices. And that's exactly the same thing with circadian rhythms. So if you take anything that has a circadian rhythm, be it a plant or a human or even a single cell, and you put it in a dark room at a constant temperature with no external information about what the time is, it will still keep this intrinsic 24h biological oscillation just fine by itself, pretty much in perpetuity. So in that sense it's just like your quartz watch.
Sally: And what is this thing? Is it a protein? Is it a gene? Is it a cell?
Priya: So it differs slightly depending on the organism, but all circadian rhythms are intrinsically a cellular property. So their smallest unit, single cells, keep time, which I think really blows my mind, that's really what I focus on, the idea that a single cell knows how long a day is I think is nuts, right?
Priya: Within every single one of these cells, we generally speaking have what we would call a negative feedback loop, which is a term that I think we take from engineering, where generally we have a gene that makes an RNA that makes a protein, and that protein goes back and inhibits the transcription of its own gene, so it prevents its own gene being made. And then eventually that protein gets degraded and then it means its gene can be made again, and that whole cycle takes around 24 hours. So that's the kind of broad model of how single cells are keeping time, this transcriptional-translational feedback loop.
Priya: And I, at the moment in particular, really think about these proteins that are made by these specific circadian genes. I say that they go back and they inhibit their own transcription, but exactly how do they do that? They often make friends with other proteins and they interact with them and they do various things in different places in the cell before they go back, or in order to go back and inhibit their own transcription.
Priya: And I really look at how these different proteins interact with each other to generate that 24h oscillation.
Sally: So the gene is coding for a protein and that protein stops the gene from making the protein. Are you saying that the gene has to make friends and join up with other proteins in order to make that switch or can it do it if it's on its own, if it's a billy-no-mates and it has no friends?
Priya: No, it has to interact with other proteins. The important thing is, initially, the thing that is making the gene is not the gene itself. It's normally another transcriptional activator, so normally one or two proteins, and then they're making another protein that then goes back and interacts with the first protein or two in order to inhibit their own transcription. That's the really simple circuit. And so you have to ask, "Well, how is it physically interacting at that point of transcription to inhibit transcription?"
Priya: There are also some what we would call post translational modifications that are really important for how these proteins work. So proteins can get phosphorylated so they can go around and have a phosphate group put on them and that can change their function as well.
Priya: And so our lab in particular spends quite a lot of time thinking about how these post-translational modifications influence protein behaviour. So it's the same protein, but it now has a slightly different quality because you've stuck another thing on the side of it.
Sally: And presumably the reason why the gene turning on making the protein that would eventually turn it off doesn't immediately cause it to switch off is because it takes time for that concentration to build up in the cell, it takes time to add all of these phosphate groups on, and so is it that kind of slow build up? Is that what gives you the 24 hours? It would be kind of useless if it turned itself off immediately after it was produced.
Priya: Yeah, it's a really good question and we don't really know the exact answer to it. So we know that these proteins get made and we know it takes them 24 hours for the whole cycle to occur, but exactly where that delay is, why it is 24 hours, is still unknown.
Priya: We know that It probably has something to do with some of these phosphorylation events and also the time it takes for it to move from the cytoplasm, where it gets made, back into the nucleus, where it's being transcribed. That also takes time. But exactly how long all these delays are, and exactly what has to happen to make it 24 hours is still actually a really open question, which seems kind of crazy, right? The idea that we know it's 24 hours, but we don't really know how it is 24 hours. So it's a good question.
Sally: So you're looking at mammal cells and the mammal cells are able to know when 24 hours is up. What does that mean for the mammal in question? Thinking beyond the cell, what does that mean for the individual? What is controlled by these clocks?
Priya: At the level of the whole organism, there's very little that is not controlled by a circadian rhythm. The kind of obvious thing for you will most certainly be the sleep-wake cycle. You get sleepy and you wake up on a 24h basis, and that isn't just reactionary to the day-night cycle. If I put you in a dark room, you would also get sleepy and wake up about once every 24 hours. That's an intrinsic thing.
Priya: But there are so many other, much less obvious circadian rhythms. You might know, for example, that you have lots of cycles in things like hormones, so women in particular have a really clear cycle in testosterone. It's much higher in the evening, so if you're someone who lifts weights and you're female, generally speaking, it's better to do that in the evening, you will find it easier.
Priya: But then, all sorts of other things; your kidney function varies on a circadian basis, your reaction time. But then if you think about the level of the single cell that makes up an organism, again, almost everything there has a circadian basis which will inherently influence the whole organism's function.
Priya: I'm struggling to give you examples of things that don't have circadian rhythms basically, almost everything does at some level.
Sally: And you mentioned that this is an intrinsic mechanism and you just said if I was to stick someone in a dark room they'd still have this cycle. But I know that, for example, blue light affects when you feel sleepy. It's why all of my computer and phone screens turn red when it gets to a certain time at night. You can get jet lag and they say one of the ways to beat jet lag is to time your meals because mealtimes affect your circadian cycles.
Sally: So how do all of these external things affect what you're describing as an intrinsic mechanism that doesn't have any other inputs?
Priya: Yeah, so you've got to what we would call the second fundamental feature of circadian rhythm. So the first fundamental feature is they have a 24 hour period. But the second fundamental feature is they are able to synchronise their phase, i.e. what time they actually think it is, to specific external events.
Priya: There's no point in having an internal clock that thinks it's a totally different time to the time in the outside world, and that's exactly what happens when you're jet lagged, right? So, I currently live in California. I'm flying back to the UK on Thursday, so I will be 8 hours out of phase, which is not fun. But my body will, fairly quickly, over a couple of days, be able to realign what time it thinks it is with the external world.
Priya: And you've picked pretty much all the right cues. So when you see light is really important, when you eat food is really important, also when you're physically active is also quite important. And if you can make sure that when you do shift, when you are jet lagged and you do change time zone, that you very quickly try to do these things on the time of the place that you've arrived at, that's generally the best way of solving jet lag.
Priya: You're not going to beat it. You can't beat that aspect of your biology; you're going to be jet lagged for a bit. But you can make it less miserable and you can realign faster if you do think about when you see light, when you eat food, and when you're physically active.
Sally: Do all of the cells in an individual have the same clock?
Priya: Yes, essentially, in that they have the same components. So every single cell in your body has the same protein components that are forming this clock. So, yes.
Sally: And do all individuals in a species have the same clock? Because you hear about 'night owls' and 'morning larks' and what have you. Is that a feature of the proteins and the genes being different or the brain and the hormonal signal bit being different?
Priya: Possibly both, but the one that we know most about is the protein. So you're absolutely right that everyone has the same core protein components, but proteins can differ very slightly from protein to protein. We can have very small mutations that are not necessarily bad, but can influence how that protein functions, just a little bit, and that gives us rise to what we call chronotypes, so these different circadian phenotypes. And this is this idea of morning larks or evening owls.
Priya: So most people often, I think, intuitively know whether they are a morning person, whether they are a late night person, or whether they sit somewhere in the middle. And that is not normally - and I always thought this was very surprising - that's not something that just is in your head about how you've been socially conditioned. That is actually controlled by your biology.
Priya: You tend to find that people who are more 'morning people' do have very small mutations in proteins that alter their circadian clock just very, very slightly that makes them slightly more likely to be alert in the morning. And people who are more night owls, like myself, tend to have very small mutations that make them slightly more likely to be better at functioning later at night.
Priya: So yeah, that's a really intrinsic part of your biology, this kind of chronotypic difference between individuals.
Sally: Other than it just being super cool, why is it important to understand the molecular biology of circadian rhythms?
Priya: There's a few reasons. So firstly, and the one that really interests me, is that if you mess with your circadian rhythm, so particularly if you do things like you engage in shift work - jet lag is one thing, but shift work is like extreme jet lag, particularly rotational shift work, so if you work two nights and then you take a day off and then you do three days and then you do two nights, it's a bit like flying across the Atlantic over and over and over and over again - your circadian travel clock really doesn't handle that very well because it's continually unclear what the actual external time is.
Priya: And we know that people who engage in shift work are much more susceptible to a whole load of disorders. They're much more likely to get metabolic syndrome, so things like type 2 diabetes. They're more susceptible to a whole load of types of cancer. They're also more likely to develop a number of mental health issues, particularly things like depression.
Priya: It's really not good for you, but we really don't know exactly why it's not good for you. Fundamentally, at a biological level, we don't know why it's not good for you, and it means that we can't always make really good recommendations about what you might be able to do to reduce your disease risk if we don't understand the fundamental biology that underlies it.
Priya: I actually think this is another socioeconomic issue, so if you actually look at shift workers, I think lots of people think that doctors are mostly shift workers. But actually most shift workers fall at the kind of lower end of the income spectrum. They're in things like transport and packaging and shipping, and I think it might be a real driver of health inequality, that these people are being, as a function of their job, being forced to effectively mess with their biology, and I think that's really an important thing that people don't think about.
Priya: It's a cool idea that you have this internal sine wave and an internal clock, but the fact that if you mess with it, it's bad for you, and it's impacting some groups of people more than others, I think is quite important.
Priya: So firstly, the idea that if you mess with your circadian rhythm at the molecular level, things go wrong at the molecular level but we don't really understand why.
Priya: And then conversely, we also know that if you get a number of diseases, particularly some of these neurological diseases, things like Parkinson's and dementia, one of the really first symptoms that we see in these patients is not cognitive deficits or motor deficits, it's actually a loss of the capacity to maintain a circadian rhythm at the whole organism level.
Priya: So one of the primary reasons that people who have dementia are put into care outside of their own family home, it's not because they have necessarily deficits that necessarily require loads of help in a cognitive capacity, but that their circadian rhythm is so disrupted that they're up and awake and they need help in the middle of the night when their family members really need to be asleep and people find that really hard.
Priya: And so we don't really understand what's going wrong there, why these disorders are associated with disruption of circadian rhythms. But again, that is a fundamentally molecular question. What's going wrong at the molecular level to mean that patients with these disorders are disrupted in this way?
Priya: And so in both ways, if we can understand the basic molecular biology that underlies it, we might be able to make either behavioural or pharmacological suggestions that might make things like shift work less bad for you, and also for things like dementia, we might be able to, in some way, restore their circadian rhythm to some extent, which we know a) makes people much easier to care for, and b) actually improves their symptoms in many cases.
Priya: So again, it would mean that people with these disorders were able to be out of care and in their own family setting for much, much longer.
