Power naps: when molecules in our bodies like to nap

Hibernating RNA polymerase (the image from Irina Artsimovitch’s laboratory)

A superpower we take for granted.

Scientists say it is impossible for a human body to go without food for longer than 8 days, with some optimists claiming that up to 21 days is sometimes possible. Even the Bible considers 40 days of fasting the ultimate feat of bodily strength. Yet what’s not possible for a human — even the legendary Christ — appears to be fairly mundane for creatures that are comparable to us in size, anatomy and lifespan. These creatures are bears.

Bears have a remarkable knack for starvation. Unlike humans, they can enjoy their breakfast in mid-September to have their lunch only in April! I guess if they would be into academic research or the literary career, it would be easy for them to implement this golden rule by Kingsley Amis: “A bad review may spoil your breakfast, but you shouldn’t allow it to spoil your lunch.”

— Hey bear, a bad review may spoil your breakfast, but you shouldn’t allow it to spoil your lunch.
— Easy as pie, pal. Just give it to me in September (proceeds to reading comments by Reviewer 2, yawns, and falls asleep).

So, what’s the trick? What makes bears so good in their ability to cope with starvation? The answer is hibernation.

All animals are equal? You’ve got to be kidding. Hibernation. We sort of know what hibernation is, but really — not quite. When I was a kid, my understanding of hibernation — mainly learned from Fozzie Bear — was plain and simple: a long nap. Over the years, however, I learned that the actual state of hibernation is much deeper and more complex than usual sleep. Although we do not fully understand this process, we now know that hibernation has many unique metabolic signatures that distinguish it from ordinary sleep, and mechanisms of hibernation appear to be wildly distinct in different species. This suggests that the ability to hibernate has evolved many times in the history of life on Earth, with many species inventing their own unique ways of hibernating.

For instance, when grizzly bears hibernate, their body temperature decreases from 38 to 31°C; their heart rate drops from 40-50 to just 8-19 beats per minute; their respiration decreases from 6-10 to just about 1 breath per minute; their circadian clocks get shut off; and their metabolism not only slows down but changes in such a way that bears do not release bodily waste for several weeks. Instead, they turn their urine into protein through a urea recycling process, along with other metabolic changes that allow them to survive cold, despondent winters.

But in other species, like Arctic ground squirrels, the process of hibernation looks strikingly different. These animals undergo the process of “supercooling,” in which their average body temperature drops to -3°C, with only their heart and brain remaining slightly warmer. Unlike most other animals, these squirrels can somehow prevent the nucleation of ice crystals in their bodies. This allows them to remain alive and soft, yet technically frozen, when the air temperature drops to -26°C. Just imagine if we, humans, would have such a skill!

Even a more impressive example of hibernation can be found in smaller animals, ironically known as water bears or tardigrades. While actively growing tardigrades are highly sensitive to various stressors, including heat and cold, things totally change as they hibernate. When these caterpillar-looking creatures encounter starvation or stress, they rapidly purge most of the water from their bodies. This “dry hibernation” allows these (not-so-much-)water bears to survive prolonged stress for decades and possibly much longer. In this state, tardigrades can survive exposure to extreme environments, including temperatures as low as -200°C and as high as 150°C, or high doses of radiation, or life in the open space outside our planet.

Thus, hibernation is a superpower: when organisms hibernate, they can do things impossible in their ordinary sleep or alert state: being able to enter a state of hibernation allows organisms to survive in some of the most extreme conditions known to science. No wonder, we, humans, would gain a lot if we could understand this process better and learn how to induce hibernation at a desired time in a target organism, including our own bodies. Putting gravely ill people or astronauts to sleep would be one immediate application of such a hibernation by design.

More common than you think. What is even more important about hibernation is how common it occurs in nature. Contrary to popular belief, hibernation is not limited to large animals or “weird” insects. In fact, hibernation is routinely exercised by practically all known microorganisms, including most studied bacteria.

One reason we know little about the hibernation of microorganisms merely stems from semantics. When bacteria hibernate, we usually do not call them ‘hibernating’. Instead, we call them ‘dormant’ or ‘persistent’. Semantics frequently screws us up. Remeber George Carlin’s ‘Soft language’? While not deliberate or malicious, this use of different terms for hibernation of animals as opposed to hibernation of germs creates a common and wrong perception that hibernation is rare, and the ability to hibernate is limited to just a handful of animal species that need to survive harsh winters.

Instead, we actually know that when bacteria face starvation or stress, including exposure to certain drugs and therapies, they undergo a conceptually similar transformation to the one observed in grizzly bears, squirells or tardigrades: some bacteria lose their water, some shut off most (but not all) of their metabolism, some produce special anti-freeze agents that prevent formation of ice crystals when bacteria are exposed to sub-freezing temperatures. This allows bacteria to survie in hostile environments for a very long time. For example, recent studies of the Greenland ice sheet have identified and ‘resurrected’ a specimen of the bacterium Chryseobacterium greenlandensis that are 120,000 years old! And it is possible that 120,000 years is very far from the actual survival limit for a hibernating microorganism.

This example goes to show that hibernation — frequently viewed as something exotic — is in fact one of the most common survival strategies of modern microorganisms. What is even more important: at least in the microbial world, the process of hibernation shows that life can be put on hold, paused, or at least marginally suspended for thousands and thousands of years without loss of viability. Thus, a typical germ can easily outperform Briar Rose, making bacteria extremely successful in surviving not only starvation and stress but also clinical drugs that we use to cure bacterial infections.

When organisms hibernate, their molecules can hibernate too. What happens inside a living cell when an organism hibernates? It was believed until recently that when a living cell encounters environmental stress, it ceases most of its metabolic activities and its key enzymes remain vacant and idle until conditions improve. However, it has become clear in recent years that organisms, from bacteria to humans, can employ a special mechanism to protect their key enzymes from degradation or unwanted activity under conditions of stress. This mechanism is based on putting their enzymes into a state akin hibernation of animals, known as molecular hibernation. Typically, molecular hibernation involve enzyme association with a specialized inhibitor/partner that occupies the active site of this enzyme.

One example of hibernating enzymes includes protasome. Proteasome is an enzyme complex that catalyzes the degradation of proteins. In some species of animals, the activity of proteasome decreases during hibernation, allowing the animal to conserve energy. This is accomplished by the binding of an inhibitor called lactacystin to the active site of proteasome, which prevents it from catalyzing the degradation of proteins.

Another example is calcineurin, an enzyme that catalyzes the dephosphorylation of target proteins in response to calcium signals. In some species of animals, the activity of calcineurin decreases during hibernation, allowing the animal to conserve energy. This is accomplished by the binding of an inhibitor called cyclosporin A, FK506, and Tacrolimus to the active site of calcineurin, which prevents it from catalyzing the dephosphorylation of target proteins.

Odds of being alive

Every time I hear people ranting about life being unfair, huffing and puffing if things don’t go their way, I recall this stunning visual: “What are the odds”. It estimates our odds of being alive, showing they are just a fraction above zero, or 1 in 102,685,000 if you like math.

Imagine: 1 in 102,685,000. As someone put it, “that probability is the same as if you handed out 2 million dice, each dice with one trillion sides… then rolled those 2 million dice and had them all land on 439,505,270,846.” It seems we are damn good at gambling! At least for once. So, when next time your dumb classmate gets into Harvard and you fail as a valedectorian, please recall this absurdly slim chance of your existance, and take a moment to appreciate this unique gift of luck — to be alive as a concious human being, to share this transient journey we call life with people we love, to get a chance to understand and explore ourselves and the universe around us, to breath air and enjoy warm rays of the morning Sun — all those things we take for granted while being obsessed with the cherry on top. Because, if scientists got it right, our life is highly improbable, and it won’t last for long. Thus, luckily for us, life is tremendously unfair, if you see what I mean.

Integrated bug management

In late 1970s, agriculture encountered a major crisis in pesticide resistance leading to the near-collapse of the cotton industry in several countries. This crisis forced the industry to devise the Integrated Pest Management (IPM), an approach that aims to minimize the risk of pesticide resistance by limiting pesticide use and by trying to manage pests rather than trying to eradicate them. Our recent paper provides a small “stone” for the emerging “building” of a similar approach – adaptive therapy – that aims to improve the way use antimicrobial and anticancer drugs: https://www.pnas.org/content/early/2020/07/10/2003132117

Please check out this wonderful blog post by Maria O’Hanlon discussing our work and this emerging new trend in more sustainable drug application: https://bit.ly/3fs45sr

New research brings us closer to understanding the origin of the eukaryotic cell

A new study by Yale scientists provides an insight into a milestone event in the early evolution of life on Earth – the origin of the cell nucleus. Dating back to around 2.5 billion years ago, the origin of the nucleus enabled the transformation of relatively simple organisms, such as bacteria, into more sophisticated ones that ultimately gave rise to modern animals, plants, and fungi. The details of this key event have remained elusive for many years. This is because not a single transitional fossil has been found to date that could point to any intermediate stages, or the logic underlying this massive transformation that took place among living cells, all that time ago.

A study led by Dr. Sergey Melnikov, from the Dieter Soll Laboratory (Department of Molecular Biophysics and Biochemistry at Yale University), has finally found these missing fossils. Yet they were found not in clay or rocks but inside currently living cells, known as Archaea – the organisms that are believed to most closely resemble the ancient intermediates between bacteria and the more complex cells that we now know as eukaryotic cells. These transitional forms are nothing like the traditional fossils we think of, such as dinosaur bones deposited in the ground or insects trapped in amber. Known as ribosomal proteins, these particular transitional forms are about 100-million times smaller than our bodies. Melnikov and his colleagues discovered that ribosomal proteins can be used as living “molecular fossils”, whose ancient origin and structure structure may hold the key to understanding the origin of the cell nucleus.

“Simple lifeforms, such as bacteria, are analogous to a studio apartment: they have a single interior space which is not subdivided into separate rooms or compartments. By contrast, more complex organisms, such as fungi, animals, and plants, are made up of cells that are separated into multiple compartments,” explained Melnikov. “These compartments are connected to one another via microscopic ‘doors’ and ‘gates’; to pass through these doors and gates, the molecules that inhabit living cells carry special IDs, some of which are called nuclear localization signals, or NLSs.”

In attempting to find and analyze NLSs in ribosomal proteins from virtually all known organisms that inhabit our planet, Melnikov and colleagues have discovered that these special IDs are present not only in complex cells but also in Archaea – the relatively simple organisms whose cells lack internal compartments linked by subcellular doors and gates. The logical question which then arose was: what was the original biological function of these IDs?

“If you think about an equivalent to our discovery in the macroscopic world, it is similar to discoveries made during the last century of bird-like dinosaurs such as Caudipteryx zoui. An example of these ancient flightless birds has illustrated that it took multiple millions of years for dinosaurs to develop wings. Yet, strikingly, for the first few million years their wings were not good enough to support flight. This fact led to fierce debates about what the evolutionary advantage was in having these seemingly useless yet complex and costly ‘half-wings’. Also, what was the driving force behind the gradual development of wings in dinosaurs, if for most of this time these wings were unable to support flight? Our discovery raised similar questions about the origin of the cell nucleus: why did the IDs that allow movement between different cell compartments initially emerge in cells that were devoid of compartments? And what was the original biological function of these IDs in non-compartmentalized cells?”

In fact, studies of bird-like dinosaurs have suggested that even though half-wings could not support flight, they could support flight-like locomotion, such as gliding and accelerated climbing, suggesting that the advantage offered by gliding and climbing (and not flight itself) was the initial driving force behind the evolution of wings. Similarly, the study by Melnikov and colleagues suggests that, even though NLSs may not initially have emerged to allow cellular molecules to pass through microscopic gates between cellular compartments, they could have emerged to fulfill a similar biological function – to help molecules get to their biological partners. As Melnikov explains: “Our analysis shows that in complex cells the very same IDs that allow proteins to pass through the microscopic gates are also used to recognize biological partners of these proteins. In other words, in complex cells the IDs fulfill two conceptually similar biological functions. In the Archaea, however, these IDs play just one of these functions – these IDs, or NLSs, help proteins to recognize their biological partners and distinguish them from the thousands of other molecules that float in a cell.”

So what was the initial trigger that led to the evolution of these IDs among cellular proteins? As Melnikov explains, “When life first emerged on the face of our planet, the earliest life forms were likely made of a very limited number of molecules. Therefore, it was relatively easy for these molecules to find one specific partner among all the other molecules in a living cell. However, as cells grew in size and complexity, it is possible, even probable, that the old rules of specific interactions between cellular molecules had to be redefined, and this is how the IDs were introduced into the structure of cellular proteins – to help these proteins identify their molecular partners more easily in the complex environment of a complex cell. Coming back to the analogy with bird-like dinosaurs, our study illustrates the remarkable similarity between how evolution happens in the macroscopic world and how evolution happens in the world that Darwin never saw – the world of invisible molecules that inhabit living cells.”

More about the work: