Protein p53 regulates learning, memory, sociability in mice

 Researchers have established the protein p53 as critical for regulating sociability, repetitive behavior, and hippocampus-related learning and memory in mice, illuminating the relationship between the protein-coding gene TP53 and neurodevelopmental and conditions like autism spectrum disorder.

"This study shows for the first time that p53 is linked directly to autism-like behavior," said Nien-Pei Tsai, an associate professor of molecular and integrative biology at the University of Illinois Urbana-Champaign and a researcher at the Beckman Institute for Advanced Science and Technology.

In living systems, genes act as a biological version of binary code, using the letters A, C, G, and T instead of ones and zeroes to spell out cellular marching orders. Some genes -- called coding genes -- instruct cells to create proteins with specific functions. For example, the gene TP53 instructs cells to create the protein p53; its job is to regulate how other genes are expressed.

In this study, Tsai and his colleagues lowered hippocampal p53 levels in mice, looking for changes in gene expressions related to behavior. They observed that the decreased p53 levels:

• Promoted repetitive behavior in mice.
• Reduced sociability in mice.
• Impaired hippocampus-dependent learning and memory, especially in male mice.

The researchers also observed that p53 levels were elevated after a period of active communication between hippocampal neurons called long-term potentiation. Flexible neuron firing -- known as plasticity -- is related to positive learning and memory outcomes.

In a 2018 study, Tsai and his colleagues identified p53 as a key protein involved in the irregular brain cell activity seen in ASD and epilepsy. In future studies, they aim to explore how p53 coordinates the expression of those autism-linked genes to guide behavior.

Compensation by healthy brain parts alleviates Parkinson symptoms

 In Parkinson's disease, the cerebral cortex can take over tasks from a deeper part of the brain that has been damaged, where cells that make dopamine have been lost. The strength of compensation by the cerebral cortex determines how many symptoms people have. This is shown in a publication by Radboud university medical center. Patients can stimulate this compensation through sports, for example, and thus slow down the disease process.

It was already known that in Parkinson's disease the cells in the brain that produce dopamine slowly disappear. This is why patients are given extra dopamine as medication. But only a limited link has been found between the loss of those cells, and the severity of symptoms in Parkinson's. Even if all the cells have disappeared, one person experiences mild symptoms, while another has many more symptoms. Researchers at the Radboudumc looked into whether something else might be going on.

They discovered that the outer layer of the brain, the cerebral cortex, can compensate for the loss of the cells that make dopamine, thereby delaying the worsening of symptoms. It turns out that the severity of symptoms is clearly related to compensation by the cerebral cortex. The more active it is in taking over tasks, the milder the slowness of movement and the better the thinking. Doctors have long suspected that such a mechanism of compensation exists, but it has now been demonstrated for the first time.

Smoothness

The conclusions are based on a study in 353 people with Parkinson's and 60 healthy volunteers. They all took a test while in an MRI scanner. The test was a kind of computer game, where participants had to make both easy and difficult choices, which demands a lot from the brain. The researchers could use the MRI scanner to identify brain regions that were active during the game. They expected that making difficult choices stimulates compensation, and that the deployment of compensation differs between people.

First, they saw that the brain structure that strongly depends on dopamine, the basal ganglia, is indeed damaged and shows much less activity in people with Parkinson's than in healthy volunteers. The basal ganglia lie deep in the brain, below the cerebral cortex. This brain area allows people to move and think smoothly. Hence, damage in this area leads to slowness of movement and thinking in Parkinson's.

Reinforcing compensation

It was also found that in people with Parkinson's there is a very clear relationship between the severity of symptoms and activity in the cerebral cortex. PhD candidate Martin Johansson: 'People with mild symptoms showed much more activity in the cerebral cortex, especially in areas that are involved in controlling movement. These areas were even more active than in healthy volunteers, which demonstrates their compensatory role. In patients with severe symptoms, on the contrary, the cerebral cortex was much less active than in healthy volunteers.'

This discovery offers new leads for treatment and lifestyle. 'In parkinson's we solve the dopamine deficiency with drugs. But with these new findings we are now going to look much more at how we can strengthen that compensation by the cerebral cortex', says Rick Helmich, neurologist at Radboudumc. 'We saw in a previous study that exercising three times a week helps against symptoms, and prevents shrinkage of the cerebral cortex. Thanks to the current study, we know why that cerebral cortex is so important.'

Parkinson's: Are our neurons more vulnerable at night?

 Disturbances in sleep patterns and the internal biological clock are frequently associated with Parkinson's disease. However, the link between biological rhythm and neuronal degeneration remains unclear. A team from the University of Geneva (UNIGE) investigated the destruction of neurons at different times of the day, using the fruit fly as a study model. The scientists discovered that the type of cellular stress involved in Parkinson's disease was more deleterious to neurons when it occurred at night. This work can be read in the journal Nature Communications.

Parkinson's disease is a progressive neurodegenerative disorder characterized by the destruction of certain neurons in the brain: dopamine neurons. The main symptoms of this disease are tremors, slowness of movement and muscular stiffness. Epidemiological studies show that other disorders may be associated, such as disturbances of the sleep and of the circadian cycle.

This cycle, defined by the alternate periods of wakefulness and sleep, lasts around 24 hours and constitutes the human body's internal clock that regulates almost all its biological functions. In particular, the circadian clock controls the secretion of the ''sleep hormone''(melatonin) at the end of the day, variations in body temperature (lower in the early morning and higher during the day), and metabolism in periods of fasting (during sleep) or energy intake (during daytime meals).

Cause or consequence?

Disruptions in circadian and sleep rhythms can be observed years before the onset of motor symptoms in Parkinson's patients. But does disruption of the circadian cycle contribute to the development of the disease, or is it a consequence?

This question is at the heart of work in the laboratory of Emi Nagoshi, associate professor in the Department of Genetics and Evolution at the UNIGE Faculty of Science. Her team uses the fruit fly as a study model for Parkinson's disease and to dissect the mechanisms of dopamine neuron degeneration. Scientists can simulate the onset of the disease by exposing the flies for a few hours to a drug that induces oxidative stress, leading to the death of dopaminergic neurons in the following days.

Flies' neurons are more sensitive at night

Despite being very different animals, the biological clocks of flies and humans are comparable. To determine whether the circadian cycle could influence the onset of Parkinson's disease, flies were exposed to oxidative stress at six different times of the day and night.

''We waited seven days to observe the survival of the targeted neurons under the microscope, and we found a greater number of destroyed dopaminergic neurons when the exposure had been made during the night hours,'' explains Michaëla Dorcikova, ex-doctoral fellow in the Department of Genetics and Evolution and first author of the study.

To understand whether these observations are dependent on circadian rhythm, the scientists exposed mutant flies with disrupted circadian cycles to the same stresses. The researchers observed that the neurons of flies without an internal clock were more sensitive to oxidative stress. These results suggest that the circadian clock exerts a protective effect on dopaminergic neurons against oxidative stress.

Exploring risk factors for Parkinson's disease

Most Parkinson's cases result from an interaction between multiple genetic risk factors and lifelong exposure to environmental factors such as pesticides, solvents and air pollution. The results show that an oxidative stressor, such as a pesticide, administered at a specific time of day can have a critical impact on the survival of dopaminergic neurons.

''Our results further suggest that genetic variations in circadian clock genes may represent a risk factor for dopaminergic neurodegeneration. We now need to ascertain the relevance of these results in humans,'' concludes Emi Nagoshi, the study's final author.

Scientists shed light on how stressed cells sequester protein-forming mRNAs

 Researchers at Weill Cornell Medicine have illuminated one of the important ways that cells respond to stress. The findings could also be relevant to Alzheimer's, ALS and other diseases in which this mechanism may be abnormally active.

When stressed by heat, toxins or other potentially damaging factors, cells gather many of their messenger RNAs (mRNAs), molecules that carry the instructions for making proteins, into droplet-like compartments called stress granules. These granules sequester affected mRNAs, preventing them from being translated into proteins. The resulting slowdown in protein production helps the cell conserve energy, declutter and focus on repairs.

In the study, which appeared Sept. 14 in Nature Structural and Molecular Biology, the researchers confirmed that a tiny chemical modification on mRNAs, known as m6A, is key to the formation of stress granules.

"We were able to show that m6A has a primary role in driving mRNAs into these granules during cell stress," said study senior author Dr. Samie Jaffrey, the Greenberg-Starr Professor of Pharmacology at Weill Cornell Medicine.

The study's first author, Dr. Ryan Ries, was a Weill Cornell Graduate School of Medical Sciences doctoral student during the research.

Understanding How Stress Granules Form

Stress granules contain many different mRNAs from the cell, but not a random selection. Dr. Jaffrey and his team previously showed that mRNAs that are found in stress granules are often chemically tagged with a small cluster of atoms called a methyl group which attaches to adenosine, one of the mRNA building blocks. The resulting mRNA has regions that are enriched in N6-methyladenosine, or m6A. They also found that m6A-rich regions bind to YTHDF proteins -- the more m6A an mRNA has, the more YTHDF proteins are present. The large amount of YTHDF proteins is needed to allow the m6A-mRNA-YTHDF complexes to accumulate into stress granules.

Dr. Jaffrey and others assumed that m6A wasn't the only factor directing mRNA into stress granules because longer mRNAs are also overrepresented. "We had thought that mRNA length was another factor, which is plausible since longer mRNAs have a tendency to stick to other mRNAs and form aggregates," Dr. Jaffrey said.

However, in this study, when the researchers engineered cells that couldn't form m6A and induced stress granule formation, they found that longer mRNAs weren't overrepresented in the granules anymore. Dr. Jaffrey concluded that the m6A in the long mRNAs, and not mRNA length per se, was the key factor making longer mRNAs disproportionately abundant in stress granules.

Why Do Longer mRNAs Dominate Stress Granules?

During protein production, mRNAs are assembled in the nucleus of a cell from smaller regions of RNA called exons. The researchers observed that m6A is added to mRNAs as soon as the mRNAs are made in the nucleus. They also discovered that exons that were unusually long strongly triggered m6A formation in the corresponding mRNA. These long exons tend to be in long mRNAs, which explained why long mRNAs have high levels of m6A, and therefore are more likely to join stress granules, compared to mRNAs that are composed of only short exons.

Why does it benefit a cell to sequester longer mRNAs during episodes of cell stress? Dr. Jaffrey and colleagues speculate that in the distant evolutionary past, longer mRNAs were more likely to be dysfunctional or even from viruses. The development of cellular pathways to direct m6A-mRNAs into stress granules may have originated as a way to lock up these suspect mRNAs and prevent them from making unsafe proteins -- though that process now appears to have evolved into a broader stress-response function.

While the new finding significantly advances the understanding of the basic biology underlying m6A and stress granule formation, it may also be relevant to neurodegenerative diseases.

"Maybe the abnormal stress granules that are formed in neurodegenerative diseases such as Alzheimer's and ALS are driving those disease processes by chronically trapping beneficial m6A-containing mRNAs," Dr. Jaffrey said. "We hope to find out whether blocking that mRNA-trapping process will help reverse pathology in these neurons."

Through the backdoor: How phosphate escapes from actin

 Actin filaments are dynamic protein-fibres in the cell built from single actin proteins. Many cellular functions, including cell movement, are regulated by constant filament assembly and disassembly. The disassembly phase is initiated by the release of a phosphate group from inside the filament, but the details of this process have puzzled scientists since decades. Researchers from the Max Planck Institute of Molecular Physiology in Dortmund and the Max Planck Institute of Biophysics in Frankfurt have joined forces to precisely identify a region in actin that functions as a "molecular backdoor" for phosphate to exit though. Using a wide variety of techniques, including cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, the scientists determined the mechanism of phosphate release from actin filaments in unprecedented molecular detail. They also described how a distorted backdoor enables the faster release of phosphate from an actin mutant linked to nemaline myopathy, a severe muscle disease. The study opens the door to further research on the dynamic actin-assembly cycle in cells and diseases related to defective actin organization.

The mysterious escape of phosphate

In eukaryotic cells, actin proteins join together (polymerize) into filaments that are part of the cell's intricate supportive network, the cytoskeleton. The disassembly of old filaments is crucial for cell movement and is regulated by ATP hydrolysis -- the reaction of ATP with water that cleaves a phosphate group and generates energy. Specifically, phosphate release from the filament core is the signal to the cell that the actin filament is old enough and can be dismantled into actin subunits. "The mechanism of phosphate release from actin filaments has remained enigmatic for decades," says Wout Oosterheert, postdoc in the group of Stefan Raunser at the MPI Dortmund and first author of the publication.

The new results are built on previous research of Raunser's group on actin that led to ground-breaking publications in 2015, 2018, and 2022 in the actin field. In the latter, the Raunser team determined high-resolution cryo-EM structures of actin filaments in three different states: bound to ATP, bound to ADP in the presence of the cleaved phosphate, and bound to ADP after release of the phosphate. However, in all structures, there was no opening or door in actin through which phosphate could escape from the filament. "Therefore, we surmised that there should be a backdoor that opens momentarily to release the phosphate, and then quickly closes again" says Raunser.

A multidisciplinary approach

MPI scientists have now tackled the problem from various angles. Since it was known that phosphate is released very rapidly from actin at the tip of the filament, called the barbed end, Raunser and his team determined its structure by cryo-EM. And indeed, only at the end of the filament, they found an open molecular backdoor, which explains the very fast phosphate release. However, it was still unclear how phosphate escapes from the actin subunits in the filament core. That's where the expertise of Gerhard Hummer's group from the MPI Frankfurt kicked in; they used the structural data from 2022 to perform molecular dynamics simulations and predict potential exit routes for the phosphate from the filament core. They then teamed up with the group of Peter Bieling (MPI Dortmund) to validate the possible routes by producing actin mutants potentially disrupting the molecular backdoor. They measured how fast they release the phosphate, and finally determined the high-resolution cryo-EM structures of the "fastest" candidates.

The mutational analysis revealed that the phosphate takes the same release route in the filament end and the filament core. The structures and interactions in the latter, however, need additional rearrangements that make it more difficult for the door to open. After phosphate cleavage, the backdoor remains predominantly closed (on average for 100 seconds) before opening for less than a second to let the phosphate leave. "This explains why we didn't see an open backdoor arrangement in our cryo-EM data of 2022," says Raunser.

The actin saga -- To be continued…

One of the actin mutants analyzed, called N111S, is linked to the muscular disease nemaline myopathy and has therefore attracted the attention of the MPI scientists: the mutant always adopts an open backdoor and hence releases phosphate much faster than normal wild-type actin. "We propose that this ultrafast release may contribute to the pathophysiology in patients harboring this actin mutation," says Oosterheert.

As a potential next step, the MPI scientists now want to uncover how phosphate release is controlled within the cell and what role the proteins that bind to actin play. In addition, their work now makes it possible to investigate other disease-related mutations in actin -- an approach that may ultimately contribute to the development of new therapeutic strategies for these diseases