How selfish genes succeed

New findings from the Stowers Institute for Medical Research uncover critical insights about how a dangerous selfish gene -- considered to be a parasitic portion of DNA -- functions and survives. Understanding this dynamic is a valuable resource for the broader community studying meiotic drive systems.

A new study, published in PLoS Genetics on Dec. 7, 2022, reveals how a selfish gene in yeast uses a poison-antidote strategy that enables its function and likely has facilitated its long-term evolutionary success. This strategy is an important addition for scientists studying similar systems including teams that are designing synthetic drive systems for pathogenic pest control. Collective and collaborative advancement on understanding drive may one day lead to the eradication of pest populations that harm crops or even humans in the case of vector borne diseases.

"It's quite dangerous for a genome to encode a protein that has the capacity to kill the organism," said Stowers Associate Investigator SaraH Zanders, Ph.D. "However, understanding the biology of these selfish elements could help us build synthetic drivers to modify natural populations."

Drivers are selfish genes that can spread in a population at higher rates than most other genes, without benefiting the organism. Previous research from the Zanders Lab revealed that a driver gene in yeast, wtf4, produces poison protein capable of destroying all offspring. However, for a given parent cell's chromosome pair, drive is achieved when wtf4 is found only on one chromosome. The effect is a simultaneous rescue of only those offspring that inherit the drive allele, by delivering a dose of a very similar protein that counteracts the poison, the antidote.

Building upon this work, the study, led by former Predoctoral Researcher Nicole Nuckolls, Ph.D., and current Predoctoral Researcher Ananya Nidamangala Srinivasa in the Zanders Lab, discovered that differences in the timing of generating poison and antidote proteins from wtf4 and their unique distribution patterns within developing spores are fundamental to the drive process.

The team has developed a model they are continuing to investigate for how the poison acts to kill the spore -- the equivalent of a human egg or sperm in yeast. Their results indicate that poison proteins cluster together, potentially disrupting proper folding of other proteins required for the cell to function. Because the wtf4 gene encodes both poison and antidote, the antidote is very similar in form and groups together with the poison. However, the antidote has an extra part that appears to isolate the poison-antidote clusters by bringing them to the cell's garbage can, the vacuole.

To understand how selfish genes function during reproduction, the researchers looked at the beginning of spore formation and found poison protein expressed within all developing spores and the sac surrounding them, while the antidote protein was only seen in low concentration throughout the sac. Later in development, the antidote was enriched inside of the spores that inherited wtf4 from the parent yeast cell.

The researchers found that spores that inherited the driver gene manufactured additional antidote protein inside the spore to neutralize the poison and ensure their survival.

The team also discovered that a particular molecular switch that controls many other genes involved in spore formation also controls the expression of poison, but not antidote, from the wtf4 gene. The switch is essential for yeast reproduction and is inextricably linked to wtf4, helping to explain why this selfish gene is so successful at evading any attempts by the host to disable the switch.

"One of the reasons we are thinking these things have stuck around for so long -- they've used this sneaky strategy of exploiting the same essential switch that turns on yeast reproduction," said Nidamangala Srinivasa.

"If we could manipulate these DNA parasites to be expressed in mosquitoes and drive their destruction, it may be a way to control pest species," said Nuckolls.

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An omega-3 that's poison for tumors

So-called "good fatty acids" are essential for human health and much sought after by those who try to eat healthily. Among the Omega-3 fatty acids, DHA or docosahexaenoic acid is crucial to brain function, vision and the regulation of inflammatory phenomena.

In addition to these virtues, DHA is also associated with a reduction in the incidence of cancer. How it works is the subject of a major discovery by a multidisciplinary team of University of Louvain (UCLouvain) researchers, who have just elucidated the biochemical mechanism that allows DHA and other related fatty acids to slow the development of tumours. This is a major advance that has recently been published in the journal Cell Metabolism.

Key to the discovery: interdisciplinarity

In 2016, Olivier Feron's UCLouvain team, which specialises in oncology, discovered that cells in an acidic microenvironment (acidosis) within tumours replace glucose with lipids as an energy source in order to multiply. In collaboration with UCLouvain's Cyril Corbet, Prof. Feron demonstrated in 2020 that these same cells are the most aggressive and acquire the ability to leave the original tumour to generate metastases. Meanwhile, Yvan Larondelle, a professor in the UCLouvain Faculty of Bioengineering, whose team is developing improved dietary lipid sources, proposed to Prof. Feron that they combine their skills in a research project, led by PhD candidate Emeline Dierge, to evaluate the behaviour of tumour cells in the presence of different fatty acids.

Thanks to the support of the Fondation Louvain, the Belgian Cancer Foundation and the Télévie telethon, the team quickly identified that these acidotic tumour cells responded in diametrically opposite ways depending on the fatty acid they were absorbing. Within a few weeks, the results were both impressive and surprising. "We soon found that certain fatty acids stimulated the tumour cells while others killed them," the researchers explained. DHA literally poisons them.

A fatal overload

The poison acts on tumour cells via a phenomenon called ferroptosis, a type of cell death linked to the peroxidation of certain fatty acids. The greater the amount of unsaturated fatty acids in the cell, the greater the risk of their oxidation. Normally, in the acidic compartment within tumours, cells store these fatty acids in lipid droplets, a kind of bundle in which fatty acids are protected from oxidation. But in the presence of a large amount of DHA, the tumour cell is overwhelmed and cannot store the DHA, which oxidises and leads to cell death. By using a lipid metabolism inhibitor that prevents the formation of lipid droplets, researchers were able to observe that this phenomenon is further amplified, which confirms the identified mechanism and opens the door to combined treatment possibilities.

For their study, UCLouvain researchers used a 3D tumour cell culture system, called spheroids. In the presence of DHA, spheroids first grow and then implode. The team also administered a DHA-enriched diet to mice with tumours. The result: tumour development was significantly slowed compared to that in mice on a conventional diet.

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Fifty years later, DDT lingers in lake ecosystems

To control pest outbreaks, airplanes sprayed more than 6,280 tons of dichlorodiphenyltrichloroethane (DDT) onto forests in New Brunswick, Canada, between 1952 and 1968, according to Environment Canada. By 1970, growing awareness of the harmful effects of DDT on wildlife led to curtailed use of the insecticide in the area. However, researchers reporting in ACS' Environmental Science & Technology have shown that DDT lingers in sediments from New Brunswick lakes, where it could alter zooplankton communities.

After being applied aerially to forests, DDT can enter lakes and rivers through atmospheric deposition and land runoff. The long-lived insecticide, now banned in most countries, and its toxic breakdown products accumulate in lake sediments and from there, could enter the food web. Previous research has shown that freshwater crustacean zooplankton such as Cladocera, otherwise known as water fleas, are sensitive to DDT. Joshua Kurek and colleagues wondered if elevated DDT use in the 1950s and 60s could have affected zooplankton populations in lakes, and whether these changes, and DDT and its breakdown products, persist today.

To find out, the researchers collected sediment core samples from five remote lakes in New Brunswick. The lake sediment cores captured environmental conditions from about the years 1890 to 2016. The team analyzed the concentrations of DDT and its breakdown products in thin sections of the sediments, finding that peak DDT levels generally occurred during the 1970s and 80s. The most recent sediments still exceeded levels considered safe for aquatic organisms. When the researchers examined the sediments for partially fossilized remains of Cladocera, they found that most lakes showed a shift from large-bodied to small-bodied zooplankton species, which are generally more tolerant to contaminants, beginning in the 1950s when DDT was widely applied in New Brunswick.

From Science Daily

Arsenic-breathing life discovered in the tropical Pacific Ocean

Jaclyn Saunders (far right) fixes the line on a McLane instrument that pumps large volumes of seawater in order to extract the DNA. The instrument on the left measures properties such as temperature, salinity and depth and collects smaller samples of seawater.

Arsenic is a deadly poison for most living things, but new research shows that microorganisms are breathing arsenic in a large area of the Pacific Ocean. A University of Washington team has discovered that an ancient survival strategy is still being used in low-oxygen parts of the marine environment.

"Thinking of arsenic as not just a bad guy, but also as beneficial, has reshaped the way that I view the element," said first author Jaclyn Saunders, who did the research for her doctoral thesis at the UW and is now a postdoctoral fellow at the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology.

The study was published this week in the Proceedings of the National Academy of Sciences.

"We've known for a long time that there are very low levels of arsenic in the ocean," said co-author Gabrielle Rocap, a UW professor of oceanography. "But the idea that organisms could be using arsenic to make a living -- it's a whole new metabolism for the open ocean."

The researchers analyzed seawater samples from a region below the surface where oxygen is almost absent, forcing life to seek other strategies. These regions may expand under climate change.

"In some parts of the ocean there's a sandwich of water where there's no measureable oxygen," Rocap said. "The microbes in these regions have to use other elements that act as an electron acceptor to extract energy from food."

The most common alternatives to oxygen are nitrogen or sulfur. But Saunders' early investigations suggested arsenic could also work, spurring her to look for the evidence.

The team analyzed samples collected during a 2012 research cruise to the tropical Pacific, off the coast of Mexico. Genetic analyses on DNA extracted from the seawater found two genetic pathways known to convert arsenic-based molecules as a way to gain energy. The genetic material was targeting two different forms of arsenic, and authors believe that the pathways occur in two organisms that cycle arsenic back and forth between different forms.

Results suggest that arsenic-breathing microbes make up less than 1% of the microbe population in these waters. The microbes discovered in the water are probably distantly related to the arsenic-breathing microbes found in hot springs or contaminated sites on land.

"What I think is the coolest thing about these arsenic-respiring microbes existing today in the ocean is that they are expressing the genes for it in an environment that is fairly low in arsenic," Saunders said. "It opens up the boundaries for where we could look for organisms that are respiring arsenic, in other arsenic-poor environments."

Biologists believe the strategy is a holdover from Earth's early history. During the period when life arose on Earth, oxygen was scarce in both the air and in the ocean. Oxygen became abundant in Earth's atmosphere only after photosynthesis became widespread and converted carbon dioxide gas into oxygen.

Early lifeforms had to gain energy using other elements, such as arsenic, which was likely more common in the oceans at that time.

"We found the genetic signatures of pathways that are still there, remnants of the past ocean that have been maintained until today," Saunders said.

Arsenic-breathing populations may grow again under climate change. Low-oxygen regions are projected to expand, and dissolved oxygen is predicted to drop throughout the marine environment.

"For me, it just shows how much is still out there in the ocean that we don't know," Rocap said. Saunders recently collected more water samples from the same region and is now trying to grow the arsenic-breathing marine microbes in a lab in order to study them more closely.

"Right now we've got bits and pieces of their genomes, just enough to say that yes, they're doing this arsenic transformation," Rocap said. "The next step would be to put together a whole genome and find out what else they can do, and how that organism fits into the environment."

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Widely used mosquito repellent proves lethal to larval salamanders

Spotted salamanders begin life in the water. During their aquatic larval phase, they are efficient predators of mosquito larvae.

Insect repellents containing picaridin can be lethal to salamanders. So reports a new study published today in Biology Letters that investigated how exposure to two common insect repellents influenced the survival of aquatic salamander and mosquito larvae.

Insect repellents are a defense against mosquito bites and mosquito-borne diseases like dengue, chikungunya, Zika, and West Nile virus. Salamanders provide natural mosquito control. During their aquatic juvenile phase, they forage on mosquito larvae, keeping populations of these nuisance insects in check.

Emma Rosi, a freshwater ecologist at Cary Institute of Ecosystem Studies and a co-author on the paper explains, "Use of insect repellents is on the rise globally. Chemicals in repellents enter aquatic ecosystems through sewage effluent and are now common in surface waters. We set out to understand the impact of repellent pollution on both larval mosquitoes and the larval salamanders that prey on them."

The paper is the first to suggest that environmentally realistic concentrations of picaridin-containing repellents in surface waters may increase the abundance of adult mosquitoes due to a decrease in predation pressure on mosquitoes at the larval stages.

Testing the two most popular repellents

The research team tested the effects of two of the most widely used insect repellents -- DEET (Repel 100 Insect Repellent) and picaridin (Sawyer Premium Insect Repellent) -- on larval salamanders and mosquitoes. In a lab, they exposed mosquito larvae and just-hatched spotted salamander larvae to three environmentally relevant concentrations of these chemicals, as well as a control treatment.

Rosi notes, "The concentrations in our experiments are conservative; we prepared them based on unadulterated commercial formulations, not concentrations of pure active compounds."

Mosquito larvae were not impacted by any of the treatments and matured unhindered. After four days of exposure to repellent with picaridin, salamanders in all of the treatment groups began to display signs of impaired development such as tail deformities. By day 25, 45-65% of picaridin-exposed salamander larvae died.

Co-author Barbara Han, a disease ecologist at Cary Institute explains, "Our findings demonstrate that larval salamanders suffer severe mortality and developmental deformities when exposed to environmentally relevant concentrations of commercially available repellent containing the active ingredient picaridin."

Adding, "The expediency of salamander mortality was disconcerting. When studying the effects of a chemical on an amphibian, we usually look for a suite of abnormalities. We couldn't collect these data because the salamanders died so quickly."

How toxic is toxic?

LC50 tests are used to define a chemical's environmental toxicity. These standard tests, based on one life stage of a single species, measure how long it takes for 50% of a test population to die with increasing exposure to a chemical in a lab over a four-day period.

Co-author Alexander Reisinger, an Assistant Professor at University of Florida, Gainesville says, "We observed heavy salamander mortality with picaridin, but not until after the fourth day of exposure. By the LC50 measure, picaridin would be deemed 'safe', but clearly, this is not the case. If a substance doesn't kill organisms within the first few days of exposure, it can still be toxic and have ecological impacts."

Results may underestimate the problem

Lethal in a controlled setting, picaridin may cause greater mortality in a natural context, where organisms are exposed to numerous stressors. Rosi notes, "Animals don't exist in isolation. In nature, competition, predation, resource limitation, and social interactions make it difficult for an organism to tolerate the added stress of exposure to a harmful substance, even in small amounts."

Timing -- of both repellent use and amphibian reproduction -- is also key. Many amphibians breed in a single seasonal pulse, putting all their eggs in one basket, so to speak. Mosquitoes have an extended breeding season, and reproduce multiple times.

Lead author Rafael Almeida, a postdoctoral researcher at Cornell University, conducted the research as a visiting PhD student at the Cary Institute. He explains, "The amount of repellents entering waterways peaks seasonally. If amphibians are exposed during a sensitive life stage, entire cohorts could perish. The population would not have a chance to recover until the following year. Meanwhile, mosquitoes would continue to reproduce. It suggests a negative feedback loop."

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Why poison frogs don't poison themselves

The phantasmal poison frog, Epipedobates anthonyi, is the original source of epibatidine, discovered by John Daly in 1974. In fact, epibatidine is named for frogs of this genus. Epibatidine has not been found in any animal outside of Ecuador, and its ultimate source, proposed to be an arthropod, remains unknown. This frog was captured at a banana plantation in the Azuay province in southern Ecuador in August 2017.

Don't let their appearance fool you: Thimble-sized, dappled in cheerful colors and squishy, poison frogs in fact harbor some of the most potent neurotoxins we know. With a new paper published in the journal Science, scientists are a step closer to resolving a related head-scratcher -- how do these frogs keep from poisoning themselves? And the answer has potential consequences for the fight against pain and addiction.

The new research, led by scientists at The University of Texas at Austin, answers this question for a subgroup of poison frogs that use the toxin epibatidine. To keep predators from eating them, the frogs use the toxin, which binds to receptors in an animal's nervous system and can cause hypertension, seizures, and even death. The researchers discovered that a small genetic mutation in the frogs -- a change in just three of the 2,500 amino acids that make up the receptor -- prevents the toxin from acting on the frogs' own receptors, making them resistant to its lethal effects. Not only that, but precisely the same change appeared independently three times in the evolution of these frogs.

"Being toxic can be good for your survival -- it gives you an edge over predators," said Rebecca Tarvin, a postdoctoral researcher at UT Austin and a co-first author on the paper. "So why aren't more animals toxic? Our work is showing that a big constraint is whether organisms can evolve resistance to their own toxins. We found evolution has hit upon this same exact change in three different groups of frogs, and that, to me, is quite beautiful."

There are hundreds of species of poisonous frogs, each of which uses dozens of different neurotoxins. Tarvin is part of a team of researchers, including professors David Cannatella and Harold Zakon in the Department of Integrative Biology, who have been studying how these frogs evolved toxic resistance.

For decades, medical researchers have known that this toxin, epibatidine, also can act as a powerful nonaddictive painkiller. They've developed hundreds of compounds from the frogs' toxin, including one that advanced in the drug-development process to human trials before being ruled out due to other side effects.

The new research -- showing how certain poison frogs evolved to block the toxin while retaining use of receptors the brain needs -- gives scientists information about epibatidine that could eventually prove helpful in designing drugs such as new pain relievers or drugs to fight nicotine addiction.

"Every bit of information we can gather on how these receptors are interacting with the drugs gets us a step closer to designing better drugs," said Cecilia Borghese, another co-first author of the paper and a research associate in the university's Waggoner Center for Alcohol and Addiction Research.

Changing the Lock

A receptor is a type of protein on the outside of cells that transmits signals between the outside and the inside. Receptors are like locks that stay shut until they encounter the correct key. When a molecule with just the right shape comes along, the receptor gets activated and sends a signal.

The receptor that Tarvin and her colleagues studied sends signals in processes like learning and memory, but usually only when a compound that is the healthy "key" comes into contact with it. Unfortunately for the frogs' predators, toxic epibatidine also works, like a powerful skeleton key, on the receptor, hijacking cells and triggering a dangerous burst of activity.

The researchers found that poison frogs that use epibatidine have developed a small genetic mutation that prevents the toxin from binding to their receptors. In a sense, they've blocked the skeleton key. They also have managed, through evolution, to retain a way for the real key to continue to work, thanks to a second genetic mutation. In the frogs, the lock became more selective.

Fighting Disease

The way that the lock changed suggests possible new ways to develop drugs to fight human disease.

The researchers found that the changes that give the frogs resistance to the toxin without changing healthy functioning occur in parts of the receptor that are close to, but don't even touch epibatidine. Borghese and Wiebke Sachs, a visiting student, studied the function of human and frog receptors in the lab of Adron Harris, another author on the paper and associate director of the Waggoner Center.

"The most exciting thing is how these amino acids that are not even in direct contact with the drug can modify the function of the receptor in such a precise way," Borghese said. The healthy compound, she continued, "keeps working as usual, no problem at all, and now the receptor is resistant to epibatidine. That for me was fascinating."

Understanding how those very small changes affect the behavior of the receptor might be exploited by scientists trying to design drugs that act on it. Because the same receptor in humans is also involved in pain and nicotine addiction, this study might suggest ways to develop new medications to block pain or help smokers break the habit.

Retracing Evolution

Working with partners in Ecuador, the researchers collected tissue samples from 28 species of frogs -- including those that use epibatidine, those that use other toxins and those that are not toxic. Tarvin and hear colleagues Juan C. Santos from St. John's University and Lauren O'Connell from Stanford University sequenced the gene that encodes the particular receptor in each species. She then compared subtle differences to build an evolutionary tree representing how the gene evolved.

This represents the second time that Cannatella, Zakon, Tarvin and Santos have played a role in discovering mechanisms that prevent frogs from poisoning themselves. In January 2016, the team identified a set of genetic mutations that they suggested might protect another subgroup of poison frogs from a different neurotoxin, batrachotoxin. Research published this month was built on their finding and conducted by researchers from the State University of New York at Albany, confirming that one of UT Austin's proposed mutations protects that set of poison frogs from the toxin.

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