In novel study, mice engineered to lack the same gene run stronger, longer and with less fatigue
Two to three million years ago, the functional loss of a single gene triggered a series of significant changes in what would eventually become the modern human species, altering everything from fertility rates to increasing cancer risk from eating red meat.
In a new paper, published in the Proceedings of the Royal Society B, researchers at University of California San Diego School of Medicine report on studies of mice engineered to lack the same gene, called CMAH, and resulting data that suggest the lost gene may also have contributed to humanity’s well-documented claim to be among the best long-distance runners in the animal kingdom.
At roughly the same time as the CMAH mutation took hold, human ancestors were transitioning from forest dwellers to life primarily upon the arid savannahs of Africa. While they were already walking upright, the bodies and abilities of these early hominids were evolving dramatically, in particular major changes in skeletal biomechanics and physiology that resulted in long, springy legs, big feet, powerful gluteal muscles and an expansive system of sweat glands able to dissipate heat much more effectively than other larger mammals.
Such changes may have helped fuel the emergence of the human ability to run long distances relatively tirelessly, allowing ancestors to hunt in the heat of the day when other carnivores were resting and to pursue prey to their point of exhaustion, a technique called persistence hunting.
“We discovered this first clear genetic difference between humans and our closest living evolutionary relatives, the chimpanzees, more than 20 years ago,” said senior author Ajit Varki, MD, Distinguished Professor of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine and co-director of the UC San Diego/Salk Center for Academic Research and Training in Anthropogeny.
Given the approximate timing of the mutation and its documented impact on fertility in a mouse model with the same mutation, Varki and Pascal Gagneux, PhD, professor of anthropology and pathology, began investigating how the genetic difference might have contributed to the origin of Homo, the genus that includes modern Homo sapiens and extinct species like Homo habilis and Homo erectus.
“Since the mice were also more prone to muscle dystrophy, I had a hunch that there was a connection to the increased long distance running and endurance of Homo,” said Varki, “but I had no expertise on the issue and could not convince anyone in my lab to organize this long-shot experiment.”
Ultimately, a graduate student named Jon Okerblom took up the task, building mouse running wheels and borrowing a mouse treadmill. “We evaluated the exercise capacity (of mice lacking the CMAH gene), and noted an increased performance during treadmill testing and after 15 days of voluntary wheel running,” said Okerblom, the study’s first author. The researchers then consulted Ellen Breen, PhD, a research scientist in the division of physiology, part of the Department of Medicine in the UC San Diego School of Medicine, who added observations that the mice displayed greater resistance to fatigue, increased mitochondrial respiration and hind-limb muscle, with more capillaries to increase blood and oxygen supply.
Taken together, Varki said the data suggest CMAH loss contributed to improved skeletal muscle capacity for oxygen utilization. “And if the findings translate to humans, they may have provided early hominids with a selective advantage in their move from trees to becoming permanent hunter-gatherers on the open range.”
When the CMAH gene mutated in the genus Homo two to three million years ago, perhaps in response to evolutionary pressures caused by an ancient pathogen, it altered how subsequent hominids and modern humans used sialic acids — a family of sugar molecules that coat the surfaces of all animal cells, where they serve as vital contact points for interaction with other cells and with the surrounding environment.
The human mutation causes loss of a sialic acid called N-glycolylneuraminic acid (Neu5Gc), and accumulation of its precursor, called N-acetylneuraminic acid or Neu5Ac, which differs by only a single oxygen atom.
This seemingly minor difference affects almost every cell type in the human body — and has proved to be a mixed blessing. Varki and others have linked the loss of the CMAH gene and sialic acids to not just improved long-distance running ability, but also enhanced innate immunity in early hominids. Sialic acids may also be a biomarker for cancer risk.
Conversely, they have also reported that certain sialic acids are associated with increased risk of type 2 diabetes; may contribute to elevated cancer risk associated with red meat consumption; and trigger inflammation.
“They are a double-edged sword,” said Varki. “The consequence of a single lost gene and a small molecular change that appears to have profoundly altered human biology and abilities going back to our origins.”
All living things use the genetic code to “translate” DNA-based genetic information into proteins, which are the main working molecules in cells. Precisely how the complex process of translation arose in the earliest stages of life on Earth more than four billion years ago has long been mysterious, but two theoretical biologists have now made a significant advance in resolving this mystery.
Charles Carter, PhD, professor of biochemistry and biophysics at the UNC School of Medicine, and Peter Wills, PhD, an associate professor of biochemistry at the University of Auckland, used advanced statistical methods to analyze how modern translational molecules fit together to perform their job – linking short sequences of genetic information to the protein building blocks they encode.
The scientists’ analysis, published in Nucleic Acids Research, reveals previously hidden rules by which key translational molecules interact today. The research suggests how the much-simpler ancestors of these molecules began to work together at the dawn of life.
“I think we have clarified the underlying rules and the evolutionary history of genetic coding,” Carter said. “This had been unresolved for 60 years.”
Wills added, “The pairs of molecular patterns we have identified may be the first that nature ever used to transfer information from one form to another in living organisms.”
The discoveries center on a cloverleaf-shaped molecule called transfer RNA (tRNA), a key player in translation. A tRNA is designed to carry a simple protein building-block, known as an amino acid, onto the assembly line of protein production within tiny molecular factories called ribosomes. When a copy or “transcript” of a gene called a messenger RNA (mRNA) emerges from the cell nucleus and enters a ribosome, it is bound to tRNAs carrying their amino acid cargoes.
The mRNA is essentially a string of genetic “letters” spelling out protein-making instructions, and each tRNA recognizes a specific three-letter sequence on the mRNA. This sequence is called a “codon.” As the tRNA binds to the codon, the ribosome links its amino acid to the amino acid that came before it, elongating the growing peptide. When completed, the chain of amino acids is released as a newly born protein.
Proteins in humans and most other life forms are made from 20 different amino acids. Thus there are 20 distinct types of tRNA molecules, each capable of linking to one particular amino acid. Partnering with these 20 tRNAs are 20 matching helper enzymes known as synthetases (aminoacyl-tRNA synthetases), whose job it is to load their partner tRNAs with the correct amino acid.
“You can think of these 20 synthetases and 20 tRNAs collectively as a molecular computer that evolution has designed to make gene-to-protein translation happen,” Carter said.
Biologists have long been intrigued by this molecular computer and the puzzle of how it originated billions of years ago. In recent years, Carter and Wills have made this puzzle their principal research focus. They have shown, for example, how the 20 synthetases, which exist in two structurally distinct classes of 10 synthetases, likely arose from just two simpler, ancestral enzymes.
A similar class division exists for amino acids, and Carter and Wills have argued that the same class division must apply to tRNAs. In other words, they propose that at the dawn of life on Earth, organisms contained just two types of tRNA, which would have worked with two types of synthetases to perform gene-to-protein translation using just two different kinds of amino acids.
The idea is that over the course of eons this system became ever more specific, as each of the original tRNAs, synthetases, and amino acids was augmented or refined by new variants until there were distinct classes of 10 in place of each of the two original tRNAs, synthetases, and amino acids.
In their most recent study, Carter and Wills examined modern tRNAs for evidence of this ancient duality. To do so they analyzed the upper part of the tRNA molecule, known as the acceptor stem, where partner synthetases bind. Their analysis showed that just three RNA bases, or letters, at the top of the acceptor stem carry an otherwise hidden code specifying rules that divide tRNAs into two classes – corresponding exactly to the two classes of synthetases. “It is simply the combinations of these three bases that determine which class of synthetase binds to each tRNA,” Carter said.
The study serendipitously found evidence for another proposal about tRNAs. Each modern tRNA has at its lower end an “anticodon” that it uses to recognize and stick to a complementary codon on an mRNA. The anticodon is relatively distant from the synthetase binding site, but scientists since the early 1990s have speculated that tRNAs were once much smaller, combining the anticodon and synthetase binding regions in one. Wills and Carter’s analysis shows that the rules associated with one of the three class-determining bases – base number 2 in the overall tRNA molecule – effectively imply a trace of the anticodon in an ancient, truncated version of tRNA.
“This is a completely unexpected confirmation of a hypothesis that has been around for almost 30 years,” Carter said.
These findings strengthen the argument that the original translational system had just two primitive tRNAs, corresponding to two synthetases and two amino acid types. As this system evolved to recognize and incorporate new amino acids, new combinations of tRNA bases in the synthetase binding region would have emerged to keep up with the increasing complexity – but in a way that left detectable traces of the original arrangement.
“These three class-defining bases in contemporary tRNAs are like a medieval manuscript whose original texts have been rubbed out and replaced by newer texts,” Carter said.
The findings narrow the possibilities for the origins of genetic coding. Moreover, they narrow the realm of future experiments scientists could conduct to reconstruct early versions of the translational system in the laboratory – and perhaps even make this simple system evolve into more complex, modern forms of the same translation system. This would further show how life evolved from the simplest of molecules into cells and complex organisms.
Almost all mammals avoid eating chili peppers and other “hot” foods, because of the pain they induce. But not the tree shrew, according to a study publishing in the journal PLOS Biology. The researchers found that this close relative of primates is unaffected by the active ingredient in chili peppers due to a subtle mutation in the receptor that detects it. They speculate that this is an evolutionary adaptation to enable tree shrews to cope with a peppery plant that makes up part of their diet.
Capsaicinoids, including the capsaicin found in chili peppers, are chemicals that deter animals from eating them. They act by triggering the activation of TRPV1, an ion channel found on the surface of pain-sensitive cells in the tongue and elsewhere. TRPV1’s normal job is to alert animal to the presence of harmful heat, which is why capsaicinoids induce a sharp burning sensation. While humans may develop a tolerance and even a liking for capsaicinoids, most animals avoid feeding on plants that contain them.
The authors observed that Chinese tree shrews (Tupaia belangeri chinensis) actively fed on chili peppers, and, in contrast with mice, did not reduce their food intake as the concentration of capsaicin increased. They found that while the levels of TRPV1 in mice and tree shrews were similar, and both mammals were similarly responsive to other painful stimuli, the TRPV1 ion channel in the tree shrew was much less responsive to capsaicin. The authors then revealed the reason for this; TRPV1 proteins of mice and tree shrews differed by a single amino acid in the binding pocket for capsaicin, a mutation that the researchers found reduced the binding ability, and thus pain-inducing potential, of capsaicin in the tree shrew’s form of the protein.
While chili peppers themselves do not grow in the tree shrew’s environment, a plant that produces abundant capsaicinoids, Piper boehmeriaefolium, does, and is an important food source for the tree shrew. The ability to feed on this plant while most other species avoid it, the authors suggest, was potentially an important driver for the spread of the TRPV1 mutation through the tree shrew population over time.
“We propose that this mutation is an evolutionary adaptation that enabled the tree shrew to acquire tolerance for capsaicinoids, thus widening the range of its diet for better survival,” Han says.
Humans and mice share approximately 98% of genes, and have similar physiology and anatomy. This is because we share a relatively recent common ancestor, around 80 million-years-ago. In contrast, the ancestor of all animals lived over 500 million-years-ago. As genomic data becomes available for more animal species a detailed family tree can be created, allowing novel insight into the genomes of long extinct species. In the guest post below Jordi Paps summarises recent research that attempts to reconstruct the genome of the ‘first animal’ by using the genomic data available on living animals.
The first animals emerged on Earth at least 541m years ago, according to the fossil record. What they looked like is the subject of an ongoing debate, but they’re traditionally thought to have been similar to sponges.
Like today’s animals, they were made up of many, many different cells doing different jobs, programmed by thousands of different genes. But where did all these genes come from? Was the emergence of animals a small step in evolution, or did it represent a big leap in the DNA that carries the instructions for life?
To answer these questions and more, my colleague and I have reconstructed the set of genetic instructions (a minimal genome) present in the last common ancestor of all animals. By comparing this ancestral animal genome to those of other ancient lifeforms, we’ve shown that the emergence of animals involved a lot of very novel changes in DNA. What’s more, some of these changes were so essential to the biology of animals that they are still found in most modern animals after more than 500m years of independent evolution. In fact, most of our own genes are descended from this “first animal”.
Previous research on lifeforms that are closely related to animals – single-celled organisms such as choanoflagellates, filastereans and ichthyosporeans – has shown they share many genes with their animal cousins. This means that these genes are older than animals themselves and date back to some common ancestor of all these creatures. So the recycling of old genes into new functions, a kind of genome tinkering, must have been an important force in the origin of animals.
But Professor Peter Holland and I wanted to find out which new genes emerged when animals evolved. We used sophisticated computer programs to compare 1.5m proteins (the molecules that genes contain the instructions for) across 62 living genomes, making a total of 2.25 trillion comparisons to find out which genes are shared between different organisms today.
We then created a computer program that could combine this information with the evolutionary relationships of the animals to reconstruct which genes were present in the last common ancestor of all animals. The results don’t represent the ancestor’s full genome, as many genes and other genetic information will no longer exist in today’s animals. But using evolutionary trees to infer what happened in the past in this way is one of the most powerful applications of evolutionary biology, as close as we can come to travelling back in time.
Our results suggest the genomes of the first animals were surprisingly similar to those of modern ones, containing the same proportions of biological functions. Around 55% of modern human genes descend from genes found in the last common ancestor of all animals, meaning the other 45% evolved later.
By applying the same techniques to the genomes of modern relatives of animals,
we also reconstructed the genome of even older ancestral organisms. We found that the first animal genome was in many ways very similar to the genomes of these unicellular ancestors.
But then we looked at the novel genes in the first animal genome that weren’t found in older lifeforms. We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors.
Finally, we looked at those novel genes from the first animal that are still found in most of the modern animals we studied. Natural selection should mean that animals keep genes with essential biological functions as the species evolve. We found 25 groups of such genes that had been kept in this way, five times more genes than in other, older, ancestors. Most of them have never been associated with the origin of animals before.
These novel genes that are still widely found today control essential functions that are specifically related to lifeforms with multiple cells. Three groups of these genes are involved in transmitting different nervous system signals. But our analyses show that these genes are also found in animals that do not have a nervous system, such as sponges. That means the genetic basis of the nervous system may have evolved before the nervous system itself did.
Our research shows that both new genes and the recycling of old genes were important in the evolution of animals. But these results raise even more questions. Were novel genes also important in the rise of other types of large multicellular lifeforms such as plants or fungi? What was behind the explosion of novel genes that drove the evolution of animals? Did it happen faster than in other groups or did animal ancestors take a long time to accumulate all the new genes? Answering those questions will require more and better genome data (or improved time-travelling capabilities).