Two people are dancing a waltz, and it is not going well. One is tall and the other short; one is graceful, the other flat-footed; and both are stepping to completely different rhythms. The result is chaos, and the dance falls apart. Their situation mirrors a problem faced by all complex life on Earth. Whether we’re animal or plant, fungus or alga, we all need two very different partners to dance in step with one another. A mismatch can be disastrous.
Virtually all complex cells – better known as eukaryotes – have at least two separate genomes. The main one sits in the central nucleus. There’s also a smaller one in tiny bean-shaped structures called mitochondria, little batteries that provide the cell with energy. Both sets of genes must work together. Neither functions properly without the other.
Mitochondria came from a free-living bacterium that was engulfed by a larger cell a few billion years ago. The two eventually became one. Their fateful partnership revolutionised life on this planet, giving it a surge of power that allowed it to become complex and big (see here for the full story). But the alliance between mitochondria and their host cells is a delicate one.
Both genomes evolve in very different ways. Mitochondrial genes are only passed down from mother to child, whereas the nuclear genome is a fusion of both mum’s and dad’s genes. This means that mitochondria genes evolve much faster than nuclear ones – around 10 to 30 times faster in animals and up to a hundred thousand times faster in some fungi. These dance partners are naturally drawn to different rhythms.
This is a big and underappreciated problem because the nuclear and mitochondrial genomes cannot afford to clash. In a new paper, Nick Lane, a biochemist at University College London, argues that some of the most fundamental aspects of eukaryotic life are driven by the need to keep these two genomes dancing in time. The pressure to maintain this “mitonuclear match” influences why species stay separate, why we typically have two sexes, how many offspring we produce, and how we age.
No expecting mother would ever wish harm to befall her children. Unfortunately, she may have no choice in the matter. Due to the rules of genetics, mums always run the risk of passing a “mother’s curse” onto their sons, but not their daughters.
The curse is an ancient one, the result of events that happened billions of years ago. At a time when all life consisted of single microscopic cells, one of these swallowed another. Normally, the engulfed cell would be digested, but not this time – this time, the two cells formed an alliance. The swallowed cell transferred many of its genes to its host, keeping only those involved in providing energy. It evolved into a mitochondrion – a tiny, efficient battery that would power its host, giving it the energy to become more complex. This alliance is the foundation of all complex life on the planet. All animals, plants, fungi and algae run on mitochondria power.
This means that all animals really have two genomes – their main nuclear one, and a far smaller secondary one in their mitochondria. The two sets of genes work together, each controlling the activity of the other. But they are inherited differently. The nuclear genome is a mash-up of genes from both parents, but the mitochondrial one only comes from mum. And this asymmetry is the reason for the mother’s curse.
The 21st century is all about conserving energy. The push towards energy-efficient buildings, vehicles and lifestyles is both fashionable and necessary, but it’s also ironic. Our pattern of ever-increasing energy consumption is deeply rooted in our history, not just since the Industrial Revolution, but since the origin of all complex life on Earth.
According to a new hypothesis, put forward by Nick Lane and Bill Martin, we are all natural-born gas-guzzlers. Our very existence, and that of every animal, plant and fungus, depended on an ancient partnership, forged a few billion years ago, which gave our ancestors access to unparalleled supplies of energy and allowed them to escape from the shackles of simplicity.
At first glance, the African elephant doesn’t look like it has much in common with us humans. We support around 70-80 kg of weight on two legs, while it carries around four to six tonnes on four. We grasp objects with opposable thumbs, while it uses its trunk. We need axes and chainsaws to knock down a tree, but it can just use its head. Yet among these differences, there is common ground. We’re both long-lived animals with rich social lives. And we have very, very large brains (well, mostly).
But all that intelligence doesn’t come cheaply. Large brains are gas-guzzling organs and they need a lot of energy. Faced with similarly pressing fuel demands, humans and elephants have developed similar adaptations in a set of genes used in our mitochondria – small power plants that supply energy to our cells. The genes in question are “aerobic energy metabolism (AEM)” genes – they govern how the mitochondria metabolise nutrients in food, in the presence of oxygen.
We already knew that the evolution of AEM genes has accelerated greatly since our ancestors split away from those of other monkeys and apes. While other mutations were reshaping our brain and nervous system, these altered AEM genes helped to provide our growing cortex with much-needed energy.
Now, Morris Goodman from Wayne State University has found evidence that the same thing happened in the evolution of modern elephants. It’s a good thing too – our brain accounts for a fifth of our total demand for oxygen but the elephant’s brain is even more demanding. It’s the largest of any land mammal, it’s four times the size of our own and it requires four times as much oxygen.
Goodman was only recently furnished with the tools that made his discovery possible – the full genome sequences of a number of oddball mammals, including the lesser hedgehog tenrec (Echinops telfairi). As its name suggests, the tenrec looks like a hedgehog, but it’s actually more closely related to elephants. Both species belong to a major group of mammals called the afrotherians, which also include aardvarks and manatees.
Goodman compared the genomes of 15 species including humans, elephants, tenrecs and eight other mammals and looked for genetic signatures of adaptive evolution. The genetic code is such as that a gene can accumulate many changes that don’t actually affect the structure of the protein it encodes. These are called “synonymous mutations” and they are effectively silent. Some genetic changes do, however, alter protein structure and these “non-synonymous mutations” are more significant and more dramatic, for even small tweaks to a protein’s shape can greatly alter its effectiveness. A high ratio of non-synonymous mutations compared to synonymous ones is a telltale sign that a gene has been the target of natural selection.
And sure enough, elephants have more than twice as many genes with high ratios of non-synonymous mutations to synonymous ones than tenrecs do, particularly among the AEM genes used in the mitochondria. In the same way, humans have more of such genes compared to mice (which are as closely related to us, as tenrecs are to elephants).
These changes have taken place against a background of less mutation, not more. Our lineage, and that of elephants, has seen slower rates of evolution among protein-coding genes, probably due to the fact that the duration of our lives and generations have increased. Goodman speculates that with lower mutation rates, we’d be less prone to developing costly faults in our DNA every time it was copied anew.
Overall, his conclusion was clear – in the animals with larger brains, a suite of AEM genes had gone through an accelerated burst of evolution compared to our mini-brained cousins. Six of our AEM genes that appear to have been strongly shaped by natural selection even have elephant counterparts that have gone through the same process.
Of course, humans and elephants are much larger than mice and tenrecs. But our genetic legacy isn’t just a reflection of our bigger size, for Goodman confirmed that AEM genes hadn’t gone through a similar evolutionary spurt in animals like cows and dogs.
Goodman’s next challenge is to see what difference the substituted amino acids would have made to us and elephants and whether they make our brains more efficient at producing aerobic energy. He also wants to better understand the specific genes that have been shaped the convergent evolution of human and elephant brains over the course of evolution. That task should certainly become easier as more and more mammal genomes are published.
Reference: PNAS doi:10.1073/pnas.0911239106
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