Hidden evolution: How the mammoth kept its cool

Last weekend I went to see an exhibition on mammoths in the Natural History Museum in London (unfortunately now closed). The descriptions and posters did a very good job of explaining our current knowledge of mammoths and how that knowledge had been gained. In particular, the curators were very keen to highlight the evolutionary relationships between different mammoth species and modern elephants.

A lot of the differences between the woolly mammoths and modern elephants are quickly apparent. The woolly mammoths are larger, hairier, and of course there are the tusks.

The tusks can be a big giveaway for a mammoth

The tusks can be a big giveaway for a mammoth

But one little sign caught my eye. It said that from the genetic material gathered from mammoth remains (we’ve recorded about 70% of their genome, so maybe not too far off until we can clone mammoths back into existence!), we can tell that woolly mammoths had a mutated form of haemoglobin that worked better in cold temperatures.

This haemoglobin discovery was published in 2010, so it isn’t anything new. But for me, this is evolution at its most interesting – not apes walking upright or fish breathing on land, but the tiny internal changes that adapt the body’s complex machinery.

Haemoglobin has a difficult balancing act to achieve – it needs to grab hold of oxygen from the lungs and it needs to release it around the body. If it holds the oxygen too tightly, the muscles can’t receive enough. If the haemoglobin holds on too weakly, it won’t be able to carry enough oxygen to where it is needed.

Elephant haemoglobin, like the human form, more readily releases oxygen at higher temperatures. That comes down to the energetics of breaking its hold, but it also means that harder-working (and therefore warm) muscles can take a greater share. This can be a serious issue if body-parts get too cold – they can suffocate to death. This is a danger for trekking around Siberia, even if you are large and hairy.

Researchers from the University of Manitoba, Canada, compared the haemoglobin genes of woolly mammoths to those of an Asian elephant from a nearby zoo. They noticed that there were four mutations that led to changes in the amino acid chains of the haemoglobin proteins.

Without any mammoth blood to hand, it can be very difficult to work out the effect of these changes. Fortunately, although we can’t resurrect a full mammoth now, we can insert the haemoglobin DNA into bacteria and resurrect one small part of them.

With the bacterium-produced mammoth haemoglobin, the researchers could run the tests needed to confirm that it was indeed adapted to the cold. Rather than the strong link to temperature seen in elephants, the mammoths’ haemoglobin can release oxygen at a similar level over a wide range of temperatures.

The structure of haemoglobin, with the blue regions showing where the mammoth mutations are

The structure of haemoglobin, with the blue regions showing where the mammoth mutations are (Credit: K Campbell et al, 2010)

The blue regions in the picture above show where the changes are in the structure of haemoglobin. These changes don’t appear to make any direct contact with the heme group (the part that carries the oxygen, shown in orange sticks), but they alter the shape of the protein subtly. This change in shape is enough to give mammoths a better chance of surviving freezing cold environments.

Mutations in haemoglobin are also seen in other animals adapted to cold environments, such as the arctic fox. The mutations seen in these animals are all different but lead to similar effects – an example of convergent evolution.

Just last year, the same researchers who made this discovery started work on an exciting new find: well-preserved mammoth blood. This could give them the chance to test the same idea on haemoglobin straight from a mammoth. There is even a (very small) chance that intact cells could be found in the sample, which would make cloning a full mammoth a lot easier.

So before long we might find out a lot more about these legendary creatures.

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Finding a needle in a haystack: How RecA slides in to the rescue

RecA is well-practiced at finding a needle in a haystack – its job is to track down the right sequence of DNA out of 3,000,000,000 letters. But until now, it was not clear how it did this: does it jump from one bit of DNA to the next or does it slide along?

Damage to DNA is one of the biggest threats that we face – it is one the main driving factors in developing cancer. However, evolution has provided us with many tools to prevent and fix any problems. One advantage of DNA being a double helix is that if only one strand of the helix breaks, the DNA is still held in place by the second and so it can be easily fixed. However, if both strands break it becomes far more difficult to piece the DNA back together.

The single strand break (left) can be easily patched up - the DNA helix is still held in one piece. However, the double strand break (right) means that the sequence is split into two and it's not possible to stitch them back together.

The single strand break (left) can be easily patched up – the DNA helix is still held in one piece. However, the double strand break (right) means that the sequence is split into two and it’s not possible to stitch them back together.

In a double-strand break, the broken strands separate from each other because they can’t be put back together. To be repaired, a broken strand needs to line up with an undamaged molecule of DNA and use it as a template. However, finding the right sequence to align with is not easy when there are 3 billion nucleotides to search through.

These broken strands rely on a protein known as RecA to act as matchmaker and find the perfect partner sequence of DNA. Several molecules of RecA attach themselves to the strand, straightening it out and forming what is called the pre-synaptic filament. Taekjip Ha from the University of Illinois wanted to find out if this filament is able to slide along the DNA or if it has to rely on jumping from place to place. To test this they used a technique known as FRET (fluorescence resonance energy transfer), which can tell you the distance between two fluorescent tags that are attached to different molecules. One tag was attached to the filament and the other was attached to a short stretch of DNA that would not match with the filament. The researchers were able to see the distance changing very quickly, showing that the RecA-DNA filament was sliding back and forth along the short length of DNA, unsuccessfully trying to find a match.

Several copies of RecA bind to a stretch of single-stranded DNA

Several copies of RecA bind to a stretch of single-stranded DNA (shown in black) to help it find a match

The ‘bait’ DNA was then changed so that it had two patches that matched the sequence of the filament. By attaching fluorescent tags to each patch, the filament could be seen sticking to one of the two sections, and then sliding along and binding to the other. From the speed of the sliding, the researchers estimated that RecA could help to slide along up to 300 base pairs of DNA before reattaching somewhere else. This could help speed up the search for the matching sequence by over 200-fold, making it a much more efficient technique than randomly hopping from sequence to sequence.

This kind of sliding movement is the first that has been seen in a protein-DNA complex and improves our understanding of this highly important process. Fortunately, one lab has made a (low-budget) video to show how RecA works. Enjoy…

…and this little piggy corrected genetic mutations

Scientists have come a step closer to being able to correct mistakes in our DNA, thanks to a new method for rewriting mutations in stem cells. This could be used to treat genetic diseases for which there are no treatments available.

The researchers made use of piggyBac, a ‘jumping gene‘ originally found in moths. These ‘jumping genes’, as their name suggests, move from place to place along the DNA and can be used to carry other genes with them. Acting as a genetic cut-and-paste, they can neatly insert a corrected gene with remarkable precision. “Our systems leave behind no trace of the genetic manipulation, save for the gene correction,” says Professor Allan Bradley of the Wellcome Trust Sanger Institute.

In the case described in Nature the team focused on a genetic liver disease.

Severe deficiency in the protein alpha 1-antitrypsin is caused by a mutation, which is found in 1 in 2000 North Europeans. This protein is produced in the liver, but is responsible for protecting the lungs. The mutation causes the protein to accumulate in the liver, leading to cirrhosis, and deplete in the lungs, causing emphysema.

The scientists converted samples of patients’ skin cells into stem cells and corrected the mutation, using piggyBac. These stem cells were then converted into liver cells, in test tubes and in mice, which were able to produce the correct form of the protein.

Despite advances in the technology, producing stem cells in this fashion introduces new mutations into the DNA. While most of these mutations are likely to be harmless, there can be potentially fatal side-effects. This risk will need to be minimized before the technique is brought forward to treating patients.

Currently the only cure for alpha 1-antitrypsin deficiency is a liver transplant, but with transplant waiting lists longer than ever, this new development can bring hope to thousands of sufferers.

Pearls of Wisdom: Oysters genome reveals hardy defences

The oyster genome has been sequenced, making it the first mollusc to have its whole DNA mapped out. Molluscs (more specifically the phylum Mollusca) are largest group of marine species, making up nearly a quarter of all known species, and naturally play an important part in maintaining the ecosystem. Analysis of the genome has revealed a highly developed response to environmental stresses.

Oysters tend to live in estuaries or by the seashore – both very changeable environments. Estuaries continuously vary in salinity, requiring a highly adaptable system for life there. The seashore, or intertidal region, also has varying salinity but also has the problem of exposure to air when the tide goes out. Although exposure to air might be the least of your concerns if you find yourself stuck in the full glare of the midday sun at low tide.

The Pacific Oyster (Crassostrea gigas) lives a difficult life, but has the tools to help it survive.
Credit: David.Monniaux

Protecting against heat is common concern and so we have specialised proteins to defend against damage, aptly known as heat shock proteins. These proteins are found in nearly all forms of life, that’s how important they are. Researchers found 88 HSP70 (heat shock protein 70) genes in the oyster genome, significantly more than the 17 genes found in humans. Not only are there many of these genes, but they are highly responsive; 14 times more Hsp70 was produced under heat stress overall, with some genes activating over 2000-fold.

Hsp70 is usually used in the cell to protect newly synthesized proteins. Proteins are often highly dependent on being folded properly to prevent them from aggregating. Aggregation not only means the protein is useless, but it may be damaging to the cell. As the protein leaves the ribosome it is in a vulnerable position until it has time to fold into shape. Hsp70 acts by cradling the protein strand and protecting it until it can be passed on for further processing.

Hsp70 is found in nearly all forms of life, that’s just how important it is

The protective ability of Hsp70 is also why it is known as a heat shock protein. When the temperature gets high, proteins begin to unfold and are again threatened by aggregation. Hsp70 recognises loose strands of protein and binds to them, protecting them in the same fashion. This may help to explain the oyster’s ability to survive at temperatures up to 49°C (120°F).

Heat is only one factor that oysters have to deal with and their genome shows just how hardy they are. They appear to have a high rate of mutations and a large number of transposons, both resulting in high genetic diversity. This has allowed them to accumulate many mechanisms to prevent apoptosis (programmed cell death) in times of stress. In fact, over 4000 genes (16% of the whole genome) responded to air exposure.

The paper in Nature detailing these results had 85 authors. This gives a good indication of how much work goes into whole genome sequencing and analysis. There is a lot to learn from studying the genomes of other organisms, but it is still difficult work.

Above Genetics: How your behaviour can affect your DNA

It is now regarded as a simple fact of life that you are stuck with the genes your parents gave you. Genetic mutations from long ago have passed down from generation to generation, whether it is joined earlobes, knobbly knees or a higher risk of breast cancer. This is Darwinian inheritance in action.

But what if that isn’t the full story? What if your actions as a ten-year-old not only affected your genes, but those of your future children and grandchildren?

Darwin wasn’t the first to offer a theory on evolution; before him was Jean-Baptiste Lamarck, who suggested that traits developed by animals during their lifetime could be passed onto their children. The classic example is a giraffe, who, after years of stretching to reach higher leaves, would have offspring with longer necks. After several generations of stretching, giraffes would have necks as long as they are today.

This made intuitive sense and even Darwin was reluctant to dismiss it — he was not quite the Darwinist he is now made out to be. However, now that DNA is known to be responsible for passing on genetic information, it is hard to see how this could work. No amount of neck-straining will change your genes, so surely this cannot happen.

How could stretching your neck be passed on to the next generation?
Source: Brocken Inaglory

The Human Genome Project aimed to transcribe our DNA and find out what makes a human. Even after decoding all three billion ‘letters’, there was still not enough information to provide all the answers. One of the problems is that many genes can be switched off, or ‘silenced’, by the body. This occurs through methylation, where a small marker, just one carbon and three hydrogen atoms, is attached to a section of DNA and switches it off. Since this silences a gene without actually altering the genetic code, methylation is described as epigenetic, from the Greek ‘epi-’ for ‘above’. This system of silencing genes is another layer of information on top of the genetic code — an epigenetic code.

Methylation of DNA is a natural way that an organism regulates itself, but external factors can affect this dramatically. When a honey bee larva is fed on royal jelly its methylation levels fall, causing it to develop ovaries, grow larger and live longer, i.e. become a queen. However, it is not just food that is important; mice change their DNA methylation patterns depending on how much attention their mothers paid them as a pup.

Methylation of DNA is a very subtle change but its effects can be enormous.
Source: Christoph Bock

Epigenetic changes due to environment can happen even before birth. Studies of several famines, including the Dutch Hunger Winter of 1944 and the Great Chinese Famine of 1958–61, have shown that children conceived during these periods were underweight at birth. Now adults, they have increased rates of obesity, heart disease and schizophrenia, and have increased methylation of genes linked to these diseases. This makes clear the importance of epigenetics as not just an aside to genetics but a powerful force in its own right.

It was long thought that epigenetic changes could not be passed to our children, as sperm and egg cells undergo ‘reprogramming’ to wipe the slate clean. However, recent experiments have shown that mice are able to pass on epigenetic changes and historical records suggest that this may be happening in humans too.

As an isolated farming community in the early 1800s, Överkalix in north Sweden suffered from extreme fluctuation in food supply; some years would be plentiful while others would be ruinous. This variation encouraged Lars Olev Bygren, a preventative health specialist, to trace the ancestries of a hundred villagers and cross-reference them with harvest records. Remarkably, he found that boys who had survived a year of famine while aged 9–12 went on to have sons and grandsons who lived on average 32 years longer than those of boys who had enjoyed a year of feasting. This prepubescent stage is when the body is most susceptible to environmental changes; however it is remarkable that the repercussions can be seen two hundred years later in the lives of their grandchildren, who were never directly exposed to famine.

This seems very similar to Lamarck’s theory that the impact of an animal’s life is passed down to the next generation. However, epigenetics cannot replace Darwinian inheritance, where a genetic mutation is permanent, as epigenetic changes should only be temporary. But how long is temporary? We have seen effects passed down at least two generations in humans, while experiments with roundworms have shown epigenetic changes surviving over 40 generations.

Epigenetics gives us the flexibility that genetics could never provide, allowing us to adapt to our environment during our lifetime. However, it is not just our own lives being adjusted; we could be determining the lives of our future children. Take heed, the sins of the father may well be visited upon the son.