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.

Listening in on Lysozyme

Researchers from the University of California have used a ‘molecular microphone’ to listen to a single protein molecule at work.

One of the world’s smallest transistors, constructed from a single carbon nanotube, was attached to a molecule of lysozyme, a bacterium-fighting protein.

Lysozyme has been the subject of thousands of publications ever since Alexander Fleming, who was suffering from a cold at the time, first tried cultivating a sample of nasal mucus and discovered its antibacterial properties.

Proteins, which are very long, string-like molecules, need to be folded in a specific way in order to function properly. Lysozyme was the first enzyme to have its structure solved, back in 1965. However, knowing the structure alone is not enough to explain how lysozyme works – the way it moves is important too.

Lysozyme folds to form two ‘jaws’, which allow it to hold sugar chains in place in order to cut them apart by breaking a chemical bond. The development of the nano-transistor allowed scientists to study how this protein behaves in unprecedented detail. The team were able to detect lysozyme cutting through chemical bonds at a rate of 15 per second, before it got stuck and started opening and closing its jaws 300 times per second trying to find more bonds to cut (think Pac-Man!).

 

As the transistor is attached to a single molecule, the researchers can see how each protein behaves, rather than just looking at the average of millions of molecules. “Our circuits are molecule-sized microphones,” says Philip Collins, associate professor of physics and astronomy, who led the project with Professor Gregory Weiss from the department of biochemistry. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

This research is the first to use carbon nanotubes for studying the activity of a single molecule. This would previously have been achieved by attaching a fluorescent dye to the protein but these often wear out within seconds. By using the nano-transistor, the team were able to ‘listen’ to the protein for ten minutes, which was crucial for them to observe the protein switching between its different forms.

This ‘microphone’ can be applied to countless other proteins, giving scientists a chance to listen to the machinery of our body at work.