Wednesday, 16 October 2013

The 2013 Nobel Prize in Medicine or Physiology - vesicle trafficking: what even is it

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On the 7th of October, 2013, the Nobel Prize for Physiology and Medicine was awarded to James Rothman, Randy Shekman and Thomas Südhof for their work on vesicle trafficking. After the usual announcements broadcast over the internet in both Swedish and English, and the ensuing explanatory lecture, the press saw fit to ask few questions. The inevitable “how did it feel,” “are there any treatments” fizzled into “…” The conference finished early, while no one seemed to grasp the full significance or profundity of the work.

The discoveries made by Rothman, Shekman and Sudhof were unique, their experiments were unique and the discoveries led to our understanding of how biomolecules like insulin and hormones are made and released, how nerve cells transmit information, and how some diseases like Alzheimer’s develop.

What is a vesicle?

A “vesicle” is a small blob of membrane that encases proteins and other substances. It’s basically the cargo packaging of the cell and transports important items – or biomolecules – around the cell.

You can think of it this way: the human body is made up of organs that have different roles – the kidneys filter blood and remove waste products, the lungs absorb oxygen, which are then carried by red blood cells around the body, pumped by the heart. Just as the human body is made up of specialized organs, so an individual cell is made up of versions of organs known as organelles. Vesicles are the packages that travel between the organelles, delivering their cargo. What our Nobel trio found was how the vesicles transport their cargo, and the order in which they do so.

Rather than a brain, the cell contains a nucleus which holds the code of life, DNA (see Figure 1). Outside the nucleus, which is bound by a membrane, is the endoplasmic reticulum, rough AND smooth, a folded series of membranes. Next up is the Golgi stack (bear with me here, it will make sense), another series of foldy membranes that always are found together. All of this is encase in the cell or plasma membrane, which holds the cell together and is made up of lipids and fats– and also why you do actually need cholesterol. Now you have a map.

Figure 1: How proteins traffic through the cell (from Conn, et al, Pharmacological Reviews (2007) vol. 59 pages 225-250).

The cell is made up largely of Stuff floating in a solution of salts (“plasma”) in water in between the cytoskeleton – which is the structure that gives the cell shape, just as the human body has a skeleton. The cytoskeleton is made up of proteins. In fact, a lot of the cell is made up of proteins – proteins called enzymes help reactions to take place in the cell: proteins are the workhorses of the cell, and indeed, the human body. And DNA codes for these proteins. So it’s important for cells to correctly make and transport proteins around the cell and out of the cell. And it’s this mode of protein transport that Rothman and Shekman studied.

How is Protein Formed?

Proteins are made by translating the linear code of DNA into a three-dimensional structure made of amino acids. Inside the nucleus, the DNA unwinds and the information is read. This information is transcribed by RNA which is then transported out of the cell to be translated into a protein code. The endoplasmic reticulum (ER) is where the magic happens. Amino acids corresponding to the code are lined up and chemically connected to form a peptide chain. The ER then has to transport this peptide to the Golgi, which takes this peptide up and completes the process of protein finishing and folding. The chain of amino acids, also known as a polypeptide chain, must be folded into the correct 3D form, so it can carry out its function as an enzyme, or as part of the cytoskeleton and so on. If you don’t have the correct 3D structure, you can end up with disease states. Mad cow disease is an example of where misfolded proteins result in disease. The transport from membrane to membrane, its direction, and working out how this happens is what won the Nobel this year.

Vesicles containing our proteins pinch off, like a piece of dough from a larger loaf, from the ER and travel through the cell. They bud off one side of the ER and move through the cell to the Golgi, fusing with the membrane and moving through the whole stack.

Inside these membranes, things are happening to the protein. They are folded with the help of other helper proteins called chaperones. If they need the addition of other things, like sugars, they are added in the Golgi. This is how substances like insulin are produced. Vesicles are then used to deliver these biomolecules to the cell membrane and release their contents.

How are proteins transported? Shekman and Rothman’s Work

Randy Shekman wanted to know how vesicles transported proteins. He used baker’s yeast as a model organism because it is cheap and easy to grow and related to human cells somewhere down the line – it contains the same basic apparatus as human cells. To work out what molecules might be involved in controlling the formation and delivery and uptake of vesicles, he induced random mutations into yeast, and then basically looked to see what happened inside the mutant yeast cells. In a ground breaking paper with Peter Novick, they showed that in some mutants, there were specific points where the vesicles would simply stop and stack, indicating that a signal was involved at that point. So they were able to identify what the checkpoints were, how it was controlled, and what direction the vesicles moved in.

Independently of Shekman, James Rothman had been trying to work out exactly how vesicles form and then merge with other membranes inside mammalian cells. How did these little blebs form without conscious control? How did they know where to go and how to dock with the other membranes and deliver their cargo? Rothman and Shekman eventually collaborated. Rothman was able to show that there were specific proteins, called clathrins which are shaped a bit like the triskelion of the Manx flag that acted liked tiny zippers, pulling the membrane into a vesicle. It’s a bit like pulling fabric into a curve by introducing shape and tension. Then once the vesicles reach their destination, there were other proteins on the ER or Golgi membranes that connected with the vesicles and “unzipped” them, so the vesicle merges into the membrane and releases its contents into the organelle. He also found that very closely related proteins were responsible for this happening in both yeast and mammals. So the process was the same for complex and simple organisms. In fact, many of these basic processes they discovered are universal to most life.

The Timed Release of Vesicles

Rothman and Shekman established that vesicles were involved in and necessary for transport of biomolecules in the cell. What German-born Thomas Südhof was interested in was how nerve cells transmitted the nerve signal. Between two nerve cells is a gap called a synapse (Figure 2). Vesicles containing neurotransmitters, chemicals that transmit the nerve signal, gather at the end of one neuron (pre-synaptic neuron). They are then released on signal into the synaptic cleft, and the neurotransmitter then binds to receptors on the second neuron. So, while it was clear that vesicle transport was involved, the real question was: how was vesicle movement controlled in nerve cells? How was it controlled so that the vesicles delivered only on cue at the right time?

Figure 2: The nerve synapse (copyright Elizabeth Morales). Here’s where the nerve signal is transmitted from one neuron to another.

Südhof’s work showed that vesicle release could be timed to occur only when the nerve signal was received. It was known that calcium ions were involved in nerve signal, and Südhof tried to work out how the ions were released and the signal picked up. He found the biomolecules, proteins that detected the rapid movement of calcium ions into the nerve cell, these molecules then induced vesicles to bind to the nerve cell membrane at the synapse and release the neurotransmitter. The neurotransmitter was then picked up by other receptors on the second cell, and the signal passed on. He showed that vesicle release could be timed perfectly, under the unconscious control of biomolecules.

And this is the essence of what Rothman, Shekman and Südhof showed us: within the cell, just like the human body at large, were elegant, well timed and carefully controlled processes that resulted in the manufacture and delivery of biomolecules – as well as the transmission of nerve signals and other cellular processes. All of these occurred because of chemistry and physics within the cell, between proteins, behaving like components of machinery. James Rothman puts it best:

“..one of the major lessons in all of biochemistry, cell biology and molecular medicine is that when proteins operate at the sub-cellular level they behave in certain way, as if they were mechanical machinery. It's absolutely fascinating. When you ... when we study chemistry, the rules of chemistry, electrons and so on, they operate at an even smaller level of atoms and molecules. But when you get to the sort of level of the nanoscale, you find that these objects start behaving as if they were mechanical. Exactly how I think about it, and always have. “

 James Rothman, Nobel Prize Interview with Adam Smith.

Like the brain unconsciously controlling our heartbeat and breathing, vesicles traffic proteins through the cell under the unconscious control of pure chemistry and physics. It just happens because, and it is exquisitely beautiful.

Upulie Divisekera

Upulie Divisekera is a cake-loving molecular biologist and science communicator with an evangelical interest in dinosaurs.

Follow her on Twitter @scienceupulie