The genetic copier unravelled
At any given moment in every body, many millions of cells are engaged in a complex process: copying DNA within the cell. Before a cell can start dividing, each piece of genetic material is copied with great precision. For many years, the workings of this so-called DNA replication were a great mystery. Bruce Stillman, professor of biochemistry and president of Cold Spring Harbor Laboratory in New York State, made important contributions to unravelling this mystery. In 2020, he received the Dr. H.P. Heineken Prize for Biochemistry and Biophysics for his work.
In Bruce Stillman’s office, there is a beautiful crystal on which a replica of the first lens made by Antoni van Leeuwenhoek is displayed. That lens opened the world of microbes and cells to the human eye. This work of art is the Heineken trophy he received for is pioneering research. One of the first things Van Leeuwenhoek saw through his microscope around 1670 was the sediment in beer. At first, he thought he was looking at some dead cells, but later he found he had seen yeast cells, alive and well and essential to the process of brewing beer. It so happens that Stillman owes many of his breakthroughs to an important choice: about forty years ago, he decided to start using yeast cells for his research. The yeast S. cerevisiae, which is used to make bread, wine, and beer, enabled him to identify many proteins that play a role in copying DNA in cells.
Indeed, while Stillman is enthusiastically talking about his research, many millions of cells in his body are busy. All DNA and associated proteins are copied with great precision before a cell can proceed to divide. For example, in the human body’s bone marrow alone, a billion metres of DNA are meticulously copied every minute – a feat of no small magnitude. But despite the insanely complex molecular machinery, equipped with various control mechanisms, this process sometimes goes wrong. ‘One of the reasons I became interested in the subject of DNA replication is because this process goes wrong in cancer,’ Stillman says. ‘I wanted to understand how this process really works, and what exactly goes wrong in that case.’ Stillman devoted his career to unravelling this biological copier. He and his colleagues identified many proteins that play an important role in the replication process and unravelled how they interact.
If you want to copy a strand of DNA, you might think: I’ll just start at one end, and copy until I get to the other end. But the hard data quickly make you face facts. ‘If you only had one starting point, a so-called origin of replication, it would take months to replicate an entire chromosome’, Stillman says. ‘In reality, there are a lot of these starting points. As a result, the copying process only takes about eight hours in human cells.’
Very efficient, but this requires good coordination. First, the copying proteins must somehow know where to start copying. ‘You cannot start in the same place twice, because then you get duplicate sections’, Stillman says. ‘You cannot skip a starting point either, because then a piece of DNA is thrown away.’ One of his major breakthroughs was to unravel how this simultaneous start is managed. ‘The replication process starts with proteins binding to DNA at specific locations’, Stillman says. ‘The breakthrough that Steve Bell, a postdoc in my lab, and I made in 1992 was the discovery of the Origin Recognition Complex, which is the enzyme machinery that gets the whole process going.’
Ready, set, go!
This Origin Recognition Complex, ORC for short, is a protein that recognises a starting point in the DNA strand and binds to it. Next, ORC gathers a series of other proteins around it, many of which Stillman has also identified. All together, they form what is known as the pre-replicative complex. This complex gives ‘permission’, as it were, to start DNA replication. Once the starting signal is given, the copying proteins begin copying from the starting points. After that, the pre-replicative complex is destroyed. ‘This complex cannot then be reassembled until the fully copied and original chromosomes are pulled apart and placed in two separate cell nuclei’, Stillman says. ‘This ensures that the copying process cannot be started multiple times within one cell cycle.’
To figure out exactly how this all works, Stillman and colleagues had to find a way to distinguish between the formation of the pre-replicative complex and the actual copying of DNA. To do this, they first studied viruses that infect cells of primates. In these cells, the virus uses much the same machinery as primates to replicate its viral DNA. So, the same proteins that copy human DNA also copy viral DNA. ‘In my lab and that of my colleague Thomas Kelly, we identified many of these proteins,’ Stillman says. ‘Thanks to this research, we discovered many proteins that play an important role in the human replication process.’
However, viruses did not solve the issue of how this replication process gets started in cell chromosomes. An important step toward unravelling this mystery was the decision to work with yeast. Stillman’s eye fell on Saccharomyces cerevisiae, a yeast used to make bread, wine, and beer. Yeast proved to be a perfect organism for his research because it allowed him to apply both biochemical and genetic techniques. ‘The reason we started working with yeast was because there was a suggestion that the starting points, the origins of replication, in yeast are defined by specific DNA sequences.’
This indeed turned out to be the case. Step by step, Stillman and student York Marahrens studied which nucleotides (the building blocks of DNA, better known by the letters A, C, G, and T) are required for DNA replication. They did this by comparing normal strands of DNA with mutated versions. ‘We identified four pieces of DNA code required for DNA replication,’ Stillman says. ‘We had origins that worked, and origins that did not work. The difference between the working and non-working versions was only one letter in the genetic code. Colleague Stephen Bell used that information to identify proteins that bound to the working origins, and not to the non-working ones.’ The proteins that bound to the working origins combined to form what they called the Origin Recognition Complex.
In their yeast research, they discovered not only ORC, but also other proteins that together with ORC formed the pre-replicative complex, not just in yeast cells. ‘Eventually in my lab we also found the human ORC, by following the evolutionary path from yeast to humans’, Stillman says. ‘I knew at the time that this would open up a whole new field of research. But when we found ORC, we were initially very cautious. Indeed, people had previously claimed to have found the critical protein that bound to the origins. But each time, it turned out not to be true. People began to believe that no such protein existed. But thanks to our analysis with the origin mutations, the evidence was very strong. It is very rewarding to spend six or seven years working on a hypothesis that could very well be wrong but turns out to be right in the end.’
Only recently did Stillman fully realise how beneficial their choice of baker’s yeast had been. In 2020, he published a paper on the evolution of ORC. In it, he showed that baker’s yeast and some related yeasts are the only species on the planet in which the origins are characterised by specific DNA sequences. This does not occur in any other organism – fungi, insects, plants, animals. So, it would have been very difficult to find ORC with their mutation analysis in any other organism. And they just might have chosen a different organism. ‘In the mid-1980s, I was talking to yeast researchers’, says Stillman. ‘I asked them what it was like to do biochemistry with yeast. Some of them said: “Don’t do it, it’s awful.” Fortunately, we did not listen to them at the time.’
In addition to the start of the replication process, Stillman unravelled many other aspects. ‘I vividly recall one moment from when I was working in the lab myself. I identified the protein we called CAF-1, Chromatin Assembly Factor 1, for the first time.’ CAF-1 helps to bind packaging proteins around the newly copied DNA. In the end, the DNA forms a structure together with these packaging proteins that ensures that it is stored well protected. ‘I will always remember that moment. I sat down and thought: “This is going to be really big.”’ Stillman and colleagues discovered many other proteins, including the so-called Replication Protein A, a protein that binds to a single strand of DNA to keep it from curling up during copying; ABF-1, one of the proteins that bind at locations where copying starts; and Replication Factor C, a protein that loads a protein called Proliferating Cell Nuclear Antigen (PCNA) that helps the copying machinery and CAF-1 to duplicate and package the copied DNA. Many patients with the autoimmune disease systemic lupus erythematosus make antibodies against PCNA.
‘It turns out that all these proteins do not just play a role in DNA replication’, Stillman says. ‘They also play an important role in DNA repair, DNA recombination (which occurs when mixing the DNA of two parents, among other things), and a process called checkpoint signalling. If damage is detected during DNA replication, such as that caused by UV light or X-rays, a signal is sent to stop the cycle of cell division until repair has taken place. Replication Protein A appears to be the primary signal for this.’
In case of damage, DNA repair enzymes digest the DNA strand that has damage, leaving single-stranded DNA behind. This does not belong in a human cell, where all the DNA is neatly contained in the double-helix structure. ‘Replication Protein A binds to that single-stranded DNA, and that is the signal for the temporary stopping process. The cell division cycle can only progress once the damage is fixed, by creating double-stranded DNA again’, Stillman says. ‘I am quite proud of the fact that these proteins play a role in many different processes. The impact is much broader than we thought when we started this.’
Not only environmental factors such as UV light or X-rays can cause damage. When you consider how complicated the DNA replication process is, and how many different proteins are involved, it is not hard to imagine that very occasionally something goes wrong in the copying process itself. ‘In the bone marrow alone, 500 million red and white blood cells are produced every minute’, Stillman says. ‘Multiply that by the 2 meters of DNA that needs to be copied in each cell, and that means a billion metres of DNA are copied every minute. You could wrap that around the earth along the equator about 25 times. We know today that about half of all cancers are caused not by environmental influences such as sunlight or smoking, but by the intrinsic process of making mistakes during DNA duplication. These mutations accumulate over a person’s lifetime. And even though the process of DNA replication is very accurate, if we could make it even more accurate, we could significantly slow down the onset of cancer in people’s lifetimes. It would be wonderful if we could get that done.’
Rare genetic disorder
In addition to cancer, Stillman’s research is making an important contribution to understanding a very different disease. In 2011, he stumbled upon a series of publications about a very rare genetic disorder: Meier-Gorlin syndrome. People with this condition suffer from a specific form of dwarfism. Unlike more common forms of dwarfism, in people with Meier-Gorlin the head is also smaller than usual, proportional to the small body size. But even though these patients have a brain that is about twice as small, their intelligence is not necessarily lower than average. According to the publications, mutations in DNA replication genes, which code for ORC and other proteins, were the cause of the syndrome. But the symptoms could not be explained purely on the basis of errors in the DNA replication process. ‘Thanks to our research, we now know that ORC and other replication proteins play a much larger role in the cell cycle’, Stillman says. ‘Many of these other functions were found to be impaired in people with Meier-Gorlin syndrome. So, thanks to our fundamental research, we were able to explain this syndrome.’
But what Stillman finds most valuable is this fundamental knowledge itself. ‘I have been very fortunate to be able to pursue the discoveries that end up in textbooks and are part of the knowledge of who we are and how our genetic information is passed on from one generation to the next. I find it quite extraordinary that the human genome shares gene sequences with bacteria that evolved many billions of years ago and with yeast that evolved hundreds of millions to a billion years ago. All that time, their DNA sequences were being copied to eventually produce modern species with related genes. Evolution has maintained processes that have been in place for a very long time. The proteins that copy DNA, which are similar in yeast and humans, have been doing so for a very long time.’
Bruce Stillman (Melbourne, Australia, 1953) studied at the University of Sydney, and received his PhD from the John Curtin School of Medical Research at the Australian National University. He continued his career in the United States, where he started as a postdoc at Cold Spring Harbor Laboratory in New York State. He has been a professor of biochemistry there since 1985. In 1994, he became director of Cold Spring Harbor Laboratory, and since 2003 he has held the position of president there. In addition to the H.P. Heineken Prize for Biochemistry and Biophysics, Stillman has received the Herbert Tabor Research Award, The Louisa Gross Horwitz Prize, the Canada Gairdner International Award, and the Australian Advance Global Impact Award, among others.
Bruce Stillman studies how the replication process of DNA works in eukaryotic cells – cells that contain a nucleus. This includes the cells of almost all multicellular organisms, such as plants, animals, and humans, as well as many unicellular organisms, such as yeast. Thanks to his research, we better understand how our genetic material is copied and how this relates to other processes in the cell. Stillman also studies where this process goes wrong in diseases such as cancer. His research provided an explanation for the rare genetic disorder Meier-Gorlin syndrome.