One of the great achievements of contemporary biology is its foundation in molecular genetics and the remarkable progress that has been made in understanding how genes work. Genes are nothing more than discrete stretches of DNA that contain within them the blueprint for producing the proteins upon which life depends. The important question is this: What regulates the genetic machinery? The mechanisms by which genes are turned on, and then turned off when their job is done, are essential to our knowledge of development and disease.
Mark Ptashne is an acknowledged founder of molecular studies of gene regulation. For three decades he has kept his scientific eye on this single target and, in so doing, laid the conceptual framework on which many other investigators have built their research. His major accomplishment has been to figure out how “regulatory molecules” control the function of genes. In the early phase of his research, focusing on bacteriophage, a simple virus that grows in a bacterium, he and his colleagues discovered a series of fundamental mechanisms for how genes are switched on and off. Then turning his attention to higher organisms his laboratory showed, much to the surprise of many, that the very principles that explain gene regulation in lower organisms apply to higher organisms as well. These discoveries are now so deeply ingrained in contemporary science that it is possible to forget their wide-ranging significance.
In 1967, exactly 3o years ago, Dr. Ptashne isolated a regulatory protein in bacteriophage called the “lambda repressor.” This key regulatory protein controls the genes of a virus, called lambda, that reproduces by invading bacterial cells. Dr. Ptashne’s extensive studies of the lambda repressor showed how a regulatory protein can recognize “information specific” sites on DNA. Through studies of the lambda repressor and related molecules, Dr. Ptashne also revealed how simple regulatory molecules can be combined to create a sophisticated “genetic switch” that also allows the virus, when dormant in the bacterium, to dramatically switch on its genes in response to a signal in its environment. Much of this insight required deciphering the molecular anatomy of lambda repressor through the techniques of structural biology, which enabled Dr. Ptashne and his colleague Dr. Stephen Harrison to show in 1987 how the repressor protein bound to DNA atom by atom. This was the first atomic view of a transcription factor touching its DNA.
Dr. Ptashne’s laboratory then turned its attention from bacteria to the more complicated organisms such as yeast and fruit flies. Working on transcription factors from these higher organisms, he defined the structure and function of “gene activators” in these organisms. As is the case for activators in bacteria, gene activators bear regions on the surface that direct the protein to the correct DNA sites and separate surfaces that activate gene expression by interacting with other proteins that bind to DNA. Experiments built on Dr. Ptashne’s data and conceptual ideas have shown the universality of regulatory gene mechanisms. The mechanisms are essentially the same in yeast and fruit flies, in plants and people, and gene regulators that work in one organism will work in others as well.
The next chapter in the gene transcription story will be told through the analysis of the thousands of proteins that are part of the complex human genome. Genetic instructions are “transcribed” as the switches that turn genes on and off enable cells to interpret information for development and homeostasis. Dr. Ptashne has laid the foundation for the complete biochemical reconstruction of the machinery of transcription and for deciphering the complicated gene regulatory networks that underlie development and cell functioning.
Understanding gene regulation in the same detail that computer experts understand microcircuits, for instance, is basic to all recent success in science’s growing comprehension of how multicellular organisms, like human beings, develop and how things sometimes go awry. In this regard, Dr. Ptashne’s work over three decades is a perfect paradigm for the relevance of very basic research on simple and primitive unicellular organisms to human disease. We now know that many genetic diseases are caused by faulty gene regulation Among these are developmental disorders, such as a pituitary hormone deficiency in which growth hormone is not produced; thyroid hormone defects that lead to mental retardation; cancers that develop because an “onco” or cancer-causing gene is turned on (leukemia due to chromosomal translocation, for instance); and cancer caused, oppositely, by the inactivation of genes whose function is to keep cell growth under proper control. Certain tumors of bone, breast, brain and even the eye are known to occur when the “repressor” molecules in the regulatory system fail to repress. Researchers have identified a host of oncogenes, with names like Myc, Fos, and Jun that are known to cause cancer because of errors in gene regulation. When these and similar errors of regulation are finally explained and treatable, Dr. Ptashne can take pride in this accomplishment.
For elegant and incisive discoveries that provided a conceptual framework for understanding how regulatory proteins control the transcription of genes, Mark Ptashne is honored with the Albert Lasker Basic Medical Research Award.
Award presentation by Joseph Goldstein
In an interview on BBC Radio in London, Francis Crick was asked, “What is the key to scientific success?” His reply went something like this: “Be bold and adventurous. Make bold theories and take a bold approach to experimentation. Don’t get bogged down in details. Think big and adventurously.”
The recipient of this year’s Lasker Basic Research Award, Mark Ptashne, passes Crick’s boldness test with flying colors. When Mark began his scientific career 35 years ago, Jacob and Monod had just advanced the theory of gene regulation by repressors. Identifying repressors became the Holy Grail of molecular biology. An understanding of repressors would tell us how genes are turned on and off in response to hormones, growth factors, drugs, and other environmental signals. Many scientists searched for repressors, including Jacob and Monod, but in the end only two scientists had the “bolds” to complete the job: Walter Gilbert working on the lac operon repressor defined by Jacob and Monod, and Mark Ptashne working on the repressor of a tiny virus that infects bacteria called bacteriophage. Mark isolated the repressor in 1967. He showed that it was a protein that specifically bound to a small stretch of DNA. These experiments earned Mark a full professorship at Harvard at age 31. Mike Brown and I had to wait until we were 36 to become full professors—and that was at the University of Texas Southwestern Medical School, not Harvard!
Shortly after Gilbert and Ptashne isolated the first repressors, Gilbert left the field of gene regulation and went on to develop a new technique for sequencing DNA, for which he received a Lasker Award in 1979 and a Nobel Prize in 1980.
Like Gilbert, Ptashne did not rest on his Harvard laurels. He continued to work on gene regulation and soon made his most notable discovery notable not only for its significance, but also for its elegance. To shorten a long story, Mark delineated the molecular basis of the lambda switch, which explains how the repressor and another regulatory protein called Cro interact with the DNA of the bacteriophage virus to switch genes on or off in response to two different environmental signals. Upon infecting a bacterial cell, the virus decides between two developmental pathways, called lysis and lysogeny. When the switch is ON, the virus multiplies exponentially. It commandeers the bacterial cell and kills it by lysis. When the switch is OFF, lysogeny occurs. The DNA of the virus inserts itself into the chromosome of the host bacteria and remains quiescent until the switch is reversed by signals from the environment.
Mark’s work explained beautifully how the lambda switch is constructed and how it is modulated by a positive and negative feedback system controlled by the two DNA-binding proteins, repressor and Cro, interacting with DNA and other components of the genetic machinery. Elucidating the lambda switch opened the field of transcriptional regulation as we know it today and provided the first general model to explain the switching between two developmental pathways that occur during the formation of embryos and cancers in higher organisms, including humans.
Mark Ptashne began a brilliant scientific career by studying lambda, a virus that infects bacteria. In a September 1997 interview with friend and colleague, Nobelist James D. Watson, President of the Cold Spring Harbor Laboratory, Ptashne talks of his work and teaching.
Part 1: Love for the lambda prompts a leap of faith
Mark Ptashne leaves the field of fly genetics to pursue his PhD and learn lambda lore. The Lasker Award winner discusses the scientific community and tells how determination, friendly competition and a unique perspective lead to eventual success in the search for the repressor.
Watson: ….the ambition to find the repressor.
Ptashne: Well, you know, in fact, I had it before I came to Harvard because I had worked — I went to school at Reed College in Portland, Oregon and well, let’s see, if we go back to my sophomore year, my introduction to the field was working as a fly geneticist with Ed Novitsky. We went to Crested Butte, Colorado and Ed, despite his continuing enmity with all things molecular, had the good graces to say look, if you really want to do science, you should go into molecular biology and you should meet Frank Stahl and Aaron Novick. And that was my introduction.
So I spent at least one summer with Aaron and Frank and that was really the generative thing. Of course, Aaron had studied with Francois Jacob and Jacques Monod in Paris, and the whole business of the repressor was very much in the air. It was the great intellectual issue, and I can even remember once mixing up some test tubes and absolutely thrilling Aaron because he thought we’d disproved the French—and of course it was just that I’d screwed up. And so then, when it came time to graduate and go do a PhD, they said well, the real person to go study with is Matt Messelson. So, I went to Cal Tech and met Matt and he said I’m going to Harvard. So that’s why I went to Harvard.
But from the beginning, I said I wanted to isolate the repressor. And Matt said, well, that’s fine. But first you have to get a license, you have to do your PhD. So that’s why I set about learning everything I could about lambda and did the initial thesis on lambda, so that I could get into a position when I got my PhD to then spend full-time doing what, of course, everyone thought was a waste of time because it couldn’t be done.
Watson: Now, when you were doing this —
Ptashne: Oh, and by the way. One of the things that was so encouraging is that as I was on the sidelines doing this other stuff and supposedly all these great labs, the Pasteur and so on, were going to isolate the repressor, they all failed. And yet, if you looked carefully at what they had done, you could convince yourself they just hadn’t done it seriously enough. In other words, they didn’t fail for what I thought were good reasons, but had anyone succeeded during that period, of course, then I wouldn’t have done it.
Watson: Did they fail because they weren’t rigorous or did they not just work as hard as you?
Ptashne: I don’t think they were willing to do things as bizarre as it turned out we had to do. Because don’t forget, there must have been 10 different things we tried, both me and Wally, and none of them were classical chemistry nor classical molecular genetics. They were all quite bizarre. And finally, as you probably remember, in our case, in the lambda case, we had to do this completely unheard of thing of giving vast doses of radiation to cells so that they were essentially just bags of protein synthetic machinery and then stick the DNA in, that is, by adding the virus and let it make the repressor. So there was this very elaborate, complicated thing that depended on a lot of luck and Nancy Hopkins’ particular touch with the cells and correlations with genetics. Looking back on it, it’s not surprising that most people —
I think having Wally there as the competitor, where the two of us were spurring each other on, is what made it possible. Otherwise, I think after a while, you try all the standard ways of doing it and then give up. So in other words, what finally worked was so bizarre and unusual, it could not have been predicted when we started, both of our methods. And it required that special kind of effort.
Watson: Did the sort of conventional lambda PhD, was that actually useful? I mean, in the sense that if you hadn’t done that, you wouldn’t have done the experiments you finally did? That is, it just gave you the background of —
Ptashne: Yeah, I think so and you learn the culture, you learn the —
Watson: That is, I guess what I’m asking you is if you’d started two years earlier, would you have gotten the answer two years earlier?
Ptashne: You mean if I had started on the repressor two years earlier?
Ptashne: Oh, I see. Well, I doubt it. I don’t know, but I sort of doubt it. Certain mutants had to be developed and certain things had to be clarified before it was possible, I think, to go ahead, but my recollection isn’t detailed enough to know for sure.
Watson: So, it was a discovery —