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Barbara McClintock, Genome Self-Repair and Cell Cognition: A Revolutionary Vision for the Future of Biology

Posted: 03/ 9/2012 11:42 am

Among the 20th Century's truly great biologists, the pioneering American geneticist Barbara McClintock is still largely unknown to the public -- except, perhaps, for the fact that her views were decidedly different from those of her mainstream colleagues. Among her accomplishments, McClintock was the first person to document genome repair by living cells. But this fundamental discovery does not appear in the introduction to the Wikipedia biography highlighting her major achievements.

Wikipedia reflects the general perception that the work for which McClintock received the 1983 Nobel Prize in Medicine or Physiology -- the discovery of transposable elements in maize (corn) -- arose more or less independently of previous work. Transposable elements are chromosome segments that can change position, or "transpose," in the genome. The results that led her to describe and document transposable elements did come as a complete surprise -- but a surprise for which she was well prepared (McClintock 1984; McClintock 1987).

Transposable elements have revolutionized our understanding of genome change. Unlike the "genes" hypothesized by pre-DNA genetic theory, transposable elements do not occupy a permanent location on a particular chromosome and can be distributed throughout the genome. In fact, they account for between 40 and 65 percent of our own DNA and exceed protein-coding sequences more than 25-fold in abundance (Lander, Linton et al. 2001; de Koning, Gu et al. 2011).

We now recognize that there are several classes of mobile genetic elements that can move from one place in the genome to a new location (Shapiro 1983; Craig 2002; Shapiro 2011). An earlier blog explained how these mobile elements have played key roles in evolutionary innovation.

X-ray mutagenesis involves cell repair functions and chromosome rearrangements, not "gene mutations"

In her Nobel lecture, McClintock took pains to explain her early work on the chromosomal basis of X-ray mutagenesis, discovered in the 1920s. X-rays were the first of many external agents that have been shown to induce mutations, or hereditary changes, in living organisms. McClintock set out in 1931 to analyze the X-ray mutants Louis Stadler had isolated from maize plants at the University of Missouri. She was well qualified for doing this; as a graduate student at Cornell in the 1920s, she had personally developed the microscopic methods that allow scientists to visualize the 10 maize chromosomes.

Based on her understanding of chromosome behavior, she made a hypothesis to explain the behavior of certain so-called "variegating" mutants. These mutants were unstable and changed (or "variegated") in their inherited properties as the organism develops. McClintock proposed that variegating plants carried ring chromosomes formed by the fusion of broken chromosome ends at either end of a previously linear chromosome. Such ring chromosomes would tend to be lost during the process of cell divisions as the plant grows, thus producing the variegated patterns.

Some colleagues scoffed at McClintock's idea, but in 1932 she went on to demonstrate that the predicted ring chromosomes were present in the variegating mutants (McClintock 1932). Other mutants induced by X-ray treatment also carried chromosome rearrangements (deletions, translocations, inversions, duplications). All of these could be explained as the results of breakage of one or more chromosomes at two sites and rejoining of the broken ends to reconstitute novel chromosome structures.

McClintock reasoned that maize cells must have an inherent capacity to join broken chromosome ends when two of them are present in the cell. In the mid 1930s, she devised experimental methods to induce new chromosome breakage events. Using these experimentally generated breaks, she demonstrated conclusively that maize cells have the ability to detect, bring together, and fuse broken chromosome ends (McClintock 1939; McClintock 1942). Because these studies on broken ends were so important to her thinking and later discoveries, she fully described and illustrated them in her Nobel lecture (McClintock 1984).

Sensitivity and responsiveness, not mechanism, were the key subjects of her Nobel lecture.

McClintock realized two things from those highly original studies of the X-ray mutants. The first was that the action of the X-rays was to break chromosomes. Breakage alone, however, was not sufficient to generate a mutant chromosome. Broken chromosomes would be lost. The cell's ability to repair the damage by fusing broken ends was essential. In other words, X-ray mutagenesis required cell action. It was not a passive consequence of the physical damage induced by the radiation.

The second realization was that maize cells have sensory and other capacities needed to identify, locate, and join the broken chromosomes. Repair was an example of action by what McClintock came to call "smart cells."

"There must be numerous homeostatic adjustments required of cells. The sensing devices and the signals that initiate these adjustments are beyond our present ability to fathom. A goal for the future would be to determine the extent of knowledge the cell has of itself and how it utilizes this knowledge in a "thoughtful" manner when challenged" (McClintock 1984).

This kind of thinking was indeed far outside the mainstream. It is the reason that the neurobiologist and bacterial behavior researcher, Dennis Bray, comments in his 2009 book, Wetware: A Computer in Every Living Cell (Bray 2009), that McClintock was the first biologist to ask what a cell knows about itself.

McClintock's studies of chromosome breakage and repair led directly to the experiment that resulted in the discovery of transposable elements. In 1944, she applied a technique to introduce broken chromosome ends in the pollen grains and egg cells that fused to generate zygotes. McClintock's original idea was to use this method to generate a series of deletions from a specific chromosome region. But, as she wrote:

Although all of this was known before the 1944 experiment was conducted, the extent of trauma perceived by cells whose nuclei receive a single newly ruptured end of a chromosome that the cell cannot repair, and the speed with which this trauma is registered, was not appreciated until the winter of 1944-45.

In addition to the predicted deletions, McClintock obtained a large number of variegating plants. Some of the variegation patterns involved chromosome breaks, which she documented by microscopic photography of cell nuclei (McClintock 1952). Over the years 1944-1947, she demonstrated that the genetic instabilities she observed were the results of activity by what she called "controlling elements" -- genomic factors that could move to new locations, alter the expression of genetic loci where they inserted, and generate a variety of chromosome structural changes.

By 1947 it was learned that the bizarre variegated phenotypes that segregated in many of the self-pollinated progenies grown on the seedling bench in the fall and winter of 1944-45, were due to the action of transposable elements.

Rather than explain how she demonstrated transposition, the process recognized by the Nobel Prize, McClintock chose instead to relate later experiments that confirmed that the "shock" from receiving a single broken chromosome end had the extraordinary effect of awakening previously latent transposable elements in the genome:

It seemed clear that these elements must have been present in the genome, and in a silent state previous to an event that activated one or another of them. To my knowledge, no progenies derived from self-pollination of plants of the same strain, or related strains, had ever been reported to have produced so many distinctly different variegated expressions of different genes as had appeared in the progenies of these closely related plants grown in the summer of 1944. It was concluded that some traumatic event was responsible for these activations.

Most of the remainder of McClintock's lecture provided "further examples of response of genomes to stress." She wished to emphasize the generality of her observations across the living world, taking examples from both plants and animals. With respect to evolutionary change, she emphasized the "shock" of interspecific hybridization, a process that leads to whole genome doubling, widespread genome reorganization, and formation of novel species. For McClintock, genome change was not accidental. Change was a response to life history challenges.

McClintock saw the future agenda for biology as part of an unending scientific revolution

Why did McClintock focus so much attention on cell sensing and not on research that provided molecular evidence in support of her previously heretical views (Shapiro 1983)? From the way she ends her lecture, we can conclude that McClintock had her perspective directed towards the years ahead rather than those behind:

In the future attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them, often by restructuring the genome. We know about the components of genomes that could be made available for such restructuring. We know nothing, however, about how the cell senses danger and instigates responses to it that often are truly remarkable.(McClintock 1984)

McClintock apparently wanted to draw special attention to the most challenging problems in biology: cognition and purposeful action by living cells. As she knew well from her long experience with 20th Century genetics and cell biology, whether life has special "vital" properties that separate it from inorganic matter has been among the most fiercely disputed topics in the history of science. In its early days, molecular biology promised to provide us with an explanation of life in terms of physics and chemistry. However, since the 1960s it has succeeded instead in amazing us with the richness and sophistication of intra- and inter-cellular control and communication networks.

In conversation, McClintock expressed the conviction that computers and information science would help open our eyes to a more inclusive and realistic picture of the genome and its place in the living cell. Near the beginning of her lecture, she predicted an ongoing series of conceptual upheavals:

Because I became actively involved in the subject of genetics only twenty-one years after the rediscovery, in 1900, of Mendel's principles of heredity, and at a stage when acceptance of these principles was not general among biologists, I have had the pleasure of witnessing and experiencing the excitement created by revolutionary changes in genetic concepts that have occurred over the past sixty-odd years. I believe we are again experiencing such a revolution. It is altering our concepts of the genome: its component parts, their organizations, mobilities, and their modes of operation. Also, we are now better able to integrate activities of nuclear genomes with those of other components of a cell. Unquestionably, we will emerge from this revolutionary period with modified views of components of cells and how they operate, but only, however, to await the emergence of the next revolutionary phase that again will bring startling changes in concepts.(McClintock 1984)

Let us hope that her expectations are fulfilled in the 21st Century with all the "pleasure" and "excitement" this extraordinary scientist experienced for much of the 20th Century.

References:

Bray, D. (2009). Wetware: A Computer in Every Living Cell New Haven, CT, Yale University Press. ISBN 978-0300141733.
Craig, N., Craigie, R, Gellert, M, Lambowitz, AM (2002). Mobile DNA II Washington, American Society for Microbiology Press. ISBN 978-1555812096.
de Koning, A. P., W. Gu, et al. (2011). "Repetitive elements may comprise over two-thirds of the human genome." PLoS Genet 7(12): e1002384. http://www.ncbi.nlm.nih.gov/pubmed/22144907.
Lander, E. S., L. M. Linton, et al. (2001). "Initial sequencing and analysis of the human genome." Nature 409(6822): 860-921. http://www.ncbi.nlm.nih.gov/pubmed/11237011.
McClintock, B. (1932). "A Correlation of Ring-Shaped Chromosomes with Variegation in Zea Mays." Proc Natl Acad Sci U S A 18(12): 677-681. http://www.ncbi.nlm.nih.gov/pubmed/16577496.
McClintock, B. (1939). "The Behavior in Successive Nuclear Divisions of a Chromosome Broken at Meiosis." Proc Nat Acad Sci USA 25(8): 405-416. http://www.ncbi.nlm.nih.gov/pubmed/16577924.
McClintock, B. (1942). "The Fusion of Broken Ends of Chromosomes Following Nuclear Fusion." Proc Nat Acad Sci USA 28(11): 458-463. http://www.ncbi.nlm.nih.gov/pubmed/16578057.
McClintock, B. (1952). "Controlling elements and the gene." Cold Spring Harb Symp Quant Biol 21: 197-216. http://www.ncbi.nlm.nih.gov/pubmed/13433592.
McClintock, B. (1984). "The significance of responses of the genome to challenge." Science 226(4676): 792-801. http://www.ncbi.nlm.nih.gov/pubmed/15739260.
McClintock, B. (1987). Discovery And Characterization of Transposable Elements: The Collected Papers of Barbara McClintock New York, Garland. ISBN 978-0824013912.
Shapiro, J. A. (1983). Mobile Genetic Elements. New York, Academic Press. ISBN 978-0126386806.
Shapiro, J. A. (2011). Evolution: A View from the 21st Century. Upper Saddle River, NJ, FT Press Science. ISBN 978-0132780933.