Life's Jumps

Nancy Marie Brown
September 01, 1995

Plants can't run away.

It's not a new thought: Anyone has pondered it who's watched a favorite oak stripped by caterpillars, a row of lettuces nipped by frost, or potted pansies wilting in the sun.

Yet said by Nina Fedoroff, tracing an imaginary root and stem and leaf on the tabletop, all ten fingers wide like a musician accustomed to the full range of the keyboard, the idea seems to deepen, to grow more resonant, to find a new key. Fedoroff, the first Verne M. Willaman Professor of Life Sciences at Penn State, thinks of plants not in terms of forests nor trees nor leaves nor even cells. Following the measure of Nobel Laureate Barbara McClintock, Fedoroff thinks of plants most intimately, at the level of the gene.

"Plants can't run away, they can't change their environment," she says. "They have to adapt."

Individually they drop leaves, wall off hurts, favor one shoot over another, juice up their output of defensive chemicals. But over evolutionary timescales, in an analogous way, the whole plant kingdom must adapt to environmental stress.

One way plants do it, Fedoroff explains, is by letting their genes jump.

It's a risk. Jumping genes (or transposable elements, as Fedoroff more formally calls them) are "by and large harmful," she says. It's a course of last resort. It's a revolution.

"Thomas Jefferson once wrote that an occasional revolution can be beneficial," Fedoroff noted in The Sciences in 1991. "So it may be on the molecular level. Like human insurgents, transposable elements are destructive and, not infrequently, self-destructive. They tend to surface when conditions are bad and change is long overdue, but the outcome of their activities is never quite certain. Sometimes change and reorganization can have a salutary effect on social—or genetic—structure, yet the possibiity of ruin always looms."

But the risk, the jump, may also be ultimately necessary. It may be the engine of evolution itself.

"It is as if transposable elements can amplify a small disturbance," Fedoroff speculated in Scientific American in 1984, "turning it into a genetic earthquake. Perhaps such genetic turbulence is an important source of genetic variability, the raw material from which natural selection can sift what is useful for the species."

Genes used to be thought of as beads on a string. Stretched tight, the strings—the chromosomes—could be laid out in neat rows and the order of their genes mapped. It took a tedious amount of sowing and cross-breeding and harvesting and comparing of traits, but a botanist could eventually learn that in corn, for example, the gene for color was on one chromosome, that for starch on another. And always would be. The strings would be passed down unbroken from corn generation to corn generation, like grandmother's pearls.

In 1945, McClintock saw a string break. She saw a gene jump.

McClintock's work at Cold Spring Harbor eventually rewrote our concept of a gene—and earned her the 1983 Nobel Prize in Medicine—but for more than 30 years she wasn't universally believed.

"When she made these ideas public in 1951, in 1953, and again in 1956," wrote her biographer, Evelyn Fox Keller, "in spite of the fact that she had long since established her reputation as an impeccable investigator"—she had been elected to the National Academy of Sciences in 1944, only the third woman to be so honored—"few listened, and fewer understood. She was described as 'obscure,' even 'mad.'"

Writing of a 1978 visit to McClintock at Cold Spring Harbor, Fedoroff recalled a biologist in the lunch line "leaning down to me from his great height to inquire whether I really believed all of that stuff of hers."

McClintock was "complex, gifted, intense, and superbly original," Fedoroff wrote in McClintock's obituary for Cell. (McClintock died in 1992, at the age of 90.) "She was acerbic and impatient; so too was she kind, generous, and patient. She saw much—too much, at times—making many uncomfortable." (One of her early supporters, T. H. Morgan, spoke in the mid-1930's "of what he called her 'personality difficulties,'" according to biographer Keller, "claiming that 'she is sore at the world because of her conviction that she would have a much freer scientific opportunity if she were a man.'")

"But she did care that her work be understood," continued Fedoroff, "and it frustrated her when it was not. She knew that part of the reponsibility was hers: her writing was dense, and she refused to make 'models'"—(elsewhere Fedoroff calls them "cartoons")—"to reify the genetic abstractions from which she inferred the existence of transposable elements (she didn't need them). Yet those who read her papers report that it was well worth the effort. Her thinking was elegant, the data irrefutable."

Reading McClintock's papers from first to last was for Fedoroff "the most remarkable learning experience of her life," she said in a Carnegie Institution of Washington brochure. "Like a detective novel, I couldn't put it down."

"It isn't that McClintock's ideas contradicted the accepted model of what a gene is," Fedoroff says now. "What McClintock's ideas contradicted was the notion that genes don't move. Today we know that there are many transposable elements in genomes, but the basic floor plan seems to hang together. That is, the relative order of many genes is conserved over long evolutionary periods. Yet there have been, and continue to be, both genomic rearrangements and small and large alterations, such as duplications and deletions. So the contemporary picture is of a much more active genome, subject to considerable change."

It is a picture with "greater appreciation," as McClintock wrote in her Nobel Prize lecture, of the genome's "significance as a highly sensitive organ of the cell that monitors genomic activities and corrects common errors, senses unusual and unexpected events, and responds to them."

When McClintock was told, in 1918, that Cornell University's plant-breeding program did not accept women, she turned to genetics. Working with Indian corn, or maize, she distinguished herself for insight and persistance, charting out the relationship between macroscopic changes in kernel patterns and microscopic changes in chromosomes. When no job offer materialized upon her receipt of a Ph.D. in 1927, she found temporary money to continue her research at Cornell and elsewhere, publishing 24 papers on corn genetics before finally gaining a permanent position in the private, non-profit Carnegie Institution's department of genetics at Cold Spring Harbor in 1942.

So it is not surprising that in the mid-1950s, again faced with an obstacle—this time her colleagues' refusal to believe her near-heretical results that genes could "jump"—McClintock shrugged off their obtuseness and got on with her work.

In The Dynamic Genome, a collection of essays honoring McClintock's Nobel, Fedoroff continued the story: "In the winter and spring of the following year, McClintock typed out her results in tabular form and wrote a full discussion of her observations, inferences, and conclusions. These texts have never been published. The originals remain as typewritten reports in McClintock's files: dozens of tables, diagrams of alternative chromosome structures, extensive discussion. They are lucid and painstaking, and the conclusions, inexorable."

They share, as well, what Fedoroff called "the subject's delicious (ferocious?) complexity." A sample she gave of a McClintock text begins: The first recognized case of transposition of Ds arose in the cross of a plant (4108C-1) having the constitution wd I Sh Bz Wx Ds in one normal chromosome 9 and Wd C sh bz wx ds in a normal homologous chromosome 9. It is not the type of prose that wins converts. Indeed, although Fedoroff was assigned a McClintock paper in graduate school at Rockefeller University ("I do not remember which paper, but I do remember being confused and not enlightened"), she began her career in frogs, not corn. It was a frog gene (the 5S rRNA gene of the frog Xenopus laevis) that was the first gene to be completely sequenced, and Fedoroff, as a post doc at the Carnegie Institution of Washington, was a member of the research team.

It was a chance meeting that changed Fedoroff into what biographer Keller called an "enthusiast." Fedoroff had been invited to present her frog gene results in 1978 at Cold Spring Harbor Laboratory, where McClintock still worked ("in solitude," noted a Science News reporter) five years before her Nobel. It was not, Fedoroff noted, "the same institution that McClintock had joined" some 30 years earlier. Not only was it no longer part of the Carnegie Institution's genetics department, none of its researchers (except McClintock) worked with plants. All were molecular biologists, their director James D. Watson, co- discoverer of the double helix and a Nobel Laureate himself. Their new science of molecular biology was "a science of molecular mechanics," as Keller put it, "rather than of living organisms, or even of 'living machines.'" It brought a change of focus to genetics that made McClintock's patient plant-breeding experiments seem old-fashioned, if not obsolete.

"Late in the day, as the mandatory round of laboratory visits was drawing to a close," Fedoroff recalled in The Dynamic Genome, "I ran into Barbara McClintock in a hall of the Demerec Laboratory. She surprised me with an apology for missing my lecture (why should she apologize?) and invited me to her laboratory for a talk (I have it firmly in my memory that we drank Cinzano and ate peanuts—Barbara says we didn't). I was very much taken with the lucidity of McClintock's casual discourse—science, scientists, politics, philosophy—the usual stuff of late afternoon laboratory visits. It did not fit her reputation for impenetrability and I was curious—curious enough to find the old Carnegie yearbooks in which she had published and to start reading upon my return to Baltimore. I had to learn McClintock's language (no surprise here, she had given words, a long time ago, to things that no one was ready to see). I had, laboriously, to figure out the genetic crosses, and I had [my own] experiments to do, too. But I found myself impatient to read on, to get back each evening to the next year's installment of work in progress and discover how she had figured it out. The stuff was complicated, but it was clear and logical and beautiful."

"I found it immensely exciting," Fedoroff continued, in the version of the story she gave in her 1990 Howard Taylor Ricketts Lecture at the University of Chicago, "and I began to entertain the notion of embarking on a molecular study of the transposable genetic elements whose existence was so beautifully revealed by McClintock's genetic experiments.

"But I'm a practical person"—(Fedoroff neglected to mention in her lecture that she was also a single mother at the time, with her postdoctoral fellowship about to expire and no permanent job promised)—"and I rapidly concluded that this was not a practical idea. I knew that plant research was difficult to fund, that molecular biology in particular was expensive, and that molecular techniques hadn't yet been applied to plants. Not a single plant gene had been cloned at the time, and some of my colleagues were even saying it couldn't be done. The notion that I could start from such ignorance and get at the molecular basis of McClintock's genetic phenomena in time to get tenure at a university was just absurd."

Then came what actors and artists would call "The Big Break." A staff researcher in the embryology department of the Carnegie Institution—"the very same institution that firmly supported McClintock's research, even when it was regarded by many as well off the deep end," Fedoroff noted of the institution where she herself was a postdoc—left for a job at the National Cancer Institute, and Fedoroff was offered his spot. "It was an unexpected gift and dislodged my tucked-away fantasy. I made an impulsive commitment to the molecular biology of maize transposable elements."

Maize, our corn, is an ancient and adaptable organism. The earliest known ears were purple, small, and dry. The best farmers' market varieties today are butter-yellow or white, plump, and bursting with sweet corn syrup. Then there's the unusual Indian Corn, its jazzy mosaic of earthtones essential to our harvest decor. How did they get those colors?

According to Fedoroff's article in The Sciences, "from a genetic standpoint the unusual kernels are the colorless ones"—the ones we eat boiled with butter and salt. "In those kernels the sequence of biochemical reactions leading to pigment synthesis has been interrupted by a genetic mutation."

Look at a cob of Indian corn closely and you might notice another mutation: pale kernels with spots or streaks of color, their rows like rows of small birds' eggs and pinto beans. "The variegation is caused by what are known as unstable mutations," Fedoroff wrote. "Wherever streaks or spots of color appear on an otherwise pale kernel, a reversion has taken place. The mutation that interrupted pigment synthesis is reversed, allowing the normal synthesis of pigment to proceed. It was understood before McClintock began her work that such odd instability was the effect of a mutant gene, but it was she who figured out that such mutations could be caused by the insertion of a transposable element into the pigment-synthesis gene. As long as the element is embedded in the gene, the gene cannot function. Yet when the element transposes out of the gene, the gene can work normally. And if the element transposes in only some of the cells during the development of the organism, the organism becomes a mosaic of normal (pigmented) and mutant (colorless) tissue." Picture within each cell of the corn kernel a gene like a tiny zipper. Stick a safety pin through the zipper's teeth so the zipper can't unzip: no color. Take the pin out: color.

It was the nature of this metaphorical pin that Fedoroff wanted to find out. What made a transposable element—a jumping gene—different from any other gene? (A pin, not a zipper.) What let it jump?

To find out, she first had to grow some corn.

From the account by McClintock's biographer, you would think that the genetics of corn was a gentlewomanly pursuit: "Each spring," wrote Keller, "she plants her corn, judiciously fertilizing the budding kernels according to a carefully worked out plan of genetic crosses, watches the plants grow over the summer, and spends the long quiet winters analyzing the results."

Of her first season, on the other hand, Fedoroff remembered "being so exhausted by the end of two months of 5 a.m. to 2 a.m. days that I seriously considered abandoning the project."

Each corn plant bears both male and female flowers, the females on the ears, the males on the tassel at the top of the cornstalk. The males' pollen, borne on the wind, is "ensnared," as Fedoroff put it, by the females' silk, and fertilization takes place. "With millions of grains [of pollen] flying around the cornfield," Fedoroff wrote, "controlling the mating process demands extreme care. Each plant is assigned a number. When an ear is ready to be fertilized, pollen from the desired male is applied to the silks of the ears. Later the ear is tagged with the numbers of the plants used in the cross. In our cornfield . . . hundreds of crosses are done every day at the height of the pollination season, and thousands are completed by early August." A month later, the mature ears, carefully tagged, have to be collected (or, as happened in a later year, rescued "from the tornado that blew over Ed Coe's field, where I was growing my plants that summer").

Using McClintock's kernels, and following her advice that first summer, Fedoroff tried to cross-breed corn plants that would contain a jumping gene in enough quantity that she could clone it, which entails duplicating it, identifying it, then working out its DNA sequence. "Barbara and I discussed this crop in advance and at great length, but we weren't communicating," Fedoroff wrote in The Dynamic Genome. "We were not even speaking the same language. I was a molecular biologist trying to figure out what materials would be optimal for cloning. Barbara had a very different perspective. . . . But we got through the summer somehow and I learned an immense amount." It was only when she began to analyze the kernels that she "realized that Barbara had slipped me a treasure trove, bits of virtually everything she had ever worked on, and I was glad I had done every cross I could push my weary body to do, even if all of them were not just the right crosses."

The first jumping gene Fedoroff isolated, in 1983, had not jumped into a pigment gene but into a gene responsible for making cornstarch. Looking among the starch genes was a tactical choice: A lot more of the enzyme for starch-making exists in a corn kernel than that for making color (or, as Fedoroff has written, "a little paint goes a long way"), and a gene is best found by tracing its products backwards. Moreover, the effects of the starch gene, called waxy, can also be seen: When the gene is working, the kernel is translucent; when a jumping gene has disabled waxy, the kernel shows spots and streaks that are opaque and waxy-looking.

To find a jumping gene using the tools of a molecular biologist, rather than those of a classical geneticist like McClintock, Fedoroff wrote in The Sciences, "we started by extracting DNA from corn plants and treating it with restriction enzymes to cut it into small fragments—just as one might strip away a book binding and spread out the pages." There were a lot of pages. Corn has a lot of DNA; its genes, like a human's, are "embedded in a sea of junk DNA that doesn't seem to be serving much purpose," Fedoroff explains. "Our task," Fedoroff wrote, "was roughly equivalent to finding a one-line message, of unknown wording, that jumps spontaneously throughout a library from book to book and page to page."

Using a now-standard trick of genetic engineering, Fedoroff and post-doctoral fellows Susan Wessler and Mavis Shure took each snippet of maize DNA from a normal corn plant amd stuck it into a bacterium. Then, while the bacteria and their maize-DNA hitchhikers multiplied, the researchers worked backwards from the plentiful cornstarch enzyme to find the corn cell's enzyme-making template (the messenger-RNA), and then the source of the mRNA, called complementary-DNA. This they tagged with radioactive atoms and fed to the bacteria. Only the bacteria harboring pieces of the waxy DNA lit up, as the cDNA found and bound to its matching gene.

Having the waxy gene from a normal translucent kernel in hand, Fedoroff and her team repeated the exercise with DNA from a corn kernel that looked haphazardly waxy and opaque. The mutant gene, they knew, should have an extra loop—the inserted jumping gene—that would make it longer than the normal waxy gene. After mixing a single strand of each gene together so that they would have to combine to form DNA's classic double-helix structure, Fedoroff looked into the electron microscope: "Single strands of each fragment bound to one another along most of their length wherever they were complementary, forming a nearly perfect double helix. The flaw was a loop, a short sequence in one strand that had no complement in the other. That loop was the elusive Ac element," the transposable element that McClintock had first seen at work in 1947 and had named Activator.

Like the trill that signals the end of a cadenza in a classical concerto, a transposable element is marked by a repetition. At each end of Activator, for example, are the same 11 nucleotides, but their order is reversed. That is, the first 11 "letters" of the code, read from left to right, spell out the same "word" as the last 11 letters, read right to left.

Also among Activator's 4,500 nucleotides is a gene that codes for a protein called "transposase." Only in the presence of this protein can a jumping gene jump—or be "transposed" to a different spot on the chromosome, as a melody is transposed to a different key. The transposable element doesn't necessarily have to be able to make its own transposase. Dissociation, another group of transposable elements named by McClintock, jumps only in the presence of Activator. The two groups can look remarkably similar, Fedoroff found: The first Dissociation element she cloned was nearly identical to Activator, only minus 194 nucleotides in the middle of its transposase gene section.

"As long as you have a sequence bounded by the correct ends," Fedoroff says, "and you have transposase, the sequence will hop. You can put whatever you want in the middle. You can put in a gene that codes for resistance to a herbicide, for example, and you can follow it when it hops."

By splicing in a resistance gene, or a gene that turns certain compounds blue, Fedoroff and her colleagues have turned jumping genes into a tool to learn about the rest of the plant's genome. Says Fedoroff, "It's a very rapid way of pulling out a gene you know nothing about." And by pairing gene sequencing with the use of transposable elements, Fedoroff adds, "As you find genes you can begin to ask questions about them genetically.

"As a plant's root grows through the soil, for example," she continues, "its tip, just like our skin, flakes off and has to be constantly replaced. We've identified a gene that operates only in this root tip. It seems to be active only at the very early stages of branching. What's the signal? This root doesn't have a brain. How does it know the tip's grown up against a stone wall, that it's time to start making lateral roots?"

But while she's been able to harness these "molecular subversives," as she's called them, to investigate other biological questions, Fedoroff has not turned from studying their essential nature. She remains intrigued by what she's called "the genetic choreography underlying development." She's particularly curious to know how the plant keeps its jumping genes standing still.

"We've identified a system that's neither conventional in the biochemical sense," she says, "nor is it totally genetic. It changes the genes, but it changes them reversably.

"The DNA itself is modified—by some process we don't yet understand at all—and the modification can be reversed. It has methyl groups put onto it. Methylation is an interesting phenomenon. It changes the way the DNA looks to a protein. It can turn genes on or turn them off. In some cases, the methylated form may be the only form the protein recognizes. In this case, it makes the DNA inactive.

"But we've identified a protein encoded by a gene on a transposable element that reverses this methylation.

"Since transposable elements are by and large harmful, the plant stores them away and keeps them from being harmful in this highly methylated form. So how does a transposable element get activated? Every time something happens to the genome, the transposable elements come back to active form. One of the things that can happen is that a chromosome breaks—by irradiation, by a spontaneous breakage. When a chromosome breaks, it's a mess. The DNA repair system gets massively activated. And the transposable elements become active. You'll see them hopping all around, if you know what to look for.

"But my deeper question is, What role does this mechanism play?

"The plant is doing something to the transposable element, and the transposable element is resisting the modification—it codes for a protein that keeps it from being inactivated. Not only that, but an active transposable element that is making this protein can wake up a dormant element. Why? What has this system developed for?"

Fedoroff pauses, spreads her hands wide on the table. "Early in the spring," she begins again, "plants can get fooled. A long period of cold can come after the plant gets the trigger. What lets a plant know that one warm day isn't the spring?

"It's not a foolproof mechanism, but by and large it works pretty well.

"The plant doesn't immediately respond. It has to be exposed to warmer temperatures, more sunlight, for a number of days. It has a way of figuring out, I've heard this sound, this signal, long enough. There must be some mechanism at the molecular level that builds in a delay.

"A system such as we've been discussing with transposable elements could do that job."

"I cannot say for sure that transposable elements are useful to the corn plant," Fedoroff wrote in The Dynamic Genome. "I do know from experience, however, that corn lines with too many active transposable elements are in trouble: Some of their offspring look more like cabbages than corn plants. If I try to think like a corn plant (although sometimes I'm convinced that I think more like a cabbage), I conclude that my best bet is to keep my options open by hanging on to some of these principles of radical change, but shackling them as securely as possible."

And what of the shackled gene's options? Writing of the Suppressor-mutator (Spm) element, which she has studied most closely, Fedoroff continued, "Spm knows how to subvert the plant's efforts to silence it and it even probably knows that being silenced is its best chance of long-term survival. It knows when it should be transcribed, how much of each transcript and protein it needs, and when to jump (and when not to)."

In her 1990 Ricketts Lecture, Fedoroff, who in 1990 was the 60th woman elected to the National Academy of Sciences, noted that "I've actually been asked by biology graduate students whether plants have DNA.

"Such ignorance is a bit frightening," she added, noting that "our agricultural success has made us complacent. So complacent that we have even begun to discard our knowledge base about plant biology, eliminating its study from all but a few biology curricula."

She points out now that the list of "model organisms" for the Human Genome Project includes no plants. "I find this appalling," she says, remarking on how difficult it makes getting funding for plant genetics research. "It reflects our anthropomorphism," she continues. "What connects us to the Earth? What helps us to survive but our agriculture and biology?" She shakes her head over "people who think that food comes from the grocery store."

"To me," she continues, "the sad part is that even as we get closer and closer to the limits of what Earth can support, we don't even know it. Five to ten years ago we had pictures on TV of massive surpluses of grain. I haven't seen those recently. Demand is going up. The amount of arable land is constant. We have to get more out of less. How? I don't know any way except to use all the knowledge we acquire about plants. We've pushed classical breeding close to its limits.

"We do know that plants harvest only a limited amount of the incident light. But we don't know enough about plants to know if we can change that. The basic research that will allow us to change plants is very sparsely supported, less than 5 percent of the level of funding for biomedical research. Yet I suspect that issues of population, environment, and food production are going to overshadow health issues in the not-too-distant future."

It's as if she had said people can't run away.

"There are 'shocks,'" McClintock said in her Nobel Prize lecture, "that a genome must face repeatedly, and for which it is prepared to respond in a programmed manner. . . . But there are also responses of genomes to unanticipated challenges that are not so precisely programmed. The genome is unprepared for these shocks. Nevertheless, they are sensed, and the genome responds in a discernible but initially unforeseen manner."

"Accidents within the cell," "virus infections," "species crosses," "poisons of various sorts," "altered surroundings"—McClintock lists these as potential genome-shaking "shocks."

"There is little doubt that genomes of some if not all organisms are fragile and that drastic changes may occur at rapid rates," she said at a 1980 symposium on genetics at Cold Spring Harbor, three years before Fedoroff had cloned her first jumping gene. "It is reasonable to believe that such genome shocks are responsible for the release of otherwise silent elements, which can then initiate changes to overcome disruptive challenges. . . . Since the types of genome restructuring induced by such elements know few limits, their extensive release, followed by stabilization, could give rise to new species or even new genera."

"We know nothing, however," she concluded her 1983 Nobel lecture by saying, "about how the cell senses danger and instigates responses to it that often are truly remarkable."

Nina V. Fedoroff, Ph.D., is professor of biology, Verne M. Willaman Professor of Life Sciences, and director of the Biotechnology Intitute at Penn State, 519 Wartik Lab, University Park, PA 16802; 814-863-3650.

Last Updated September 01, 1995