Last fall, members of the European Molecular Biology Organization (EMBO) elected MCB Professor Nancy E. Kleckner as one of three new associate members for 2004. This is a tremendous honor for the Herchel Smith Professor of Molecular Biology, because EMBO has only 100 non-European associates in addition to 1,200 European members. In October, Kleckner will travel to Warsaw and present two seminars on her work at the annual meeting for members.
“Nancy Kleckner is an unusually imaginative and unorthodox scientist, which leads her to novel and groundbreaking ideas,” Erik Boye wrote when he proposed her election. Boye, head of the department of cell biology at Norway’s Institute for Cancer Research, knows Kleckner’s work first-hand: the two began collaborating in the early 1990s, when they coauthored several papers on the control of DNA replication in E. coli; more recently they’ve extended their collaboration to DNA damage responses in fission yeast.
Kleckner’s work on bacterial DNA replication is essentially a quest to understand how cells ensure that each round of cell division is accompanied by one and only one round of replication. But this is only one facet of her scientific life. When she dived into these topics, she was already a leading expert on transposable elements, bits of genetic material that move around, thereby changing the wording of the text encoded by DNA. Equally important are her seminal contributions to the understanding of meiosis, the process that makes sexual reproduction possible.
Stress relief for chromosomes?
As pleased as Kleckner is about her election to EMBO, she is not resting on her laurels. Instead, she is charging ahead with what she calls “phase three of my career – investigating the basic principles of chromosome function with an eye toward chromosomes as mechanical objects.” Kleckner has experienced many sudden brainstorms about biology, and one of her most compelling is the idea that mechanical stresses could explain why, during meiosis, every pair of homologous chromosomes undergoes at least one crossover event that forms a chiasma, and why multiple crossovers/chiasmata are spaced relatively evenly along any given chromosome pair.
About five years ago, Kleckner turned to John W. Hutchinson, Professor of Engineering and Applied Mechanics in the Division of Engineering and Applied Sciences (DEAS), to help devise a model for exploring the plausibility of stress as a mechanism for chiasma formation. At first the two spoke very different languages, but over time, as Hutchinson recalled, Kleckner “took my hand and led me through the biology.”
Hutchinson came up with a classical mechanics model: he coated an elastic metal beam with a thin, ceramic film marked by tiny flaws on its edges. Heat causes the beam to expand, building up tensile stress in the brittle film until it cracks at the site of a flaw. Stress is relieved on both sides of the break, which prevents other cracks from occurring nearby. However, applying more stress may eventually lead to other breaks, which will then occur outside the area where relaxation occurred. These phenomena were shown to closely resemble patterns of chiasma formation during meiosis. Kleckner and colleagues have further proposed that mechanical forces are important for many chromosomal phenomena and have suggested that the requisite mechanical forces might be generated internally within chromosomes via programmed chromatin expansion. All of this work was published in the Proceedings of the National Academy of Sciences in 2004. (Kleckner et al. 2004. A mechanical basis for chromosome function. Proc. Natl. Acad. Sci. USA 101: 12592-12597).
In Leonardo’s footsteps
Hutchinson says the opportunity to work with Kleckner came at an auspicious moment. Thirty years ago, the best opportunities for mechanical engineers were in material science; now, “the future for mechanical engineering is in biology,” Hutchinson says. His ongoing dialogue with Kleckner spawned a course for DEAS graduate students taught during the 2002-2003 academic year. For a semester, MCB and DEAS faculty and students collaboratively explored the interface of biology and physical sciences.
This course, in turn, gave rise to a new initiative called The da Vinci Center for Physical Biology. The Center’s mission – formulated by Kleckner, Hutchinson and other interested faculty during a retreat in September 2004 – is to view biological processes “through the lens of engineering and physics.”
The da Vinci Center planners advocate launching a new PhD program in Engineering and Physical Biology (EPB), “because teaching is the core of everything at the University,” Kleckner says. She characterizes the center and the graduate program as “emerging,” and hopes that the first EPB graduate students might enroll in fall 2006.
Inspecting the house
Although a sudden interest in physical science may seem like a radical departure for someone trained in genetics, biochemistry, and molecular biology, Kleckner doesn’t see it that way. Instead, she says she is merely applying new principles and methods to what she has studied all along.
“My work can be summarized by the word ‘chromosome,’” she says. “The chromosome is the repository of genetic information. It comprises not just the DNA, but also the house in which the information content lives.” Although observers may think she is pursuing many different avenues of research, for her all roads lead to the same place.
Kleckner’s interest in genetic material began in high school, where she was introduced to the structure of DNA by a remarkable science teacher, Arnold Small, also one-time president of the American Birding Association. Kleckner then graduated from Harvard, where she did her undergraduate research with Matthew Meselson, studying the reciprocity of recombination genetically in bacteriophage lambda. She earned a PhD at Massachusetts Institute of Technology in 1974 and stayed on for a postdoc with geneticist David Botstein. Kleckner’s initial paper with Botstein presented the first identification of a transposable drug resistance element, a tetracycline-resistance transposon known as Tn10. Her findings over the next 25 years revised how textbooks describe the plasticity of genomes and elucidated the existence and biochemical mechanism of transposons that work by a “cut-and-paste” mechanism. Her work also identified an entire constellation of unique host- and element-encoded regulatory processes which serve to impede explosive transposon self-proliferation, including one of the first identifications of functionally relevant anti-sense RNA. There has been great clinical interest in elements like Tn10 because antibiotic-resistant infections cause death and disease in hospitals worldwide.
Moving beyond moveable elements
The second phase of Kleckner’s life in science began in 1985, when she was the nineteenth woman awarded tenure at Harvard. “Once you have tenure you have the freedom and the time to try new things,” she says. She continued to study transposons while adding two new lines of research: one was E. coli replication and cell cycle and the other was yeast meiosis.
Both have been highly productive, and Erik Boye asserts that, “Dr. Kleckner’s work on yeast has revolutionized our molecular and mechanistic understanding of meiosis.” Her first major finding was that meiotic recombination is initiated by programmed double-strand breaks which occur at “hot spots” determined by chromatin structure. Other important discoveries followed. One of these studies Boye calls “a seminal and still unmatched study” defining temporal relationships among DNA replication, initiation of recombination, formation of crossover products, and formation and elimination of the synaptonemal complex, a highly evolutionarily conserved structure integral to meiosis. A second landmark finding was the discovery by Scott Keeney, then a post-doctoral fellow in the Kleckner laboratory, that Spo11 protein, which is a topoisomerase-like protein rather than a nuclease, is responsible for making programmed double-strand breaks. Most recently, just last year, she and her colleagues published a landmark paper that is the culmination of meiosis research in her laboratory thus far. This paper reveals that the critical point at which crossover positions are determined is much earlier than in the models presented in textbooks for the past 40 years. (Börner et al. 2004. Crossover/Noncrossover Differentiation, Synaptonemal Complex Formation, and Regulatory Surveillance at the Leptotene/Zygotene Transition of Meiosis, Cell 117, 29-45).
Kleckner’s lab has also advanced the study of DNA replication and cell cycle control in both E. coli and in eukaryotes. The laboratory’s studies of eukaryotic DNA replication are aimed at understanding how cells modulate the length of the DNA replication period, and the temporal program of firing of the chromosomes’ multiple origins. Their work in this area has led to the identification of genetically-encoded replication “slow zones;” to the important finding that a key signal transduction protein, ATR, previously thought only to respond when chromosomes are damaged, is also involved in modulating progression of normal DNA replication; and to a new model for temporal control of replication. (Cha and Kleckner. 2002. ATR homolog Mec1 promotes replication fork progression, thus averting breaks in replication slow zones. Science vol 297, 602-606).
With respect to E.coli, Kleckner’s best known contribution is discovery of a previously unknown component of this system, SeqA, and the demonstration that this protein is a key regulator of replication initiation, according to Susan Gottesman, Chief of the Biochemical Genetics Section of the Molecular Biology Laboratory at the National Cancer Institute at NIH.
Gottesman and other experts on regulatory mechanisms in E. coli are currently excited about “the baby cell column,” a novel method for generating and harvesting large populations of bacteria that are “synchronized” at the same point in the cell cycle. Scientists are eager to try their hand with this new process, which was developed in the Kleckner lab by postdoc David Bates. Indeed, Bates and Kleckner have already used this method to show that sister chromosomes in E.coli cells undergo cohesion and loss of cohesion in a process which, the authors argue, is a primordial precursor to microtubule-based chromosome segregation in eukaryotic organisms (Bates and Kleckner. 2005. Chromosome and Replisome Dynamics in E.coli: Loss of Sister Cohesion Promotes Global Chromosome Movement and Mediates Chromosome Segregation, Cell in press).
Bates is one of the latest in a long line of postdocs who have risen to the challenge of developing creative and innovative new assays and experimental techniques. Highlights include the first method for chromosome-wide mapping of protein interaction sites, genetic, physical and cytological approaches to analysis of interactions between homologs, and the “3C” technique for “capturing chromosome conformation.”
“Elegant and rigorous experimental designs” are the hallmarks of Kleckner’s work, according to Allan Campbell, Browning Professor in the School of Humanities and Sciences at Stanford University. A pioneering phage biologist, Campbell nominated Kleckner for membership in the National Academy of Sciences; she was elected in 1993 at age 46.
Kleckner’s mix of creativity and tough-mindedness may be at least partly genetic. She was born and raised in Southern California, the only child of an aviation engineer and an artist. The walls of her office are decorated with her mother’s drawings and paintings and with black-and-white photographs of her father posed beside an X-3 aircraft – one of his early designs and the second plane to break the sound barrier.
Compared with biologists who philosophize about why genetic diversity or evolution occurs, “I am the engineering department: I want to know how stuff works,” Kleckner says. “I am my father’s daughter.” At the same time, Kleckner acknowledges the importance of maternal DNA: “I didn’t inherit my mother’s drawing abilities, but I may have gotten a little of her imagination.”
While nature and nurture may each play a role in Kleckner’s accomplishments so far, former postdoc Douglas Bishop has another explanation. “She is the hardest working person I have ever known. She lives and breaths biology,” says Bishop, an Associate Professor of Radiation and Cellular Oncology at the University of Chicago’s Pritzker School of Medicine.