Model Builder

Kris Niyogi (pictured left) likes model organisms. In graduate school at the Massachusetts Institute of Technology (MIT), he was part of one of the first groups to work with Arabidopsis. As a postdoc, he did early work with the green alga Chlamydomonas reinhardtii. As a professor in the department of plant and microbial biology at the University of California, Berkeley, he works with both, applying insights from one to the study of the other. This approach helped him identify a key protein that helps plants avoid photooxidative damage in high-light conditions.

Spreading His Leaves

As an undergraduate biology major at Johns Hopkins University in Baltimore, Maryland, Niyogi focused on molecular and cell biology and thought about immunology or transcription factors as a potential field of study. As a senior, he took a plant biochemistry course and enjoyed it. After graduating, he did a master's degree at the University of Cambridge, where he studied plant cell differentiation, although he admits that he "didn't accomplish all that much."

Niyogi chose MIT for graduate school, even though he didn't know if MIT's biology department included any plant biologists. In his first-year coursework he returned to immunology, assuming that his Cambridge experience had been the end of his foray into plant science. But he took one plant biology course and discovered that one lab, headed by Gerald Fink, a professor of genetics, was working with Arabidopsis and yeast genetics.

Niyogi joined Fink's lab and found himself in an unusual situation: As a graduate student in a group of about 20, he was surrounded by postdocs, because he was focused on Arabidopsis and all the other graduate students worked with yeast. It was hardly a handicap. "All of [the postdocs] acted as mentors, both when I was a graduate student and later when I became a postdoc. They had gone through the same experience a few years before."

Niyogi worked on identifying tryptophan biosynthesis pathways in Arabidopsis, which at the time was a relatively new model organism. "One of the things that appealed to me [about Fink's lab] was working on more than one model organism, applying insights from yeast genetics to Arabidopsis," Niyogi recalls. Arabidopsis was an extremely useful model organism for plants. Before its advent, researchers often used maize, but maize has a long life cycle and a large genome, limiting its utility. Arabidopsis grows quickly and has a small genome, with little repetitive DNA. "It made a lot of the molecular biology very easy [to perform]," Niyogi says. He identified some genes in the pathway and studied how it was regulated, comparing it to bacteria and yeast.

Niyogi's experience with yeast piqued his interest in other organisms with very fast life cycles. Reading a meeting summary, he learned about some novel techniques for working with a new model organism, the green alga Chlamydomonas reinhardtii. "I had the feeling that [it] was going to take off as a model organism, so I wanted to get in on the ground floor, so to speak," Niyogi says.


Postelsia observed during a Nyogi lab field trip in 2005.

One Postdoc, Two Labs

In 1993, he began a postdoc at the Carnegie Institution's Department of Plant Biology in Stanford, California. He wound up with a joint position in two labs, with two separate postdoc advisers, Arthur Grossman and Olle Björkman, and set about applying his knowledge of yeast and Arabidopsis genetics to the new model organism.

His timing was good. Molecular-genetics tools were coming into their own. "Before that, it was isolating mutants and studying the physiology and biochemistry without being able to get at the genes. It seemed like the tool kit was getting better." He was particularly interested in using Chlamydomonas to study photosynthesis. "I realized [photosynthesis] was a core metabolic pathway, which was what really attracted me to it," says Niyogi. The ability of Chlamydomonas to survive in the absence of light (and photosynthesis) meant that he could identify mutants with faulty photosynthesis pathways, mutants that in Arabidopsis or another model system would likely die before they could be isolated within a batch. "I guess I was looking for something where I could find my niche, some area where it was obviously an important problem that hadn't been investigated because the tools had not been available. It was an opportunity to develop projects I could call my own and eventually start a lab with."

At Carnegie, he designed a system to identify Chlamydomonas mutants that are impaired in a process called nonphotochemical quenching (NPQ), which evolved because plants often absorb more light energy than can be used for photosynthesis. Stray chlorophyll, excited by excess photons, can cause oxidative damage. NPQ quenches the excess excited chlorophyll, releasing the energy as heat. Previous work had suggested that this process would be vital to a plant's survival in high-light conditions. Niyogi grew Chlamydomonas mutants in low light and then videotaped chlorophyll fluorescence during a few minutes of illumination with high light, singling out mutants that didn't respond normally.

He succeeded in identifying NPQ-deficient mutants, but he was surprised to find that they grew just fine even in high-light conditions. "They weren't photosensitive at all. We realized we could do the same screen in Arabidopsis," says Niyogi. Soon he had isolated similar mutants in Arabidopsis, and these parallel studies revealed that a carotenoid pigment was common to the NPQ pathway in both plants. "The process is conserved, but there were some interesting differences when you got to the details of the proteins involved."

Near the end of his postdoc, Niyogi experienced a crisis. His ambition had been to get an academic position, but he watched his friends who had been postdocs ahead of him as they went into similar positions and gave up doing experimental science in favor of managing their labs. "I agonized over it because I love doing experiments," he recalls. After some thought, he made an effort, during the final year of his postdoc, to get involved in projects where he could supervise other people in the lab. To his relief, he says, "I kind of liked it."


Nyogi lab field trip in 2004.

Playing One Against the Other

When he joined Berkeley's faculty in 1997, Niyogi continued to study both Arabidopsis and Chlamydomonas. Most labs focus on just one model organism, he says, but he believes that keeping both in play was an important factor in his success. "My rationale was that you could learn things from one organism that could be applied to the other. I think of Arabidopsis and Chlamydomonas as two model organisms that bracket the green clade of life, much the way yeast and mice bracket the clade of life that includes fungi and animals. Chlamydomonas and Arabidopsis are about as evolutionarily distinct from each other as yeast and mice. There are some interesting similarities, and some of the differences are quite interesting and illuminating."

Within a couple of years of starting his faculty position, Niyogi had generated several interesting mutants and discovered a protein that is a major component of nonphotochemical quenching. The discovery "helped me get tenure, and it got me known in the international community," he says. He has reason to think that the protein, called PsbS, may be acting differently in his two model organisms.

Niyogi attributes his willingness to investigate two model systems in part to his experience as a graduate student at MIT, where he worked on Arabidopsis but was surrounded by yeast geneticists. "That was a little bit inspirational," he says. The breadth of expertise in the group gave him a strong base, and the postdocs working on Arabidopsis provided much guidance throughout his graduate years and beyond.

"It is definitely an asset to work with more than one system," says Sabeeha Merchant, a professor of biochemistry at the University of Wisconsin, Madison. "It opens us up to different ways of thinking--and keeps us flexible and less likely to sink into dogma. The differences in how the various systems are wired are as important as the similarities."

"Kris is unusual not only in his willingness to work with several different organisms, but also to take on high-risk problems," says MIT's Fink, Niyogi's graduate adviser.

In retrospect, he feels lucky that he landed in such an unusual group at MIT. "Had I known I wanted to be a plant biologist, I never would have applied to MIT in the first place."

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