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Biofuels from bacteria is biochemist's goal

Lipton studies the protein tools that microbes use to get their jobs done



Biochemist Mary Lipton at DOE's Pacific Northwest National Laboratory wants to make a noticeable impact on the use of biofuels in the US. She is using her expertise in proteomics and mass spectrometry toward that goal.

When you ask Mary Lipton what her strengths are, she quickly responds with her personality type. "I'm an Expressive," she says, aptly punctuating her words with her hands. "The plus side is that I communicate and collaborate well, and I look at the bigger picture. On the other hand, I don't concentrate on details. But I can incorporate the details into a larger vision."

Regardless of how they are perceived, these traits have served Lipton well as a scientist at DOE's Pacific Northwest National Laboratory. She is nationally recognized for applying new mass-spectrometry-based technologies to characterize environmental microbes and microbial communities, particularly for their use in generating biofuels.

"I work on biofuels because, at some point, everyone pays for the high cost of fuel. It affects all of us, whether directly at the gas pump or by higher food and materials costs," Lipton said.

Lipton categorizes her biofuels research area as environmental proteomics, which she defines as the application of advanced protein-based techniques to understanding environmental and biological systems. However, she is quick to note that environmental proteomics does not just aid development of new biofuels but helps further understanding of the impact of climate change and the use of organisms for bioremediation.

So what, again, is a proteome? According to Lipton, it is a complement of proteins expressed by a cell at any given time, under any given condition, or a subset of those proteins.

She used the following analogy: "Let's say that you have a village with a bakery, butcher shop, drug store, and flower shop that are all the same size along a street. The blueprint of each is identical. But when you look into each one of them, you see the tools of the trade for that store: baking equipment and supplies, raw meat and knives, pharmaceuticals and sundries, flowers and plants, and so on. Each defines what that store is. Those are the proteome.

"The proteome defines what the cell is," Lipton continued. "Every cell has the same DNA, but in humans, for example, the liver cell is different from those in the brain and kidney. What makes them different are the proteins expressed to do the jobs they have to do. In the environment, every plant or organism has a static genome, but how the organism responds to the environment depends on its proteome. The proteome is what gives you the perspective."

Her expressiveness and ability to explain science in layperson's terms also help Lipton provide direction in her lab, where she currently has four postdocs, a post-bachelor's student, a grad student, and two staff.

Lipton has been a researcher on DOE programs since starting at PNNL as a postdoc in mass spectrometry in 1993. She received her bachelor's degree in chemistry from Juniata College in Pennsylvania and her doctorate in biochemistry from the University of South Carolina.

"Working at PNNL was supposed to be a two-year stint," Lipton said. "I had other job offers and was applying for other postdoc positions. Then in 1995, someone coined the term 'proteomics,' which combines mass spectrometry and protein biochemistry. I was in the right place at the right time with the right expertise."

She was hired as a scientist in 1998 by Dick Smith, who is conducting pioneering work in developing proteomics, mass spectrometry, and separations technologies.

"Mary joined us with a background in biochemistry, a willingness to tackle new problems, and an appreciation for what the new technology we were developing in the EMSL could contribute as we began to focus our efforts on proteomics," Smith said. "Combined with her inherent drive, she has continually explored new and increasingly challenging areas of biological research."

Lipton describes her research at PNNL as working "in a multidisciplinary group where I get to apply bleeding-edge technologies toward solving problems of concern to everybody." And since coming to the lab, the list of DOE programs to which she has contributed continues to grow.

Among these, Lipton is part of the Great Lakes Bioenergy Research Center, one of three Centers established by DOE's Office of Science to focus the most advanced biotechnology-based resources on the biological challenges of biofuel production. She serves as the Associate Director of the Genome Science Program's Pan-omics effort at PNNL focused on developing and applying multiple-omics measurements to biological systems critical to DOE missions.

She led a team that mapped nearly 300 mobile elements within the genome of Shewanella oneidensis MR-1 and identified more than 200 pseudogenes, which are genes with mutations predicted to prevent production of functional proteins, advancing knowledge and understanding of the bacterium's evolution.

Lipton has contributed to research showing that bacteria as diverse as ocean-dwelling Pelagibacter ubique and bubonic plague-causing Yersinia pestis produce identical proteins. Called the "core proteome," this research represents six years of gathering and evaluating proteomics measurements.

These projects are challenging and exciting to Lipton, but she admits that her favorite one is PNNL's Foundational Scientific Focus Area for DOE with its research on the interaction between microbial photoautotrophs-organisms that use photosynthesis for growth-and heterotrophs-organisms that use organic carbon.

"We're characterizing the proteome of the organisms in nature, using stable isotope probing in the environment to see, in real time, which proteins are being synthesized under different light conditions. I'm very excited about it," she said.

On the road and at home

Lipton's expertise also takes her out of the lab to participate in advisory groups, workshops, and scientific conferences. At DOE's request, she has given presentations on mass spectrometry and biofuels at Pittcon and other national meetings and offered tutorials in proteomics at international scientific meetings.

She serves on editorial boards for scientific journals and review panels for DOE, the National Institutes of Health, and the Department of Agriculture. Lipton is also part of the National Alliance for Advanced Biofuels and Bioproducts consortium funded by DOE to help find ecologically sustainable and economically viable renewable fuel options through further investigating and commercializing algal biofuels.

She combines her more-than-40-hour workweek with a full personal life. Lipton and her husband Andrew, also a scientist at PNNL, have two teenagers with myriad outside interests.

"I run from the lab, to dance and tennis lessons, to baseball games, to band concerts," Lipton added.

She takes advantage of her love of tennis to spend time with her 15-year-old daughter and 13-year-old son, who are her doubles partners in tournaments.

Whether in the lab, on travel, or on the tennis courts, Lipton's expressiveness, expertise, reputation, and enthusiasm promise to keep her at the top of her game.

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By Julie Wiley, PNNL

 

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