Rising Stars Seek to Learn from the Master: Mother Nature

If you want to be better than the best, you first must understand what makes them best—in detail. That's a daunting task when the best is Mother Nature. Two of her highly efficient creations, bacteria and algae, have great potential to produce fuels using fewer resources than today's industries. To improve fuel and chemical production, we need to understand and mimic these simple and yet complex microbes. The Department of Energy's (DOE's) Office of Science is leading the effort to uncover nature's biochemical secrets to answer some of the toughest questions about mechanisms Mother Nature uses to perform some amazing chemical feats.

The editors of ACS Biochemistry recognized a trio of rising stars supported by the Office of Basic Energy Sciences within DOE's Office of Science. Each of the scientists is doing work made possible by an Early Career Research Program grant.

Here are three rising stars in the field of physical biosciences.

Dave Savage: Tiny compartments hold the machinery of photosynthesis.

Carrots, cranberries, corn, and other crops that supply our caloric needs use photosynthesis, a process that uses carbon dioxide to create sugary fuels, structural building blocks, and the many larger structures that enable life as we know it. Certain bacteria use the same process; in fact, nearly a quarter of the carbon dioxide that's pulled from the air via photosynthesis passes through bacteria. Learning the secrets of bacterial photosynthesis and its efficiency in handling carbon dioxide could be applied to plants. For example, we could alter plants to take in more carbon dioxide, producing bumper crops of food and biofuel feedstock.

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Photo courtesy of Dave Savage

Dave Savage, former competitor in DOE's Science Bowl, one of the rising stars in biochemistry, is working on carbon dioxide uptake that could, one day, enhance the outputs of food and biomass for fuel conversion.

For Dave Savage, the key is bacterial microcompartments, which are like soap bubbles inside the bacterial cell. Each bubble is packed full of machinery. The machinery does the jobs necessary to keep the cells alive. The machinery-packed bubbles enhance the efficiency by which carbon dioxide can be taken into the cell from the air and converted into "starter compounds" bacteria can use. "There is tremendous importance in understanding how these amazing molecular machines work," said Savage, an associate professor at the University of California, Berkeley. "From a practical perspective, this is where inorganic carbon enters the organic world," said Savage. "There is, thus, great potential in using microcompartments—or at least the principles behind how they function—to improve plant-based photosynthetic carbon uptake and assimilation."

Over the course of his research, Savage and his colleagues have discovered that it's possible to take a compartment containing specific molecular machinery from bacterium A and put it into bacterium B. This is significant for two reasons. First, being able to transplant a compartment full of specialized proteins is like sending in the cavalry; the transplanted machinery amps up the host's ability to capture carbon dioxide and use it. Second, the research defines what it takes to build compartments to protect the reactions.

Developing the interdisciplinary skills needed to address the biological questions is an ongoing challenge for Savage. This means that to make progress, Savage and his colleagues need to become experts in many fields and reach out to others to collaborate when necessary. "I'm fortunate to have attracted great trainees and received help along the way from collaborators at Berkeley and other facilities, but it takes time to develop these resources," he explained.

Savage credits an early career award from DOE's Office of Science with giving him and his team that time. Also, the award confirmed that his research had merit. "I was just beginning to start my laboratory," he noted, "and the early career award was tremendous validation for our science."

Steven Mansoorabadi: Getting proteins what they need.

At Auburn University in Alabama, Steven Mansoorabadi studies microbes that produce methane or ammonia, potential fuels. Also, his work could lead to new ways to consume methane when it presents safety or environmental risks, such as at oil wells.

Mansoorabadi was making great progress elucidating methane-related processes, including a study published in Science. Much of his work focused on the F430 coenzyme. A coenzyme is a helper molecule.

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Photo courtesy of Auburn University

One of the rising stars in biochemistry, Steven Mansoorabadi's research could bring us closer to using microbes to produce renewable methane, the key component in natural gas.

It's not a protein; it's a small molecule that plays an important role in enabling larger catalytic proteins, or enzymes, to run. It's sort of like the spark plug in a pickup truck. While he was studying the biochemical pathway by which F430 is made, he discovered a protein that looked an awful lot like the enzyme (nitrogenase) that produces ammonia.

"The nitrogenase enzyme is the biological equivalent of the Haber-Bosch process, used in industry to produce ammonia," said Mansoorabadi. Unlike the industrial process, nitrogenase pumps out ammonia without needing massive quantities of heat, natural gas, and physical space.

The similarities between the enzymes involved in producing the F430 cofactor and ammonia made his research a potential two-for-one deal: learn how nature produces this cofactor involved in methane production and perhaps gain new insights on ammonia formation. This idea led Mansoorabadi to a successful early career grant from DOE.

Mansoorabadi and his colleagues went on to write a dossier on the F430 coenzyme. The individual steps that describe how it is formed. How it works. Where it goes in the cell. Ultimately, they determined how this and other helper molecules start up the methane-generating protein engine known as methyl-coenzyme M reductase. "If you know how it works," said Mansoorabadi, "you know what it needs."

The most frustrating challenge for the assistant professor and his colleagues was the months it took to grow each batch of microbes involved. "In biosciences, you're sometimes at the mercy of whether things want to grow or not," he said. Or at least how fast they want to grow, as that's how you obtain the materials used to support these kinds of studies.

Kyle Lancaster: Trading electrons and controlling nitrogen.

Bacteria can thrive on the fringes of our environment. These bacteria and other organisms—living next to underwater volcanic vents—have a rather odd nutritional plan: They digest nitrogen, not the usual diet of carbon. This odd diet requires a chain of biochemical reactions that continually give and take electrons from nitrogen atoms. Kyle Lancaster delved into these reactions to uncover how they work.

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Photo courtesy of Cornell University

Kyle Lancaster is conducting research that could change how we produce ammonia, vital for crop growth, or better ways to minimize its loss from productive farmlands.

Understanding how those electrons move could lead to more efficient ammonia production. Ammonia is vital in fertilizers used to grow everything from corn, to cotton, to canola oil. Globally, farmers use around 120 million tons of nitrogen each year to raise crops. Ammonia could also be fuel for cars and trucks, enriching our energy landscape.

In microbes, proteins control electron transfers. Nitrogen atoms are quite useful in these transfers, as the atoms can accept up to three electrons and donate as many as five. After each exchange, the molecule changes. For example, one exchange turns ammonia into a form that microbes can consume. A major player in this transformation is a monstrous protein.

"It has a lot of hemes [massive iron-containing structures], but only three get the job done. To understand the chemistry, we need to understand the critical heme center," noted Lancaster. "Our challenge is to pull the information out from the noise."

He and his colleagues at Cornell University began by delving into a model protein; it's smaller but has the same active heme group they wanted to study. They have already overturned a 50-year-old assumption, about how the heme-containing protein packs away electrons.

Further, they changed how scientists understand the protein's end game. They found that the protein produces a simple nitrogen compound that can, under the right circumstances, turn into nitrous oxide. Nitrous oxide has serious environmental implications; it's an ozone-depleting gas that's also linked to acid rain. "It was one of those serendipitous discoveries," said Lancaster. "We ended up answering questions for agricultural scientists and others."

More secrets to uncover

Nature has many more secrets to share, and these rising stars are among the crew providing a foundational understanding of the complex biochemistry that is involved in biological energy capture, conversion, and storage.

The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information please visit https://science.energy.gov.

Kristin Manke is on detail as a communications specialist in the Office of Science, [email protected].