Hot springs microbe yields record-breaking, heat-tolerant enzyme

ScienceDaily (July 5, 2011) — Bioprospectors from the University of California, Berkeley, and the University of Maryland School of Medicine have found a microbe in a Nevada hot spring that happily eats plant material -- cellulose -- at temperatures near the boiling point of water.

In fact, the microbe's cellulose-digesting enzyme, called a cellulase, is most active at a record 109 degrees Celsius (228 degrees Fahrenheit), significantly above the 100oC (212oF) boiling point of water.

This so-called hyperthermophilic microbe, discovered in a 95oC (203oF) geothermal pool, is only the second member of the ancient group Archaea known to grow by digesting cellulose above 80oC. And the microbe's cellulase is the most heat tolerant enzyme found in any cellulose-digesting microbe, including bacteria.

"These are the most thermophilic Archaea discovered that will grow on cellulose and the most thermophilic cellulase in any organism," said coauthor Douglas S. Clark, UC Berkeley professor of chemical and biomolecular engineering. "We were surprised to find this bug in our first sample."

Clark and coworkers at UC Berkeley are teaming with colleagues, led by Frank T. Robb, at the University of Maryland (U-Md) School of Medicine in Baltimore, to analyze microbes scooped from hot springs and other extreme environments around the United States in search of new enzymes that can be used in extreme industrial processes, including the production of biofuels from hard-to-digest plant fiber. Their team is supported by a grant from the Energy Biosciences Institute (EBI), a public-private collaboration that includes UC Berkeley, in which bioscience and biological techniques are being applied to help solve the global energy challenge.

"Our hope is that this example and examples from other organisms found in extreme environments -- such as high-temperature, highly alkaline or acidic, or high salt environments -- can provide cellulases that will show improved function under conditions typically found in industrial applications, including the production of biofuels," Clark said.

Clark, Robb and their colleagues, including UC Berkeley professor Harvey W. Blanch and postdoctoral researcher Melinda E. Clark, and U-Md postdoctoral researcher Joel E. Graham, will publish their results on July 5, in the online-only journal Nature Communications.

Many industrial processes employ natural enzymes, some of them isolated from organisms that live in extreme environments, such as hot springs. The enzyme used in the popular polymerase chain reaction to amplify DNA originally came from a thermophilic organism found in a geyser in Yellowstone National Park.

But many of these enzymes are not optimized for industrial processes, Clark said. For example, a fungal enzyme is currently used to break down tough plant cellulose into its constituent sugars so that the sugars can be fermented by yeast into alcohol. But the enzyme's preferred temperature is about 50oC (122oF), and it is not stable at the higher temperatures desirable to prevent other microbes from contaminating the reaction.

Hence the need to look in extreme environments for better enzymes, he said.

"This discovery is interesting because it helps define the range of natural conditions under which cellulolytic organisms exist and how prevalent these bugs are in the natural world," Clark said. "It indicates that there are a lot of potentially useful cellulases in places we haven't looked yet."

Robb and his colleagues collected sediment and water samples from the 95oC (203oF) Great Boiling Springs near the town of Gerlach in northern Nevada and grew microbes on pulverized Miscanthus gigas, a common biofuel feedstock, to isolate those that could grow with plant fiber as their only source of carbon.

After further growth on microcrystalline cellulose, the U-Md and UC Berkeley labs worked together to sequence the community of surviving microbes to obtain a metagenome, which indicated that three different species of Archaea were able to utilize cellulose as food. Using genetic techniques, they plucked out the specific genes involved in cellulose degradation, and linked the most active high-temperature cellulase, dubbed EBI-244, to the most abundant of the three Archaea.

Based on the structure of the enzyme, "this could represent a new type of cellulase or a very unusual member of a previously known family," Clark said.

The enzyme is so stable that it works in hot solutions approaching conditions that could be used to pretreat feedstocks like Miscanthus to break down the lignocelluloses and liberate cellulose. This suggests that cellulases may someday be used in the same reaction vessel in which feedstocks are pretreated.

The newly discovered hyperthermophilic cellulase may actually work at too high a temperature for some processes, Clark said. By collecting more hyperthermophilic cellulases, protein engineers may be able to create a version of the enzyme optimized to work at a lower temperature, but with the robust structural stability of the wild microbe.

"We might even find a cellulase that could be used as-is," he said, "but at least they will give us information to engineer new cellulases, and a better understanding of the diversity of nature."

The EBI partnership, which is funded with $500 million for 10 years from the energy company BP, includes researchers from the UC Berkeley; the University of Illinois at Urbana-Champaign; and the Lawrence Berkeley National Laboratory.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of California - Berkeley.

Journal Reference:

Joel E. Graham, Melinda E. Clark, Dana C. Nadler, Sarah Huffer, Harshal A. Chokhawala, Sara E. Rowland, Harvey W. Blanch, Douglas S. Clark, Frank T. Robb. Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment. Nature Communications, 2011; 2: 375 DOI: 10.1038/ncomms1373

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Warming dents corn and wheat yields

CEREAL KILLERBetween 1980 and 2008, climbing global temperatures took millions of tons of wheat off the dinner table, scientists say. Some countries experienced big losses due to weather (red), while in others, wheat production held steady (blue).Images courtesy of Science/AAAS

Set a place at the table for climate change; hotter weather may have already taken a bite out of food crops worldwide.

Farms across the planet produced 3.8 percent less corn and 5.5 percent less wheat than they could have between 1980 and 2008 thanks to rising temperatures, a new analysis estimates. These wilting yields may have contributed to the current sky-high price of food, a team of U.S. researchers reports online May 5 in Science. Climate-induced losses could have driven up prices of corn by 6.4 percent and wheat by 18.9 percent since 1980.

The researchers tracked country-by-country yields of these common foodstuffs over nearly three decades. Harvests of corn and wheat have climbed steadily since 1980 due in part to technological advancements, says David Lobell, a land-use scientist at Stanford University. But based on the team’s statistical analysis, farmers could have produced a lot more food if the weather had been cooler. For corn, global losses amount to millions of tons — about equal to Mexico’s yearly production of the crop. “For every decade of climate change, it sets you back a year,” Lobell says.

CORN ON THE RUN Corn is feeling the heat from climate change, with yields dropping close to 4 percent due to weather-related factors between 1980 and 2008.Images courtesy of Science/AAAS

For reasons still up for debate, temperatures largely held steady in the U.S. over the study period. So Iowa, by and large, doesn’t seem to have lost out. Rice and soybean yields have also proved resilient to rising temperatures so far, the team discovered.

This analysis of the past three decades largely falls in line with what other studies have projected for the coming century, says Andy Challinor of the University of Leeds in England, who studies the impacts of climate on agriculture. With enough complementary analyses, scientists may start to feel more certain about predicting the future of food. Still, when it comes to agriculture, researchers rely on a very murky crystal ball. Humans can, and probably will, adapt to warmer temperatures, switching to hardier crops or developing new technology to keep harvests high.

While it’s far from a prediction, Lobell says his study identifies a number of problem areas that do need attention — not later but now. “If we really invest a lot in the development of crops that can withstand really high temperatures,” he says, “that would potentially change things a lot.”

Even today, food scarcity is a pressing problem, says Navin Ramankutty, a geographer at McGill University in Montreal. As populations climb steeply, putting added pressure on agricultural production, an estimated one in seven people go hungry across the globe.

Found in: Climate Change, Earth, Earth Science, Ecology and Environment

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Understanding how crops deal with stress -- yield's biggest enemy

ScienceDaily (Apr. 25, 2011) — Like people, plants experience stress. And also, like people, the response to that stress can determine success.

People can exercise, or rest, or talk about the problem.

For plants, ways to deal with stress are internal. And ISU researchers are trying to understand how they do it.

Stephen Howell is a professor of genetics, development and cell biology and former director of the Plant Sciences Institute at ISU. His research is featured in the current issue of the Proceedings of the National Academy of Sciences.

"We've discovered a new arm of the pathway by which plants activate a response to environmental stress," he said.

Adverse environmental conditions, such as drought, flood, heat and other stresses, affect yield more than crop pests and diseases. Finding a way to maintain high yields for plants under stress is a goal of plant breeders and other agriculture stakeholders, said Howell.

"These are environmental stresses that the farmers can't control," Howell said. "They are acts of nature. And now seed companies are interested in trying to equip plants with the ability to tolerate stress."

Plant cells produce proteins and ship them to different parts of the cell. During production and shipment, these proteins move through an area of the cell called the endoplasmic reticulum (ER).

Under normal conditions, these proteins are folded into their normal, healthy three-dimensional structures as they are produced.

When a plant is under stress, its cells produce poorly folded or unfolded proteins. Inside the ER, a built-in, quality-control system senses this and "sets off an alarm in the cell," said Howell.

In response to the alarm, another protein (IRE1) cuts apart an important RNA molecule, but then splices it back together to create a different sequence.

This cut-and-splice event activates a cascade of stress response genes whose products bring about internal defensive measures that help the plant survive.

"As it turns out, responses that are activated under stress conditions actually inhibit the growth of plants," said Howell. "This allows them to conserve their energy to survive the stress conditions."

For plants in the wild, this response is a survival tactic, he said.

In production agriculture crops, however, these responses reduce yields.

"You don't want crop plants to [stop growing]," Howell said. "You want them to continue to grow and produce even though they are under stress."

With the new understanding of this stress response pathway, Howell says, the next step may be to silence the alarm system.

"What may be important is to disable some of these stress responses," said Howell. "That may make the plant be more productive under stress conditions."

Howell's research team included Yan Deng and Renu Srivastava, both of the Plant Sciences Institute, Ames; Sabrina Humbert and Steven Rothstein, both of University of Guelph, Canada; and Jian-Xiang Liu formerly of the Plant Sciences Institute and now a faculty member at Fudan University, China.

Howell is currently on leave from ISU and is director of the Division of Molecular and Cellular Biosciences for the National Science Foundation in Washington, D.C.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Iowa State University.

Journal Reference:

Yan Deng, Sabrina Humbert, Jian-Xiang Liu, Renu Srivastava, Steven J. Rothstein, and Stephen H. Howell. Heat induces the splicing by IRE1 of a mRNA encoding a transcription factor involved in the unfolded protein response in Arabidopsis. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1102117108

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Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

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