Salk Institute for Biological Studies

These bacterial smears show common E. coli strains that allow unnatural amino acid (Uaas) incorporation at one site only (left side), and an engineered strain that enables the incorporation of Uaas at multiple sites simultaneously (right side). The glow indicates the bacteria are producing full-length proteins with Uaas incorporated at different numbers of sites (as indicated by the surrounding numbers), a necessary step for their potential use in the production of new drugs and biofuels.

Scientists have successfully added multiple "unnatural" amino acids to a strain of bacteria, a breakthrough on the path to genetically engineered microbes that create useful things for people such as life-saving medicines and biofuels.

"We are adding components to the bug so that the bug can do something that a natural bug usually can't do," Lei Wang at the Salk Institute for Biological Studies told me today. "We are trying to make it do new tricks."

Amino acids are molecules built primarily from carbon, hydrogen, oxygen, and nitrogen. They assemble into various shapes and patterns to form the larger proteins. Proteins, in turn, carry out specific biological functions.

All life on Earth relies on a standard set of 20 amino acids. For years, researchers have genetically altered bacteria to perform certain tasks, such as produce the synthetic insulin diabetics use to regulate blood sugar levels. But until now, all such genetic engineering has relied on the 20 natural amino acids.

In the eyes of Wang, the world might be a better place if there were more building blocks available.

"If you can provide more building blocks, then you may be able to generate a new function for the proteins," he said. "And if you can create new functions for the proteins, then you may be able to synthesize new compounds using these proteins."

Examples of the potential compounds include drugs, industrial chemicals, and biofuels. 

Expanded genetic code
To do this, Wang's team created an essentially expanded genetic code for the bacteria, a strain of E. coli, with instructions to use multiple unnatural amino acids in the construction of proteins. 

The technology to put one unnatural amino acid at one place in the DNA has been around for about a decade, Wang said. The problem is that with just one position, "you cannot evolve anything, you cannot produce anything useful," he said. 

This limitation stemmed from that fact that bacteria produce another protein called release factor 1 (RF1) that stops the production of the protein containing the unnatural amino acid. To get around this, Wang's team removed RF1 and altered another protein, RF2, to keep the bug alive in the absence of RF1.

"We can now put unnatural amino acids at multiple places simultaneously and with very, very high efficiency … therefore you significantly increase your chance of generating new protein function and therefore generating new biosynthesis ability," he said. 

Complementary to 'synthetic life'
This approach to creating useful products with genetically enhanced bugs is complementary to efforts such as Craig Venter's well publicized effort to create synthetic lifeforms that could, potentially, produce biofuels, Wang said.

That effort, Wang explained, essentially attempts to reorganize and optimize the natural components of the genome to "make it better." The Salk team's effort gives the bug new building blocks. 

"They sort of help each other out," Wang said of the two approaches. "What they achieve can help us and what we helped achieve here can also help them."

Both approaches along with other efforts to genetically engineer microbes to produce useful products such as butanol may one day allow us to fill up our cars with fuel made by the genetically enhanced bugs or visit the pharmacy for a new class of drugs.

"We are not there yet, but that is exactly what we want to do in the next stage," Wang said.

More stories on engineered bacteria:

• Bacteria turned into biofuel factories
• Bacteria rebuilt to make oil
• It's alive! Artificial DNA controls life
• First synthetic life form holds promise, peril
• Synthetic life could help humans colonize Mars

A paper on the findings appear in the Sept. 19 issue of the journal Nature Chemical Biology. 

John Roach is a contributing writer for msnbc.com.

Joel Graham, University of Maryland

A 94°C geothermal pool, with a level-maintaining siphon, near Gerlach, Nevada. Sediment from the floor of this pool was enriched on pulverized miscanthus at 90°C and subsequently transferred to filter paper in order to isolate microbes able to subsist on cellulose alone.

A record-breaking microbe that thrives while munching plant material at near boiling temperatures has been discovered in a Nevada hot spring, researchers announced in a study published today.

Scientists are eyeing the microbe's enzyme responsible for breaking down cellulose — called a cellulase — as a potential workhouse in the production of biofuels and other industrial processes.

Cellulose is a chain of linked sugar molecules that makes up the woody fiber of plants. To produce biofuels, enzymes are required to breakdown cellulose into its constituent sugars so that yeasts can then ferment them into the type of alcohol that makes cars (not people) go vroom.

At the industrial scale, this process is done most efficiently at high temperatures that kill other microbes that could otherwise contaminate the reaction, Douglas Clark, a chemical and biomolecular engineer at the University of California at Berkeley, told me today.

"So finding cellulases that can operate at those temperatures are of interest," he said.

Hot spring
That's what led Clark, microbiologist Frank Robb from the University of Maryland, and colleagues to collect sediment and water samples from the Great Boiling Springs near Gerlach, Nevada. The spring is 203 degrees F, just short of boiling.

"It's on private land and has been surrounded by a low wall to keep cattle from going into it and that maintains the temperature," Robb explained to me today, noting that most hot springs have varying temperatures depending on the weather and water levels in the spring.

In addition, a siphon has been added to Gerlach hot spring to keep it from overflowing. The combination gives whatever microbes that are in there no choice but to grow at high temperatures, Robb noted. Bits of grass and woody material blown into the spring serve as a food source.

The team grew microbes found in the samples on pulverized miscanthus, a type of grass that is a common biofuel feedstock, to isolate the microbes that grow with plant fiber as their only source of carbon.

They then sequenced the community of surviving microbes, which indicated three species of Archaea, a type of single celled microorganism, were able to utilize cellulose as food. Genetic techniques identified the specific cellulase involved in the breakdown of cellulose.

This cellulase, dubbed EBI-244, was found in the most abundant of the three Archaea.

"We didn't really expect to find an organism that could grow at such a high temperature and degrade cellulose in this particular environment. But you never know," Clark told me. "It really underscores the diversity of life. And, obviously, if you don't look, you won't find it."

Too hot
The enzyme EBI-244 works optimally at 228 degrees F (109 degrees C), which is actually too hot for the efficient breakdown of cellulose into fermentable sugars due to side reactions that can occur, Clark noted.

"But it is interesting to know that such cellulases are out there," Clark said. "And then this cellulase might also serve as a good starting point to be engineered to work at a lower temperature but maintain the high stability that it has naturally evolved to work at such high temperatures."

Robb likened this engineering process to building a street car from parts used on cars found at the racetrack. "The enzyme itself could be the parts bin," he said.

So, the enzyme itself probably won't be hard at work anytime soon producing fuel to put in your gas tank, but it does lead researchers down the road to engineering the biofuels of the future. What's more, EBI-244 is a record holder for heat tolerance in cellulase.

"It is always nice to have a record breaker," Clark noted. "It adds to that wow factor a little bit."

A paper on the findings appears in the July 5 issue of the journal Nature Communications. Other authors are Dana C. Nadler, Sarah Huffer, Harshal A. Chokhawala and Harvey W. Blanch of UC Berkeley; and Sara E. Rowland of the University of Maryland Marine, Estuarine and Environmental Sciences graduate program.

More on heat-loving microbes:

• Yellowstone microbe converts light to energy
• Got milk? Convert it into biofuel
• How bacteria could help power the future
• How biology will help fill your fuel tank
• Hole-y Cow! Guts could lead to holy grail for cheap biofuels
• Not-so-stupid microbe tricks