Scientists discover how ocean bacterium turns carbon into fuel (w/ Video)

Mar 04, 2010 by Elizabeth Dougherty
Fluorescent labeling of proteins inside the carboxysome show that cyanobacteria create carboxysomes in numbers proportional to length and space them evenly along their longest axis.

(PhysOrg.com) -- Reduce. Reuse. Recycle. We hear this mantra time and again. When it comes to carbon‹the "Most Wanted" element in terms of climate change‹nature has got reuse and recycle covered. However, it's up to us to reduce. Scientists at Harvard Medical School are trying to meet this challenge by learning more about the carbon cycle, that is, the process by which carbon moves from the atmosphere into plants, oceans, soils, the earth's crust, and back into the atmosphere again.

One of the biggest movers and shakers is the lowly cyanobacteria, an ocean-dwelling, one-celled organism. Pamela Silver, HMS professor of , and colleagues have uncovered details about how this fixes, or digests, carbon. These bacteria build miniature factories inside themselves that turn carbon into fuel.

Silver and her colleagues report that the bacteria organize these factories spatially, revealing a structural sophistication not often seen in single-celled organisms. This regular and predictable spacing improves the efficiency of carbon processing. In the future, an understanding of the mechanisms that govern this spatial organization may help improve the efficiency of designer bacteria engineered to produce carbon-neutral fuels such as and hydrogen.

These findings will be published online March 5 in the journal Science.

The rod-shaped cyanobacteria are among the most abundant organisms on earth. Forty percent of the carbon in the carbon cycle is reused and recycled through these tiny creatures. To process carbon, cyanobacteria build soccer-ball-shaped structures inside themselves called carboxysomes. These tiny factories absorb and convert it into sugar, which the bacteria then use to produce energy.

"The ocean is just packed with these bacteria. By studying them, we're understanding more about how the earth works," said Silver, who is also on the faculty of the Wyss Institute for Biologically Inspired Engineering at HMS. "I'm blown away by what's happening in the ocean and what we don't understand about it. There are a lot of things in the ocean that are going to be useful to us."

The research team, led by co-first authors, research fellows David Savage and Bruno Afonso, attached a fluorescent tag to proteins involved in building the carboxysome, then grew the tagged bacteria under a microscope.

The resulting images revealed that, instead of being randomly numbered and haphazardly placed, cyanobacteria build carboxysomes in numbers that scale with their size, and they space the factories evenly along their length. (see image, end of release)

The finding adds evidence for new ways to think about bacteria. "We had this idea of bacteria as a bag of enzymes, but that has been completely shattered," said Afonso. A single protein, called parA, acts as a kind of inner-bacterium stage manager, arranging the carboxysomes in a neat, single-file row, the researchers found. When they disabled the bacteria's ability to make the protein, the carboxysomes were distributed far more randomly.

The lacking parA were also less "fit" for survival, said Savage. While wild-type bacteria cells have a consistent number of carboyxsomes, which in turn optimizes carbon processing and fitness, the knockout bacterium created daughter cells whose numbers of carboxysomes ranged from none to an excess. The daughter cells with few or no carboxysomes divide more slowly and also process fifty percent less than daughter cells at the other end of the spectrum. (see video 1)

This video is not supported by your browser at this time.
Knock-out bacteria, like the ones shown here who lack in parA, are less fit for survival. While wild-type bacteria cells have a consistent number of carboyxsomes, the knockouts either don't have enough or have too many, which leads to slower cell division and less carbon processing.

By tagging parA in wild-type bacteria, they discovered interesting dynamics in the protein. Thousands of parA proteins repeatedly cluster together and shoot quickly from one end of the bacterium to the other. (see video 2)

This video is not supported by your browser at this time.
Green tagged parA proteins gather at one side of the bacterium, shoot to the other end as a cluster, then shoot back. This dynamic seems to be associated with the even spacing of carboxysomes.

"It's amazing that you can generate this regularity and symmetry potentially from a single protein," said Savage. "It's amazing that it is somehow tuned by the dynamics of the protein." The researchers have not yet identified the exact mechanism parA uses to govern the spacing.

Many other bacteria also have the parA protein, which is known for separating chromosomes during cell division. "This work highlights how bacteria cobble together spare parts to achieve similar goals such as organization and segregation," said David Rudner, HMS assistant professor of microbiology and molecular genetics, who was not involved in the study.

These findings may help synthetic biologists one day create designer bacteria.

"Knowledge about how cells create and deploy specialized factories like the carboxysome opens the way to creating other kinds of mini factories that could perform useful functions," said Richard Losick, Harvard University professor of molecular and cellular biology, who was not involved in the study.

Silver's lab is looking into whether the carboxysome might be useful for optimizing the production of hydrogen by engineered bacteria. One challenge in designing hydrogen-producing bacteria is that the enzymes that produce hydrogen are sensitive to oxygen. The carboxysome may help solve this problem because its outer shell blocks out oxygen, protecting the enzymes inside from its toxic effects.

Explore further: Sugar mimics guide stem cells toward neural fate

More information: "Spatially Ordered Dynamics of the Bacterial Carbon Fixation Machinery", David F. Savage, Bruno Afonso, Anna Chen, and Pamela A. Silver, Science, 5 March 2010, Vol 327, Issue 5970

Related Stories

Food source threatened by carbon dioxide

Dec 10, 2007

Carbon dioxide increasing in the atmosphere may affect the microbial life in the sea, which could have an impact on a major food source, warned Dr Ian Joint at a Science Media Centre press briefing today.

Fuel from food waste: bacteria provide power

Jul 17, 2008

Researchers have combined the efforts of two kinds of bacteria to produce hydrogen in a bioreactor, with the product from one providing food for the other. According to an article in the August issue of Microbiology Today, this t ...

Odd energy mechanism in bacteria analyzed

Nov 04, 2005

Scientists at Oregon State University have successfully cultured in a laboratory a microorganism with a gene for an alternate form of photochemistry – an advance that may ultimately help shed light on the ecology of the ...

Are microbes the answer to the energy crisis?

Jun 04, 2008

The answer to the looming fuel crisis in the 21st century may be found by thinking small, microscopic in fact. Microscopic organisms from bacteria and cyanobacteria, to fungi to microalgae, are biological factories that ...

From microbes to hydrogen fuel

Mar 24, 2009

Searching for an environmentally friendly way to produce cheap hydrogen as a fuel, researchers at Oregon State University are turning to microbes that have been doing the job for billions of years.

Recommended for you

Sugar mimics guide stem cells toward neural fate

17 hours ago

Embryonic stem cells can develop into a multitude of cells types. Researchers would like to understand how to channel that development into the specific types of mature cells that make up the organs and other structures of ...

Researchers uncover secrets of internal cell fine-tuning

Jul 29, 2014

New research from scientists at the University of Kent has shown for the first time how the structures inside cells are regulated – a breakthrough that could have a major impact on cancer therapy development.

User comments : 3

Adjust slider to filter visible comments by rank

Display comments: newest first

Mesafina
3.8 / 5 (5) Mar 04, 2010
Grow bacteria -> bacteria turn carbon-dioxide into sugar -> bioreact bacteria to turn sugar into electricity = power source that consumes rather then produces carbon dioxide. Next, balance the amount of energy sources which produce co2 with those that consume it so they are carbon neutral. Voila! In one fell swoop, you get the annoying people on both sides of the GW argument to shut up. And without solve the problem if it even exists. And all without cap and trade nonsense.
RJ32
Mar 05, 2010
This comment has been removed by a moderator.
PPihkala
not rated yet Mar 05, 2010
@Mesafina: Who is going to pay for that expensive energy? Coal is too cheap, it will currently win any price comparison to carbon neutral production.
RETT
not rated yet Mar 13, 2010
Mesfina,

And just how do you know that such energy would be expensive. If all that it requires is bacteria, seawater, and CO2, I'd say that is a bit of a rash conclusion. Until a process is developed and optimized, commenting about the economics is meaningless. Coal is not cheap in the long run, but ruinously expensive. We just don't assess all the costs to the producers. If we did, coal would disappear as a fuel in about five minutes. We choose to ignore the full costs, thus assuring that we all will pay them in the most difficult of ways.