Microbial Juggling

Researchers discovered how a soil microbe could rev up artificial photosynthesis

May 09, 2022

Researchers discovered how a a bacterial enzyme converts carbon dioxide into carbon compounds 20 times faster than plant enzymes do during photosynthesis. The results stand to accelerate progress toward converting carbon dioxide into a variety of products.

Plants rely on a process called carbon fixation – turning carbon dioxide from the air into carbon-rich biomolecules ¬ for their very existence. That’s the whole point of photosynthesis, and a cornerstone of the vast interlocking system that cycles carbon through plants, animals, microbes and the atmosphere to sustain life on Earth.  

But the carbon fixing champs are not plants, but soil bacteria. Some bacterial enzymes carry out a key step in carbon fixation 20 times faster than plant enzymes do.  Now an international research team, among them researchers from the Max Planck Institute for Terrestrial Microbiology, has discovered how a bacterial enzyme – a molecular machine that facilitates chemical reactions – revs up to perform this feat.

Rather than grabbing carbon dioxide molecules and attaching them to biomolecules one at a time, they found, this enzyme consists of pairs of molecules that work in sync, like the hands of a juggler who simultaneously tosses and catches balls, to get the job done faster. One member of each enzyme pair opens wide to catch a set of reaction ingredients while the other closes over its captured ingredients and carries out the carbon-fixing reaction; then, they switch roles in a continual cycle. 

This animation shows two of the paired molecules (blue and white) within the ECR enzyme, which fixes carbon in soil microbes, in action. They work together, like the hands of a juggler who simultaneously tosses and catches balls, to get the job done faster. One member of each enzyme pair opens wide to catch a set of reaction ingredients (shown coming in from top and bottom) while the other closes over its captured ingredients and carries out the carbon-fixing reaction; then, they switch roles in a continual cycle. Scientists are trying to harness and improve these reactions for artificial photosynthesis to make a variety of products.

Microbial Juggling

This animation shows two of the paired molecules (blue and white) within the ECR enzyme, which fixes carbon in soil microbes, in action. They work together, like the hands of a juggler who simultaneously tosses and catches balls, to get the job done faster. One member of each enzyme pair opens wide to catch a set of reaction ingredients (shown coming in from top and bottom) while the other closes over its captured ingredients and carries out the carbon-fixing reaction; then, they switch roles in a continual cycle. Scientists are trying to harness and improve these reactions for artificial photosynthesis to make a variety of products.

A single spot of molecular “glue” holds each pair of enzymatic hands together so they can alternate opening and closing in a coordinated way, the team discovered, while a twisting motion helps hustle ingredients and finished products in and out of the pockets where the reactions take place. When both glue and twist are present, the carbon-fixing reaction goes 100 times faster than without them.  

Figuring out how they do this could help scientists develop forms of artificial photosynthesis to convert the greenhouse gas into fuels, fertilizers, antibiotics and other products.
“This bacterial enzyme is the most efficient carbon fixer that we know of, and we came up with a neat explanation of what it can do,” said Soichi Wakatsuki, a professor at SLAC National Accelerator Laboratory  and Stanford and one of the senior leaders of the study. Now that they know the mechanism, he said, scientists can engineer enzymes that do a very fast job with all sorts of starting materials.

Improving on nature

The enzyme the team studied is part of a family called enoyl-CoA carboxylases/reductases, or ECRs. It comes from soil bacteria called Kitasatospora setae, which in addition to their carbon-fixing skills can also produce antibiotics.

Wakatsuki heard about this enzyme family half a dozen years ago from Tobias Erb of the Max Planck Institute for Terrestrial Microbiology in Germany and Yasuo Yoshikuni of Joint Genome Institute (JGI). Erb’s research team had been working to develop bioreactors for artificial photosynthesis to convert carbon dioxide (CO2) from the atmosphere into all sorts of products.

“As important as photosynthesis is to life on Earth”, Tobias Erb explains, “it isn’t very efficient. Like all things shaped by evolution over the eons, it’s only as good as it needs to be, the result of slowly building on previous developments but never inventing something entirely new from scratch.”

The step in natural photosynthesis that fixes CO2 from the air, which relies on an enzyme called Rubisco, is a bottleneck that bogs the whole chain of photosynthetic reactions down. So using speedy ECR enzymes to carry out this step, and engineering them to go even faster, could bring a big boost in efficiency.

“We aren’t trying to make a carbon copy of photosynthesis,” Tobias Erb says. “We want to design a process that’s much more efficient by using our understanding of engineering to rebuild the concepts of nature. This ‘photosynthesis 2.0’ could take place in living or synthetic systems such as artificial chloroplasts – droplets of water suspended in oil.”

Portraits of an enzyme

While the collaboration partners from SLAC National Accelerator Laboratory and JGI revealed the molecular structure of the enzyme using both X-ray crystallography and X-ray free-electron laser, Tobias Erb’s group in Germany together with Esteban Vöhringer-Martinez’s group from the University of Concepción in Chile carried out detailed biochemical studies and extensive dynamic simulations to make sense of the structural data.
The simulations revealed that the opening and closing of the enzyme’s two parts don’t just involve molecular glue, but also twisting motions around the central axis of each enzyme pair.

“This twist is almost like a rachet that can push a finished product out or pull a new set of ingredients into the pocket where the reaction takes place,” Soichi Wakatskuki said. Together, the twisting and synchronization of the enzyme pairs allow them to fix carbon 100 times a second.

From static shots to fluid movies

So far the experiments have produced static snapshots of the enzyme, the reaction ingredients and the final products in various configurations.

“Our dream experiment,” Soichi Wakatsuki said, “would be to combine all the ingredients as they flow into the path of the X-ray laser beam so we could watch the reaction take place in real time.”

The team actually tried that, he said, but it didn’t work. “The CO2 molecules are really small, and they move so fast that it’s hard to catch the moment when they attach to the substrate,” he said. “Plus the X-ray laser beam is so strong that we couldn’t keep the ingredients in it long enough for the reaction to take place. When we pressed hard to do this, we managed to break the crystals.”

An upcoming high-energy upgrade to SLAC`s X-ray electron laser will likely solve that problem, he added, with pulses that arrive much more frequently -- a million times per second – and can be individually adjusted to the ideal strength for each sample. The international team continues to collaborate to find a way to make this approach work.

(Source: Press release by SLAC National Accelerator Laboratory, with kind permission by Glennda Chui, Office of Communications)

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