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, and 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.
Now a team of researchers from the Department of Energy’s SLAC National Accelerator Laboratory, Stanford University, Max Planck Institute for Terrestrial Microbiology in Germany, DOE’s Joint Genome Institute (JGI) and the University of Concepción in Chile 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.
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.
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 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, Erb said, 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.
Portraits of an enzyme
Wakatsuki and his group had been investigating a related system, nitrogen fixation, which converts nitrogen gas from the atmosphere into compounds that living things need. Intrigued by the question of why ECR enzymes were so fast, he started collaborating with Erb’s group to find answers.
The SLAC team made samples of the ECR enzyme and crystallized them for examination with X-rays at the Advanced Photon Source at DOE’s Argonne National Laboratory. The X-rays revealed the molecular structure of the enzyme — the arrangement of its atomic scaffolding — both on its own and when attached to a small helper molecule that facilitates its work.
Further X-ray studies at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) showed how the enzyme’s structure shifted when it attached to a substrate, a kind of molecular workbench that assembles ingredients for the carbon fixing reaction and spurs the reaction along.
Finally, a team of researchers from SLAC’s Linac Coherent Light Source (LCLS) carried out more detailed studies of the enzyme and its substrate at Japan’s SACLA X-ray free-electron laser. The choice of an X-ray laser was important because it allowed them to study the enzyme’s behavior at room temperature — closer to its natural environment.
Meanwhile, Erb’s group in Germany and Associate Professor Esteban Vo?hringer-Martinez’s group at the University of Concepción in Chile carried out detailed biochemical studies and extensive dynamic simulations to make sense of the structural data collected by Wakatsuki and his team.
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, Wakatsuki said.
The ECR enzyme family also includes a more versatile branch that can interact with many different kinds of biomolecules to produce a variety of products. But since they aren’t held together by molecular glue, they can’t coordinate their movements and therefore operate much more slowly.
From static shots to fluid movies
An upcoming high-energy upgrade to LCLS 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.
Wakatsuki said his team continues to collaborate with Erb’s group, and it’s working with the LCLS sample delivery group and with researchers at the SLAC-Stanford cryogenic electron microscopy (cryo-EM) facilities to find a way to make this approach work.
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