How a soil microbe could rev up artificial photosynthesis

Date:
April 29, 2022
Source:
DOE/SLAC National Accelerator Laboratory
Summary:
When it comes to fixing carbon, plants have nothing on soil
bacteria that can do it 20 times faster. The secret is an enzyme
that 'juggles' reaction ingredients. Scientists hope to optimize
this process for producing fuels, antibiotics and other products
from CO2.



FULL STORY ========================================================================== 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, 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 Concepcio'n 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.

"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 and Stanford and one of the senior leaders
of the study, which was published in ACS Central Science this week.



========================================================================== "Some of the enzymes in this family act slowly but in a very specific
way to produce just one product," he said. "Others are much faster and
can craft chemical building blocks for all sorts of products. Now that
we know the mechanism, we can engineer enzymes that combine the best
features of both approaches and 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 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.



========================================================================== What's more, he said, 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," Erb
explained. "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 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.

Hasan DeMirci, a research associate in Wakatsuki's group who is now an assistant professor at Koc University and investigator with the Stanford
PULSE Institute, led the effort at SLAC with help from half a dozen SLAC
summer interns he supervised. "We train six or seven of them every year,
and they were fearless," he said. "They came with open minds, ready
to learn, and they did amazing things." 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 -- with almost
no radiation damage.

Meanwhile, Erb's group in Germany and Associate Professor Esteban
Vo?hringer- Martinez's group at the University of Concepcio'n 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.

"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," he said. Together, the twisting and synchronization of
the enzyme pairs allow them to fix carbon 100 times a second.

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.

"If we can increase the rate of those sophisticated reactions to make
new biomolecules," Wakatsuki said, "that would be a significant jump in
the field." 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," 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 at SACLA, 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 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.

Researchers from the RIKEN Spring-8 Center and Japan Synchrotron Radiation Research Institute also contributed to this work, which received major
funding from the DOE Office of Science. Much of the preliminary work for
this study was carried out by SLAC summer intern Yash Rao; interns Brandon Hayes, E. Han Dao and Manat Kaur also made key contributions. DOE's Joint Genome Institute provided the DNA used to produce the ECR samples. SSRL,
LCLS, the Advanced Photon Source and the Joint Genome Institute are all
DOE Office of Science user facilities.

Citation: Hasan DeMirci et al., ACS Central Science, 25 April 2022
(10.1021/ acscentsci.2c00057) SLAC is a vibrant multiprogram laboratory
that explores how the universe works at the biggest, smallest and
fastest scales and invents powerful tools used by scientists around
the globe. With research spanning particle physics, astrophysics and
cosmology, materials, chemistry, bio- and energy sciences and scientific computing, we help solve real-world problems and advance the interests
of the nation.

SLAC is operated by Stanford University for theU.S. Department of Energy's Office of Science. The Office of Science is the single largest supporter
of basic research in the physical sciences in the United States and is
working to address some of the most pressing challenges of our time.


========================================================================== Story Source: Materials provided by
DOE/SLAC_National_Accelerator_Laboratory. Original written by Glennda
Chui. Note: Content may be edited for style and length.


========================================================================== Related Multimedia:
* Kitasatospora_setae ========================================================================== Journal Reference:
1. Hasan DeMirci, Yashas Rao, Gabriele M. Stoffel, Bastian Vo"geli,
Kristina
Schell, Aharon Gomez, Alexander Batyuk, Cornelius Gati, Raymond G.

Sierra, Mark S. Hunter, E. Han Dao, Halil I. Ciftci, Brandon Hayes,
Fredric Poitevin, Po-Nan Li, Manat Kaur, Kensuke Tono, David Adrian
Saez, Samuel Deutsch, Yasuo Yoshikuni, Helmut Grubmu"ller, Tobias
J. Erb, Esteban Vo"hringer-Martinez, Soichi Wakatsuki. Intersubunit
Coupling Enables Fast CO2-Fixation by Reductive Carboxylases. ACS
Central Science, 2022; DOI: 10.1021/acscentsci.2c00057 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/04/220429185744.htm

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