How a soil microbe could rev up artificial photosynthesis
The secret is an enzyme that “juggles” reaction ingredients
Greg Stewart, SLAC National Accelerator Laboratory
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.
“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 Vöhringer-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.
“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.
Other news from the department science
Leibniz Prize for chemist Prof. Dr. Peter R. Schreiner
Germany's most important research funding prize goes to scientist at the University of Giessen
Non-toxic plasticisers for use in elastomers and thermoplastics
Bio-based plasticizers from Central Germany
Wood materials make for reliable organic solar cells
Kraft lignin improves the stability in organic solar cells thanks to its ability to form hydrogen bonds that acts as a sort of glue
Argonne and Idaho National Laboratories partner with CMBlu Energy for innovative long-duration energy storage project
The project aims to improve microgrids in cold climates and make fast charging of electric vehicles more affordable in underserved communities
Blue-green algae sugar instead of glyphosate
Cooperation project develops environmentally friendly glyphosate alternative
Using clay to combat eternal toxins
TU Freiberg clarifies basis for innovative PFAS filter made of clay
Unveiling a new era of imaging: Boston University engineers lead breakthrough microscopy techniques
Researchers made significant advancements in the field of vibrational imaging
Phasing out fossil fuels could save millions of lives
The mortality burden attributable to air pollution from fossil fuel use is considerably higher than most previous estimates - a phaseout of fossil fuels would have tremendous, positive health outcomes
Replicating the structure of bird feathers
The new material could be used in batteries or filtration
Quantum tool opens door to uncharted phenomena
Method can contribute to a better understanding of quantum materials
Recovering instead of shredding: recycling batteries more efficiently
KIT researchers are working with industry to develop a more sustainable recycling process to recycle materials from lithium-ion batteries more effectively
Industry 4.0: No impact on energy consumption?
To what extent does the digitalisation of industrial and manufacturing processes (Industry 4.0) improve energy efficiency and thus reduce energy intensity?
New approach to the sensible utilisation of carbon dioxide from car exhaust gases
"A method has been discovered that uses impure CO2 streams and enables a breakthrough in the synthesis of valuable chemicals and pharmaceuticals"
Most read news
Microbes could help reduce the need for chemical fertilizers
A coating protects nitrogen-fixing bacteria: Start-up to commercialise coated bacteria for large-scale use in regenerative agriculture
Inauguration of the world’s first pilot plant for the cost-efficient production of green methanol
Start-up C1 Green Chemicals AG and research partners develop fundamentally new production process
This is a battery
Two colored liquids bubbling through tubes: Is this what the battery of the future looks like?
Not so silver lining: Microplastics found in clouds could affect the weather
Low-altitude and denser clouds contained greater amounts of microplastics
New designs for solid-state electrolytes may soon revolutionize the battery industry
Scientists achieve monumental improvements in lithium-metal-chloride solid-state electrolytes
Converting PFAS “forever chemicals” into valuable compounds
Scientists develop a new method to incorporate harmful perfluoroalkenes into N-heterocyclic carbene ligands
Graphene's proton permeability: A switch for future energy technologies
This discovery could lead to the development of more efficient hydrogen fuel cells and solar water-splitting devices
Lithium-ion batteries are no longer the gold standard in battery tech
On the way to safer and more powerful energy sources
Vulcan officially opened its Lithium Extraction Optimisation Plant
Europe’s first plant for fully domestic lithium chemicals production, to secure Europe’s lithium supply chain for Battery Electric Vehicle manufacturers
CO2-free hydrogen: BASF receives funding approval for 54-megawatt water electrolysis plant
Proton exchange membrane (PEM) electrolyzer expected to produce up to 8,000 metric tons of hydrogen per year
More news from our other portals
New drug delivery system could reduce daily diabetes shots to just three a year
Dietary management drugs have transformed Type 2 diabetes care, but daily injection routines are challenging for some patients
Dunning-Kruger effect with muesli bars
Those who know the least consider themselves highly competent
Aston University technology to combat the not-so sweet practice of honey fraud
Light technology to be used to detect if honey is blended with cheap additions
Naked Clams: The New Superfood Sensation Emerging from the Depths
Researchers found Naked Clams contain almost twice the amount of Vitamin B12 as blue mussels and have developed an efficient way to farm them
Scientists use quantum biology, AI to sharpen genome editing tool
"This study represents an exciting advancement toward, understanding how we can avoid making costly ‘typos’ in an organism’s genetic code"
How stem cells and immune cells communicate
Lisec Artz Award for Simon Haas: Groundbreaking discovery of an unknown protective mechanism against blood cancer from stem cells
Fatty acid factory filmed at work
High-resolution images provide new insights into cellular fatty acid production: Potential for medicine and biotechnology
Pushers, overcrowded trains and phone zombies
Sprite presents the world's first vending machine that responds to the things that bother Generation Z the most
‘Hot’ new form of microscopy examines materials using evanescent waves
“This microscope technology is completely new, so we’re still learning specifically how and where it can be applied”
Tönnies Group launches first nationwide "Meat Climate Platform"
100 guests at the Future Forum for Agriculture
Award for innovation in the detection of PFAS compounds
Thuringian startup and Fraunhofer Institute receive Lothar Späth Award
From the trough to the plate - digitally calculated
Computer program "ConTrans" estimates how much of an undesirable substance is transferred from animal feed to food
analytica 2024: Food analysis for sustainable nutrition
From PFAS to microplastics: focus on new harmful substances
The Largest Biotech City in Europe Will Soon Be Built
The entire BIO CITY complex will span an area equivalent to 10 football fields, total investment expected to reach around 7 billion euros
Could eating turkey ease colitis?
According to data in mice, extra tryptophan could reduce the risk of future colitis flares
Breakthrough in the synthesis of artificial cells
Researchers develop artificial cells from synthetic materials
Are healthy foods automatically sustainable, too?
Perceptions about sustainability and healthy food choices are closely linked
The weight of pollution: exposure linked to obesity
Chronic exposure to environmental pollutants found to increase risk of cardiovascular disease