{"id":109181,"date":"2022-05-16T07:03:00","date_gmt":"2022-05-16T05:03:00","guid":{"rendered":"https:\/\/renewable-carbon.eu\/news\/?p=109181"},"modified":"2022-05-11T11:31:14","modified_gmt":"2022-05-11T09:31:14","slug":"how-a-soil-microbe-could-rev-up-artificial-photosynthesis","status":"publish","type":"post","link":"https:\/\/renewable-carbon.eu\/news\/how-a-soil-microbe-could-rev-up-artificial-photosynthesis\/","title":{"rendered":"How a soil microbe could rev up artificial photosynthesis"},"content":{"rendered":"\n\n\n

Plants rely on a process called carbon fixation \u2013 turning carbon dioxide from the air into carbon-rich biomolecules \u00ad\u2013 for their very existence. That\u2019s 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. <\/strong><\/p>\n\n\n\n

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.<\/p>\n\n\n\n

Now a team of researchers from the Department of Energy\u2019s SLAC National Accelerator Laboratory, Stanford University, Max Planck Institute for Terrestrial Microbiology in Germany, DOE\u2019s Joint Genome Institute (JGI) and the University of Concepci\u00f3n in Chile has discovered how a bacterial enzyme \u2013 a molecular machine that facilitates chemical reactions \u2013 revs up to perform this feat.<\/p>\n\n\n\n

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.  <\/p>\n\n\n\n

A single spot of molecular \u201cglue\u201d 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.  <\/p>\n\n\n\n

\u201cThis 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,\u201d 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<\/em><\/a> this week.<\/p>

\u201cSome of the enzymes in this family act slowly but in a very specific way to produce just one product,\u201d he said. \u201cOthers 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.”<\/p><\/blockquote>\n\n\n\n

\"This
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. (H. DeMirci et al., ACS Central Science, 2022)<\/em> \u00a9<\/strong> SLAC National Accelerator Laboratory<\/figcaption><\/figure><\/div>\n\n\n\n

Improving on nature<\/strong><\/h3>\n\n\n\n

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, <\/em>which in addition to their carbon-fixing skills can also produce antibiotics.<\/p>\n\n\n\n

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\u2019s research team had been working to develop bioreactors for artificial photosynthesis<\/a> to convert carbon dioxide (CO2<\/sub>) from the atmosphere into all sorts of products.<\/p>\n\n\n\n

As important as photosynthesis is to life on Earth, Erb said, it isn\u2019t very efficient. Like all things shaped by evolution over the eons, it\u2019s only as good as it needs to be, the result of slowly building on previous developments but never inventing something entirely new from scratch.<\/p>\n\n\n\n

What\u2019s more, he said, the step in natural photosynthesis that fixes CO2<\/sub> from the air, which relies on an enzyme called Rubisco<\/a>, 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.<\/p>\n\n\n\n

\u201cWe aren\u2019t trying to make a carbon copy of photosynthesis,\u201d Erb explained. \u201cWe want to design a process that\u2019s much more efficient by using our understanding of engineering to rebuild the concepts of nature. This \u2018photosynthesis 2.0\u2019 could take place in living or synthetic systems such as artificial chloroplasts \u2013 droplets of water<\/a> suspended in oil.\u201d<\/p><\/blockquote>\n\n\n\n

\"A
A close-up look at Kitasatospora setae, a bacterium isolated from soil in Japan. These bacteria fix carbon \u2013 turn carbon dioxide from their environment into biomolecules they need to survive \u2013 thanks to enzymes called ECRs. Researchers are looking for ways to harness and improve ECRs for artificial photosynthesis to produce fuels, antibiotics and other products. (Y. Takahashi & Y. Iwai, atlas.actino.jp)<\/em>
\u00a9<\/strong> SLAC National Accelerator Laboratory<\/figcaption><\/figure><\/div>\n\n\n\n

Portraits of an enzyme<\/strong><\/h3>\n\n\n\n

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\u2019s group to find answers.<\/p>\n\n\n\n

Hasan DeMirci, a research associate in Wakatsuki\u2019s group who is now an assistant professor at Koc University and investigator with the Stanford PULSE Institute<\/a>, led the effort at SLAC with help from half a dozen SLAC summer interns he supervised. \u201cWe train six or seven of them every year, and they were fearless,\u201d he said. \u201cThey came with open minds, ready to learn, and they did amazing things.\u201d<\/p>\n\n\n\n

The SLAC team made samples of the ECR enzyme and crystallized them for examination with X-rays at the Advanced Photon Source at DOE\u2019s Argonne National Laboratory. The X-rays revealed the molecular structure of the enzyme \u2013 the arrangement of its atomic scaffolding \u2013 both on its own and when attached to a small helper molecule that facilitates its work.<\/p>\n\n\n\n

Further X-ray studies at SLAC\u2019s Stanford Synchrotron Radiation Lightsource (SSRL)<\/a> showed how the enzyme\u2019s 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.<\/p>\n\n\n\n

Finally, a team of researchers from SLAC\u2019s Linac Coherent Light Source (LCLS<\/a>) carried out more detailed studies of the enzyme and its substrate at Japan\u2019s SACLA X-ray free-electron laser. The choice of an X-ray laser was important because it allowed them to study the enzyme\u2019s behavior at room temperature \u2013 closer to its natural environment \u2013 with almost no radiation damage.<\/p>\n\n\n\n

\"This
This depiction of ECR, an enzyme found in soil bacteria, shows each of its four identical molecules in a different color. These molecules work together in pairs \u2013 blue with white and green with orange \u2013 to turn carbon dioxide from the microbe\u2019s environment into biomolecules it needs to survive. A new study shows that a spot of molecular glue and a timely swing and twist allow these pairs to sync their motions and fix carbon 20 times faster than plant enzymes do during photosynthesis. (H. DeMirci et al., ACS Central Science, 2022)<\/em> \u00a9<\/strong> SLAC National Accelerator Laboratory<\/figcaption><\/figure><\/div>\n\n\n\n

Meanwhile, Erb\u2019s group in Germany and Associate Professor Esteban V\u00f6hringer-Martinez\u2019s group at the University of Concepci\u00f3n in Chile carried out detailed biochemical studies and extensive dynamic simulations to make sense of the structural data collected by Wakatsuki and his team.<\/p>\n\n\n\n

The simulations revealed that the opening and closing of the enzyme\u2019s two parts don\u2019t just involve molecular glue, but also twisting motions around the central axis of each enzyme pair, Wakatsuki said.<\/p>\n\n\n\n

\u201cThis 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,\u201d he said. Together, the twisting and synchronization of the enzyme pairs allow them to fix carbon 100 times a second.<\/p><\/blockquote>\n\n\n\n

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\u2019t held together by molecular glue, they can\u2019t coordinate their movements and therefore operate much more slowly.<\/p>\n\n\n\n

\u201cIf we can increase the rate of those sophisticated reactions to make new biomolecules,\u201d Wakatsuki said, \u201cthat would be a significant jump in the field.\u201d<\/p><\/blockquote>\n\n\n\n

From static shots to fluid movies<\/strong><\/h3>\n\n\n\n

So far the experiments have produced static snapshots of the enzyme, the reaction ingredients and the final products in various configurations.<\/p>\n\n\n\n

\u201cOur dream experiment,\u201d Wakatsuki said, \u201cwould 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.\u201d<\/p><\/blockquote>\n\n\n\n

The team actually tried that at SACLA, he said, but it didn\u2019t work. \u201cThe CO2<\/sub> molecules are really small, and they move so fast that it\u2019s hard to catch the moment when they attach to the substrate,\u201d he said. \u201cPlus the X-ray laser beam is so strong that we couldn\u2019t 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.\u201d<\/p>\n\n\n\n

An upcoming high-energy upgrade<\/a> to LCLS will likely solve that problem, he added, with pulses that arrive much more frequently – a million times per second \u2013 and can be individually adjusted to the ideal strength for each sample.<\/p>\n\n\n\n

Wakatsuki said his team continues to collaborate with Erb\u2019s group, and it\u2019s working with the LCLS sample delivery group and with researchers at the SLAC-Stanford cryogenic electron microscopy (cryo-EM) facilities<\/a> to find a way to make this approach work.<\/p>\n\n\n\n

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\u2019s 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.<\/p>\n\n\n\n

Original publication<\/strong><\/h2>\n\n\n\n

Hasan DeMirci et al.,\u00a0ACS Central Science<\/em>, 25 April 2022 (10.1021\/acscentsci.2c00057<\/a>)<\/strong><\/p>\n\n\n\n

<\/p>\n\n\n\n

About SLAC<\/h3>\n\n\n\n

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.<\/em><\/p>\n\n\n\n

SLAC is operated by Stanford University for the <\/em>U.S. Department of Energy\u2019s Office of Science<\/em><\/a>. 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.<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"

Plants rely on a process called carbon fixation \u2013 turning carbon dioxide from the air into carbon-rich biomolecules \u00ad\u2013 for their very existence. That\u2019s 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 […]<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_seopress_robots_primary_cat":"none","nova_meta_subtitle":"Researchers discover that a spot of molecular glue and a timely twist help a bacterial enzyme convert 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","footnotes":""},"categories":[5572,5571],"tags":[5796,10744,5840,10408,13634],"supplier":[20344,20329,16064,6679,20331,1122,7513,4844],"class_list":["post-109181","post","type-post","status-publish","format-standard","hentry","category-bio-based","category-co2-based","tag-biotechnology","tag-carboncapture","tag-enzymes","tag-greenchemistry","tag-photosynthesis","supplier-doe-joint-genome-institute-jgi","supplier-max-planck-institute-for-terrestrial-microbiology-in-germany","supplier-riken","supplier-slac-national-accelerator-laboratory","supplier-stanford-pulse-institute","supplier-stanford-university","supplier-university-concepcion","supplier-us-department-of-energy-joint-genome-institute"],"_links":{"self":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/posts\/109181","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/comments?post=109181"}],"version-history":[{"count":0,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/posts\/109181\/revisions"}],"wp:attachment":[{"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/media?parent=109181"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/categories?post=109181"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/tags?post=109181"},{"taxonomy":"supplier","embeddable":true,"href":"https:\/\/renewable-carbon.eu\/news\/wp-json\/wp\/v2\/supplier?post=109181"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}