Hydrogenases Enhance Bacterial Carbon Dioxide Fixation

Studying regulatory mechanisms of acetogenic bacteria can help researchers identify and engineer microbes to more efficiently use carbon dioxide.

Rising levels of atmospheric carbon dioxide (CO₂) represent an urgent global issue, with communities already experiencing more extreme weather because of a changing climate. One strategy that companies are exploring to reduce the level of this greenhouse gas is to capture it and store it deep underground.

“That’s not an ultimate solution to solve this CO₂ problem, so we have to convert CO₂ into other forms of things,” said Byung-Kwan Cho, a synthetic biologist at the Korean Advanced Institute of Science and Technology. One way to do this would be to take advantage of acetogenic bacteria, which use CO₂ and hydrogen to generate energy and produce byproducts like acetate. These bacteria could serve as biocatalysts to metabolize and remove CO₂ from the atmosphere. However, differences in metabolic strategies and regulatory mechanisms among various acetogenic bacteria lead to differences in their rates of CO₂ fixation.

Cho and his team recently isolated and characterized a new acetogen, Sporomusa sphaeroides KIAC (KIAC), that rapidly consumes CO₂. Using multiple genomic analyses, the team demonstrated that this isolate contains several different hydrogenase enzymes, pointing to these proteins as important mediators in the rate of CO₂ fixation.¹ The findings, published in mSystems, offer important insights into leveraging acetogenic bacteria to address the climate crisis.

Although their new isolate was most genetically similar to S. sphaeroides, Cho and his team saw that KIAC grew faster and consumed CO₂ more rapidly than its relative. To explore what could be contributing to KIAC’s rapid CO₂ fixation, the researchers compared the genes in its metabolic pathways to a closely related and well-characterized species in the same genus, S. ovata. While these two species shared many genes, KIAC’s genome included genes for different hydrogenases, as well as unique formate dehydrogenase genes, which is an enzyme tied to CO₂ metabolism, suggesting potential versatility in metabolic capacity in this bacterium.

“I’m not entirely convinced if this microbe is now really faster [than most other acetogens],” said Jo Philips, a biotechnologist and microbiologist at Aarhus University who was not involved in the study. “They did a lot of genomic comparisons, but the real comparison of the rates [between KIAC and S. ovata] there, I think that is missing.”

To study the regulation of these genes in CO₂ fixation further, the team identified transcriptional start sites and studied these regions for promoter motifs. They identified six sequences used by distinct sigma factors. They observed that the expression of one sigma factor, SigH, increased in hydrogen and CO₂ conditions. Additionally, many genes involved in energy production and acetogenesis contained binding sites for this sigma factor. While several other acetogens, including those from the Sporomusa genus, contained the motif for SigH, it was not universal among acetogens, highlighting a potential novel regulatory role.

Next, the team used RNA sequencing to study KIAC’s gene expression when given four different carbon sources for energy. They showed that KIAC constitutively expressed some energy-producing genes as well as four hydrogenases. “That, I think, is surprising. That was not really what I expected,” Philips said, adding that since the hydrogenases are expressed in the absence of hydrogen, it could indicate they have other functions. Cho’s team also saw that KIAC expressed genes related to formate dehydrogenase differently depending on the carbon substrates available.

To study the role of these different hydrogenases in CO₂ fixation, Cho’s team expressed three of these genes individually in another acetogen, Eubacterium limosum, which typically encodes one hydrogenase. Each KIAC hydrogenase increased the growth rate and consumption of hydrogen and CO₂ as well as the production of acetate in E. limosum compared to a control strain. The metabolism of formate occurred faster in KIAC hydrogenase-expressing strains compared to the original E. limosum.

Cho’s team concluded that diverse hydrogenases increase a bacteria’s metabolic capacity, possibly through their unique pathways available to produce and conserve energy, leading to improved CO₂ fixation. “There is a kind of regulatory network to more efficiently utilize those hydrogenases because the energy level outside changes a lot,” Cho said.

Philips said that the hypothesis was interesting but added that subsequent studies removing these hydrogenase genes from the KIAC strain to see how it affects its growth and CO₂ fixation rates would add more support to it. However, she acknowledged that, given the constraints of working with anaerobic bacteria, this is a difficult experiment to conduct.

Cho and his team plan to explore using KIAC in larger fermentation reactions to determine its industrial potential in CO₂ conversion.