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How Microbes Deal With "Toxic" Oxygen

This graphic shows the enzyme F420H2-Oxidase and the way it works. The cyan y-formed part is the gas-channel. The red arrow shows the way in of the oxygen to the catalytic cavity containing iron. The green arrow symbolizes the way out of the water. Yet, the blue-red sticks in the middle shows the flavin (FMN) accepting electrons from the reduced coenzyme F420, which brings the hydrogen necessary to convert the oxygen into water. Credit: S. Engilberge and T. Wagner.

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We humans need oxygen to breathe - but for many microbes it is a deadly poison. That is why microorganisms have developed ways of rendering oxygen molecules harmless. Researchers from Bremen, Marburg and Grenoble have now succeeded in deciphering such a mechanism. They show how methane bacteria transform oxygen, which is so dangerous for them, into harmless water without being harmed. These findings are relevant for future bio-inspired processes in industry.

Methane is a powerful greenhouse gas that plays a central role in the global carbon cycle. At the same time, it serves as an important source of energy for us humans. Around half of the methane produced annually is caused by microorganisms known as methanogens. The gas is mainly produced when the methanogens decompose organic material such as plant residues. This usually happens in oxygen-free environments, as oxygen acts like a powerful poison on methane bacteria and kills them. But even in habitats that are actually oxygen-free, oxygen molecules occasionally appear. In order to render these intruders harmless, methanogens have a special enzyme that can convert oxygen into water.

“Enzymes are vital components of the metabolism of all living organisms. The aim of our research is to understand how these nano-machines work on a molecular level, ”says Tristan Wagner, head of the research group Microbial Metabolisms at the Max Planck Institute for Marine Microbiology and one of the two first authors of the study, which is now in the scientific journal Chemical Communication was published. For the study, Wagner cultivated the anaerobic microorganisms Methanothermococcus thermolithotrophicus , which come from the seabed of the Gulf of Naples. He isolated the enzyme F 420Oxidase (a flavodiirone protein) and crystallized it - a common way to study how enzymes work.

“It was already known that F 420 oxidase can convert oxygen into water,” says Wagner. “But we managed to decipher the mechanism.” Scientists from the Max Planck Institute for Marine Microbiology, the Max Planck Institute for Terrestrial Microbiology, the Paul Scherrer Institute, the Interdisciplinary Research Institute of Grenoble and the European Synchrotron Radiation Facility.

Oxygen is locked in

The mechanism that the researchers discovered has an important prerequisite: Oxygen is a very reactive molecule, so it is crucial that the enzyme precisely controls the reaction. For example, water must not be present that would "accidentally" convert the oxygen into superoxide and kill the anaerobic microbe. The trick that the enzyme F 420-Oxidase used for this is a combination of a gas duct and a door. In order to render the oxygen molecules harmless, the enzyme uses the gas channel through which it leads the oxygen into an anhydrous cavity. The oxygen is locked in this cavity, which does not contain water, but contains iron. The iron acts as a catalyst and converts the oxygen into water. The necessary hydrogen molecules are supplied by the coenzyme F 420 . Then the cavity begins to move and opens a small "door". Thanks to the movement of the room, the water is carried outside through this opening. The cavity closes again and is available for the next oxygen molecule.  

To investigate this mechanism, the researchers used X-ray crystallography. They first received the crystal structure of the enzyme without oxygen and could see the anhydrous catalytic cavity. Then they first fumigate the enzyme crystals with the noble gas krypton, which, unlike oxygen, can be made visible by X-rays. They then X-rayed the crystals and were able to detect krypton atoms that showed the gas channel leading to the catalytic cave. The flavodiirone protein and its gas channels have not only been detected in methanogens, but also in other microorganisms such as clostridia (mainly found in soil and in the digestive tract), in sulfur bacteria such as Desulfovibrio gigas or even in the intestinal parasiteGiardia intestinalis.

The faster the better

"This reaction takes place very quickly," says Sylvain Engilberge from the Paul Scherrer Institute, who is first author of the study alongside Wagner. “The speed is also what makes our results so important.” Enzymes similar to laccase are much slower. "For the future application of bio-inspired electrochemical processes, it is important that we learn more about the chemical reaction, structure and function of the various groups of oxygen-reducing enzymes," says Engilberge. This could, for example, pave the way for protein engineering in order to use fast oxygen detoxifiers for industrial processes.

“The next step is now to understand the diversity of the flavodiirone protein,” says Tristan Wagner. For example, some identical bacteria do not target oxygen, but rather the toxic nitric oxide, whereby the enzyme can precisely differentiate between the two gases. But what is the crucial filter - the gas duct? Or the environmental conditions in the cavity? “More research needs to be done to understand how the protein can differentiate between oxygen and nitric oxide,” explains Wagner. With this knowledge it will then be possible to read from the genetic information whether a flavodiirone protein is an oxygen scavenger or a nitric oxide scavenger.

Engilberge S, Wagner T, Carpentier P, Girard E, Shima S. Krypton-derivatization highlights O2-channeling in a four-electron reducing oxidase. Chem Commun. 2020;56(74):10863-10866. doi:10.1039/D0CC04557H

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