Lipid formation could enable past climate detection, finds university study

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A team of biochemists from Penn State and the University of Illinois Urbana-Champaign has determined the missing step in the formation of a molecule called GDGT, which is a promising candidate for use as an indicator of past climate.

The missing step in the formation of a lipid molecule enables certain single-celled organisms to survive the most extreme environments on Earth. This new understanding could improve the ability of the lipids to be used as an indicator of temperature across geological time.

The lipid, called glycerol dibiphytanyl glycerol tetraether (GDGT), is found in the cell membrane of some species of archaea, single-celled organisms that were originally thought to be bacteria but now are considered a separate group. This lipid provides the stability for some species to thrive in environments with extremely high temperatures, salinity or acidity, like thermal vents in the ocean, hot springs and hypersaline waters. The unique stability of GDGT also enables it to be detected hundreds or even thousands of years after the organism dies. As these organisms tend to produce more GDGT at higher temperatures, it has been considered by the researchers to be a promising candidate for estimating temperature over geologic time.

Squire Booker, a biochemist at Penn State, an investigator with the Howard Hughes Medical Institute, and leader of the research team, said, “For GDGT to be accurately used as a proxy to reconstruct changes in geological temperatures, scientists need to better understand how it is made, what genes code for it, and which species can create it. But, until now, there has been a missing step in the formation of this lipid. We used imaging techniques coupled with chemical and biochemical methods to deconstruct the chemical pathway for this missing step.”

Cody Lloyd, a graduate student at Penn State and a member of the research team, said, “Coupling the carbons at the end of the two hydrocarbon chains is really challenging chemistry because they are inert – they are chemically inactive. We identified the enzyme that activates these terminal carbons and makes this coupling possible. Additionally, we now know the gene that encodes this enzyme, which should improve the use of GDGT as an indicator of past climates.”

The enzyme that facilitates the coupling of the two hydrocarbon chains belongs to a class of proteins called radical S-adenosyl-L-methionine (SAM) proteins, which are known to play an important role in a variety of chemical reactions, including the production of antibiotics, the modification of proteins, DNA and RNA, and the creation of various biomolecules.

The first step is similar to that of other reactions that involve radical SAM enzymes: the radical SAM enzyme uses one of its iron-sulfur clusters to cleave a molecule called S-adenosyl-L-methionine (SAM), producing a “free radical” or an unpaired electron that is highly reactive and helps move the reaction forward. Then, the radical plucks a hydrogen atom off the carbon at the end of the chain. At a later step, this process repeats with the second chain using the second molecule of SAM.

Lloyd continued, “Ultimately, the carbons at the end of each of the chains end up binding to each other at the position where the hydrogen atoms were removed. But once the hydrogen on the first chain is removed, it becomes so unstable that it could react with pretty much anything. To temporarily keep the first chain from reacting with any off-targets, the carbon binds to a sulfur atom from another one of the enzyme’s three iron-sulfur clusters.”

Once the hydrogen has been removed from the second chain, the resulting radical encourages the first chain to remove itself from the iron-sulfur cluster on the enzyme and instead bind to the second chain. This results in the two chains being bound together, completing the missing step in GDGT’s formation. The researchers presented their results in a paper appearing online and in print in the September 1 issue of the journal Nature.

Booker added, “This is a completely novel use of an iron-sulfur cluster, and this is the first example in nature of the coupling of two completely inert carbon atoms with this electron configuration, which chemists call sp3 hybridized. There has been a lot of interest in creating these kinds of carbon-carbon bonds from sp3-hybridized carbons as part of pharmaceuticals and other industrial products. Nature has had millions of years to figure this stuff out, so we continue to look to nature for inspiration for synthetic reactions – like this novel use of an iron-sulfur cluster.”

This research was funded by the National Institutes of Health, the Penn State Eberly Family Distinguished Chair in Science, and the Howard Hughes Medical Institute.

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