Defining enzyme structure a step in the right direction to better understand bacteria function

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The green sphere in the cofactor diagram represents nickel. (view larger image)

In the world of bacteria, Lactobacillus plantarum is as versatile as they come. The microorganism produces a large amount of lactic acid and can interconvert between its two forms, L-lactate and D-lactate, through the use of an enzyme known as lactate racemase. But L. plantarum is not just impressive on the molecular level — it has many applications on a much grander scale. Making silage, a fermented animal feed, or fermented foods such as sauerkraut for humans are just a couple of L. plantarum’s capabilities. But the headliner may be the potential it holds in the area of human health.

Studies on L. plantarum as a probiotic — live bacteria that can be helpful in digestion and immune system function — have been promising. And there’s a significant market. Consumers have responded well to the growing scientific support for a wide range of probiotic supplements, foods and beverages, making it a global industry worth more than $28 billion per year.

“I’ve seen articles mentioning L. plantarum’s ability to enhance iron uptake, produce bacteriocin, and decrease levels of triglycerides and other lipid-associated components, including cholesterol,” said Robert Hausinger, a professor of microbiology and molecular genetics at Michigan State University (MSU).

Although Hausinger hasn’t yet delved into the human health applications of L. plantarum, his laboratory is studying a key component of the bacteria — lactate racemase. After reading a report from a Belgian group in 2014, which identified lactate racemase as a nickel-containing enzyme, Hausinger was intrigued.

A team consisting of Hausinger; Benoît Desguin, a postdoctoral researcher from the Belgian group; and Jian Hu, an assistant professor in biochemistry and molecular biology at MSU, has since made some important discoveries.

“I’ve been interested in nickel for a long time,” Hausinger said. “I’ve done a lot of work over the years with another enzyme called urease. It contains nickel, and to put that nickel in place there’s a protein assembly ‘machine’ in the cell. There’s an entirely different approach used in lactate racemase. In particular, what happens is that the enzyme has a cofactor that’s not just nickel — it has a niacin [vitamin B3]- derived organic component to it as well. That cofactor — the organic and inorganic components — is attached to the protein. That was surprising and unusual.”

In a paper published in the July 3, 2015, issue of Science, Desguin, the lead author, detailed the process by which the group defined the structure of the lactate racemase enzyme and its cofactor, something never seen before. Seeing the makeup of the enzyme will help researchers learn more about how it helps L. plantarum and other bacteria function.

Using the sophisticated method of mass spectrometry and Hu’s expertise in crystallography, the team elucidated the lactate racemase enzyme structure in the lab. The researchers saw that the cofactor they found contains an organic and inorganic component, including a nickel ion bonded in a planar manner to a carbon atom and two sulfur atoms. The discovery marks the first instance of this unique configuration, known as a pincer complex, in biology. Inorganic chemists work with pincer complexes regularly.

“Desguin was able to identify exactly where the cofactor was bound to the protein and characterize it,” Hausinger said. “It’s really elegant work that he and Tuo Zhang [a postdoctoral researcher with Hu] did to sort out how it all fits together. Additionally, the great thing is that now the studies by research inorganic chemists with pincer complexes have biological significance and can have a great impact on the work we’re doing.”

The Hausinger team believes it has just scratched the service of understanding lactate racemase and the roles of the novel cofactor in L. plantarum and other bacteria. Hausinger is excited to continue the research with a broad array of partners.

“Making this connection among various scientific disciplines is what led to this discovery,” Hausinger said. “We are continuing to work with scientists in Belgium. Inorganic chemists across the country are also interested in this research. Hopefully, it will lead to a better understanding of lactate racemase’s chemistry. That could have significant implications on other biological reactions.”

The project is funded by the National Science Foundation, the Department of Microbiology and Molecular Genetics at MSU, and MSU AgBioResearch.

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