Mysterious soil virus gene appears for the first time

Soil virus AMG product crystals (chitosanase) at 400 times magnification. The individual crystals were cryo-cooled in liquid nitrogen before being exposed to powerful SSRL X-ray beams for structure analysis. Credit: Clyde Smith National Accelerator Laboratory/SLAC

In every handful of soil, there are billions of bacteria, fungi, and viruses, all working to maintain the life cycle. Understanding how these microorganisms interact with each other helps scientists analyze soil health, soil carbon, the nutrient cycle, and even the ways in which dead insects decompose.

Soil viruses contain genes that they seem to have metabolic function, but it is clearly not required for normal viral replication. These genes are called metabolic auxiliary genes (AMGs) and they produce proteins, some of which are enzymes with diverse functions. So far, scientists have wondered whether certain AMG proteins play a role in critical soil processes, such as the carbon cycle. To learn more about soil AMGs, the researchers determined the atomic structure of a protein that is expressed by a particular AMG.

Specifically, the researchers irradiated brittle crystalline protein samples using high-brightness X-rays generated by the Stanford Synchrotron Lightsource (SSRL) 12-2 beamline at the Department of Energy’s (DOE) SLAC National Accelerator Laboratory. X-rays hit the proteins inside the crystal samples, revealing their presence molecular structures And a bit of a mystery behind their makeup.

AMGs, like many viral genes, do not help the virus to reproduce. Instead, they encode a variety of proteins, each with its own expected function. The expressed AMG was a putative enzyme that plays a key role in how soils are treated and the carbon cycle in the biosphere.

“We saw the location of every single atom in the viral protein, which helps us figure out how it works,” said Clyde Smith, SSRL’s senior researcher and co-author. “We were surprised to see that the protein resembled the known atomic structures of related bacterial and fungal enzyme families, but it also contained completely new pieces.”

The detailed atomic structure is unprecedented and reveals for the first time the potential mechanism of this new enzyme that could play an important role in the soil environment, Janet K. , He said.

“Our collaboration with SLAC has enabled us to decipher previously unknown functions carried out by soil viruses,” Janson said.

The research team from SSRL, PNNL, and the Joint Genome Institute (JGI) at the Department of Energy’s Lawrence Berkeley National Laboratory published their findings today in Nature Communications.

Mysterious soil virus gene appears for the first time

Three-dimensional structure of the soil virus AMG product, an enzyme known as chitosanase. Chitosanase is composed of two structural domains (domain 1 in green and domain 2 in pink). The active site at which the chemical reaction takes place is marked by the four yellow and red sticks. Credit: Clyde Smith National Accelerator Laboratory/SLAC

break down chitin

The researchers believe that the viral AMG in the study encodes an enzyme that performs the chitin-degradation reaction. Chitin is the second most abundant carbon polymer on the planet after cellulose and is part of the insect’s exoskeleton and the cell walls of most fungi.

The viral AMG in the study is known as a chitosanase protein, and from sequence analysis it was identified as a member of the glycosyl hydrolase family GH75. This protein can act like a garden hoe for soil – any tool that helps prepare the soil for vegetables, trees, flowers, and all kinds of other life.

Capturing the atomic structure of chitosanase requires more than 5,000 images taken from crystal samples. Putting these images together showed that parts of the protein structure resemble a known group of carbohydrate-metabolizing enzymes from the GH45 glycosyl hydrolase family. However, the chitosanase protein contains other molecular segments that are not similar to those of GH45, or any other known molecular segments. protein The structures, which means their role in soil circulation, remain open to further studies, Smith said.

“There’s a bit of the enzyme that’s completely new and new,” Smith said. “That’s the exciting thing for me as a structural biologist — to see something we haven’t seen before, and then try to figure out its role,” Smith said.

Smith said future research could lead to an understanding of why AMGs are there in the first place, because they don’t help the virus reproduce. In addition, researchers can learn more about other AMGs carried by soil viruses and whether or not they play a functional role in the soil ecosystem.

“One of the big questions coming out of this discovery is, ‘What does soil need for the carbon in chitin,'” Smith said. “.” Answers to questions like these will lead to a deeper understanding of the interaction between the many soil microorganisms, the movement of nutrients and essential molecules, and the overall health of Soil. ”


Scientists discover new viruses in the soil


more information:
Ruonan Wu et al, Structural characterization of a soil interferon-functional chitosanase metabolic helper gene product, Nature Communications (2022). DOI: 10.1038 / s41467-022-32993-8

the quote: mysterious soil virus gene first seen (2022, September 20) Retrieved September 21, 2022 from

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