Mysterious soil virus gene seen for the first time

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

Soil viruses contain genes that appear to have some metabolic function, but they are clearly not required for normal virus replication. These genes are called metabolic auxiliary genes (AMGs) and produce proteins, some of which are enzymes that have a variety of functions. Until now, scientists have wondered if some AMG proteins play a role in critical soil processes like carbon cycling. To find out more about soil AMGs, the researchers determined the atomic structure of a protein expressed by a particular AMG.

Specifically, the researchers irradiated fragile crystallized protein samples with high-intensity X-rays generated by the Stanford Synchrotron Radiation Lightsource (SSRL) beamline 12-2 at the SLAC National Accelerator Laboratory of the Department of Energy (DOE). The X-rays hit the proteins in the crystal samples, revealing their molecular structures and a bit of the mystery behind their composition.

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

“We’ve seen the position of every atom in the viral protein, which helps us figure out how it works,” said Clyde Smith, lead researcher and co-author of the SSRL. “We were amazed to see that the protein resembled known atomic structures of related bacterial and fungal enzyme families, but also contained completely new parts.”

The detailed atomic structure is unprecedented and reveals for the first time the potential mechanism of this novel enzyme that could play an important role in soil ecology, said Janet K. Jansson, senior scientist at DOE’s Pacific Northwest National Laboratory (PNNL) and co-author .

“Our collaboration with SLAC has enabled us to unravel previously unknown functions of soil viruses,” said Jansson.

The research team from SSRL, PNNL and the Joint Genome Institute (JGI) at DOE’s Lawrence Berkeley National Laboratory today published their findings in nature communication.

degradation of chitin

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

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

Capturing the atomic structure of the chitosanase protein required more than 5,000 images taken of the crystal samples. Putting these images together revealed that parts of the protein structure resembled a known group of carbohydrate-metabolizing enzymes from the glycosyl hydrolase GH45 family. However, the chitosanase protein contained other molecular parts that didn’t look like those found in GH45 or other known protein structures, meaning its role in soil cycling remains open to further study, Smith said.

“There is a part of the enzyme that is completely new and novel. That’s what excites me as a structural biologist — to see something we’ve never seen before and then try to figure out what its role might be,” Smith said.

Future research could lead to an understanding of why AMGs exist in the first place, since they don’t help a virus replicate, Smith said. In addition, the researchers were able to learn more about other AMGs transmitted by soil viruses and whether or not they play a functional role in the soil ecosystem.

“One of the big questions that arises from this finding is, ‘What in the soil needs this carbon in the chitin?'” Smith said. “Answers to questions like these will lead to a deeper understanding of how the soil’s multitude of microorganisms interact, the movement of nutrients and essential molecules, and the overall health of the soil.”