The research shed new light on metabolic helper genes.
The protein could be important in both soil decomposition and soil carbon cycling.
There are billions of bacteria, fungi and viruses in every handful of soil, all of which contribute to sustaining the cycle of life. Understanding how these microorganisms interact with each other allows scientists to better understand soil health, soil carbon and nutrient cycling, and even how dead insects decompose.
Soil viruses have genes that appear to have a metabolic role, but are not essential for normal viral replication. These genes are known as auxiliary metabolic genes (AMGs) and produce proteins, some of which are enzymes with a variety of functions. Scientists have previously speculated whether certain AMG proteins have a role in crucial soil processes, such as the carbon cycle. To learn more about soil AMGs, the researchers determined the atomic structure of a protein expressed by a specific AMG.
A three-dimensional structure of the AMG product of the soil virus, an enzyme known as chitosanase. Chitosanase is composed of two structural domains (Domain-1 in green and Domain-2 in pink). The active site where the chemical reaction takes place is highlighted by the four yellow and red sticks. Credit: Clyde Smith/SLAC National Accelerator Lab
The researchers used high-brightness X-rays generated by the 12-2 beamline of the Stanford Synchrotron Radiation (SSRL) light source at the Department of Energy’s (DOE) SLAC National Accelerator Laboratory to irradiate fragile samples of crystallized proteins. The X-rays struck the proteins in the crystal samples, exposing their molecular structures, as well as some of the mystery surrounding their composition.
AMGs, like many viral genes, do not help a virus replicate. Instead, they code for a variety of proteins, each with its own predicted function. The AMG that was expressed was a putative enzyme that plays a key role in how carbon is processed and cycled by soils in the biosphere.
“We saw the location of each
” data-gt-translate-attributes=”[{“attribute=””>atom[{“attribute=””>atom[{“atributo=””>átomo[{“attribute=””>atom on the viral protein, which helps us figure out how it works,” said Clyde Smith, SSRL principal investigator and co-author. “We were surprised to see that the protein resembles known atomic structures of related bacterial and fungal enzyme families, but that it also contained entirely 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 soil ecology, Janet K. Jansson, chief scientist at DOE’s Pacific Northwest National Laboratory (PNNL). and co-author, she said.
“Our collaboration with SLAC has allowed us to decipher previously unknown functions performed by soil viruses,” Jansson said.
The research team of SSRL, PNNL, and the Joint Genome Institute (JGI) at DOE’s Lawrence Berkeley National Laboratory recently published their results in
” data-gt-translate-attributes=”[{“attribute=””>NatureCommunications[{“attribute=””>NatureCommunications[{“atributo=””>Comunicacionesdelanaturaleza[{“attribute=””>NatureCommunications.
break the chitin
The researchers believe that the viral AMG in the study encodes an enzyme that performs a chitin degradation reaction. Chitin is the second most abundant carbon biopolymer on the planet after cellulose and is part of the exoskeleton of an insect and the cell walls of most fungi.
The viral AMG in the study is known as a chitosanase protein and was identified from sequence analysis as a member of the GH75 glycosyl hydrolase family. This protein could be acting as a garden hoe for the soil, that is, a tool that helps prepare the soil for vegetables, trees, flowers and all kinds of life.
Capturing the atomic structure of the chitosanase protein required more than 5,000 images taken from the crystal samples. Assembling these images revealed that parts of the protein’s structure resembled a known group of carbohydrate-metabolizing enzymes from the GH45 glycosyl hydrolase family. However, the chitosanase protein contained other molecular pieces that did not resemble those found in GH45 or any other known protein structure, meaning its role in the soil cycle 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: seeing something we haven’t seen before and then trying 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, researchers could 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 that arises from this finding is, ‘What in the soil needs that carbon in chitin?'” Smith said. “Answers to questions like this will lead to a deeper understanding of the interaction of the multitude of microorganisms in the soil, the movement of essential nutrients and molecules, and the overall health of the soil.”
Reference: “Structural characterization of a soil viral helper metabolic gene product: a functional chitosanase” by Ruonan Wu, Clyde A. Smith, Garry W. Buchko, Ian K. Blaby, David Paez-Espino, Nikos C. Kyrpides, Yasuo Yoshikuni , Jason E. McDermott, Kirsten S. Hofmockel, John R. Cort, and Janet K. Jansson, September 19, 2022, Nature Communications.
DOI: 10.1038/s41467-022-32993-8
The study was funded by DOE’s Office of Biological and Environmental Research (BER), JGI, and DOE’s Environmental Molecular Sciences Laboratory (EMSL). The project was initiated by PNNL researchers through the BER-funded SFA soil microbiome. It was also supported by a FICUS grant for the support of JGI and EMSL. The Structural Molecular Biology Program at SSRL is supported by the DOE BER and the National Institutes of Health and the National Institute of General Medical Sciences.
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