Scientists find a never-seen-before protein structure in a virus

It does not help the virus replicate but has a vital role in the carbon cycle.
Ameya Paleja
Scientist examining soil sample
Scientist examining soil sample

megaflopp/iStock 

Researchers at the SLAC National Accelerator Laboratory in California have for the first time spotted a gene that could provide insights into the interactions that occur between organisms in the soil and why viruses carry genes that are not essential for their survival, Phys.org reported.

Across the world, even small quantities of soil contain billions of microorganisms such as bacteria, viruses, and fungi, all working in tandem to circulate essential molecules and nutrients and keep the soil healthy. Among them, viruses seem to carry genes that are necessary to carry out such functions but are not needed for their replication. These are called auxiliary metabolic genes (AMGs).

Studying AMG proteins for possible functions

AMGs are not entirely understood, but scientists have wondered if they play a role in carbon cycling. To find out more, the researchers at the SLAC laboratory scanned under high brightness X-rays a highly crystallized sample of a protein encoded by one of the AMGs. X-ray crystallography reveals the molecular structure of the protein, which is then used to determine its function.

"We saw the location of every atom in the viral protein, which helps us figure out how it functions," said Clyde Smith, senior researcher at Stanford Synchrotron Radiation Lightsource's (SSRL) Beam Line at the SLAC. "We were amazed to see that the protein resembles known atomic structures of related bacterial and fungal enzyme families but also contained totally new pieces."

Zeroing down on the protein structure wasn't straightforward through. Scientists had to take over 5,000 images of the crystallized protein under the X-ray and then piece them together to determine the structure. The unprecedented details of the molecular structure have helped researchers identify a potential mechanism for the enzyme's function.

What does the protein do?

The AMG protein studied by the researchers is called chitosanase, which is the scientific way of saying an enzyme that breaks down chitin. Part of the cell walls of most fungi as well as the exoskeleton of insects, chitin is the second most abundant carbon biopolymer on the planet. The first is cellulose. The AMG protein works to break down the chitin in the soil.

Scientists find a never-seen-before protein structure in a virus
Two domains of the Chitosanase protein

From the analysis of captured images and gene sequence of the protein, the researchers could also classify the protein as one that resembled a group of carbohydrate metabolizing enzymes called glycosyl hydrolase GH45. However, the similarities between chitosanase and GH45 were limited. The bits that did not look like the GH45 family enzyme did not look like any other enzyme seen before either.

"There is a part of the enzyme that is completely new and novel. That's what's exciting to me as a structural biologist—to see something we have not seen before, and then try to figure out what its role might be", Smith added in the press release.

This opens up more avenues of research to determine how the protein functions and its possible role in soil cycling. It would also help explore the role of AMGs and the role they play in interaction with other organisms in the soil.

The research findings were published in the journal Nature Communications.

Abstract

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

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