Mysterious soil virus genes

This protein may be important
in both soil decomposition and soil carbon cycling.

Every handful of soil contains billions of bacteria, fungi and viruses, all of which contribute
to the maintenance of life cycles.
Understanding how these microbes interact could give scientists a better understanding of soil health, soil carbon and nutrient cycling, and even how dead insects break down
.

Characteristic genes of soil viruses appear to have metabolic roles, but they are not required for
normal viral replication.
These genes are called helper metabolic genes (AMGs), and they produce proteins, some of which are enzymes
with multiple roles.
Scientists have previously speculated whether certain AMG proteins play a role
in key soil processes, such as the carbon cycle.
To further understand soil AMG, the researchers determined the atomic structure
of a specific AMG-expressing protein.

The three-dimensional structure of the AMG product of the soil virus, an enzyme
called chitosanase.
Chitosanase consists of
two domains (domain-1 is green and domain-2 is pink).
The active site where the chemical reaction took place is marked with four yellow and red sticks
.

The researchers used high-brightness X-rays generated by the Stanford Synchrotron Radiation Light Source (SSRL) Beamline 12-2 at the Department of Energy's SLAC National Accelerator Laboratory to irradiate fragile crystalline protein samples
.
X-rays hit the proteins in the crystal samples, exposing their molecular structure and some of the mysteries
surrounding their composition.

AMG does not help viruses replicate
like many viral genes.
Instead, they encode multiple proteins, each with its own predictive function
.
The expressed AMG is thought to be an enzyme that plays a key role
in soil processing and recycling carbon in the biosphere.

"We saw the location of each atom in the viral protein, which helped us figure out how it works," said
Clyde Smith, senior researcher and co-author at SSRL.
"We were surprised to find that this protein is similar in structure to the known atomic structure of related bacterial and fungal enzyme families, but also contains completely new fragments
.
"

Janet K.
Jansson, chief scientist and co-author of the Department of Energy's Pacific Northwest National Laboratory (PNNL), said this detailed atomic structure is unprecedented, revealing for the first potential mechanism
by which this new enzyme may play an important role in soil ecology.

"Our collaboration with SLAC allowed us to decipher previously unknown functions of soil viruses," Jansson said
.

A team of researchers from the National Scientific Research Laboratory, the National Laboratory, and the Joint Genomic Research Institute (JGI) of the U.
S.
Department of Energy's Lawrence Berkeley National Laboratory recently published their findings
in Nature Communications.