‘Treasure trove’ of antiviral proteins could inspire powerful molecular tools
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Escherichia coli produce a diverse array of proteins to help protect them against bacteriophages (green). Credit: M. Maeder/Dept of Microbiology, Biozentrum/SPL
Bacteria have been fighting off viruses using a huge arsenal of molecular weaponry that scientists did not know about — until now.
In studies published in Science today, two research teams describe the machine-learning algorithms they developed to screen bacterial genomes and identify proteins that are involved in protecting the microorganisms against viral invaders. Their analyses identified hundreds of thousands of potential antiviral proteins, which researchers could harness to develop innovative biotechnologies.
“This is a treasure trove for any biochemist,” says José Antonio Escudero, a microbiologist at the CSIC National Center for Biotechnology in Madrid, who was not involved in either study.
Previous discoveries of antiviral immune systems in bacteria include the gene-editing system CRISPR–Cas9 and DNA-snipping proteins called restriction enzymes. Researchers have repurposed both systems to create molecular tools for genetic engineering.
“There’s a hope that maybe there’s a next generation of molecular tools that would come from some of these new systems,” says Michael Laub, a microbiologist at the Massachusetts Institute of Technology in Cambridge and a co-author on one of the studies1.
Protein defences
When looking at the genome of a bacterium, “most of it is still dark matter”, says Escudero. “There are many things that we don’t know how they work or what they are.”
Previous studies had confirmed that bacteria use more than 250 proteins to protect themselves from viral infections. Researchers had suggested that the true bacterial immune system was much larger and more diverse than this, “But the big question was how much diversity and how can we actually predict it at scale?”, says Aude Bernheim, a microbiologist at the Pasteur Institute in Paris and a co-author on one of the papers2.
Bacteria use a decoy defence molecule to set a trap for viruses