A New Tool For Exploring Phage Genomes
Bacteriophages — tiny moon lander-shaped viruses that infect bacteria — are everywhere. They’ve adapted to a tremendous range of environments and to infect a tremendous range of bacteria. Phage genomes represent an enormous pool of untapped potential, full of mysterious proteins of unknown function or importance, but that could potentially be harnessed to create genomic and biological tools.
A new paper from the labs of IGI Investigators Jennifer Doudna and Brady Cress, and co-first authors Ben Adler and Muntathar Jamal Al-Shimary, was published today in Nature Microbiology. The paper details a new method for studying phages and their genomes.
“Phage genomes are some of the most diverse biological entities on earth,” says Adler. “But a lot of the tools that we’ve been using in the lab to study and edit human genomes, like most CRISPR tools, actually come from an arms race between bacteria and bacteriophages. Bacteriophages actually have billions of years of evolution to protect them from these tools! But early on in my postdoc, I realized that we might be able to study them by targeting their mRNA instead of the genome itself.”
Just like humans, bacteriophages have a genome that contains the genetic code for all of the proteins they need to make, like an instruction manual. Because the genome is so critical, it’s well protected. And when it’s time to actually make proteins, the bacteriophage (or human cell) makes copies of gene sequences in the form of messenger RNA, also known as mRNA. Protein factories attach to the phage mRNA, following its code to make a protein.
The team used a version of the CRISPR-associated protein Cas13 known as dCas13d that recognizes and binds to specific mRNAs, stopping the cell’s protein factories from being able to make the phage protein that mRNA codes for. By eliminating the function of different phage proteins, the team could see which are essential for phage infection and what processes they are involved in.
We are only shooting the messenger here.
“We are only shooting the messenger here,” says Adler. “At the level of protein expression, we can shut off a protein — programmably. Our tool, CRISPRi-ART, lets us highlight what proteins are most important for bacteriophage infection and figure out why certain proteins matter so much.”
This paper is the first from the lab of IGI Investigator Brady Cress, a PI who is part of IGI’s work to edit human, plant, and animal microbiomes to improve human health and fight climate change.
“My lab is focused on microbiome editing,” says Cress. “And one of our goals is to use bacteriophages as a way to deliver DNA editing tools to microbes in a microbiome. For instance, to reduce methane emissions coming from a farm animal or a rice paddy, we might want to use a phage to deliver DNA that codes for a gene that helps break down methane. Or DNA that codes for a CRISPR-editing tool that could interrupt a methane production pathway. To successfully harness bacteriophages, we first need a blueprint specifying which genes help them infect bacteria and circumvent bacterial defenses. CRISPRi-ART helps us get there.”
The team’s collaborators at UC San Diego, led by Joe Pogliano, have used CRISPRi-ART to study unusual bacteriophages in the Chimalliviridae family. Check out the preprint here and stay tuned for more papers exploring the wonderful world of phages!
By
Hope Henderson
