UC Berkeley researchers and their collaborators found hundreds of relatively large viruses with genome sizes thought to only be characteristic of living organisms.
The study was co-authored by Basem Al-Shayeb and Rohan Sachdeva, who work in the Banfield Laboratory. Jillian Banfield is a UC Berkeley professor of earth and planetary science and of environmental science, policy and management, and was also a senior author of this study.
These viruses are called bacteriophages, or phages, and they infect bacteria. According to the study, most of the research on phages prior to the study was conducted on phages with genomes that are few tens of kilobases in length. This study, however, found hundreds of phage genomes that were over 200 kilobases long, the longest of which was 735 kilobases.
“We didn’t know at first (that) these things are pretty much found everywhere because there’s a bias assumption that viruses are small particles,” Al-Shayeb said. “For our approach, we looked at much bigger phages.”
The fact that the genomes for these phages are of this size blurs the lines between living and nonliving organisms, according to Sachdeva.
Viruses are viewed as nonliving organisms, as they need hosts to replicate. Some symbiotic bacteria operate in a similar way, however, requiring a host bacterium. Sachdeva said viruses often don’t have the genes needed to make proteins.
“These phages have the protein-making genes,” Sachdeva said. “It kind of pushes viruses more towards the side of living, but the thing is that they can’t make any of this without a host.”
Sachdeva concluded that phages, regardless of size, cannot be classified as living organisms.
Another result from this study was the discovery of a phage that can make a protein that is similar to the Cas9 protein in the CRISPR-Cas9 tool used for gene editing.
“We’ve found that these CRISPR-Cas systems on these viruses, which is weird because why would a virus carry this system?” Al-Shayeb said. “These target other viruses that are attempting to attack the same bacterium.”
Al-Shayeb added that this protein is most often found on bacteria, and it is used to target cells and cut mutated genes out of DNA.
Al-Shayeb and Sachdeva hypothesized in the study that these phages could be used for medical purposes by taming the phages with CRISPR-Cas9 systems and using them to eliminate unwanted bacteria.
Sachdeva said these results are just the first findings about these large phages.
“Phages which have large genomes are related, which means that these are established lineages with a long history of large genome size,” Banfield said in a Berkeley News article. “Having large genomes is one successful strategy for existence, and a strategy we know very little about.”