FEB 17, 2020 7:30 AM PST

Giant Viruses Blur the Line Between Life and Non-Life

WRITTEN BY: Carmen Leitch

Not all viruses infect people, some, called bacteriophages, infect bacteria. Bacteriophages, also known as phages, are more complex than many viruses that we're familiar with and carry large genes that can be used to attack the bacteria they infect. Researchers have now found giant phages in samples from almost thirty different environments, including a Tibetan hot spring, oceans, hospital rooms, and pregnant women. The work, reported in Nature, revealed 351 massive phages, which all carry genomes that are four or more times bigger than the genomes of typical viruses that have been identified. This includes the largest bacteriophage ever found, which has a genome of 735,000 base pairs, roughly fifteen times bigger than average phages.

"We are exploring Earth's microbiomes, and sometimes unexpected things turn up. These viruses of bacteria are a part of biology, of replicating entities, that we know very little about," said the senior study author Jill Banfield, a UC Berkeley professor of earth and planetary science and of environmental science, policy, and management. "These huge phages bridge the gap between non-living bacteriophages, on the one hand, and bacteria and archaea. There definitely seem to be successful strategies of existence that are hybrids between what we think of as traditional viruses and traditional living organisms."

The CRISPR gene-editing system comes from a bacterial defense mechanism against phages, and some of that CRISPR system can be found in large phage genomes. The phages may infect bacteria, and a viral CRISPR can alter the bacterial CRISPR, potentially to target other viruses. One phage is even able to generate a Cas9 protein that is similar to what's used in the CRISPR editing system. The team called this protein CasØ.

"It is fascinating how these phages have repurposed this system we thought of as bacterial or archaeal to use for their own benefit against their competition, to fuel warfare between these viruses," said UC Berkeley graduate student and study co-first author Basem Al-Shayeb.

"In these huge phages, there is a lot of potential for finding new tools for genome engineering," said study co-first author, research associate Rohan Sachdeva. "A lot of the genes we found are unknown, they don't have a putative function and may be a source of new proteins for industrial, medical or agricultural applications."

Viruses are able to move genes between cells, and live in the human gut microbiome with bacteria and archaea, so this work may have implications for human disease.

Depiction of huge phages (red, left) and normal phages infecting a bacterial cell. The huge phage injects its DNA into the host cell, where Cas proteins -- part of the CRISPR immune system typically found only in bacteria and archaea -- manipulate the host cell's response to other viruses. The UC Berkeley team has not yet photographed any huge phages, so all are depicted resembling the most common type of phage, T4. / Credit: UC Berkeley image courtesy of Jill Banfield lab

"Some diseases are caused indirectly by phages, because phages move around genes involved in pathogenesis and antibiotic resistance," said Banfield. "And the larger the genome, the larger the capacity you have to move around those sorts of genes, and the higher the probability that you will be able to deliver undesirable genes to bacteria in human microbiomes."

Most of the genes carried in the bacteriophage genomes encode unknown proteins, but the scientists found genes that are crucial for generating cellular machinery called the ribosome, which makes proteins (in eukaryotic cells this machinery is an organelle but it's also found as a complex in prokaryotes). They also identified genes that move amino acids to this machinery when proteins are being translated.

"Typically, what separates life from non-life is to have ribosomes and the ability to do translation; that is one of the major defining features that separate viruses and bacteria, non-life and life," Sachdeva said. "Some large phages have a lot of this translational machinery, so they are blurring the line a bit."

"The high-level conclusion is that phages with large genomes are quite prominent across Earth's ecosystems, they are not a peculiarity of one ecosystem," Banfield said. "And phages which have large genomes are related, which means that these are established lineages with a long history of large genome size. Having large genomes is one successful strategy for existence, and a strategy we know very little about."


Sources: AAAS/Eurekalert! via University of California - Berkeley, Nature

About the Author
  • Experienced research scientist and technical expert with authorships on 28 peer-reviewed publications, traveler to over 60 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
JAN 13, 2020
Microbiology
JAN 13, 2020
Using Food to 'Sculpt' the Gut Microbiome
Scientists are learning more about how the antimicrobial effect of some foods and how it alters the microbial community in the gut....
MAR 09, 2020
Microbiology
MAR 09, 2020
Chlamydiae Bacteria are Found Deep in the Arctic Ocean
Scientists studying microbial life near a hydrothermal vent were surprised to find Chlamydiae bacteria....
MAR 10, 2020
Microbiology
MAR 10, 2020
Study Suggests 14-Day Quarantine for SARS-CoV-2 is Reasonable
The vast majority (97.5%) of people will develop symptoms of infection within 11.5 days of exposure to the virus....
MAR 25, 2020
Clinical & Molecular DX
MAR 25, 2020
A coronavirus testing kit with glow-in-the-dark Mango?
A group of Canadian researchers is responding to a desperate need for COVID-19 diagnostic kits with their fluorescent imaging technology, known as Mango. M...
MAR 29, 2020
Microbiology
MAR 29, 2020
Plastic-Eating Microbe is Found
Plastics entered the consumer market after World War II and since then it's been used in countless ways....
APR 05, 2020
Microbiology
APR 05, 2020
How Life Beneath the Sea Informs the Search for Life on Mars
Single-celled microbes that live beneath the floor of the ocean have provided insight into how scientists might be able to find life on Mars....
Loading Comments...