To easily understand what bacteriophages (bacterial viruses) are, just picture them as microscopic genetic machines that use a host’s cells as material and fuel to produce and pump out more copies of themselves. The mission of these simple biological machines is to multiply and spread. It’s a basic system of input-output. Their hosts are always bacteria, hence why they’re called bacteriophages.
Now, scientists have come across more sophisticated versions of these bacteriophages (called phages for short). They are huge and carry with them a heap of bacterial proteins – additional tools to more efficiently manipulate their microbial hosts. For example, one of the proteins is involved with the CRISPR bacterial immune system and another ribosomal production of proteins. These are features of a living microbe, which makes these phages a hybrid between viral machines and living microbes. However, because the phages cannot carry out biological processes without the help and cellular machinery of another organism, they are not considered living organisms.
Rohan Sachdeva, a UC Berkeley microbial ecologist, said:
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. Some large phages have a lot of this translational machinery, so they are blurring the line a bit.
Basem Al-Shayeb, UC Berkeley microbiologists, added:
They have an unusual number of components of the translation machinery that you do not find on a typical virus.
These big phages can be found lurking in ecosystems all over the planet – in freshwater lakes, rivers, and hot springs. They are very successful at instigating significant ecological changes because they prey on populations of bacteria and alter their metabolism, carry compounds that cause disease in humans and animals, and spread antibiotic resistance.
An international team of researchers eager to learn more about these sneaky invaders, collected samples from almost 30 different environments around the world – ranging from a Tibetan hot spring, to a South African bioreactor, to the guts of an Alaskan moose, and the saliva of humans. The team led by scientists from the University of California, Berkeley, created a DNA database from all the samples and analyzed it. The research has been published in Nature.
The team found 351 huge phages that had genomes at least four times larger than the average genome of phages. One of those was the largest phage discovered yet with a genome of 735,000 base pairs (the set of nucleotides that make up the “steps” of the DNA molecule’s “ladder” structure), which is almost 15 times bigger than the average phage.
Senior author Jill Banfield, a professor of Earth and planetary science and of environmental science, policy and management at University of California, Berkeley, said:
These phages are hybrids between what we think of as traditional viruses and traditional living organisms, such as bacteria and archaea. This huge phages’ genome is much larger than the genomes of many bacteria.
Many of these extra genes coded for proteins that have never been seen before and that are typical of bacteria, not typical of viruses. For example, some of the genes are part of a CRISPR system that bacteria use to fight viruses. The same system humans adapted (CRISPR-Cas9) to edit genes. The scientists believe that the phages inject their DNA into bacteria to hijack the bacteria CRISPR system and combine it with theirs – to then use it in warfare against other phages and get rid of the competition.
Another example, the team found genes that code for proteins necessary for the functioning of ribosomes – which translates genetic material into proteins. Proteins are the molecules that implement DNA’s instructions. The scientists believe the phages are using these proteins to hijack the ribosomes in their microbial host and generate more copies of their own proteins.
The phages are taking over all the victim’s gene replication equipment to make copies of themselves. It is imperative we know more about this because our physical and mental health is linked with the microbes that we share our bodies and the environment with. What affects them can profoundly impact us.
Al-Shayeb said:
Phages are also known to transfer genes for bacterial toxins and antibiotic resistance between bacteria, which contribute to disease. Since we have both harmful and useful bacteria living on us and within us, understanding what kinds of phages coexist with them in humans and animals and how they affect those environments is of great value.
Next, the researchers are working on growing some of these whopper phages in a laboratory setting to study how their unique CRISPR systems work. They hope to “discover their roles and test for value in genome editing.” Meaning, they are interested in seeing if the CRISPR systems some of these phages have could be used to help us control our microbiomes by eliminating the troublesome bacteria or even altering their function to be beneficial to us.
