Phages fight back: how anti-CRISPRs interfere with the bacterial immune system

A transmission electron micrograph of phage JBD93, which contains an anti-CRISPR gene. (Credit: Joe Bondy-Denomy)
A transmission electron micrograph of phage JBD93, which contains an anti-CRISPR gene. (Credit: Joe Bondy-Denomy)

So nat’ralists observe, a flea
Hath smaller fleas that on him prey;
And these have smaller fleas to bite ‘em.
And so proceeds Ad infinitum.

Jonathan Swift, 1733

When the Anglo-Irish satirist wrote these words nearly two centuries ago, he could not have known just how far down the tree of life his observations would hold true. These predator-prey relationships exist beyond the plains of Africa or the jungles of Borneo. They extend to the realm of microscopic organisms and to the world of bacteria and the teeny tiny, itsy bitsy viruses that prey on them. These viruses are called bacteriophages, or phages for short.

Like human and other animal viruses, phages rely completely on their host for reproduction. They enter a bacterial cell and hijack the cellular machinery to make new phages until the cell is literally bursting with viral cargo. A torrent of phages is unleashed that go on to infect more bacteria and continue the cycle.

But bacteria are not helpless victims in this story. They have a large arsenal of anti-phage weapons to keep phages out and prevent them from taking over. Perhaps the coolest of these weapons is the CRISPR-Cas system. First discovered in 2007, the CRISPR-Cas system functions as the bacteria’s immune system. It is both a memory keeper and a hitman. Every time a bacteria survives a phage infection (which doesn’t happen often), the CRISPR-Cas complex takes a small piece of phage DNA and adds it to the bacteria’s own DNA, gradually building a database of unique DNA fingerprints from every phage that has ever tried to kill it. In other words, bacteria with CRISPR-Cas systems are able to “learn” from their previous phage encounters and acquire immunological memory based on those experiences—a trait that was previously thought to be unique to animals.

“It’s the first example of a single cell, simple [bacteria] having an adaptive immune system,” says Dr. Joseph Bondy-Denomy, a faculty fellow at the University of California, San Francisco. “The adaptability of CRISPR is very, very rapid. I think that’s why it’s so exciting.” Continue reading

Less toxic staph cause more severe disease

A scanning electron micrograph of methicillin-resistant Staphylococcus aureus and dead human immune cells. (Credit: National Institute of Allergy and Infectious Diseases. CC BY 2.0)
A scanning electron micrograph of methicillin-resistant Staphylococcus aureus and dead human immune cells. (Credit: National Institute of Allergy and Infectious Diseases. CC BY 2.0)

We hear a lot about toxins in the news these days. Specifically, the hidden toxins lurking in the food we eat, the household products we use, the air we breathe and why we need to go on a juice cleanse to detox our bodies, lose weight and feel great!

But right now, let’s ignore those exaggerations and pseudoscience (because that’s a lengthy post in and of itself) and talk about real toxins. Real bacterial toxins. These toxins are proteins made and secreted by bacteria that help them establish an infection and cause disease. Staphylococcus aureus, commonly known as staph, is one species of bacteria that deploys a large and diverse arsenal of toxins. Most people carry staph bacteria asymptomatically on their skin and in their noses. In certain individuals, such as those with a weakened immune system, the bacteria can cause a wide spectrum of diseases from minor skin and soft tissue infections to life-threatening pneumonia and bloodstream infections. A key component of the bacteria’s survival strategy are the toxins that damage tissues and attack immune cells to interfere with the host’s defense system. Toxins are also responsible for disease symptoms such as the skin lesions commonly seen in patients with a staph infection.

Given the important role that toxins play in establishing and maintaining an infection, it would be logical to assume that the more toxins a bacteria produces, the more severe the infection. Until recently, that was the prevailing belief in the research community. Continue reading

Bacteria from tobacco plant roots provide protection against sudden-wilt disease

A tobacco field in Tennessee (Credit: ajgarrison3. CC BY 2.0)
A tobacco field in Tennessee (Credit: ajgarrison3 via Flickr. CC BY 2.0)

As humans, we rely on the community of microbes in our gut to help us thrive. These microorganisms, collectively known as the gut microbiome, serve many purposes. Chief among them are helping us breakdown food into nutrients that our bodies can absorb and use and preventing harmful pathogens from taking hold.

So what is a poor plant to do without a gut? Use its root microbiome of course! The root microbiome is the collection of bacteria and fungi that live in the soil in and around the plant’s roots. The root microbiome is remarkably diverse and fluid in its composition. One gram of soil from the roots can contain up to one billion bacteria from as many as 10,000 different species. To compare, one millilitre of intestinal fluid from a human contains similar numbers of microbial cells but they represent only 500 to 1000 different species.1

The relationship between a plant and its microbial co-dwellers is generally one of give and take—the plant secretes carbon-rich sugars through its roots to feed the microbes and the microbes help the plants take up more nutrients from the soil and prime its immune system. Beyond this, we know surprisingly little about just what and how exactly all those microbial partnerships are contributing to plant health.

Dr. Ian Baldwin leads a group of researchers in the department of molecular ecology at the Max Planck Institute for Chemical Ecology in Germany. His team uses the wild tobacco plant Nicotiana attenuata to study the complex interactions between plants and microbes. In a paper published last week in the Proceedings of the National Academy of Sciences, the researchers describe how the root microbiome rescued plants from sudden-wilt disease. Continue reading