CRISPR-induced immune diversification in host-virus populations

October 19, 2020

Just like humans, microbes have equipped themselves with tools to recognize and defend themselves against viral invaders. In a continual evolutionary battle between virus and host, CRISPR-Cas act as a major driving force of strain diversity in host-virus systems.

A new study led by Professor of Life Sciences Shai Pilosof (Ben-Gurion University of the Negev, Beer-Sheva, Israel), Professor of Microbiology Rachel Whitaker (University of Illinois Urbana-Champaign), and Professor of Ecology and Evolution Mercedes Pascual (University of Chicago) highlights the role of diversified immunity in mediating host-pathogen interactions and its eco-evolutionary dynamics. The study also included Professor of Bioengineering and Bliss Faculty Scholar Sergei Maslov (University of Illinois Urbana-Champaign), Sergio A. Alcal´a-Corona (University of Chicago), and PhD graduate students Ted Kim and Tong Wang (University of Illinois Urbana-Champaign).

Their findings were reported in the journal Nature Ecology & Evolution.

"The motivation for this study was to figure out how the structure of immunity in microbial populations impacts the dynamics of virus-host interactions," said Whitaker.

Now famous for its application in genetic engineering (Nobel Prize in Chemistry, 2020), the CRISPR-Cas system originated as an adaptive immune system for microbes. In this system, "protospacers" -- segments of DNA from the infecting virus -- are incorporated into the microbial host genome, termed "spacers." The host molecular machinery uses these spacers to recognize, target and destroy viruses, analogous to the human adaptive immune system.

Researchers used computational models to explore the influence of microbial immune diversity on population dynamics of host-virus interactions. Their simulations revealed two alternating major regimes: the virus diversification regime (VDR) where viruses proliferate and diversify, and the host-controlled regime (HCR) where hosts constrain virus diversification, leading to their extinction.

As the viruses diversified in VDR regimes, so too did the hosts. The viruses that were able to escape host control harbored mutations in their protospacers, thereby leading to higher encounter rates with hosts. From these increased encounters, hosts were able to acquire new spacers, increasing CRISPR diversity. In turn, the immunity network exhibited weighted-nestedness, which enabled host control.

"Weighted-nestedness means that some microbial strains have redundant immunity to many viruses while others have limited immunity to a few," said Whitaker. "It is this structure that leads to the dynamics of host stability punctuated by viral epidemics."

To test the weighted-nestedness immunity structure predicted by their theory, researchers compared the data to empirical datasets from natural systems. Their findings revealed the presence of virus control via distributed and redundant immunity in these static empirical datasets.

"We next want to test this model in dynamic natural systems," said Whitaker. "We are focused on collecting high-resolution temporal data on hot springs and wastewater treatment because they are relatively simple with few viruses and microbial species."

By understanding the dynamics of host-virus populations in natural systems, researchers can better control microbes in industrial settings.

"Some industrial applications like wastewater treatment, yogurt, and solvent production depend on stable microbial populations," said Whitaker. "Often, these applications fail because of viral epidemics that kill these microbes. We believe that understanding CRISPRs diversity and structure can support the design of stable microbial populations that are immune to virus infection."
This work was funded by the Paul G. Allen Family Foundation through an Allen Distinguished Investigator award.

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

Related Microbes Articles from Brightsurf:

A new look at deep-sea microbes
Microbes found deeper in the ocean are believed to have slow population turnover rates and low amounts of available energy.

Microbes might manage your cholesterol
Researchers discover a link between human blood cholesterol levels and a gene in the microbiome that could one day help people manage their cholesterol through diet, probiotics, or entirely new types of treatment.

Can your gut microbes tell you how old you really are?
Harvard longevity researchers in collaboration with Insilico Medicine develop the first AI-powered microbiomic aging clock

What can be learned from the microbes on a turtle's shell?
Research published in the journal Microbiology has found that a unique type of algae, usually only seen on the shells of turtles, affects the surrounding microbial communities.

Life, liberty -- and access to microbes?
Poverty increases the risk for numerous diseases by limiting people's access to healthy food, environments and stress-free conditions.

Rye is healthy, thanks to an interplay of microbes
Eating rye comes with a variety of health benefits. A new study from the University of Eastern Finland now shows that both lactic acid bacteria and gut bacteria contribute to the health benefits of rye.

Gut microbes may affect the course of ALS
Researchers isolated a molecule that may be under-produced in the guts of patients.

Gut microbes associated with temperament traits in children
Scientists in the FinnBrain research project of the University of Turku discovered that the gut microbes of a 2.5-month-old infant are associated with the temperament traits manifested at six months of age.

Gut microbes eat our medication
Researchers have discovered one of the first concrete examples of how the microbiome can interfere with a drug's intended path through the body.

Microbes can grow on nitric oxide
Nitric oxide (NO) is a central molecule of the global nitrogen cycle.

Read More: Microbes News and Microbes Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to