CRISPR-induced immune diversification in host-virus populations

Date:
October 19, 2020
Source:
Carl R. Woese Institute for Genomic Biology, University of Illinois
at Urbana-Champaign
Summary:
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.



FULL STORY ==========================================================================
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.


========================================================================== Story Source: Materials provided by Carl_R._Woese_Institute_for_Genomic_Biology,_University of_Illinois_at_Urbana-Champaign. Original written by Alisa King. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Shai Pilosof, Sergio A. Alcala'-Corona, Tong Wang, Ted Kim, Sergei
Maslov, Rachel Whitaker, Mercedes Pascual. The network
structure and eco- evolutionary dynamics of CRISPR-induced
immune diversification. Nature Ecology & Evolution, 2020; DOI:
10.1038/s41559-020-01312-z ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/10/201019145546.htm

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