A molecular on/off switch for CRISPR

March 28, 2017, The Scripps Research Institute
This image shows how the CRISPR surveillance complex is disabled by two copies of anti-CRISPR protein AcrF1 (red) and one AcrF2 (light green). These anti-CRISPRs block access to the CRISPR RNA (green tube) preventing the surveillance complex from scanning and targeting invading viral DNA for destruction (Image from Lander Lab). Credit: The Scripps Research Institute

Picture bacteria and viruses locked in an arms race. For many bacteria, one line of defense against viral infection is a sophisticated RNA-guided "immune system" called CRISPR-Cas. At the center of this system is a surveillance complex that recognizes viral DNA and triggers its destruction. However, viruses can strike back and disable this surveillance complex using "anti-CRISPR" proteins, though no one has figured out exactly how these anti-CRISPRs work—until now.

For the first time, researchers have solved the structure of viral anti-CRISPR proteins attached to a bacterial CRISPR surveillance complex, revealing precisely how viruses incapacitate the bacterial defense system. The research team, co-led by biologist Gabriel C. Lander of The Scripps Research Institute (TSRI), discovered that anti-CRISPR proteins work by locking down CRISPR's ability to identify and attack the . One anti-CRISPR protein even "mimics" DNA to throw the CRISPR-guided detection machine off its trail.

"It's amazing what these systems do to one-up each other," said Lander. "It all comes back to this evolutionary ."

The new research, co-led by Blake Wiedenheft of Montana State University, was published recently in the journal Cell. If CRISPR complexes sound familiar, that's because they are at the forefront in a new wave of genome-editing technologies. CRISPR (pronounced "crisper") stands for "clustered regularly interspaced short palindromic repeats." Scientists have discovered that they can take advantage of CRISPR's natural ability to degrade sections of viral RNA and use CRISPR systems to remove unwanted genes from nearly any organism.

"Although CRISPR-Cas9 is the 'celebrity' CRISPR system, there are 19 different types of CRISPR systems, each of which may have unique advantages for genetic engineering. They are a massive, untapped resource," said Lander. "The more we learn about the structures of these systems, the more we can take advantage of them as genome-editing tools."

Using a high-resolution imaging technique called cryo-electron microscopy, the researchers discovered three important aspects of CRISPR and anti-CRISPR systems.

First, the researchers saw exactly how the CRISPR surveillance complex analyzes a virus's genetic material to see where it should attack. Proteins within the complex wrap around the CRISPR RNA like a grasping hand, exposing specific sections of bacterial RNA. These sections of RNA scan viral DNA, looking for genetic sequences they recognize.

"This system can quickly read through massive lengths of DNA and accurately hit its target," said Lander. If the CRISPR complex identifies a viral DNA target, the surveillance machine recruits other molecules to destroy the virus's genome.

Next, the researchers analyzed how viral anti-CRISPR proteins paralyze the surveillance complex. They found that one type of anti-CRISPR protein covers up the exposed section of CRISPR RNA, thereby preventing the CRISPR system from scanning the viral DNA.

"These anti-CRISPR proteins keep the bacteria from recognizing the viral DNA," Lander explained. He called these anti-CRISPR proteins "exceptionally clever" because they appear to have evolved to target a crucial piece of the CRISPR machinery. If bacteria were to mutate this machinery to avoid viral attacks, the CRISPR system would cease to function. "CRISPR systems cannot escape from these anti-CRISPR proteins without completely changing the mechanism they use to recognize DNA," he said.

Another anti-CRISPR protein uses a different trick. Based on its location and negative charge, the researchers believe this anti-CRISPR protein acts as a DNA mimic, fooling CRISPR into binding this immobilizing , rather than an invading viral DNA.

"These findings are important because we knew that anti-CRISPR proteins were blocking bacterial defenses, but we had no idea how," said Lander.

The researchers believe this new understanding of anti-CRISPR proteins may eventually lead to more sophisticated and efficient tools for gene editing. Perhaps anti-CRISPR proteins can be used in CRISPR systems to swoop in to block gene editing—or researchers could degrade anti-CRISPR proteins to trigger gene editing. "That might work as an on-off switch for CRISPR," Lander said.

Explore further: An anti-CRISPR for gene editing

Related Stories

An anti-CRISPR for gene editing

December 8, 2016

Researchers have discovered a way to program cells to inhibit CRISPR-Cas9 activity. "Anti-CRISPR" proteins had previously been isolated from viruses that infect bacteria, but now University of Toronto and University of Massachusetts ...

Off-switch for CRISPR-Cas9 gene editing system discovered

December 29, 2016

UC San Francisco researchers have discovered a way to switch off the widely used CRISPR-Cas9 gene-editing system using newly identified anti-CRISPR proteins that are produced by bacterial viruses. The technique has the potential ...

Video: Genetically modified humans? CRISPR/Cas 9 explained

September 6, 2016

Thanks to a new, cheap and accurate DNA-editing technique called CRISPR-Cas9, targeted genetic modification in humans is no longer just the realm of science fiction. Both the British and U.S. governments recently gave scientists ...

Video: The legal battle over CRISPR

January 9, 2017

CRISPR could potentially engineer super crops, make designer animal models for research and even snip out genetic diseases. Experts say that billions of dollars are at stake.

Recommended for you

Elephants resist cancer by waking a zombie gene

August 14, 2018

An estimated 17 percent of humans worldwide die from cancer, but less than five percent of captive elephants—who also live for about 70 years, and have about 100 times as many potentially cancerous cells as humans—die ...

Models give synthetic biologists a head start

August 14, 2018

Synthetic biologists have the tools to build complex, computer-like DNA circuits that sense or trigger activities in cells, and thanks to scientists at Rice University and the University of Houston they now they have a way ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.