Navigation Links
Puzzling question in bacterial immune system answered
Date:1/29/2014

A central question has been answered regarding a protein that plays an essential role in the bacterial immune system and is fast becoming a valuable tool for genetic engineering. A team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have determined how the bacterial enzyme known as Cas9, guided by RNA, is able to identify and degrade foreign DNA during viral infections, as well as induce site-specific genetic changes in animal and plant cells. Through a combination of single-molecule imaging and bulk biochemical experiments, the research team has shown that the genome-editing ability of Cas9 is made possible by the presence of short DNA sequences known as "PAM," for protospacer adjacent motif.

"Our results reveal two major functions of the PAM that explain why it is so critical to the ability of Cas9 to target and cleave DNA sequences matching the guide RNA," says Jennifer Doudna, the biochemist who led this study. "The presence of the PAM adjacent to target sites in foreign DNA and its absence from those targets in the host genome enables Cas9 to precisely discriminate between non-self DNA that must be degraded and self DNA that may be almost identical. The presence of the PAM is also required to activate the Cas9 enzyme."

With genetically engineered microorganisms, such as bacteria and fungi, playing an increasing role in the green chemistry production of valuable chemical products including therapeutic drugs, advanced biofuels and biodegradable plastics from renewables, Cas9 is emerging as an important genome-editing tool for practitioners of synthetic biology.

"Understanding how Cas9 is able to locate specific 20-base-pair target sequences within genomes that are millions to billions of base pairs long may enable improvements to gene targeting and genome editing efforts in bacteria and other types of cells," says Doudna who holds joint appointments with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry, and is also an investigator with the Howard Hughes Medical Institute (HHMI).

Doudna is one of two corresponding authors of a paper describing this research in the journal Nature. The paper is titled "DNA interrogation by the CRISPR RNA-guided endonuclease Cas9." The other corresponding author is Eric Greene of Columbia University. Co-authoring this paper were Samuel Sternberg, Sy Redding and Martin Jinek.

Bacterial microbes face a never-ending onslaught from viruses and invasive snippets of nucleic acid known as plasmids. To survive, the microbes deploy an adaptive nucleic acid-based immune system that revolves around a genetic element known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. Through the combination of CRISPRs and RNA-guided endonucleases, such as Cas9, ("Cas" stands for CRISPR-associated), bacteria are able to utilize small customized crRNA molecules (for CRISPR RNA) to guide the targeting and degradation of matching DNA sequences in invading viruses and plasmids to prevent them from replicating. There are three distinct types of CRISPRCas immunity systems. Doudna and her research group have focused on the Type II system which relies exclusively upon RNA-programmed Cas9 to cleave double-stranded DNA at target sites.

"What has been a major puzzle in the CRISPRCas field is how Cas9 and similar RNA-guided complexes locate and recognize matching DNA targets in the context of an entire genome, the classic needle in a haystack problem," says Samuel Sternberg, lead author of the Nature paper and a member of Doudna's research group. "All of the scientists who are developing RNA-programmable Cas9 for genome engineering are relying on its ability to target unique 20-base-pair long sequences inside the cell. However, if Cas9 were to just blindly bind DNA at random sites across a genome until colliding with its target, the process would be incredibly time-consuming and probably too inefficient to be effective for bacterial immunity, or as a tool for genome engineers. Our study shows that Cas9 confines its search by first looking for PAM sequences. This accelerates the rate at which the target can be located, and minimizes the time spent interrogating non-target DNA sites."

Doudna, Sternberg and their colleagues used a unique DNA curtains assay and total internal reflection fluorescence microscopy (TIRFM) to image single molecules of Cas9 in real time as they bound to and interrogated DNA. The DNA curtains technology provided unprecedented insights into the mechanism of the Cas9 target search process. Imaging results were verified using traditional bulk biochemical assays.

"We found that Cas9 interrogates DNA for a matching sequence using RNADNA base-pairing only after recognition of the PAM, which avoids accidentally targeting matching sites within the bacterium's own genome," Sternberg says. "However, even if Cas9 somehow mistakenly binds to a matching sequence on its own genome, the catalytic nuclease activity is not triggered without a PAM being present. With this mechanism of DNA interrogation, the PAM provides two redundant checkpoints that ensure that Cas9 can't mistakenly destroy its own genomic DNA."


'/>"/>

Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
Source:Eurekalert  

Related biology news :

1. Fielding questions about climate change
2. New CU-NOAA monitoring system clarifies murky atmospheric questions
3. Researchers question pulling plug on pacifiers
4. Study raises questions about use of anti-epilepsy drugs in newborns
5. Just a question of time?
6. Questionnaire completed by parents may help identify 1-year-olds at risk for autism
7. New research questions how fat influences flavor perception
8. Paddlefishs doubled genome may question theories on limb evolution
9. Chicken and egg question (and answer) for rural Uganda
10. Georgetown Lombardi researcher awarded Provocative Question grant from NCI
11. Columbia awarded 1 of first Provocative Questions grants from NCI
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Puzzling question in bacterial immune system answered
(Date:3/22/2016)... 2016 According to ... for Consumer Industry by Type (Image, Motion, Pressure, ... & IT, Entertainment, Home Appliances, & Wearable ... 2022", published by MarketsandMarkets, the market for ... USD 26.76 Billion by 2022, at a ...
(Date:3/15/2016)... , March 15, 2016 ... report published by Transparency Market Research "Digital Door Lock Systems ... Forecast 2015 - 2023," the global digital door lock systems ... Mn in 2014 and is forecast to grow at a ... of micro, small and medium enterprises (MSMEs) across the world ...
(Date:3/11/2016)... -- --> --> ... Market by Technology (Pattern Recognition), by Component (Hardware, Software, ... (On-Premises and Cloud), by Industry Vertical and by Region ... global market is expected to grow from USD 12.49 ... at a CAGR of 19.1%. , ...
Breaking Biology News(10 mins):
(Date:4/29/2016)... ... 2016 , ... During a two day program for start-up ... CereScan’s CEO, John Kelley, joined other Denver business leaders in providing business basics ... Denver area business community, shared his top fundamental learnings in building an effective, ...
(Date:4/28/2016)... , April 28, 2016 ... reports the Company,s CEO  was featured in an ... Enter When VCs Fear To Tread: http://www.lifescienceleader.com/doc/accelerators-enter-when-vcs-fear-to-tread-0001 ... magazine is an essential business journal ... from emerging biotechs to Big Pharmas. Their content ...
(Date:4/27/2016)... ... 2016 , ... Cambridge Semantics, the leading provider of Smart Data ... has been named to The Silicon Review’s “20 Fastest Growing Big Data Companies of ... serves the needs of end users facing some of the most complex data challenges ...
(Date:4/27/2016)... and RESEARCH TRIANGLE PARK, N.C. , ... UTHR ) announced today that Martine Rothblatt ... Therapeutics will provide an overview and update on the ... Annual Health Care Conference. The presentation will ... a.m. Eastern Time, and can be accessed via a ...
Breaking Biology Technology: