Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation

Liu, Tina Y.; Doudna, Jennifer A.

doi:10.1074/jbc.rev120.007034

Cited by 75 publications

(45 citation statements)

References 143 publications

(248 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The classification section above details relevant proteins and cleavage types. Structural and mechanistic details of CRISPR interference have been recently reviewed ( Murugan et al., 2017 ; Liu and Doudna, 2020 ). Interference involves R-loop formation as the crRNA guide-region hybridizes to target DNA or base-pairing between the crRNA guide region and target RNA.…”

Section: Crispr-cas In Immunitymentioning

confidence: 99%

“…Over the past decade, detailed molecular mechanisms were discovered which established CRISPR-Cas not just as a phage defense system, but also as a regulator of bacterial physiology such as virulence and group behaviors. ( Murugan et al., 2017 ; Faure et al., 2019 ; Liu and Doudna, 2020 ). In this review, we cover the roles of CRISPR-Cas systems within and outside the realm of adaptive immunity and detail the repertoire of biotechnological tools developed from them.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

Newsom

Parameshwaran

Martin

et al. 2021

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

Bacterial and archaeal CRISPR-Cas systems offer adaptive immune protection against foreign mobile genetic elements (MGEs). This function is regulated by sequence specific binding of CRISPR RNA (crRNA) to target DNA/RNA, with an additional requirement of a flanking DNA motif called the protospacer adjacent motif (PAM) in certain CRISPR systems. In this review, we discuss how the same fundamental mechanism of RNA-DNA and/or RNA-RNA complementarity is utilized by bacteria to regulate two distinct functions: to ward off intruding genetic materials and to modulate diverse physiological functions. The best documented examples of alternate functions are bacterial virulence, biofilm formation, adherence, programmed cell death, and quorum sensing. While extensive complementarity between the crRNA and the targeted DNA and/or RNA seems to constitute an efficient phage protection system, partial complementarity seems to be the key for several of the characterized alternate functions. Cas proteins are also involved in sequence-specific and non-specific RNA cleavage and control of transcriptional regulator expression, the mechanisms of which are still elusive. Over the past decade, the mechanisms of RNA-guided targeting and auxiliary functions of several Cas proteins have been transformed into powerful gene editing and biotechnological tools. We provide a synopsis of CRISPR technologies in this review. Even with the abundant mechanistic insights and biotechnology tools that are currently available, the discovery of new and diverse CRISPR types holds promise for future technological innovations, which will pave the way for precision genome medicine.

show abstract

Section: Crispr-cas In Immunitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

Newsom

Parameshwaran

Martin

et al. 2021

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Three types of class 1 CRISPR-Cas systems are type I, III and IV systems with different characteristic nucleases, including the enzymes Cas3, Cas10 and Cas8-like (csf1), respectively [65][66][67]. Type I systems are composed of Cas protein complexes and a crRNA molecule.…”

Section: Class 1 Crispr-cas System Classificationmentioning

confidence: 99%

Applications of the CRISPR-Cas system for infectious disease diagnostics

Wang

Yang³

et al. 2021

Expert Review of Molecular Diagnostics

View full text Add to dashboard Cite

Introduction: Rapid and accurate diagnostic approaches are essential for impeding the spread of infectious diseases. This review aims to summarize current progress of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) systems in the applications for diagnostics of infectious diseases including the ongoing COVID-19 epidemic. Areas covered: In this review, we discuss class 2 CRISPR-Cas biosensing systems-based diagnostics in various emerging and reemerging infectious diseases, CRISPR-Cas systems have created a new era for early diagnostics of infectious diseases, especially with the discovery of the collateral cleavage activity of Cas12 and Cas13. We mainly focus on different CRISPR-Cas effectors for the detection of pathogenic microorganisms as well as provide a detailed explanation of the pros and cons of CRISPR-Cas biosensing systems. In addition, we also introduce future research perspectives. Expert commentary: However, further improvement of newly discovered systems and engineering existing ones should be developed to increase the specificity, sensitivity or stability of the diagnostic tools. It may be a long journey to finish the clinical transition from research use. CRISPR-Cas approaches will emerge as more promising and robust tools for infectious disease diagnosis in the future.

show abstract

“…E. coli CRISPR-Cas3 is generally well-characterized type I CRISPR complexes in vitro and in vivo [31][32][33][34] . However, recombinant EcoCas3 protein is difficult to purify because of poor solubility and propensity to aggregate at 37°C 24,25,29,35 .…”

Section: In Vitro Reconstitution Of Escherichia Coli Crispr-cas3 Interferencementioning

confidence: 99%

Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3

Yoshimi

Takeshita

Kodera

et al. 2021

Preprint

View full text Add to dashboard Cite

Type I CRISPR-Cas3 uses an RNA-guided multi Cas-protein complex, Cascade, which detects and degrades foreign nucleic acids via the helicase-nuclease Cas3 protein. Despite many studies using cryoEM and smFRET, the precise mechanism of Cas3-mediated cleavage and degradation of target DNA remains elusive. Here we reconstitute the CRISPR-Cas3 system in vitro to show how the Escherichia coli Cas3 (EcoCas3) with EcoCascade exhibits collateral non-specific ssDNA cleavage and target specific DNA degradation. Partial binding of EcoCascade to target DNA with tolerated mismatches within the spacer sequence, but not the PAM, elicits collateral ssDNA cleavage activity of recruited EcoCas3. Conversely, stable binding with complete R-loop formation drives EcoCas3 to nick the non-target strand (NTS) in the bound DNA. Helicase-dependent unwinding then combines with trans ssDNA cleavage of the target strand and repetitive cis cleavage of the NTS to degrade the target dsDNA substrate. High-speed atomic force microscopy demonstrates that EcoCas3 bound to EcoCascade repeatedly reels and releases the target DNA, followed by target fragmentation. Together, these results provide a revised model for collateral ssDNA cleavage and target dsDNA degradation by CRISPR-Cas3, furthering understanding of type I CRISPR priming and interference and informing future genome editing tools.

show abstract

Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation

Cited by 75 publications

References 143 publications

The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies

Applications of the CRISPR-Cas system for infectious disease diagnostics

Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3

Contact Info

Product

Resources

About